Showing papers by "University of Vienna published in 2011"

The ERA-Interim reanalysis: configuration and performance of the data assimilation system

Abstract: ERA-Interim is the latest global atmospheric reanalysis produced by the European Centre for Medium-Range Weather Forecasts (ECMWF). The ERA-Interim project was conducted in part to prepare for a new atmospheric reanalysis to replace ERA-40, which will extend back to the early part of the twentieth century. This article describes the forecast model, data assimilation method, and input datasets used to produce ERA-Interim, and discusses the performance of the system. Special emphasis is placed on various difficulties encountered in the production of ERA-40, including the representation of the hydrological cycle, the quality of the stratospheric circulation, and the consistency in time of the reanalysed fields. We provide evidence for substantial improvements in each of these aspects. We also identify areas where further work is needed and describe opportunities and objectives for future reanalysis projects at ECMWF. Copyright © 2011 Royal Meteorological Society

Communication and Persuasion: Central and Peripheral Routes to Attitude Change

Abstract: Das Elaboration Likelihood Modell (ELM) wurde in den 1980er Jahren von den Sozialpsychologen Richard E. Petty und John T. Cacioppo mit dem Ziel entwickelt, die prozesshafte Verarbeitung persuasiver Botschaften zu erklaren und Einstellungsveranderungen in Abhangigkeit von der Rezeptionssituation, den Eigenschaften einer persuasiven Botschaft und individuellen Voraussetzungen des Rezipienten vorherzusagen. Die zentrale Veroffentlichung dieser Persuasionstheorie ist das 1986 erschienene Buch Communication and persuasion: Central and peripheral routes to attitude change. In diesem Schlusselwerk der Medienwirkungsforschung werden das ELM und seine Basiskonzepte theoretisch definiert und durch eine Vielzahl empirischer Studien untermauert. Daruber hinaus diskutieren die Autoren methodische Schwierigkeiten bei der Uberprufung ihrer Annahmen sowie Konsequenzen der verschiedenen Elaborationsrouten. Communication and persuasion bietet damit einen detaillierten Uberblick zu einem der wichtigsten Zwei-Prozess-Modelle der persuasiven Kommunikationsforschung.

ViennaRNA Package 2.0

Abstract: Background Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters, exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties.

Laser cooling of a nanomechanical oscillator into its quantum ground state

Abstract: The simple mechanical oscillator, canonically consisting of a coupled mass–spring system, is used in a wide variety of sensitive measurements, including the detection of weak forces and small masses. On the one hand, a classical oscillator has a well-defined amplitude of motion; a quantum oscillator, on the other hand, has a lowest-energy state, or ground state, with a finite-amplitude uncertainty corresponding to zero-point motion. On the macroscopic scale of our everyday experience, owing to interactions with its highly fluctuating thermal environment a mechanical oscillator is filled with many energy quanta and its quantum nature is all but hidden. Recently, in experiments performed at temperatures of a few hundredths of a kelvin, engineered nanomechanical resonators coupled to electrical circuits have been measured to be oscillating in their quantum ground state. These experiments, in addition to providing a glimpse into the underlying quantum behaviour of mesoscopic systems consisting of billions of atoms, represent the initial steps towards the use of mechanical devices as tools for quantum metrology or as a means of coupling hybrid quantum systems. Here we report the development of a coupled, nanoscale optical and mechanical resonator formed in a silicon microchip, in which radiation pressure from a laser is used to cool the mechanical motion down to its quantum ground state (reaching an average phonon occupancy number of 0.85±0.08). This cooling is realized at an environmental temperature of 20 K, roughly one thousand times larger than in previous experiments and paves the way for optical control of mesoscale mechanical oscillators in the quantum regime.

Oncogene-induced Nrf2 transcription promotes ROS detoxification and tumorigenesis

Abstract: Reactive oxygen species (ROS) are mutagenic and may thereby promote cancer. Normally, ROS levels are tightly controlled by an inducible antioxidant program that responds to cellular stressors and is predominantly regulated by the transcription factor Nrf2 (also known as Nfe2l2) and its repressor protein Keap1 (refs 2-5). In contrast to the acute physiological regulation of Nrf2, in neoplasia there is evidence for increased basal activation of Nrf2. Indeed, somatic mutations that disrupt the Nrf2-Keap1 interaction to stabilize Nrf2 and increase the constitutive transcription of Nrf2 target genes were recently identified, indicating that enhanced ROS detoxification and additional Nrf2 functions may in fact be pro-tumorigenic. Here, we investigated ROS metabolism in primary murine cells following the expression of endogenous oncogenic alleles of Kras, Braf and Myc, and found that ROS are actively suppressed by these oncogenes. K-Ras(G12D), B-Raf(V619E) and Myc(ERT2) each increased the transcription of Nrf2 to stably elevate the basal Nrf2 antioxidant program and thereby lower intracellular ROS and confer a more reduced intracellular environment. Oncogene-directed increased expression of Nrf2 is a new mechanism for the activation of the Nrf2 antioxidant program, and is evident in primary cells and tissues of mice expressing K-Ras(G12D) and B-Raf(V619E), and in human pancreatic cancer. Furthermore, genetic targeting of the Nrf2 pathway impairs K-Ras(G12D)-induced proliferation and tumorigenesis in vivo. Thus, the Nrf2 antioxidant and cellular detoxification program represents a previously unappreciated mediator of oncogenesis.

