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Yezo virus (YEZV), in the order Bunyavirales, family Nairoviridae, genus Orthonairovirus, possesses a negative-sense single-stranded RNA genome comprising 3 segments: large (L), medium (M), and small (S) (1). Each segment [...]

Background: Previously, MDR1 T-129C polymorphism, encoding multidrug resistant transporter MDR1/P-glycoprotein, was reported to be predictive of poorly-differentiated colorectal adenocarcinomas. Here, VEGF T-1498C, C-634G and C-7T polymorphisms, encoding vascular endothelial growth factor (VEGF), were investigated in terms of their association with differentiation grade. Methods: VEGF genotypes were determined by TaqManR MGB probe based polymerase chain reaction and evaluated were confirmed by direct sequencing in 36 Japanese patients. Results: VEGF T-1498C, but not C-634G or C-7T, was predictive of poorly-differentiated ones, and thereby a poor prognosis (p = 0.064 for genotype, p = 0.037 for allele), and this effect can be explained by that on VEGF expression. Treatment of a colorectal adenocarcinoma cell line, HCT-15, with sodium butyrate, a typical differentiating agent, resulted in an increase of alkaline phosphatase activity and MDR1 mRNA expression, but in a decrease of VEGF mRNA expression. The transfection of VEGF small interfering RNA (siRNA) induced the expression of MDR1 mRNA to 288-332% of the control level, whereas MDR1 siRNA had no effect on VEGF mRNA expression. Conclusions: VEGF T-1498C polymorphism is also a candidate marker predictive of poorly-differentiated colorectal adenocarcinomas, but further investigations with a large number of patients should be addressed to draw a conclusion.

A diagnostic relationship between finite-amplitude wave activity and the associated adiabatic adjustments to the zonal-mean zonal wind and temperature is developed in the quasigeostrophic (QG) framework and is applied to a 23-yr segment (1979-2001) of the 40-yr ECMWF Re-Analysis (ERA-40) data. Wave activity is defined in terms of an instantaneous areal displacement of QG potential vorticity (PV) from zonal symmetry. Unlike previous forms, the tendency of wave activity equals exactly the negative of the eddy PV flux (Eliassen--Palm flux divergence) in the conservative limit, even at finite amplitude. This allows one to integrate the transformed Eulerian mean (TEM) theory in time and quantify the departure (adiabatic adjustment) of the zonal-mean state from an eddy-free reference state in terms of the observed wave activity. The structure of wave activity identifies synoptic eddies in the extratropics and planetary waves in the high latitudes of winter-to-spring stratosphere. In addition, a thin layer of high wave activity is found at the top of the lowermost stratosphere (~17 km) in the summer extratropics. The reference state is constructed by 'zonalizing' the PV contours conservatively (preserving area) on the isobaric surface and by inverting the resultant PV gradient for the mean flow. The adjustment associated with wave activity depends on the assumed surface boundary condition for the reference state. With a no-slip condition, the observed zonal-mean temperature is on average ~33 (90) K higher than the reference state in the troposphere (stratosphere) of the Arctic winter, while the zonal-mean zonal wind is ~30 m [s.sup.-1] slower in the upper stratosphere. Since the reference state filters out the advective eddy-mean flow interaction, it fluctuates less than the zonal-mean state, potentially improving the signal-to-noise ratio for climate diagnosis. DOI: 10.1175/2010JAS3503.1

