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  • Springer Nature  (17,922)
  • American Meteorological Society
  • 2010-2014  (19,915)
  • 2005-2009
  • 1995-1999
  • 2012  (19,915)
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  • 2010-2014  (19,915)
  • 2005-2009
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  • 1
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    Assimilating Along-Track Altimetric Observations through Local Hydrostatic Adjustment in a Global Ocean Variational Assimilation System (2012)
    American Meteorological Society
    Details
    Publication Date: 2017-04-03
    Description: A global ocean three-dimensional variational data assimilation system was developed with the aim of assimilating along-track sea level anomaly observations, along with in situ observations from bathythermographs and conventional sea stations. All the available altimetric data within the period October 1992–January 2006 were used in this study. The sea level corrections were covariated with vertical profiles of temperature and salinity according to the bivariate definition of the background-error vertical covariances. Sea level anomaly observational error variance was carefully defined as a sum of instrumental, representativeness, observation operator, and mean dynamic topography error variances. The mean dynamic topography was computed from the model long-term mean sea surface height and adjusted through an optimal interpolation scheme to account for observation minus first-guess biases. Results show that the assimilation of sea level anomaly observations improves the model sea surface height skill scores as well as the subsurface temperature and salinity fields. Furthermore, the estimate of the tropical and subtropical surface circulation is clearly improved after assimilating altimetric data. Nonnegligible impacts of the mean dynamic topography used have also been found: compared to a gravimeter-based mean dynamic topography the use of the mean dynamic topography discussed in this paper improves both the consistency with sea level anomaly observations and the verification skill scores of temperature and salinity in the tropical regions. Furthermore, the use of a mean dynamic topography computed from the model long-term sea surface height mean without observation adjustments results in worsened verification skill scores and highlights the benefits of the current approach for deriving the mean dynamic topography.
    Description: European Commission WP4 Fondazione Cassa di Risparmio di Bologna Cnes
    Description: Published
    Description: 738-754
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: 4.6. Oceanografia operativa per la valutazione dei rischi in aree marine
    Description: 5.4. Banche dati di geomagnetismo, aeronomia, clima e ambiente
    Description: JCR Journal
    Description: partially_open
    Keywords: Data assimilation ; Satellite observations ; Ocean models ; Sea level ; In situ observations ; Variational analysis ; 03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modeling ; 03. Hydrosphere::03.01. General::03.01.03. Global climate models ; 03. Hydrosphere::03.01. General::03.01.04. Ocean data assimilation and reanalysis
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    Baroclinic Stationary Waves in Aquaplanet Models (2012)
    American Meteorological Society
    Details
    Publication Date: 2020-02-24
    Description: An aquaplanet model is used to study the nature of the highly persistent low-frequency waves that have been observed in models forced by zonally symmetric boundary conditions. Using the Hayashi spectral analysis of the extratropical waves, the authors find that a quasi-stationary wave 5 belongs to a wave packet obeying a well-defined dispersion relation with eastward group velocity. The components of the dispersion relation with k ≥ 5 baroclinically convert eddy available potential energy into eddy kinetic energy, whereas those with k 〈 5 are baroclinically neutral. In agreement with Green’s model of baroclinic instability, wave 5 is weakly unstable, and the inverse energy cascade, which had been previously proposed as a main forcing for this type of wave, only acts as a positive feedback on its predominantly baroclinic energetics. The quasi-stationary wave is reinforced by a phase lock to an analogous pattern in the tropical convection, which provides further amplification to the wave. It is also found that the Pedlosky bounds on the phase speed of unstable waves provide guidance in explaining the latitudinal structure of the energy conversion, which is shown to be more enhanced where the zonal westerly surface wind is weaker. The wave’s energy is then trapped in the waveguide created by the upper tropospheric jet stream. In agreement with Green’s theory, as the equator-to-pole SST difference is reduced, the stationary marginally stable component shifts toward higher wavenumbers, while wave 5 becomes neutral and westward propagating. Some properties of the aquaplanet quasi-stationary waves are found to be in interesting agreement with a low frequency wave observed by Salby during December–February in the Southern Hemisphere so that this perspective on low frequency variability, apart from its value in terms of basic geophysical fluid dynamics, might be of specific interest for studying the earth’s atmosphere.
    Description: Published
    Description: 1023–1040.
    Description: JCR Journal
    Description: restricted
    Keywords: Boundary conditions ; 03. Hydrosphere::03.02. Hydrology::03.02.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    Quality Assessment of a 1985–2007 Mediterranean Sea Reanalysis (2012)
    American Meteorological Society
    Details
    Publication Date: 2020-02-24
    Description: A simulation and two reanalyses from 1985 to 2007 have been produced for the Mediterranean Sea using different assimilation schemes: a reduced-order optimal interpolation [System for Ocean Forecast and Analysis (SOFA)] and a three-dimensional variational scheme (OceanVar). The observational dataset consists of vertical temperature and salinity in situ profiles and along-track satellite sea level anomalies; daily mean fields of satellite sea surface temperature are used for correcting the air–sea fluxes. This paper assesses the quality of the reanalyses with respect to observations and the simulation. Both the SOFA and OceanVar schemes give very similar root-mean-square errors and biases for temperature and salinity fields compared with the assimilated observations. The largest errors are at the thermocline level and in regions of large eddy field variability. However, OceanVar gives 20% better results for sea level anomaly root-mean-square error.
    Description: Published
    Description: 569-59
    Description: JCR Journal
    Description: open
    Keywords: Mediterranean Sea ; 03. Hydrosphere::03.01. General::03.01.05. Operational oceanography
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Parameterisation of the Sedimentation of Raindrops with Finite Maximum Diameter (2012)
    American Meteorological Society
    In:  EPIC3Monthly Weather Review., American Meteorological Society, 140(5), pp. 1589-1602
    Details
    Publication Date: 2014-04-17
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 5
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    A comparison of methods for estimating Reynolds stress from ADCP measurements in wavy environments (2012)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2011. 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 28 (2011): 1539–1553, doi:10.1175/JTECH-D-11-00001.1.
    Description: Turbulent Reynolds stresses are now routinely estimated from acoustic Doppler current profiler (ADCP) measurements in estuaries and tidal channels using the variance method, yet biases due to surface gravity waves limit its use in the coastal ocean. Recent modifications to this method, including spatially filtering velocities to isolate the turbulence from wave velocities and fitting a cospectral model to the below-wave band cospectra, have been used to remove this bias. Individually, each modification performed well for the published test datasets, but a comparative analysis over the range of conditions in the coastal ocean has not yet been performed. This work uses ADCP velocity measurements from five previously published coastal ocean and estuarine datasets, which span a range of wave and current conditions as well as instrument configurations, to directly compare methods for estimating stresses in the presence of waves. The computed stresses from each were compared to bottom stress estimates from a quadratic drag law and, where available, estimates of wind stress. These comparisons, along with an analysis of the cospectra, indicated that spectral fitting performs well when the wave climate is wide-banded and/or multidirectional as well as when instrument noise is high. In contrast, spatial filtering performs better when waves are narrow-banded, low frequency, and when wave orbital velocities are strong relative to currents. However, as spatial filtering uses vertically separated velocity bins to remove the wave bias, spectral fitting is able to resolve stresses over a larger fraction of the water column.
    Description: J. Rosman acknowledges funding from the National Science Foundation (OCE-1061108).
    Keywords: Coastal flows ; Momentum ; Ocean circulation ; Waves, oceanic ; In situ observations ; Instrumentation/sensors
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Turbulent kinetic energy dissipation in Barrow Canyon (2012)
    American Meteorological Society
    Details
    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): 1012–1021, doi:10.1175/JPO-D-11-0184.1.
    Description: Pacific Water flows across the shallow Chukchi Sea before reaching the Arctic Ocean, where it is a source of heat, freshwater, nutrients, and carbon. A substantial portion of Pacific Water is routed through Barrow Canyon, located in the northeast corner of the Chukchi. Barrow Canyon is a region of complex geometry and forcing where a variety of water masses have been observed to coexist. These factors contribute to a dynamic physical environment, with the potential for significant water mass transformation. The measurements of turbulent kinetic energy dissipation presented here indicate diapycnal mixing is important in the upper canyon. Elevated dissipation rates were observed near the pycnocline, effectively mixing winter and summer water masses, as well as within the bottom boundary layer. The slopes of shear/stratification layers, combined with analysis of rotary spectra, suggest that near-inertial wave activity may be important in modulating dissipation near the bottom. Because the canyon is known to be a hotspot of productivity with an active benthic community, mixing may be an important factor in maintenance of the biological environment.
    Description: ELS was supported as a WHOI Postdoctoral Scholar through the WHOI Ocean and Climate Change Institute.
    Description: 2012-12-01
    Keywords: Arctic ; Continental shelf/slope ; Mixing ; Small scale processes
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Variability of the Atlantic meridional overturning circulation in CCSM4 (2012)
    American Meteorological Society
    Details
    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 Climate 25 (2012): 5153–5172, doi:10.1175/JCLI-D-11-00463.1.
    Description: Atlantic meridional overturning circulation (AMOC) variability is documented in the Community Climate System Model, version 4 (CCSM4) preindustrial control simulation that uses nominal 1° horizontal resolution in all its components. AMOC shows a broad spectrum of low-frequency variability covering the 50–200-yr range, contrasting sharply with the multidecadal variability seen in the T85 × 1 resolution CCSM3 present-day control simulation. Furthermore, the amplitude of variability is much reduced in CCSM4 compared to that of CCSM3. Similarities as well as differences in AMOC variability mechanisms between CCSM3 and CCSM4 are discussed. As in CCSM3, the CCSM4 AMOC variability is primarily driven by the positive density anomalies at the Labrador Sea (LS) deep-water formation site, peaking 2 yr prior to an AMOC maximum. All processes, including parameterized mesoscale and submesoscale eddies, play a role in the creation of salinity anomalies that dominate these density anomalies. High Nordic Sea densities do not necessarily lead to increased overflow transports because the overflow physics is governed by source and interior region density differences. Increased overflow transports do not lead to a higher AMOC either but instead appear to be a precursor to lower AMOC transports through enhanced stratification in LS. This has important implications for decadal prediction studies. The North Atlantic Oscillation (NAO) is significantly correlated with the positive boundary layer depth and density anomalies prior to an AMOC maximum. This suggests a role for NAO through setting the surface flux anomalies in LS and affecting the subpolar gyre circulation strength.
    Description: The CCSM project is supported by NSF and the Office of Science (BER) of the U.S. Department of Energy. SGY and YOK were supported by the NOAA Climate Program Office under Climate Variability and Predictability Program Grants NA09OAR4310163 and NA10OAR4310202, respectively.
    Description: 2013-02-01
    Keywords: Meridional overturning circulation ; Coupled models ; Ocean models ; Oceanic variability
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Energy transfer from high-shear, low-frequency internal waves to high-frequency waves near Kaena Ridge, Hawaii (2012)
    American Meteorological Society
    Details
    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): 1524–1547, doi:10.1175/JPO-D-11-0117.1.
