The transient IDEMIX model as a nonorographic gravity wave parameterization in an atmospheric circulation model

The Internal wave Dissipation, Energy and Mixing (IDEMIX) model presents a novel way of parameterizing internal gravity waves in the atmosphere. Using a continuous full wave spectrum in the energy balance equation and integrating over all vertical wavenumbers and frequencies results in prognostic equations for the energy density of gravity waves in multiple azimuthal compartments. It includes their non-dissipative interaction with the mean flow, allowing for an evolving and local description of momentum flux and gravity wave drag. A saturation mechanism maintains the wave field within convective stability limits, and an energetically consistent closure for critical-layer effects controls how much wave flux propagates from the troposphere into the middle atmosphere. IDEMIX can simulate zonal gravity wave drag around the mesopause, similar to a traditional gravity wave parameterization and to a state-of-the-art wave ray tracing model in an atmospheric circulation model. In addition, IDEMIX shows a reversal of the gravity wave drag around the mesopause region due to changes in the momentum flux there. When compared to empirical model data, IDEMIX captures well the summer hemisphere flow reversal, the cold summer mesospheric pole and the alternate positive and negative structures in the meridional mean flow.Comment: 21 pages, 19 figure

MS-GWaM: A 3-dimensional transient gravity wave parametrization for atmospheric models

Parametrizations for internal gravity waves in atmospheric models are traditionally subject to a number of simplifications. Most notably, they rely on both neglecting wave propagation and advection in the horizontal direction (single-column assumption) and an instantaneous balance in the vertical direction (steady-state assumption). While these simplifications are well justified to cover some essential dynamic effects and keep the computational effort small it has been shown that both mechanisms are potentially significant. In particular, the recently introduced Multiscale Gravity Wave Model (MS-GWaM) successfully applied ray-tracing methods in a novel type of transient but columnar internal gravity wave parameterization (MS-GWaM-1D). We extend this concept to a three-dimensional version of the parameterization (MS-GWaM-3D) to simulate subgrid-scale non-orographic internal gravity waves. The resulting global wave model -- implemented into the weather-forecast and climate code ICON -- contains three-dimensional transient propagation with accurate flux calculations, a latitude-dependent background source, and convectively generated waves. MS-GWaM-3D helps reproducing expected temperature and wind patterns in the mesopause region in the climatological zonal mean state and thus proves a viable IGW parameterization. Analyzing the global wave action budget, we find that horizontal wave propagation is as important as vertical wave propagation. The corresponding wave refraction includes previously missing but well-known effects such as wave refraction into the polar jet streams. On a global scale, three-dimensional wave refraction leads to a horizontal flow-dependent redistribution of waves such that the structures of the zonal mean wave drag and consequently the zonal mean winds are modified.Comment: 39 pages, 9 figures; This Work has been submitted to the Journal of Atmospheric Sciences. Copyright in this Work may be transferred without further notic

TP53 mutation p.R337H in gastric cancer tissues of a 12-year-old male child - evidence for chimerism involving a common mutant founder haplotype: case report

<p>Abstract</p> <p>Background</p> <p>Gastric adenocarcinoma is rare in children and adolescents, with about 17 cases under age 21 in the world's literature. We report a case of invasive well-differentiated metastatic gastric cancer in a Brazilian 12-year-old boy without documented familial history of cancer.</p> <p>Case presentation</p> <p>The patient, diagnosed with metastatic disease, died seven months after surgery. DNA from intra-surgical specimens revealed a <it>TP53 </it>mutation at codon 337 (p.R337H) in samples with neoplastic cells (dysplasia, tumor and metastasis) but not in non-transformed cells (incomplete intestinal metaplasia and non-involved celiac lymph node). In all mutation-positive tissues, p.R337H occurred on the same background, a founder allele identified by a specific haplotype previously described in Brazilian Li-Fraumeni syndrome patients. The same mutant haplotype, corresponding to a founder mutation present in 0.3% of the general population in Southern Brazil, was found in the genome of the father. Presence of this inherited haplotype in the tumor as well as in the father's germline, suggests a rare case of microchimerism in this patient, who may have harbored a small number of mutant cells originating in another individual, perhaps a dizygotic twin that died early in gestation.</p> <p>Conclusion</p> <p>This case represents one of the earliest ages at diagnosis of gastric cancer ever reported. It shows that cancer inheritance can occur in the absence of an obvious germline mutation, calling for caution in assessing early cancers in populations with common founder mutations such as p.R337H in Southern Brazil.</p

