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Abstract: A simple k–ε turbulence closure is introduced which has no stability functions but instead a Richardson number-dependent turbulent Prandtl number. Its free parameters are determined in a comparison with microstructure observations from a stratified and sheared tidal estuary and laboratory measurements. The closure is able to simulate observed turbulent dissipation rates (ε) and turbulent length scales (l th) in regions of strong mean shear and small gradient Richardson number (R g) to within factors of 2–3. It fails in regions of small shear and large R g, presumably because of the dominance of internal wave-driven mixing. Additional simulations with a k–ε closure with stability functions taken from Canuto et al. [Canuto, V.M., Howard, A., Cheng, Y., Dubovikov, M.S., 2001. Ocean turbulence I: one-point closure model. Momentum and heat vertical diffusivities. J. Phys. Oceanogr. 31, 1413–1426] and with the closure of Baumert and Peters [Baumert, H., Peters, H., 2004. Turbulence closure, steady state, and collapse into waves. J. Phys. Oceanogr. 34, 505–512] show poor performance. Establishing a valid 1:1 comparison of simulated and observed ε and l th requires nudging the model velocity and density toward observed values because free model integrations quickly diverge from the observations. Steady state gradient Richardson numbers are constrained to a range of 0.18–0.25, while flux Richardson numbers are constrained to the range of 0.1–0.22. The closure output is rather insensitive to such parameter variations. The simulations are sensitive, however, to the treatment of the observed velocity and density used to nudge the model. Good closure performance requires averaging the measured tidal flow over about an hour, a time scale for which conventional numerical models of estuarine circulations should be able to match observed shears. In the closure simulations the TKE balance stays close to a production–dissipation balance. The time rate of change and vertical diffusion of TKE are small, of the same order of magnitude, and vary in magnitude relative to each other systematically across the water column. [Copyright &y& Elsevier]

Summary: Aims: The hereditary occurrence of cherubism indicates a probable genetic aetiology: a correlation with a mutation in the gene SH3BP2 has been demonstrated. A convincing concept of formal pathogenesis is not yet available. The study was aimed at advancing the understanding of the pathogenesis of cherubism by presenting a case study including genetic findings and an evaluation of the literature. Results and conclusion: Because of its association with the development of the second and third molars, cherubism could be defined as a genetically determined alteration of tooth development. In this context, disturbed PTHrP – PTHrP receptor interaction induced by the mutation in SH3BP2 is discussed. The temporal and spatial determination of the clinical symptoms is explained by an interaction of SH3BP2-dependent signal transduction pathways with jaw morphogenesis (e.g. Hox-gene Msx-1). Because of the disease-induced lack of determination of the cap phase of the second and third molar, a spatial compartmentation, which is necessary for normal dental development, does not take place. This leads to dysregulation of mesenchymal bone building tissue areas, and to the development of giant cell granulomas with high osteoclastic activity. Because of the genetic determination of cherubism and the associated dedifferentiation of the diseased tissue, a surgical removal should be exclusively restricted to specific indications. Therefore an attitude of wait and see is preferred. [Copyright &y& Elsevier]

Abstract: The overflows of cold, heavy waters from the Nordic Seas across the Greenland–Iceland–Scotland Ridges are simulated using the Hybrid Coordinate Model in a North Atlantic configuration. Results at three different horizontal model resolutions are compared to each other, to recent hydrographic sections and moored observations. Simulations in the finest grid employed, 1/12° resolution, show realistic overflow pathways, reasonable overflow and Deep Western Boundary Current mean velocities and transports, and overall reasonable North Atlantic three-dimensional temperature and salinity fields, namely the Atlantic Meridional Overturning Circulation (AMOC). In contrast, simulations at coarser grids of 1/3° and 1° resolution exhibit a range of significant problems owing to unresolved, dynamically vital features in the seafloor topography. This lack of resolution, for example of the Faroe Bank Channel, leads to unrealistic overflow pathways between Iceland and Scotland in the 1/3° and 1° cases. Accordingly, overflow mass transports are also unrealistic in this area. In the Denmark Strait Overflow the underlying topographical scales are larger, and pathways are reasonable even at coarse resolution. However, overflow speeds are too small in the 1/3° and 1° cases. Underestimated velocities in the 1° simulations are compensated by an overestimated sill cross-section, whereas it is too small in 1/3°. As such, the 1/3° and 1° simulations show both large under- and overestimations of volume transport at several locations. No significant improvement in modeled overflows takes place when the grid spacing is decreased from 1° to 1/3°. An experiment conducted with hand-tuned topography shows improved volume transports near the regions of modification, but somewhat increased errors in other parts of the deep circulation, indicating the complex response of the system to perturbations in bathymetry. These results demonstrate the importance of an accurate representation of the domain geometry, in particular the channels of the complex Iceland–Scotland ridge system, in order to reproduce the pathways of the deep AMOC. [Copyright &y& Elsevier]

