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  • Springer Nature  (30,231)
  • Oxford University Press  (25,011)
  • American Meteorological Society
  • 2010-2014  (45,850)
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  • 2013  (45,850)
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  • 1
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    Oxford University Press
    In:  EPIC3Journal of Experimental Botany, Oxford University Press, ISSN: 0022-0957
    Publication Date: 2019-07-17
    Repository Name: EPIC Alfred Wegener Institut
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  • 2
    Publication Date: 2017-04-04
    Description: Global-scale variations in the climate system over the last half of the twentieth century. including long-term increases in global-mean near-surface temperatures. are consistent with concurrent human-induced emissions of radiatively active gases and aerosols. However, such consistency does not preclude the possible influence of other forcing agents, including internal modes of climate variability or unaccounted for aerosol effects. To test whether other unknown forcing agents may have contributed to multidecadal increases in global-mean near-surface temperatures from 1950 to 2000. data pertaining to observed changes in global-scale sea surface temperatures and observed changes in radiatively active atmospheric constituents are incorporated into numerical global climate models. Results indicate that the radiative forcing needed to produce the observed long-term trends in sea surface temperatures-and global-mean near-surface temperatures-is provided predominantly by known changes in greenhouse gases and aerosols. Further, results indicate that less than 10% of the long-term historical increase in global-mean near-surface temperatures over the last half of the twentieth century could have been the result of internal climate variability. In addition. they indicate that less than 25% of the total radiative forcing needed to produce the observed long-term trend in global-mean near-surface temperatures could have been provided by changes in net radiative forcing from unknown sources (either positive or negative). These results, which are derived from simple energy balance requirements. emphasize the important role humans have played in modifying the global climate over the last half of the twentieth century.
    Description: Published
    Description: 7163-7172
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: restricted
    Keywords: climate forcing ; temperature increase ; AGCM ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
    Publication Date: 2017-04-04
    Description: In this work the authors investigate possible changes in the distribution of heavy precipitation events under a warmer climate, using the results of a set of 20 climate models taking part in the Coupled Model Intercomparison Project phase 5 effort (CMIP5). Future changes are evaluated as the difference between the last four decades of the 21st and the 20th Century assuming the Representative Concentration Pathway RCP8.5 scenario. As a measure of the width of the right tail of the precipitation distribution, we use the difference between the 99th and the 90th percentiles. Despite a slight tendency to underestimate the observed heavy precipitation, the considered CMIP5 models well represent the observed patterns in terms of the ensemble average, during both summer and winter seasons for the 1997-2005 period. Future changes in average precipitation are consistentwith previous findings based on CMIP3 models. CMIP5 models show a projected increase for the end of the twenty-first century of the width of the right tail of the precipitation distribution, particularly pronounced over India, South East Asia, Indonesia and Central Africa during borealsummer, as well as over South America and southern Africa during boreal winter.
    Description: Published
    Description: 7902–7911
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: open
    Keywords: precipitation ; extreme events ; climate change ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 93 (2012): 1547–1566, doi:10.1175/BAMS-D-11-00201.1.
    Description: The Geostationary Coastal and Air Pollution Events (GEO-CAPE) mission was recommended by the National Research Council's (NRC's) Earth Science Decadal Survey to measure tropospheric trace gases and aerosols and coastal ocean phytoplankton, water quality, and biogeochemistry from geostationary orbit, providing continuous observations within the field of view. To fulfill the mandate and address the challenge put forth by the NRC, two GEO-CAPE Science Working Groups (SWGs), representing the atmospheric composition and ocean color disciplines, have developed realistic science objectives using input drawn from several community workshops. The GEO-CAPE mission will take advantage of this revolutionary advance in temporal frequency for both of these disciplines. Multiple observations per day are required to explore the physical, chemical, and dynamical processes that determine tropospheric composition and air quality over spatial scales ranging from urban to continental, and over temporal scales ranging from diurnal to seasonal. Likewise, high-frequency satellite observations are critical to studying and quantifying biological, chemical, and physical processes within the coastal ocean. These observations are to be achieved from a vantage point near 95°–100°W, providing a complete view of North America as well as the adjacent oceans. The SWGs have also endorsed the concept of phased implementation using commercial satellites to reduce mission risk and cost. GEO-CAPE will join the global constellation of geostationary atmospheric chemistry and coastal ocean color sensors planned to be in orbit in the 2020 time frame.
    Description: Funding for GEO-CAPE definition activities is provided by the Earth Science Division of the National Aeronautics and Space Administration.
    Description: 2013-04-01
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 17–28, doi:10.1175/JPO-D-11-0108.1.
    Description: Observational evidence is presented for transfer of energy from the internal tide to near-inertial motions near 29°N in the Pacific Ocean. The transfer is accomplished via parametric subharmonic instability (PSI), which involves interaction between a primary wave (the internal tide in this case) and two smaller-scale waves of nearly half the frequency. The internal tide at this location is a complex superposition of a low-mode waves propagating north from Hawaii and higher-mode waves generated at local seamounts, making application of PSI theory challenging. Nevertheless, a statistically significant phase locking is documented between the internal tide and upward- and downward-propagating near-inertial waves. The phase between those three waves is consistent with that expected from PSI theory. Calculated energy transfer rates from the tide to near-inertial motions are modest, consistent with local dissipation rate estimates. The conclusion is that while PSI does befall the tide near a critical latitude of 29°N, it does not do so catastrophically.
    Description: This work was sponsored by NSF OCE 04-25283.
    Description: 2013-07-01
    Keywords: Diapycnal mixing ; Internal waves ; Nonlinear dynamics
    Repository Name: Woods Hole Open Access Server
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  • 6
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 418–431, doi:10.1175/JPO-D-12-087.1.
    Description: The overflow of the dense water mass across the Greenland–Scotland Ridge (GSR) from the Nordic Seas drives the Atlantic meridional overturning circulation (AMOC). The Nordic Seas is a large basin with an enormous reservoir capacity. The volume of the dense water above the GSR sill depth in the Nordic Seas, according to previous estimates, is sufficient to supply decades of overflow transport. This large capacity buffers overflow’s responses to atmospheric variations and prevents an abrupt shutdown of the AMOC. In this study, the authors use a numerical and an analytical model to show that the effective reservoir capacity of the Nordic Seas is actually much smaller than what was estimated previously. Basin-scale oceanic circulation is nearly geostrophic and its streamlines are basically the same as the isobaths. The vast majority of the dense water is stored inside closed geostrophic contours in the deep basin and thus is not freely available to the overflow. The positive wind stress curl in the Nordic Seas forces a convergence of the dense water toward the deep basin and makes the interior water even more removed from the overflow-feeding boundary current. Eddies generated by the baroclinic instability help transport the interior water mass to the boundary current. But in absence of a robust renewal of deep water, the boundary current weakens rapidly and the eddy-generating mechanism becomes less effective. This study indicates that the Nordic Seas has a relatively small capacity as a dense water reservoir and thus the overflow transport is sensitive to climate changes.
    Description: This study has been supported by National Science Foundation (OCE0927017,ARC1107412).
    Description: 2013-08-01
    Keywords: Bottom currents ; Drainage flow ; Meridional overturning circulation ; Ocean dynamics ; Potential vorticity ; Topographic effects
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 283–300, doi:10.1175/JPO-D-11-0240.1.
    Description: Motivated by the recent interest in ocean energetics, the widespread use of horizontal eddy viscosity in models, and the promise of high horizontal resolution data from the planned wide-swath satellite altimeter, this paper explores the impacts of horizontal eddy viscosity and horizontal grid resolution on geostrophic turbulence, with a particular focus on spectral kinetic energy fluxes Π(K) computed in the isotropic wavenumber (K) domain. The paper utilizes idealized two-layer quasigeostrophic (QG) models, realistic high-resolution ocean general circulation models, and present-generation gridded satellite altimeter data. Adding horizontal eddy viscosity to the QG model results in a forward cascade at smaller scales, in apparent agreement with results from present-generation altimetry. Eddy viscosity is taken to roughly represent coupling of mesoscale eddies to internal waves or to submesoscale eddies. Filtering the output of either the QG or realistic models before computing Π(K) also greatly increases the forward cascade. Such filtering mimics the smoothing inherent in the construction of present-generation gridded altimeter data. It is therefore difficult to say whether the forward cascades seen in present-generation altimeter data are due to real physics (represented here by eddy viscosity) or to insufficient horizontal resolution. The inverse cascade at larger scales remains in the models even after filtering, suggesting that its existence in the models and in altimeter data is robust. However, the magnitude of the inverse cascade is affected by filtering, suggesting that the wide-swath altimeter will allow a more accurate determination of the inverse cascade at larger scales as well as providing important constraints on smaller-scale dynamics.
    Description: BKA received support from Office of Naval Research Grant N00014-11-1-0487, National Science Foundation (NSF) Grants OCE-0924481 and OCE- 09607820, and University of Michigan startup funds. KLP acknowledges support from Woods Hole Oceanographic Institution bridge support funds. RBS acknowledges support from NSF grants OCE-0960834 and OCE-0851457, a contract with the National Oceanography Centre, Southampton, and a NASA subcontract to Boston University. JFS and JGR were supported by the projects ‘‘Global and remote littoral forcing in global ocean models’’ and ‘‘Agesotrophic vorticity dynamics of the ocean,’’ respectively, both sponsored by the Office of Naval Research under program element 601153N.
    Description: 2013-08-01
    Keywords: Eddies ; Nonlinear dynamics ; Ocean dynamics ; Satellite observations ; Ocean models
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 744–765, doi:10.1175/JPO-D-12-067.1.
    Description: This study investigates the coherence between ocean bottom pressure signals at the Rapid Climate Change programme (RAPID) West Atlantic Variability Experiment (WAVE) array on the western North Atlantic continental slope, including the Woods Hole Oceanographic Institution Line W. Highly coherent pressure signals propagate southwestward along the slope, at speeds in excess of 128 m s−1, consistent with expectations of barotropic Kelvin-like waves. Coherent signals are also evidenced in the smaller pressure differences relative to 1000-m depth, which are expected to be associated with depth-dependent basinwide meridional transport variations or an overturning circulation. These signals are coherent and almost in phase for all time scales from 3.6 years down to 3 months. Coherence is still seen at shorter time scales for which group delay estimates are consistent with a propagation speed of about 1 m s−1 over 990 km of continental slope but with large error bounds on the speed. This is roughly consistent with expectations for propagation of coastally trapped waves, though somewhat slower than expected. A comparison with both Eulerian currents and Lagrangian float measurements shows that the coherence is inconsistent with a propagation of signals by advection, except possibly on time scales longer than 6 months.
    Description: This work was funded by the U.K. Natural Environment Research Council. Sofia Olhede was supported by EPSRC Grant EP/I005250/1. Initial observations at StationW(2001–04) were made possible by a grant from the G. Unger Vetlesen Foundation and support from the Woods Hole Oceanographic Institution. Since 2004, the Line W program has been supported by the U.S. National Science Foundation with supplemental contribution from WHOIs Ocean and Climate Change Institute.
    Description: 2013-10-01
    Keywords: Atlantic Ocean ; Boundary currents ; Meridional overturning circulation ; Pressure ; Waves, oceanic ; In situ oceanic observations
    Repository Name: Woods Hole Open Access Server
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  • 9
    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 Conservation Physiology 1 (2013): cot006, doi:10.1093/conphys/cot006.
    Description: Large whales are subjected to a variety of conservation pressures that could be better monitored and managed if physiological information could be gathered readily from free-swimming whales. However, traditional approaches to studying physiology have been impractical for large whales, because there is no routine method for capture of the largest species and there is presently no practical method of obtaining blood samples from free-swimming whales. We review the currently available techniques for gathering physiological information on large whales using a variety of non-lethal and minimally invasive (or non-invasive) sample matrices. We focus on methods that should produce information relevant to conservation physiology, e.g. measures relevant to stress physiology, reproductive status, nutritional status, immune response, health, and disease. The following four types of samples are discussed: faecal samples, respiratory samples (‘blow’), skin/blubber samples, and photographs. Faecal samples have historically been used for diet analysis but increasingly are also used for hormonal analyses, as well as for assessment of exposure to toxins, pollutants, and parasites. Blow samples contain many hormones as well as respiratory microbes, a diverse array of metabolites, and a variety of immune-related substances. Biopsy dart samples are widely used for genetic, contaminant, and fatty-acid analyses and are now being used for endocrine studies along with proteomic and transcriptomic approaches. Photographic analyses have benefited from recently developed quantitative techniques allowing assessment of skin condition, ectoparasite load, and nutritional status, along with wounds and scars from ship strikes and fishing gear entanglement. Field application of these techniques has the potential to improve our understanding of the physiology of large whales greatly, better enabling assessment of the relative impacts of many anthropogenic and ecological pressures.