The R337H mutation in TP53 and breast cancer in Brazil

<p>Abstract</p> <p>Background</p> <p>Germline mutations in p53 are associated with the Li-Fraumeni Syndrome which is characterized by childhood cancers, including pediatric adrenal cortical carcinomas and early onset breast cancer. The high incidence of adrenal cortical carcinomas in southern Brazil is mostly attributed to the <it>R337H </it>mutation in <it>TP53</it>. The relatively high population frequency of this mutation in southern Brazil, along with the clustering of early onset breast cancer in Li-Frameni families, suggests this mutation may also be a low-penetrance breast cancer susceptibility polymorphism.</p> <p>Methods</p> <p>We undertook this study to evaluate the frequency of the <it>R337H </it>mutation in breast cancer patients from Rio de Janeiro, Brazil. <it>R337H </it>mutation status was determined in 390 unselected breast cases and 324 controls identified from clinics in Rio de Janeiro, Brazil using a PCR-based assay.</p> <p>Results</p> <p>Two of the breast cancer cases (0.5%) and none of the controls carried the mutation. Both cases had an early age at diagnosis (< 40 years old) and a family history of breast and other cancers.</p> <p>Conclusions</p> <p>These data suggest genetic screening of young onset breast cancer patients should include testing for the <it>R337H </it>mutation.</p

Ancestry of the Brazilian TP53 c.1010G>A (p.Arg337His, R337H) founder mutation : clues from haplotyping of short tandem repeats on Chromosome 17p

Rare germline mutations in TP53 (17p13.1) cause a highly penetrant predisposition to a specific spectrum of early cancers, defining the Li-Fraumeni Syndrome (LFS). A germline mutation at codon 337 (p.Arg337His, c1010G>A) is found in about 0.3% of the population of Southern Brazil. This mutation is associated with partially penetrant LFS traits and is found in the germline of patients with early cancers of the LFS spectrum unselected for familial his- tory. To characterize the extended haplotypes carrying the mutation, we have genotyped 9 short tandem repeats on chromosome 17p in 12 trios of Brazilian p.Arg337His carriers. Results confirm that all share a common ancestor haplotype of Caucasian/Portuguese-Ibe- ric origin, distant in about 72–84 generations (2000 years assuming a 25 years intergenera- tional distance) and thus pre-dating European migration to Brazil. So far, the founder p. Arg337His haplotype has not been detected outside Brazil, with the exception of two resi- dents of Portugal, one of them of Brazilian origin. On the other hand, increased meiotic recombination in p.Arg337His carriers may account for higher than expected haplotype diversity. Further studies comparing haplotypes in populations of Brazil and of other areas of Portuguese migration are needed to understand the historical context of this mutation in Brazil.This study was funded by grant # 478430/2012-4 from CNPq (RFA MCT/CNPq - No 14/2012; Universal), Brazil.We would like to thank UFRGS, UFPA, AC Camargo, HC Barretos and University of Minho for their support during this work

Modeling nuclei of radio galaxies from VLBI radio observations. Application to the BL Lac Object S5 1803+784

We present a new method to fit the variations of both coordinates of a VLBI component as a function of time, assuming that the nucleus of the radio source contains a binary black hole system (BBH system). The presence of a BBH system produces 2 perturbations of the trajectory of the ejected VLBI components. By using only the VLBI coordinates, the problem we have to solve reduces to an astrometric problem. Knowledge of the variations of the VLBI coordinates as a function of time contains the kinematical information, thus we are able to deduce the inclination angle of the source and the bulk Lorentz factor of the ejected component. Generally, there is a family of the BBH system producing the same fit to our data. To illustrate this method, we apply it to the source 1807+784. We find that the inclination of the source is i = 5.8+-1.8 degrees and the VLBI component is ejected with a bulk Lorentz factor of 3.7+-0.3. We determine the family of the BBH system which provides the best fit, assuming at first that the masses of the 2 black holes are equal and then that the masses are different. Each family of BBH systems is characterized by Tp/Tb~1.967, where Tp and Tb are the precession period of the accretion disk of the black hole ejecting the VLBI component and the orbiting period of the BBH system.Comment: 15 pages, 12 figure