    Description: Evidence is presented for the transfer of energy from low-frequency inertial–diurnal internal waves to high-frequency waves in the band between 6 cpd and the buoyancy frequency. This transfer links the most energetic waves in the spectrum, those receiving energy directly from the winds, barotropic tides, and parametric subharmonic instability, with those most directly involved in the breaking process. Transfer estimates are based on month-long records of ocean velocity and temperature obtained continuously over 80–800 m from the research platform (R/P) Floating Instrument Platform (FLIP) in the Hawaii Ocean Mixing Experiment (HOME) Nearfield (2002) and Farfield (2001) experiments, in Hawaiian waters. Triple correlations between low-frequency vertical shears and high-frequency Reynolds stresses, uiw∂Ui/∂z, are used to estimate energy transfers. These are supported by bispectral analysis, which show significant energy transfers to pairs of waves with nearly identical frequency. Wavenumber bispectra indicate that the vertical scales of the high-frequency waves are unequal, with one wave of comparable scale to that of the low-frequency parent and the other of much longer scale. The scales of the high-frequency waves contrast with the classical pictures of induced diffusion and elastic scattering interactions and violates the scale-separation assumption of eikonal models of interaction. The possibility that the observed waves are Doppler shifted from intrinsic frequencies near f or N is explored. Peak transfer rates in the Nearfield, an energetic tidal conversion site, are on the order of 2 × 10−7 W kg−1 and are of similar magnitude to estimates of turbulent dissipation that were made near the ridge during HOME. Transfer rates in the Farfield are found to be about half the Nearfield values.
    Description: This work was supported by the National Science Foundation and the Office of Naval Research.
    Description: 2013-03-01
    Keywords: Diapycnal mixing ; Energy transport ; Internal waves ; Nonlinear dynamics ; Ship observations ; Spectral analysis/models/distribution
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Improving HF radar estimates of surface currents using signal quality metrics, with application to the MVCO high-resolution radar system (2012)
    American Meteorological Society
    Details
    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 Atmospheric and Oceanic Technology 29 (2012): 1377–1390, doi:10.1175/JTECH-D-11-00160.1.
    Description: Estimates of surface currents over the continental shelf are now regularly made using high-frequency radar (HFR) systems along much of the U.S. coastline. The recently deployed HFR system at the Martha’s Vineyard Coastal Observatory (MVCO) is a unique addition to these systems, focusing on high spatial resolution over a relatively small coastal ocean domain with high accuracy. However, initial results from the system showed sizable errors and biased estimates of M2 tidal currents, prompting an examination of new methods to improve the quality of radar-based velocity data. The analysis described here utilizes the radial metric output of CODAR Ocean Systems’ version 7 release of the SeaSonde Radial Site Software Suite to examine both the characteristics of the received signal and the output of the direction-finding algorithm to provide data quality controls on the estimated radial currents that are independent of the estimated velocity. Additionally, the effect of weighting spatial averages of radials falling within the same range and azimuthal bin is examined to account for differences in signal quality. Applied to two month-long datasets from the MVCO high-resolution system, these new methods are found to improve the rms difference comparisons with in situ current measurements by up to 2 cm s−1, as well as reduce or eliminate observed biases of tidal ellipses estimated using standard methods.
    Description: 2013-03-01
    Keywords: Coastal flows ; Currents ; Data processing ; Data quality control ; In situ atmospheric observations ; Remote sensing
    Repository Name: Woods Hole Open Access Server
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  • 10
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    Cross-shelf and out-of-bay transport driven by an open-ocean current (2012)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2011. 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 41 (2011): 2168–2186, doi:10.1175/JPO-D-11-08.1.
    Description: This paper studies the interaction of an Antarctic Circumpolar Current (ACC)–like wind-driven channel flow with a continental slope and a flat-bottomed bay-shaped shelf near the channel’s southern boundary. Interaction between the model ACC and the topography in the second layer induces local changes of the potential vorticity (PV) flux, which further causes the formation of a first-layer PV front near the base of the topography. Located between the ACC and the first-layer slope, the newly formed PV front is constantly perturbed by the ACC and in turn forces the first-layer slope with its own variability in an intermittent but persistent way. The volume transport of the slope water across the first-layer slope edge is mostly directly driven by eddies and meanders of the new front, and its magnitude is similar to the maximum Ekman transport in the channel. Near the bay’s opening, the effect of the topographic waves, excited by offshore variability, dominates the cross-isobath exchange and induces a mean clockwise shelf circulation. The waves’ propagation is only toward the west and tends to be blocked by the bay’s western boundary in the narrow-shelf region. The ensuing wave–coast interaction amplifies the wave amplitude and the cross-shelf transport. Because the interaction only occurs near the western boundary, the shelf water in the west of the bay is more readily carried offshore than that in the east and the mean shelf circulation is also intensified along the bay’s western boundary.
    Description: Y. Zhang acknowledges the support of the MIT-WHOI Joint Program in Physical Oceanography and NSF OCE-9901654 and OCE- 0451086. J. Pedlosky acknowledges the support of NSF OCE-9901654 and OCE-0451086.
    Keywords: Baroclinic flows ; Eddies ; Fronts ; Mass fluxes/transport ; Mesoscale processes ; Topographic effects
    Repository Name: Woods Hole Open Access Server
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  • 11
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    An equatorial ocean bottleneck in global climate models (2012)
    American Meteorological Society
    Details
    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 Climate 25 (2012): 343–349, doi:10.1175/JCLI-D-11-00059.1.
    Description: The Equatorial Undercurrent (EUC) is a major component of the tropical Pacific Ocean circulation. EUC velocity in most global climate models is sluggish relative to observations. Insufficient ocean resolution slows the EUC in the eastern Pacific where nonlinear terms should dominate the zonal momentum balance. A slow EUC in the east creates a bottleneck for the EUC to the west. However, this bottleneck does not impair other major components of the tropical circulation, including upwelling and poleward transport. In most models, upwelling velocity and poleward transport divergence fall within directly estimated uncertainties. Both of these transports play a critical role in a theory for how the tropical Pacific may change under increased radiative forcing, that is, the ocean dynamical thermostat mechanism. These findings suggest that, in the mean, global climate models may not underrepresent the role of equatorial ocean circulation, nor perhaps bias the balance between competing mechanisms for how the tropical Pacific might change in the future. Implications for model improvement under higher resolution are also discussed.
    Description: KBK gratefully acknowledges the J. Lamar Worzel Assistant Scientist Fund. GCJ is supported by NOAA’s Office of Oceanic and Atmospheric Research. RM gratefully acknowledges the generous support and hospitality of the Divecha Centre for Climate Change and CAOS at IISc, Bangalore, and partial support by NASA PO grants.
    Description: 2012-07-01
    Keywords: Tropics ; Ocean circulation ; Ocean dynamics ; Climate models ; Coupled models ; Ocean models
    Repository Name: Woods Hole Open Access Server
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  • 12
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    The global subduction/obduction rates : their interannual and decadal variability (2012)
    American Meteorological Society
    Details
    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 Climate 25 (2012): 1096–1115, doi:10.1175/2011JCLI4228.1.
    Description: Ventilation, including subduction and obduction, for the global oceans was examined using Simple Ocean Data Assimilation (SODA) outputs. The global subduction rate averaged over the period from 1959 to 2006 is estimated at 505.8 Sv (1 Sv ≡ 106 m3 s−1), while the corresponding global obduction rate is estimated at 482.1 Sv. The annual subduction/obduction rates vary greatly on the interannual and decadal time scales. The global subduction rate is estimated to have increased 7.6% over the past 50 years, while the obduction rate is estimated to have increased 9.8%. Such trends may be insignificant because errors associated with the data generated by ocean data assimilation could be as large as 10%. However, a major physical mechanism that induced these trends is primarily linked to changes in the Southern Ocean. While the Southern Ocean plays a key role in global subduction and obduction rates and their variability, both the Southern Ocean and equatorial regions are critically important sites of water mass formation/erosion.
    Description: This work was supported by the Key State Basic Research Program of China under Grant 2012CB417401, the National Natural Science Foundation of China (Grants 40906007, 40890152), and the Open Foundation of Physical Oceanography Laboratory, OUC, under Grant 200902.
    Description: 2012-08-15
    Keywords: Decadal variability ; Southern Ocean ; Trends ; Water masses ; Convergence ; Mixing
    Repository Name: Woods Hole Open Access Server
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  • 13
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    Horizontal density structure and restratification of the Arctic Ocean surface layer (2012)
    American Meteorological Society
    Details
    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): 659–668, doi:10.1175/JPO-D-11-0125.1.
    Description: Ice-tethered profiler (ITP) measurements from the Arctic Ocean’s Canada Basin indicate an ocean surface layer beneath sea ice with significant horizontal density structure on scales of hundreds of kilometers to the order 1 km submesoscale. The observed horizontal gradients in density are dynamically important in that they are associated with restratification of the surface ocean when dense water flows under light water. Such restratification is prevalent in wintertime and competes with convective mixing upon buoyancy forcing (e.g., ice growth and brine rejection) and shear-driven mixing when the ice moves relative to the ocean. Frontal structure and estimates of the balanced Richardson number point to the likelihood of dynamical restratification by isopycnal tilt and submesoscale baroclinic instability. Based on the evidence here, it is likely that submesoscale processes play an important role in setting surface-layer properties and lateral density variability in the Arctic Ocean.
    Description: Funding was provided by the National Science Foundation Office of Polar Programs Arctic Sciences Section under Awards ARC-0519899, ARC-0856479, and ARC-0806306. Support was also provided by the Woods Hole Oceanographic Institution Arctic Research Initiative.
    Description: 2012-10-01
    Keywords: Arctic ; Ocean dynamics
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  • 14
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    ENSO and Pacific decadal variability in the Community Climate System Model Version 4 (2012)
    American Meteorological Society
    Details
    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 Climate 25 (2012): 2622–2651, doi:10.1175/JCLI-D-11-00301.1.
    Description: This study presents an overview of the El Niño–Southern Oscillation (ENSO) phenomenon and Pacific decadal variability (PDV) simulated in a multicentury preindustrial control integration of the NCAR Community Climate System Model version 4 (CCSM4) at nominal 1° latitude–longitude resolution. Several aspects of ENSO are improved in CCSM4 compared to its predecessor CCSM3, including the lengthened period (3–6 yr), the larger range of amplitude and frequency of events, and the longer duration of La Niña compared to El Niño. However, the overall magnitude of ENSO in CCSM4 is overestimated by ~30%. The simulated ENSO exhibits characteristics consistent with the delayed/recharge oscillator paradigm, including correspondence between the lengthened period and increased latitudinal width of the anomalous equatorial zonal wind stress. Global seasonal atmospheric teleconnections with accompanying impacts on precipitation and temperature are generally well simulated, although the wintertime deepening of the Aleutian low erroneously persists into spring. The vertical structure of the upper-ocean temperature response to ENSO in the north and south Pacific displays a realistic seasonal evolution, with notable asymmetries between warm and cold events. The model shows evidence of atmospheric circulation precursors over the North Pacific associated with the “seasonal footprinting mechanism,” similar to observations. Simulated PDV exhibits a significant spectral peak around 15 yr, with generally realistic spatial pattern and magnitude. However, PDV linkages between the tropics and extratropics are weaker than observed.
    Description: M. Alexander, A. Capotondi, and J. Scott’s participation was supported by a grant from the NSF Climate and Large-scale Dynamics Program. Y.-O. Kwon gratefully acknowledges support from a WHOI Heyman fellowship and a grant from the NSF Climate and Largescale Dynamics Program. The CESM project is supported by the National Science Foundation and the Office of Science (BER) of the U.S. Department of Energy.
