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  • American Meteorological Society
  • Public Library of Science (PLoS)
  • 2015-2019  (10,811)
  • 2018  (10,811)
  • 1
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    Towards a Solution of the Closure Problem for Non-Homogeneous and Anisotropic Turbulence: Non-Gaussian Closures for Convective Atmospheric Boundary Layer Turbulence Based on an Analytically Solvable Multivariate Delta-PDF Model. (2018)
    American Meteorological Society
    In:  EPIC323rd Symposium on Boundary Layers and Turbulence, Renaissance Oklahoma City Convention Center Hotel - Ballroom E, 2018-06-2018-06Renaissance Oklahoma City Convention Center Hotel - Ballroom E, American Meteorological Society
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    Publication Date: 2018-08-08
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
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  • 2
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    Ecological impacts of the 2015/16 El Niño in the Central Equatorial Pacific (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 99, Suppl. S (2018): S21-S26, doi:10.1175/BAMS-D-17-0128.1.
    Description: NOAA Coral Reef Conservation Program; National Science Foundation OCE 1537338, OCE 1605365, OCE 1031971
    Repository Name: Woods Hole Open Access Server
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  • 3
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    Coral reef drag coefficients—surface gravity wave enhancement (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 1555-1566, doi:10.1175/JPO-D-17-0231.1.
    Description: A primary challenge in modeling flow over shallow coral reefs is accurately characterizing the bottom drag. Previous studies over continental shelves and sandy beaches suggest surface gravity waves should enhance the drag on the circulation over coral reefs. The influence of surface gravity waves on drag over four platform reefs in the Red Sea is examined using observations from 6-month deployments of current and pressure sensors burst sampling at 1Hz for 4–5min. Depth-average current fluctuations U0 within each burst are dominated by wave orbital velocities uw that account for 80%–90%of the burst variance and have a magnitude of order 10 cm s21, similar to the lower-frequency depth-average current Uavg. Previous studies have shown that the cross-reef bottom stress balances the pressure gradient over these reefs. A bottom stress estimate that neglects the waves (rCdaUavgjUavgj, where r is water density and Cda is a drag coefficient) balances the observed pressure gradient when uw is smaller than Uavg but underestimates the pressure gradient when uw is larger than Uavg (by a factor of 3–5 when uw 5 2Uavg), indicating the neglected waves enhance the bottom stress. In contrast, a bottom stress estimate that includes the waves [rCda(Uavg 1 U0)jUavg 1 U0j)] balances the observed pressure gradient independent of the relative size of uw and Uavg, indicating that this estimate accounts for the wave enhancement of the bottom stress. A parameterization proposed by Wright and Thompson provides a reasonable estimate of the total bottom stress (including the waves) given the burst-averaged current and the wave orbital velocity.
    Description: The Red Sea field program was supported by Awards USA 00002 and KSA 00011 made by KAUST. S. Lentz was supported for the analysis by NSF Award OCE-1558343.
    Description: 2019-01-13
    Keywords: Coastal flows ; Currents ; Dynamics ; Gravity waves ; Turbulence
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Results of the first Arctic Heat Open Science Experiment (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 99 (2018): 513-520, doi:10.1175/BAMS-D-16-0323.1.
    Description: Seasonally ice-covered marginal seas are among the most difficult regions in the Arctic to study. Physical constraints imposed by the variable presence of sea ice in all stages of growth and melt make the upper water column and air–sea ice interface especially challenging to observe. At the same time, the flow of solar energy through Alaska’s marginal seas is one of the most important regulators of their weather and climate, sea ice cover, and ecosystems. The deficiency of observing systems in these areas hampers forecast services in the region and is a major contributor to large uncertainties in modeling and related climate projections. The Arctic Heat Open Science Experiment strives to fill this observation gap with an array of innovative autonomous floats and other near-real-time weather and ocean sensing systems. These capabilities allow continuous monitoring of the seasonally evolving state of the Chukchi Sea, including its heat content. Data collected by this project are distributed in near–real time on project websites and on the Global Telecommunications System (GTS), with the objectives of (i) providing timely delivery of observations for use in weather and sea ice forecasts, for model, and for reanalysis applications and (ii) supporting ongoing research activities across disciplines. This research supports improved forecast services that protect and enhance the safety and economic viability of maritime and coastal community activities in Alaska. Data are free and open to all (see www.pmel.noaa.gov/arctic-heat/).
    Description: This work was supported by NOAA Ocean and Atmospheric Research and the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) under NOAA Cooperative Agreement NA15OAR4320063 and by the Innovative Technology for Arctic Exploration (ITAE) program at JISAO/PMEL. Jayne, Robbins, and Ekholm were supported by ONR (N00014-12-10110).
    Repository Name: Woods Hole Open Access Server
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  • 5
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    A method to quantify bedform height and asymmetry from a low-mounted sidescan sonar (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 35 (2018): 893-910, doi:10.1175/JTECH-D-17-0102.1.
    Description: Rotary sidescan sonars are widely used to image the seabed given their high temporal and spatial resolution. This high resolution is necessary to resolve bedform dynamics and evolution; however, sidescan sonars do not directly measure bathymetry, limiting their utility. When sidescan sonars are mounted close to the seabed, bedforms may create acoustical “shadows” that render previous methods that invert the backscatter intensity to estimate bathymetry and are based on the assumption of a fully insonified seabed ineffective. This is especially true in coastal regions, where bedforms are common features whose large height relative to the water depth may significantly influence the surrounding flow. A method is described that utilizes sonar shadows to estimate bedform height and asymmetry. The method accounts for the periodic structure of bedform fields and the projection of the shadows onto adjacent bedforms. It is validated with bathymetric observations of wave-orbital ripples, with wavelengths ranging from 0.3 to 0.8 m, and tidally reversing megaripples, with wavelengths from 5 to 8 m. In both cases, bathymetric-measuring sonars were deployed in addition to a rotary sidescan sonar to provide a ground truth; however, the bathymetric sonars typically measure different and smaller areas than the rotary sidescan sonar. The shadow-based method and bathymetric-measuring sonar data produce estimates of bedform height that agree by 34.0% ± 27.2% for wave-orbital ripples and 16.6% ± 14.7% for megaripples. Errors for estimates of asymmetry are 1.9% ± 2.1% for wave-orbital ripples and 11.2% ± 9.6% for megaripples.
    Description: This project is partially supported by the National Science Foundation through a Graduate Research Fellowship and a Massachusetts Institute of Technology Energy Initiative Fellowship. Additionally, funding used in developing the method was obtained from NSF Grants OCE-1634481 and OCE-1635151. Field work was funded under ONR Grants N00014-06-10329 and N00014-13-1-0364.
    Keywords: Ocean ; Acoustic measurements/effects ; Algorithms ; In situ oceanic observations ; Instrumentation/sensors
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Evolution of the freshwater coastal current at the southern tip of Greenland (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 2127-2140, doi:10.1175/JPO-D-18-0035.1.
    Description: Shipboard hydrographic and velocity measurements collected in summer 2014 are used to study the evolution of the freshwater coastal current in southern Greenland as it encounters Cape Farewell. The velocity structure reveals that the coastal current maintains its identity as it flows around the cape and bifurcates such that most of the flow is diverted to the outer west Greenland shelf, while a small portion remains on the inner shelf. Taking into account this inner branch, the volume transport of the coastal current is conserved, but the freshwater transport decreases on the west side of Cape Farewell. A significant amount of freshwater appears to be transported off the shelf where the outer branch flows adjacent to the shelfbreak circulation. It is argued that the offshore transposition of the coastal current is caused by the flow following the isobaths as they bend offshore because of the widening of the shelf on the west side of Cape Farewell. An analysis of the potential vorticity shows that the subsequent seaward flux of freshwater can be enhanced by instabilities of the current. This set of circumstances provides a pathway for the freshest water originating from the Arctic, as well as runoff from the Greenland ice sheet, to be fluxed into the interior Labrador Sea where it could influence convection in the basin.
    Description: Funding for this project was provided by the National Science Foundation under Grant OCE-1259618.
    Description: 2019-03-11
    Keywords: Boundary currents ; Coastal flows ; Instability ; Ocean circulation ; Potential vorticity ; Transport
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Turbulence from breaking surface waves at a river mouth (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 435-453, doi:10.1175/JPO-D-17-0122.1.
    Description: Observations of surface waves, currents, and turbulence at the Columbia River mouth are used to investigate the source and vertical structure of turbulence in the surface boundary layer. Turbulent velocity data collected on board freely drifting Surface Wave Instrument Float with Tracking (SWIFT) buoys are corrected for platform motions to estimate turbulent kinetic energy (TKE) and TKE dissipation rates. Both of these quantities are correlated with wave steepness, which has previously been shown to determine wave breaking within the same dataset. Estimates of the turbulent length scale increase linearly with distance from the free surface, and roughness lengths estimated from velocity statistics scale with significant wave height. The vertical decay of turbulence is consistent with a balance between vertical diffusion and dissipation. Below a critical depth, a power-law scaling commonly applied in the literature works well to fit the data. Above this depth, an exponential scaling fits the data well. These results, which are in a surface-following reference frame, are reconciled with results from the literature in a fixed reference frame. A mapping between free-surface and mean-surface reference coordinates suggests 30% of the TKE is dissipated above the mean sea surface.
    Description: Funding for this project was provided by the Office of Naval Research as part of the RIVET-II DRI, and for the DARLA group.
    Keywords: Ocean ; Estuaries ; Gravity waves ; Turbulence ; Wave breaking ; In situ oceanic observations
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  • 8
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    The interaction of recirculation gyres and a deep boundary current (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 573-590, doi:10.1175/JPO-D-17-0206.1.
    Description: Motivated by the proximity of the Northern Recirculation Gyre and the deep western boundary current in the North Atlantic, an idealized model is used to investigate how recirculation gyres and a deep flow along a topographic slope interact. In this two-layer quasigeostrophic model, an unstable jet imposed in the upper layer generates barotropic recirculation gyres. These are maintained by an eddy-mean balance of potential vorticity (PV) in steady state. The authors show that the topographic slope can constrain the northern recirculation gyre meridionally and that the gyre’s adjustment to the slope leads to increased eddy PV fluxes at the base of the slope. When a deep current is present along the topographic slope in the lower layer, these eddy PV fluxes stir the deep current and recirculation gyre waters. Increased proximity to the slope dampens the eddy growth rate within the unstable jet, altering the geometry of recirculation gyre forcing and leading to a decrease in overall eddy PV fluxes. These mechanisms may shape the circulation in the western North Atlantic, with potential feedbacks on the climate system.
    Description: We gratefully acknowledge an AMS graduate fellowship (IALB) and U.S. National Science Foundation Grants OCE-1332667 and 1332834 (IALB and JMT).
    Description: 2018-09-06
    Keywords: Boundary currents ; Meridional overturning circulation ; Mesoscale processes ; Ocean circulation ; Potential vorticity ; Quasigeostrophic models
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  • 9
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    Comment on “Abyssal upwelling and downwelling driven by near-boundary mixing” (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 739-748, doi:10.1175/JPO-D-17-0089.1.
    Description: McDougall and Ferrari have estimated the global deep upward diapycnal flow in the boundary layer overlying continental slopes that must balance both downward diapycnal flow in the deep interior and the formation of bottom water around Antarctica. The decrease of perimeter of isopycnal surfaces with depth and the observed decay with height above bottom of turbulent dissipation in the deep ocean play a key role in their estimate. They argue that because the perimeter of seamounts increases with depth, the net effect of mixing around seamounts is to produce net downward diapycnal flow. While this is true along much of a seamount, it is shown here that diapycnal flow of the densest water around the seamount is upward, with buoyancy being transferred from water just above. The same is true for midocean ridges, whose perimeter is constant with depth. It is argued that mixing around seamounts and especially midocean ridges contributes positively to the global deep overturning circulation, reducing the amount of turbulence demanded over the continental slopes to balance the buoyancy budget for the bottom and deep water.
    Description: This work was supported by National Science Foundation Grant OCE- 1232962.
    Description: 2018-09-29
    Keywords: Abyssal circulation ; Boundary currents ; Buoyancy ; Diapycnal mixing ; Mass fluxes/transport ; Ocean circulation
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  • 10
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    A note on interior pathways in the meridional overturning circulation (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 643-646, doi:10.1175/JPO-D-17-0240.1.
    Description: A simple oceanic model is presented for source–sink flow on the β plane to discuss the pathways from source to sink when transport boundary layers have large enough Reynolds numbers to be inertial in their dynamics. A representation of the flow as a Fofonoff gyre, suggested by prior work on inertial boundary layers and eddy-driven circulations in two-dimensional turbulent flows, indicates that even when the source and sink are aligned along the same western boundary the flow must intrude deep into the interior before exiting at the sink. The existence of interior pathways for the flow is thus an intrinsic property of an inertial circulation and is not dependent on particular geographical basin geometry.
    Description: 2018-09-12
    Keywords: Abyssal circulation ; Bottom currents ; Nonlinear dynamics ; Ocean circulation ; Ocean dynamics ; Potential vorticity
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  • 11
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    Submesoscale processes at shallow salinity fronts in the Bay of Bengal : observations during the winter monsoon (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 479-509, doi:10.1175/JPO-D-16-0283.1.
    Description: Lateral submesoscale processes and their influence on vertical stratification at shallow salinity fronts in the central Bay of Bengal during the winter monsoon are explored using high-resolution data from a cruise in November 2013. The observations are from a radiator survey centered at a salinity-controlled density front, embedded in a zone of moderate mesoscale strain (0.15 times the Coriolis parameter) and forced by winds with a downfront orientation. Below a thin mixed layer, often ≤10 m, the analysis shows several dynamical signatures indicative of submesoscale processes: (i) negative Ertel potential vorticity (PV); (ii) low-PV anomalies with O(1–10) km lateral extent, where the vorticity estimated on isopycnals and the isopycnal thickness are tightly coupled, varying in lockstep to yield low PV; (iii) flow conditions susceptible to forced symmetric instability (FSI) or bearing the imprint of earlier FSI events; (iv) negative lateral gradients in the absolute momentum field (inertial instability); and (v) strong contribution from differential sheared advection at O(1) km scales to the growth rate of the depth-averaged stratification. The findings here show one-dimensional vertical processes alone cannot explain the vertical stratification and its lateral variability over O(1–10) km scales at the radiator survey.
    Description: S. Ramachandran acknowledges support from the National Science Foundation through award OCE 1558849 and the U.S. Office of Naval Research, Grants N00014-13-1-0456 and N00014-17- 1-2355. A. Tandon acknowledges support from the U.S. Office of Naval Research, Grants N00014-13-1-0456 and N00014-17-1-2355. J. T. Farrar and R. A. Weller were supported by the U.S. Office of Naval Research, Grant N00014-13-1-0453, to collect the UCTD data and process theUCTD and shipboard meteorological data. J. Nash, J. Mackinnon, and A. F. Waterhouse acknowledge support from the U. S. Office of Naval Research, Grants N00014-13-1-0503 and N00014-14-1-0455. E. Shroyer acknowledges support from the U. S. Office of Naval Research, Grants N00014-14-10236 and N00014-15- 12634. A. Mahadevan acknowledges support fromthe U. S. Office of Naval Research, Grant N00014-13-10451. A. J. Lucas and R. Pinkel acknowledge support from the U. S. Office of Naval Research, Grant N00014-13-1-0489.
    Description: 2018-08-26
    Keywords: Indian Ocean ; Baroclinic flows ; Potential vorticity ; Fronts ; Monsoons ; Oceanic mixed layer
    Repository Name: Woods Hole Open Access Server
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  • 12
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    The transformation of salinity variance : a new approach to quantifying the influence of straining and mixing on estuarine stratification (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 607-623, doi:10.1175/JPO-D-17-0189.1.
    Description: The roles of straining and dissipation in controlling stratification are derived analytically using a vertical salinity variance method. Stratification is produced by converting horizontal variance to vertical variance via straining, that is, differential advection of horizontal salinity gradients, and stratification is destroyed by the dissipation of vertical variance through turbulent mixing. A numerical model is applied to the Changjiang estuary in order to demonstrate the salinity variance balance and how it reveals the factors controlling stratification. The variance analysis reveals that dissipation reaches its maximum during spring tide in the Changjiang estuary, leading to the lowest stratification. Stratification increases from spring tide to neap tide because of the increasing excess of straining over dissipation. Throughout the spring–neap tidal cycle, straining is almost always larger than dissipation, indicating a net excess of production of vertical variance relative to dissipation. This excess is balanced on average by advection, which exports vertical variance out of the estuarine region into the plume. During neap tide, tidal straining shows a general tendency of destratification during the flood tide and restratification during ebb, consistent with the one-dimensional theory of tidal straining. During spring tide, however, positive straining occurs during flood because of the strong baroclinicity induced by the intensified horizontal salinity gradient. These results indicate that the salinity variance method provides a valuable approach for examining the spatial and temporal variability of stratification in estuaries and coastal environments.
    Description: X. Li was supported by the China Scholarship Council. W. R. Geyer was supported by NSF Grants OCE 1736539 and OCE 1634480. J. Zhu was supported by the National Natural Science Foundation of China (41476077 and 41676083). H. Wu was supported by the National Natural Science Foundation of China (41576088 and 41776101).
    Description: 2018-09-08
    Keywords: Ocean ; Estuaries ; Freshwater ; Mixing ; Numerical analysis/modeling ; Regional models
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  • 13
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    A role for the equatorial undercurrent in the ocean dynamical thermostat (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 6245-6261, doi:10.1175/JCLI-D-17-0513.1.
    Description: Reconstructions of sea surface temperature (SST) based on instrumental observations suggest that the equatorial Pacific zonal SST gradient has increased over the twentieth century. While this increase is suggestive of the ocean dynamical thermostat mechanism of Clement et al., observations of a concurrent weakening of the zonal atmospheric (Walker) circulation are not. Here we show, using heat and momentum budget calculations on an ocean reanalysis dataset, that a seasonal weakening of the zonal atmospheric circulation is in fact consistent with cooling in the eastern equatorial Pacific (EEP) and thus an increase in the zonal SST gradient. This cooling is driven by a strengthening Equatorial Undercurrent (EUC) in response to decreased upper-ocean westward momentum associated with weakening equatorial zonal wind stress. This process can help to reconcile the seemingly contradictory twentieth-century trends in the tropical Pacific atmosphere and ocean. Moreover, it is shown that coupled general circulation models (CGCMs) do not correctly simulate this process; we identify a systematic bias in the relationship between changes in equatorial surface zonal wind stress in the EEP and EUC strength that may help to explain why observations and CGCMs have opposing trends in the zonal SST gradient over the twentieth century.
    Description: 2019-01-11
    Keywords: Tropics ; Atmosphere-ocean interaction ; Climate change ; Climate models ; Trends
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  • 14
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    Propagation of North Atlantic Deep Water anomalies (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 1831-1848, doi:10.1175/JPO-D-18-0068.1.
