Electronic structure and properties of Cu2O

The structural and electronic properties of Cu2O have been investigated using the periodic Hartree-Fock method and a posteriori density-functional corrections. The lattice parameter, bulk modulus, and elastic constants have been calculated. The electronic structure of and bonding in Cu2O are analyzed and compared with x-ray photoelectron spectroscopy spectra, showing a good agreement for the valence-band states. To check the quality of the calculated electron density, static structure factors and Compton profiles have been calculated, showing a good agreement with the available experimental data. The effective electron and hole masses have been evaluated for Cu2O at the center of the Brillouin zone. The calculated interaction energy between the two interpenetrated frameworks in the cuprite structure is estimated to be around -6.0 kcal/mol per Cu2O formula. The bonding between the two independent frameworks has been analyzed using a bimolecular model and the results indicate an important role of d10-d10 type interactions between copper atoms.

Electronic structure and properties of Cu2O

The structural and electronic properties of Cu2O have been investigated using the periodic Hartree-Fock method and a posteriori density-functional corrections. The lattice parameter, bulk modulus, and elastic constants have been calculated. The electronic structure of and bonding in Cu2O are analyzed and compared with x-ray photoelectron spectroscopy spectra, showing a good agreement for the valence-band states. To check the quality of the calculated electron density, static structure factors and Compton profiles have been calculated, showing a good agreement with the available experimental data. The effective electron and hole masses have been evaluated for Cu2O at the center of the Brillouin zone. The calculated interaction energy between the two interpenetrated frameworks in the cuprite structure is estimated to be around -6.0 kcal/mol per Cu2O formula. The bonding between the two independent frameworks has been analyzed using a bimolecular model and the results indicate an important role of d10-d10 type interactions between copper atoms.

GSVA: gene set variation analysis for microarray and RNA-seq data

Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as well as greater biological interpretability. As molecular profiling experiments move beyond simple case-control studies, robust and flexible GSE methodologies are needed that can model pathway activity within highly heterogeneous data sets. To address this challenge, we introduce Gene Set Variation Analysis (GSVA), a GSE method that estimates variation of pathway activity over a sample population in an unsupervised manner. We demonstrate the robustness of GSVA in a comparison with current state of the art sample-wise enrichment methods. Further, we provide examples of its utility in differential pathway activity and survival analysis. Lastly, we show how GSVA works analogously with data from both microarray and RNA-seq experiments. GSVA provides increased power to detect subtle pathway activity changes over a sample population in comparison to corresponding methods. While GSE methods are generally regarded as end points of a bioinformatic analysis, GSVA constitutes a starting point to build pathway-centric models of biology. Moreover, GSVA contributes to the current need of GSE methods for RNA-seq data. GSVA is an open source software package for R which forms part of the Bioconductor project and can be downloaded at http://www.bioconductor.org.

Genesis of self-organized zebra textures in burial dolomites: Displacive veins, induced stress, and dolomitization

The dolomite veins making up rhythmites common in burial dolomites are not cement infillings of supposed cavities, as in the prevailing view, but are instead displacive veins, veins that pushed aside the host dolostone as they grew. Evidence that the veins are displacive includes a) small transform-fault-like displacements that could not have taken place if the veins were passive cements, and b) stylolites in host rock that formed as the veins grew in order to compensate for the volume added by the veins. Each zebra vein consists of crystals that grow inward from both sides, and displaces its walls via the local induced stress generated by the crystal growth itself. The petrographic criterion used in recent literature to interpret zebra veins in dolomites as cements - namely, that euhedral crystals can grow only in a prior void - disregards evidence to the contrary. The idea that flat voids did form in dolostones is incompatible with the observed optical continuity between the saddle dolomite euhedra of a vein and the replacive dolomite crystals of the host. The induced stress is also the key to the self-organization of zebra veins: In a set of many incipient, randomly-spaced, parallel veins just starting to grow in a host dolostone, each vein¿s induced stress prevents too-close neighbor veins from nucleating, or redissolves them by pressure-solution. The veins that survive this triage are those just outside their neighbors¿s induced stress haloes, now forming a set of equidistant veins, as observed.

Marine benthic algae of Namibia

The first comprehensive study of the marine algal flora of Namibia including descriptions and illustrations of most species is presented. The main objective of this work is to report a flora that, until now, has scarcely been studied. The work compiles all the available information on the marine benthic flora of Namibia and provides new data about it composition and biogeography, as well as detailed descriptions and remarks of most of its species. The samples on which this study is based were collected between 1986 and 1989 in the eulittoral and the upper sublittoral zones of the north half of the Namibian coast. According to the present data, the marine benthic flora of Namibia comprises 196 taxa (147 Rhodophyceae, 20 Phaeophyceae, 15 Ulvophyceae, 6 Cladophorophyceae and 8 Bryopsidophyceae), 21 of which has not been recorded from this coasts. This temperate flora is mainly characterized by a low number of species, a low proportion of Phaeophyceae and a high degree of endemism. Concerning the species number, the flora is quite poor due to both the scarce availability of colonizable substratum and the low diversity of habitats. On the other hand, the low proportion of Phaeophyceae is the reason for which the R/P and (R+C)/P ratios take disproportionately high values and so they are not useful in this geographical area. As regards the degree of endemism, the marine benthic flora of Namibia includes quite a high number of taxa endemic to southern Africa (55 taxa; 28.1% of the flora); 25 of these 55 taxa (12.8% of the flora) are endemic to the biogeographic Benguela Marine Province and only Acrosorium cincinnatum is endemic to the Namibian coasts.