    Description: 2012-10-15
    Keywords: Atmosphere-ocean interaction ; El Nino ; ENSO ; La Nina ; Pacific decadal oscillation ; Climate models
    Repository Name: Woods Hole Open Access Server
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  • 15
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    High-latitude contribution to global variability of air–sea sensible heat flux (2012)
    American Meteorological Society
    Details
    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 Climate 25 (2012): 3515–3531, doi:10.1175/JCLI-D-11-00028.1.
    Description: The study examined global variability of air–sea sensible heat flux (SHF) from 1980 to 2009 and the large-scale atmospheric and ocean circulations that gave rise to this variability. The contribution of high-latitude wintertime SHF was identified, and the relative importance of the effect of the sea–air temperature difference versus the effect of wind on decadal SHF variability was analyzed using an empirical orthogonal function (EOF) approach. The study showed that global SHF anomalies are strongly modulated by SHF at high latitudes (poleward of 45°) during winter seasons. Decadal variability of global wintertime SHF can be reasonably represented by the sum of two leading EOF modes, namely, the boreal wintertime SHF in the northern oceans and the austral wintertime SHF in the southern oceans. The study also showed that global wintertime SHF is modulated by the prominent modes of the large-scale atmospheric circulation at high latitudes. The increase of global SHF in the 1990s is attributable to the strengthening of the Southern Hemisphere annular mode index, while the decrease of global SHF after 2000 is due primarily to the downward trend of the Arctic Oscillation index. This study identified the important effects of wind direction and speed on SHF variability. Changes in winds modify the sea–air temperature gradient by advecting cold and dry air from continents and by imposing changes in wind-driven oceanic processes that affect sea surface temperature (SST). The pattern of air temperature anomalies dominates over the pattern of SST anomalies and dictates the pattern of decadal SHF variability.
    Description: The study is supported by the NOAA Office of Climate Observations (OCO) and the WHOI Arctic Climate Initiative. X. Song acknowledges the support from the China Scholarship Council, National Natural Science Foundation of China (NSFC) (40930844, 40976004, and 40921004) and the Ministry of Education’s 111 Project (B07036).
    Description: 2012-11-15
    Keywords: Atmosphere-ocean interaction
    Repository Name: Woods Hole Open Access Server
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    On the response of a buoyant plume to downwelling-favorable wind stress (2012)
    American Meteorological Society
    Details
    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): 1083–1098, doi:10.1175/JPO-D-11-015.1.
    Description: Here, the response of a coastally trapped buoyant plume to downwelling-favorable wind forcing is explored using a simplified two-dimensional numerical model and a prognostic theory for the resulting width, depth, and density anomaly and along-shelf transport of the plume. Consistent with the numerical simulations, the analytical model shows that the wind causes mixing of the plume water and that the forced cross-shelf circulation can also generate significant deepening and surface narrowing, as well as increased along-shelf transport. The response is due to a combination of the purely advective process that leads to the steepening of the isopycnals and the entrainment of ambient water into the plume. The advective component depends on the initial plume geometry: plumes that have a large fraction of their total width in contact with the bottom (“bottom trapped”) suffer relatively small depth and width changes compared to plumes that have a large fraction of their total width detached from the bottom (“surface trapped”). Key theoretical parameters are Wγ/Wα, the ratio of the width of the plume detached from the bottom to the width of the plume in contact with it, and the ratio of the wind-generated mixed layer δe to the initial plume depth hp, which determines the amount of water initially entrained into the plume. The model results also show that the cross-shelf circulation can be strongly influenced by the wind-driven response in combination with the geostrophic shear of the plume. The continuous entrainment into the plume, as well as transient events, is also discussed.
    Description: This work has been supported by FONDECYT Grant 1070501. S. Lentz received support by theNational Science Foundation GrantOCE-0751554. C. Moffat had additional support from the National Science Foundation Office of Polar Programs through U.S. Southern Ocean GLOBEC Grants OPP 99-10092 and 06- 23223.
    Description: 2013-01-01
    Keywords: Baroclinic flows ; Boundary currents ; Coastal flows ; Upwelling/downwelling ; Wind ; Ocean models
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    ENSO’s impact on the gap wind regions of the eastern tropical Pacific Ocean (2012)
    American Meteorological Society
    Details
    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 Climate 25 (2012): 3549–3565, doi:10.1175/JCLI-D-11-00320.1.
    Description: The recently released NCEP Climate Forecast System Reanalysis (CFSR) is used to examine the response to ENSO in the northeast tropical Pacific Ocean (NETP) during 1979–2009. The normally cool Pacific sea surface temperatures (SSTs) associated with wind jets through the gaps in the Central American mountains at Tehuantepec, Papagayo, and Panama are substantially warmer (colder) than the surrounding ocean during El Niño (La Niña) events. Ocean dynamics generate the ENSO-related SST anomalies in the gap wind regions as the surface fluxes damp the SSTs anomalies, while the Ekman heat transport is generally in quadrature with the anomalies. The ENSO-driven warming is associated with large-scale deepening of the thermocline; with the cold thermocline water at greater depths during El Niño in the NETP, it is less likely to be vertically mixed to the surface, particularly in the gap wind regions where the thermocline is normally very close to the surface. The thermocline deepening is enhanced to the south of the Costa Rica Dome in the Papagayo region, which contributes to the local ENSO-driven SST anomalies. The NETP thermocline changes are due to coastal Kelvin waves that initiate westward-propagating Rossby waves, and possibly ocean eddies, rather than by local Ekman pumping. These findings were confirmed with regional ocean model experiments: only integrations that included interannually varying ocean boundary conditions were able to simulate the thermocline deepening and localized warming in the NETP during El Niño events; the simulation with variable surface fluxes, but boundary conditions that repeated the seasonal cycle, did not.
    Description: This research was supported by grants from the NOAA office of Global Programs and the NSF Climate and Global Dynamics Division.
    Description: 2012-11-15
    Keywords: North Pacific Ocean ; Atmosphere-ocean interaction ; ENSO ; Thermocline circulation ; Waves, oceanic ; Ocean models
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    A surface mooring for air–sea interaction research in the Gulf Stream. Part I : mooring design and instrumentation (2012)
    American Meteorological Society
    Details
    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 Atmospheric and Oceanic Technology 29 (2012): 1363–1376, doi:10.1175/JTECH-D-12-00060.1.
    Description: The design of a surface mooring for deployment in the Gulf Stream in the Mid-Atlantic Bight is described. The authors' goals were to observe the surface meteorology; upper-ocean variability; and air–sea exchanges of heat, freshwater, and momentum in and near the Gulf Stream during two successive 1-yr deployments. Of particular interest was quantifying these air–sea fluxes during wintertime events that carry cold, dry air from the land over the Gulf Stream. Historical current data and information about the surface waves were used to guide the design of the surface mooring. The surface buoy provided the platform for both bulk meteorological sensors and a direct covariance flux system. Redundancy in the meteorological sensors proved to be a largely successful strategy to obtain complete time series. Oceanographic instrumentation was limited in size by considerations of drag; and two current meters, three temperature–salinity recorders, and 15 temperature recorders were deployed. Deployment from a single-screw vessel in the Gulf Stream required a controlled-drift stern first over the anchor sites. The first deployment lasted the planned full year. The second deployment ended after 3 months when the mooring was cut by unknown means at a depth of about 3000 m. The mooring was at times in the core of the Gulf Stream, and a peak surface current of over 2.7 m s−1 was observed. The 15-month records of surface meteorology and air–sea fluxes captured the seasonal variability as well as several cold-air outbreaks; the peak observed heat loss was in excess of 1400 W m−2.
    Description: This work was funded by the National Science Foundation Grant OCE04-24536 as part of the CLIVAR Mode Water Dynamics Experiment (CLIMODE). The Vetlesen Foundation is also acknowledged for the early support of SB.
    Description: 2013-03-01
    Keywords: Buoy observations
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  • 19
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    The unpredictable nature of internal tides on continental shelves (2012)
    American Meteorological Society
    Details
    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): 1981–2000, doi:10.1175/JPO-D-12-028.1.
    Description: Packets of nonlinear internal waves (NLIWs) in a small area of the Mid-Atlantic Bight were 10 times more energetic during a local neap tide than during the preceding spring tide. This counterintuitive result cannot be explained if the waves are generated near the shelf break by the local barotropic tide since changes in shelfbreak stratification explain only a small fraction of the variability in barotropic to baroclinic conversion. Instead, this study suggests that the occurrence of strong NLIWs was caused by the shoaling of distantly generated internal tides with amplitudes that are uncorrelated with the local spring-neap cycle. An extensive set of moored observations show that NLIWs are correlated with the internal tide but uncorrelated with barotropic tide. Using harmonic analysis of a 40-day record, this study associates steady-phase motions at the shelf break with waves generated by the local barotropic tide and variable-phase motions with the shoaling of distantly generated internal tides. The dual sources of internal tide energy (local or remote) mean that shelf internal tides and NLIWs will be predictable with a local model only if the locally generated internal tides are significantly stronger than shoaling internal tides. Since the depth-integrated internal tide energy in the open ocean can greatly exceed that on the shelf, it is likely that shoaling internal tides control the energetics on shelves that are directly exposed to the open ocean.
    Description: This research was supported by ONR Grants N00014-05-1-0271, N00014-08-1-0991, N00014-04- 1-0146, and N00014-11-1-0194.
    Description: 2013-05-01
    Keywords: Internal waves ; Nonlinear dynamics ; Tides
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  • 20
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    Two configurations of the Western Arctic Shelfbreak Current in summer (2012)
    American Meteorological Society
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    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): 329-351, doi:10.1175/JPO-D-11-026.1.
    Description: Data from a closely spaced array of moorings situated across the Beaufort Sea shelfbreak at 152°W are used to study the Western Arctic Shelfbreak Current, with emphasis on its configuration during the summer season. Two dynamically distinct states of the current are revealed in the absence of wind, with each lasting approximately one month. The first is a surface-intensified shelfbreak jet transporting warm and buoyant Alaskan Coastal Water in late summer. This is the eastward continuation of the Alaskan Coastal Current. It is both baroclinically and barotropically unstable and hence capable of forming the surface-intensified warm-core eddies observed in the southern Beaufort Sea. The second configuration, present during early summer, is a bottom-intensified shelfbreak current advecting weakly stratified Chukchi Summer Water. It is baroclinically unstable and likely forms the middepth warm-core eddies present in the interior basin. The mesoscale instabilities extract energy from the mean flow such that the surface-intensified jet should spin down over an e-folding distance of 300 km beyond the array site, whereas the bottom-intensified configuration should decay within 150 km. This implies that Pacific Summer Water does not extend far into the Canadian Beaufort Sea as a well-defined shelfbreak current. In contrast, the Pacific Winter Water configuration of the shelfbreak jet is estimated to decay over a much greater distance of approximately 1400 km, implying that it should reach the first entrance to the Canadian Arctic Archipelago.
    Description: This work was supported by National Science Foundation GrantsOCE-0726640,OPP-0731928, and OPP-0713250.
    Description: 2012-09-01
    Keywords: Arctic ; Continental shelf/slope ; Boundary currents
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  • 21
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    Estuarine exchange flow quantified with isohaline coordinates : contrasting long and short estuaries (2012)
    American Meteorological Society
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    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): 748–763, doi:10.1175/JPO-D-11-086.1.