    Description: This work was supported by the United States Office of Naval Research (award #N000141110435 to K.E.H., award #N000141110540 to R.M.R., and award #N0001412WX20890 to L.C.Y. and C.E.D.); the United Kingdom Natural Environmental Research Council (supporting A.J.H.); the National Center for Research Resources, a component of the United States National Institutes of Health (NIH; supporting C.E.D.); the NIH Roadmap for Medical Research (UL1 RR024146 supporting C.E.D.); The Hartwell Foundation (supporting C.E.D.) and the 2012 Marine Mammal Breath Workshop, which was funded by the National Oceanic and Atmospheric Administration’s Marine Mammal Health and Stranding Response Program.
    Keywords: Blow ; Biopsy dart ; Cetacea ; Faecal samples ; Non-invasive ; Visual health assessment
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 26 (2013): 2453–2466, doi:10.1175/JCLI-D-12-00023.1.
    Description: The North Atlantic Oscillation (NAO) is one of the most important modes of variability in the global climate system and is characterized by a meridional dipole in the sea level pressure field, with centers of action near Iceland and the Azores. It has a profound influence on the weather, climate, ecosystems, and economies of Europe, Greenland, eastern North America, and North Africa. It has been proposed that around 1980, there was an eastward secular shift in the NAO’s northern center of action that impacted sea ice export through Fram Strait. Independently, it has also been suggested that the location of its southern center of action is tied to the phase of the NAO. Both of these attributes of the NAO have been linked to anthropogenic climate change. Here the authors use both the one-point correlation map technique as well as empirical orthogonal function (EOF) analysis to show that the meridional dipole that is often seen in the sea level pressure field over the North Atlantic is not purely the result of the NAO (as traditionally defined) but rather arises through an interplay among the NAO and two other leading modes of variability in the North Atlantic region: the East Atlantic (EA) and the Scandinavian (SCA) patterns. This interplay has resulted in multidecadal mobility in the two centers of action of the meridional dipole since the late nineteenth century. In particular, an eastward movement of the dipole has occurred during the 1930s to 1950s as well as more recently. This mobility is not seen in the leading EOF of the sea level pressure field in the region.
    Description: GWKM was supported by the Natural Sciences and Engineering Research Council of Canada. IAR was supported in part by NE/C003365/1. RSP was supported by Grant OCE-0959381 from the U.S. National Science Foundation.
    Description: 2013-10-15
    Keywords: North Atlantic Ocean ; North Atlantic Oscillation ; Climate variability ; Climatology ; Empirical orthogonal functions
    Repository Name: Woods Hole Open Access Server
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  • 11
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 42 (2012): 2234–2253, doi:10.1175/JPO-D-12-033.1.
    Description: Meridional velocity, mass, and heat transport in the equatorial oceans are difficult to estimate because of the nonapplicability of the geostrophic balance. For this purpose a steady-state model is utilized in the equatorial Indian Ocean using NCEP wind stress and temperature and salinity data from the World Ocean Atlas 2005 (WOA05) and Argo. The results show a Somali Current flowing to the south during the winter monsoon carrying −11.5 ± 1.3 Sv (1 Sv ≡ 106 m3 s−1) and −12.3 ± 0.3 Sv from WOA05 and Argo, respectively. In the summer monsoon the Somali Current reverses to the north transporting 16.8 ± 1.2 Sv and 19.8 ± 0.6 Sv in the WOA05 and Argo results. Transitional periods are considered together and in consequence, there is not a clear Somali Current present in this period. Model results fit with in situ measurements made around the region, although Argo data results are quite more realistic than WOA05 data results.
    Description: This study has been partly funded by the MOC Project (CTM 2008- 06438) and the Spanish contribution to the Argo network (AC2009 ACI2009-0998), financed by the Spanish Government and Feder.
    Description: 2013-06-01
    Keywords: Indian Ocean ; Subtropics ; Currents ; Ocean circulation ; Transport ; Wind stress
    Repository Name: Woods Hole Open Access Server
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  • 12
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 2132–2141, doi:10.1175/JPO-D-12-0182.1.
    Description: Repeated occupations of two hydrographic sections in the southwest Pacific basin from the 1990s to 2000s track property changes of Antarctic Bottom Water (AABW). The largest property changes—warming, freshening, increase in total carbon, and decrease in oxygen—are found near the basin’s deep western boundary between 50° and 20°S. The magnitude of the property changes decreases with increasing distance from the western boundary. At the deep western boundary, analysis of the relative importance of AABW (γn 〉 28.1 kg m−3) freshening, heating, or isopycnal heave suggests that the deep ocean stratification change is the result of both warming and freshening processes. The consistent deep ocean changes near the western boundary of the southwest Pacific basin dispel the notion that the deep ocean is quiescent. High-latitude climate variability is being directly transmitted into the deep southwest Pacific basin and the global deep ocean through dynamic deep western boundary currents.
    Description: BMS, SEW, and BT were supported by the Australian Climate Change Science Program, funded jointly by the Department of Climate Change and Energy Efficiency and CSIRO. Funding for AM was provided through NOAA GrantNA110AR4310063.
    Description: 2014-04-01
    Keywords: Circulation/ Dynamics ; Waves ; Oceanic
    Repository Name: Woods Hole Open Access Server
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  • 13
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 1589–1610, doi:10.1175/JPO-D-12-0173.1.
    Description: This study investigates the exchange of momentum between the atmosphere and ocean using data collected from four oceanic field experiments. Direct covariance estimates of momentum fluxes were collected in all four experiments and wind profiles were collected during three of them. The objective of the investigation is to improve parameterizations of the surface roughness and drag coefficient used to estimate the surface stress from bulk formulas. Specifically, the Coupled Ocean–Atmosphere Response Experiment (COARE) 3.0 bulk flux algorithm is refined to create COARE 3.5. Oversea measurements of dimensionless shear are used to investigate the stability function under stable and convective conditions. The behavior of surface roughness is then investigated over a wider range of wind speeds (up to 25 m s−1) and wave conditions than have been available from previous oversea field studies. The wind speed dependence of the Charnock coefficient α in the COARE algorithm is modified to , where m = 0.017 m−1 s and b = −0.005. When combined with a parameterization for smooth flow, this formulation gives better agreement with the stress estimates from all of the field programs at all winds speeds with significant improvement for wind speeds over 13 m s−1. Wave age– and wave slope–dependent parameterizations of the surface roughness are also investigated, but the COARE 3.5 wind speed–dependent formulation matches the observations well without any wave information. The available data provide a simple reason for why wind speed–, wave age–, and wave slope–dependent formulations give similar results—the inverse wave age varies nearly linearly with wind speed in long-fetch conditions for wind speeds up to 25 m s−1.
    Description: This work was funded by the National Science Foundation Grant OCE04-24536 as part of the CLIVAR Mode Water Dynamics Experiment (CLIMODE) and the Office of Naval Research Grant N00014-05-1-0139 as part of the CBLAST-LOW program.
    Description: 2014-02-01
    Keywords: Wind shear ; Wind stress ; Atmosphere-ocean interaction ; Fluxes ; Momentum ; Algorithms
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  • 14
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 30 (2013): 1767–1788, doi:10.1175/JTECH-D-12-00140.1.
    Description: Seismic images of oceanic thermohaline finestructure record vertical displacements from internal waves and turbulence over large sections at unprecedented horizontal resolution. Where reflections follow isopycnals, their displacements can be used to estimate levels of turbulence dissipation, by applying the Klymak–Moum slope spectrum method. However, many issues must be considered when using seismic images for estimating turbulence dissipation, especially sources of random and harmonic noise. This study examines the utility of seismic images for estimating turbulence dissipation in the ocean, using synthetic modeling and data from two field surveys, from the South China Sea and the eastern Pacific Ocean, including the first comparison of turbulence estimates from seismic images and from vertical shear. Realistic synthetic models that mimic the spectral characteristics of internal waves and turbulence show that reflector slope spectra accurately reproduce isopycnal slope spectra out to horizontal wavenumbers of 0.04 cpm, corresponding to horizontal wavelengths of 25 m. Using seismic reflector slope spectra requires recognition and suppression of shot-generated harmonic noise and restriction of data to frequency bands with signal-to-noise ratios greater than about 4. Calculation of slope spectra directly from Fourier transforms of the seismic data is necessary to determine the suitability of a particular dataset to turbulence estimation from reflector slope spectra. Turbulence dissipation estimated from seismic reflector displacements compares well to those from 10-m shear determined by coincident expendable current profiler (XCP) data, demonstrating that seismic images can produce reliable estimates of turbulence dissipation in the ocean, provided that random noise is minimal and harmonic noise is removed.
    Description: This work was funded by NSF Grants 0452744, 0405654, and 0648620, and ONR/DEPSCoR Grant DODONR40027.
    Description: 2014-02-01
    Keywords: Mixing ; Thermocline ; Acoustic measurements/effects
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  • 15
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 94 (2013): 1131–1144, doi:10.1175/BAMS-D-12-00100.1.
    Description: The recent retreat and speedup of outlet glaciers, as well as enhanced surface melting around the ice sheet margin, have increased Greenland's contribution to sea level rise to 0.6 ± 0.1 mm yr−1 and its discharge of freshwater into the North Atlantic. The widespread, near-synchronous glacier retreat, and its coincidence with a period of oceanic and atmospheric warming, suggests a common climate driver. Evidence points to the marine margins of these glaciers as the region from which changes propagated inland. Yet, the forcings and mechanisms behind these dynamic responses are poorly understood and are either missing or crudely parameterized in climate and ice sheet models. Resulting projected sea level rise contributions from Greenland by 2100 remain highly uncertain. This paper summarizes the current state of knowledge and highlights key physical aspects of Greenland's coupled ice sheet–ocean–atmosphere system. Three research thrusts are identified to yield fundamental insights into ice sheet, ocean, sea ice, and atmosphere interactions, their role in Earth's climate system, and probable trajectories of future changes: 1) focused process studies addressing critical glacier, ocean, atmosphere, and coupled dynamics; 2) sustained observations at key sites; and 3) inclusion of relevant dynamics in Earth system models. Understanding the dynamic response of Greenland's glaciers to climate forcing constitutes both a scientific and technological frontier, given the challenges of obtaining the appropriate measurements from the glaciers' marine termini and the complexity of the dynamics involved, including the coupling of the ocean, atmosphere, glacier, and sea ice systems. Interdisciplinary and international cooperation are crucial to making progress on this novel and complex problem.
    Description: 2014-02-01
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  • 16
    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 Nucleic Acids Research 40 (2012): W82-W87, doi:10.1093/nar/gks418.
    Description: Amplicon sequencing of the hypervariable regions of the small subunit ribosomal RNA gene is a widely accepted method for identifying the members of complex bacterial communities. Several rRNA gene sequence reference databases can be used to assign taxonomic names to the sequencing reads using BLAST, USEARCH, GAST or the RDP classifier. Next-generation sequencing methods produce ample reads, but they are short, currently ∼100–450 nt (depending on the technology), as compared to the full rRNA gene of ∼1550 nt. It is important, therefore, to select the right rRNA gene region for sequencing. The primers should amplify the species of interest and the hypervariable regions should differentiate their taxonomy. Here, we introduce TaxMan: a web-based tool that trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. It allows interactive plotting of taxa, both amplified and missed in silico by the primers used. Additionally, using the trimmed sequences improves the speed of sequence matching algorithms. The smaller database greatly improves run times (up to 98%) and memory usage, not only of similarity searching (BLAST), but also of chimera checking (UCHIME) and of clustering the reads (UCLUST). TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/.
