Numerical representation of internal waves propagation

Similar to surface waves propagating at the interface of two fluid of different densities (like air and water), internal waves in the oceanic interior travel along surfaces separating waters of different densities (e.g. at the thermocline). Due to their key role in the global distribution of (physical) diapycnal mixing and mass transport, proper representation of internal wave dynamics in numerical models should be considered a priority since global climate models are now configured with increasingly higher horizontal/vertical resolution. However, in most state-of-the-art oceanic models, important terms involved in the propagation of internal waves (namely the horizontal pressure gradient and horizontal divergence in the continuity equation) are generally discretized using very basic numerics (i.e. second-order approximations) in space and time. In this paper, we investigate the benefits of higher-order approximations in terms of the discrete dispersion relation (in the linear theory) on staggered and nonstaggered computational grids. A fourth-order scheme discretized on a C-grid to approximate both pressure gradient and horizontal divergence terms provides clear improvements but, unlike nonstaggered grids, prevents the use of monotonic or non- oscillatory schemes. Since our study suggests that better numerics is required, second and fourth order direct space-time algorithms are designed, thus paving the way toward the use of efficient high-order discretizations of internal gravity waves in oceanic models, while maintaining good sta- bility properties (those schemes are stable for Courant numbers smaller than 1). Finally, important results obtained at a theoretical level are illustrated at a discrete level using two-dimensional (x,z) idealized experiments

Group Strategyproof Pareto-Stable Marriage with Indifferences via the Generalized Assignment Game

We study the variant of the stable marriage problem in which the preferences of the agents are allowed to include indifferences. We present a mechanism for producing Pareto-stable matchings in stable marriage markets with indifferences that is group strategyproof for one side of the market. Our key technique involves modeling the stable marriage market as a generalized assignment game. We also show that our mechanism can be implemented efficiently. These results can be extended to the college admissions problem with indifferences

Desastres, responsabilidade civil e áreas de preservação permanente: paradoxo do progresso nômade

- Divulgação dos SUMÁRIOS das obras recentemente incorporadas ao acervo da Biblioteca Ministro Oscar Saraiva do STJ. Em respeito à Lei de Direitos Autorais, não disponibilizamos a obra na íntegra.- Localização na estante: 34:504(81) D371

The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications

Background: Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals. Results: We have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes. Conclusion: Because the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently evolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as previously suggested

Open problems on graph coloring for special graph classes.

For a given graph G and integer k, the Coloring problem is that of testing whether G has a k-coloring, that is, whether there exists a vertex mapping c:V→{1,2,…}c:V→{1,2,…} such that c(u)≠c(v)c(u)≠c(v) for every edge uv∈Euv∈E. We survey known results on the computational complexity of Coloring for graph classes that are hereditary or for which some graph parameter is bounded. We also consider coloring variants, such as precoloring extensions and list colorings and give some open problems in the area of on-line coloring

An Improved Approximation Bound for Spanning Star Forest and Color Saving

Abstract. We present a simple algorithm for the maximum spanning star forest problem. We take advantage of the fact that the problem is a special case of complementary set cover and we adapt an algorithm of Duh and Fürer in order to solve it. We prove that this algorithm computes 193/240 ≈ 0.804-approximate spanning star forests; this result improves a previous lower bound of 0.71 by Chen et al. Although the algorithm is purely combinatorial, our analysis defines a linear program that uses a parameter f and which is feasible for values of the parameter f not smaller than the approximation ratio of the algorithm. The analysis is tight and, interestingly, it also applies to complementary versions of set cover such as color saving; it yields the same approximation guarantee of 193/240 that marginally improves the previously known upper bound of Duh and Fürer. We also show that, in general, a natural class of local search algorithms do not provide better than 1/2-approximate spanning star forests.

