CABARET in the ocean gyres

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Ocean Modelling 30 (2009): 155-168, doi:10.1016/j.ocemod.2009.06.009.A new high-resolution Eulerian numerical method is proposed for modelling quasigeostrophic ocean dynamics in eddying regimes. The method is based on a novel, second-order non-dissipative and lowdispersive conservative advection scheme called CABARET. The properties of the new method are compared with those of several high-resolution Eulerian methods for linear advection and gas dynamics. Then, the CABARET method is applied to the classical model of the double-gyre ocean circulation and its performance is contrasted against that of the common vorticity-preserving Arakawa method. In turbulent regimes, the new method permits credible numerical simulations on much coarser computational grids.Supports from the Royal Society of London and from the Mary Sears Visitor Grant are acknowledged by SK with gratitude. The work of VG was supported by the Russian Foundation for Basic Research (RFBR), grant 06-01-00819a. Funding for PB was provided by the NSF grant 0725796

Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles

Machine learning approaches offer the potential to systematically identify transcriptional regulatory interactions from a compendium of microarray expression profiles. However, experimental validation of the performance of these methods at the genome scale has remained elusive. Here we assess the global performance of four existing classes of inference algorithms using 445 Escherichia coli Affymetrix arrays and 3,216 known E. coli regulatory interactions from RegulonDB. We also developed and applied the context likelihood of relatedness (CLR) algorithm, a novel extension of the relevance networks class of algorithms. CLR demonstrates an average precision gain of 36% relative to the next-best performing algorithm. At a 60% true positive rate, CLR identifies 1,079 regulatory interactions, of which 338 were in the previously known network and 741 were novel predictions. We tested the predicted interactions for three transcription factors with chromatin immunoprecipitation, confirming 21 novel interactions and verifying our RegulonDB-based performance estimates. CLR also identified a regulatory link providing central metabolic control of iron transport, which we confirmed with real-time quantitative PCR. The compendium of expression data compiled in this study, coupled with RegulonDB, provides a valuable model system for further improvement of network inference algorithms using experimental data

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

Recent genomic analyses of pathologically-defined tumor types identify “within-a-tissue” disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head & neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multi-platform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All datasets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Structural and mechanic modelling of metallic materials failure and forecasting of high-loaded construction elements durability

In this work samples out of steels of the types 15H2MFA, 15 H2NMFA, 12 HN3ND and alloy HN55MVC, welded compounds of mixed type, constructive elements of power equipment are investigated. The purpose of this study is to develop the methods of forecasting construction elements durability by complex thermo-force loading in volumetric stressed state conditions. There have been formulated main principles of structural and mechanical modelling of brittle, viscous and endurance failure of materials in conditions of complex thermoforce loading and volumetric stressed state. The methods of forecasting durability of deep sea-apparatus welded constructions and constructions of power equipment have been developed. New criteria of brittle, viscous and endurance failure have been formulated, forecasting constructions working capacity in volumetric stressed state conditions. The results of investigations have been used in defining the resource and in working out the approaches on deep-sea apparatus and power equipment safe workAvailable from VNTIC / VNTIC - Scientific & Technical Information Centre of RussiaSIGLERURussian Federatio

PVP 2009-77095 STRUCTURAL INTEGRITY ASSESSMENT OF WWER INTERNALS ON STRESS CORROSION CRACKING CRITERION

ABSTRACT Stress-damage dose curve (SDDC) is introduced on the basis of the analysis of experimental data on susceptibility to intergranular stress corrosion cracking (IGSCC) of irradiated stainless steels (SS). Approaches to determination of the SDDC parameters are considered. Based on SDDC calculative procedure for estimation of reactor vessel internals (RVI) lifetime by criterion of initiation crack due to IGSCC is proposed

Geochemistry of basalts from DSDP Leg 65 holes

Petrological investigations of oceanic rocks carried out during the past several years have shed considerable light on the geochemistry of basalts from various structural provinces in the ocean basins. It is evident from these studies that variations in chemistry exist between volcanics in different provinces and even within individual provinces