    Description: University of Amsterdam under the research priority area ‘Oral Infections and Inflammation’ (to B.W.B.); National Science Foundation [NSF/BDI 0960626 to S.M.H.]; the European Union Seventh Framework Programme (FP7/ 2007-2013) under ANTIRESDEV grant agreement no 241446 (to E.Z.).
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  • 17
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 42 (2012): 2143–2152, doi:10.1175/JPO-D-12-027.1.
    Description: Direct measurements of turbulence levels in the Drake Passage region of the Southern Ocean show a marked enhancement over the Phoenix Ridge. At this site, the Antarctic Circumpolar Current (ACC) is constricted in its flow between the southern tip of South America and the northern tip of the Antarctic Peninsula. Observed turbulent kinetic energy dissipation rates are enhanced in the regions corresponding to the ACC frontal zones where strong flow reaches the bottom. In these areas, turbulent dissipation levels reach 10−8 W kg−1 at abyssal and middepths. The mixing enhancement in the frontal regions is sufficient to elevate the diapycnal turbulent diffusivity acting in the deep water above the axis of the ridge to 1 × 10−4 m2 s−1. This level is an order of magnitude larger than the mixing levels observed upstream in the ACC above smoother bathymetry. Outside of the frontal regions, dissipation rates are O(10−10) W kg−1, comparable to the background levels of turbulence found throughout most mid- and low-latitude regions of the global ocean.
    Description: This work was supported by the U.S. National Science Foundation and by the Natural Environment Research Council of the United Kingdom.
    Description: 2013-06-01
    Keywords: Southern Ocean ; Turbulence ; Diapycnal mixing
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  • 18
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    Unknown
    American Meteorological Society
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 698–705, doi:10.1175/JPO-D-12-0119.1.
    Description: Owing to the larger thermal expansion coefficient at higher temperatures, more buoyancy is put into the ocean by heating than is removed by cooling at low temperatures. The authors show that, even with globally balanced thermal and haline surface forcing at the ocean surface, there is a negative density flux and hence a positive buoyancy flux. As shown by McDougall and Garrett, this must be compensated by interior densification on mixing due to the nonlinearity of the equation of state (cabbeling). Three issues that arise from this are addressed: the estimation of the annual input of density forcing, the effects of the seasonal cycle, and the total cabbeling potential of the ocean upon complete mixing. The annual expansion through surface density forcing in a steady-state ocean driven by balanced evaporation–precipitation–runoff (E–P–R) and net radiative budget at the surface Qnet is estimated as 74 000 m3 s−1 (0.07 Sv; 1 Sv ≡ 106 m3 s−1), which would be equivalent to a sea level rise of 6.3 mm yr−1. This is equivalent to approximately 3 times the estimated rate of sea level rise or 450% of the average Mississippi River discharge. When seasonal variations are included, this density forcing increases by 35% relative to the time-mean case to 101 000 m3 s−1 (0.1 Sv). Likely bounds are established on these numbers by using different Qnet and E–P–R datasets and the estimates are found to be robust to a factor of ~2. These values compare well with the cabbeling-induced contraction inferred from independent thermal dissipation rate estimates. The potential sea level decrease upon complete vertical mixing of the ocean is estimated as 230 mm. When horizontal mixing is included, the sea level drop is estimated as 300 mm.
    Description: The authors would like to acknowledge support from the National Aeronautics and Space Administration, Grant NNX12AF59G and the National Science Foundation, Grant OCE-0647949.
    Description: 2013-10-01
    Keywords: Buoyancy ; Conservation equations ; Diapycnal mixing ; Heating ; Mixing ; Heat budgets/fluxes
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  • 19
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 42 (2012): 2206–2228, doi:10.1175/JPO-D-11-0191.1.
    Description: This study investigates the anisotropic properties of the eddy-induced material transport in the near-surface North Atlantic from two independent datasets, one simulated from the sea surface height altimetry and one derived from real-ocean surface drifters, and systematically examines the interactions between the mean- and eddy-induced material transport in the region. The Lagrangian particle dispersion, which is widely used to characterize the eddy-induced tracer fluxes, is quantified by constructing the “spreading ellipses.” The analysis consistently demonstrates that this dispersion is spatially inhomogeneous and strongly anisotropic. The spreading is larger and more anisotropic in the subtropical than in the subpolar gyre, and the largest ellipses occur in the Gulf Stream vicinity. Even at times longer than half a year, the spreading exhibits significant nondiffusive behavior in some parts of the domain. The eddies in this study are defined as deviations from the long-term time-mean. The contributions from the climatological annual cycle, interannual, and subannual (shorter than one year) variability are investigated, and the latter is shown to have the strongest effect on the anisotropy of particle spreading. The influence of the mean advection on the eddy-induced particle spreading is investigated using the “eddy-following-full-trajectories” technique and is found to be significant. The role of the Ekman advection is, however, secondary. The pronounced anisotropy of particle dispersion is expected to have important implications for distributing oceanic tracers, and for parameterizing eddy-induced tracer transfer in non-eddy-resolving models.
    Description: IR was supported by Grant NSF-OCE-0725796. IK would like to acknowledge support by the National Science foundation Grant OCE-0842834.
    Description: 2013-06-01
    Keywords: North Atlantic Ocean ; Diffusion ; Dispersion ; Eddies ; Lagrangian circulation/transport ; Trajectories
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  • 20
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 905–919, doi:10.1175/JPO-D-12-0150.1.
    Description: Interactions between vortices and a shelfbreak current are investigated, with particular attention to the exchange of waters between the continental shelf and slope. The nonlinear, three-dimensional interaction between an anticyclonic vortex and the shelfbreak current is studied in the laboratory while varying the ratio ε of the maximum azimuthal velocity in the vortex to the maximum alongshelf velocity in the shelfbreak current. Strong interactions between the shelfbreak current and the vortex are observed when ε 〉 1; weak interactions are found when ε 〈 1. When the anticyclonic vortex comes in contact with the shelfbreak front during a strong interaction, a streamer of shelf water is drawn offshore and wraps anticyclonically around the vortex. Measurements of the offshore transport and identification of the particle trajectories in the shelfbreak current drawn offshore from the vortex allow quantification of the fraction of the shelfbreak current that is deflected onto the slope; this fraction increases for increasing values of ε. Experimental results in the laboratory are strikingly similar to results obtained from observations in the Middle Atlantic Bight (MAB); after proper scaling, measurements of offshore transport and offshore displacement of shelf water for vortices in the MAB that span a range of values of ε agree well with laboratory predictions.
    Description: Laboratory work was supported by the National Science Foundation through Grant OCE- 0081756. Glider observations in March–April 2006 were supported by the National Science Foundation through Grant OCE-0220769. Glider observations in July– October 2007 were supported by a grant from Raytheon. 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. The REMUS observations were funded by the Office of Naval Research. GGG was supported by the National Science Foundation through Grant OCE-1129125 for analysis and writing.
    Description: 2013-11-01
    Keywords: Continental shelf/slope ; Eddies ; Fronts ; Transport ; Laboratory/physical models
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  • 21
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 30 (2013): 1576–1582, doi:10.1175/JTECH-D-12-00204.1.
    Description: Onset's HOBO U22 Water Temp Pros are small, reliable, relatively inexpensive, self-contained temperature loggers that are widely used in studies of oceans, lakes, and streams. An in-house temperature bath calibration of 158 Temp Pros indicated root-mean-square (RMS) errors ranging from 0.01° to 0.14°C, with one value of 0.23°C, consistent with the factory specifications. Application of a quadratic calibration correction substantially reduced the RMS error to less than 0.009°C in all cases. The primary correction was a bias error typically between −0.1° and 0.15°C. Comparison of water temperature measurements from Temp Pros and more accurate temperature loggers during two oceanographic studies indicates that calibrated Temp Pros have an RMS error of ~0.02°C throughout the water column at night and beneath the surface layer influenced by penetrating solar radiation during the day. Larger RMS errors (up to 0.08°C) are observed near the surface during the day due to solar heating of the black Temp Pro housing. Errors due to solar heating are significantly reduced by wrapping the housing with white electrical tape.
    Description: This work is based on research supported by Awards USA 00002 and KSA 00011 made by King Abdullah University of Science and Technology (KAUST) and by the Ocean Sciences Division of the National Science Foundation under Grant OCE- 0548961.
    Description: 2014-01-01
    Keywords: In situ oceanic observations ; Instrumentation/sensors
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  • 22
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 26 (2013): 4447–4475, doi:10.1175/JCLI-D-12-00589.1.
    Description: Changes in atmospheric CO2 variability during the twenty-first century may provide insight about ecosystem responses to climate change and have implications for the design of carbon monitoring programs. This paper describes changes in the three-dimensional structure of atmospheric CO2 for several representative concentration pathways (RCPs 4.5 and 8.5) using the Community Earth System Model–Biogeochemistry (CESM1-BGC). CO2 simulated for the historical period was first compared to surface, aircraft, and column observations. In a second step, the evolution of spatial and temporal gradients during the twenty-first century was examined. The mean annual cycle in atmospheric CO2 was underestimated for the historical period throughout the Northern Hemisphere, suggesting that the growing season net flux in the Community Land Model (the land component of CESM) was too weak. Consistent with weak summer drawdown in Northern Hemisphere high latitudes, simulated CO2 showed correspondingly weak north–south and vertical gradients during the summer. In the simulations of the twenty-first century, CESM predicted increases in the mean annual cycle of atmospheric CO2 and larger horizontal gradients. Not only did the mean north–south gradient increase due to fossil fuel emissions, but east–west contrasts in CO2 also strengthened because of changing patterns in fossil fuel emissions and terrestrial carbon exchange. In the RCP8.5 simulation, where CO2 increased to 1150 ppm by 2100, the CESM predicted increases in interannual variability in the Northern Hemisphere midlatitudes of up to 60% relative to present variability for time series filtered with a 2–10-yr bandpass. Such an increase in variability may impact detection of changing surface fluxes from atmospheric observations.
    Description: The CESM project is supported by the National Science Foundation and the Office of Science (BER) of the U.S. Department of Energy. Computing resources were provided by the Climate Simulation Laboratory at NCAR’s Computational and Information Systems Laboratory (CISL), sponsored by the National Science Foundation and other agencies. G.K.A. acknowledges support of a NOAA Climate and Global Change postdoctoral fellowship. J.T.R., N.M.M., S.C.D., K.L., and J.K.M. acknowledge support of Collaborative Research: Improved Regional and Decadal Predictions of the Carbon Cycle (NSF AGS-1048827, AGS-1021776,AGS-1048890). TheHIPPO Programwas supported byNSF GrantsATM-0628575,ATM-0628519, and ATM-0628388 to Harvard University, University of California (San Diego), and by University Corporation for Atmospheric Research, University of Colorado/ CIRES, by the NCAR and by the NOAAEarth System Research Laboratory. Sunyoung Park, Greg Santoni, Eric Kort, and Jasna Pittman collected data during HIPPO. The ACME project was supported by the Office of Biological and Environmental Research of the U.S. Department of Energy under Contract DE-AC02- 05CH11231 as part of the Atmospheric Radiation Measurement Program (ARM), the ARM Aerial Facility, and the Terrestrial EcosystemScience Program. TCCON measurements at Eureka were made by the Canadian Network for Detection of Atmospheric Composition Change (CANDAC) with additional support from the Canadian Space Agency. The Lauder TCCON program was funded by the New Zealand Foundation for Research Science and Technology contracts CO1X0204, CO1X0703, and CO1X0406. Measurements at Darwin andWollongong were supported by Australian Research Council Grants DP0879468 and DP110103118 and were undertaken by David Griffith, Nicholas Deutscher, and Ronald Macatangay. We thank Pauli Heikkinen, Petteri Ahonen, and Esko Kyr€o of the Finnish Meteorological Institute for contributing the Sodankyl€a TCCON data. Measurements at Park Falls, Lamont, and Pasadena were supported byNASAGrant NNX11AG01G and the NASA Orbiting Carbon Observatory Program. Data at these sites were obtained by Geoff Toon, Jean- Francois Blavier, Coleen Roehl, and Debra Wunch.