    Description: We present a simplified theory using reduced-gravity equations for North Atlantic Deep Water (NADW) and its variation driven by high-latitude deep-water formation. The theory approximates layer thickness on the eastern boundary with domain-averaged layer thickness and, in tandem with a mass conservation argument, retains fundamental physics for cross-equatorial flows on interannual and longer forcing time scales. Layer thickness anomalies are driven by a time-dependent northern boundary condition that imposes a southward volume flux representative of a variable source of NADW and damped by diapycnal mixing throughout the basin. Moreover, an outflowing southern boundary condition imposes a southward volume flux that generally differs from the volume flux at the northern boundary, giving rise to temporal storage of NADW within the Atlantic basin. Closed form analytic solutions for the amplitude and phase are provided when the variable source of NADW is sinusoidal. We provide a nondimensional analysis that demonstrates that solution behavior is primarily controlled by two parameters that characterize the meridional extent of the southern basin and the width of the basin relative to the equatorial deformation radius. Similar scaling applied to the time-lagged equations of Johnson and Marshall provides a clear connection to their results. Numerical simulations of reduced-gravity equations agree with analytic predictions in linear, turbulent, and diabatic regimes. The theory introduces a simple analytic framework for studying idealized buoyancy- and wind-driven cross-equatorial flows on interannual and longer time scales.
    Description: This research was supported by the National Science Foundation under Grant OCE- 1634468.
    Description: 2019-02-15
    Keywords: North Atlantic Ocean ; Tropics ; Meridional overturning circulation ; Ocean circulation ; Shallow-water equations
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  • 15
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    Revisiting the relationship among metrics of tropical expansion (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 7565-7581, doi:10.1175/JCLI-D-18-0108.1.
    Description: There is mounting evidence that the width of the tropics has increased over the last few decades, but there are large differences in reported expansion rates. This is, likely, in part due to the wide variety of metrics that have been used to define the tropical width. Here we perform a systematic investigation into the relationship among nine metrics of the zonal-mean tropical width using preindustrial control and abrupt quadrupling of CO2 simulations from a suite of coupled climate models. It is shown that the latitudes of the edge of the Hadley cell, the midlatitude eddy-driven jet, the edge of the subtropical dry zones, and the Southern Hemisphere subtropical high covary interannually and exhibit similar long-term responses to a quadrupling of CO2. However, metrics based on the outgoing longwave radiation, the position of the subtropical jet, the break in the tropopause, and the Northern Hemisphere subtropical high have very weak covariations with the above metrics and/or respond differently to increases in CO2 and thus are not good indicators of the expansion of the Hadley cell or subtropical dry zone. The differing variability and responses to increases in CO2 among metrics highlights that care is needed when choosing metrics for studies of the width of the tropics and that it is important to make sure the metric used is appropriate for the specific phenomena and impacts being examined.
    Description: DW acknowledges support from NSF AGS-1403676.
    Description: 2019-02-08
    Keywords: Hadley circulation ; Hydrologic cycle ; Meridional overturning circulation
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  • 16
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    On the dynamics and water mass transformation of a boundary current connecting alpha and beta oceans (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 2457-2475, doi:10.1175/JPO-D-17-0186.1.
    Description: A subpolar marginal sea, like the Nordic seas, is a transition zone between the temperature-stratified subtropics (the alpha ocean) and the salinity-stratified polar regions (the beta ocean). An inflow of Atlantic Water circulates these seas as a boundary current that is cooled and freshened downstream, eventually to outflow as Deep and Polar Water. Stratification in the boundary region is dominated by a thermocline over the continental slope and a halocline over the continental shelves, separating Atlantic Water from Deep and Polar Water, respectively. A conceptual model is introduced for the circulation and water mass transformation in a subpolar marginal sea to explore the potential interaction between the alpha and beta oceans. Freshwater input into the shelf regions has a slight strengthening effect on the Atlantic inflow, but more prominently impacts the water mass composition of the outflow. This impact of freshwater, characterized by enhancing Polar Water outflow and suppressing Deep Water outflow, is strongly determined by the source location of freshwater. Concretely, perturbations in upstream freshwater sources, like the Baltic freshwater outflow into the Nordic seas, have an order of magnitude larger potential to impact water mass transports than perturbations in downstream sources like the Arctic freshwater outflow. These boundary current dynamics are directly related to the qualitative stratification in transition zones and illustrate the interaction between the alpha and beta oceans.
    Description: This research was supported by the Research Council of Norway project NORTH. Support for the publication was provided by the University of Bergen. Ocean Outlook has supported a research visit for EL to Woods Hole Oceanographic Institute where much of the current work has been carried out. Support forMAS was provided by the National Science Foundation Grant OCE-1558742.
    Keywords: Continental shelf/slope ; Baroclinic flows ; Boundary currents ; Buoyancy ; Freshwater ; Thermohaline circulation
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    Wind-driven circulation in a shelf valley. Part II : Dynamics of the along-valley velocity and transport (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 883-904, doi:10.1175/JPO-D-17-0084.1.
    Description: The dynamics controlling the along-valley (cross shelf) flow in idealized shallow shelf valleys with small to moderate Burger number are investigated, and analytical scales of the along-valley flows are derived. This paper follows Part I, which shows that along-shelf winds in the opposite direction to coastal-trapped wave propagation (upwelling regime) force a strong up-valley flow caused by the formation of a lee wave. In contrast, along-shelf winds in the other direction (downwelling regime) do not generate a lee wave and consequently force a relatively weak net down-valley flow. The valley flows in both regimes are cyclostrophic with 0(1) Rossby number. A major difference between the two regimes is the along-shelf length scales of the along-valley flows L. In the upwelling regime Ls, depends on the valley width W, and the wavelength lambda(1w) of the coastal-trapped lee wave arrested by the along-shelf flow U-s. In the downwelling regime L depends on the inertial length scale U-s|'f and W-c. The along-valley velocity scale in the upwelling regime, given by V-u approximate to root pi H-c/H-s integral W-c lambda(1w)/2 pi L-x (1+L-x(2)/L-c(2))(-1) e(-(pi Wc)/(lambda 1w),) is based on potential vorticity (PV) conservation and lee-wave dynamics (Hs and H, are the shelf and valley depth scales, respectively, and fis the Coriolis parameter). The velocity scale in the downwelling regime, given by |v(d)| approximate to (H-s/H-s)[1 + (L-x(2)/L-x(2))](-1) fL, is based on PV conservation. The velocity scales are validated by the numerical sensitivity simulations and can be useful for observational studies of along -valley transports. The work provides a framework for investigating cross -shelf transport induced by irregular shelf bathymetry and calls for future studies of this type under realistic environmental conditions and over a broader parameter space.
    Description: Both WGZ and SJL were supported by the National Science Foundation (NSF) through Grant OCE 1154575.WGZis also supported by the NSF Grant OCE 1634965 and SJL by NSF Grant OCE 1558874.
    Description: 2018-10-16
    Keywords: Ocean circulation ; Topographic effects ; Upwelling/downwelling ; Waves, oceanic ; Wind stress ; Ocean models
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    The dynamics of shelf forcing in Greenlandic fjords (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 2799-2827, doi:10.1175/JPO-D-18-0057.1.
    Description: The fjords that connect Greenland’s glaciers to the ocean are gateways for importing heat to melt ice and for exporting meltwater into the ocean. The transport of heat and meltwater can be modulated by various drivers of fjord circulation, including freshwater, local winds, and shelf variability. Shelf-forced flows (also known as the intermediary circulation) are the dominant mode of variability in two major fjords of east Greenland, but we lack a dynamical understanding of the fjord’s response to shelf forcing. Building on observations from east Greenland, we use numerical simulations and analytical models to explore the dynamics of shelf-driven flows. For the parameter space of Greenlandic fjords, we find that the fjord’s response is primarily a function of three nondimensional parameters: the fjord width over the deformation radius (W/Rd), the forcing time scale over the fjord adjustment time scale, and the forcing amplitude (shelf pycnocline displacements) over the upper-layer thickness. The shelf-forced flows in both the numerical simulations and the observations can largely be explained by a simple analytical model for Kelvin waves propagating around the fjord. For fjords with W/Rd 〉 0.5 (most Greenlandic fjords), 3D dynamics are integral to understanding shelf forcing—the fjord dynamics cannot be approximated with 2D models that neglect cross-fjord structure. The volume flux exchanged between the fjord and shelf increases for narrow fjords and peaks around the resonant forcing frequency, dropping off significantly at higher- and lower-frequency forcing.
    Description: This work was funded by NSF Grant OCE-1536856 and by the NOAA Climate and Global Change Postdoctoral Fellowship.
    Keywords: Estuaries ; Glaciers ; Baroclinic flows ; Coastal flows ; Kelvin waves ; Regional models
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  • 19
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    Large changes in sea ice triggered by small changes in Atlantic water temperature (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 4847-4863, doi:10.1175/JCLI-D-17-0802.1.
    Description: The sensitivity of sea ice to the temperature of inflowing Atlantic water across the Greenland–Scotland Ridge is investigated using an eddy-resolving configuration of the Massachusetts Institute of Technology General Circulation Model with idealized topography. During the last glacial period, when climate on Greenland is known to have been extremely unstable, sea ice is thought to have covered the Nordic seas. The dramatic excursions in climate during this period, seen as large abrupt warming events on Greenland and known as Dansgaard–Oeschger (DO) events, are proposed to have been caused by a rapid retreat of Nordic seas sea ice. Here, we show that a full sea ice cover and Arctic-like stratification can exist in the Nordic seas given a sufficiently cold Atlantic inflow and corresponding low transport of heat across the Greenland–Scotland Ridge. Once sea ice is established, continued sea ice formation and melt efficiently freshens the surface ocean and makes the deeper layers more saline. This creates a strong salinity stratification in the Nordic seas, similar to today’s Arctic Ocean, with a cold fresh surface layer protecting the overlying sea ice from the warm Atlantic water below. There is a nonlinear response in Nordic seas sea ice to Atlantic water temperature with simulated large abrupt changes in sea ice given small changes in inflowing temperature. This suggests that the DO events were more likely to have occurred during periods of reduced warm Atlantic water inflow to the Nordic seas.
    Description: The research was supported by the Centre for Climate Dynamics at the Bjerknes Centre for Climate Research. The research leading to these results is part of the ice2ice project funded by the European Research Council under the European Community Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 610055.
    Keywords: Ocean ; Arctic ; Sea ice ; Ocean dynamics ; Paleoclimate ; General circulation models
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    Hydrography of the Gulf of Mexico using autonomous floats (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 773-794, doi:10.1175/JPO-D-17-0205.1.
    Description: Fourteen autonomous profiling floats, equipped with CTDs, were deployed in the deep eastern and western basins of the Gulf of Mexico over a four-year interval (July 2011–August 2015), producing a total of 706 casts. This is the first time since the early 1970s that there has been a comprehensive survey of water masses in the deep basins of the Gulf, with better vertical resolution than available from older ship-based surveys. Seven floats had 14-day cycles with parking depths of 1500 m, and the other half from the U.S. Argo program had varying cycle times. Maps of characteristic water masses, including Subtropical Underwater, Antarctic Intermediate Water (AAIW), and North Atlantic Deep Water, showed gradients from east to west, consistent with their sources being within the Loop Current (LC) and the Yucatan Channel waters. Altimeter SSH was used to characterize profiles being in LC or LC eddy water or in cold eddies. The two-layer nature of the deep Gulf shows isotherms being deeper in the warm anticyclonic LC and LC eddies and shallower in the cold cyclones. Mixed layer depths have an average seasonal signal that shows maximum depths (~60 m) in January and a minimum in June–July (~20 m). Basin-mean steric heights from 0–50-m dynamic heights and altimeter SSH show a seasonal range of ~12 cm, with significant interannual variability. The translation of LC eddies across the western basin produces a region of low homogeneous potential vorticity centered over the deepest part of the western basin.
    Description: The authors were supported by the Department of the Interior, Bureau of Ocean Energy Management (BOEM), Contract M08PC20043 to Leidos, Inc., Raleigh, North Carolina.
    Description: 2018-10-04
    Keywords: Eddies ; Mixing ; Potential vorticity ; Surface layer ; Water masses
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    Wind-wave effects on estuarine turbulence : a comparison of observations and second-moment closure predictions (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 905-923, doi:10.1175/JPO-D-17-0133.1.
    Description: Observations of turbulent kinetic energy, dissipation, and turbulent stress were collected in the middle reaches of Chesapeake Bay and were used to assess second-moment closure predictions of turbulence generated beneath breaking waves. Dissipation scaling indicates that the turbulent flow structure observed during a 10-day wind event was dominated by a three-layer response that consisted of 1) a wave transport layer, 2) a surface log layer, and 3) a tidal, bottom boundary layer limited by stable stratification. Below the wave transport layer, turbulent mixing was limited by stable stratification. Within the wave transport layer, where dissipation was balanced by a divergence in the vertical turbulent kinetic energy flux, the eddy viscosity was significantly underestimated by second-moment turbulence closure models, suggesting that breaking waves homogenized the mixed surface layer to a greater extent than the simple model of TKE diffusing away from a source at the surface. While the turbulent transport of TKE occurred largely downgradient, the intermittent downward sweeps of momentum generated by breaking waves occurred largely independent of the mean shear. The underprediction of stress in the wave transport layer by second-moment closures was likely due to the inability of the eddy viscosity model to capture the nonlocal turbulent transport of the momentum flux beneath breaking waves. Finally, the authors hypothesize that large-scale coherent turbulent eddies played a significant role in transporting momentum generated near the surface to depth.
    Description: This work was supported by National Science Foundation Grants OCE-1061609 and OCE-1339032.
    Description: 2018-10-19
    Keywords: Mixing ; Turbulence ; Waves, oceanic ; Boundary layer
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    An observing system simulation experiment for the calibration and validation of the surface water ocean topography sea surface height measurement using in situ platforms (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 35 (2018): 281-297, doi:10.1175/JTECH-D-17-0076.1.
    Description: The wavenumber spectrum of sea surface height (SSH) is an important indicator of the dynamics of the ocean interior. While the SSH wavenumber spectrum has been well studied at mesoscale wavelengths and longer, using both in situ oceanographic measurements and satellite altimetry, it remains largely unknown for wavelengths less than ~70 km. The Surface Water Ocean Topography (SWOT) satellite mission aims to resolve the SSH wavenumber spectrum at 15–150-km wavelengths, which is specified as one of the mission requirements. The mission calibration and validation (CalVal) requires the ground truth of a synoptic SSH field to resolve the targeted wavelengths, but no existing observational network is able to fulfill the task. A high-resolution global ocean simulation is used to conduct an observing system simulation experiment (OSSE) to identify the suitable oceanographic in situ measurements for SWOT SSH CalVal. After fixing 20 measuring locations (the minimum number for resolving 15–150-km wavelengths) along the SWOT swath, four instrument platforms were tested: pressure-sensor-equipped inverted echo sounders (PIES), underway conductivity–temperature–depth (UCTD) sensors, instrumented moorings, and underwater gliders. In the context of the OSSE, PIES was found to be an unsuitable tool for the target region and for SSH scales 15–70 km; the slowness of a single UCTD leads to significant aliasing by high-frequency motions at short wavelengths below ~30 km; an array of station-keeping gliders may meet the requirement; and an array of moorings is the most effective system among the four tested instruments for meeting the mission’s requirement. The results shown here warrant a prelaunch field campaign to further test the performance of station-keeping gliders.
    Description: The authors would like to acknowledge the funding sources: the SWOT mission (JW, LF, DM); NASA Projects NNX13AE32G, NNX16AH76G, and NNX17AH54G (TF); and NNX16AH66G and NNX17AH33G (BQ). AF and MF were funded by the Keck Institute for Space Studies (which is generously supported by the W. M. Keck Foundation) through the project Science-driven Autonomous and Heterogeneous Robotic Networks: A Vision for Future Ocean Observations (http://kiss.caltech.edu/?techdev/seafloor/seafloor.html).
    Description: 2018-08-07
    Keywords: Altimetry ; In situ oceanic observations ; Profilers, oceanic ; Satellite observations ; Sensitivity studies ; Planning
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  • 23
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    Shelf–open ocean exchange forced by wind jets (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 163-174, doi:10.1175/JPO-D-17-0161.1.
    Description: The general problem of exchange from a shallow shelf across sharp topography to the deep ocean forced by narrow, cross-shelf wind jets is studied using quasigeostrophic theory and an idealized primitive equation numerical model. Interest is motivated by katabatic winds that emanate from narrow fjords in southeast Greenland, although similar topographically constrained wind jets are found throughout the world’s oceans. Because there is no net vorticity input by the wind, the circulation is largely confined to the region near the forcing. Circulation over the shelf is limited by bottom friction for weakly stratified flows, but stratification allows for much stronger upper-layer flows that are regulated by weak coupling to the lower layer. Over the sloping topography, the topographic beta effect limits the deep flow, while, for sufficient stratification, the upper-layer flow can cross the topography to connect the shelf to the open ocean. This can be an effective transport mechanism even for short, strong wind events because damping of the upper-layer flow is weak. A variety of transients are generated for an abrupt onset of winds, including short topography Rossby waves, long topographic Rossby waves, and inertial waves. Using parameters representative of southeast Greenland, katabatic wind events will force an offshore transport of O(0.4) Sv (1 Sv ≡ 106 m3 s−1) that, when considered for 2 days, will result in an offshore flux of O(5 × 1010) m3.
    Description: MAS was supported by the National Science Foundation under Grant OCE-1533170.
    Description: 2018-07-18
    Keywords: Coastal flows ; Downslope winds ; Ocean dynamics
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    On estimating the surface wind stress over the sea (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 1533-1541, doi:10.1175/JPO-D-17-0267.1.
    Description: Our study analyzes measurements primarily from two Floating Instrument Platform (FLIP) field programs and from the Air–Sea Interaction Tower (ASIT) site to examine the relationship between the wind and sea surface stress for contrasting conditions. The direct relationship of the surface momentum flux to U2 is found to be better posed than the relationship between and U, where U is the wind speed and is the friction velocity. Our datasets indicate that the stress magnitude often decreases significantly with height near the surface due to thin marine boundary layers and/or enhanced stress divergence close to the sea surface. Our study attempts to correct the surface stress estimated from traditional observational levels by using multiple observational levels near the surface and extrapolating to the surface. The effect of stability on the surface stress appears to be generally smaller than errors due to the stress divergence. Definite conclusions require more extensive measurements close to the sea surface.
    Description: This work was supported by the U.S. Office of Naval Research through Award N00014-16-1-2600. We
    Description: 2019-01-10
    Keywords: Atmosphere-ocean interaction ; Marine boundary layer
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  • 25
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    Observed variations in turbulent mixing efficiency in the deep ocean (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 1815-1830, doi:10.1175/JPO-D-17-0275.1.
