eggNOG: automated construction and annotation of orthologous groups of genes

The identification of orthologous genes forms the basis for most comparative genomics studies. Existing approaches either lack functional annotation of the identified orthologous groups, hampering the interpretation of subsequent results, or are manually annotated and thus lag behind the rapid sequencing of new genomes. Here we present the eggNOG database ('evolutionary genealogy of genes: Non-supervised Orthologous Groups'), which contains orthologous groups constructed from Smith-Waterman alignments through identification of reciprocal best matches and triangular linkage clustering. Applying this procedure to 312 bacterial, 26 archaeal and 35 eukaryotic genomes yielded 43 582 course-grained orthologous groups of which 9724 are extended versions of those from the original COG/KOG database. We also constructed more fine-grained groups for selected subsets of organisms, such as the 19 914 mammalian orthologous groups. We automatically annotated our non-supervised orthologous groups with functional descriptions, which were derived by identifying common denominators for the genes based on their individual textual descriptions, annotated functional categories, and predicted protein domains. The orthologous groups in eggNOG contain 1 241 751 genes and provide at least a broad functional description for 77% of them. Users can query the resource for individual genes via a web interface or download the complete set of orthologous groups at http://eggnog.embl.d

Multi-Dimensional Simulations of the Accretion-Induced Collapse of White Dwarfs to Neutron Stars

We present 2.5D radiation-hydrodynamics simulations of the accretion-induced collapse (AIC) of white dwarfs, starting from 2D rotational equilibrium configurations of a 1.46-Msun and a 1.92-Msun model. Electron capture leads to the collapse to nuclear densities of these cores within a few tens of milliseconds. The shock generated at bounce moves slowly, but steadily, outwards. Within 50-100ms, the stalled shock breaks out of the white dwarf along the poles. The blast is followed by a neutrino-driven wind that develops within the white dwarf, in a cone of ~40deg opening angle about the poles, with a mass loss rate of 5-8 x 10^{-3} Msun/yr. The ejecta have an entropy on the order of 20-50 k_B/baryon, and an electron fraction distribution that is bimodal. By the end of the simulations, at >600ms after bounce, the explosion energy has reached 3-4 x 10^{49}erg and the total ejecta mass has reached a few times 0.001Msun. We estimate the asymptotic explosion energies to be lower than 10^{50}erg, significantly lower than those inferred for standard core collapse. The AIC of white dwarfs thus represents one instance where a neutrino mechanism leads undoubtedly to a successful, albeit weak, explosion. We document in detail the numerous effects of the fast rotation of the progenitors: The neutron stars are aspherical; the ``nu_mu'' and anti-nu_e neutrino luminosities are reduced compared to the nu_e neutrino luminosity; the deleptonized region has a butterfly shape; the neutrino flux and electron fraction depend strongly upon latitude (a la von Zeipel); and a quasi-Keplerian 0.1-0.5-Msun accretion disk is formed.Comment: 25 pages, 19 figures, accpeted to ApJ, high resolution of the paper and movies available at http://hermes.as.arizona.edu/~luc/aic/aic.htm

Coulomb drag in mesoscopic rings

We develop a Luttinger liquid theory of the Coulomb drag of persistent currents flowing in concentric mesoscopic rings, by incorporating non-linear corrections to the electron dispersion relation. We demonstrate that at low temperatures, interactions between electrons in different rings generate an additional phase and thus alter the period of Aharonov-Bohm oscillations. The resulting nondissipative drag depends strongly on the relative parity of the electron numbers. We also show that interactions set a new temperature scale below which the linear response theory does not apply at certain values of external flux.Comment: Latex 10 pages + 2 Figure

Si/SiGe quantum cascade superlattice designs for terahertz emission

Quantum cascade lasers are compact sources that have demonstrated high output powers at THz frequencies. To date all THz quantum cascade lasers have been realized in III-V materials. Results are presented from Si1−xGex quantum cascade superlattice designs emitting at around 3 THz which have been grown in two different chemical vapor deposition systems. The key to achieving successful electroluminescence at THz frequencies in a p-type system has been to strain the light-hole states to energies well above the radiative subband states. To accurately model the emission wavelengths, a 6-band k.p tool which includes the effects of non-abrupt heterointerfaces has been used to predict the characteristics of the emitters. X-ray diffraction and transmission electron microscopy have been used along with Fourier transform infrared spectroscopy to fully characterise the samples. A number of methods to improve the gain from the designs are suggested

Sharks of the order Carcharhiniformes from the British Coniacian, Santonian and Campanian (Upper Cretaceous).