    Description: 2014-01-01
    Keywords: Carbon cycle ; Carbon dioxide ; Aircraft observations ; In situ atmospheric observations ; Remote sensing ; Tracers
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  • 23
    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 Briefings in Bioinformatics 15 (2014): 783-787, doi:10.1093/bib/bbt010.
    Description: The extremely high error rates reported by Keegan et al. in ‘A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE’ (PLoS Comput Biol 2012;8:e1002541) for many next-generation sequencing datasets prompted us to re-examine their results. Our analysis reveals that the presence of conserved artificial sequences, e.g. Illumina adapters, and other naturally occurring sequence motifs accounts for most of the reported errors. We conclude that DRISEE reports inflated levels of sequencing error, particularly for Illumina data. Tools offered for evaluating large datasets need scrupulous review before they are implemented.
    Description: National Institutes of Health [1UH2DK083993 to M.L.S.]; National Science Foundation [BDI- 096026 to S.M.H.].
    Keywords: Next-generation sequencing ; Sequencing error ; Adapter ligation ; PCR ; Quality score
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  • 24
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 42 (2012): 2283–2296, doi:10.1175/JPO-D-11-0227.1.
    Description: The dynamic influence of thermohaline circulation on wind-driven circulation in the South China Sea (SCS) is studied using a simple reduced gravity model, in which the upwelling driven by mixing in the abyssal ocean is treated in terms of an upward pumping distributed at the base of the upper layer. Because of the strong upwelling of deep water, the cyclonic gyre in the northern SCS is weakened, but the anticyclonic gyre in the southern SCS is intensified in summer, while cyclonic gyres in both the southern and northern SCS are weakened in winter. For all seasons, the dynamic influence of thermohaline circulation on wind-driven circulation is larger in the northern SCS than in the southern SCS. Analysis suggests that the upwelling associated with the thermohaline circulation in the deep ocean plays a crucial role in regulating the wind-driven circulation in the upper ocean.
    Description: G. Wang is supported by the National Science Foundation of China (NSFC Grants 41125019, 40725017, and 40976017).D.Chen is supported by grants from the Ministry of Science and Technology (2010DFA21012), the State Oceanic Administration (201105018), and the NSFC (91128204).
    Description: 2013-06-01
    Keywords: Abyssal circulation ; Dynamics ; Ocean circulation ; Upwelling/downwelling
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  • 25
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 259–282, doi:10.1175/JPO-D-11-0194.1.
    Description: This study reports on observations of turbulent dissipation and internal wave-scale flow properties in a standing meander of the Antarctic Circumpolar Current (ACC) north of the Kerguelen Plateau. The authors characterize the intensity and spatial distribution of the observed turbulent dissipation and the derived turbulent mixing, and consider underpinning mechanisms in the context of the internal wave field and the processes governing the waves’ generation and evolution. The turbulent dissipation rate and the derived diapycnal diffusivity are highly variable with systematic depth dependence. The dissipation rate is generally enhanced in the upper 1000–1500 m of the water column, and both the dissipation rate and diapycnal diffusivity are enhanced in some places near the seafloor, commonly in regions of rough topography and in the vicinity of strong bottom flows associated with the ACC jets. Turbulent dissipation is high in regions where internal wave energy is high, consistent with the idea that interior dissipation is related to a breaking internal wave field. Elevated turbulence occurs in association with downward-propagating near-inertial waves within 1–2 km of the surface, as well as with upward-propagating, relatively high-frequency waves within 1–2 km of the seafloor. While an interpretation of these near-bottom waves as lee waves generated by ACC jets flowing over small-scale topographic roughness is supported by the qualitative match between the spatial patterns in predicted lee wave radiation and observed near-bottom dissipation, the observed dissipation is found to be only a small percentage of the energy flux predicted by theory. The mismatch suggests an alternative fate to local dissipation for a significant fraction of the radiated energy.
    Description: SW acknowledges the support of the Grantham Institute for Climate Change, Imperial College London. ACNG acknowledges the support of a NERC Advanced Research Fellowship (Grant NE/C517633/1). KLP acknowledges support from Woods Hole Oceanographic Institution bridge support funds.
    Description: 2013-08-01
    Keywords: Diapycnal mixing ; Internal waves ; Turbulence
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  • 26
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 766–789, doi:10.1175/JPO-D-12-0141.1.
    Description: Nonlinear energy transfers from the semidiurnal internal tide to high-mode, near-diurnal motions are documented near Kaena Ridge, Hawaii, an energetic generation site for the baroclinic tide. Data were collected aboard the Research Floating Instrument Platform (FLIP) over a 35-day period during the fall of 2002, as part of the Hawaii Ocean Mixing Experiment (HOME) Nearfield program. Energy transfer terms for a PSI resonant interaction at midlatitude are identified and compared to those for near-inertial PSI close to the M2 critical latitude. Bispectral techniques are used to demonstrate significant energy transfers in the Nearfield, between the low-mode M2 internal tide and subharmonic waves with frequencies near M2/2 and vertical wavelengths of O(120 m). A novel prefilter is used to test the PSI wavenumber resonance condition, which requires the subharmonic waves to propagate in opposite vertical directions. Depth–time maps of the interactions, formed by directly estimating the energy transfer terms, show that energy is transferred predominantly from the tide to subharmonic waves, but numerous reverse energy transfers are also found. A net forward energy transfer rate of 2 × 10−9 W kg−1 is found below 400 m. The suggestion is that the HOME observations of energy transfer from the tide to subharmonic waves represent a first step in the open-ocean energy cascade. Observed PSI transfer rates could account for a small but significant fraction of the turbulent dissipation of the tide within 60 km of Kaena Ridge. Further extrapolation suggests that integrated PSI energy transfers equatorward of the M2 critical latitude may be comparable to PSI energy transfers previously observed near 28.8°N.
    Description: This work was supported by the National Science Foundation and the Office of Naval Research.
    Description: 2013-10-01
    Keywords: Diapycnal mixing ; Energy transport ; Internal waves ; Nonlinear dynamics ; Topographic effects ; In situ oceanic observations
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  • 27
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 26 (2013): 2833–2844, doi:10.1175/JCLI-D-12-00181.1.
    Description: The Community Climate System Model, version 4 (CCSM4) is used to assess the climate impact of wind-generated near-inertial waves (NIWs). Even with high-frequency coupling, CCSM4 underestimates the strength of NIWs, so that a parameterization for NIWs is developed and included into CCSM4. Numerous assumptions enter this parameterization, the core of which is that the NIW velocity signal is detected during the model integration, and amplified in the shear computation of the ocean surface boundary layer module. It is found that NIWs deepen the ocean mixed layer by up to 30%, but they contribute little to the ventilation and mixing of the ocean below the thermocline. However, the deepening of the tropical mixed layer by NIWs leads to a change in tropical sea surface temperature and precipitation. Atmospheric teleconnections then change the global sea level pressure fields so that the midlatitude westerlies become weaker. Unfortunately, the magnitude of the real air-sea flux of NIW energy is poorly constrained by observations; this makes the quantitative assessment of their climate impact rather uncertain. Thus, a major result of the present study is that because of its importance for global climate the uncertainty in the observed tropical NIW energy has to be reduced.
    Description: This research was funded as part of the Climate Process Team on internal wave-driven mixing with NSF Grant Nr E0968771 at NCAR.
    Description: 2013-11-01
    Keywords: Fronts ; Inertia-gravity waves ; Mesoscale processes ; Mixing ; Nonlinear dynamics
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  • 28
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    Unknown
    American Meteorological Society
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 1028–1041, doi:10.1175/JPO-D-12-0159.1.
    Description: The circulation induced by the interaction of surface Ekman transport with an island is considered using both numerical models and linear theory. The basic response is similar to that found for the interaction of Ekman layers and an infinite boundary, namely downwelling (upwelling) in narrow boundary layers and deformation-scale baroclinic boundary layers with associated strong geostrophic flows. The presence of the island boundary, however, allows the pressure signal to propagate around the island so that the regions of upwelling and downwelling are dynamically connected. In the absence of stratification the island acts as an effective barrier to the Ekman transport. The presence of stratification supports baroclinic boundary currents that provide an advective pathway from one side of the island to the other. The resulting steady circulation is quite complex. Near the island, both geostrophic and ageostrophic velocity components are typically large. The density anomaly is maximum below the surface and, for positive wind stress, exhibits an anticyclonic phase rotation with depth (direction of Kelvin wave propagation) such that anomalously warm water can lie below regions of Ekman upwelling. The horizontal and vertical velocities exhibit similar phase changes with depth. The addition of a sloping bottom can act to shield the deep return flow from interacting with the island and providing mass transport into/out of the surface Ekman layer. In these cases, the required transport is provided by a pair of recirculation gyres that connect the narrow upwelling/downwelling boundary layers on the eastern and western sides of the island, thus directly connecting the Ekman transport across the island.
    Description: This study was supported by the National Science Foundation under Grants OCE-0826656 and OCE-0959381 (MAS), and OCE-0925061 (JP).
    Description: 2013-11-01
    Keywords: Coastal flows ; Ekman pumping/transport ; Ocean dynamics
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  • 29
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 222–230, doi:10.1175/JPO-D-12-099.1.
    Description: Observations with fine horizontal resolution are used to identify the horizontal scales of variability over the Middle Atlantic Bight (MAB) shelf break and continental rise. Spray gliders collected observations along two alongshelf transects over the continental rise in March–April 2006 and along 16 cross-shelf transects over the shelf break and continental rise during July–October 2007. Horizontal resolution varied from 1 km or finer over the shelf to 6 km in deep water. These observations allow horizontal thermohaline variability offshore of the MAB shelf break to be examined for the first time. Structure functions of temperature and salinity, the mean square difference between observations separated by specified distances, reveal the horizontal spatial scales in the region. Exponential (e-folding) scales of temperature and salinity increase from 8–13 km near the shelf break to about 30 km over the continental rise. Just offshore of the shelf break, alongshelf structure functions exhibit periodicity with a 40–50-km wavelength that matches the wavelength of shelfbreak frontal meanders. Farther offshore, alongshelf structure functions suggest a dominant wavelength of 175–250 km, but these scales are only marginally resolved by the available observations. Examination of structure functions of along-isopycnal salinity (i.e., spice) suggests that interleaving of shelf and slope water masses contributes most of the horizontal variability near the MAB shelf break, but heaving of isopycnals is the primary source of horizontal variability over the continental rise.
    Description: Glider observations in March–April 2006 were supported by the National Science Foundation through Grant OCE-0220769. Glider observations in July–October 2007 were supported by a grant from Raytheon. 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. GGG was supported by the National Science Foundation under Grant OCE-1129125.
    Description: 2013-07-01
    Keywords: Continental shelf/slope ; North Atlantic Ocean ; Fronts ; In situ oceanic observations ; Profilers, oceanic
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  • 30
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013]. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 26 (2013): 6775–6800, doi:10.1175/JCLI-D-12-00184.1.
    Description: Ocean carbon uptake and storage simulated by the Community Earth System Model, version 1–Biogeochemistry [CESM1(BGC)], is described and compared to observations. Fully coupled and ocean-ice configurations are examined; both capture many aspects of the spatial structure and seasonality of surface carbon fields. Nearly ubiquitous negative biases in surface alkalinity result from the prescribed carbonate dissolution profile. The modeled sea–air CO2 fluxes match observationally based estimates over much of the ocean; significant deviations appear in the Southern Ocean. Surface ocean pCO2 is biased high in the subantarctic and low in the sea ice zone. Formation of the water masses dominating anthropogenic CO2 (Cant) uptake in the Southern Hemisphere is weak in the model, leading to significant negative biases in Cant and chlorofluorocarbon (CFC) storage at intermediate depths. Column inventories of Cant appear too high, by contrast, in the North Atlantic. In spite of the positive bias, this marks an improvement over prior versions of the model, which underestimated North Atlantic uptake. The change in behavior is attributable to a new parameterization of density-driven overflows. CESM1(BGC) provides a relatively robust representation of the ocean–carbon cycle response to climate variability. Statistical metrics of modeled interannual variability in sea–air CO2 fluxes compare reasonably well to observationally based estimates. The carbon cycle response to key modes of climate variability is basically similar in the coupled and forced ocean-ice models; however, the two differ in regional detail and in the strength of teleconnections.