    Description: Recent progress in direct numerical simulations (DNSs) of stratified turbulent flows has led to increasing attention to the validity of the constancy of the dissipation flux coefficient Γ in the Osborn’s eddy diffusivity model. Motivated by lack of observational estimates of Γ, particularly under weakly stratified deep-ocean conditions, this study estimates Γ using deep microstructure profiles collected in various regions of the North Pacific and Southern Oceans. It is shown that Γ is not constant but varies significantly with the Ozmidov/Thorpe scale ratio ROT in a fashion similar to that obtained by previous DNS studies. Efficient mixing events with Γ ~ O(1) and ROT ~ O(0.1) tend to be frequently observed in the deep ocean (i.e., weak stratification), while moderate mixing events with Γ ~ O(0.1) and ROT ~ O(1) tend to be observed in the upper ocean (i.e., strong stratification). The observed negative relationship between Γ and ROT is consistent with a simple scaling that can be derived from classical turbulence theories. In contrast, the observed results exhibit no definite relationships between Γ and the buoyancy Reynolds number Reb, although Reb has long been thought to be another key parameter that controls Γ.
    Description: This study was supported by MEXT KAKENHI Grant JP15H05824 and JSPS KAKENHI Grant JP15H02131.
    Description: 2019-02-15
    Keywords: Abyssal circulation ; Mixing ; Subgrid-scale processes ; Turbulence ; In situ oceanic observations
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  • 26
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    Distinct mechanisms of decadal subsurface heat content variations in the eastern and western Indian Ocean modulated by tropical Pacific SST (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 7751-7769, doi:10.1175/JCLI-D-18-0184.1.
    Description: Decadal variability of the subsurface ocean heat content (OHC) in the Indian Ocean is investigated using a coupled climate model experiment, in which observed eastern tropical Pacific sea surface temperature (EPSST) anomalies are specified. This study intends to understand the contributions of external forcing relative to those of internal variability associated with EPSST, as well as the mechanisms by which the Pacific impacts Indian Ocean OHC. Internally generated variations associated with EPSST dominate decadal variations in the subsurface Indian Ocean. Consistent with ocean reanalyses, the coupled model reproduces a pronounced east–west dipole structure in the southern tropical Indian Ocean and discontinuities in westward-propagating signals in the central Indian Ocean around 100°E. This implies distinct mechanisms by which the Pacific impacts the eastern and western Indian Ocean on decadal time scales. Decadal variations of OHC in the eastern Indian Ocean are attributed to 1) western Pacific surface wind anomalies, which trigger oceanic Rossby waves propagating westward through the Indonesian Seas and influence Indonesian Throughflow transport, and 2) zonal wind anomalies over the central tropical Indian Ocean, which trigger eastward-propagating Kelvin waves. Decadal variations of OHC in the western Indian Ocean are linked to conditions in the Pacific via changes in the atmospheric Walker cell, which trigger anomalous wind stress curl and Ekman pumping in the central tropical Indian Ocean. Westward-propagating oceanic Rossby waves extend the influence of this anomalous Ekman pumping to the western Indian Ocean.
    Description: This research was supported by the Independent Research and Development Program at WHOI to CCU, an NSF OCE PO grant (NSF OCE- 1242989) to Young-Oh Kwon, NOAA CP CVP grants (NA15OAR4310176 and NA17OAR4310255) to Hyodae Seo, and a research grant fromtheMinistry of Science and Technology of the People’s Republic of China to Tsinghua University (2017YFA0603902).
    Description: 2019-02-13
    Keywords: Air-sea interaction
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    Dynamics of three-dimensional turbulent wall plumes and implications for estimates of submarine glacier melting (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018):1941-1950, doi:10.1175/JPO-D-17-0194.1.
    Description: Subglacial discharges have been observed to generate buoyant plumes along the ice face of Greenland tidewater glaciers. These plumes have been traditionally modeled using classical plume theory, and their characteristic parameters (e.g., velocity) are employed in the widely used three-equation melt parameterization. However, the applicability of plume theory for three-dimensional turbulent wall plumes is questionable because of the complex near-wall plume dynamics. In this study, corrections to the classical plume theory are introduced to account for the presence of a wall. In particular, the drag and entrainment coefficients are quantified for a three-dimensional turbulent wall plume using data from direct numerical simulations. The drag coefficient is found to be an order of magnitude larger than that for a boundary layer flow over a flat plate at a similar Reynolds number. This result suggests a significant increase in the melting estimates by the current parameterization. However, the volume flux in a wall plume is found to be one-half that of a conical plume that has 2 times the buoyancy flux. This finding suggests that the total entrainment (per unit area) of ambient water is the same and that the plume scalar characteristics (i.e., temperature and salinity) can be predicted reasonably well using classical plume theory.
    Description: This work was supported by the Linné FLOW Centre at KTH and the Academy of Finland Center of Excellence Programme Grant 307331 (author Ezhova) and by VR Swedish Research Council GrantVR2014-5001 (author Brandt). Support to author Cenedese was given by NSF Project OCE-1434041.
    Description: 2019-02-27
    Keywords: Buoyancy ; Entrainment ; Turbulence
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  • 28
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    Dominant circulation patterns of the deep Gulf of Mexico (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 511-529, doi:10.1175/JPO-D-17-0140.1.
    Description: The large-scale circulation of the bottom layer of the Gulf of Mexico is analyzed, with special attention to the historically least studied western basin. The analysis is based on 4 years of data collected by 158 subsurface floats parked at 1500 and 2500 m and is complemented with data collected by current meter moorings in the western basin during the same period. Three main circulation patterns stand out: a cyclonic boundary current, a cyclonic gyre in the abyssal plain, and the very high eddy kinetic energy observed in the eastern Gulf. The boundary current and the cyclonic gyre appear as distinct features, which interact in the western tip of the Yucatan shelf. The persistence and continuity of the boundary current is addressed. Although high variability is observed, the boundary flow serves as a pathway for water to travel around the western basin in approximately 2 years. An interesting discovery is the separation of the boundary current over the northwestern slope of the Yucatan shelf. The separation and retroflection of the along-slope current appears to be a persistent feature and is associated with anticyclonic eddies whose genesis mechanism remains to be understood. As the boundary flow separates, it feeds into the westward flow of the deep cyclonic gyre. The location of this gyre—named the Sigsbee Abyssal Gyre—coincides with closed geostrophic contours, so eddy–topography interaction via bottom form stresses may drive this mean flow. The contribution to the cyclonic vorticity of the gyre by modons traveling under Loop Current eddies is discussed.
    Description: This work was supported by the Bureau of Ocean Energy Management (BOEM) under Contract M10PC00112 assigned to Leidos, Inc.
    Keywords: Seas/gulfs/bays ; Abyssal circulation ; Boundary currents ; Lagrangian circulation/transport ; Large-scale motions ; Trajectories
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    Influences of Pacific climate variability on decadal subsurface ocean heat content variations in the Indian Ocean (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 4157-4174, doi:10.1175/JCLI-D-17-0654.1.
    Description: Decadal variabilities in Indian Ocean subsurface ocean heat content (OHC; 50–300 m) since the 1950s are examined using ocean reanalyses. This study elaborates on how Pacific variability modulates the Indian Ocean on decadal time scales through both oceanic and atmospheric pathways. High correlations between OHC and thermocline depth variations across the entire Indian Ocean Basin suggest that OHC variability is primarily driven by thermocline fluctuations. The spatial pattern of the leading mode of decadal Indian Ocean OHC variability closely matches the regression pattern of OHC on the interdecadal Pacific oscillation (IPO), emphasizing the role of the Pacific Ocean in determining Indian Ocean OHC decadal variability. Further analyses identify different mechanisms by which the Pacific influences the eastern and western Indian Ocean. IPO-related anomalies from the Pacific propagate mainly through oceanic pathways in the Maritime Continent to impact the eastern Indian Ocean. By contrast, in the western Indian Ocean, the IPO induces wind-driven Ekman pumping in the central Indian Ocean via the atmospheric bridge, which in turn modifies conditions in the southwestern Indian Ocean via westward-propagating Rossby waves. To confirm this, a linear Rossby wave model is forced with wind stresses and eastern boundary conditions based on reanalyses. This linear model skillfully reproduces observed sea surface height anomalies and highlights both the oceanic connection in the eastern Indian Ocean and the role of wind-driven Ekman pumping in the west. These findings are also reproduced by OGCM hindcast experiments forced by interannual atmospheric boundary conditions applied only over the Pacific and Indian Oceans, respectively.
    Description: This research was supported by a scholarship from the China Scholarship Council (CSC) to X. J., a research fellowship by the Alexander von Humboldt Foundation to C. C. U., an NSF OCE PO Grant (OCE- 1242989) to Y.-O. K., the ONR Young Investigator Award (N00014-15-1-2588) to H. S., and a research grant from the Ministry of Science and Technology of the People’s Republic of China to Tsinghua University (2017YFA0603902).
    Description: 2018-10-30
    Keywords: Atmosphere-ocean interaction
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    A multivariate estimate of the cold season atmospheric response to North Pacific SST variability (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 2771-2796, doi:10.1175/JCLI-D-17-0061.1.
    Description: The Generalized Equilibrium Feedback Analysis (GEFA) is used to distinguish the influence of the Oyashio Extension (OE) and the Kuroshio Extension (KE) variability on the atmosphere from 1979 to 2014 from that of the main SST variability modes, using seasonal mean anomalies. Remote SST anomalies are associated with each single oceanic regressor, but the multivariate approach efficiently confines their SST footprints. In autumn [October–December (OND)], the OE meridional shifts are followed by a North Pacific Oscillation (NPO)-like signal. The OE influence is not investigated in winter [December–February (DJF)] because of multicollinearity, but a robust response with a strong signal over the Bering Sea is found in late winter/early spring [February–April (FMA)], a northeastward strengthening of the Aleutian low following a northward OE shift. A robust response to the KE variability is found in autumn, but not in winter and late winter when the KE SST footprint becomes increasingly small and noisy as regressors are added in GEFA. In autumn, a positive PDO is followed by a northward strengthening of the Aleutian low and a southward shift of the storm track in the central Pacific, reflecting the surface heat flux footprint in the central Pacific. In winter, the PDO shifts the maximum baroclinicity and storm track southward, the response strongly tilts westward with height in the North Pacific, and there is a negative NAO-like teleconnection. In late winter, the North Pacific NPO-like response to the PDO interferes negatively with the response to the OE and is only detected when the OE is represented in GEFA. A different PDO influence on the atmospheric circulation is found from 1958 to 1977.
    Description: This research has received funding from the European Union 7th Framework Program (FP7 2007-2013) under Grant Agreement 308299 (NACLIM) and from NSF Grants AGS CLD 1035423 and OCE PO 1242989.
    Keywords: Atmosphere-ocean interaction ; Boundary currents ; Pacific decadal oscillation ; Atmosphere-ocean interaction ; Empirical orthogonal functions ; Regression analysis
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    A laboratory study of iceberg side melting in vertically sheared flows (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 1367-1373, doi:10.1175/JPO-D-17-0185.1.
    Description: An earlier study indicates that the side melting of icebergs subject to vertically homogeneous horizontal velocities is controlled by two distinct regimes, which depend on the melt plume behavior and produce a nonlinear dependence of side melt rate on velocity. Here, we extend this study to consider ice blocks melting in a two-layer vertically sheared flow in a laboratory setting. It is found that the use of the vertically averaged flow speed in current melt parameterizations gives an underestimate of the submarine side melt rate, in part because of the nonlinearity of the dependence of the side melt rate on flow speed but also because vertical shear in the horizontal velocity profile fundamentally changes the flow splitting around the ice block and consequently the velocity felt by the ice surface. An observational record of 90 icebergs in a Greenland fjord suggests that this effect could produce an average underestimate of iceberg side melt rates of 21%.
    Description: A. F. was supported by NA14OAR4320106 from the National Oceanic and Atmospheric Administration, U.S. Department of Commerce. C. C. was supported by NSF OCE-1658079 and F. S. was supported by NSF OCE-1657601 and NSF PLR-1743693.
    Description: 2018-12-12
    Keywords: Ocean ; Antarctica ; Arctic ; Laboratory/physical models ; Parameterization
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    A global glacial ocean state estimate constrained by upper-ocean temperature proxies (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 8059-8079, doi:10.1175/JCLI-D-17-0769.1.
    Description: We use the method of least squares with Lagrange multipliers to fit an ocean general circulation model to the Multiproxy Approach for the Reconstruction of the Glacial Ocean Surface (MARGO) estimate of near sea surface temperature (NSST) at the Last Glacial Maximum (LGM; circa 23–19 thousand years ago). Compared to a modern simulation, the resulting global, last-glacial ocean state estimate, which fits the MARGO data within uncertainties in a free-running coupled ocean–sea ice simulation, has global-mean NSSTs that are 2°C lower and greater sea ice extent in all seasons in both the Northern and Southern Hemispheres. Increased brine rejection by sea ice formation in the Southern Ocean contributes to a stronger abyssal stratification set principally by salinity, qualitatively consistent with pore fluid measurements. The upper cell of the glacial Atlantic overturning circulation is deeper and stronger. Dye release experiments show similar distributions of Southern Ocean source waters in the glacial and modern western Atlantic, suggesting that LGM NSST data do not require a major reorganization of abyssal water masses. Outstanding challenges in reconstructing LGM ocean conditions include reducing effects from model biases and finding computationally efficient ways to incorporate abyssal tracers in global circulation inversions. Progress will be aided by the development of coupled ocean–atmosphere–ice inverse models, by improving high-latitude model processes that connect the upper and abyssal oceans, and by the collection of additional paleoclimate observations.
    Description: DEA was supported by a NSF Graduate Research Fellowship and NSF Grant OCE-1060735. OM acknowledges support from the NSF. GF was supported by NASA Award 1553749 and Simons Foundation Award 549931.
    Keywords: Ocean ; Abyssal circulation ; Sea surface temperature ; Paleoclimate ; Inverse methods ; Ocean models
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    Internal tidal modal ray refraction and energy ducting in baroclinic Gulf Stream currents (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 1969-1993, doi:10.1175/JPO-D-18-0031.1.
    Description: Upstream mean semidiurnal internal tidal energy flux has been found in the Gulf Stream in hydrodynamical model simulations of the Atlantic Ocean. A major source of the energy in the simulations is the south edge of Georges Bank, where strong and resonant Gulf of Maine tidal currents are found. An explanation of the flux pattern within the Gulf Stream is that internal wave modal rays can be strongly redirected by baroclinic currents and even trapped (ducted) by current jets that feature strong velocities above the thermocline that are directed counter to the modal wavenumber vector (i.e., when the waves travel upstream). This ducting behavior is analyzed and explained here with ray-based wave propagation studies for internal wave modes with anisotropic wavenumbers, as occur in mesoscale background flow fields. Two primary analysis tools are introduced and then used to analyze the strong refraction and ducting: the generalized Jones equation governing modal properties and ray equations that are suitable for studying waves with anisotropic wavenumbers.
    Description: The Woods Hole research was supported by National Science Foundation Grant OCE-1060430 and by the Office of Naval Research Grants N00014-11-1-0701 and N00014-17-1-2624. The USM research was supported by ONR Grant N00014-15-1-2288 and National Science Foundation Grant OCE-1537449.
    Description: 2019-02-28
    Keywords: Internal waves ; Wave properties ; Tides ; Differential equations ; Numerical analysis/modeling
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    Estuarine exchange flow is related to mixing through the salinity variance budget (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 1375-1384, doi:10.1175/JPO-D-17-0266.1.
    Description: The relationship between net mixing and the estuarine exchange flow may be quantified using a salinity variance budget. Here “mixing” is defined as the rate of destruction of volume-integrated salinity variance, and the exchange flow is quantified using the total exchange flow. These concepts are explored using an idealized 3D model estuary. It is shown that in steady state (e.g., averaging over the spring–neap cycle) the volume-integrated mixing is approximately given by Mixing ≅ SinSoutQr, where Sin and Sout are the representative salinities of in- and outflowing layers at the mouth and Qr is the river volume flux. This relationship provides an extension of the familiar Knudsen relation, in which the exchange flow is diagnosed based on knowledge of these same three quantities, quantitatively linking mixing to the exchange flow.
    Description: The work was supported by the National Science Foundation through Grants OCE-1736242 to PM and OCE-1736539 to WRG and by the German Research Foundation through Grants TRR 181 and GRK 2000 to HB.
    Keywords: Coastal flows ; Diapycnal mixing ; Ocean dynamics ; Streamflow ; Diagnostics ; Isopycnal coordinates
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    Deep eddies in the Gulf of Mexico observed with floats (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 2703-2719, doi:10.1175/JPO-D-17-0245.1.
    Description: A new set of deep float trajectory data collected in the Gulf of Mexico from 2011 to 2015 at 1500- and 2500-m depths is analyzed to describe mesoscale processes, with particular attention paid to the western Gulf. Wavelet analysis is used to identify coherent eddies in the float trajectories, leading to a census of the basinwide coherent eddy population and statistics of the eddies’ kinematic properties. The eddy census reveals a new formation region for anticyclones off the Campeche Escarpment, located northwest of the Yucatan Peninsula. These eddies appear to form locally, with no apparent direct connection to the upper layer. Once formed, the eddies drift westward along the northern edge of the Sigsbee Abyssal Gyre, located in the southwestern Gulf of Mexico over the abyssal plain. The formation mechanism and upstream sources for the Campeche Escarpment eddies are explored: the observational data suggest that eddy formation may be linked to the collision of a Loop Current eddy with the western boundary of the Gulf. Specifically, the disintegration of a deep dipole traveling under the Loop Current eddy Kraken, caused by the interaction with the northwestern continental slope, may lead to the acceleration of the abyssal gyre and the boundary current in the Bay of Campeche region.
    Description: The authors were supported by the Department of the Interior, Bureau of Ocean Energy Management (BOEM), Contract M10PC00112 to Leidos, Inc., Raleigh, North Carolina.
    Description: 2019-05-07
    Keywords: Abyssal circulation ; Currents ; Eddies ; Mesoscale processes ; Trajectories ; In situ oceanic observations
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    Structure and forcing of observed exchanges across the Greenland–Scotland Ridge (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 9881-9901, doi:10.1175/JCLI-D-17-0889.1.
    Description: The Atlantic meridional overturning circulation and associated poleward heat transport are balanced by northern heat loss to the atmosphere and corresponding water-mass transformation. The circulation of northward-flowing Atlantic Water at the surface and returning overflow water at depth is particularly manifested—and observed—at the Greenland–Scotland Ridge where the water masses are guided through narrow straits. There is, however, a rich variability in the exchange of water masses across the ridge on all time scales. Focusing on seasonal and interannual time scales, and particularly the gateways of the Denmark Strait and between the Faroe Islands and Shetland, we specifically assess to what extent the exchanges of water masses across the Greenland–Scotland Ridge relate to wind forcing. On seasonal time scales, the variance explained of the observed exchanges can largely be related to large-scale wind patterns, and a conceptual model shows how this wind forcing can manifest via a barotropic, cyclonic circulation. On interannual time scales, the wind stress impact is less direct as baroclinic mechanisms gain importance and observations indicate a shift in the overflows from being more barotropically to more baroclinically forced during the observation period. Overall, the observed Greenland–Scotland Ridge exchanges reflect a horizontal (cyclonic) circulation on seasonal time scales, while the interannual variability more represents an overturning circulation.
