Recent Advances Concerning Certain Class of Geophysical Flows

This paper is devoted to reviewing several recent developments concerning certain class of geophysical models, including the primitive equations (PEs) of atmospheric and oceanic dynamics and a tropical atmosphere model. The PEs for large-scale oceanic and atmospheric dynamics are derived from the Navier-Stokes equations coupled to the heat convection by adopting the Boussinesq and hydrostatic approximations, while the tropical atmosphere model considered here is a nonlinear interaction system between the barotropic mode and the first baroclinic mode of the tropical atmosphere with moisture. We are mainly concerned with the global well-posedness of strong solutions to these systems, with full or partial viscosity, as well as certain singular perturbation small parameter limits related to these systems, including the small aspect ratio limit from the Navier-Stokes equations to the PEs, and a small relaxation-parameter in the tropical atmosphere model. These limits provide a rigorous justification to the hydrostatic balance in the PEs, and to the relaxation limit of the tropical atmosphere model, respectively. Some conditional uniqueness of weak solutions, and the global well-posedness of weak solutions with certain class of discontinuous initial data, to the PEs are also presented.Comment: arXiv admin note: text overlap with arXiv:1507.0523

Synthesis of Alkaline Earth Diazenides MAEN2 (MAE = Ca, Sr, Ba) by Controlled Thermal Decomposition of Azides under High Pressure

The alkaline earth diazenides MAEN2 with MAE = Ca, Sr and Ba were synthesized by a novel synthetic approach, namely, a controlled decomposition of the corresponding azides in a multianvil press at highpressure/ high-temperature conditions. The crystal structure of hitherto unknown calcium diazenide (space group I4/mmm (no. 139), a = 3.5747(6) Å, c = 5.9844(9) Å, Z = 2, wRp = 0.078) was solved and refined on the basis of powder X-ray diffraction data as well as that of SrN2 and BaN2. Accordingly, CaN2 is isotypic with SrN2 (space group I4/mmm (no. 139), a = 3.8054(2) Å, c = 6.8961(4) Å, Z = 2, wRp = 0.057) and the corresponding alkaline earth acetylenides (MAEC2) crystallizing in a tetragonally distorted NaCl structure type. In accordance with literature data, BaN2 adopts a more distorted structure in space group C2/c (no. 15) with a = 7.1608(4) Å, b = 4.3776(3) Å, c = 7.2188(4) Å, β = 104.9679(33)°, Z = 4 and wRp = 0.049). The N−N bond lengths of 1.202(4) Å in CaN2 (SrN2 1.239(4) Å, BaN2 1.23(2) Å) correspond well with a double-bonded dinitrogen unit confirming a diazenide ion [N2]2−. Temperature-dependent in situ powder X-ray diffractometry of the three alkaline earth diazenides resulted in formation of the corresponding subnitrides MAE2N (MAE = Ca, Sr, Ba) at higher temperatures. FTIR spectroscopy revealed a band at about 1380 cm−1 assigned to the N−N stretching vibration of the diazenide unit. Electronic structure calculations support the metallic character of alkaline earth diazenides

Characterization of human mesothelin transcripts in ovarian and pancreatic cancer

BACKGROUND: Mesothelin is an attractive target for cancer immunotherapy due to its restricted expression in normal tissues and high level expression in several tumor types including ovarian and pancreatic adenocarcinomas. Three mesothelin transcript variants have been reported, but their relative expression in normal tissues and tumors has been poorly characterized. The goal of the present study was to clarify which mesothelin transcript variants are commonly expressed in human tumors. METHODS: Human genomic and EST nucleotide sequences in the public databases were used to evaluate sequences reported for the three mesothelin transcript variants in silico. Subsequently, RNA samples from normal ovary, ovarian and pancreatic carcinoma cell lines, and primary ovarian tumors were analyzed by reverse transcription-polymerase chain reaction (RT-PCR) and nucleotide sequencing to directly identify expressed transcripts. RESULTS: In silico comparisons of genomic DNA sequences with available EST sequences supported expression of mesothelin transcript variants 1 and 3, but there were no sequence matches for transcript variant 2. Newly-derived nucleotide sequences of RT-PCR products from tissues and cell lines corresponded to mesothelin transcript variant 1. Mesothelin transcript variant 2 was not detected. Transcript variant 3 was observed as a small percentage of total mesothelin amplification products from all studied cell lines and tissues. Fractionation of nuclear and cytoplasmic RNA indicated that variant 3 was present primarily in the nuclear fraction. Thus, mesothelin transcript variant 3 may represent incompletely processed hnRNA. CONCLUSION: Mesothelin transcript variant 1 represents the predominant mature mRNA species expressed by both normal and tumor cells. This conclusion should be important for future development of cancer immunotherapies, diagnostic tests, and gene microarray studies targeting mesothelin

The roles of static stability and tropical – extratropical interactions in the summer interannual variability of the North Atlantic sector

Summer seasonal forecast skill in the North Atlantic sector is lower than winter skill. To identify potential controls on predictability, the sensitivity of North Atlantic baroclinicity to atmospheric drivers is quantified. Using ERA-INTERIM reanalysis data, North Atlantic storm-track baroclinicity is shown to be less sensitive to meridional temperature-gradient variability in summer. Static stability shapes the sector’s interannual variability by modulating the sensitivity of baroclinicity to variations in meridional temperature gradients and tropopause height and by modifying the baroclinicity itself. High static stability anomalies at upper levels result in more zonal extratropical cyclone tracks and higher eddy kinetic energy over the British Isles in the summertime. These static stability anomalies are not strongly related to the summer NAO; but they are correlated with the suppression of convection over the tropical Atlantic and with a poleward-shifted subtropical jet. These results suggest a non-local driver of North Atlantic variability. Furthermore, they imply that improved representations of convection over the south-eastern part of North America and the tropical Atlantic might improve summer seasonal forecast skill