    Description: The CESM project is supported by the National Science Foundation and the Office of Science (BER) of the U.S. Department of Energy. SCD acknowledges support of Collaborative Research: Improved Regional and Decadal Predictions of the Carbon Cycle (NSFAGS- 1048827).
    Description: 2014-03-15
    Keywords: Carbon cycle ; Carbon dioxide ; Climate change ; Climate models ; Coupled models ; Oceanic chemistry
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  • 31
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 26 (2013): 2546–2556, doi:10.1175/JCLI-D-12-00062.1.
    Description: Diurnal sea surface warming affects the fluxes of latent heat, sensible heat, and upwelling longwave radiation. Diurnal warming most typically reaches maximum values of 3°C, although very localized events may reach 7°–8°C. An analysis of multiple years of diurnal warming over the global ice-free oceans indicates that heat fluxes determined by using the predawn sea surface temperature can differ by more than 100% in localized regions over those in which the sea surface temperature is allowed to fluctuate on a diurnal basis. A comparison of flux climatologies produced by these two analyses demonstrates that significant portions of the tropical oceans experience differences on a yearly average of up to 10 W m−2. Regions with the highest climatological differences include the Arabian Sea and the Bay of Bengal, as well as the equatorial western and eastern Pacific Ocean, the Gulf of Mexico, and the western coasts of Central America and North Africa. Globally the difference is on average 4.45 W m−2. The difference in the evaporation rate globally is on the order of 4% of the total ocean–atmosphere evaporation. Although the instantaneous, year-to-year, and seasonal fluctuations in various locations can be substantial, the global average differs by less than 0.1 W m−2 throughout the entire 10-yr time period. A global heat budget that uses atmospheric datasets containing diurnal variability but a sea surface temperature that has removed this signal may be underestimating the flux to the atmosphere by a fairly constant value.
    Description: We acknowledge, with pleasure, NASA Physical Oceanography program support and the support of the NOAA Climate Data Records program. A. Bogdanoff was also supported by the NASA Graduate Student Researchers Program and the Department of Defense through the National Defense Science & Engineering Graduate (NDSEG) Fellowship Program.
    Description: 2013-10-15
    Keywords: Air-sea interaction ; Heat budgets/fluxes ; Moisture/moisture budget ; Surface fluxes ; Surface temperature
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  • 32
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 26 (2013): 2719–2740, doi:10.1175/JCLI-D-12-00436.1.
    Description: The estimate of surface irradiance on a global scale is possible through radiative transfer calculations using satellite-retrieved surface, cloud, and aerosol properties as input. Computed top-of-atmosphere (TOA) irradiances, however, do not necessarily agree with observation-based values, for example, from the Clouds and the Earth’s Radiant Energy System (CERES). This paper presents a method to determine surface irradiances using observational constraints of TOA irradiance from CERES. A Lagrange multiplier procedure is used to objectively adjust inputs based on their uncertainties such that the computed TOA irradiance is consistent with CERES-derived irradiance to within the uncertainty. These input adjustments are then used to determine surface irradiance adjustments. Observations by the Atmospheric Infrared Sounder (AIRS), Cloud–Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO), CloudSat, and Moderate Resolution Imaging Spectroradiometer (MODIS) that are a part of the NASA A-Train constellation provide the uncertainty estimates. A comparison with surface observations from a number of sites shows that the bias [root-mean-square (RMS) difference] between computed and observed monthly mean irradiances calculated with 10 years of data is 4.7 (13.3) W m−2 for downward shortwave and −2.5 (7.1) W m−2 for downward longwave irradiances over ocean and −1.7 (7.8) W m−2 for downward shortwave and −1.0 (7.6) W m−2 for downward longwave irradiances over land. The bias and RMS error for the downward longwave and shortwave irradiances over ocean are decreased from those without constraint. Similarly, the bias and RMS error for downward longwave over land improves, although the constraint does not improve downward shortwave over land. This study demonstrates how synergetic use of multiple instruments (CERES, MODIS, CALIPSO, CloudSat, AIRS, and geostationary satellites) improves the accuracy of surface irradiance computations.
    Description: The work was supported by theNASACERES and, in part, Energy Water Cycle Study (NEWS) projects.
    Description: 2013-11-01
    Keywords: Energy budget/balance ; Radiation budgets ; Radiative fluxes ; Radiative transfer
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  • 33
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 1611–1626, doi:10.1175/JPO-D-12-0204.1.
    Description: A new method is proposed for extrapolating subsurface velocity and density fields from sea surface density and sea surface height (SSH). In this, the surface density is linked to the subsurface fields via the surface quasigeostrophic (SQG) formalism, as proposed in several recent papers. The subsurface field is augmented by the addition of the barotropic and first baroclinic modes, whose amplitudes are determined by matching to the sea surface height (pressure), after subtracting the SQG contribution. An additional constraint is that the bottom pressure anomaly vanishes. The method is tested for three regions in the North Atlantic using data from a high-resolution numerical simulation. The decomposition yields strikingly realistic subsurface fields. It is particularly successful in energetic regions like the Gulf Stream extension and at high latitudes where the mixed layer is deep, but it also works in less energetic eastern subtropics. The demonstration highlights the possibility of reconstructing three-dimensional oceanic flows using a combination of satellite fields, for example, sea surface temperature (SST) and SSH, and sparse (or climatological) estimates of the regional depth-resolved density. The method could be further elaborated to integrate additional subsurface information, such as mooring measurements.
    Description: JW and AM were supported by NASA (NNX12AD47G) and NSF (OCE 0928617). JLM was supported by the Office of Naval Research and the Office of Science (BER), U.S. Department of Energy under DE-GF0205ER64119. GRF is supported by OCE-0752346 and JHL by NORSEE (Nordic Seas Eddy Exchanges) funded by the Norwegian Research Council.
    Description: 2014-02-01
    Keywords: Eddies ; Ocean dynamics ; Potential vorticity ; Surface pressure ; Surface temperature ; Inverse methods
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  • 34
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 26 (2013): 9291–9312, doi:10.1175/JCLI-D-12-00566.1.
    Description: The authors compare Community Earth System Model results to marine observations for the 1990s and examine climate change impacts on biogeochemistry at the end of the twenty-first century under two future scenarios (Representative Concentration Pathways RCP4.5 and RCP8.5). Late-twentieth-century seasonally varying mixed layer depths are generally within 10 m of observations, with a Southern Ocean shallow bias. Surface nutrient and chlorophyll concentrations exhibit positive biases at low latitudes and negative biases at high latitudes. The volume of the oxygen minimum zones is overestimated. The impacts of climate change on biogeochemistry have similar spatial patterns under RCP4.5 and RCP8.5, but perturbation magnitudes are larger under RCP8.5. Increasing stratification leads to weaker nutrient entrainment and decreased primary and export production (〉30% over large areas). The global-scale decreases in primary and export production scale linearly with the increases in mean sea surface temperature. There are production increases in the high nitrate, low chlorophyll (HNLC) regions, driven by lateral iron inputs from adjacent areas. The increased HNLC export partially compensates for the reductions in non-HNLC waters (~25% offset). Stabilizing greenhouse gas emissions and climate by the end of this century (as in RCP4.5) will minimize the changes to nutrient cycling and primary production in the oceans. In contrast, continued increasing emission of CO2 (as in RCP8.5) will lead to reduced productivity and significant modifications to ocean circulation and biogeochemistry by the end of this century, with more drastic changes beyond the year 2100 as the climate continues to rapidly warm.
    Description: The CESM project is supported by the National Science Foundation and the Office of Science (BER) of the U.S. Department of Energy. S.C.D. acknowledges support of Collaborative Research: Improved Regional and Decadal Predictions of the Carbon Cycle (NSF AGS-1048827). This work was supported by NSF grants (ARC-0902045 and AGS-1021776 to Moore and AGS- 1048890 to Moore, Lindsay, and Doney).
    Description: 2014-06-01
    Keywords: Climate prediction ; Forecast verification/skill ; Climate models ; Ecological models ; Model evaluation/performance ; Ocean models
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  • 35
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 26 (2013): 9247–9290, doi:10.1175/JCLI-D-12-00593.1.
    Description: This is the second part of a three-part paper on North American climate in phase 5 of the Coupled Model Intercomparison Project (CMIP5) that evaluates the twentieth-century simulations of intraseasonal to multidecadal variability and teleconnections with North American climate. Overall, the multimodel ensemble does reasonably well at reproducing observed variability in several aspects, but it does less well at capturing observed teleconnections, with implications for future projections examined in part three of this paper. In terms of intraseasonal variability, almost half of the models examined can reproduce observed variability in the eastern Pacific and most models capture the midsummer drought over Central America. The multimodel mean replicates the density of traveling tropical synoptic-scale disturbances but with large spread among the models. On the other hand, the coarse resolution of the models means that tropical cyclone frequencies are underpredicted in the Atlantic and eastern North Pacific. The frequency and mean amplitude of ENSO are generally well reproduced, although teleconnections with North American climate are widely varying among models and only a few models can reproduce the east and central Pacific types of ENSO and connections with U.S. winter temperatures. The models capture the spatial pattern of Pacific decadal oscillation (PDO) variability and its influence on continental temperature and West Coast precipitation but less well for the wintertime precipitation. The spatial representation of the Atlantic multidecadal oscillation (AMO) is reasonable, but the magnitude of SST anomalies and teleconnections are poorly reproduced. Multidecadal trends such as the warming hole over the central–southeastern United States and precipitation increases are not replicated by the models, suggesting that observed changes are linked to natural variability.
    Description: The authors acknowledge the support of NOAA/Climate Program Office/Modeling, Analysis, Predictions and Projections (MAPP) program as part of the CMIP5 Task Force.
    Description: 2014-06-01
    Keywords: North America ; Regional effects ; Coupled models ; Decadal variability ; Interannual variability ; Intraseasonal variability
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  • 36
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    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 193(3), pp. 1399-1414, ISSN: 0956-540X
    Publication Date: 2019-07-16
    Description: The Boreas Basin is located in the Norwegian-Greenland Sea between Northeast Greenland and Svalbard. Towards the east, it is bounded by the ultraslow mid-ocean Knipovich Ridge. Here, we present a 340-km-long seismic refraction line acquired during the expedition ARK-XXIV/3 of research vessel Polarstern in 2009, using 18 ocean bottom seismometers. It crosses the central Boreas Basin from the Knipovich Ridge to the Northeast Greenland margin. Thus, the line provides the first reliable crustal structure information of this basin. In addition, the gravity data acquired parallel to the seismic refraction line are used to calculate a 2.5-D gravity model. The P-wave velocity model shows an unusual ∼3-km-thin oceanic crust with seismic velocities less than 6.3 km s−1, indicating the absence of a significant oceanic layer 3. Mantle velocities vary between 7.5 kms−1 in the uppermost mantle and 8.0 km s−1 at approximately 15 km depth. The low velocities within the upper mantle may be explained by 13 per cent serpentinisation, which is negligible at about 15 km depth. Furthermore, the S-wave velocity model shows low Vp/Vs ratios in the mantle, indicating a highly serpentinised mantle at shallow depths. The gravity model has crustal densities between 2.3 and 2.9 g cm−3, which also point towards the absence of a significant thick oceanic layer 3. The results of our seismic refraction line and other geophysical data indicate that the entire Boreas Basin opened at ultraslow spreading rates since at least ∼28 Ma. No evidence for an extinct spreading ridge in the centre of the Boreas Basin was found.
    Repository Name: EPIC Alfred Wegener Institut
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  • 37
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 1841–1861, doi:10.1175/JPO-D-12-0231.1.