    Description: This research was supported by the Research Council of Norway project NORTH (Grant 229763). Additional support for M. A. Spall was provided by National Science Foundation Grant OCE- 1558742, for T. Eldevik and S. Østerhus by the European Union’s Horizon 2020 research and innovation program project Blue-Action (Grant 727852), and for S. Østerhus by the European Framework Programs under Grant Agreement 308299 (NACLIM).
    Keywords: Ocean circulation ; Thermocline circulation ; Atmosphere-ocean interaction ; North Atlantic Oscillation ; Statistical techniques ; Time series
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    AXIS—an Autonomous Expendable Instrument System (2018)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2017. 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 34 (2017): 2673-2682, doi:10.1175/JTECH-D-17-0054.1.
    Description: Expendable bathythermographs (XBT) to profile upper-ocean temperatures from vessels in motion have been in use for some 50 years now. Developed originally for navy use, they were soon adapted by oceanographers to map out upper-ocean thermal structure and its space–-time variability from both research vessels and merchant marine vessels in regular traffic. These activities continue today. This paper describes a new technology—the Autonomous Expendable Instrument System (AXIS)—that has been developed to provide the capability to deploy XBT probes on a predefined schedule, or adaptively in response to specific events without the presence of an observer on board. AXIS is a completely self-contained system that can hold up to 12 expendable probes [XBTs, XCTDs, expendable sound velocimeter (XSV)] in any combination. A single-board Linux computer keeps track of what probes are available, takes commands from ashore via Iridium satellite on what deployment schedule to follow, and records and forwards the probe data immediately with a time stamp and the GPS position. This paper provides a brief overview of its operation, capabilities, and some examples of how it is improving coverage along two lines in the Atlantic.
    Description: Initial development of AXIS mechanical design elements wasmade possible by awards from the Cecil H. and Ida M. Green Technology Innovation Fund and the Sealark Foundation to the team of Dave Fratantoni, Keith von der Heydt (WHOI), and Terry Hammar (WHOI). Construction of the first full AXIS prototype was supported by a technology grant from the National Science Foundation (OCE-0926853) and the second one through an NSF-funded (OCE-1061185) subcontract from the University of Rhode Island.
    Description: 2018-06-28
    Keywords: In situ oceanic observations ; Instrumentation/sensors ; Profilers, oceanic ; Ship observations
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    Surface cooling, winds, and eddies over the continental shelf (2018)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2017. 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 47 (2017): 879-894, doi:10.1175/JPO-D-16-0196.1.
    Description: Models show that surface cooling over a sloping continental shelf should give rise to baroclinic instability and thus tend toward gravitationally stable density stratification. Less is known about how alongshore winds affect this process, so the role of surface momentum input is treated here by means of a sequence of idealized, primitive equation numerical model calculations. The effects of cooling rate, wind amplitude and direction, bottom slope, bottom friction, and rotation rate are all considered. All model runs lead to instability and an eddy field. While instability is not strongly affected by upwelling-favorable alongshore winds, wind-driven downwelling substantially reduces eddy kinetic energy, largely because the downwelling circulation plays a similar role to baroclinic instability by flattening isotherms and so reducing available potential energy. Not surprisingly, cross-shelf winds appear to have little effect. Analysis of the model runs leads to quantitative relations for the wind effect on eddy kinetic energy for the equilibrium density stratification (which increases as the cooling rate increases) and for eddy length scale.
    Description: This research was supported by the National Science Foundation Physical Oceanography Program through Grant OCE-1433953.
    Keywords: Continental shelf/slope ; Baroclinic flows ; Eddies ; Instability
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    The nexus between sea ice and polar emissions of marine biogenic aerosols (2018)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 99 (2018): 61-82, doi:10.1175/BAMS-D-16-0254.1.
    Description: Accurate estimation of the climate sensitivity requires a better understanding of the nexus between polar marine ecosystem responses to warming, changes in sea ice extent, and emissions of marine biogenic aerosol (MBA). Sea ice brine channels contain very high concentrations of MBA precursors that, once ventilated, have the potential to alter cloud microphysical properties, such as cloud droplet number, and the regional radiative energy balance. In contrast to temperate latitudes, where the pelagic phytoplankton are major sources of MBAs, the seasonal sea ice dynamic plays a key role in determining MBA concentration in both the Arctic and Antarctic. We review the current knowledge of MBA sources and the link between ice melt and emissions of aerosol precursors in the polar oceans. We illustrate the processes by examining decadal-scale time series in various satellite-derived parameters such as aerosol optical depth (AOD), sea ice extent, and phytoplankton biomass in the sea ice zones of both hemispheres. The sharpest gradients in aerosol indicators occur during the spring period of ice melt. In sea ice–covered waters, the peak in AOD occurs well before the annual maximum in biomass in both hemispheres. The results provide strong evidence that suggests seasonal changes in sea ice and ocean biology are key drivers of the polar aerosol cycle. The positive trend in annual-mean Antarctic sea ice extent is now almost one-third of the magnitude of the annual-mean decrease in Arctic sea ice, suggesting the potential for different patterns of aerosol emissions in the future.
    Description: Matrai and Middleton were supported by the National Science Foundation (PLR-1417517). Jones was partially funded by a grant from the Australian Research Council (DP150101649).
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    Eddy memory mode of multidecadal variability in residual-mean ocean circulations with application to the Beaufort Gyre (2018)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2017. 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 47 (2017): 855-866, doi:10.1175/JPO-D-16-0194.1.
    Description: Mesoscale eddies shape the Beaufort Gyre response to Ekman pumping, but their transient dynamics are poorly understood. Climate models commonly use the Gent–McWilliams (GM) parameterization, taking the eddy streamfunction to be proportional to an isopycnal slope s and an eddy diffusivity K. This local-in-time parameterization leads to exponential equilibration of currents. Here, an idealized, eddy-resolving Beaufort Gyre model is used to demonstrate that carries a finite memory of past ocean states, violating a key GM assumption. As a consequence, an equilibrating gyre follows a spiral sink trajectory implying the existence of a damped mode of variability—the eddy memory (EM) mode. The EM mode manifests during the spinup as a 15% overshoot in isopycnal slope (2000 km3 freshwater content overshoot) and cannot be explained by the GM parameterization. An improved parameterization is developed, such that is proportional to an effective isopycnal slope , carrying a finite memory γ of past slopes. Introducing eddy memory explains the model results and brings to light an oscillation with a period ≈ 50 yr, where the eddy diffusion time scale TE ~ 10 yr and γ ≈ 6 yr are diagnosed from the eddy-resolving model. The EM mode increases the Ekman-driven gyre variance by γ/TE ≈ 50% ± 15%, a fraction that stays relatively constant despite both time scales decreasing with increased mean forcing. This study suggests that the EM mode is a general property of rotating turbulent flows and highlights the need for better observational constraints on transient eddy field characteristics.
    Description: GEM acknowledges the Stanback Postdoctoral Fellowship Fund at Caltech and the Howland Postdoctoral Program Fund at WHOI. MAS was supported by NSF Grants PLR-1415489 and OCE- 1232389. AFT acknowledges support from NSF OCE- 1235488.
    Keywords: Arctic ; Eddies ; Ekman pumping/transport ; Mesoscale processes ; Parameterization ; Multidecadal variability
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    Rossby waves with continuous stratification and bottom friction (2018)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 2209-2219, doi:10.1175/JPO-D-18-0070.1.
    Description: Published observations of subinertial ocean current variability show that the vertical structure is often well described by a vertical mode that has a node of horizontal velocity at the bottom rather than the traditional node of vertical velocity. The theory of forced and free linear Rossby waves in a continuously stratified ocean with a sloping bottom and bottom friction is treated here to see if frictional effects can plausibly contribute to this phenomenon. For parameter values representative of the mesoscale, bottom dissipation by itself appears to be too weak to be an explanation, although caution is required because the present approach uses a linear model to address a nonlinear phenomenon. One novel outcome is the emergence of a short-wave, bottom-trapped, strongly damped mode that is present even with a flat bottom.
    Description: Partial funding for this article is provided by the National Science Foundation Physical Oceanography section through Award OCE-1433953.
    Description: 2019-03-17
    Keywords: Baroclinic flows ; Ekman pumping/transport ; Rossby waves
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    Daily to decadal modulation of jet variability (2018)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2018. 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 30 (2018): 1297-1314, doi:10.1175/JCLI-D-17-0286.1.
    Description: The variance of a jet’s position in latitude is found to be related to its average speed: when a jet becomes stronger, its variability in latitude decreases. This relationship is shown to hold for observed midlatitude jets around the world and also across a hierarchy of numerical models. North Atlantic jet variability is shown to be modulated on decadal time scales, with decades of a strong, steady jet being interspersed with decades of a weak, variable jet. These modulations are also related to variations in the basinwide occurrence of high-impact blocking events. A picture emerges of complex multidecadal jet variability in which recent decades do not appear unusual. An underlying barotropic mechanism is proposed to explain this behavior, related to the change in refractive properties of a jet as it strengthens, and the subsequent effect on the distribution of Rossby wave breaking.
    Description: We would like to acknowledge funding from NERC and the Research Council of Norway project jetSTREAM under Grants NE/ L01047X/1 (IMPETUS) and 231716, respectively, for a contribution to the work presented here. EAB is supported in part by the NSF Climate and Large-Scale Dynamics Program under Grant 1545675. Y-OK was supported by the NSF Climate and Large-Scale Dynamics Program under Grant 1355339. KW was supported by the Joint UK BEIS/Defra Met Office Hadley Centre Climate Programme (GA01101). RL was supported by the Met Office and the National Centre for Atmospheric Science.
    Description: 2018-07-29
    Keywords: Atmospheric circulation ; Jets ; North Atlantic Oscillation ; Baroclinic models ; Decadal variability
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    Climate variability, volcanic forcing, and last millennium hydroclimate extremes (2018)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 4309-4327, doi:10.1175/JCLI-D-17-0407.1.
    Description: Multidecadal hydroclimate variability has been expressed as “megadroughts” (dry periods more severe and prolonged than observed over the twentieth century) and corresponding “megapluvial” wet periods in many regions around the world. The risk of such events is strongly affected by modes of coupled atmosphere–ocean variability and by external impacts on climate. Accurately assessing the mechanisms for these interactions is difficult, since it requires large ensembles of millennial simulations as well as long proxy time series. Here, the Community Earth System Model (CESM) Last Millennium Ensemble is used to examine statistical associations among megaevents, coupled climate modes, and forcing from major volcanic eruptions. El Niño–Southern Oscillation (ENSO) strongly affects hydroclimate extremes: larger ENSO amplitude reduces megadrought risk and persistence in the southwestern United States, the Sahel, monsoon Asia, and Australia, with corresponding increases in Mexico and the Amazon. The Atlantic multidecadal oscillation (AMO) also alters megadrought risk, primarily in the Caribbean and the Amazon. Volcanic influences are felt primarily through enhancing AMO amplitude, as well as alterations in the structure of both ENSO and AMO teleconnections, which lead to differing manifestations of megadrought. These results indicate that characterizing hydroclimate variability requires an improved understanding of both volcanic climate impacts and variations in ENSO/AMO teleconnections.
    Description: This work is supported by NSF EaSM Grants AGS-1243125 and NCAR-1243107 to The University of Arizona.
    Description: 2018-11-03
    Keywords: Drought ; Climate variability ; ENSO ; Paleoclimate ; Climate models ; Multidecadal variability
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    The continuum of drought in southwestern North America (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 8627-8643, doi:10.1175/JCLI-D-18-0010.1.
    Description: Drought has severe consequences for humans and their environment, yet we have a limited understanding of the drivers of drought across the full range of time scales on which it occurs. Here, the atmosphere and ocean conditions that drive this continuum of drought variability in southwestern North America (SWNA) are studied using the latest observationally based products, paleoclimate reconstructions, and state-of-the-art Earth system model simulations of the last millennium. A novel application of the self-organizing maps (SOM) methodology allows for a visualization of the continuum of climate states coinciding with thousands of droughts of varying lengths in last millennium simulations from the Community Earth System Model (CESM), the Goddard Institute for Space Studies Model E2-R (GISS E2-R), and eight other members from phase 5 of the Coupled Model Intercomparison Project (CMIP5). It is found that most droughts are associated with a cool Pacific decadal oscillation (PDO) pattern, but persistent droughts can coincide with a variety of ocean–atmosphere states, including time periods showing a warm PDO or weak ocean–atmosphere anomalies. Many CMIP5 models simulate similar SWNA teleconnection patterns, but the SOM analysis demonstrates that models simulate different continuums of ocean–atmosphere states coinciding with droughts of different lengths, suggesting fundamental differences in their drought dynamics. These findings have important implications for our understanding and simulation of the drivers of persistent drought, and for their potential predictability.
    Description: The National Science Foundation EaSM2 Grant (AGS1243125) supported this work.
    Keywords: Atmosphere-ocean interaction ; Drought ; Paleoclimate ; Ensembles ; General circulation models ; Climate variability
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    High-frequency variability in the circulation and hydrography of the Denmark Strait Overflow from a high-resolution numerical model (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2017. 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 47 (2017): 2999-3013, doi:10.1175/JPO-D-17-0129.1.
    Description: Initial results are presented from a yearlong, high-resolution (~2 km) numerical simulation covering the east Greenland shelf and the Iceland and Irminger Seas. The model hydrography and circulation in the vicinity of Denmark Strait show good agreement with available observational datasets. This study focuses on the variability of the Denmark Strait overflow (DSO) by detecting and characterizing boluses and pulses, which are the two dominant mesoscale features in the strait. The authors estimate that the yearly mean southward volume flux of the DSO is about 30% greater in the presence of boluses and pulses. On average, boluses (pulses) are 57.1 (27.5) h long, occur every 3.2 (5.5) days, and are more frequent during the summer (winter). Boluses (pulses) increase (decrease) the overflow cross-sectional area, and temperatures around the overflow interface are colder (warmer) by about 2.6°C (1.8°C). The lateral extent of the boluses is much greater than that of the pulses. In both cases the along-strait equatorward flow of dense water is enhanced but more so for pulses. The sea surface height (SSH) rises by 4–10 cm during boluses and by up to 5 cm during pulses. The SSH anomaly contours form a bowl (dome) during boluses (pulses), and the two features cross the strait with a slightly different orientation. The cross streamflow changes direction; boluses (pulses) are associated with veering (backing) of the horizontal current. The model indicates that boluses and pulses play a major role in controlling the variability of the DSO transport into the Irminger Sea.
    Description: This work was supported by the NSF Grants OCE-1433448, OCE-1633124, and OCE- 1259618 and the Institute for Data Intensive Engineering and Science (IDIES) seed grant funding.
    Description: 2018-06-13
    Keywords: North Atlantic Ocean ; Mesoscale processes ; Ocean models ; Regional models
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    Wind-driven circulation in a shelf valley. Part I : Mechanism of the asymmetrical response to along-shelf winds in opposite directions (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2017. 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 47 (2017): 2927-2947, doi:10.1175/JPO-D-17-0083.1.
    Description: Motivated by observations in Hudson shelf valley showing stronger onshore than offshore flows, this study investigates wind-driven flows in idealized shallow shelf valleys. This first part of a two-part sequence focuses on the mechanism of the asymmetrical flow response in a valley to along-shelf winds of opposite directions. Model simulations show that (i) when the wind is in the opposite direction to coastal-trapped wave (CTW) phase propagation, the shelf flow turns onshore in the valley and generates strong up-valley transport and a standing meander on the upstream side (in the sense of CTW phase propagation) of the valley, and (ii) when the wind is in the same direction as CTW phase propagation, the flow forms a symmetric onshore detour pattern over the valley with negligible down-valley transport. Comparison of the modeled upstream meanders in the first scenario with CTW characteristics confirms that the up-valley flow results from CTWs being arrested by the wind-driven shelf flow establishing lee waves. The valley bathymetry generates an initial excessive onshore pressure gradient force that drives the up-valley flow and induces CTW lee waves that sustain the up-valley flow. When the wind-driven shelf flow aligns with CTW phase propagation, the initial disturbance generated in the valley propagates away, allowing the valley flow to adjust to roughly follow isobaths. Because of the similarity in the physical setup, this mechanism of arrested CTWs generating stronger onshore than offshore flow is expected to be applicable to the flow response in slope canyons to along-isobath background flows of opposite directions.
    Description: WGZ and SJL were supported by the National Science Foundation through GrantOCE1154575.WGZ is also supported by the NSF Grant OCE 1634965 and SJL by NSF Grant OCE 1558874.
    Description: 2018-06-08
    Keywords: Ocean circulation ; Topographic effects ; Transport ; Vertical motion ; Waves, oceanic ; Wind stress
    Repository Name: Woods Hole Open Access Server
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    The cospectrum of stress-carrying turbulence in the presence of surface gravity waves (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2017. 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 48 (2018): 29-44, doi:10.1175/JPO-D-17-0016.1.
    Description: The cospectrum of the horizontal and vertical turbulent velocity fluctuations, an essential tool for understanding measurements of the turbulent Reynolds shear stress, often departs in the ocean from the shape that has been established in the atmospheric surface layer. Here, we test the hypothesis that this departure is caused by advection of standard boundary layer turbulence by the random oscillatory velocities produced by surface gravity waves. The test is based on a model with two elements. The first is a representation of the spatial structure of the turbulence, guided by rapid distortion theory, and consistent with the one-dimensional cospectra that have been measured in the atmosphere. The second model element is a map of the spatial structure of the turbulence to the temporal fluctuations measured at fixed sensors, assuming advection of frozen turbulence by the velocities associated with surface waves. The model is adapted to removal of the wave velocities from the turbulent fluctuations using spatial filtering. The model is tested against previously published laboratory measurements under wave-free conditions and two new sets of measurements near the seafloor in the coastal ocean in the presence of waves. Although quantitative discrepancies exist, the model captures the dominant features of the laboratory and field measurements, suggesting that the underlying model physics are sound.
    Description: This research was supported by National Science Foundation Ocean Sciences Division Award 1356060 and the U.S. Geological Survey Coastal and Marine Geology Program.
    Keywords: Ocean
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    Estimation of the SST response to anthropogenic and external forcing and its impact on the Atlantic multidecadal oscillation and the Pacific decadal oscillation (2018)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2017. 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 30 (2017): 9871-9895, doi:10.1175/JCLI-D-17-0009.1.