Resectable adenocarcinomas in the pancreatic head: the retroperitoneal resection margin is an independent prognostic factor

Pancreatic cancer is a lethal disease, and even after assumed margin-free pancreatoduodenectomy, most patients die within few years. The aims were to evaluate the importance of standardised histopathologic assessment for adequacy of reporting and survival estimates, and to report on prognostic factors in a setting of standardised histopathologic assessment. We performed immunohistochemical evaluation, slide review, and review of histopathologic reports from all pancreatoduodenectomies at Rikshospitalet University Hospital in 1980–2004. Reports from 1998-2004 at this institution were compared with reports from all other Norwegian institutions in the same period. Standardised histopathologic assessment and reporting was found necessary to avoid underestimation of poor prognostic factors, and to avoid misdiagnosis of tumours originating from non-pancreatic tissue (ampulla, distal bile duct, duodenum). Standardised histopathology was more important than surgical volume for completeness of reporting and for reliability of survival estimates, particularly with respect to lymph node evaluation. Immunostaining for MUC1 and MUC4 identified a subgroup of patients with particularly poor prognosis. Standardised histopathologic evaluation should be a first prerequisite to assure adequate histopathology after pancreatoduodenectomy. Immunostaining may identify tumour markers potentially targetable in future adjuvant treatments for pancreatic cancer

Challenges and opportunities for improved understanding of regional climate dynamics

Dynamical processes in the atmosphere and ocean are central to determining the large-scale drivers of regional climate change, yet their predictive understanding is poor. Here, we identify three frontline challenges in climate dynamics where significant progress can be made to inform adaptation: response of storms, blocks and jet streams to external forcing; basin-to-basin and tropical–extratropical teleconnections; and the development of non-linear predictive theory. We highlight opportunities and techniques for making immediate progress in these areas, which critically involve the development of high-resolution coupled model simulations, partial coupling or pacemaker experiments, as well as the development and use of dynamical metrics and exploitation of hierarchies of models

Crystal Structure of Reovirus Attachment Protein σ1 in Complex with Sialylated Oligosaccharides

Many viruses attach to target cells by binding to cell-surface glycans. To gain a better understanding of strategies used by viruses to engage carbohydrate receptors, we determined the crystal structures of reovirus attachment protein σ1 in complex with α-2,3-sialyllactose, α-2,6-sialyllactose, and α-2,8-di-siallylactose. All three oligosaccharides terminate in sialic acid, which serves as a receptor for the reovirus serotype studied here. The overall structure of σ1 resembles an elongated, filamentous trimer. It contains a globular head featuring a compact β-barrel, and a fibrous extension formed by seven repeating units of a triple β-spiral that is interrupted near its midpoint by a short α -helical coiled coil. The carbohydrate-binding site is located between β-spiral repeats two and three, distal from the head. In all three complexes, the terminal sialic acid forms almost all of the contacts with σ1 in an identical manner, while the remaining components of the oligosaccharides make little or no contacts. We used this structural information to guide mutagenesis studies to identify residues in σ1 that functionally engage sialic acid by assessing hemagglutination capacity and growth in murine erythroleukemia cells, which require sialic acid binding for productive infection. Our studies using σ1 mutant viruses reveal that residues 198, 202, 203, 204, and 205 are required for functional binding to sialic acid by reovirus. These findings provide insight into mechanisms of reovirus attachment to cell-surface glycans and contribute to an understanding of carbohydrate binding by viruses. They also establish a filamentous, trimeric carbohydrate-binding module that could potentially be used to endow other trimeric proteins with carbohydrate-binding properties

Transcription profiling of lung adenocarcinomas of c-myc-transgenic mice: Identification of the c-myc regulatory gene network

<p>Abstract</p> <p>Background</p> <p>The transcriptional regulator c-Myc is the most frequently deregulated oncogene in human tumors. Targeted overexpression of this gene in mice results in distinct types of lung adenocarcinomas. By using microarray technology, alterations in the expression of genes were captured based on a female transgenic mouse model in which, indeed, c-Myc overexpression in alveolar epithelium results in the development of bronchiolo-alveolar carcinoma (BAC) and papillary adenocarcinoma (PLAC). In this study, we analyzed exclusively the promoters of induced genes by different in silico methods in order to elucidate the c-Myc transcriptional regulatory network.</p> <p>Results</p> <p>We analyzed the promoters of 361 transcriptionally induced genes with respect to c-Myc binding sites and found 110 putative binding sites in 94 promoters. Furthermore, we analyzed the flanking sequences (+/- 100 bp) around the 110 c-Myc binding sites and found Ap2, Zf5, Zic3, and E2f binding sites to be overrepresented in these regions. Then, we analyzed the promoters of 361 induced genes with respect to binding sites of other transcription factors (TFs) which were upregulated by c-Myc overexpression. We identified at least one binding site of at least one of these TFs in 220 promoters, thus elucidating a potential transcription factor network. The analysis correlated well with the significant overexpression of the TFs Atf2, Foxf1a, Smad4, Sox4, Sp3 and Stat5a. Finally, we analyzed promoters of regulated genes which where apparently not regulated by c-Myc or other c-Myc targeted TFs and identified overrepresented Oct1, Mzf1, Ppargamma, Plzf, Ets, and HmgIY binding sites when compared against control promoter background.</p> <p>Conclusion</p> <p>Our in silico data suggest a model of a transcriptional regulatory network in which different TFs act in concert upon c-Myc overexpression. We determined molecular rules for transcriptional regulation to explain, in part, the carcinogenic effect seen in mice overexpressing the c-Myc oncogene.</p