An exact diagnostic formalism for finite-amplitude eddy--mean flow interaction is developed for barotropic and quasigeostrophic baroclinic flows on the beta plane. Based on the advection--diffusion--reaction equation for potential vorticity (PV), the formalism quantifies both advective and diffusive contributions to the mean flow modification by eddies, of which the latter is the focus of the present article. The present theory adopts a hybrid Eulerian--Lagrangian-mean description of the flow and defines finite-amplitude wave activity in terms of the areal displacement of PV contours from zonal symmetry. Unlike previous formalisms, wave activity is readily calculable from data and the local Eliassen---Palm relation does not involve cubic or higher-order terms in eddy amplitude. This leads to a natural finite-amplitude extension to the local nonacceleration theorem, as well as the global stability theorems, in the inviscid and unforced limit. The formalism incorporates mixing with effective diffusivity of PV, and the diffusive flux of PV is shown to be a sink of wave activity. The relationship between the advective and diffusive fluxes of PV and its implications for parameterization are discussed in the context of wave activity budget. If all momentum associated with wave activity were returned to the zonal-mean flow, a balanced eddy-free flow would ensue. It is shown that this hypothetical flow [u.sub.REF] is unaffected by the advective PV flux and is driven solely by the diffusive PV flux and forcing. For this reason, [u.sub.REF], rather than the zonal-mean flow, is proposed as a diagnostic for the diffusive mean-flow modification. The formalism is applied to a freely decaying beta-plane turbulence to evaluate the contribution of the diffusive PV flux to the jet formation. DOI: 10.1175/2010JAS3432.1

Formation of multiple jets in forced beta-plane turbulence is studied from the perspective of nonuniform nonconservative arrangement of potential vorticity (PV). Numerical simulations are analyzed to show that mixing and forcing reinforce jets by concentrating PV gradients at the axes of prograde jets. Based on the formalism developed in the companion paper, the nonconservative driving of jets is diagnosed and parameterized through the diffusive flux of PV and the source of wave activity. It is found that the two terms nearly balance on a long time scale, and they are both strongly anticorrelated with the PV gradient, which suggests that PV controls the nonconservative processes and that these processes could be parameterized as functions of the PV gradient. The flux is modeled using the effective diffusivity formula recently obtained by Ferrari and Nikurashin. Consistent with the PV barrier concept, the nonlinear diffusivity is a decreasing function of the squared PV gradient and agrees well with the diffusivity diagnosed from the numerical simulation. The source term is assumed to be inversely proportional to the PV gradient. The parameterization gives rise to a nonlinear partial differential equation (PDE) for the mean flow. A finite-difference model of the PDE predicts formation of a piecewise linear PV (staircase) and piecewise parabolic jets from a near-uniform initial condition when anisotropy and mixing of the flow are sufficiently strong. The origin of the discontinuities is antidiffusive instability of PV gradients, and although nonlinearity allows the discrete model to integrate stably, the solution is sensitive to the initial condition and resolution. The emerging jets in the 1D model have similar characteristics to those in the numerical simulation, but the details of the transient behavior are distinct. Similar discrete models of ill-posed PDEs in which discontinuities form also appear in image processing and granular matter dynamics. DOI: 10.1175/2009JAS3159.1

Effects of isolated transport barriers on the global mixing and fluxes of a tracer are investigated, where a barrier is defined as a local minimum in effective diffusivity. An idealized 1D model with a prescribed diffusivity profile, with or without forcing, is used to show that the structure, flux, and decay rates of the tracer are all very sensitive to the barrier geometry, particularly when it is deep and narrow. Although the tracer gradients and the variance dissipation are concentrated to the barrier region, the flux shows a more global response to the barrier, decreasing everywhere. The harmonic mean of effective diffusivity is proposed as a useful first-order predictor of the global transport. This 1D model is used to diagnose the isentropic transport in the upper troposphere and lower stratosphere with offline transport calculations driven by the Met Office winds. The global tracer variance in these calculations decays approximately exponentially, and the time-mean decay rate and tracer structure are well captured by the gravest 1D eigenmode with the time-averaged effective diffusivity. However, the decay rate and the flux of the full solution are 15%-20% smaller than those of the eigenmode because of a negative temporal correlation between the effective diffusivity and the gradient. The vertical and decadal variations of the decay rates are consistent with the corresponding variations in the harmonic mean effective diffusivity. To the extent that the global mixing is sensitive to the local barrier properties, and to the extent that the latter are sensitive to the errors in advecting winds and model numerics, modeling of global atmospheric transport remains a challenge. This may explain, at least partially, the disparate model estimates reported in the literature.