    Description: Two large ensembles (LEs) of historical climate simulations are used to compare how various statistical methods estimate the sea surface temperature (SST) changes due to anthropogenic and other external forcing, and how their removal affects the internally generated Atlantic multidecadal oscillation (AMO), Pacific decadal oscillation (PDO), and the SST footprint of the Atlantic meridional overturning circulation (AMOC). Removing the forced SST signal by subtracting the global mean SST (GM) or a linear regression on it (REGR) leads to large errors in the Pacific. Multidimensional ensemble empirical mode decomposition (MEEMD) and quadratic detrending only efficiently remove the forced SST signal in one LE, and cannot separate the short-term response to volcanic eruptions from natural SST variations. Removing a linear trend works poorly. Two methods based on linear inverse modeling (LIM), one where the leading LIM mode represents the forced signal and another using an optimal perturbation filter (LIMopt), perform consistently well. However, the first two LIM modes are sometimes needed to represent the forced signal, so the more robust LIMopt is recommended. In both LEs, the natural AMO variability seems largely driven by the AMOC in the subpolar North Atlantic, but not in the subtropics and tropics, and the scatter in the AMOC–AMO correlation is large between individual ensemble members. In three observational SST reconstructions for 1900–2015, linear and quadratic detrending, MEEMD, and GM yield somewhat different AMO behavior, and REGR yields smaller PDO amplitudes. Based on LIMopt, only about 30% of the AMO variability is internally generated, as opposed to more than 90% for the PDO. The natural SST variability contribution to global warming hiatus is discussed.
    Description: Support from the NOAA Climate Program Office Climate Variability and Predictability program (NA13OAR4310139), NSF EaSM2 (OCE-84298900), the European Community Horizon 2020 Framework under Grant Agreement 727852 (Blue-Action), and the ANR MORDICUS project (ANR-13-SENV-0002-02) is gratefully acknowledged.
    Description: 2018-05-16
    Keywords: Pattern detection ; Decadal variability ; Multidecadal variability ; Pacific decadal oscillation ; Trends
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    100 Years of Research on Mesoscale Convective Systems (2018)
    American Meteorological Society
    Details
    Publication Date: 2018-01-01
    Description: When cumulonimbus clouds aggregate, developing into a single entity with precipitation covering a horizontal scale of hundreds of kilometers, they are called mesoscale convective systems (MCSs). They account for much of Earth’s precipitation, generate severe weather events and flooding, produce prodigious cirriform anvil clouds, and affect the evolution of the larger-scale circulation. Understanding the inner workings of MCSs has resulted from developments in observational technology and modeling. Time–space conversion of ordinary surface and upper-air observations provided early insight into MCSs, but deeper understanding has followed field campaigns using increasingly sophisticated radars, better aircraft instrumentation, and an ever-widening range of satellite instruments, especially satellite-borne radars. High-resolution modeling and theoretical insights have shown that aggregated cumulonimbus clouds induce a mesoscale circulation consisting of air overturning on a scale larger than the scale of individual convective up- and downdrafts. These layers can be kilometers deep and decoupled from the boundary layer in elevated MCSs. Cooling in the lower troposphere and heating aloft characterize the stratiform regions of MCSs. As a result, long-lived MCSs with large stratiform regions have a top-heavy heating profile that generates potential vorticity in midlevels, thus influencing the larger-scale circulation within which the MCSs occur. Global satellite data show MCSs varying in structure, depending on the prevailing large-scale circulation and topography. These patterns are likely to change with global warming. In addition, environmental pollution affects MCS structure and dynamics subtly. Feedbacks of MCSs therefore need to be included or parameterized in climate models.
    Print ISSN: 0065-9401
    Electronic ISSN: 1943-3646
    Topics: Geography , Geosciences , Physics
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    100 Years of Progress in Hydrology (2018)
    American Meteorological Society
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    Publication Date: 2018-01-01
    Print ISSN: 0065-9401
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    Topics: Geography , Geosciences , Physics
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    100 Years of the Ocean General Circulation (2018)
    American Meteorological Society
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    Publication Date: 2018-01-01
    Description: The central change in understanding of the ocean circulation during the past 100 years has been its emergence as an intensely time-dependent, effectively turbulent and wave-dominated, flow. Early technologies for making the difficult observations were adequate only to depict large-scale, quasi-steady flows. With the electronic revolution of the past 50+ years, the emergence of geophysical fluid dynamics, the strongly inhomogeneous time-dependent nature of oceanic circulation physics finally emerged. Mesoscale (balanced), submesoscale oceanic eddies at 100-km horizontal scales and shorter, and internal waves are now known to be central to much of the behavior of the system. Ocean circulation is now recognized to involve both eddies and larger-scale flows with dominant elements and their interactions varying among the classical gyres, the boundary current regions, the Southern Ocean, and the tropics.
    Print ISSN: 0065-9401
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    Topics: Geography , Geosciences , Physics
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    100 Years of Progress in Atmospheric Observing Systems (2018)
    American Meteorological Society
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    Publication Date: 2018-01-01
    Description: Although atmospheric observing systems were already an important part of meteorology before the American Meteorological Society was established in 1919, the past 100 years have seen a steady increase in their numbers and types. Examples of how observing systems were developed and how they have enabled major scientific discoveries are presented. These examples include observing systems associated with the boundary layer, the upper air, clouds and precipitation, and solar and terrestrial radiation. Widely used specialized observing systems such as radar, lidar, and research aircraft are discussed, and examples of applications to weather forecasting and climate are given. Examples drawn from specific types of chemical measurements, such as ozone and carbon dioxide, are included. Sources of information on observing systems, including other chapters of this monograph, are also discussed. The past 100 years has been characterized by synergism between societal needs for weather observations and the needs of fundamental meteorological research into atmospheric processes. In the latter half of the period, observing system improvements have been driven by the increasing demands for higher-resolution data for numerical models, the need for long-term measurements, and for more global coverage. This has resulted in a growing demand for data access and for integrating data from an increasingly wide variety of observing system types and networks. These trends will likely continue.
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    Topics: Geography , Geosciences , Physics
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    Social Sciences, Weather, and Climate Change (2018)
    American Meteorological Society
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    Publication Date: 2018-01-01
    Print ISSN: 0065-9401
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    Topics: Geography , Geosciences , Physics
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    100 Years of Progress in Polar Meteorology (2018)
    American Meteorological Society
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    Publication Date: 2018-01-01
    Description: The polar regions present several unique challenges to meteorology, including remoteness and a harsh environment. We summarize the evolution of polar meteorology in both hemispheres, beginning with measurements made during early expeditions and concluding with the recent decades in which polar meteorology has been central to global challenges such as the ozone hole, weather prediction, and climate change. Whereas the 1800s and early 1900s provided data from expeditions and only a few subarctic stations, the past 100 years have seen great advances in the observational network and corresponding understanding of the meteorology of the polar regions. For example, a persistent view in the early twentieth century was of an Arctic Ocean dominated by a permanent high pressure cell, a glacial anticyclone. With increased observations, by the 1950s it became apparent that, while anticyclones are a common feature of the Arctic circulation, cyclones are frequent and may be found anywhere in the Arctic. Technology has benefited polar meteorology through advances in instrumentation, especially autonomously operated instruments. Moreover, satellite remote sensing and computer models revolutionized polar meteorology. We highlight the four International Polar Years and several high-latitude field programs of recent decades. We also note outstanding challenges, which include understanding of the role of the Arctic in variations of midlatitude weather and climate, the ability to model surface energy exchanges over a changing Arctic Ocean, assessments of ongoing and future trends in extreme events in polar regions, and the role of internal variability in multiyear-to-decadal variations of polar climate.
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    Topics: Geography , Geosciences , Physics
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    100 Years of Progress in Applied Meteorology. Part I: Basic Applications (2018)
    American Meteorological Society
    Details
    Publication Date: 2018-01-01
    Description: The field of atmospheric science has been enhanced by its long-standing collaboration with entities with specific needs. This chapter and the two subsequent ones describe how applications have worked to advance the science at the same time that the science has served the needs of society. This chapter briefly reviews the synergy between the applications and advancing the science. It specifically describes progress in weather modification, aviation weather, and applications for security. Each of these applications has resulted in enhanced understanding of the physics and dynamics of the atmosphere, new and improved observing equipment, better models, and a push for greater computing power.
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    Topics: Geography , Geosciences , Physics
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    American Meteorological Society: 100 Years of Supporting the Scientific Community (2018)
    American Meteorological Society
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    Publication Date: 2018-01-01
    Description: Over the past century, the atmospheric and related sciences have seen incredible advances in our understanding of Earth’s environment and our ability to monitor and predict its behavior. These advances have had a profound impact on society and have been integrated into every aspect of daily life. The American Meteorological Society (AMS) has been instrumental in supporting these advances throughout its first 100 years of existence as a scientific and professional society serving the community of professionals in the atmospheric and related oceanic and hydrologic sciences. AMS has provided opportunities for researchers and practitioners to share their scientific findings and build fruitful collaborations to further the science and its application. Through strategic initiatives at key points in its history, AMS has pushed the science forward—highlighting areas ripe for development, creating frameworks for interdisciplinary interactions, and providing innovative approaches to the dissemination of research results. As a society made up of the scientific community and led by many of the most prominent scientists of their time, AMS has been able to respond to, and often anticipate, the needs of its community.
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    100 Years of Progress in Tropical Cyclone Research (2018)
    American Meteorological Society
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    Publication Date: 2018-01-01
    Description: A century ago, meteorologists regarded tropical cyclones as shallow vortices, extending upward only a few kilometers into the troposphere, and nothing was known about their physics save that convection was somehow involved. As recently as 1938, a major hurricane struck the densely populated northeastern United States with no warning whatsoever, killing hundreds. In the time since the American Meteorological Society was founded, however, tropical cyclone research blossomed into an endeavor of great breadth and depth, encompassing fields ranging from atmospheric and oceanic dynamics to biogeochemistry, and the precision and scope of forecasts and warnings have achieved a level of success that would have been regarded as impossible only a few decades ago. This chapter attempts to document the extraordinary progress in tropical cyclone research over the last century and to suggest some avenues for productive research over the next one.
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    Measuring biological age to assess colony demographics in honeybees (2018)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2018-12-14
    Description: by Cedric Alaux, Samuel Soubeyrand, Alberto Prado, Mathilde Peruzzi, Alban Maisonnasse, Julien Vallon, Julie Hernandez, Pascal Jourdan, Yves Le Conte Honeybee colonies are increasingly exposed to environmental stress factors, which can lead to their decline or failure. However, there are major gaps in stressor risk assessment due to the difficulty of assessing the honeybee colony state and detecting abnormal events. Since stress factors usually induce a demographic disturbance in the colony (e.g. loss of foragers, early transition from nurse to forager state), we suggest that disturbances could be revealed indirectly by measuring the age- and task-related physiological state of bees, which can be referred to as biological age (an indicator of the changes in physiological state that occur throughout an individual lifespan). We therefore estimated the biological age of bees from the relationship between age and biomarkers of task specialization (vitellogenin and the adipokinetic hormone receptor). This relationship was determined from a calibrated sample set of known-age bees and mathematically modelled for biological age prediction. Then, we determined throughout the foraging season the evolution of the biological age of bees from colonies with low (conventional apiary) or high Varroa destructor infestation rates (organic apiary). We found that the biological age of bees from the conventional apiary progressively decreased from the spring (17 days) to the fall (6 days). However, in colonies from the organic apiary, the population aged from spring (13 days) to summer (18.5 days) and then rejuvenated in the fall (13 days) after Varroa treatment. Biological age was positively correlated with the amount of brood (open and closed cells) in the apiary with low Varroa pressure, and negatively correlated with Varroa infestation level in the apiary with high Varroa pressure. Altogether, these results show that the estimation of biological age is a useful and effective method for assessing colony demographic state and likely detrimental effects of stress factors.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Prevalence of antiretroviral therapy treatment failure among HIV-infected pregnant women at first antenatal care: PMTCT Option B+ in Malawi (2018)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2018-12-14
    Description: by Maganizo B. Chagomerana, William C. Miller, Jennifer H. Tang, Irving F. Hoffman, Bryna J. Harrington, Bethany DiPrete, Shaphil Wallie, Allan Jumbe, Laura Limarzi, Mina C. Hosseinipour Background In Malawi’s PMTCT Option B+ program, HIV-infected pregnant women who are already receiving ART are continued on their current therapy regimen without testing for treatment failure at the first antenatal care (ANC) visit. HIV RNA screening at ANC may identify women with treatment failure and ensure that viral suppression is maintained throughout the pregnancy. Methods We conducted a cross-sectional study of HIV-infected pregnant women who had been receiving ART for at least 6 months at the first ANC visit under the PMTCT Option B+ program at Bwaila Hospital in Lilongwe, Malawi from June 2015 to December 2017. Poisson regression models with robust variance were used to investigate the predictors of ART treatment failure defined as viral load ≥1000 copies/ml. Results The median age of 864 women tested for ART failure was 31.1 years (interquartile range: 26.9–34.5). The prevalence of treatment failure was 7.6% (95% confidence interval (CI): 6.0–9.6). CD4 cell count (adjusted prevalence ratio (aPR) = 0.57; 95% CI: 0.50–0.65) was strongly associated with treatment failure. Conclusion The low prevalence of treatment failure among women presenting for their first ANC in urban Malawi demonstrates success of Option B+ in maintaining viral suppression and suggests progress towards the last 90% of the UNAIDS 90-90-90 targets. Women failing on ART should be identified early for adherence counseling and may require switching to an alternative ART regimen.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Sphingosine 1-phosphate (S1P) reduces hepatocyte growth factor-induced migration of hepatocellular carcinoma cells via S1P receptor 2 (2018)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2018-12-14
    Description: by Rie Matsushima-Nishiwaki, Noriko Yamada, Kouki Fukuchi, Osamu Kozawa A bioactive lipid, sphingosine 1-phosphate (S1P), acts extracellularly as a potent mediator, and is implicated in the progression of various cancers including hepatocellular carcinoma (HCC). S1P exerts its functions by binding to five types of specific receptors, S1P receptor 1 (S1PR1), S1PR2, S1PR3, S1PR4 and S1PR5 on the plasma membrane. However, the exact roles of S1P and each S1PR in HCC cells remain to be clarified. In the present study, we investigated the effect of S1P on the hepatocyte growth factor (HGF)-induced migration of human HCC-derived HuH7 cells, and the involvement of each S1PR. S1P dose-dependently reduced the HGF-induced migration of HuH7 cells. We found that all S1PRs exist in the HuH7 cells. Among each selective agonist for five S1PRs, CYM5520, a selective S1PR2 agonist, significantly suppressed the HGF-induced HuH7 cell migration whereas selective agonists for S1PR1, S1PR3, S1PR4 or S1PR5 failed to affect the migration. The reduction of the HGF-induced migration by S1P was markedly reversed by treatment of JTE013, a selective antagonist for S1PR2, and S1PR2- siRNA. These results strongly suggest that S1P reduces the HGF-induced HCC cell migration via S1PR2. Our findings may provide a novel potential of S1PR2 to therapeutic strategy for metastasis of HCC.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Digital Identity: The effect of trust and reputation information on user judgement in the Sharing Economy (2018)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2018-12-14
    Description: by Mircea Zloteanu, Nigel Harvey, David Tuckett, Giacomo Livan The Sharing Economy (SE) is a growing ecosystem focusing on peer-to-peer enterprise. In the SE the information available to assist individuals (users) in making decisions focuses predominantly on community-generated trust and reputation information. However, how such information impacts user judgement is still being understood. To explore such effects, we constructed an artificial SE accommodation platform where we varied the elements related to hosts’ digital identity, measuring users’ perceptions and decisions to interact. Across three studies, we find that trust and reputation information increases not only the users’ perceived trustworthiness, credibility, and sociability of hosts, but also the propensity to rent a private room in their home. This effect is seen when providing users both with complete profiles and profiles with partial user-selected information. Closer investigations reveal that three elements relating to the host’s digital identity are sufficient to produce such positive perceptions and increased rental decisions, regardless of which three elements are presented. Our findings have relevant implications for human judgment and privacy in the SE, and question its current culture of ever increasing information-sharing.
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    Topics: Medicine , Natural Sciences in General
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    Rapid antibiotic susceptibility testing from blood culture bottles with species agnostic real-time polymerase chain reaction (2018)
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    In: PLoS ONE
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    Publication Date: 2018-12-14
    Description: by Tucker Maxson, Candace D. Blancett, Amanda S. Graham, Christopher P. Stefan, Timothy D. Minogue Development and implementation of rapid antimicrobial susceptibility testing is critical for guiding patient care and improving clinical outcomes, especially in cases of sepsis. One approach to reduce the time-to-answer for antimicrobial susceptibility is monitoring the inhibition of DNA production, as differences in DNA concentrations are more quickly impacted compared to optical density changes in traditional antimicrobial susceptibility testing. Here, we use real-time PCR to rapidly determine antimicrobial susceptibility after short incubations with antibiotic. Application of this assay to a collection of 144 isolates in mock blood culture, covering medically relevant pathogens displaying high rates of resistance, provided susceptibility data in under 4 hours. This assay provided categorical agreement with a reference method in 96.3% of cases across all species. Sequencing of a subset of PCR amplicons showed accurate genus level identification. Overall, implementation of this method could provide accurate susceptibility results with a reduced time-to-answer for a number of medically relevant bacteria commonly isolated from blood culture.
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    Developmental and tissue specific changes of ubiquitin forms in Drosophila melanogaster (2018)
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    Publication Date: 2018-12-14
    Description: by Ágota Nagy, Levente Kovács, Zoltán Lipinszki, Margit Pál, Péter Deák In most Eukaryotes, ubiquitin either exists as free monoubiquitin or as a molecule that is covalently linked to other proteins. These two forms cycle between each other and due to the concerted antagonistic activity of ubiquitylating and deubiquitylating enzymes, an intracellular ubiquitin equilibrium is maintained that is essential for normal biological function. However, measuring the level and ratio of these forms of ubiquitin has been difficult and time consuming. In this paper, we have adapted a simple immunoblotting technique to monitor ubiquitin content and equilibrium dynamics in different developmental stages and tissues of Drosophila . Our data show that the level of total ubiquitin is distinct in different developmental stages, lowest at the larval-pupal transition and in three days old adult males, and highest in first instar larvae. Interestingly, the ratio of free mono-ubiquitin remains within 30–50% range of the total throughout larval development, but peaks to 70–80% at the larval-pupal and the pupal-adult transitions. It stays within the 70–80% range in adults. In developmentally and physiologically active tissues, the ratio of free ubiquitin is similarly high, most likely reflecting a high demand for ubiquitin availability. We also used this method to demonstrate the disruption of the finely tuned ubiquitin equilibrium by the abolition of proteasome function or the housekeeping deubiquitylase, Usp5. Our data support the notion that the ubiquitin equilibrium is regulated by tissue- and developmental stage-specific mechanisms.