Bulk sampling of phosphate-rich horizons within the British Coniacian to Campanian (Upper Cretaceous) yielded very large samples of shark and ray teeth. All of these samples yielded teeth of diverse members of the Carcharhiniformes, which commonly dominate the fauna. The following species are recorded and described: Pseudoscyliorhinus reussi (Herman, 1977) comb. nov., Crassescyliorhinus germanicus (Herman, 1982) gen. nov., Scyliorhinus elongatus (Davis, 1887), Scyliorhinus brumarivulensis sp. nov., ? Palaeoscyllium sp., Prohaploblepharus riegrafi (Müller, 1989) gen. nov., ? Cretascyliorhinus sp., Scyliorhinidae inc. sedis 1, Scyliorhinidae inc. sedis 2, Pteroscyllium hermani sp. nov., Protoscyliorhinus sp., Leptocharias cretaceus sp. nov., Palaeogaleus havreensis Herman, 1977, Paratriakis subserratus sp. nov., Paratriakis tenuis sp. nov., Paratriakis sp. indet. and ? Loxodon sp. Taxa belonging to the families ?Proscylliidae, Leptochariidae, and Carcharhinidae are described from the Cretaceous for the first time. The evolutionary and palaeoecological implications of these newly recognised faunas are discussed

Impact of STROBE Statement Publication on Quality of Observational Study Reporting: Interrupted Time Series versus Before-After Analysis

Background:In uncontrolled before-after studies, CONSORT was shown to improve the reporting of randomised trials. Before-after studies ignore underlying secular trends and may overestimate the impact of interventions. Our aim was to assess the impact of the 2007 STROBE statement publication on the quality of observational study reporting, using both uncontrolled before-after analyses and interrupted time series.Methods:For this quasi-experimental study, original articles reporting cohort, case-control, and cross-sectional studies published between 2004 and 2010 in the four dermatological journals having the highest 5-year impact factors (≥4) were selected. We compared the proportions of STROBE items (STROBE score) adequately reported in each article during three periods, two pre STROBE period (2004-2005 and 2006-2007) and one post STROBE period (2008-2010). Segmented regression analysis of interrupted time series was also performed.Results:Of the 456 included articles, 187 (41%) reported cohort studies, 166 (36.4%) cross-sectional studies, and 103 (22.6%) case-control studies. The median STROBE score was 57% (range, 18%-98%). Before-after analysis evidenced significant STROBE score increases between the two pre-STROBE periods and between the earliest pre-STROBE period and the post-STROBE period (median score2004-0548% versus median score2008-1058%, p<0.001) but not between the immediate pre-STROBE period and the post-STROBE period (median score2006-0758% versus median score2008-1058%, p = 0.42). In the pre STROBE period, the six-monthly mean STROBE score increased significantly, by 1.19% per six-month period (absolute increase 95%CI, 0.26% to 2.11%, p = 0.016). By segmented analysis, no significant changes in STROBE score trends occurred (-0.40%; 95%CI, -2.20 to 1.41; p = 0.64) in the post STROBE statement publication.Interpretation:The quality of reports increased over time but was not affected by STROBE. Our findings raise concerns about the relevance of uncontrolled before-after analysis for estimating the impact of guidelines

Unknown Quantum States: The Quantum de Finetti Representation

We present an elementary proof of the quantum de Finetti representation theorem, a quantum analogue of de Finetti's classical theorem on exchangeable probability assignments. This contrasts with the original proof of Hudson and Moody [Z. Wahrschein. verw. Geb. 33, 343 (1976)], which relies on advanced mathematics and does not share the same potential for generalization. The classical de Finetti theorem provides an operational definition of the concept of an unknown probability in Bayesian probability theory, where probabilities are taken to be degrees of belief instead of objective states of nature. The quantum de Finetti theorem, in a closely analogous fashion, deals with exchangeable density-operator assignments and provides an operational definition of the concept of an ``unknown quantum state'' in quantum-state tomography. This result is especially important for information-based interpretations of quantum mechanics, where quantum states, like probabilities, are taken to be states of knowledge rather than states of nature. We further demonstrate that the theorem fails for real Hilbert spaces and discuss the significance of this point.Comment: 30 pages, 2 figure

eggNOG: automated construction and annotation of orthologous groups of genes

The identification of orthologous genes forms the basis for most comparative genomics studies. Existing approaches either lack functional annotation of the identified orthologous groups, hampering the interpretation of subsequent results, or are manually annotated and thus lag behind the rapid sequencing of new genomes. Here we present the eggNOG database (‘evolutionary genealogy of genes: Non-supervised Orthologous Groups’), which contains orthologous groups constructed from Smith–Waterman alignments through identification of reciprocal best matches and triangular linkage clustering. Applying this procedure to 312 bacterial, 26 archaeal and 35 eukaryotic genomes yielded 43 582 course-grained orthologous groups of which 9724 are extended versions of those from the original COG/KOG database. We also constructed more fine-grained groups for selected subsets of organisms, such as the 19 914 mammalian orthologous groups. We automatically annotated our non-supervised orthologous groups with functional descriptions, which were derived by identifying common denominators for the genes based on their individual textual descriptions, annotated functional categories, and predicted protein domains. The orthologous groups in eggNOG contain 1 241 751 genes and provide at least a broad functional description for 77% of them. Users can query the resource for individual genes via a web interface or download the complete set of orthologous groups at http://eggnog.embl.de

Infrared Properties of QCD from Dyson-Schwinger equations

I review recent results on the infrared properties of QCD from Dyson-Schwinger equations. The topics include infrared exponents of one-particle irreducible Green's functions, the fixed point behaviour of the running coupling at zero momentum, the pattern of dynamical quark mass generation and properties of light mesons.Comment: 47 pages, 19 figures, Topical Review to be published in J.Phys.G, v2: typos corrected and some references adde