Effective diffusivity calculated from a scalar field that obeys the advection-diffusion equation has proved useful for estimating the permeability of unsteady boundaries of air masses such as the edge of the stratospheric polar vortex and the extratropical tropopause. However, the method does not discriminate the direction of transport--whereas some material crosses the boundary from one side to the other, some material does so in the other direction--yet the extant method concerns only the net transport. In this paper, the diagnostic is extended to allow partitioning of fluxes of mass and tracer into opposing directions. This is accomplished by discriminating the regions of 'inward' and ''outward' wave breaking with the local curvature of the tracer field. The utility of the new method is demonstrated for nonlinear Kelvin-Helmholtz instability and Rossby wave breaking in the stratosphere using a numerically generated tracer. The method successfully quantifies two-way transport and hence the direction of wave breaking--the predominantly equatorward breaking of Rossby waves in the extratropical middle stratosphere, for example. Isolated episodes of mixing are identified well, particularly by the mass flux that primarily arises from the tracer filaments. Comparison of different transport schemes suggests that the results are reasonably robust under a varying subgrid representation of the model.

Area equivalent latitude based on potential vorticity (PV) is a widely used diagnostic for isentropic transport in the stratosphere and upper troposphere. Here, an alternate method for calculating equivalent latitude is explored, namely, a numerical synthesis of a PV-like tracer from a long-term integration of the advection-diffusion equation on isentropic surfaces. It is found that the tracer equivalent latitude (TrEL) behaves much like the traditional PV equivalent latitude (PVEL) despite the simplified governing physics; this is evidenced by examining the kinematics of the Arctic lower stratospheric vortex. Yet in some cases TrEL performs markedly better as a coordinate for long-lived trace species such as ozone. These instances include analysis of lower tratospheric ozone during the Stratospheric Aerosol and Gas Experiment (SAGE) III Ozone Loss and Validation Experiment (SOLVE) campaign and three-dimensional reconstruction of total column ozone during November-December 1999 from fitted ozone-equivalent latitude relationship. It is argued that the improvement is due to the tracer being free from the diagnostic errors and certain diabatic processes that affect PV. The sensitivity of TrEL to spatial and temporal resolution, advection scheme, and driving winds is also examined.

It is shown that the Eulerian-mean advection-diffusion equation for a passive tracer, q, can be cast, uniquely and exactly into [delta]/[delta]t[bar]q + [gradient] * ([bar][v.sup.*][bar]q) = [gradient] * ([K.sup.*] [gradient] [bar]q), where the bar denotes an arbitrary Eulerian average (spatial, temporal, or both), [[bar]v.sup.*] is a nondivergent effective transport velocity, and [K.sup.*] is a scalar that varies in space and time. Furthermore, [K.sup.*] = [K.sub.k] + [K.sub.m], where [K.sub.k] represents (possibly nonlocal) along-gradient dispersion of tracer isosurface, whereas [K.sub.m] = D[bar]|[gradient]q[|.sup.2]/|[gradient][bar]q[|.sup.2] [greater than or equal to] D represents local mixing due to diffusion at unresolved scales (D) amplified by resolved (but averaged) fluid dynamical stirring. The amplifying factor, [bar]|[gradient]q[|.sup.2]/|[gradient][bar]q[|.sup.2] measures local roughness of tracer field and determines the spatiotemporal structure of [K.sub.m]. This factor is called 'mixing efficiency' and it is proposed as a diagnostic of mixing. The mixing efficiency diagnostic is demonstrated using potential vorticity and nitrous oxide from the outputs of the Geophysical Fluid Dynamics Laboratory (GFDL) SKYHI general circulation model (GCM) analyzed on the 320-K isentropic surface for the month of March. It is found that mixing is severely suppressed along the jet axes at the midlatitude tropopause with marked zonal localization in the Northern Hemisphere. The formalism's relationship to the previously derived modified Lagrangian-mean theory is also discussed.