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    Relative miRNA and mRNA expression involved in arsenic methylation (2018)
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    Publication Date: 2018-12-14
    Description: by Huirong Cheng, Pei Hu, Weihua Wen, Ling Liu Three arsenic species in urine are measured using an atomic absorption spectrophotometer. RT-PCR is performed to detect the expression levels of AS3MT, 3 miRNAs, and 17 relative mRNAs in 43 workers producing arsenic trioxide, 36 workers who stopped exposure to arsenic for 85 days, and 24 individuals as the control group. The concentrations of urinary arsenic are very high in workers. A negative correlation between AS3MT and MiR-5 48c-3p is found. There exist significant changes for most selected miRNAs and mRNAs in workers. There are no significant differences between workers who stopped exposure to arsenic and the control group for most miRNAs and mRNAs, but the MiR-5 48c-3p levels show significant changes. Similar positive correlations between the expression of AS3MT and all selected mRNAs are found. Negative correlations between the expression of MiR-5 48c-3p and many relative mRNAs are found as well. AS3MT and MiR-5 48c-3p may regulate arsenic methylation jointly, which when involved in a group of relative mRNAs may play roles in arsenic metabolism and epigenetic changes caused by this metabolism.
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    Moving developmental social neuroscience toward a second-person approach (2018)
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    Publication Date: 2018-12-14
    Description: by Stefanie Hoehl, Gabriela Markova Infants’ cognitive development and learning rely profoundly on their interactions with other people. In the first year, infants become increasingly sensitive to others’ gaze and use it to focus their own attention on relevant visual input. However, infants are not passive observers in early social interactions, and these exchanges are characterized by high levels of contingency and reciprocity. Wass and colleagues offer first insights into the neurobehavioral dynamics of caregiver–infant interactions, demonstrating that caregivers’ scalp-recorded theta band activity responds to their infant’s changes in attention, and parental brain activation is associated with infants’ sustenance of attention. This research opens up entirely new ways of exploring caregiver–infant interactions and to understand early social attention as a reciprocal and dynamic process.
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    Correction: Journey to the east: Diverse routes and variable flowering times for wheat and barley en route to prehistoric China (2018)
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    Publication Date: 2018-12-14
    Description: by Xinyi Liu, Diane L. Lister, Zhijun Zhao, Cameron A. Petrie, Xiongsheng Zeng, Penelope J. Jones, Richard A. Staff, Anil K. Pokharia, Jennifer Bates, Ravindra N. Singh, Steven A. Weber, Giedre Motuzaite Matuzeviciute, Guanghui Dong, Haiming Li, Hongliang Lü, Hongen Jiang, Jianxin Wang, Jian Ma, Duo Tian, Guiyun Jin, Liping Zhou, Xiaohong Wu, Martin K. Jones
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    Coherent chaos in a recurrent neural network with structured connectivity (2018)
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    Publication Date: 2018-12-14
    Description: by Itamar Daniel Landau, Haim Sompolinsky We present a simple model for coherent, spatially correlated chaos in a recurrent neural network. Networks of randomly connected neurons exhibit chaotic fluctuations and have been studied as a model for capturing the temporal variability of cortical activity. The dynamics generated by such networks, however, are spatially uncorrelated and do not generate coherent fluctuations, which are commonly observed across spatial scales of the neocortex. In our model we introduce a structured component of connectivity, in addition to random connections, which effectively embeds a feedforward structure via unidirectional coupling between a pair of orthogonal modes. Local fluctuations driven by the random connectivity are summed by an output mode and drive coherent activity along an input mode. The orthogonality between input and output mode preserves chaotic fluctuations by preventing feedback loops. In the regime of weak structured connectivity we apply a perturbative approach to solve the dynamic mean-field equations, showing that in this regime coherent fluctuations are driven passively by the chaos of local residual fluctuations. When we introduce a row balance constraint on the random connectivity, stronger structured connectivity puts the network in a distinct dynamical regime of self-tuned coherent chaos. In this regime the coherent component of the dynamics self-adjusts intermittently to yield periods of slow, highly coherent chaos. The dynamics display longer time-scales and switching-like activity. We show how in this regime the dynamics depend qualitatively on the particular realization of the connectivity matrix: a complex leading eigenvalue can yield coherent oscillatory chaos while a real leading eigenvalue can yield chaos with broken symmetry. The level of coherence grows with increasing strength of structured connectivity until the dynamics are almost entirely constrained to a single spatial mode. We examine the effects of network-size scaling and show that these results are not finite-size effects. Finally, we show that in the regime of weak structured connectivity, coherent chaos emerges also for a generalized structured connectivity with multiple input-output modes.
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    Micropeptide (2018)
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    Publication Date: 2018-12-14
    Description: by Maria E. Sousa, Michael H. Farkas
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    Skin-tone discrimination by Whites and Africans is associated with the acculturation of African immigrants in Norway (2018)
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    Publication Date: 2018-12-14
    Description: by Jonas R. Kunst, Esther N. Phillibert It is well-established that experiences of discrimination influence immigrants’ acculturation. Yet, whereas a large body of research has demonstrated the role of discrimination by members of the dominant societal group, surprisingly little is known about how being discriminated by members of one’s own group relates to the way immigrants acculturate. With a sample of 162 African first- and second-generation immigrants living in Norway, the present research investigated the relationship between both types of discrimination, acculturation and psychological well-being. It did so, focusing on discrimination based on one’s skin tone, a type of discrimination Africans can experience from White as well as African individuals. Results showed that skin-tone discrimination by Whites was associated with a lower host culture orientation. By contrast, skin-tone discrimination by Africans was associated with a lower heritage culture orientation. Mediation analyses showed that the positive relationship of skin-tone discrimination by Whites and Africans with life satisfaction was mediated by a lower host and heritage culture orientation respectively. This indirect relationship did not reach significance with self-esteem as dependent variable. Participants’ actual skin tone was unrelated to experiences of skin-tone discrimination. We discuss our results in light of previous research and highlight potential limitations.
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    Correction: A Randomized Study of the Effects of Additional Fruit and Nuts Consumption on Hepatic Fat Content, Cardiovascular Risk Factors and Basal Metabolic Rate (2018)
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    Publication Date: 2018-12-14
    Description: by Christian Agebratt, Edvin Ström, Thobias Romu, Olof Dahlqvist-Leinhard, Magnus Borga, Per Leandersson, Fredrik H. Nystrom
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    Interhomolog polymorphism shapes meiotic crossover within the Arabidopsis RAC1 and RPP13 disease resistance genes (2018)
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    Publication Date: 2018-12-14
    Description: by Heïdi Serra, Kyuha Choi, Xiaohui Zhao, Alexander R. Blackwell, Juhyun Kim, Ian R. Henderson During meiosis, chromosomes undergo DNA double-strand breaks (DSBs), which can be repaired using a homologous chromosome to produce crossovers. Meiotic recombination frequency is variable along chromosomes and tends to concentrate in narrow hotspots. We mapped crossover hotspots located in the Arabidopsis thaliana RAC1 and RPP13 disease resistance genes, using varying haplotypic combinations. We observed a negative non-linear relationship between interhomolog divergence and crossover frequency within the hotspots, consistent with polymorphism locally suppressing crossover repair of DSBs. The fancm , recq4a recq4b , figl1 and msh2 mutants, or lines with increased HEI10 dosage, are known to show increased crossovers throughout the genome. Surprisingly, RAC1 crossovers were either unchanged or decreased in these genetic backgrounds, showing that chromosome location and local chromatin environment are important for regulation of crossover activity. We employed deep sequencing of crossovers to examine recombination topology within RAC1 , in wild type, fancm , recq4a recq4b and fancm recq4a recq4b backgrounds. The RAC1 recombination landscape was broadly conserved in the anti-crossover mutants and showed a negative relationship with interhomolog divergence. However, crossovers at the RAC1 5'-end were relatively suppressed in recq4a recq4b backgrounds, further indicating that local context may influence recombination outcomes. Our results demonstrate the importance of interhomolog divergence in shaping recombination within plant disease resistance genes and crossover hotspots.
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    G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide (2018)
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    Publication Date: 2018-12-14
    Description: by Enrico Lavezzo, Michele Berselli, Ilaria Frasson, Rosalba Perrone, Giorgio Palù, Alessandra R. Brazzale, Sara N. Richter, Stefano Toppo G-quadruplexes are non-canonical nucleic-acid structures that control transcription, replication, and recombination in organisms. G-quadruplexes are present in eukaryotes, prokaryotes, and viruses. In the latter, mounting evidence indicates their key biological activity. Since data on viruses are scattered, we here present a comprehensive analysis of potential quadruplex-forming sequences (PQS) in the genome of all known viruses that can infect humans. We show that occurrence and location of PQSs are features characteristic of each virus class and family. Our statistical analysis proves that their presence within the viral genome is orderly arranged, as indicated by the possibility to correctly assign up to two-thirds of viruses to their exact class based on the PQS classification. For each virus we provide: i) the list of all PQS present in the genome (positive and negative strands), ii) their position in the viral genome, iii) the degree of conservation among strains of each PQS in its genome context, iv) the statistical significance of PQS abundance. This information is accessible from a database to allow the easy navigation of the results: http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=g4virus. The availability of these data will greatly expedite research on G-quadruplex in viruses, with the possibility to accelerate finding therapeutic opportunities to numerous and some fearsome human diseases.
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    Impaired cognitive modification for estimating time duration in Parkinson’s disease (2018)
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    Publication Date: 2018-12-14
    Description: by Motoyasu Honma, Yuri Masaoka, Shinichi Koyama, Takeshi Kuroda, Akinori Futamura, Azusa Shiromaru, Yasuo Terao, Kenjiro Ono, Mitsuru Kawamura Parkinson's disease (PD) is associated with various cognitive impairments. However, the nature of cognitive modification in patients with PD remains to be elucidated. In the present study, we examined whether patients with PD could correct and maintain subjective time duration and line length estimation. After training sessions, in which participants repeatedly memorized either a duration or a length, we compared a learning performance in 20 PD patients with 20 healthy controls. In the case of duration in the PD patients, the learned durations immediately returned to baseline of pre-training within a few minutes. However, the patients’ ability to learn length estimation remained unimpaired. In contrast, healthy controls were able to retain the learned duration and length estimations. Time compression in PD's internal clock may become entrained to their altered duration estimation even after learning of accurate time duration. These deficits may be associated with disrupting cognitive modification in PD.
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    Perceptually relevant speech tracking in auditory and motor cortex reflects distinct linguistic features (2018)
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    Publication Date: 2018-03-13
    Description: by Anne Keitel, Joachim Gross, Christoph Kayser During online speech processing, our brain tracks the acoustic fluctuations in speech at different timescales. Previous research has focused on generic timescales (for example, delta or theta bands) that are assumed to map onto linguistic features such as prosody or syllables. However, given the high intersubject variability in speaking patterns, such a generic association between the timescales of brain activity and speech properties can be ambiguous. Here, we analyse speech tracking in source-localised magnetoencephalographic data by directly focusing on timescales extracted from statistical regularities in our speech material. This revealed widespread significant tracking at the timescales of phrases (0.6–1.3 Hz), words (1.8–3 Hz), syllables (2.8–4.8 Hz), and phonemes (8–12.4 Hz). Importantly, when examining its perceptual relevance, we found stronger tracking for correctly comprehended trials in the left premotor (PM) cortex at the phrasal scale as well as in left middle temporal cortex at the word scale. Control analyses using generic bands confirmed that these effects were specific to the speech regularities in our stimuli. Furthermore, we found that the phase at the phrasal timescale coupled to power at beta frequency (13–30 Hz) in motor areas. This cross-frequency coupling presumably reflects top-down temporal prediction in ongoing speech perception. Together, our results reveal specific functional and perceptually relevant roles of distinct tracking and cross-frequency processes along the auditory–motor pathway.
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    Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state (2018)
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    Publication Date: 2018-03-13
    Description: by Hao Ge, Pingping Wu, Hong Qian, Sunney Xiaoliang Xie Within an isogenic population, even in the same extracellular environment, individual cells can exhibit various phenotypic states. The exact role of stochastic gene-state switching regulating the transition among these phenotypic states in a single cell is not fully understood, especially in the presence of positive feedback. Recent high-precision single-cell measurements showed that, at least in bacteria, switching in gene states is slow relative to the typical rates of active transcription and translation. Hence using the lac operon as an archetype, in such a region of operon-state switching, we present a fluctuating-rate model for this classical gene regulation module, incorporating the more realistic operon-state switching mechanism that was recently elucidated. We found that the positive feedback mechanism induces bistability (referred to as deterministic bistability), and that the parameter range for its occurrence is significantly broadened by stochastic operon-state switching. We further show that in the absence of positive feedback, operon-state switching must be extremely slow to trigger bistability by itself. However, in the presence of positive feedback, which stabilizes the induced state, the relatively slow operon-state switching kinetics within the physiological region are sufficient to stabilize the uninduced state, together generating a broadened parameter region of bistability (referred to as stochastic bistability). We illustrate the opposite phenotype-transition rate dependence upon the operon-state switching rates in the two types of bistability, with the aid of a recently proposed rate formula for fluctuating-rate models. The rate formula also predicts a maximal transition rate in the intermediate region of operon-state switching, which is validated by numerical simulations in our model. Overall, our findings suggest a biological function of transcriptional “variations” among genetically identical cells, for the emergence of bistability and transition between phenotypic states.
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    The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen–encoding var genes (2018)
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    Publication Date: 2018-03-13
    Description: by Gerry Q. Tonkin-Hill, Leily Trianty, Rintis Noviyanti, Hanh H. T. Nguyen, Boni F. Sebayang, Daniel A. Lampah, Jutta Marfurt, Simon A. Cobbold, Janavi S. Rambhatla, Malcolm J. McConville, Stephen J. Rogerson, Graham V. Brown, Karen P. Day, Ric N. Price, Nicholas M. Anstey, Anthony T. Papenfuss, Michael F. Duffy Within the human host, the malaria parasite Plasmodium falciparum is exposed to multiple selection pressures. The host environment changes dramatically in severe malaria, but the extent to which the parasite responds to—or is selected by—this environment remains unclear. From previous studies, the parasites that cause severe malaria appear to increase expression of a restricted but poorly defined subset of the PfEMP1 variant, surface antigens. PfEMP1s are major targets of protective immunity. Here, we used RNA sequencing (RNAseq) to analyse gene expression in 44 parasite isolates that caused severe and uncomplicated malaria in Papuan patients. The transcriptomes of 19 parasite isolates associated with severe malaria indicated that these parasites had decreased glycolysis without activation of compensatory pathways; altered chromatin structure and probably transcriptional regulation through decreased histone methylation; reduced surface expression of PfEMP1; and down-regulated expression of multiple chaperone proteins. Our RNAseq also identified novel associations between disease severity and PfEMP1 transcripts, domains, and smaller sequence segments and also confirmed all previously reported associations between expressed PfEMP1 sequences and severe disease. These findings will inform efforts to identify vaccine targets for severe malaria and also indicate how parasites adapt to—or are selected by—the host environment in severe malaria.
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    Particle-based simulations of polarity establishment reveal stochastic promotion of turing pattern formation (2018)
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    Publication Date: 2018-03-13
    Description: by Michael Pablo, Samuel A. Ramirez, Timothy C. Elston Polarity establishment, the spontaneous generation of asymmetric molecular distributions, is a crucial component of many cellular functions. Saccharomyces cerevisiae (yeast) undergoes directed growth during budding and mating, and is an ideal model organism for studying polarization. In yeast and many other cell types, the Rho GTPase Cdc42 is the key molecular player in polarity establishment. During yeast polarization, multiple patches of Cdc42 initially form, then resolve into a single front. Because polarization relies on strong positive feedback, it is likely that the amplification of molecular-level fluctuations underlies the generation of multiple nascent patches. In the absence of spatial cues, these fluctuations may be key to driving polarization. Here we used particle-based simulations to investigate the role of stochastic effects in a Turing-type model of yeast polarity establishment. In the model, reactions take place either between two molecules on the membrane, or between a cytosolic and a membrane-bound molecule. Thus, we developed a computational platform that explicitly simulates molecules at and near the cell membrane, and implicitly handles molecules away from the membrane. To evaluate stochastic effects, we compared particle simulations to deterministic reaction-diffusion equation simulations. Defining macroscopic rate constants that are consistent with the microscopic parameters for this system is challenging, because diffusion occurs in two dimensions and particles exchange between the membrane and cytoplasm. We address this problem by empirically estimating macroscopic rate constants from appropriately designed particle-based simulations. Ultimately, we find that stochastic fluctuations speed polarity establishment and permit polarization in parameter regions predicted to be Turing stable. These effects can operate at Cdc42 abundances expected of yeast cells, and promote polarization on timescales consistent with experimental results. To our knowledge, our work represents the first particle-based simulations of a model for yeast polarization that is based on a Turing mechanism.
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    Across-subjects classification of stimulus modality from human MEG high frequency activity (2018)
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    Publication Date: 2018-03-13
    Description: by Britta U. Westner, Sarang S. Dalal, Simon Hanslmayr, Tobias Staudigl Single-trial analyses have the potential to uncover meaningful brain dynamics that are obscured when averaging across trials. However, low signal-to-noise ratio (SNR) can impede the use of single-trial analyses and decoding methods. In this study, we investigate the applicability of a single-trial approach to decode stimulus modality from magnetoencephalographic (MEG) high frequency activity. In order to classify the auditory versus visual presentation of words, we combine beamformer source reconstruction with the random forest classification method. To enable group level inference, the classification is embedded in an across-subjects framework. We show that single-trial gamma SNR allows for good classification performance (accuracy across subjects: 66.44%). This implies that the characteristics of high frequency activity have a high consistency across trials and subjects. The random forest classifier assigned informational value to activity in both auditory and visual cortex with high spatial specificity. Across time, gamma power was most informative during stimulus presentation. Among all frequency bands, the 75 Hz 95 Hz band was the most informative frequency band in visual as well as in auditory areas. Especially in visual areas, a broad range of gamma frequencies (55 Hz 125 Hz) contributed to the successful classification. Thus, we demonstrate the feasibility of single-trial approaches for decoding the stimulus modality across subjects from high frequency activity and describe the discriminative gamma activity in time, frequency, and space.
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    Controlled branched-chain amino acids auxotrophy in Listeria monocytogenes allows isoleucine to serve as a host signal and virulence effector (2018)
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    Publication Date: 2018-03-13
    Description: by Moran Brenner, Lior Lobel, Ilya Borovok, Nadejda Sigal, Anat A. Herskovits Listeria monocytogenes ( Lm ) is a saprophyte and intracellular pathogen. Transition to the pathogenic state relies on sensing of host-derived metabolites, yet it remains unclear how these are recognized and how they mediate virulence gene regulation. We previously found that low availability of isoleucine signals Lm to activate the virulent state. This response is dependent on CodY, a global regulator and isoleucine sensor. Isoleucine-bound CodY represses metabolic pathways including branched-chain amino acids (BCAA) biosynthesis, however under BCAA depletion, as occurs during infection, BCAA biosynthesis is upregulated and isoleucine-unbound CodY activates virulence genes. While isoleucine was revealed as an important input signal, it was not identified how internal levels are controlled during infection. Here we show that Lm regulates BCAA biosynthesis via CodY and via a riboregulator located upstream to the BCAA biosynthesis genes, named Rli60. rli60 is transcribed when BCAA levels drop, forming a ribosome-mediated attenuator that cis -regulates the downstream genes according to BCAA supply. Notably, we found that Rli60 restricts BCAA production, essentially starving Lm , a mechanism that is directly linked to virulence, as it controls the internal isoleucine pool and thereby CodY activity. This controlled BCAA auxotrophy likely evolved to enable isoleucine to serve as a host signal and virulence effector.