    Description: Isohaline coordinate analysis is used to compare the exchange flow in two contrasting estuaries, the long (with respect to tidal excursion) Hudson River and the short Merrimack River, using validated numerical models. The isohaline analysis averages fluxes in salinity space rather than in physical space, yielding the isohaline exchange flow that incorporates both subtidal and tidal fluxes and precisely satisfies the Knudsen relation. The isohaline analysis can be consistently applied to both subtidally and tidally dominated estuaries. In the Hudson, the isohaline exchange flow is similar to results from the Eulerian analysis, and the conventional estuarine theory can be used to quantify the salt transport based on scaling with the baroclinic pressure gradient. In the Merrimack, the isohaline exchange flow is much larger than the Eulerian quantity, indicating the dominance of tidal salt flux. The exchange flow does not scale with the baroclinic pressure gradient but rather with tidal volume flux. This tidal exchange is driven by tidal pumping due to the jet–sink flow at the mouth constriction, leading to a linear dependence of exchange flow on tidal volume flux. Finally, a tidal conversion parameter Qin/Qprism, measuring the fraction of tidal inflow Qprism that is converted into net exchange Qin, is proposed to characterize the exchange processes among different systems. It is found that the length scale ratio between tidal excursion and salinity intrusion provides a characteristic to distinguish estuarine regimes.
    Description: SNC is supported by a WHOI postdoctoral scholarship, a NSF Grant OCE-0926427, and a Taiwan National Science Council Grant NSC 100- 2199-M-002-028.WRGis supported byNSFGrantOCE- 0926427. JAL is supported by NSF Grant OCE-0452054.
    Description: 2012-11-01
    Keywords: Coastal flows
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  • 22
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    The role of advection, straining, and mixing on the tidal variability of estuarine stratification (2012)
    American Meteorological Society
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    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): 855–868, doi:10.1175/JPO-D-10-05010.1.
    Description: Data from the Hudson River estuary demonstrate that the tidal variations in vertical salinity stratification are not consistent with the patterns associated with along-channel tidal straining. These observations result from three additional processes not accounted for in the traditional tidal straining model: 1) along-channel and 2) lateral advection of horizontal gradients in the vertical salinity gradient and 3) tidal asymmetries in the strength of vertical mixing. As a result, cross-sectionally averaged values of the vertical salinity gradient are shown to increase during the flood tide and decrease during the ebb. Only over a limited portion of the cross section does the observed stratification increase during the ebb and decrease during the flood. These observations highlight the three-dimensional nature of estuarine flows and demonstrate that lateral circulation provides an alternate mechanism that allows for the exchange of materials between surface and bottom waters, even when direct turbulent mixing through the pycnocline is prohibited by strong stratification.
    Description: The funding for this research was obtained from NSF Grant OCE-08-25226.
    Description: 2012-11-01
    Keywords: Mixing ; Ocean circulation ; Shear structure/flows ; Transport ; Turbulence
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    On the nature and variability of the east Greenland Spill Jet : a case study in Summer 2003 (2012)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2011. 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 41 (2011): 2307–2327, doi:10.1175/JPO-D-10-05004.1.
    Description: Results from a high-resolution (~2 km) numerical simulation of the Irminger Basin during summer 2003 are presented. The focus is on the East Greenland Spill Jet, a recently discovered component of the circulation in the basin. The simulation compares well with observations of surface fields, the Denmark Strait overflow (DSO), and the hydrographic structure of typical sections in the basin. The model reveals new aspects of the circulation on scales of O(0.1–10) days and O(1–100) km. The model Spill Jet results from the cascade of dense waters over the East Greenland shelf. Spilling can occur in various locations southwest of the strait, and it is present throughout the simulation but exhibits large variations on periods of O(0.1–10) days. The Spill Jet sometimes cannot be distinguished in the velocity field from surface eddies or from the DSO. The vorticity structure of the jet confirms its unstable nature with peak relative and tilting vorticity terms reaching twice the planetary vorticity term. The average model Spill Jet transport is 4.9 ±1.7 Sv (1 Sv ≡ 106 m3 s−1) equatorward, about 2½ times larger than has been previously reported from a single ship transect in August 2001. Kinematic analysis of the model results suggests two different types of spilling events. In the first case (type I), a local perturbation results in dense waters descending over the shelf break into the Irminger Basin. In the second case (type II), surface cyclones associated with DSO deep domes initiate the spilling process. During summer 2003, more than half of the largest Spill Jet transport values are of type II.
    Description: The research is supported by the National Science Foundation Grants OCE-0726393 and OCI-0904640 (MGM and TWNH) and OCE-0726640 (RSP).
    Description: 2012-06-01
    Keywords: North Atlantic Ocean ; In situ observations ; Regional models
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    Subtropical mode water variability in a climatologically forced model in the northwestern Pacific Ocean (2012)
    American Meteorological Society
    Details
    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): 126–140, doi:10.1175/2011JPO4513.1.
    Description: A climatologically forced high-resolution model is used to examine variability of subtropical mode water (STMW) in the northwestern Pacific Ocean. Despite the use of annually repeating atmospheric forcing, significant interannual to decadal variability is evident in the volume, temperature, and age of STMW formed in the region. This long time-scale variability is intrinsic to the ocean. The formation and characteristics of STMW are comparable to those observed in nature. STMW is found to be cooler, denser, and shallower in the east than in the west, but time variations in these properties are generally correlated across the full water mass. Formation is found to occur south of the Kuroshio Extension, and after formation STMW is advected westward, as shown by the transport streamfunction. The ideal age and chlorofluorocarbon tracers are used to analyze the life cycle of STMW. Over the full model run, the average age of STMW is found to be 4.1 yr, but there is strong geographical variation in this, from an average age of 3.0 yr in the east to 4.9 yr in the west. This is further evidence that STMW is formed in the east and travels to the west. This is qualitatively confirmed through simulated dye experiments known as transit-time distributions. Changes in STMW formation are correlated with a large meander in the path of the Kuroshio south of Japan. In the model, the large meander inhibits STMW formation just south of Japan, but the export of water with low potential vorticity leads to formation of STMW in the east and an overall increase in volume. This is correlated with an increase in the outcrop area of STMW. Mixed layer depth, on the other hand, is found to be uncorrelated with the volume of STMW.
    Description: E.M.D. acknowledges support of the Doherty Foundation and National Science Foundation (OCE-0849808). S.R.J was sponsored by the National Science Foundation (OCE-0849808). Participation of S.P. and F.B. was supported by the National Science Foundation by its sponsorship of the National Center for Atmospheric Research.
    Description: 2012-07-01
    Keywords: Water masses ; Pacific Ocean ; Tracers ; Advection ; Forcing ; Interannual variuability
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  • 25
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    The modification of bottom boundary layer turbulence and mixing by internal waves shoaling on a barrier reef (2012)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2011. 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 41 (2011): 2223–2241, doi:10.1175/2011JPO4344.1.
    Description: Results are presented from an observational study of stratified, turbulent flow in the bottom boundary layer on the outer southeast Florida shelf. Measurements of momentum and heat fluxes were made using an array of acoustic Doppler velocimeters and fast-response temperature sensors in the bottom 3 m over a rough reef slope. Direct estimates of flux Richardson number Rf confirm previous laboratory, numerical, and observational work, which find mixing efficiency not to be a constant but rather to vary with Frt, Reb, and Rig. These results depart from previous observations in that the highest levels of mixing efficiency occur for Frt 〈 1, suggesting that efficient mixing can also happen in regions of buoyancy-controlled turbulence. Generally, the authors find that turbulence in the reef bottom boundary layer is highly variable in time and modified by near-bed flow, shear, and stratification driven by shoaling internal waves.
    Description: Funding was provided by grants from the National Oceanic and Atmospheric Administration’s National Undersea Research Program, National Science Foundation Grants OCE-0622967 and OCE- 0824972 to SGM, and the Singapore Stanford Program. Kristen Davis was supported by a National Defense Science and Engineering Graduate Fellowship and an ARCS Foundation Fellowship.
    Keywords: Boundary layer ; Turbulence ; Bottom currents ; Mixing ; Internal waves
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    Resonant and near-resonant internal wave interactions (2012)
    American Meteorological Society
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    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): 669–691, doi:10.1175/2011JPO4129.1.
    Description: The spectral energy density of the internal waves in the open ocean is considered. The Garrett and Munk spectrum and the resonant kinetic equation are used as the main tools of the study. Evaluations of a resonant kinetic equation that suggest the slow time evolution of the Garrett and Munk spectrum is not in fact slow are reported. Instead, nonlinear transfers lead to evolution time scales that are smaller than one wave period at high vertical wavenumber. Such values of the transfer rates are inconsistent with the viewpoint expressed in papers by C. H. McComas and P. Müller, and by P. Müller et al., which regards the Garrett and Munk spectrum as an approximate stationary state of the resonant kinetic equation. It also puts the self-consistency of a resonant kinetic equation at a serious risk. The possible reasons for and resolutions of this paradox are explored. Inclusion of near-resonant interactions decreases the rate at which the spectrum evolves. Consequently, this inclusion shows a tendency of improving of self-consistency of the kinetic equation approach.
    Description: YL is supported by NSF DMS Grant 0807871 and ONR Award N00014-09-1-0515.
    Description: 2012-11-01
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  • 27
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    Mechanisms behind the temporary shutdown of deep convection in the Labrador Sea : lessons from the Great Salinity Anomaly years 1968–71 (2012)
    American Meteorological Society
    Details
    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 Climate 25 (2012): 6743–6755, doi:10.1175/JCLI-D-11-00549.1.
    Description: From 1969 to 1971 convection in the Labrador Sea shut down, thus interrupting the formation of the intermediate/dense water masses. The shutdown has been attributed to the surface freshening induced by the Great Salinity Anomaly (GSA), a freshwater anomaly in the subpolar North Atlantic. The abrupt resumption of convection in 1972, in contrast, is attributed to the extreme atmospheric forcing of that winter. Here oceanic and atmospheric data collected in the Labrador Sea at Ocean Weather Station Bravo and a one-dimensional mixed layer model are used to examine the causes of the shutdown and resumption of convection in detail. These results highlight the tight coupling of the ocean and atmosphere in convection regions and the need to resolve both components to correctly represent convective processes in the ocean. They are also relevant to present-day conditions given the increased ice melt in the Arctic Ocean and from the Greenland Ice Sheet. The analysis herein shows that the shutdown was initiated by the GSA-induced freshening as well as the mild 1968/69 winter. After the shutdown had begun, however, the continuing lateral freshwater flux as well as two positive feedbacks [both associated with the sea surface temperature (SST) decrease due to lack of convective mixing with warmer subsurface water] further inhibited convection. First, the SST decrease reduced the heat flux to the atmosphere by reducing the air–sea temperature gradient. Second, it further reduced the surface buoyancy loss by reducing the thermal expansion coefficient of the surface water. In 1972 convection resumed because of both the extreme atmospheric forcing and advection of saltier waters into the convection region.
    Description: This research was funded by a grant from the NWO/SRON User Support Programme Space Research. FS acknowledges support from OCE- 0850416 and NOAA NA08OAR4310569.
    Description: 2013-04-01
    Keywords: Atmosphere-ocean interaction ; Intermediate waters ; Oceanic variability
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  • 28
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    Wavenumber–frequency spectra of inertia–gravity and mixed Rossby–gravity waves in the equatorial Pacific Ocean (2012)
    American Meteorological Society
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    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): 1859–1881, doi:10.1175/JPO-D-11-0235.1.
