On the Sensitivity of 3-D Thermal Convection Codes to Numerical Discretization: A Model Intercomparison

Fully 3-D numerical simulations of thermal convection in a spherical shell have become a standard for studying the dynamics of pattern formation and its stability under perturbations to various parameter values. The question arises as to how does the discretization of the governing equations affect the outcome and thus any physical interpretation. This work demonstrates the impact of numerical discretization on the observed patterns, the value at which symmetry is broken, and how stability and stationary behavior is dependent upon it. Motivated by numerical simulations of convection in the Earth\u27s mantle, we consider isoviscous Rayleigh-Bénard convection at infinite Prandtl number, where the aspect ratio between the inner and outer shell is 0.55. We show that the subtleties involved in development mantle convection models are considerably more delicate than has been previously appreciated, due to the rich dynamical behavior of the system. Two codes with different numerical discretization schemes: an established, community-developed, and benchmarked finite element code (CitcomS) and a novel spectral method that combines Chebyshev polynomials with radial basis functions (RBF) are compared. A full numerical study is investigated for the following three cases. The first case is based on the cubic (or octahedral) initial condition (spherical harmonics of degree ℓ =4). How variations in the behavior of the cubic pattern to perturbations in the initial condition and Rayleigh number between the two numerical discrezations is studied. The second case investigates the stability of the dodecahedral (or icosahedral) initial condition (spherical harmonics of degree ℓ = 6). Although both methods converge first to the same pattern, this structure is ultimately unstable and systematically degenerates to cubic or tetrahedral symmetries, depending on the code used. Lastly, a new steady state pattern is presented as a combination of order 3 and 4 spherical harmonics leading to a five cell or a hexahedral pattern and stable up to 70 times the critical Rayleigh number. This pattern can provide the basis for a new accuracy benchmark for 3-D spherical mantle convection codes

FGF receptor genes and breast cancer susceptibility: results from the Breast Cancer Association Consortium

Background:Breast cancer is one of the most common malignancies in women. Genome-wide association studies have identified FGFR2 as a breast cancer susceptibility gene. Common variation in other fibroblast growth factor (FGF) receptors might also modify risk. We tested this hypothesis by studying genotyped single-nucleotide polymorphisms (SNPs) and imputed SNPs in FGFR1, FGFR3, FGFR4 and FGFRL1 in the Breast Cancer Association Consortium. Methods:Data were combined from 49 studies, including 53 835 cases and 50 156 controls, of which 89 050 (46 450 cases and 42 600 controls) were of European ancestry, 12 893 (6269 cases and 6624 controls) of Asian and 2048 (1116 cases and 932 controls) of African ancestry. Associations with risk of breast cancer, overall and by disease sub-type, were assessed using unconditional logistic regression. Results:Little evidence of association with breast cancer risk was observed for SNPs in the FGF receptor genes. The strongest evidence in European women was for rs743682 in FGFR3; the estimated per-allele odds ratio was 1.05 (95 confidence interval=1.02-1.09, P=0.0020), which is substantially lower than that observed for SNPs in FGFR2. Conclusion:Our results suggest that common variants in the other FGF receptors are not associated with risk of breast cancer to the degree observed for FGFR2. © 2014 Cancer Research UK

Evaluation and improvement of the Defense Central Index of Invesitigations (DCII), A Report to the Naval Postgraduate School

The Defense Central Index of Investigations DCII is the primary DoD automated data base containing personnel security information. The DCII is delivered quarterly to the Defense Manpower Data Center DMDC, Monterey, California. The DCII was carefully reviewed and edited at the U.S. Naval Postgraduate School and several problems were revealed. For example, the records were ordered by phonetic name making them difficult to link to other personnel security files, approximately 15 percent of the records lacked social security numbers SSN, and another 15 percent of the records contained redundant information. Software was developed by BDM Services Company at DMDC to edit the DCII file. The improvements included reconfiguring the file so that the records were arranged by SSN. Duplicate SSNs and duplicate investigative data were dropped. This editing reduced the March 1985 DCII from eleven to six tapes, while providing a more accurate and efficient-to-use file.Approved for public release, distribution unlimite

Reconstructing the Coronal Magnetic Field: The Role of Cross-field Currents in Solution Uniqueness

We present a new 3D magnetohydrostatic (MHS) direct elliptic solver for extrapolating the coronal magnetic field from photospheric boundary conditions in a manner consistent with an assumed plasma distribution. We use it to study the uniqueness of the reconstructed magnetic field as a function of how significant the plasma forcing is on the force balance of the magnetic field. To this end, we consider an analytic MHS model as ground truth. The model uses two free parameters to decompose the current into two parts: a magnetic-field-aligned component and a cross-field component. We perform a comprehensive study of the 2D parameter space to understand under what conditions the ground truth can be reproduced uniquely. We find that current oriented perpendicular to the magnetic field has a smaller solution space than the same amount of current oriented parallel to the magnetic field, and so MHS regimes with larger proportions of plasma-related forcing may be a promising avenue toward finding unique magnetic field reconstructions

References

www.geosci-model-dev-discuss.net/7/2033/2014

A first meshless approach to simulation of the elastic behaviour of the diaphragm

eSSENC

Structural variations in the H-2 genes of AKR lymphomas.

K36.16 is an AKR H-2k thymoma which expresses an aberrant H-2Dd-like allospecificity, does not have a detectable amount of the H-2Kk syngeneic antigen and grows very easily in syngeneic mice. By DNA-mediated gene transfer experiments, we were able to obtain transformed clones which do express the H-2Kk molecules and are rejected by AKR mice. Southern hybridization was performed to assess whether any gross changes had occurred in the K36.16 H-2K locus or elsewhere in the MHC, which might explain the lack of H-2K expression and/or the presence of the aberrant H-2Dd-like allospecificity. Specific H-2 class I DNA probes were used to compare the K36.16 genomic DNA with normal AKR thymus DNA after digestion with a variety of restriction enzymes. After hybridization with the pH-2IIa probe a 2.8 kb 'Hind III' fragment was identified in the K36.16 genomic DNA which is absent from AKR DNA. The pH-2IIa probe detects the third, transmembrane and cytoplasmic domains of class I genes. Although these changes are indicative of MHC genome modifications it is not yet possible to link these specific Southern blot pattern variations with the phenotypic changes mentioned above