Abstract: Mixing of overflows released from polar and marginal seas is a key process shaping the structure of the meridional overturning circulation. Ocean general circulation models have difficulty in resolving the overflows, and therefore they must rely on parameterizations. In this study, the performance of a set of turbulence closures in reproducing mixing of an overflow is quantified. We simulate the Red Sea overflow by employing standard k–ε, k–ω and Mellor–Yamada schemes with various stability functions, as well as a modified k–ε model that relies on the prescription of the turbulent Prandtl number rather than on stability functions. The simpler KPP mixing scheme and experiments without turbulent fluxes serve as useful references. To our knowledge, this is the first time that the performance of two-equation turbulence models has been examined so closely using data from an overflow. It is found that without turbulence closures, the hydrodynamic model has difficulty in reproducing the correct three-dimensional pathway of the Red Sea overflow, consisting of a distinct bifurcation into two diverging channels. All turbulence models capture the vertical structure of this overflow consisting of an interfacial layer, characterized by the density gradient, and a well-mixed bottom layer. Mean eddy diffusivity values from most closures are comparable those from observations. But we find that KPP leads to eddy diffusivity values that are too small while those from Mellor–Yamada with Galperin [Galperin, B., Kantha, L.H., Hassid, S., Rosati, A., 1988. A quasi-equilibrium turbulent energy model for geophysical flows. J. Atmos. Sci. 45, 55–62] stability functions are too large. Such high diffusivities lead to excessive mixing in the bottom layer of the overflow, ultimately resulting in a salinity deficit of approximately 1psu in the product water mass. Salinity deviations between the models and observations are quantified using both data taken along the channels and two sections across the overflow. KPP and Mellor–Yamada with Galperin (1988) stability functions produce the largest deviations from the observations, while the modified k–ε exhibits the smallest deviations. The other four closures fall in between, showing results similar to one another. The performance of the Mellor–Yamada turbulence closure is improved considerably by using the stability functions by Kantha and Clayson [Kantha, L.H., Clayson, C.A., 1994. An improved mixed layer model for geophysical applications. J. Geophys. Res. 99 (December), 25235–25266], which allow for a stationary Richardson number of 0.21. In conclusion, we find that most turbulence closures lead to a satisfactory reproduction of the Red Sea overflow, within the temporal and spatial sampling uncertainties of the REDSOX data, provided that fairly high-resolution regional models are used. [Copyright &y& Elsevier]

Abstract: Mixing between overflows and ambient water masses is a critical problem of deep-water mass formation in the downwelling branch of the meridional overturning circulation of the ocean. Modeling approaches that have been tested so far rely either on algebraic parameterizations in hydrostatic ocean circulation models, or on large eddy simulations that resolve most of the mixing using nonhydrostatic models. In this study, we examine the performance of a set of turbulence closures, that have not been tested in comparison to observational data for overflows before. We employ the so-called very large eddy simulation (VLES) technique, which allows the use of models in nonhydrostatic models. This is done by applying a dynamic spatial filtering to the equations. To our knowledge, this is the first time that the VLES approach is adopted for an ocean modeling problem. The performance of and VLES models are evaluated by conducting numerical simulations of the Red Sea overflow and comparing them to observations from the Red Sea Outflow Experiment (REDSOX). The computations are constrained to one of the main channels transporting the overflow, which is narrow enough to permit the use of a two-dimensional (and nonhydrostatic) model. A large set of experiments are conducted using different closure models, Reynolds numbers and spatial resolutions. It is found that, when no turbulence closure is used, the basic structure of the overflow, consisting of a well-mixed bottom layer (BL) and entraining interfacial layer (IL), cannot be reproduced. The model leads to unrealistic thicknesses for both BL and IL, while VLES results in the most realistic reproduction of the REDSOX observations. [Copyright &y& Elsevier]

