Angular momentum transport modeling: achievements of a gyrokinetic quasi-linear approach

QuaLiKiz, a model based on a local gyrokinetic eigenvalue solver is expanded to include momentum flux modeling in addition to heat and particle fluxes. Essential for accurate momentum flux predictions, the parallel asymmetrization of the eigenfunctions is successfully recovered by an analytical fluid model. This is tested against self-consistent gyrokinetic calculations and allows for a correct prediction of the ExB shear impact on the saturated potential amplitude by means of a mixing length rule. Hence, the effect of the ExB shear is recovered on all the transport channels including the induced residual stress. Including these additions, QuaLiKiz remains ~10 000 faster than non-linear gyrokinetic codes allowing for comparisons with experiments without resorting to high performance computing. The example is given of momentum pinch calculations in NBI modulation experiments

Segmentation of epidermal tissue with histopathological damage in images of haematoxylin and eosin stained human skin.

Background: Digital image analysis has the potential to address issues surrounding traditional histological techniques including a lack of objectivity and high variability, through the application of quantitative analysis. A key initial step in image analysis is the identification of regions of interest. A widely applied methodology is that of segmentation. This paper proposes the application of image analysis techniques to segment skin tissue with varying degrees of histopathological damage. The segmentation of human tissue is challenging as a consequence of the complexity of the tissue structures and inconsistencies in tissue preparation, hence there is a need for a new robust method with the capability to handle the additional challenges materialising from histopathological damage.Methods: A new algorithm has been developed which combines enhanced colour information, created following a transformation to the L*a*b* colourspace, with general image intensity information. A colour normalisation step is included to enhance the algorithm's robustness to variations in the lighting and staining of the input images. The resulting optimised image is subjected to thresholding and the segmentation is fine-tuned using a combination of morphological processing and object classification rules. The segmentation algorithm was tested on 40 digital images of haematoxylin & eosin (H&E) stained skin biopsies. Accuracy, sensitivity and specificity of the algorithmic procedure were assessed through the comparison of the proposed methodology against manual methods.Results: Experimental results show the proposed fully automated methodology segments the epidermis with a mean specificity of 97.7%, a mean sensitivity of 89.4% and a mean accuracy of 96.5%. When a simple user interaction step is included, the specificity increases to 98.0%, the sensitivity to 91.0% and the accuracy to 96.8%. The algorithm segments effectively for different severities of tissue damage.Conclusions: Epidermal segmentation is a crucial first step in a range of applications including melanoma detection and the assessment of histopathological damage in skin. The proposed methodology is able to segment the epidermis with different levels of histological damage. The basic method framework could be applied to segmentation of other epithelial tissues

Diagnostic yield of next-generation sequencing in very early-onset inflammatory bowel diseases: a multicenter study (vol 12, pg 1104, 2021)

Transplantation and immunomodulatio

Stable and unstable roots of ion temperature gradient driven mode using curvature modified plasma dispersion functions

Basic, local kinetic theory of ion temperature gradient driven (ITG) mode, with adiabatic electrons is reconsidered. Standard unstable, purely oscillating as well as damped solutions of the local dispersion relation are obtained using a bracketing technique that uses the argument principle. This method requires computing the plasma dielectric function and its derivatives, which are implemented here using modified plasma dispersion functions with curvature and their derivatives, and allows bracketing/following the zeros of the plasma dielectric function which corresponds to different roots of the ITG dispersion relation. We provide an open source implementation of the derivatives of modified plasma dispersion functions with curvature, which are used in this formulation. Studying the local ITG dispersion, we find that near the threshold of instability the unstable branch is rather asymmetric with oscillating solutions towards lower wave numbers (i.e. drift waves), and damped solutions toward higher wave numbers. This suggests a process akin to inverse cascade by coupling to the oscillating branch towards lower wave numbers may play a role in the nonlinear evolution of the ITG, near the instability threshold. Also, using the algorithm, the linear wave diffusion is estimated for the marginally stable ITG mode

Generalized curvature modified plasma dispersion functions and Dupree renormalization of toroidal ITG

A new generalization of curvature modified plasma dispersion functions is introduced in order to express Dupree renormalized dispersion relations used in quasi-linear theory. For instance the Dupree renormalized dispersion relation for gyrokinetic, toroidal ion temperature gradient driven (ITG) modes, where the Dupree's diffusion coefficient is assumed to be a low order polynomial of the velocity, can be written entirely using generalized curvature modified plasma dispersion functions: K-nm's. Using those, Dupree's formulation of renormalized quasi-linear theory is revisited for the toroidal ITG mode. The Dupree diffusion coefficient has been obtained as a function of velocity using an iteration scheme, first by assuming that the diffusion coefficient is constant at each v (i.e. applicable for slow dependence), and then substituting the resulting v dependence in the form of complex polynomial coefficients into the K-nm's for verification. The algorithm generally converges rapidly after only a few iterations. Since the quasi-linear calculation relies on an assumed form for the wave-number spectrum, especially around its peak, practical usefulness of the method is to be determined in actual applications. A parameter scan of eta(i) shows that the form of the diffusion coefficient is better represented by the polynomial form as eta(i) is increased

Turbulent Equipartition Theory of Toroidal Momentum Pinch

The mode-independet part of magnetic curvature driven turbulent convective (TuroCo) pinch of the angular momentum density [Hahm et al., Phys. Plasmas 14,072302 (2007)] which was originally derived from the gyrokinetic equation, can be interpreted in terms of the turbulent equipartition (TEP) theory. It is shown that the previous results can be obtained from the local conservation of "magnetically weighted angular momentum density," nmi U|| R⁄B2, and its homogenization due to turbulent flows. It is also demonstrated that the magnetic curvature modification of the parallel acceleration in the nonlinear gyrokinetic equation in the laboratory frame, which was shown to be responsible for the TEP part of the TurCo pinch of angular momentum density in the previous work, is closely related to the Coriolis drift coupling to the perturbed electric field. In addition, the origin of the diffusive flux in the rotating frame is highlighted. Finally, it is illustratd that there should be a difference in scalings between the momentum pinch originated from inherently toroidal effects and that coming from other mechanisms which exist in a simpler geometry

Symmetry breaking effects of density gradient on parallel momentum transport: A new ρ* effect

Symmetry breaking effects of density gradient on parallel momentum transport is studied via quasilinear theory. It is shown that finite (equivalent to rho(s)/L-n), where rho(s) is ion sound radius and L-n is density scale length, leads to symmetry breaking of the ion temperature gradient (ITG) eigenfunction. This broken symmetry persists even in the absence of mean poloidal (from radial electric field shear) and toroidal flows. This effect, as explained in the text, originates from the divergence of polarization particle current in the ion continuity equation. The form of the eigenfunction allows the microturbulence to generate parallel residual stress via symmetry breaking. Comparison with the (E) over right arrow x (B) over right arrow shear driven parallel residual stress, parallel polarization stress and turbulence intensity gradient driven parallel residual stress are discussed. It is shown that this rho(s)* driven parallel residual stress may become comparable to (E) over right arrow x (B) over right arrow shear driven parallel residual stress in small L-n region. In the regular drift wave ordering, where rho(s)