    Description: In the 1970s and 1980s, there was considerable interest in near-equatorial variability at periods of days to weeks associated with oceanic equatorial inertia–gravity waves and mixed Rossby–gravity waves. At that time, the measurements available for studying these waves were much more limited than today: most of the available observations were from scattered island tide gauges and a handful of short mooring records. More than a decade of the extensive modern data record from the Tropical Atmosphere Ocean (TAO)/Triangle Trans-Ocean Buoy Network (TRITON) mooring array in the Pacific Ocean is used to reexamine the internal-wave climate in the equatorial Pacific, with a focus on interpretation of the zonal-wavenumber/frequency spectrum of surface dynamic height relative to 500 decibars at periods of 3–15 days and zonal wavelengths exceeding 30° of longitude. To facilitate interpretation of the dynamic height spectrum and identification of equatorial wave modes, the spectrum is decomposed into separate spectra associated with dynamic height fluctuations that are symmetric or antisymmetric about the equator. Many equatorial-wave meridional modes can be identified, for both the first and second baroclinic mode. Zonal-wavenumber/frequency spectra of the zonal and meridional wind stress components are also examined. The observed wind stress spectra are used with linear theory of forced equatorial waves to provide a tentative explanation for the zonal-wavenumber extent of the spectral peaks seen in dynamic height. Examination of the cross-equatorial symmetry properties of the wind stress suggests that virtually all of the large-scale equatorial inertia–gravity and mixed Rossby–gravity waves examined may be sensitive to both zonal and meridional wind stress.
    Description: This research was funded by NASA Grant NNX10AO93G.
    Description: 2013-05-01
    Keywords: Inertia-gravity waves
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    The mean age of ocean waters inferred from radiocarbon observations : sensitivity to surface sources and accounting for mixing histories (2012)
    American Meteorological Society
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    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 Physical Oceanography 42 (2012): 291–305, doi:10.1175/JPO-D-11-043.1.
    Description: A number of previous observational studies have found that the waters of the deep Pacific Ocean have an age, or elapsed time since contact with the surface, of 700–1000 yr. Numerical models suggest ages twice as old. Here, the authors present an inverse framework to determine the mean age and its upper and lower bounds given Global Ocean Data Analysis Project (GLODAP) radiocarbon observations, and they show that the potential range of ages increases with the number of constituents or sources that are included in the analysis. The inversion requires decomposing the World Ocean into source waters, which is obtained here using the total matrix intercomparison (TMI) method at up to 2° × 2° horizontal resolution with 11 113 surface sources. The authors find that the North Pacific at 2500-m depth can be no younger than 1100 yr old, which is older than some previous observational estimates. Accounting for the broadness of surface regions where waters originate leads to a reservoir-age correction of almost 100 yr smaller than would be estimated with a two or three water-mass decomposition and explains some of the discrepancy with previous observational studies. A best estimate of mean age is also presented using the mixing history along circulation pathways. Subject to the caveats that inference of the mixing history would benefit from further observations and that radiocarbon cannot rule out the presence of extremely old waters from exotic sources, the deep North Pacific waters are 1200–1500 yr old, which is more in line with existing numerical model results.
    Description: GG is supported by the J. Lamar Worzel Assistant Scientist Fund and the Penzance Endowed Fund in Support of Assistant Scientists. PJH is supported by NSF Award 0960787.
    Description: 2012-08-01
    Keywords: North Pacific Ocean ; Mass fluxes/transport ; Ocean circulation ; Tracers ; Optimization ; Variational analysis
    Repository Name: Woods Hole Open Access Server
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    The CCSM4 ocean component (2012)
    American Meteorological Society
    Details
    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): 1361–1389, doi:10.1175/JCLI-D-11-00091.1.
    Description: The ocean component of the Community Climate System Model version 4 (CCSM4) is described, and its solutions from the twentieth-century (20C) simulations are documented in comparison with observations and those of CCSM3. The improvements to the ocean model physical processes include new parameterizations to represent previously missing physics and modifications of existing parameterizations to incorporate recent new developments. In comparison with CCSM3, the new solutions show some significant improvements that can be attributed to these model changes. These include a better equatorial current structure, a sharper thermocline, and elimination of the cold bias of the equatorial cold tongue all in the Pacific Ocean; reduced sea surface temperature (SST) and salinity biases along the North Atlantic Current path; and much smaller potential temperature and salinity biases in the near-surface Pacific Ocean. Other improvements include a global-mean SST that is more consistent with the present-day observations due to a different spinup procedure from that used in CCSM3. Despite these improvements, many of the biases present in CCSM3 still exist in CCSM4. A major concern continues to be the substantial heat content loss in the ocean during the preindustrial control simulation from which the 20C cases start. This heat loss largely reflects the top of the atmospheric model heat loss rate in the coupled system, and it essentially determines the abyssal ocean potential temperature biases in the 20C simulations. There is also a deep salty bias in all basins. As a result of this latter bias in the deep North Atlantic, the parameterized overflow waters cannot penetrate much deeper than in CCSM3.
    Description: NCAR is sponsored by the National Science Foundation. The CCSM is also sponsored by the Department of Energy. SGY was supported by the NOAA Climate Program Office under Climate Variability and Predictability Program Grant NA09OAR4310163.
    Description: 2012-09-01
    Keywords: Ocean circulation ; Climate models ; General circulation models ; Ocean models
    Repository Name: Woods Hole Open Access Server
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    Buoyancy arrest and shelf–ocean exchange (2012)
    American Meteorological Society
    Details
    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 Physical Oceanography 42 (2012): 644–658, doi:10.1175/JPO-D-11-0143.1.
    Description: When steady flow in a stratified ocean passes between the continental slope and open ocean, its ability to cross isobaths is potentially limited by buoyancy arrest. If the bottom Ekman transport vanishes and there are no interior stresses, then steady linear flow on an f plane must be geostrophic and follow isobaths exactly. The influence of arrest on cross-shelf transport is investigated here to establish 1) whether there are substantial penetration asymmetries between cases with upwelling and downwelling in the bottom boundary layer; 2) over what spatial scales, hence in what parameter regime, buoyancy arrest is important; and 3) the effects of depth-dependent interior flow. The problem is approached using scalings and idealized numerical models. The results show that there is little or no asymmetry introduced by bottom boundary layer behavior. Further, if the stratification is weak or moderate, as measured by a slope Burger number s = αN/f (where α is the bottom slope, N is buoyancy frequency, and f is the Coriolis parameter), buoyancy arrest does not exert a strong constraint on cross-isobath exchange.
    Description: This research was supported by the National Science Foundation Physical Oceanography program through Grant OCE-0849498.
    Description: 2012-10-01
    Keywords: Coastal flows ; Ekman pumping/transport
    Repository Name: Woods Hole Open Access Server
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    Influences of precipitation on water mass transformation and deep convection (2012)
    American Meteorological Society
    Details
    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 Physical Oceanography 42 (2012): 1684–1700, doi:10.1175/JPO-D-11-0230.1.
    Description: The influences of precipitation on water mass transformation and the strength of the meridional overturning circulation in marginal seas are studied using theoretical and idealized numerical models. Nondimensional equations are developed for the temperature and salinity anomalies of deep convective water masses, making explicit their dependence on both geometric parameters such as basin area, sill depth, and latitude, as well as on the strength of atmospheric forcing. In addition to the properties of the convective water, the theory also predicts the magnitude of precipitation required to shut down deep convection and switch the circulation into the haline mode. High-resolution numerical model calculations compare well with the theory for the properties of the convective water mass, the strength of the meridional overturning circulation, and also the shutdown of deep convection. However, the numerical model also shows that, for precipitation levels that exceed this critical threshold, the circulation retains downwelling and northward heat transport, even in the absence of deep convection.
    Description: This study was supported by the National Science Foundation underGrantsOCE-0850416, OCE-0959381, andOCE-0859381.
    Description: 2013-04-01
    Keywords: Boundary currents ; Deep convection ; Eddies ; Meridional overturning circulation ; Ocean dynamics ; Stability
    Repository Name: Woods Hole Open Access Server
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    The wavenumber–frequency content of resonantly excited equatorial waves (2012)
    American Meteorological Society
    Details
    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 Physical Oceanography 42 (2012): 1834–1858, doi:10.1175/JPO-D-11-0234.1.
    Description: The theoretical resonant excitation of equatorial inertia–gravity waves and mixed Rossby–gravity waves is examined. Contrary to occasionally published expectations, solutions show that winds that are broadband in both zonal wavenumber and frequency do not in general produce peaks in the wavenumber–frequency spectrum of sea surface height (SSH) at wavenumbers associated with vanishing zonal group velocity. Excitation of total wave energy in inertia–gravity modes by broadband zonal winds is virtually wavenumber independent when the meridional structure of the winds does not impose a bias toward negative or positive zonal wavenumbers. With increasing wavenumber magnitude |k|, inertia–gravity waves asymptote toward zonally propagating pure gravity waves, in which the magnitude of meridional velocity υ becomes progressively smaller relative to the magnitude of zonal velocity u and pressure p. When the total wave energy is independent of wavenumber, this effect produces a peak in |υ|2 near the wavenumber where group velocity vanishes, but a trough in |p|2 (or SSH variance). Another consequence of the shift toward pure gravity wave structure is that broadband meridional winds excite inertia–gravity modes progressively less efficiently as |k| increases and υ becomes less important to the wave structure. Broadband meridional winds produce a low-wavenumber peak in total wave energy leading to a subtle elevation of |p|2 at low wavenumbers, but this is due entirely to the decrease in the forcing efficiency of meridional winds with increasing |k|, rather than to the vanishing of the group velocity. Physical conditions that might alter the above conclusions are discussed.
    Description: This research was funded by NASA Grant NNX10AO93G.
    Description: 2013-05-01
    Keywords: Inertia-gravity waves ; Ocean dynamics
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    A century of Turing (2012)
    Springer Nature
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    Publication Date: 2012-11-30
    Print ISSN: 1745-2473
    Electronic ISSN: 1745-2481
    Topics: Physics
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    RET, ROS1 and ALK fusions in lung cancer (2012)
    Springer Nature
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    Publication Date: 2012-02-12
    Print ISSN: 1078-8956
    Electronic ISSN: 1546-170X
    Topics: Biology , Medicine
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    Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies (2012)
    Springer Nature
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    Publication Date: 2012-02-12
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    Chipping away at the lung cancer genome (2012)
    Springer Nature
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    Publication Date: 2012-03-01
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    miR-486 sustains NF-κB activity by disrupting multiple NF-κB-negative feedback loops (2012)
    Springer Nature
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    Publication Date: 2012-12-18
    Print ISSN: 1001-0602
    Electronic ISSN: 1748-7838
    Topics: Biology , Medicine
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    KIF5B-RET fusions in lung adenocarcinoma (2012)
    Springer Nature
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    Publication Date: 2012-02-12
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    Mapping identifies best targets for malaria prevention (2012)
    Springer Nature
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    Publication Date: 2012-06-06
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Money matters (2012)
    Springer Nature
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    Publication Date: 2012-02-25
    Description: Money matters Nature Climate Change 2, 133 24022012 doi: 10.1038/nclimate1446 Soulless economics as well as corporate and personal greed constrain climate-friendly behaviour. But explaining climate change in cultural and artistic terms may soften hardened hearts.