An efficient solution procedure is developed for a nonseparable semigeostrophic Eady problem on a semi-infinite f plane. A model is designed to study the effects of meridionally isolated jets and tropopause morphology on baroclinic instability. Potential vorticity (PV) is assumed to be piecewise constant and discontinuous at the tropopause, whose height is allowed to vary with latitude. The computational domain is discretized in a stretched coordinate to maintain adequate resolution in the vicinity of the tropopause and axis of the jet. The basic state is numerically inverted from the two PV values with the specification of only the meridional profiles of potential temperature (PT) at the surface and (unspecified) tropopause height. The nonseparable eigenvalue problem about this basic state is solved for the discrete (zero-PV) normal modes. Since continuum modes are not sought, the size of the problem is reduced greatly, keeping the storage and CPU requirements moderate even at relatively high spatial resolutions. This model is used to investigate changes in the zonal-mean state and the stability thereof, in response to arrangements of the zonal-mean PT at the surface and tropopause. In particular, (a) partial mixing of surface PT and (b) appearance of a local minimum of PT on the tropopause are considered as models of baroclinic adjustment and tropopause folds, respectively. The former renders the mean flow more barotropic and shifts up the zonal scale of baroclinic instability. The latter gives rise to a markedly dipped tropopause that is barotropically unstable at various ranges of wavenumbers. The results' implications on the life cycle simulations and roll-up of stratospheric intrusions are discussed.

Two-dimensional mixing of a tracer is diagnosed using A, the area between the tracer contour and a reference contour, as the horizontal coordinate. In the absence of sources or sinks, the tracer distribution in the area coordinate is governed by [Mathematical Expression Omitted], where [Mathematical Expression Omitted] is the square of the equivalent length of the tracer contour and k is the constant microscale diffusion coefficient. While diffusion is necessary to invoke transport, the large-scale kinematics regulates the evolution of q through the stretching and redistribution of ??. It is argued that ??, is a useful, easy to compute diagnostic for irreversible transport, especially for identifying a barrier. Typical behaviors of ?? in various flow regimes are illustrated using the numerically simulated Kelvin-Helmholtz billow. Signature of mixing is found in the irreversible growth of ??, but the precise time dependence is complex due to interplay between advection and diffusion. Formation of the edges (concentrated gradients) and their permeability to mass are addressed using a kinematic model with prescribed ??. Relevance of this model to the stratospheric polar vortex, midlatitude tropopause, and oceanic thermocline is discussed.

An exact, two-dimensional (height-latitude type) diagnostic model of tracer transport in the stratosphere is formulated. The model is a generalization of the area analysis method devised by Butchart and Remsberg but uses the mass element enclosed by the contours of a quasi-conservative tracer on a given isentropic surface as a 'meridional' coordinate. This modified Lagrangian-mean coordinate is transparent to the advective effects of the winds, and thus unambiguously extracts the nonconservative effects on the tracer distribution. The derived transport equation takes an equivalent advective form; that is, the tracer contours are 'advected' by the mean nonconservative mass flow while there are no 'eddy flux' contributions. Hence, the mass flux is implied in the motion of the tracer contours. Not only is this model conceptually simple, it is also computationally economical for analyzing large, high-resolution datasets since time averaging can be omitted to define a robust mean field of the tracer. The model is used to diagnose the [N.sub.2]O mixing ratio and potential vorticity simulated in the high-resolution, Geophysical Fluid Dynamics Laboratory SKYHI GCM. The analysis not only identifies the boundary of the polar vortex better than the Eulerian zonal-mean models but highlights how the nonconservative processes (diabatic heating and friction) contribute to the formation of the vortex edge. It also reveals the different kinematics for potential vorticity and chemical tracers.