    Description: In this idealized numerical modeling study, the composition of residual sediment fluxes in energetic (e.g., weakly or periodically stratified) tidal estuaries is investigated by means of one-dimensional water column models, with some focus on the sediment availability. Scaling of the underlying dynamic equations shows dependence of the results on the Simpson number (relative strength of horizontal density gradient) and the Rouse number (relative settling velocity) as well as impacts of the Unsteadiness number (relative tidal frequency). Here, the parameter space given by the Simpson and Rouse numbers is mainly investigated. A simple analytical model based on the assumption of stationarity shows that for small Simpson and Rouse numbers sediment flux is down estuary and vice versa for large Simpson and Rouse numbers. A fully dynamic water column model coupled to a second-moment turbulence closure model allows to decompose the sediment flux profiles into contributions from the transport flux (product of subtidal velocity and sediment concentration profiles) and the fluctuation flux profiles (tidal covariance between current velocity and sediment concentration). Three different types of bottom sediment pools are distinguished to vary the sediment availability, by defining a time scale for complete sediment erosion. For short erosion times scales, the transport sediment flux may dominate, but for larger erosion time scales the fluctuation sediment flux largely dominates the tidal sediment flux. When quarter-diurnal components are added to the tidal forcing, up-estuary sediment fluxes are strongly increased for stronger and shorter flood tides and vice versa. The theoretical results are compared to field observations in a tidally energetic inlet.
    Description: Project funding was provided by the German Research Foundation (DFG) in the framework of the Project ECOWS (Role of Estuarine Circulation for Transport of Suspended Particulate Matter in the Wadden Sea, BU 1199/11) and by the German Federal Ministry of Research and Education in the framework of the Project PACE [The future of the Wadden Sea sediment fluxes: still keeping pace with sea level rise? (FKZ 03F0634A)].
    Description: 2014-03-01
    Keywords: Channel flows ; Coastal flows ; Mixing ; Transport ; Turbulence ; Single column models
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  • 38
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 1940–1958, doi:10.1175/JPO-D-13-020.1.
    Description: The spatial structure of the tidal and background circulation over the inner shelf south of Martha's Vineyard, Massachusetts, was investigated using observations from a high-resolution, high-frequency coastal radar system, paired with satellite SSTs and in situ ADCP velocities. Maximum tidal velocities for the dominant semidiurnal constituent increased from 5 to 35 cm s−1 over the 20-km-wide domain with phase variations up to 60°. A northeastward jet along the eastern edge and a recirculation region inshore dominated the annually averaged surface currents, along with a separate along-shelf jet offshore. Owing in part to this variable circulation, the spatial structure of seasonal SST anomalies had implications for the local heat balance. Cooling owing to the advective heat flux divergence was large enough to offset more than half of the seasonal heat gain owing to surface heat flux. Tidal stresses were the largest terms in the mean along- and across-shelf momentum equations in the area of the recirculation, with residual wind stress and the Coriolis term dominating to the west and south, respectively. The recirculation was strongest in summer, with mean winds and tidal stresses accounting for much of the differences between summer and winter mean circulation. Despite the complex bathymetry and short along-shelf spatial scales, a simple model of tidal rectification was able to recreate the features of the northeastward jet and match an estimate of the across-shelf structure of sea surface height inferred from the residual of the momentum analysis.
    Description: 2014-03-01
    Keywords: Coastal flows ; Momentum ; Sea surface temperature ; Tides ; Surface observations
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  • 39
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 26 (2013): 1685–1701, doi:10.1175/JCLI-D-12-00267.1.
    Description: The influence of the atmospheric circulation on the winter air–sea heat fluxes over the northern Red Sea is investigated during the period 1985–2011. The analysis based on daily heat flux values reveals that most of the net surface heat exchange variability depends on the behavior of the turbulent components of the surface flux (the sum of the latent and sensible heat). The large-scale composite sea level pressure (SLP) maps corresponding to turbulent flux minima and maxima show distinct atmospheric circulation patterns associated with each case. In general, extreme heat loss (with turbulent flux lower than −400 W m−2) over the northern Red Sea is observed when anticyclonic conditions prevail over an area extending from the Mediterranean Sea to eastern Asia along with a recession of the equatorial African lows system. Subcenters of high pressure associated with this pattern generate the required steep SLP gradient that enhances the wind magnitude and transfers cold and dry air masses from higher latitudes. Conversely, turbulent flux maxima (heat loss minimization with values from −100 to −50 W m−2) are associated with prevailing low pressures over the eastern Mediterranean and an extended equatorial African low that reaches the southern part of the Red Sea. In this case, a smooth SLP field over the northern Red Sea results in weak winds over the area that in turn reduce the surface heat loss. At the same time, southerlies blowing along the main axis of the Red Sea transfer warm and humid air northward, favoring heat flux maxima.
    Description: The authors acknowledge the Red Sea Research Center (RSRC) at King Abdullah University for Science and Technology (KAUST) for kindly sponsoring this study. Amy Bower was supported by Awards USA 00002, KSA 00011, and KSA 00011/02 made by KAUST to the Woods Hole Oceanographic Institution.
    Description: 2013-09-01
    Keywords: Extreme events ; Air-sea interaction ; Forcing ; Surface fluxes ; Trends
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  • 40
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 26 (2013): 1669–1684, doi:10.1175/JCLI-D-12-00246.1.
    Description: Climate change west of the Antarctic Peninsula is the most rapid of anywhere in the Southern Hemisphere, with associated changes in the rates and distributions of freshwater inputs to the ocean. Here, results from the first comprehensive survey of oxygen isotopes in seawater in this region are used to quantify spatial patterns of meteoric water (glacial discharge and precipitation) separately from sea ice melt. High levels of meteoric water are found close to the coast, due to orographic effects on precipitation and strong glacial discharge. Concentrations decrease offshore, driving significant southward geostrophic flows (up to ~30 cm s−1). These produce high meteoric water concentrations at the southern end of the sampling grid, where collapse of the Wilkins Ice Shelf may also have contributed. Sea ice melt concentrations are lower than meteoric water and patchier because of the mobile nature of the sea ice itself. Nonetheless, net sea ice production in the northern part of the sampling grid is inferred; combined with net sea ice melt in the south, this indicates an overall southward ice motion. The survey is contextualized temporally using a decade-long series of isotope data from a coastal Antarctic Peninsula site. This shows a temporal decline in meteoric water in the upper ocean, contrary to expectations based on increasing precipitation and accelerating deglaciation. This is driven by the increasing occurrence of deeper winter mixed layers and has potential implications for concentrations of trace metals supplied to the euphotic zone by glacial discharge. As the regional freshwater system evolves, the continuing isotope monitoring described here will elucidate the ongoing impacts on climate and the ecosystem.
    Description: The Palmer LTER participants acknowledge Award 0823101 from the Organisms and Ecosystems program in NSF OPP
    Description: 2013-09-01
    Keywords: Southern Ocean ; Ocean circulation ; Freshwater ; Precipitation ; Snowmelt/icemelt ; Isotopic analysis
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  • 41
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 39 (2013): 450–469, doi:10.1175/JTECH-D-12-00078.1.
    Description: A surface mooring was deployed in the Gulf Stream for 15 months to investigate the role of air–sea interaction in mode water formation and other processes. The accuracies of the near-surface meteorological and oceanographic measurements are investigated. In addition, the impacts of these measurement errors on the estimation and study of the air–sea fluxes in the Gulf Stream are discussed. Pre- and postdeployment calibrations together with in situ comparison between shipboard and moored sensors supported the identification of biases due to sensor drifts, sensor electronics, and calibration errors. A postdeployment field study was used to further investigate the performance of the wind sensors. The use of redundant sensor sets not only supported the filling of data gaps but also allowed an examination of the contribution of random errors. Air–sea fluxes were also analyzed and computed from both Coupled Ocean–Atmosphere Response Experiment (COARE) bulk parameterization and using direct covariance measurements. The basic conclusion is that the surface buoy deployed in the Gulf Stream to support air–sea interaction research was successful, providing an improved 15-month record of surface meteorology, upper-ocean variability, and air–sea fluxes with known accuracies. At the same time, the coincident deployment of mean meteorological and turbulent flux sensors proved to be a successful strategy to certify the validity of the bulk formula fluxes over the midrange of wind speeds and to support further work to address the present shortcomings of the bulk formula methods at the low and high wind speeds.
    Description: The National Science Foundation (Grant OCE04-24536) funded this work, as part of the CLIVAR Mode Water Dynamics Experiment (CLIMODE). The Vetlesen Foundation is also acknowledged for the early support of S. Bigorre.
    Description: 2013-09-01
    Keywords: Atmosphere-ocean interaction ; Buoy observations
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  • 42
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 602–615, doi:10.1175/JPO-D-12-055.1.
    Description: The ocean interior stratification and meridional overturning circulation are largely sustained by diapycnal mixing. The breaking of internal tides is a major source of diapycnal mixing. Many recent climate models parameterize internal-tide breaking using the scheme of St. Laurent et al. While this parameterization dynamically accounts for internal-tide generation, the vertical distribution of the resultant mixing is ad hoc, prescribing energy dissipation to decay exponentially above the ocean bottom with a fixed-length scale. Recently, Polzin formulated a dynamically based parameterization, in which the vertical profile of dissipation decays algebraically with a varying decay scale, accounting for variable stratification using Wentzel–Kramers–Brillouin (WKB) stretching. This study compares two simulations using the St. Laurent and Polzin formulations in the Climate Model, version 2G (CM2G), ocean–ice–atmosphere coupled model, with the same formulation for internal-tide energy input. Focusing mainly on the Pacific Ocean, where the deep low-frequency variability is relatively small, the authors show that the ocean state shows modest but robust and significant sensitivity to the vertical profile of internal-tide-driven mixing. Therefore, not only the energy input to the internal tides matters, but also where in the vertical it is dissipated.
    Description: This work is a component of the Internal- Wave Driven Mixing Climate Process Team funded by the National Science Foundation Grant OCE-0968721 and the National Oceanic and Atmospheric Administration, U.S. Department of Commerce, Award NA08OAR4320752.
    Description: 2013-09-01
    Keywords: Diapycnal mixing ; Internal waves ; Subgrid-scale processes ; Ocean models ; Parameterization
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  • 43
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 25 (2012): 7781–7801, doi:10.1175/JCLI-D-11-00442.1.
    Description: Air–sea fluxes from the Community Climate System Model version 4 (CCSM4) are compared with the Coordinated Ocean-Ice Reference Experiment (CORE) dataset to assess present-day mean biases, variability errors, and late twentieth-century trend differences. CCSM4 is improved over the previous version, CCSM3, in both air–sea heat and freshwater fluxes in some regions; however, a large increase in net shortwave radiation into the ocean may contribute to an enhanced hydrological cycle. The authors provide a new baseline for assessment of flux variance at annual and interannual frequency bands in future model versions and contribute a new metric for assessing the coupling between the atmospheric and oceanic planetary boundary layer (PBL) schemes of any climate model. Maps of the ratio of CCSM4 variance to CORE reveal that variance on annual time scales has larger error than on interannual time scales and that different processes cause errors in mean, annual, and interannual frequency bands. Air temperature and specific humidity in the CCSM4 atmospheric boundary layer (ABL) follow the sea surface conditions much more closely than is found in CORE. Sensible and latent heat fluxes are less of a negative feedback to sea surface temperature warming in the CCSM4 than in the CORE data with the model’s PBL allowing for more heating of the ocean’s surface.
    Description: The CESM project is supported by the National Science Foundation and the Office of Science (BER) of the U.S. Department of Energy. S. Stevensonwas supported byNASAGrantNNX09A020H and B. Fox-Kemper by Grants NSF 0934737 and NASA NNX09AF38G.