Identification of a BRCA2-Specific modifier locus at 6p24 related to breast cancer risk

Common genetic variants contribute to the observed variation in breast cancer risk for BRCA2 mutation carriers; those known to date have all been found through population-based genome-wide association studies (GWAS). To comprehensively identify breast cancer risk modifying loci for BRCA2 mutation carriers, we conducted a deep replication of an ongoing GWAS discovery study. Using the ranked P-values of the breast cancer associations with the imputed genotype of 1.4 M SNPs, 19,029 SNPs were selected and designed for inclusion on a custom Illumina array that included a total of 211,155 SNPs as part of a multi-consortial project. DNA samples from 3,881 breast cancer affected and 4,330 unaffected BRCA2 mutation carriers from 47 studies belonging to the Consortium of Investigators of Modifiers of BRCA1/2 were genotyped and available for analysis. We replicated previously reported breast cancer susceptibility alleles in these BRCA2 mutation carriers and for several regions (including FGFR2, MAP3K1, CDKN2A/B, and PTHLH) identified SNPs that have stronger evidence of association than those previously published. We also identified a novel susceptibility allele at 6p24 that was inversely associated with risk in BRCA2 mutation carriers (rs9348512; per allele HR = 0.85, 95% CI 0.80-0.90, P = 3.9×10−8). This SNP was not associated with breast cancer risk either in the general population or in BRCA1 mutation carriers. The locus lies within a region containing TFAP2A, which encodes a transcriptional activation protein that interacts with several tumor suppressor genes. This report identifies the first breast cancer risk locus specific to a BRCA2 mutation background. This comprehensive update of novel and previously reported breast cancer susceptibility loci contributes to the establishment of a panel of SNPs that modify breast cancer risk in BRCA2 mutation carriers. This panel may have clinical utility for women with BRCA2 mutations weighing options for medical prevention of breast cancer

Azotobacter genomes: the genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412)

The genome of the soil-dwelling heterotrophic N2-fixing Gram-negative bacterium Azotobacter chroococcum NCIMB 8003 (ATCC 4412) (Ac-8003) has been determined. It consists of 7 circular replicons totalling 5,192,291 bp comprising a circular chromosome of 4,591,803 bp and six plasmids pAcX50a, b, c, d, e, f of 10,435 bp, 13,852, 62,783, 69,713, 132,724, and 311,724 bp respectively. The chromosome has a G+C content of 66.27% and the six plasmids have G+C contents of 58.1, 55.3, 56.7, 59.2, 61.9, and 62.6% respectively. The methylome has also been determined and 5 methylation motifs have been identified. The genome also contains a very high number of transposase/inactivated transposase genes from at least 12 of the 17 recognised insertion sequence families. The Ac-8003 genome has been compared with that of Azotobacter vinelandii ATCC BAA-1303 (Av-DJ), a derivative of strain O, the only other member of the Azotobacteraceae determined so far which has a single chromosome of 5,365,318 bp and no plasmids. The chromosomes show significant stretches of synteny throughout but also reveal a history of many deletion/insertion events. The Ac-8003 genome encodes 4628 predicted protein-encoding genes of which 568 (12.2%) are plasmid borne. 3048 (65%) of these show > 85% identity to the 5050 protein-encoding genes identified in Av-DJ, and of these 99 are plasmid-borne. The core biosynthetic and metabolic pathways and macromolecular architectures and machineries of these organisms appear largely conserved including genes for CO-dehydrogenase, formate dehydrogenase and a soluble NiFe-hydrogenase. The genetic bases for many of the detailed phenotypic differences reported for these organisms have also been identified. Also many other potential phenotypic differences have been uncovered. Properties endowed by the plasmids are described including the presence of an entire aerobic corrin synthesis pathway in pAcX50f and the presence of genes for retro-conjugation in pAcX50c. All these findings are related to the potentially different environmental niches from which these organisms were isolated and to emerging theories about how microbes contribute to their communities

Strategy-Proofness and Efficiency with Nonquasi-Linear Preferences: A Characterization of Minimum Price Walrasian Rule

We consider the problems of allocating several heterogeneous objects owned by governments to a group of agents and how much agents should pay. Each agent receives at most one object and has nonquasi-linear preferences. Nonquasi-linear preferences describe environments in which large-scale payments influence agents' abilities to utilize objects or derive benefits from them. The minimum price Walrasian (MPW) rule is the rule that assigns a minimum price Walrasian equilibrium allocation to each preference profile. We establish that the MPW rule is the unique rule that satisfies the desirable properties of strategy-proofness, Pareto-efficiency, individual rationality, and nonnegative payment on the domain that includes nonquasi-linear preferences. This result does not only recommend the MPW rule based on those desirable properties, but also suggest that governments cannot improve upon the MPW rule once they consider them essential. Since the outcome of the MPW rule coincides with that of the simultaneous ascending (SA) auction, our result explains the pervasive use of the SA auction