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    Topics: Geosciences
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    Peak timber (2012)
    Springer Nature
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    Publication Date: 2012-02-25
    Description: Peak timber Nature Climate Change 2, 141 24022012 doi: 10.1038/nclimate1432 Nicola Jones
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    Enhanced warming over the global subtropical western boundary currents (2012)
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    Publication Date: 2012-02-25
    Description: Enhanced warming over the global subtropical western boundary currents Nature Climate Change 2, 161 29012012 doi: 10.1038/nclimate1353 Lixin Wu Wenju Cai Liping Zhang Hisashi Nakamura Axel Timmermann Terry Joyce Michael J. McPhaden Michael Alexander Bo Qiu Martin Visbeck Ping Chang Benjamin Giese An analysis indicates that the warm, powerful currents that flow along the western edges of ocean basins warmed more than twice as quickly than the global ocean as a whole over the past century. This enhanced warming could have important effects on climate because these currents affect the air–sea exchange of heat, moisture and carbon dioxide.
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    Evolutionary ecology: Survival of the fittest (2012)
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    Publication Date: 2012-02-25
    Description: Evolutionary ecology: Survival of the fittest Nature Climate Change 2, 147 24022012 doi: 10.1038/nclimate1443 Anna Petherick
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    Economics: The rising costs of hurricanes (2012)
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    Publication Date: 2012-02-25
    Description: Economics: The rising costs of hurricanes Nature Climate Change 2, 148 24022012 doi: 10.1038/nclimate1427 Stéphane Hallegatte The impact of climate change on economic losses from tropical cyclones is a major concern. New research shows that — like changes in population and assets — climate change may double global losses from hurricanes.
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    Estimated carbon dioxide emissions from tropical deforestation improved by carbon-density maps (2012)
    Springer Nature
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    Publication Date: 2012-02-25
    Description: Estimated carbon dioxide emissions from tropical deforestation improved by carbon-density maps Nature Climate Change 2, 182 29012012 doi: 10.1038/nclimate1354 A. Baccini S. J. Goetz W. S. Walker N. T. Laporte M. Sun D. Sulla-Menashe J. Hackler P. S. A. Beck R. Dubayah M. A. Friedl S. Samanta R. A. Houghton Deforestation contributes 6–17% of anthropogenic carbon dioxide emissions. However, much uncertainty in the calculation of deforestation emissions stems from the inadequacy of forest carbon-density and deforestation data. Now an analysis provides the most-detailed estimate so far of the carbon density of vegetation and the associated carbon dioxide emissions from deforestation for ecosystems across the tropics.
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    Extreme heat effects on wheat senescence in India (2012)
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    Publication Date: 2012-02-25
    Description: Extreme heat effects on wheat senescence in India Nature Climate Change 2, 186 29012012 doi: 10.1038/nclimate1356 David B. Lobell Adam Sibley J. Ivan Ortiz-Monasterio One difficulty in anticipating the effects of climate change on agriculture is accounting for crop responses to extremely high temperatures. Now a remote-sensing study demonstrates accelerated ageing of wheat in northern India in response to extreme heat (〉34 °C); an effect that reduces crop yields but is underestimated in most crop models.
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    The impact of climate change on global tropical cyclone damage (2012)
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    Publication Date: 2012-02-25
    Description: The impact of climate change on global tropical cyclone damage Nature Climate Change 2, 205 15012012 doi: 10.1038/nclimate1357 Robert Mendelsohn Kerry Emanuel Shun Chonabayashi Laura Bakkensen Greenhouse-gas emissions are likely to have an impact on the damage caused by extreme weather events, such as tropical cyclones. A study predicts that climate change will increase the frequency of these high-intensity storms in selected ocean basins and double their economic damage. Almost all tropical cyclone damage tends to be concentrated in North America, East Asia and the Caribbean-Central American region.
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    Near-future carbon dioxide levels alter fish behaviour by interfering with neurotransmitter function (2012)
    Springer Nature
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    Publication Date: 2012-02-25
    Description: Near-future carbon dioxide levels alter fish behaviour by interfering with neurotransmitter function Nature Climate Change 2, 201 15012012 doi: 10.1038/nclimate1352 Göran E. Nilsson Danielle L. Dixson Paolo Domenici Mark I. McCormick Christina Sørensen Sue-Ann Watson Philip L. Munday A study of two species of coral reef fish demonstrates that the anticipated increase in atmospheric carbon dioxide directly interferes with neurotransmitter function in their larvae, a hitherto unrecognized problem for marine fishes.
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    Schizophrenia is a TH2 dominant autoimmune disease possibly against acetylcholine receptors of CNS (2012)
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    Publication Date: 2012-03-13
    Description: Schizophrenia is a very common psychiatric disorder. However, its etiology and pathogenesis is still unknown. Current theory saying that neurotransmitter imbalance such as serotonin or dopamine only provides limited effectiveness in schizophrenia treatment by drugs changing serotonin and dopamine concentration. Despite of such treatment, majority of schizophrenia patients still have very poor prognosis. Thus, the neurotransmitter imbalance theory is not correct. Here, I propose that schizophrenia is actually a TH2 dominant autoimmune disorder. The candidate of autoantigen could be acetylcholine receptors of CNS. My theory can explain the positive as well as negative symptoms of schizophrenia. By microarray analysis of PBMCS, one-tenth of the total 519 significantly expressed genes are immune-related genes. Among them, TH2 related genes are significantly up-regulated including IL-4, histidine decarboxylase, aldehyde dehydrogenase, CCR9, IgE Fc receptor, GATA2, serotonin receptor, phospholipase A2, and prostaglandin D2 synthase. Besides, TH1 and TH17 related genes are down-regulated including CXCL5, cathepsin C, and neutrophil related S100 binding proteins. The new theory sheds a light to better control this detrimental illness. Anti-inflammatory agents could be used to manage schizophrenia in the near future.
    Electronic ISSN: 1756-0357
    Topics: Natural Sciences in General , Geosciences , Physics , Chemistry and Pharmacology , Biology , Medicine
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    Translational neuroscience requires better design and analysis of preclinical studies (2012)
    Springer Nature
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    Publication Date: 2012-03-15
    Description: Animal models are often used to obtain a better understanding of psychiatric, neurodegenerative, and neurodevelopmental disorders. Despite many years of research, these models have not led to many novel therapies or treatments. Translating results between species will always be difficult, and it is argued that inappropriate statistical analyses, failure to identify the experimental unit, lack of random assignment to treatment conditions, and unblinded assessment of outcomes contribute to the low rate of translating preclinical in vivo studies into successful therapies. It is known that these shortcomings can generate biased estimates, too many false positives and false negatives, and unreproducible results. These issues have been raised repeatedly, but have largely gone unheeded by scientists. Two recommendations are made to improve the situation.
    Electronic ISSN: 1756-0357
    Topics: Natural Sciences in General , Geosciences , Physics , Chemistry and Pharmacology , Biology , Medicine
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    Mobile Image Ratiometry for the Detection of Botrytis cinerea (Gray Mold) (2012)
    Springer Nature
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    Publication Date: 2012-03-15
    Description: Mobile Platform Informatics (MPI) and Smartphone Informatics (SPI) methods like Mobile Image Ratiometry (MIR) are potentially transformative point-of-use instantaneous analysis tools that are useful across a variety of industries. In agriculture, MIR-compatible immuno test strips allow early detection of a number of biotic stressors before devastating crop losses occur. Here we describe a low-cost and easy-to-use Smartphone and/or tablet-based protocol (Mobile Assay Inc., www.mobileassay.com) for the detection and on-sight instantaneous analysis of B. cinerea, a fungus that causes significant damage to a variety of plants and flowers. Early detection and tracking of the B. cinerea fungus before the visible gray mold appears has the potential to increase agricultural productivity especially in the developing world.
    Electronic ISSN: 1756-0357
    Topics: Natural Sciences in General , Geosciences , Physics , Chemistry and Pharmacology , Biology , Medicine
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    Inter-Tunneling Mechanism of Colliding Population Waves (2012)
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    Publication Date: 2012-03-16
    Description: Here we show a new interaction mechanism of colliding population waves. It provides a stable coexistence of two similar but different species competing for the same limiting resource during their asexual propagation in a limited homogeneous environment under constant conditions. The revealed mechanism opens new opportunities in conservation biology.
    Electronic ISSN: 1756-0357
    Topics: Natural Sciences in General , Geosciences , Physics , Chemistry and Pharmacology , Biology , Medicine
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    The phyogenetic principles of mma: A hypothetical biostratigraphic model (2012)
    Springer Nature
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    Publication Date: 2012-03-16
    Description: Two erectoid hominids from Sarstedt prompted a detailed examination of the course of the impressions of the Arteria meningea media and their characteristics within the line of hominidae.
    Electronic ISSN: 1756-0357
    Topics: Natural Sciences in General , Geosciences , Physics , Chemistry and Pharmacology , Biology , Medicine
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    Genomic Replikin Counts of Infectious Salmon Anemia Virus (ISAV) in Canada Exceed the Counts in Lethal Outbreaks in Norway, Chile, and Scotland. Real-Time Tracking of the Evolution of the ISAV Genome and the Resultant Replikins Solid Phase ISAV Vacci (2012)
    Springer Nature
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    Publication Date: 2012-03-16
    Description: Genomic Replikin CountsTM of Infectious Salmon Anemia Virus (ISAV) in Canada Exceed the Counts in Lethal Outbreaks in Norway, Chile, and Scotland. Real-Time Tracking of the Evolution of the ISAV Genome and the Resultant Replikins Solid Phase ISAV Vaccine Make ISAV Pandemic Prevention Possible.
    Electronic ISSN: 1756-0357
    Topics: Natural Sciences in General , Geosciences , Physics , Chemistry and Pharmacology , Biology , Medicine
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    HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions (2012)
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    Publication Date: 2012-03-16
    Description: Background: The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes. In the case of human TF-TG interactions, there is no database at present that explicitly provides such information even though many databases containing human TF-TG interaction data have been available. In an effort to provide researchers with a repository of TF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).Description: The HTRIdb is an open-access database of experimentally validated interactions among human TFs and their TGs. HTRIdb can be searched via a user-friendly web interface and the retrieved TF-TG interactions data and the associated protein-protein interactions can be downloaded or interactively visualized as a network using the Cytoscape Web software. Moreover, users can improve the database quality by uploading their own interactions and indicating inconsistencies in the data. So far, HTRIdb has been populated with 283 TFs that regulate 11886 genes, totaling 18160 TF-TG interactions. HTRIdb is freely available at http://www.lbbc.ibb.unesp.br/htri.Conclusions: HTRIdb is a powerful user-friendly tool from which human experimentally validated TF-TG interactions can be easily extracted and used to construct transcriptional regulation interaction networks enabling researchers to decipher the regulation of biological processes.
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    AntEpiSeeker2.0: extending epistasis detection to epistasis-associated pathway inference using ant colony optimization (2012)
    Springer Nature
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    Publication Date: 2012-03-16
    Description: Genome-wide association studies (GWAS) have become a standard method for finding genetic variations that contribute to common, complex diseases. Recently, it is suggested that these diseases may be caused by epistatic interactions of multiple genetic variations. Although tens of software tools have been developed for epistasis detection, few are able to infer pathway importance from the identified epistatic interactions. AntEpiSeeker is originally an algorithm for detecting epistatic interactions in case-control studies, using a two-stage ant colony optimization (ACO) algorithm. We have developed AntEpiSeeker2.0, which extends the AntEpiSeeker algorithm to inference of epistasis-associated pathways, based on a natural use of the ACO pheromones. By looking at pheromone distribution across pathways, epistasis-associated pathways can be easily identified. The effectiveness of AntEpiSeeker2.0 in inferring epistasis-associated pathways is demonstrated through a simulation study and a real data application. AntEpiSeeker 2.0 was designed to provide efficient inference of epistasis-associated pathways based on ant colony optimization and is freely available at http://lambchop.ads.uga.edu/antepiseeker2/.