    Description: 2013-05-15
    Keywords: Atmosphere-ocean interaction ; Boundary layer ; Sea surface temperature ; Climate models ; Coupled models ; Model evaluation/performance
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  • 44
    Publication Date: 2013-06-17
    Print ISSN: 1552-4450
    Electronic ISSN: 1552-4469
    Topics: Biology , Chemistry and Pharmacology
    Published by Springer Nature
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    Publication Date: 2013-05-12
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    Topics: Biology , Chemistry and Pharmacology
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    Publication Date: 2013-05-22
    Print ISSN: 1476-1122
    Electronic ISSN: 1476-4660
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Natural Sciences in General , Physics
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  • 48
    Publication Date: 2013-11-21
    Print ISSN: 1476-1122
    Electronic ISSN: 1476-4660
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Natural Sciences in General , Physics
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  • 49
    Publication Date: 2013-05-22
    Print ISSN: 1476-1122
    Electronic ISSN: 1476-4660
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Natural Sciences in General , Physics
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  • 50
    Publication Date: 2013-05-24
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 51
    Publication Date: 1995-07-01
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
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    Publication Date: 1995-06-01
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    Publication Date: 1995-09-01
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    Publication Date: 1995-12-01
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    Publication Date: 1995-11-01
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  • 56
    Publication Date: 1995-12-01
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    Publication Date: 1995-10-01
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    Publication Date: 1995-10-01
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    Publication Date: 1995-11-01
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    Publication Date: 1995-10-01
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    Publication Date: 1995-05-01
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    Publication Date: 1995-05-01
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    Publication Date: 1995-05-01
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    Publication Date: 1995-09-01
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    Publication Date: 1995-12-01
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    Publication Date: 1995-11-01
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    Publication Date: 1995-11-01
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    Publication Date: 1995-09-01
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  • 71
    Publication Date: 1995-06-01
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  • 72
    Publication Date: 2013-01-23
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 73
    Publication Date: 2013-09-07
    Description: The predicted effect of effective population size on the distribution of fitness effects and substitution rate is critically dependent on the relationship between sequence and fitness. This highlights the importance of using models that are informed by the molecular biology, biochemistry, and biophysics of the evolving systems. We describe a computational model based on fundamental aspects of biophysics, the requirement for (most) proteins to be thermodynamically stable. Using this model, we find that differences in population size have minimal impact on the distribution of population-scaled fitness effects, as well as on the rate of molecular evolution. This is because larger populations result in selection for more stable proteins that are less affected by mutations. This reduction in the magnitude of the fitness effects almost exactly cancels the greater selective pressure resulting from the larger population size. Conversely, changes in the population size in either direction cause transient increases in the substitution rate. As differences in population size often correspond to changes in population size, this makes comparisons of substitution rates in different lineages difficult to interpret.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 74
    Publication Date: 2013-09-07
    Description: The magnetism of graphene has remained divergent and controversial due to absence of reliable experimental results. Here we show the intrinsic magnetism of graphene edge states revealed based on unidirectional aligned graphene sheets derived from completely carbonized SiC crystals. It is found that ferromagnetism, antiferromagnetism and diamagnetism along with a probable superconductivity exist in the graphene with irregular zigzag edges. A phase diagram is constructed to show the evolution of the magnetism. The ferromagnetic ordering curie-temperature of the fundamental magnetic order unit (FMOU) is 820 ± 80 K. The antiferromagnetic ordering Neel temperature of the FMOUs belonging to different sublattices is about 54 ± 2 K. The diamagnetism is similar to that of graphite and can be well described by the Kotosonov's equation. Our experimental results provide new evidences to clarify the controversial experimental phenomena observed in graphene and contribute to a deeper insight into the nature of magnetism in graphene based system. Scientific Reports 3 doi: 10.1038/srep02599
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 75
    Publication Date: 2013-09-07
    Description: The detection, differentiation and visualization of compounds such as gases, liquids or ions are key challenges for the design of selective optical chemosensors. Optical chemical sensors employ a transduction mechanism that converts a specific analyte recognition event into an optical signal. Here we report a novel concept for fluoride ion sensing where a porous crystalline framework serves as a host for a fluorescent reporter molecule. The detection is based on the decomposition of the host scaffold which induces the release of the fluorescent dye molecule. Specifically, the hybrid composite of the metal-organic framework NH2-MIL-101(Al) and fluorescein acting as reporter shows an exceptional turn-on fluorescence in aqueous fluoride-containing solutions. Using this novel strategy, the optical detection of fluoride is extremely sensitive and highly selective in the presence of many other anions. Scientific Reports 3 doi: 10.1038/srep02562
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 76
    Publication Date: 2013-09-07
    Description: Despite the pathological importance of fibrin clot formation, little is known about the structure of these clots because X-ray and nuclear magnetic resonance (NMR) analyses are not applicable to insoluble proteins. In contrast to previously reported anti-fibrin monoclonal antibodies (mAbs), our anti-fibrin clot mAb (clone 102–10) recognises an uncovered region that is exposed only when a fibrin clot forms. The epitope of the 102–10 mAb was mapped to a hydrophobic region on the Bβ chain that interacted closely with a counterpart region on the γ chain in a soluble state. New anti-Bβ and anti-γ mAbs specific to peptides lining the discovered region appeared to bind exclusively to fibrin clots. Furthermore, the radiolabelled 102–10 mAb selectively accumulated in mouse spontaneous tumours, and immunohistochemistry using this mAb revealed greater fibrin deposition in World Health Organization (WHO) grade 4 glioma than in lower-grade gliomas. Because erosive tumours are apt to cause micro-haemorrhages, even early asymptomatic tumours detected with a radiolabelled 102-10 mAb may be aggressively malignant. Scientific Reports 3 doi: 10.1038/srep02604
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 77
    Publication Date: 2013-09-07
    Description: An electrical pumped microscopic active display with integration of plasmonic polarizer and light-emitting-diode is proposed. Thanks to the strong polarized emission through the rectangular nanoholes, well designed pixels with respect to different polarizations are engineered, which give rise to flexible and controllable active display. As results, polarization multiplexed letter encoding, single and double gray-scale images and animation movies are successfully realized. Our results demonstrate a new strategy in electro-optical integration and indicate potential applications in designing new type of microscopic electro-optical devices. Scientific Reports 3 doi: 10.1038/srep02603
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 78
    Publication Date: 2013-09-07
    Description: We compare the three most commonly used scanning probe techniques to obtain a reliable value of the work function in graphene domains of different thickness. The surface potential (SP) of graphene is directly measured in Hall bar geometry via a combination of electrical functional microscopy and spectroscopy techniques, which enables calibrated work function measurements of graphene domains in ambient conditions with values Φ1LG ~4.55 ± 0.02 eV and Φ2LG ~ 4.44 ± 0.02 eV for single- and bi-layer, respectively. We demonstrate that frequency-modulated Kelvin probe force microscopy (FM-KPFM) provides more accurate measurement of the SP than amplitude-modulated (AM)-KPFM. The discrepancy between experimental results obtained by different techniques is discussed. In addition, we use FM-KPFM for contactless measurements of the specific components of the device resistance. We show a strong non-Ohmic behavior of the electrode-graphene contact resistance and extract the graphene channel resistivity. Scientific Reports 3 doi: 10.1038/srep02597
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 79
    Publication Date: 2013-09-07
    Description: The non-canonical NF-κB pathway is crucial for the immune system. A critical event in activation of the non-canonical pathway is the attenuation of NF-κB-inducing kinase (NIK) degradation, which is promoted by continuous polyubiquitination of NIK catalyzed by the NIK ubiquitin-ligase complex composed of cellular inhibitor of apoptosis protein 1 and 2 (cIAP1/2), TNF receptor-associated factor 2 (TRAF2), and TRAF3. However, the molecular mechanism of stimulation-dependent NIK stabilization remains poorly understood. Here, we show that A20, a ubiquitin-editing enzyme, promotes efficient activation of the non-canonical pathway independent of its catalytic activity. A20 directly binds to cIAP1 through the seventh zinc finger of A20, resulting in dissociation of the TRAF2/TRAF3 interaction, thereby inactivating the ligase complex to stabilize NIK. Given that A20 negatively regulates the canonical pathway, A20 is likely involved in the molecular switch that promotes the transition from canonical to non-canonical activation for proper control of the immune system. Scientific Reports 3 doi: 10.1038/srep02568
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 80
    Publication Date: 2013-09-07
    Description: Plasmon-enhanced photocurrent generation and water oxidation from visible to near-infrared wavelengths NPG Asia Materials 5, e61 (September 2013). doi:10.1038/am.2013.42 Authors: Kosei Ueno & Hiroaki Misawa
    Keywords: gold nanorodlocalized surface plasmon resonancenear-infrared lightphotoelectric conversionplasmonic chemistrywater oxidation
    Print ISSN: 1884-4049
    Electronic ISSN: 1884-4057
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 81
    Publication Date: 2013-09-08
    Description: O -GlcNAcylation is an inducible, highly dynamic and reversible post-translational modification, mediated by a unique enzyme named O -linked N -acetyl- d -glucosamine ( O -GlcNAc) transferase (OGT). In response to nutrients, O -GlcNAc levels are differentially regulated on many cellular proteins involved in gene expression, translation, immune reactions, protein degradation, protein–protein interaction, apoptosis and signal transduction. In contrast to eukaryotic cells, little is known about the role of O -GlcNAcylation in the viral life cycle. Here, we show that the overexpression of the OGT reduces the replication efficiency of Kaposi's sarcoma-associated herpesvirus (KSHV) in a dose-dependent manner. In order to investigate the global impact of O -GlcNAcylation in the KSHV life cycle, we systematically analyzed the 85 annotated KSHV-encoded open reading frames for O -GlcNAc modification. For this purpose, an immunoprecipitation (IP) strategy with three different approaches was carried out and the O -GlcNAc signal of the identified proteins was properly controlled for specificity. Out of the 85 KSHV-encoded proteins, 18 proteins were found to be direct targets for O -GlcNAcylation. Selected proteins were further confirmed by mass spectrometry for O -GlcNAc modification. Correlation of the functional annotation and the O -GlcNAc status of KSHV proteins showed that the predominant targets were proteins involved in viral DNA synthesis and replication. These results indicate that O -GlcNAcylation plays a major role in the regulation of KSHV propagation.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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  • 82
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2013-09-08
    Print ISSN: 0959-6658
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  • 83
    Publication Date: 2013-09-08
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  • 84
    Publication Date: 2013-09-08
    Description: Galectins are potent adhesion/growth-regulatory effectors with characteristic expression profiles. Understanding the molecular basis of gene regulation in each case requires detailed information on copy number of genes and sequence(s) of their promoter(s). Our report reveals plasticity in this respect between galectins and species. We here describe occurrence of a two-gene constellation for human galectin (Gal)-7 and define current extent of promoter-sequence divergence. Interestingly, cross-species genome analyses also detected single-copy display. Because the regulatory potential will then be different, extrapolations of expression profiles are precluded between respective species pairs. Gal-4 coding in chromosomal vicinity was found to be confined to one gene, whereas copy-number variation also applied to Gal-9. The example of rat Gal-9 teaches the lesson that the presence of multiple bands in Southern blotting despite a single-copy gene constellation is attributable to two pseudogenes. The documented copy-number variability should thus be taken into consideration when studying regulation of galectin genes, in a species and in comparison between species.
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  • 85
    Publication Date: 2013-09-08
    Description: In studying the molecular basis for the potent immune activity of previously described gamma and delta inulin particles and to assist in production of inulin adjuvants under Good Manufacturing Practice, we identified five new inulin isoforms, bringing the total to seven plus the amorphous form. These isoforms comprise the step-wise inulin developmental series amorphous -〉 alpha-1 (AI-1) -〉 alpha-2 (AI-2) -〉 gamma (GI) -〉 delta (DI) -〉 zeta (ZI) -〉 epsilon (EI) -〉 omega (OI) in which each higher isoform can be made either by precipitating dissolved inulin or by direct conversion from its precursor, both cases using regularly increasing temperatures. At higher temperatures, the shorter inulin polymer chains are released from the particle and so the key difference between isoforms is that each higher isoform comprises longer polymer chains than its precursor. An increasing trend of degree of polymerization is confirmed by end-group analysis using 1 H nuclear magnetic resonance spectroscopy. Inulin isoforms were characterized by the critical temperatures of abrupt phase-shifts (solubilizations or precipitations) in water suspensions. Such (aqueous) "melting" or "freezing" points are diagnostic and occur in strikingly periodic steps reflecting quantal increases in noncovalent bonding strength and increments in average polymer lengths. The (dry) melting points as measured by modulated differential scanning calorimetry similarly increase in regular steps. We conclude that the isoforms differ in repeated increments of a precisely repeating structural element. Each isoform has a different spectrum of biological activities and we show the higher inulin isoforms to be more potent alternative complement pathway activators.