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    A model for hydrophobic protrusions on peripheral membrane proteins (2018)
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    Publication Date: 2018-07-27
    Description: by Edvin Fuglebakk, Nathalie Reuter With remarkable spatial and temporal specificities, peripheral membrane proteins bind to biological membranes. They do this without compromising solubility of the protein, and their binding sites are not easily distinguished. Prototypical peripheral membrane binding sites display a combination of patches of basic and hydrophobic amino acids that are also frequently present on other protein surfaces. The purpose of this contribution is to identify simple but essential components for membrane binding, through structural criteria that distinguish exposed hydrophobes at membrane binding sites from those that are frequently found on any protein surface. We formulate the concepts of protruding hydrophobes and co-insertability and have analysed more than 300 families of proteins that are classified as peripheral membrane binders. We find that this structural motif strongly discriminates the surfaces of membrane-binding and non-binding proteins. Our model constitutes a novel formulation of a structural pattern for membrane recognition and emphasizes the importance of subtle structural properties of hydrophobic membrane binding sites.
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    Auditory midbrain coding of statistical learning that results from discontinuous sensory stimulation (2018)
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    Publication Date: 2018-07-27
    Description: by Hugo Cruces-Solís, Zhizi Jing, Olga Babaev, Jonathan Rubin, Burak Gür, Dilja Krueger-Burg, Nicola Strenzke, Livia de Hoz Detecting regular patterns in the environment, a process known as statistical learning, is essential for survival. Neuronal adaptation is a key mechanism in the detection of patterns that are continuously repeated across short (seconds to minutes) temporal windows. Here, we found in mice that a subcortical structure in the auditory midbrain was sensitive to patterns that were repeated discontinuously, in a temporally sparse manner, across windows of minutes to hours. Using a combination of behavioral, electrophysiological, and molecular approaches, we found changes in neuronal response gain that varied in mechanism with the degree of sound predictability and resulted in changes in frequency coding. Analysis of population activity (structural tuning) revealed an increase in frequency classification accuracy in the context of increased overlap in responses across frequencies. The increase in accuracy and overlap was paralleled at the behavioral level in an increase in generalization in the absence of diminished discrimination. Gain modulation was accompanied by changes in gene and protein expression, indicative of long-term plasticity. Physiological changes were largely independent of corticofugal feedback, and no changes were seen in upstream cochlear nucleus responses, suggesting a key role of the auditory midbrain in sensory gating. Subsequent behavior demonstrated learning of predictable and random patterns and their importance in auditory conditioning. Using longer timescales than previously explored, the combined data show that the auditory midbrain codes statistical learning of temporally sparse patterns, a process that is critical for the detection of relevant stimuli in the constant soundscape that the animal navigates through.
    Print ISSN: 1544-9173
    Electronic ISSN: 1545-7885
    Topics: Biology
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    C-type natriuretic peptide analog treatment of craniosynostosis in a Crouzon syndrome mouse model (2018)
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    Publication Date: 2018-07-27
    Description: by Greg Holmes, Lening Zhang, Joshua Rivera, Ryan Murphy, Claudia Assouline, Lorraine Sullivan, Todd Oppeneer, Ethylin Wang Jabs Activating mutations of fibroblast growth factor receptors (FGFRs) are a major cause of skeletal dysplasias, and thus they are potential targets for pharmaceutical intervention. BMN 111, a C-type natriuretic peptide analog, inhibits FGFR signaling at the level of the RAF1 kinase through natriuretic peptide receptor 2 (NPR2) and has been shown to lengthen the long bones and improve skull morphology in the Fgfr3 Y367C/+ thanatophoric dysplasia mouse model. Here we report the effects of BMN 111 in treating craniosynostosis and aberrant skull morphology in the Fgfr2c C342Y/+ Crouzon syndrome mouse model. We first demonstrated that NPR2 is expressed in the murine coronal suture and spheno-occipital synchondrosis in the newborn period. We then gave Fgfr2c C342Y/+ and Fgfr2c +/+ (WT) mice once-daily injections of either vehicle or reported therapeutic levels of BMN 111 between post-natal days 3 and 31. Changes in skeletal morphology, including suture patency, skull dimensions, and long bone length, were assessed by micro-computed tomography. Although BMN 111 treatment significantly increased long bone growth in both WT and mutant mice, skull dimensions and suture patency generally were not significantly affected. A small but significant increase in the relative length of the anterior cranial base was observed. Our results indicate that the differential effects of BMN 111 in treating various skeletal dysplasias may depend on the process of bone formation targeted (endochondral or intramembranous), the specific FGFR mutated, and/or the specific signaling pathway changes due to a given mutation.
    Electronic ISSN: 1932-6203
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    Vertically and horizontally directed muscle power exercises: Relationships with top-level sprint performance (2018)
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    Publication Date: 2018-07-27
    Description: by Irineu Loturco, Bret Contreras, Ronaldo Kobal, Victor Fernandes, Neilton Moura, Felipe Siqueira, Ciro Winckler, Timothy Suchomel, Lucas Adriano Pereira The capacity to rapidly generate and apply a great amount of force seems to play a key role in sprint running. However, it has recently been shown that, for sprinters, the technical ability to effectively orient the force onto the ground is more important than its total amount. The force-vector theory has been proposed to guide coaches in selecting the most adequate exercises to comprehensively develop the neuromechanical qualities related to the distinct phases of sprinting. This study aimed to compare the relationships between vertically-directed (loaded and unloaded vertical jumps, and half-squat) and horizontally-directed (hip-thrust) exercises and the sprint performance of top-level track and field athletes. Sixteen sprinters and jumpers (including three Olympic athletes) executed vertical jumps, loaded jump squats and hip-thrusts, and sprinting speed tests at 10-, 20-, 40-, 60-, 100-, and 150-m. Results indicated that the hip-thrust is more associated with the maximum acceleration phase (i.e., from zero to 10-m; r = 0.93), whereas the loaded and unloaded vertical jumps seem to be more related to top-speed phases (i.e., distances superior to 40-m; r varying from 0.88 to 0.96). These findings reinforce the mechanical concepts supporting the force-vector theory, and provide coaches and sport scientists with valuable information about the potential use and benefits of using vertically- or horizontally-based training exercises.
    Electronic ISSN: 1932-6203
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    Effects of motor fatigue on walking stability and variability during concurrent cognitive challenges (2018)
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    Publication Date: 2018-07-27
    Description: by Pei-Chun Kao, Michaela A. Pierro, Konstantina Booras Cognitive-motor interference, a negative influence on the performance of one or both tasks, is manifested when simultaneously performing a cognitive and a motor task. Motor fatigue reduces the ability of generating a required force level. However, little is known about the effects of motor fatigue on the cognitive-motor dual-tasking performance, an important capability during our daily lives. This study investigated how motor fatigue affects dual-task walking performance. Eighteen healthy younger adults walked on a treadmill under three different conditions: walking only, walking while receiving the Paced Auditory Serial Addition Test (PASAT) or a modified Stroop test before and after a lower-extremity fatiguing exercise. We computed dynamic margins of stability (MOS), step and joint kinematic variability, and short-term local divergence exponent (LDE) of the trunk motion. We found that subjects had similar values of short-term LDE during all conditions, indicating that local stability was not affected by the motor fatigue or dual-task conditions. Compared to the baseline, subjects had significantly greater mean MOS after the fatiguing exercise by walking with greater step length and width while having significantly greater gait variability. In contrast, subjects walked with similar mean MOS but significantly less gait variability during the dual-task conditions, indicating that subjects used different adaptive strategies when walking with motor fatigue and during dual-task conditions. There were no significant differences in the number of errors for the two cognitive tests before and after the fatiguing exercise. The current findings demonstrate that motor fatigue does not affect cognitive but motor performance in younger adults.
    Electronic ISSN: 1932-6203
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    Investigation of wound healing process guided by nano-scale topographic patterns integrated within a microfluidic system (2018)
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    Publication Date: 2018-07-27
    Description: by Insu Lee, Daegyu Kim, Ga-Lahm Park, Tae-Joon Jeon, Sun Min Kim When living tissues are injured, they undergo a sequential process of homeostasis, inflammation, proliferation and maturation, which is called wound healing. The working mechanism of wound healing has not been wholly understood due to its complex environments with various mechanical and chemical factors. In this study, we propose a novel in vitro wound healing model using a microfluidic system that can manipulate the topography of the wound bed. The topography of the extracellular matrix (ECM) in the wound bed is one of the most important mechanical properties for rapid and effective wound healing. We focused our work on the topographical factor which is one of crucial mechanical cues in wound healing process by using various nano-patterns on the cell attachment surface. First, we analyzed the cell morphology and dynamic cellular behaviors of NIH-3T3 fibroblasts on the nano-patterned surface. Their morphology and dynamic behaviors were investigated for relevance with regard to the recovery function. Second, we developed a highly reproducible and inexpensive research platform for wound formation and the wound healing process by combining the nano-patterned surface and a microfluidic channel. The effect of topography on wound recovery performance was analyzed. This in vitro wound healing research platform will provide well-controlled topographic cue of wound bed and contribute to the study on the fundamental mechanism of wound healing.
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    Surface deposited one-dimensional copper-doped TiO 2 nanomaterials for prevention of health care acquired infections (2018)
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    Publication Date: 2018-07-27
    Description: by Tilen Koklic, Iztok Urbančič, Irena Zdovc, Majda Golob, Polona Umek, Zoran Arsov, Goran Dražić, Štefan Pintarič, Martin Dobeic, Janez Štrancar Bacterial infections acquired in healthcare facilities including hospitals, the so called healthcare acquired or nosocomial infections, are still of great concern worldwide and represent a significant economical burden. One of the major causes of morbidity is infection with Methicillin Resistant Staphylococcus aureus (MRSA), which has been reported to survive on surfaces for several months. Bactericidal activity of copper-TiO 2 thin films, which release copper ions and are deposited on glass surfaces and heated to high temperatures, is well known even when illuminated with very weak UVA light of about 10 μW/cm 2 . Lately, there is an increased intrerest for one-dimensional TiO 2 nanomaterials, due to their unique properties, low cost, and high thermal and photochemical stability. Here we show that copper doped TiO 2 nanotubes produce about five times more ·OH radicals as compared to undoped TiO 2 nanotubes and that effective surface disinfection, determined by a modified ISO 22196:2011 test, can be achieved even at low intensity UVA light of 30 μW/cm 2 . The nanotubes can be deposited on a preformed surface at room temperature, resulting in a stable deposition resistant to multiple washings. Up to 10 3 microorganisms per cm 2 can be inactivated in 24 hours, including resistant strains such as Methicillin-resistant Staphylococcus aureus (MRSA) and Extended-spectrum beta-lactamase Escherichia coli ( E . coli ESBL). This disinfection method could provide a valuable alternative to the current surface disinfection methods.
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    A low FODMAP diet is associated with changes in the microbiota and reduction in breath hydrogen but not colonic volume in healthy subjects (2018)
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    Publication Date: 2018-07-27
    Description: by Tim J. Sloan, Jonna Jalanka, Giles A. D. Major, Shanthi Krishnasamy, Sue Pritchard, Salah Abdelrazig, Katri Korpela, Gulzar Singh, Claire Mulvenna, Caroline L. Hoad, Luca Marciani, David A. Barrett, Miranda C. E. Lomer, Willem M. de Vos, Penny A. Gowland, Robin C. Spiller Background & aims Ingestion of poorly digested, fermentable carbohydrates (fermentable oligo-, di-, mono-saccharides and polyols; FODMAPs) have been implicated in exacerbating intestinal symptoms and the reduction of intake with symptom alleviation. Restricting FODMAP intake is believed to relieve colonic distension by reducing colonic fermentation but this has not been previously directly assessed. We performed a randomised controlled trial comparing the effect of a low FODMAP diet combined with either maltodextrin or oligofructose on colonic contents, metabolites and microbiota. Methods A parallel randomised controlled trial in healthy adults (n = 37). All subjects followed a low FODMAP diet for a week and supplemented their diet with either maltodextrin (MD) or oligofructose (OF) 7g twice daily. Fasted assessments performed pre- and post-diet included MRI to assess colonic volume, breath testing for hydrogen and methane, and stool collection for microbiota analysis. Results The low FODMAP diet was associated with a reduction in Bifidobacterium and breath hydrogen, which was reversed by oligofructose supplementation. The difference in breath hydrogen between groups post-intervention was 27ppm (95% CI 7 to 50, P
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    Catabolism of mucus components influences motility of Vibrio cholerae in the presence of environmental reservoirs (2018)
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    Publication Date: 2018-07-27
    Description: by Geethika Reddi, Kali Pruss, Kathryn L. Cottingham, Ronald K. Taylor, Salvador Almagro-Moreno Vibrio cholerae O1, the etiological agent of cholera, is a natural inhabitant of aquatic ecosystems. Motility is a critical element for the colonization of both the human host and its environmental reservoirs. In this study, we investigated the molecular mechanisms underlying the chemotactic response of V . cholerae in the presence of some of its environmental reservoirs. We found that, from the several oligosaccharides found in mucin, two specifically triggered motility of V . cholerae O1: N -acetylneuraminic acid (Neu5Ac) and N -acetylglucosamine (GlcNAc). We determined that the compounds need to be internally catabolized in order to trigger motility of V . cholerae . Interestingly, the catabolism of Neu5Ac and GlcNAc converges and the production of one molecule common to both pathways, glucosamine-6-phosphate (GlcN-6P), is essential to induce motility in the presence of both compounds. Mutants unable to produce GlcN-6P show greatly reduced motility towards mucin. Furthermore, we determined that the production of GlcN-6P is necessary to induce motility of V . cholerae in the presence of some of its environmental reservoirs such as crustaceans or cyanobacteria, revealing a molecular link between the two distinct modes of the complex life cycle of V . cholerae . Finally, cross-species comparisons revealed varied chemotactic responses towards mucin, GlcNAc, and Neu5Ac for environmental (non-pathogenic) strains of V . cholerae , clinical and environmental isolates of the human pathogens Vibrio vulnificus and Vibrio parahaemolyticus , and fish and squid isolates of the symbiotic bacterium Vibrio fischeri . The data presented here suggest nuance in convergent strategies across species of the same bacterial family for motility towards suitable substrates for colonization.
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    Skills attained by infants with congenital Zika syndrome: Pilot data from Brazil (2018)
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    Publication Date: 2018-07-27
    Description: by Anne C. Wheeler, Camila V. Ventura, Ty Ridenour, Danielle Toth, Lucélia Lima Nobrega, Lana Claudia Silva de Souza Dantas, Camilla Rocha, Donald B. Bailey Jr., Liana O. Ventura The recent Zika outbreak and its link to microcephaly and other birth defects in infants exposed in utero have garnered widespread international attention. Based on the severity of birth defects the extent of impairment in these infants is expected to be profound; however, virtually nothing is known regarding the developmental and behavioral sequela of congenital Zika syndrome. This pilot study collected parent-reported patterns of development and sleep in 47 infants with confirmed congenital Zika syndrome who are being followed for clinical services at the Altino Ventura Foundation (FAV) in Recife, Brazil. With assistance from clinicians at FAV, caregivers completed Brazilian Portuguese versions of the Ages and Stages Questionnaire, 3 rd edition (ASQ-3) and the Brief Infant Sleep Questionnaire (BISQ). All infants were between 13–22 months of age at the time of the assessment. At 16 months of age, none of the children displayed age appropriate developmental skills. Most (~ 75%) mastered some communication and gross motor skills at around a 6–8-month level. Communication and gross motor skills were relative strengths for the sample, while problem-solving and fine motor skills were relative weaknesses. Sleep was noted to be a problem for around 18% of the sample. In utero exposure to the Zika virus will have lifelong consequences for affected children and their families. Understanding the developmental and behavioral trajectories of affected infants will help identify appropriate family supports to improve quality of life.
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    Effects of heart rate variability biofeedback training in athletes exposed to stress of university examinations (2018)
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    Publication Date: 2018-07-27
    Description: by Veronique Deschodt-Arsac, Romain Lalanne, Beatrice Spiluttini, Claire Bertin, Laurent M. Arsac Introduction Heart rate variability biofeedback (HRV-BFB) training, a method whereby one controls an unusually low breathing rate to reach cardiac coherence, has been shown to reduce anxiety and improve cardiac autonomic markers in diseased people, but much less is known about HRV-BFB benefits in healthy people. Here we investigated potential benefits in young competitors experiencing stress during university examinations as well as persistence of benefits after HRV-BFB training cessation. Methods A group of sports students (n = 12) practiced 5-min HRV-BFB training twice a day for 5-weeks using URGOfeel ® (URGOTECH) and was compared to a control group (n = 6). University examinations occurred immediately after HRV-BFB training (Exam1), then 12-weeks later (Exam2). Anxiety markers and cardiac autonomic markers were assessed at baseline, Exam1 and Exam2. Principal Component Analyses (PCA) that combined all these markers were computed at Exam1 and Exam2 to emphasize covariations. Results At Exam 1, immediately after HRV-BFB training cessation, the experimental group demonstrated greater autonomic markers but similar states of anxiety when compared to the Control group. Twelve weeks later at Exam2, autonomic markers were greater and anxiety scores were lesser among the experimental group. PCA highlighted covariations only within cardiac autonomic markers at Exam1. Rather, variations in cardiac markers were associated with anxiety markers at Exam2. Conclusion Short sessions of HRV-BFB training for a brief period of 5 weeks bring substantial benefits to autonomic markers and anxiety levels in young competitors. Here beneficial effects persisted for 12 weeks. Dissociated profiles of anxiety and cardiac autonomic adaptations shed new light on the role of the amygdala in heart-brain interactions after cardiac coherence training.