Abstract: Building on the work by Turner [Turner, J.S., 1986. The development of the entrainment assumption and its application to geophysical flows. J. Fluid Mech. 173, 431–471] and Hallberg [Hallberg, R., 2000. Time integration of diapycnal diffusion and Richardson number dependent mixing in isopycnal coordinate ocean models. Mon. Weather Rev. 128, 1402–1419], an algebraic parameterization of the entrainment process in gravity current has been derived for isopycnic coordinate ocean models. It casts the entrainment into layers as a function of the layer Richardson number (Ri) times the velocity difference across layers. In order to determine the function f(Ri), simulations of generic gravity currents over various bottom slope angle are conducted with the HYbrid Coordinate Ocean Model (HYCOM) and compared to similar experiments with the high-resolution, three-dimensional, nonhydrostatic model Nek5000, which serves as ground truth. A simple linear function, E =0.20(1− Ri/0.25), is found to reproduce quite well the entrainment, salt flux, Richardson number, velocity profile and plume propagation speed in Nek5000. The parameterization is then applied to a realistic-topography simulation of the Mediterranean outflow with HYCOM and shown to produce realistic equilibration depth and water mass properties of the outflow plume. [Copyright &y& Elsevier]

The Mediterranean Water leaves the western end of the Strait of Gibraltar as a bottom wedge of salty and warm waters flowing down the continental slope. The salinity of the onset Mediterranean Outflow Water (MOW) is so high that leads to water much denser (initially in excess of 1.5 kg m −3 ) than the overlying central waters. During much of its initial descent, the MOW retains large salinity anomalies – causing density anomalies that induce its gravity current character – and relatively high westward speeds – causing a substantial Coriolis force over long portions of its course. We use hydrographic data from six cruises (a total of 1176 stations) plus velocity data from two cruises, together with high-resolution bathymetric data, to track the preferential MOW pathways from the Strait of Gibraltar into the western Gulf of Cadiz and to examine the relation of these pathways to the bottom topography. A methodology for tributary systems in drainage basins, modified to account for the Coriolis force, emphasizes the good agreement between the observed trajectories and those expected from a topographically-constrained flow. Both contour avenues and cross-slope channels are important and have complementary roles steering the MOW along the upper and middle continental slope before discharging as a neutrally buoyant flow into the western Gulf of Cadiz. Our results show that the interaction between bottom flow and topography sets the path and final equilibrium depths of the modern MOW. Furthermore, they support the hypothesis that, as a result of the high erosive power of the bottom flow and changes in bottom-water speed, the MOW pathways and mixing rates have changed in the geological past. [ABSTRACT FROM AUTHOR]

Amelogenesis imperfecta (AI) is a clinically and genetically heterogeneous disorder of tooth development which is due to aberrant deposition or composition of enamel. Both syndromic and isolated forms exist; they may be inherited in an X-linked, autosomal recessive, or autosomal dominant manner. WDR72 is one of ten currently known genes for recessive isolated AI; nine WDR72 mutations affecting single nucleotides have been described to date. Based on whole exome sequencing in a large consanguineous AI pedigree, we obtained evidence for presence of a multi-exonic WDR72 deletion. A home-made multiplex ligation-dependent probe amplification assay was used to confirm the aberration, to narrow its extent, and to identify heterozygous carriers. Our study extends the mutational spectrum for WDR72 to include large deletions, and supports a relevance of the previously proposed loss-of-function mechanism. It also introduces an easy-to-use and highly sensitive tool for detecting WDR72 copy number alterations. [ABSTRACT FROM AUTHOR]

Abstract: In light of the pressing need for development and testing of reliable parameterizations of gravity current entrainment in ocean general circulation models, two existing entrainment parameterization schemes, K-profile parameterization (KPP) and one based on Turner’s work (TP), are compared using idealized experiments of dense water flow over a constant-slope wedge using the HYbrid Coordinate Ocean Model (HYCOM). It is found that the gravity current entrainment resulting from KPP and TP differ significantly from one another. Parameters of KPP and TP are then calibrated using results from the high-order nonhydrostatic spectral element model Nek5000. It is shown that a very good agreement can be reached between the HYCOM simulations with KPP and TP, even though these schemes are quite different from each other. [Copyright &y& Elsevier]