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  • 86
    Publication Date: 2013-09-08
    Description: The methylotrophic yeast, Pichia pastoris , is an important organism used for the production of therapeutic proteins. Previously, we have reported the glycoengineering of this organism to produce human-like N -linked glycans but up to now no one has addressed engineering the O -linked glycosylation pathway. Typically, O -linked glycans produced by wild-type P. pastoris are linear chains of four to five α-linked mannose residues, which may be capped with β- or phospho-mannose. Previous genetic engineering of the N-linked glycosylation pathway of P. pastoris has eliminated both of these two latter modifications, resulting in O -linked glycans which are linear α-linked mannose structures. Here, we describe a method for the co-expression of an α-1,2-mannosidase, which reduces these glycans to primarily a single O -linked mannose residue. In doing so, we have reduced the potential of these glycans to interact with carbohydrate-binding proteins, such as dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin. Furthermore, the introduction of the enzyme protein- O -linked-mannose β-1,2- N -acetylglucosaminyltransferase 1, resulted in the capping of the single O -linked mannose residues with N -acetylglucosamine. Subsequently, this glycoform was extended into human-like sialylated glycans, similar in structure to α-dystroglycan-type glycoforms. As such, this represents the first example of sialylated O -linked glycans being produced in yeast and extends the utility of the P. pastoris production platform beyond N -linked glycosylated biotherapeutics to include molecules possessing O -linked glycans.
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  • 87
    Publication Date: 2013-09-08
    Description: Neurons and other cells require intracellular transport of essential components for viability and function. Previous work has shown that while net amyloid precursor protein (APP) transport is generally anterograde, individual vesicles containing APP move bi-directionally. This discrepancy highlights our poor understanding of the in vivo regulation of APP-vesicle transport. Here, we show that reduction of presenilin (PS) or suppression of gamma-secretase activity substantially increases anterograde and retrograde velocities for APP vesicles. Strikingly, PS deficiency has no effect on an unrelated cargo vesicle class containing synaptotagmin, which is powered by a different kinesin motor. Increased velocities caused by PS or gamma-secretase reduction require functional kinesin-1 and dynein motors. Together, our findings suggest that a normal function of PS is to repress kinesin-1 and dynein motor activity during axonal transport of APP vesicles. Furthermore, our data suggest that axonal transport defects induced by loss of PS-mediated regulatory effects on APP-vesicle motility could be a major cause of neuronal and synaptic defects observed in Alzheimer's Disease (AD) pathogenesis. Thus, perturbations of APP/PS transport could contribute to early neuropathology observed in AD, and highlight a potential novel therapeutic pathway for early intervention, prior to neuronal loss and clinical manifestation of disease.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
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  • 88
    Publication Date: 2013-09-08
    Description: Article The Broca area is located in the human prefrontal cortex and is involved in voluntary speech. Hage and Nieder now show that a monkey homologue of Broca’s area is similarly responsible for monkey volitional vocalizations. Nature Communications doi: 10.1038/ncomms3409 Authors: Steffen R. Hage, Andreas Nieder
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 89
    Publication Date: 2013-09-08
    Description: Article B lymphocytes respond to stimulation by proliferating and differentiating. Here the authors quantify and model the responses of B lymphocytes to TLR and CD40-dependent stimulation, and find that the latter induces a more complex response to signals of varying strength. Nature Communications doi: 10.1038/ncomms3406 Authors: E.D. Hawkins, M.L. Turner, C.J. Wellard, J.H.S. Zhou, M.R. Dowling, P.D. Hodgkin
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 90
    Publication Date: 2013-09-08
    Description: With age, muscle mass and integrity are progressively lost leaving the elderly frail, weak and unable to independently care for themselves. Defined as sarcopenia, this age-related muscle atrophy appears to be multifactorial but its definite cause is still unknown. Mitochondrial dysfunction has been implicated in this process. Using a novel transgenic mouse model of mitochondrial DNA (mtDNA) double-strand breaks (DSBs) that presents a premature aging-like phenotype, we studied the role of mtDNA damage in muscle wasting. We caused DSBs in mtDNA of adult mice using a ubiquitously expressed mitochondrial-targeted endonuclease, mito- Pst I. We found that a short, transient systemic mtDNA damage led to muscle wasting and a decline in locomotor activity later in life. We found a significant decline in muscle satellite cells, which decreases the muscle's capacity to regenerate and repair during aging. This phenotype was associated with impairment in acetylcholinesterase (AChE) activity and assembly at the neuromuscular junction (NMJ), also associated with muscle aging. Our data suggests that systemic mitochondrial dysfunction plays important roles in age-related muscle wasting by preferentially affecting the myosatellite cell pool.
    Print ISSN: 0964-6906
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  • 91
    Publication Date: 2013-09-08
    Description: Erratum Nature Communications doi: 10.1038/ncomms3309 Authors: Ralph P. Schneider, Ianire Garrobo, Miguel Foronda, Jose A. Palacios, Rosa M. Marión, Ignacio Flores, Sagrario Ortega, Maria A. Blasco
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 92
    Publication Date: 2013-09-08
    Description: Article It has long been suggested, but never shown, than nanometre-sized particles precede mineral formation in magmatic systems. Here, Helmy et al. demonstrate that platinum and arsenic self-organize to nanoparticle precursors in magmatic liquids before mineral crystallization. Nature Communications doi: 10.1038/ncomms3405 Authors: Hassan M. Helmy, Chris Ballhaus, Raúl O.C. Fonseca, Richard Wirth, Thorsten Nagel, Marian Tredoux
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 93
    Publication Date: 2013-09-08
    Description: Article Messenger RNAs and their associated proteins are transported from the nucleus through highly selective nuclear pore complexes. Using ultrahigh resolution single-molecule imaging, the authors visualise the path taken by each messenger RNA as it negotiates the pore’s selectivity filter. Nature Communications doi: 10.1038/ncomms3414 Authors: Jiong Ma, Zhen Liu, Nicole Michelotti, Sethuramasundaram Pitchiaya, Ram Veerapaneni, John R. Androsavich, Nils G. Walter, Weidong Yang
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 94
    Publication Date: 2013-09-08
    Description: Article TRPA1 is a transient receptor potential channel family member and is involved in the detection of nociceptive stimuli. Zhou et al. identify an alternative splice variant of TRPA1, which increases TRPA1 plasma expression and channel function, and enhances pain-like behaviour in mice. Nature Communications doi: 10.1038/ncomms3399 Authors: Yiming Zhou, Yoshiro Suzuki, Kunitoshi Uchida, Makoto Tominaga
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 95
    Publication Date: 2013-09-08
    Description: Corrigendum Nature Communications doi: 10.1038/ncomms3358 Authors: Qilong Wang, Xiaoying Zhuang, Jingyao Mu, Zhong-Bin Deng, Hong Jiang, Lifeng Zhang, Xiaoyu Xiang, Baomei Wang, Jun Yan, Donald Miller, Huang-Ge Zhang
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 96
    Publication Date: 2013-09-08
    Description: Article Despite its importance for non-volatile memory, the origin of resistive switching in a metal insulator-metal structure is unclear. Park et al. fabricate such a structure inside a transmission electron microscope to show that switching occurs via oxygen-vacancy migration, which changes the conduction channels. Nature Communications doi: 10.1038/ncomms3382 Authors: Gyeong-Su Park, Young Bae Kim, Seong Yong Park, Xiang Shu Li, Sung Heo, Myoung-Jae Lee, Man Chang, Ji Hwan Kwon, M. Kim, U-In Chung, Regina Dittmann, Rainer Waser, Kinam Kim
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 97
    Publication Date: 2013-09-09
    Description: Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 98
    Publication Date: 2013-09-10
    Description: We present a methodology for infrasonic remote sensing of winds in the stratosphere that does not require discrete ground-truth events. Our method uses measured time delays between arrays of sensors to provide group velocities (referred to here as celerities) and then minimizes the difference between observed and predicted celerities by perturbing an initial atmospheric specification. Because we focus on interarray propagation effects, it is not necessary to simulate the full propagation path from source to receiver. This feature allows us to use a relatively simple forward model that is applicable over short-regional distances. By focusing on stratospheric returns, we show that our non-linear inversion scheme converges much better if the starting model contains a strong stratospheric duct. Using the Horizontal Wind Model (HWM)/Mass Spectrometer Incoherent Scatter (MSISE) empirical climatology as a starting model, we demonstrate that the inversion scheme is robust to large uncertainties in backazimuth, but that uncertainties in the measured trace velocity and celerity require the use of prior constraints to ensure suitable convergence. The inversion of synthetic data, using realistic estimates of measurement error, shows that our scheme will nevertheless improve upon a starting model under most scenarios. The inversion scheme is applied to infrasound data recorded from a large event on 2010 December 25, which is presumed to be a bolide, using data from a nine-element infrasound network in Utah. We show that our recorded data require a stronger zonal wind speed in the stratosphere than is present in the HWM profile, and are more consistent with the Ground-to-Space (G2S) profile.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 99
    Publication Date: 2013-09-10
    Description: Coda- Q is a stochastic parameter reflecting the heterogeneities of medium that seismic waves travel through. We confirmed that coda- Q would vary with the stress loaded to an elastic medium using numerical simulations of seismic wave propagation. When the stress is loaded, cracks in the crust could either close or newly open. The closure and opening of the cracks are not random but depending on the magnitude and the direction of the stress and the crack aspect ratio. The cracks in the medium after loading stress could be aligned in a specific orientation, and elastic wave velocity field would become anisotropic due to the alignment of specific crack orientations. Elastic wave velocity is in general faster along the direction corresponding with the crack orientation while slower along the perpendicular direction. In the numerical simulation, the effect of anisotropy in elastic wave velocity field due to the selective closure and opening of the cracks is calculated using a 2-D finite difference method assuming elastic wave velocity to be a function of the magnitude of loaded stress. The coda- Q calculated from seismic waves simulated for a model varies when the averaged normal stress changes. Our simulation indicated that the sensitivity of coda- Q –1 , that is the reciprocal of the coda- Q , would be 1.0 10 –2 (1.0 MPa –1 ) against the magnitude of the confining pressure and 1.0 10 –3 (1.0 deg –1 ) against the direction of principal stress. We would like to conclude that coda- Q , a stochastic parameter reflecting heterogeneities of subsurface medium, could become a quantitative state indicator of the stress field of the medium where seismic waves propagate through. Spatiotemporal variation of coda- Q reflects change in the stress field in the crust.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 100
    Publication Date: 2013-09-10
    Description: How do body-wave traveltimes constrain the Earth's radial (1-D) seismic structure? Existing 1-D seismological models underpin 3-D seismic tomography and earthquake location algorithms. It is therefore crucial to assess the quality of such 1-D models, yet quantifying uncertainties in seismological models is challenging and thus often ignored. Ideally, quality assessment should be an integral part of the inverse method. Our aim in this study is twofold: (i) we show how to solve a general Bayesian non-linear inverse problem and quantify model uncertainties, and (ii) we investigate the constraint on spherically symmetric P -wave velocity ( V P ) structure provided by body-wave traveltimes from the EHB bulletin (phases Pn , P , PP and PKP ). Our approach is based on artificial neural networks, which are very common in pattern recognition problems and can be used to approximate an arbitrary function. We use a Mixture Density Network to obtain 1-D marginal posterior probability density functions (pdfs), which provide a quantitative description of our knowledge on the individual Earth parameters. No linearization or model damping is required, which allows us to infer a model which is constrained purely by the data. We present 1-D marginal posterior pdfs for the 22 V P parameters and seven discontinuity depths in our model. P -wave velocities in the inner core, outer core and lower mantle are resolved well, with standard deviations of ~0.2 to 1 per cent with respect to the mean of the posterior pdfs. The maximum likelihoods of V P are in general similar to the corresponding ak135 values, which lie within one or two standard deviations from the posterior means, thus providing an independent validation of ak135 in this part of the radial model. Conversely, the data contain little or no information on P -wave velocity in the D '' layer, the upper mantle and the homogeneous crustal layers. Further, the data do not constrain the depth of the discontinuities in our model. Using additional phases available in the ISC bulletin, such as PcP , PKKP and the converted phases SP and ScP , may enhance the resolvability of these parameters. Finally, we show how the method can be extended to obtain a posterior pdf for a multidimensional model space. This enables us to investigate correlations between model parameters.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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