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    Control of cytokine-driven eosinophil migratory behavior by TGF-beta-induced protein (TGFBI) and periostin (2018)
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    Publication Date: 2018-07-27
    Description: by Karina T. Barretto, Calvin M. Swanson, Christopher L. Nguyen, Douglas S. Annis, Stephane J. Esnault, Deane F. Mosher, Mats W. Johansson Periostin, which is induced by interleukin (IL)-13, is an extracellular matrix (ECM) protein that supports α M β 2 integrin-mediated adhesion and migration of IL-5-stimulated eosinophils. Transforming growth factor (TGF)-β-induced protein (TGFBI) is a widely expressed periostin paralog known to support monocyte adhesion. Our objective was to compare eosinophil adhesion and migration on TGFBI and periostin in the presence of IL-5-family cytokines. Eosinophil adhesion after 1 h and random motility over 20 h in the presence of various concentrations of IL-5, IL-3, or granulocyte macrophage-colony stimulating factor (GM-CSF) were quantified in wells coated with various concentrations of TGFBI or periostin. Results were compared to video microscopy of eosinophils. Cytokine-stimulated eosinophils adhered equivalently well to TGFBI or periostin in a coating concentration-dependent manner. Adhesion was blocked by anti-α M β 2 and stimulated at the lowest concentration by GM-CSF. In the motility assay, periostin was more potent than TGFBI, the coating-concentration effect was bimodal, and IL-3 was the most potent cytokine. Video microscopy revealed that under the optimal coating condition of 5 μg/ml periostin, most eosinophils migrated persistently and were polarized and acorn-shaped with a ruffling forward edge and granules gathered together, in front of the nucleus. On 10 μg/ml periostin or TGFBI, more eosinophils adopted a flattened pancake morphology with dispersed granules and nuclear lobes, and slower migration. Conversion between acorn and pancake morphologies were observed. We conclude that TGFBI or periostin supports two modes of migration by IL-5 family cytokine-activated eosinophils. The rapid mode is favored by intermediate protein coatings and the slower by higher coating concentrations. We speculate that eosinophils move by haptotaxis up a gradient of adhesive ECM protein and then slow down to surveil the tissue.
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    The effects of a gamified approach avoidance training and verbal suggestions on food outcomes (2018)
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    Publication Date: 2018-07-27
    Description: by Lemmy Schakel, Dieuwke S. Veldhuijzen, Henriët van Middendorp, Pieter Van Dessel, Jan De Houwer, Rafael Bidarra, Andrea W. M. Evers There is initial support for the effectiveness of approach-avoidance trainings in altering food-related health behaviors. Furthermore, outcome expectancies induced by verbal suggestions might optimize the effectiveness of these interventions, as shown in placebo research. The present study investigated the effectiveness of a gamified approach-avoidance training on food-related outcomes and whether verbal suggestions could strengthen those effects. A total of 120 participants were randomly assigned to 1 of 4 conditions: serious gaming only, verbal suggestions only, serious gaming combined with verbal suggestions, or a gaming control condition. Virtual food preference and food choice were assessed with a food choice task, with pairs differing in healthiness or in healthiness and attractiveness. Implicit food preference was assessed with an Implicit Association Test and food intake with a bogus taste test. Participants in both serious gaming conditions made healthier food choices for pairs differing in healthiness and attractiveness and had healthier implicit food preferences compared to gaming control. No effects were found on food intake. These findings provide the first preliminary support for the effects of a gamified approach-avoidance training on virtual food choice and implicit food preference. Future studies should further elucidate these effects, also in other health domains such as physical activity.
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    StartReact effects in first dorsal interosseous muscle are absent in a pinch task, but present when combined with elbow flexion (2018)
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    Publication Date: 2018-07-27
    Description: by Juan M. Castellote, Markus Kofler Objective To provide a neurophysiological tool for assessing sensorimotor pathways, which may differ for those involving distal muscles in simple tasks from those involving distal muscles in a kinetic chain task, or proximal muscles in both. Methods We compared latencies and magnitudes of motor responses in a reaction time paradigm in a proximal (biceps brachii, BB) and a distal (first dorsal interosseous, FDI) muscle following electrical stimuli used as imperative signal (IS) delivered to the index finger. These stimuli were applied during different motor tasks: simple tasks involving either one muscle, e.g. flexing the elbow for BB (FLEX), or pinching a pen for FDI (PINCH); combined tasks engaging both muscles by pinching and flexing simultaneously (PINCH-FLEX). Stimuli were of varying intensity and occasionally elicited a startle response, and a StartReact effect. Results In BB, response latencies decreased gradually and response amplitudes increased progressively with increasing IS intensities for non-startling trials, while for trials containing startle responses, latencies were uniformly shortened and response amplitudes similarly augmented across all IS intensities in both FLEX and PINCH-FLEX. In FDI, response latencies decreased gradually and response amplitudes increased progressively with increasing IS intensities in both PINCH and PINCH-FLEX for non-startling trials, but, unlike in BB for the simple task, in PINCH for trials containing startle responses as well. In PINCH-FLEX, FDI latencies were uniformly shortened and amplitudes similarly increased across all stimulus intensities whenever startle signs were present. Conclusions Our results suggest the presence of different sensorimotor pathways supporting a dissociation between simple tasks that involve distal upper limb muscles (FDI in PINCH) from simple tasks involving proximal muscles (BB in FLEX), and combined tasks that engage both muscles (FDI and BB in PINCH-FLEX), all in accordance with differential importance in the control of movements by cortical and subcortical structures. Significance Simple assessment tools may provide useful information regarding the differential involvement of sensorimotor pathways in the control of both simple and combined tasks that engage proximal and distal muscles.
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    Optimal cut-off value for equol-producing status in women: The Japan Nurses’ Health Study urinary isoflavone concentration survey (2018)
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    Publication Date: 2018-07-27
    Description: by Yuki Ideno, Kunihiko Hayashi, Junko Nakajima-Shimada, Yoko Onizuka, Mikiko Kishi, Tomomi Ueno, Shigeto Uchiyama Equol is one of the most active soy isoflavones. When the association between soy food intake in daily life and health outcomes is examined in epidemiological studies, it is important to define the equol-producing status of each individual. However, few studies have assessed equol-producing status without a soy challenge test. To determine a robust cutoff criterion for equol producer classification in observational studies, we conducted a urinary isoflavone concentration survey in daily life among women. Furthermore, we examined the association between eating habits regarding soy foods and equol-producing status. A total of 4,412 participants were included in the analyses. Urinary isoflavones were analyzed using a high-performance liquid chromatography method. We examined the distribution of the log 10 equol/daidzein ratios, finding a mixture of two normal distributions, corresponding to equol producer and non-producer subpopulations. Applying a finite mixture model, we estimated the means, standard deviations, and mixing proportions of these two distributions. The estimation was carried out using the SAS NLIN procedure. The optimal cutoff point for the log 10 equol/daidzein ratio in the study population was determined to be −1.42, according to the estimated parameters of the mixture distribution. Based on this criterion, 1,830 (41.5%) of the participants were identified as equol producers. Compared with non-consumers of soy foods, consumers of soy foods had significantly higher odds of being equol producers. Using log 10 -transformed equol/daidzein ratios ≥ −1.42 to define equol producers among Japanese women is reasonable and suitable for determining equol-producing status in epidemiological studies. We found that soy food eating habits were associated with equol-producing status. Further investigation is required to evaluate associations between equol-producing status in daily life and health outcomes. The results of this study suggest the best cutoff point to use in the definition of equol-producing status in daily life.
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    A mathematical and computational model of the calcium dynamics in Caenorhabditis elegans ASH sensory neuron (2018)
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    Publication Date: 2018-07-27
    Description: by Ehsan Mirzakhalili, Bogdan I. Epureanu, Eleni Gourgou We propose a mathematical and computational model that captures the stimulus-generated Ca 2+ transients in the C . elegans ASH sensory neuron. The rationale is to develop a tool that will enable a cross-talk between modeling and experiments, using modeling results to guide targeted experimental efforts. The model is built based on biophysical events and molecular cascades known to unfold as part of neurons' Ca 2+ homeostasis mechanism, as well as on Ca 2+ signaling events. The state of ion channels is described by their probability of being activated or inactivated, and the remaining molecular states are based on biochemically defined kinetic equations or known biochemical motifs. We estimate the parameters of the model using experimental data of hyperosmotic stimulus-evoked Ca 2+ transients detected with a FRET sensor in young and aged worms, unstressed and exposed to oxidative stress. We use a hybrid optimization method composed of a multi-objective genetic algorithm and nonlinear least-squares to estimate the model parameters. We first obtain the model parameters for young unstressed worms. Next, we use these values of the parameters as a starting point to identify the model parameters for stressed and aged worms. We show that the model, in combination with experimental data, corroborates literature results. In addition, we demonstrate that our model can be used to predict ASH response to complex combinations of stimulation pulses. The proposed model includes for the first time the ASH Ca 2+ dynamics observed during both "on" and "off" responses. This mathematical and computational effort is the first to propose a dynamic model of the Ca 2+ transients' mechanism in C . elegans neurons, based on biochemical pathways of the cell's Ca 2+ homeostasis machinery. We believe that the proposed model can be used to further elucidate the Ca 2+ dynamics of a key C . elegans neuron, to guide future experiments on C . elegans neurobiology, and to pave the way for the development of more mathematical models for neuronal Ca 2+ dynamics.
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    First trimester prenatal screening biomarkers and gestational diabetes mellitus: A systematic review and meta-analysis (2018)
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    Publication Date: 2018-07-27
    Description: by Brittney M. Donovan, Nichole L. Nidey, Elizabeth A. Jasper, Jennifer G. Robinson, Wei Bao, Audrey F. Saftlas, Kelli K. Ryckman Biomarkers commonly assessed in prenatal screening have been associated with a number of adverse perinatal and birth outcomes. However, it is not clear whether first trimester measurements of prenatal screening biomarkers are associated with subsequent risk of gestational diabetes mellitus (GDM). We aimed to systematically review and statistically summarize studies assessing the relationship between first trimester prenatal screening biomarker levels and GDM development. We comprehensively searched PubMed/MEDLINE, EMBASE, CINAHL, and Scopus (from inception through January 2018) and manually searched the reference lists of all relevant articles. We included original, published, observational studies examining the association of first trimester pregnancy associated plasma protein-A (PAPP-A) and/or free β-human chorionic gonadotropin (free β-hCG) levels with GDM diagnosis. Mean differences were calculated comparing PAPP-A and free β-hCG multiples of median (MoM) levels between women who developed GDM and those who did not and were subsequently pooled using two-sided random-effects models. Our meta-analysis of 13 studies on PAPP-A and nine studies on free β-hCG indicated that first trimester MoM levels for both biomarkers were lower in women who later developed GDM compared to women who remained normoglycemic throughout pregnancy (MD -0.17; 95% CI -0.24, -0.10; MD -0.04; 95% CI -0.07–0.01). There was no evidence for between-study heterogeneity among studies on free β-hCG (I 2 = 0%). A high level of between-study heterogeneity was detected among the studies reporting on PAPP-A (I 2 = 90%), but was reduced after stratifying by geographic location, biomarker assay method, and timing of GDM diagnosis. Our meta-analysis indicates that women who are diagnosed with GDM have lower first trimester levels of both PAPP-A and free β-hCG than women who remain normoglycemic throughout pregnancy. Further assessment of the predictive capacity of these biomarkers within large, diverse populations is needed.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Risk of autoimmune rheumatic diseases in patients with palindromic rheumatism: A nationwide, population-based, cohort study (2018)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2018-07-27
    Description: by Hsin-Hua Chen, Wen-Cheng Chao, Tsai-Ling Liao, Ching-Heng Lin, Der-Yuan Chen Objective To estimate the relative risk of autoimmune rheumatic diseases, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), systemic sclerosis (SSc), Sjogren’s syndrome (SS), dermatomyositis (DM) and polymyositis (PM), among patients with palindromic rheumatism (PR) compared with non-PR individuals. Methods The study utilized 2003–2013 claims data from the Taiwanese National Health Insurance Research Database. We identified 4,421 cases of PR from 2007 to 2012 and randomly chose 44,210 non-PR individuals who matched (1:10) for age, sex and the year of index date without prior history of RA, SLE, SSc, SS, DM, or PM. After adjusting for age, sex, and the Charlson comorbidity index, we calculated the hazard ratios (HRs) with 95% confidence intervals (CIs) using the Cox proportional hazard model to quantify the risk of RA, SLE, SS, DM and PM in PR patients compared with that in matched non-PR individuals. Results Among the 4,421 patients with PR, 569 (12.87%) developed RA, 269 (6.08%) developed SS, 113 (2.56%) developed SLE, 5 (0.11%) developed SSc, 8 (0.18%) developed PM, and 1 (0.02%) developed DM. After adjusting for potential confounders, the patients with PR had an increased risk of RA (HR, 118.76; 95% CI, 89.81–157.04), SS (HR, 59.57; 95% CI, 43.87–80.88), SLE (HR, 51.56; 95% CI, 32.96–80.66) PM (HR, 57.38; 95% CI, 6.90–476.83), and SSc (HR, 13.42; 95% CI, 3.79–47.55) but not of DM (HR, 3.44; 95% CI, 0.34–34.59). Conclusion Patients with PR had an increased risk of developing RA, SS, SLE, PM, and SSc.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    HIV induces synaptic hyperexcitation via cGMP-dependent protein kinase II activation in the FIV infection model (2018)
    Public Library of Science (PLoS)
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    Publication Date: 2018-07-28
    Description: by Keira Sztukowski, Kaila Nip, Paige N. Ostwald, Matheus F. Sathler, Julianna L. Sun, Jiayi Shou, Emily T. Jorgensen, Travis E. Brown, John H. Elder, Craig Miller, Franz Hofmann, Sue VandeWoude, Seonil Kim Over half of individuals infected with human immunodeficiency virus (HIV) suffer from HIV-associated neurocognitive disorders (HANDs), yet the molecular mechanisms leading to neuronal dysfunction are poorly understood. Feline immunodeficiency virus (FIV) naturally infects cats and shares its structure, cell tropism, and pathology with HIV, including wide-ranging neurological deficits. We employ FIV as a model to elucidate the molecular pathways underlying HIV-induced neuronal dysfunction, in particular, synaptic alteration. Among HIV-induced neuron-damaging products, HIV envelope glycoprotein gp120 triggers elevation of intracellular Ca 2+ activity in neurons, stimulating various pathways to damage synaptic functions. We quantify neuronal Ca 2+ activity using intracellular Ca 2+ imaging in cultured hippocampal neurons and confirm that FIV envelope glycoprotein gp95 also elevates neuronal Ca 2+ activity. In addition, we reveal that gp95 interacts with the chemokine receptor, CXCR4, and facilitates the release of intracellular Ca 2+ by the activation of the endoplasmic reticulum (ER)-associated Ca 2+ channels, inositol triphosphate receptors (IP3Rs), and synaptic NMDA receptors (NMDARs), similar to HIV gp120. This suggests that HIV gp120 and FIV gp95 share a core pathological process in neurons. Significantly, gp95’s stimulation of NMDARs activates cGMP-dependent protein kinase II (cGKII) through the activation of the neuronal nitric oxide synthase (nNOS)-cGMP pathway, which increases Ca 2+ release from the ER and promotes surface expression of AMPA receptors, leading to an increase in synaptic activity. Moreover, we culture feline hippocampal neurons and confirm that gp95-induced neuronal Ca 2+ overactivation is mediated by CXCR4 and cGKII. Finally, cGKII activation is also required for HIV gp120-induced Ca 2+ hyperactivation. These results thus provide a novel neurobiological mechanism of cGKII-mediated synaptic hyperexcitation in HAND.
    Print ISSN: 1544-9173
    Electronic ISSN: 1545-7885
    Topics: Biology
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    CCL20 triggered by chemotherapy hinders the therapeutic efficacy of breast cancer (2018)
    Public Library of Science (PLoS)
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    Publication Date: 2018-07-28
    Description: by Weilong Chen, Yuanyuan Qin, Dong Wang, Lei Zhou, Yin Liu, Sheng Chen, Liang Yin, Yaoxing Xiao, Xiao-Hong Yao, Xiaoli Yang, Wei Ma, Weifeng Chen, Xueyan He, Lixing Zhang, Qifeng Yang, Xiuwu Bian, Zhi-ming Shao, Suling Liu Chemotherapeutic resistance in triple-negative breast cancer (TNBC) has brought great challenges to the improvement of patient survival. The mechanisms of taxane chemoresistance in TNBC have not been well investigated. Our results illustrated C-C motif chemokine ligand 20 (CCL20) was significantly elevated during taxane-containing chemotherapy in breast cancer patients with nonpathologic complete response. Furthermore, CCL20 promoted the self-renewal and maintenance of breast cancer stem cells (BCSCs) or breast cancer stem-like cells through protein kinase Cζ (PKCζ) or p38 mitogen-activated protein kinase (MAPK)-mediated activation of p65 nuclear factor kappa B (NF-κB) pathway, significantly increasing the frequency and taxane resistance of BCSCs. Moreover, CCL20-promoted NF-κB activation increased ATP-binding cassette subfamily B member 1 (ABCB1)/multidrug resistance 1 (MDR1) expression, leading to the extracellular efflux of taxane. These results suggested that chemotherapy-induced CCL20 mediated chemoresistance via up-regulating ABCB1. In addition, NF-κB activation increased CCL20 expression, forming a positive feedback loop between NF-κB and CCL20 pathways, which provides sustained impetus for chemoresistance in breast cancer cells. Our results suggest that CCL20 can be a novel predictive marker for taxane response, and the blockade of CCL20 or its downstream pathway might reverse the taxane resistance in breast cancer patients.
    Print ISSN: 1544-9173
    Electronic ISSN: 1545-7885
    Topics: Biology
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    Bayesian comparison of explicit and implicit causal inference strategies in multisensory heading perception (2018)
    Public Library of Science (PLoS)
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    Publication Date: 2018-07-28
    Description: by Luigi Acerbi, Kalpana Dokka, Dora E. Angelaki, Wei Ji Ma The precision of multisensory perception improves when cues arising from the same cause are integrated, such as visual and vestibular heading cues for an observer moving through a stationary environment. In order to determine how the cues should be processed, the brain must infer the causal relationship underlying the multisensory cues. In heading perception, however, it is unclear whether observers follow the Bayesian strategy, a simpler non-Bayesian heuristic, or even perform causal inference at all. We developed an efficient and robust computational framework to perform Bayesian model comparison of causal inference strategies, which incorporates a number of alternative assumptions about the observers. With this framework, we investigated whether human observers’ performance in an explicit cause attribution and an implicit heading discrimination task can be modeled as a causal inference process. In the explicit causal inference task, all subjects accounted for cue disparity when reporting judgments of common cause, although not necessarily all in a Bayesian fashion. By contrast, but in agreement with previous findings, data from the heading discrimination task only could not rule out that several of the same observers were adopting a forced-fusion strategy, whereby cues are integrated regardless of disparity. Only when we combined evidence from both tasks we were able to rule out forced-fusion in the heading discrimination task. Crucially, findings were robust across a number of variants of models and analyses. Our results demonstrate that our proposed computational framework allows researchers to ask complex questions within a rigorous Bayesian framework that accounts for parameter and model uncertainty.
    Print ISSN: 1553-734X
    Electronic ISSN: 1553-7358
    Topics: Biology , Computer Science
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