    Electronic ISSN: 1756-0357
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    The next generation (2012)
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    Publication Date: 2012-02-17
    Description: The next generation Nature Reviews Microbiology 10, 157 (2012). doi:10.1038/nrmicro2759 A better understanding of the factors that affect children's desire to follow a career in science is vital if we are to inspire the next generation of scientists.
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    Bacterial pathogenesis: Controlling Fic proteins (2012)
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    Publication Date: 2012-02-17
    Description: Bacterial pathogenesis: Controlling Fic proteins Nature Reviews Microbiology 10, 160 (2012). doi:10.1038/nrmicro2757 Author: Sheilagh Molloy A general mechanism for controlling the adenylylation activity of Fic proteins has been identified.
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    Cellular microbiology: An unconventional exit for Brucella (2012)
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    Publication Date: 2012-02-17
    Description: Cellular microbiology: An unconventional exit for Brucella Nature Reviews Microbiology 10, 160 (2012). doi:10.1038/nrmicro2749 Author: Rachel David Brucella abortus hijacks autophagy components to complete its life cycle.
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    Bacterial genomics: Universal bacterial barcode (2012)
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    Publication Date: 2012-02-17
    Description: Bacterial genomics: Universal bacterial barcode Nature Reviews Microbiology 10, 161 (2012). doi:10.1038/nrmicro2754 Author: Andrew Jermy Although analysis of 16S ribosomal RNA has revolutionized the ability to classify bacteria and understand their phylogenetic relationships, it is less useful for classifying related strains of bacteria that share similar or identical 16S rRNA gene sequences but exhibit distinct properties. To address this, Jolley
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    Viral infection: Promiscuous packaging (2012)
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    Publication Date: 2012-02-17
    Description: Viral infection: Promiscuous packaging Nature Reviews Microbiology 10, 161 (2012). doi:10.1038/nrmicro2755 Author: Andrew Jermy The high error rate of viral polymerases allows viruses to rapidly adapt to a new host, and each replication cycle results in a heterogeneous population of viruses with distinct genetic content. Routh et al. used an unbiased next-generation sequencing approach to look at the
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    Biofilms: Biofilms take shape (2012)
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    Description: Biofilms: Biofilms take shape Nature Reviews Microbiology 10, 162 (2012). doi:10.1038/nrmicro2756 Author: Sheilagh Molloy Phenol-soluble modulins have a key role in the structuring and detachment of Staphylococcus aureus biofilms.
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    Adapting to domesticity (2012)
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    Description: Adapting to domesticity Nature Reviews Microbiology 10, 163 (2012). doi:10.1038/nrmicro2752 Author: Adam J. Reid This month's Genome Watch highlights new insights into the impact of food production on the evolution of microorganisms.
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    In the news (2012)
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    Publication Date: 2012-02-17
    Description: In the news Nature Reviews Microbiology 10, 164 (2012). doi:10.1038/nrmicro2760 Our monthly round up of infectious diseases news, which this month includes the spread of a new virus affecting livestock in Europe, the H5N1 controversy and a report that mortality from malaria may be much higher than was previously suspected.
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    Bacterial pathogenesis: UPEC helps host to exfoliate (2012)
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    Publication Date: 2012-02-17
    Description: Bacterial pathogenesis: UPEC helps host to exfoliate Nature Reviews Microbiology 10, 159 (2012). doi:10.1038/nrmicro2758 Author: Andrew Jermy UPEC pore-forming toxin α-haemolysin (HlyA) stimulates the proteolysis of host proteins involved in cell adhesion, resulting in uroepithelial cell exfoliation.
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    A bacterial siren song: intimate interactions between Neisseria and neutrophils (2012)
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    Publication Date: 2012-02-17
    Description: A bacterial siren song: intimate interactions between Neisseria and neutrophils Nature Reviews Microbiology 10, 178 (2012). doi:10.1038/nrmicro2713 Authors: Alison K. Criss & H. Steven Seifert Neisseria gonorrhoeae and Neisseria meningitidis are Gram-negative bacterial pathogens that are exquisitely adapted for growth at human mucosal surfaces and for efficient transmission between hosts. One factor that is essential to neisserial pathogenesis is the interaction between the bacteria and neutrophils, which are
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    Phage biology: T4 to TA, checkmate (2012)
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    Publication Date: 2012-02-17
    Description: Phage biology: T4 to TA, checkmate Nature Reviews Microbiology 10, 160 (2012). doi:10.1038/nrmicro2748 Author: Andrew Jermy Phage T4 encodes an antitoxin that is active against multiple Escherichia coli toxins.
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    ppGpp: magic beyond RNA polymerase (2012)
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    Description: ppGpp: magic beyond RNA polymerase Nature Reviews Microbiology 10, 203 (2012). doi:10.1038/nrmicro2720 Authors: Zachary D. Dalebroux & Michele S. Swanson During stress, bacteria undergo extensive physiological transformations, many of which are coordinated by ppGpp. Although ppGpp is best known for enhancing cellular resilience by redirecting the RNA polymerase (RNAP) to certain genes, it also acts as a signal in many other cellular processes in bacteria.
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    Structural insights into the coupling of virion assembly and rotavirus replication (2012)
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    Publication Date: 2012-02-17
    Description: Structural insights into the coupling of virion assembly and rotavirus replication Nature Reviews Microbiology 10, 165 (2012). doi:10.1038/nrmicro2673 Authors: Shane D. Trask, Sarah M. McDonald & John T. Patton Viral replication is rapid and robust, but it is far from a chaotic process. Instead, successful production of infectious progeny requires that events occur in the correct place and at the correct time. Rotaviruses (segmented double-stranded RNA viruses of the Reoviridae family) seem to
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    Genome analyses highlight the different biological roles of cellulases (2012)
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    Publication Date: 2012-02-17
    Description: Genome analyses highlight the different biological roles of cellulases Nature Reviews Microbiology 10, 227 (2012). doi:10.1038/nrmicro2729 Authors: Felix Mba Medie, Gideon J. Davies, Michel Drancourt & Bernard Henrissat Cellulolytic enzymes have been the subject of renewed interest owing to their potential role in the conversion of plant lignocellulose to sustainable biofuels. An analysis of ∼1,500 complete bacterial genomes, presented here, reveals that ∼40% of the genomes of sequenced bacteria encode at least one
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    Host response: Phagocytosis runs like clockwork (2012)
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    Publication Date: 2012-02-17
    Description: Host response: Phagocytosis runs like clockwork Nature Reviews Microbiology 10, 162 (2012). doi:10.1038/nrmicro2751 Author: Christina Tobin Kåhrström In Drosophila melanogaster, phagocytosis of specific bacteria is regulated by a circadian protein.
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    From self sufficiency to dependence: mechanisms and factors important for autotransporter biogenesis (2012)
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    Publication Date: 2012-02-17
    Description: From self sufficiency to dependence: mechanisms and factors important for autotransporter biogenesis Nature Reviews Microbiology 10, 213 (2012). doi:10.1038/nrmicro2733 Authors: Denisse L. Leyton, Amanda E. Rossiter & Ian R. Henderson Autotransporters are a superfamily of proteins that use the type V secretion pathway for their delivery to the surface of Gram-negative bacteria. At first glance, autotransporters look to contain all the functional elements required to promote their own secretion: an amino-terminal signal peptide to mediate
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    Virophages question the existence of satellites (2012)
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    Description: Virophages question the existence of satellites Nature Reviews Microbiology 10, 234 (2012). doi:10.1038/nrmicro2676-c3 Authors: Christelle Desnues & Didier Raoult In a recent Comment (Virophages or satellite viruses? Nature Rev. Microbiol.9 762–763(2011)), Mart Krupovic and Virginija Cvirkaite-Krupovic argued that the recently described virophages, Sputnik and Mavirus, should be classified as satellite viruses. In a response, to which Krupovic and
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    Evolution: Co-evolution promotes innovation (2012)
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    Description: Evolution: Co-evolution promotes innovation Nature Reviews Microbiology 10, 161 (2012). doi:10.1038/nrmicro2753 Author: Christina Tobin Kåhrström The interaction between a viral ligand and its cellular receptor is highly specific and limits host range. A recent paper describes a mutant form of bacteriophage λ that targets an alternative receptor after co-evolution with Escherichia coli. When phage cI26 was cultured with E.
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    Towards a more comprehensive classification of satellite viruses (2012)
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    Publication Date: 2012-02-17
    Description: Towards a more comprehensive classification of satellite viruses Nature Reviews Microbiology 10, 234 (2012). doi:10.1038/nrmicro2676-c4 Authors: Mart Krupovic & Virginija Cvirkaite-Krupovic Our recent Comment on the nature and place of the so-called virophages in the viral world (Virophages or satellite viruses? Nature Rev. Microbiol.9 762–763 (2011)) has caught the attention of researchers favouring the virophage concept and initiated a debate on this
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    Computational tools for the synthetic design of biochemical pathways (2012)
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    Publication Date: 2012-02-17
    Description: Computational tools for the synthetic design of biochemical pathways Nature Reviews Microbiology 10, 191 (2012). doi:10.1038/nrmicro2717 Authors: Marnix H. Medema, Renske van Raaphorst, Eriko Takano & Rainer Breitling As the field of synthetic biology is developing, the prospects for de novo design of biosynthetic pathways are becoming more and more realistic. Hence, there is an increasing need for computational tools that can support these efforts. A range of algorithms has been developed
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    Agriculture: Nanotechnology’s Green Field (2012)
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    Publication Date: 2012-02-22
    Description: Natural agricultural production functions in open system, where energy and matter are exchanged freely between geosphere (especially pedosphere), biosphere, and atmosphere. The self regulation of biophysical processes in these spheres is crucial for global sustainability. However, modern farming practices have stressed the system to the extent that damaged C, N, and P cycles are threatening catastrophic consequences. High food-wastage coupled with high food price, high soil fertility zones but low crop productivity, and highly productive irrigated farming marred with ecological disasters are examples of global paradoxes associated with modern farming. High incidence of pesticide residues in soil and water bodies, low use efficiency of agricultural inputs, vulnerability to climate, and low conversion of energy by crops leaving high amount of residues and their subsequent burden on environment, and hunger and malnutrition in many parts of the world are threatening civilizations to crumble. Nanotechnology promises to break these vicious cycles, because technology is based on applying exact amounts of inputs for use by the crops, and only when they are required. Some of the examples are: nanofabricating nutrient ions to improve nutrient use efficiency, targeted use of nano-pesticides, holding of water and then releasing it at the time of crop need by nps, forecasting and elimination of diseases, packaging of food to improve shelf-life, protecting food during storage, DNA nanotechnology, smart treatment delivery systems, bioanalytical nanosensors, bioselective surfaces, nanobioprocessing, protection of the environment by the reduction and conversion of agricultural materials into valuable products, design and development of new nanocatalysts to convert vegetable oils into biobased fuels and biodegradable industrial solvents, and controlled ecological life support system.
    Electronic ISSN: 1756-0357
    Topics: Natural Sciences in General , Geosciences , Physics , Chemistry and Pharmacology , Biology , Medicine
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    Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties (2012)
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    Publication Date: 2012-12-19
    Description: Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties The ISME Journal 7, 37 (January 2013). doi:10.1038/ismej.2012.77 Authors: Anja B Dohrmann, Meike Küting, Sebastian Jünemann, Sebastian Jaenicke, Andreas Schlüter & Christoph C Tebbe
    Keywords: Bt-maizeCry proteinsbacterial community analysisrhizospherepyrosequencinggenetically modified maize
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    Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years (2012)
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    Publication Date: 2012-12-19
    Description: Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years The ISME Journal 7, 72 (January 2013). doi:10.1038/ismej.2012.83 Authors: Júlia Rosa de Rezende, Kasper Urup Kjeldsen, Casey R J Hubert, Kai Finster, Alexander Loy & Bo Barker Jørgensen
    Keywords: biogeographydispersalendosporespopulation half-lifesulfate-reducing bacteria
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    Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat (2012)
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    Publication Date: 2012-12-19
    Description: Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat The ISME Journal 7, 50 (January 2013). doi:10.1038/ismej.2012.79 Authors: J Kirk Harris, J Gregory Caporaso, Jeffrey J Walker, John R Spear, Nicholas J Gold, Charles E Robertson, Philip Hugenholtz, Julia Goodrich, Daniel McDonald, Dan Knights, Paul Marshall, Henry Tufo, Rob Knight & Norman R Pace
    Keywords: Guerrero NegrorRNA phylogenymicrobial matsmicrobial ecologyQIIME
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    Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation (2012)
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    Publication Date: 2012-12-19
    Description: Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation The ISME Journal 7, 122 (January 2013). doi:10.1038/ismej.2012.82 Authors: María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V Del Pozo, José María Vieites, Martin von Bergen, José Luis R Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert & Manuel Ferrer
    Keywords: biodiversitybio-stimulationlabel-free protein quantificationmetagenomicsmetaproteomicspolyaromatic hydrocarbon
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    Extracellular Ca2+ is a danger signal activating the NLRP3 inflammasome through G protein-coupled calcium sensing receptors (2012)
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    Publication Date: 2012-12-28
    Description: Extracellular Ca2+ is a danger signal activating the NLRP3 inflammasome through G protein-coupled calcium sensing receptors Nature Communications 3, 1329 (2012). doi:10.1038/ncomms2339 Authors: Manuela Rossol, Matthias Pierer, Nora Raulien, Dagmar Quandt, Undine Meusch, Kathrin Rothe, Kristin Schubert, Torsten Schöneberg, Michael Schaefer, Ute Krügel, Sanela Smajilovic, Hans Bräuner-Osborne, Christoph Baerwald & Ulf Wagner
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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    Phospho-dependent ubiquitination and degradation of PAR-1 regulates synaptic morphology and tau-mediated Aβ toxicity in Drosophila (2012)
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    Publication Date: 2012-12-28
    Description: Phospho-dependent ubiquitination and degradation of PAR-1 regulates synaptic morphology and tau-mediated Aβ toxicity in Drosophila Nature Communications 3, 1312 (2012). doi:10.1038/ncomms2278 Authors: Seongsoo Lee, Ji-Wu Wang, Wendou Yu & Bingwei Lu
    Electronic ISSN: 2041-1723
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    Atomic-scale engineering of magnetic anisotropy of nanostructures through interfaces and interlines (2012)
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    Publication Date: 2012-12-28
    Description: Atomic-scale engineering of magnetic anisotropy of nanostructures through interfaces and interlines Nature Communications 3, 1313 (2012). doi:10.1038/ncomms2316 Authors: S. Ouazi, S. Vlaic, S. Rusponi, G. Moulas, P. Buluschek, K. Halleux, S. Bornemann, S. Mankovsky, J. Minár, J.B. Staunton, H. Ebert & H. Brune
    Electronic ISSN: 2041-1723
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    Organic Single-Crystal Light-Emitting Transistor Coupling with Optical Feedback Resonators (2012)
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    Publication Date: 2012-12-18
    Description: Organic light-emitting transistors (OLETs) are of great research interest because they combine the advantage of the active channel of a transistor that can control the luminescence of an in-situ light-emitting diode in the same device. Here we report a novel single-crystal OLET (SCLET) that is coupled with single crystal optical feedback resonators. The combination of single-crystal waveguides with native Fabry-Perot cavities, formed by parallel crystal edges, drastically lowers the threshold energy for spectral narrowing and non-linear intensity enhancement. We apply this structure to SCLETs and demonstrate the first fabrication of a SCLET with the optical feedback resonators. Scientific Reports 2 doi: 10.1038/srep00985
    Electronic ISSN: 2045-2322
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    Ordering Ag nanowire arrays by a glass capillary: A portable, reusable and durable SERS substrate (2012)
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    Publication Date: 2012-12-18
    Description: Assembly of nanowires into ordered macroscopic structures with new functionalities has been a recent focus. In this Letter, we report a new route for ordering hydrophilic Ag nanowires with high aspect ratio by flowing through a glass capillary. The present glass capillary with well-defined silver nanowire films inside can serve as a portable and reusable substrate for surface-enhanced Raman spectroscopy (SERS), which may provide a versatile and promising platform for detecting mixture pollutions. By controlling the flow parameters of nanowire suspensions, initially random Ag nanowires can be aligned to form nanowire arrays with tunable density, forming cambered nanowire films adhered onto the inner wall of the capillary. Compared with the planar ordered Ag nanowire films by the Langmuir-Blodgett (LB) technique, the cambered nanowire films show better SERS performance. Scientific Reports 2 doi: 10.1038/srep00987
    Electronic ISSN: 2045-2322
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    Growth patterns for acervuli in human pineal gland (2012)
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    Publication Date: 2012-12-18
    Description: Acervuli are calcified concretions in the pineal gland (PG). Particularly interesting are their incidence and size, which are believed to affect neurological disorders and many physiological functions of PG such as regulating circadian rhythm. Despite long investigations for a century, detailed growth mechanism of acervuli has yet to be studied. Here we study the growth morphology of acervuli in human PGs by a direct visualization in 3-dimension (3-D) using a synchrotron X-ray imaging method. For an entire PG, non-aggregated acervuli show Gaussian distribution in size with 47±28 µm. The 3-D volume rendered images of acervuli reveal that the bumpy surfaces developed by lamination result in the mulberry-like structure. In addition, coalescence of multiple acervuli leads to large-scale lamination on the whole aggregate. We suggest a novel hypothesis on the growth patterns of acervuli by their nucleation density (Nd): i) mulberry-like structure at low Nd, and ii) large-scale lamination on an aggregate at high Nd. Scientific Reports 2 doi: 10.1038/srep00984
    Electronic ISSN: 2045-2322
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    A singular thermodynamically consistent temperature at the origin of the anomalous behavior of liquid water (2012)
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    Publication Date: 2012-12-19
    Description: The density maximum of water dominates the thermodynamics of the system under ambient conditions, is strongly P-dependent, and disappears at a crossover pressure Pcross ~ 1.8 kbar. We study this variable across a wide area of the T–P phase diagram. We consider old and new data of both the isothermal compressibility KT(T, P) and the coefficient of thermal expansion αP(T, P). We observe that KT(T) shows a minimum at T* ~ 315±5 K for all the studied pressures. We find the behavior of αP to also be surprising: all the αP(T) curves measured at different P cross at T*. The experimental data show a “singular and universal expansivity point” at T* ~ 315 K and αP(T*) ≃ 0.44 10−3 K−1. Unlike other water singularities, we find this temperature to be thermodynamically consistent in the relationship connecting the two response functions. Scientific Reports 2 doi: 10.1038/srep00993
    Electronic ISSN: 2045-2322
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    Stability of miRNA 5′terminal and seed regions is correlated with experimentally observed miRNA-mediated silencing efficacy (2012)
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    Publication Date: 2012-12-19
    Description: MicroRNAs (miRNAs) are key regulators of sequence-specific gene silencing. However, crucial factors that determine the efficacy of miRNA-mediated target gene silencing are poorly understood. Here we mathematized base-pairing stability and showed that miRNAs with an unstable 5′ terminal duplex and stable seed-target duplex exhibit strong silencing activity. The results are consistent with the previous findings that an RNA strand with unstable 5′ terminal in miRNA duplex easily loads onto the RNA-induced silencing complex (RISC), and miRNA recognizes target mRNAs with seed-complementary sequences to direct posttranscriptional repression. Our results suggested that both the unwinding and target recognition processes of miRNAs could be proficiently controlled by the thermodynamics of base-pairing in protein-free condition. Interestingly, such thermodynamic parameters might be evolutionarily well adapted to the body temperatures of various species. Scientific Reports 2 doi: 10.1038/srep00996
    Electronic ISSN: 2045-2322
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    Absence of a Spin Liquid Phase in the Hubbard Model on the Honeycomb Lattice (2012)
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    Publication Date: 2012-12-19
    Description: A spin liquid is a novel quantum state of matter with no conventional order parameter where a finite charge gap exists even though the band theory would predict metallic behavior. Finding a stable spin liquid in two or higher spatial dimensions is one of the most challenging and debated issues in condensed matter physics. Very recently, it has been reported that a model of graphene, i.e., the Hubbard model on the honeycomb lattice, can show a spin liquid ground state in a wide region of the phase diagram, between a semi-metal (SM) and an antiferromagnetic insulator (AFMI). Here, by performing numerically exact quantum Monte Carlo simulations, we extend the previous study to much larger clusters (containing up to 2592 sites), and find, if any, a very weak evidence of this spin liquid region. Instead, our calculations strongly indicate a direct and continuous quantum phase transition between SM and AFMI. Scientific Reports 2 doi: 10.1038/srep00992
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    On the Horizon (2012)
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    Publication Date: 2012-12-18
    Description: Nature Physics 8, 851 (2012). doi:10.1038/nphys2511 Emotions run high as the European Commission's ambitious framework for research and development forms the focus of a special budget summit in Brussels.
    Print ISSN: 1745-2473
    Electronic ISSN: 1745-2481
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    Man and machine (2012)
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    Publication Date: 2012-12-18
    Description: Nature Physics 8, 853 (2012). doi:10.1038/nphys2500 Author: Andreas Trabesinger
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    Exhibition: A life decoded (2012)
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    Description: Nature Physics 8, 855 (2012). doi:10.1038/nphys2499 Author: David Gevaux
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    Gone in a flash (2012)
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    Description: Nature Physics 8, 857 (2012). doi:10.1038/nphys2506 Author: Iulia Georgescu
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    Battle of the bulge (2012)
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    Description: Nature Physics 8, 857 (2012). doi:10.1038/nphys2507 Author: May Chiao
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    Description: Nature Physics 8, 857 (2012). doi:10.1038/nphys2505 Author: Abigail Klopper
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    Branching out (2012)
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    Description: Nature Physics 8, 857 (2012). doi:10.1038/nphys2509 Author: Alison Wright
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    Sisyphus again (2012)
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    Description: Nature Physics 8, 857 (2012). doi:10.1038/nphys2508 Author: David Gevaux
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    Quantum causality: Information insights (2012)
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    Description: Nature Physics 8, 860 (2012). doi:10.1038/nphys2470 Author: Terry Rudolph Answers to fundamental questions about the nature of non-locality shed new light onto the spacetime structure and the role of causality in quantum theory, topics that have traditionally been studied within the quantum gravity community.
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