Why intraspecific trait variation matters in community ecology

Abstract: Natural populations consist of phenotypically diverse individuals that exhibit variation in their demographic parameters and intra- and inter-specific interactions. Recent experimental work indicates that such variation can have significant ecological effects. However, ecological models typically disregard this variation and focus instead on trait means and total population density. Under what situations is this simplification appropriate? Why might intraspecific variation alter ecological dynamics? In this review we synthesize recent theory and identify six general mechanisms by which trait variation changes the outcome of ecological interactions. These mechanisms include several direct effects of trait variation per se and indirect effects arising from the role of genetic variation in trait evolution.

Evolutionary Game Dynamics

Abstract: Evolutionary game dynamics is the application of population dynamical methods to game theory. It has been introduced by evolutionary biologists, anticipated in part by classical game theorists. In this survey, we present an overview of the many brands of deterministic dynamical systems motivated by evolutionary game theory, including ordinary differential equations (and, in particular, the replicator equation), differential inclusions (the best response dynamics), difference equations (as, for instance, fictitious play) and reaction-diffusion systems. A recurrent theme (the so-called `folk theorem of evolutionary game theory') is the close connection of the dynamical approach with the Nash equilibrium, but we show that a static, equilibrium-based viewpoint is, on principle, unable to always account for the long-term behaviour of players adjusting their behaviour to maximise their payoff.

Role of sulphuric acid, ammonia and galactic cosmic rays in atmospheric aerosol nucleation

Abstract: Atmospheric aerosols exert an important influence on climate through their effects on stratiform cloud albedo and lifetime and the invigoration of convective storms. Model calculations suggest that almost half of the global cloud condensation nuclei in the atmospheric boundary layer may originate from the nucleation of aerosols from trace condensable vapours, although the sensitivity of the number of cloud condensation nuclei to changes of nucleation rate may be small. Despite extensive research, fundamental questions remain about the nucleation rate of sulphuric acid particles and the mechanisms responsible, including the roles of galactic cosmic rays and other chemical species such as ammonia. Here we present the first results from the CLOUD experiment at CERN. We find that atmospherically relevant ammonia mixing ratios of 100 parts per trillion by volume, or less, increase the nucleation rate of sulphuric acid particles more than 100–1,000-fold. Time-resolved molecular measurements reveal that nucleation proceeds by a base-stabilization mechanism involving the stepwise accretion of ammonia molecules. Ions increase the nucleation rate by an additional factor of between two and more than ten at ground-level galactic-cosmic-ray intensities, provided that the nucleation rate lies below the limiting ion-pair production rate. We find that ion-induced binary nucleation of H_(2)SO_(4)–H_(2)O can occur in the mid-troposphere but is negligible in the boundary layer. However, even with the large enhancements in rate due to ammonia and ions, atmospheric concentrations of ammonia and sulphuric acid are insufficient to account for observed boundary-layer nucleation.

Field test of quantum key distribution in the Tokyo QKD Network

Abstract: A secure communication network with quantum key distribution in a metropolitan area is reported. Six different QKD systems are integrated into a mesh-type network. GHz-clocked QKD links enable us to demonstrate the world-first secure TV conferencing over a distance of 45km. The network includes a commercial QKD product for long-term stable operation, and application interface to secure mobile phones. Detection of an eavesdropper, rerouting into a secure path, and key relay via trusted nodes are demonstrated in this network.

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function.

Abstract: This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors. We provide an overview on the structure and composition of the plastid genome of land plants as well as the functions of its genes in an explicit phylogenetic and evolutionary context. We will discuss the architecture of land plant plastid chromosomes, including gene content and synteny across land plants. Moreover, we will explore the functions and roles of plastid encoded genes in metabolism and their evolutionary importance regarding gene retention and conservation. We suggest that the slow mode at which the plastome typically evolves is likely to be influenced by a combination of different molecular mechanisms. These include the organization of plastid genes in operons, the usually uniparental mode of plastid inheritance, the activity of highly effective repair mechanisms as well as the rarity of plastid fusion. Nevertheless, structurally rearranged plastomes can be found in several unrelated lineages (e.g. ferns, Pinaceae, multiple angiosperm families). Rearrangements and gene losses seem to correlate with an unusual mode of plastid transmission, abundance of repeats, or a heterotrophic lifestyle (parasites or myco-heterotrophs). While only a few functional gene gains and more frequent gene losses have been inferred for land plants, the plastid Ndh complex is one example of multiple independent gene losses and will be discussed in detail. Patterns of ndh-gene loss and functional analyses indicate that these losses are usually found in plant groups with a certain degree of heterotrophy, might rendering plastid encoded Ndh1 subunits dispensable.

Rotating massive main-sequence stars - I. Grids of evolutionary models and isochrones

Abstract: We present a dense grid of evolutionary tracks and isochrones of rotating massive main-sequence stars. We provide three grids with different initial compositions tailored to compare with early OB stars in the Small and Large Magellanic Clouds and in the Galaxy. Each grid covers masses ranging from 5 to 60 M ⊙ and initial rotation rates between 0 and about 600 km s-1 . To calibrate our models we used the results of the VLT-FLAMES Survey of Massive Stars. We determine the amount of convective overshooting by using the observed drop in rotation rates for stars with surface gravities log g < 3.2 to determine the width of the main sequence. We calibrate the efficiency of rotationally induced mixing using the nitrogen abundance determinations for B stars in the Large Magellanic cloud. We describe and provide evolutionary tracks and the evolution of the central and surface abundances. In particular, we discuss the occurrence of quasi-chemically homogeneous evolution, i.e. the severe effects of efficient mixing of the stellar interior found for the most massive fast rotators. We provide a detailed set of isochrones for rotating stars. Rotation as an initial parameter leads to a degeneracy between the age and the mass of massive main sequence stars if determined from its observed location in the Hertzsprung-Russell diagram. We show that the consideration of surface abundances can resolve this degeneracy.

Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil

Abstract: Genes of archaea encoding homologues of ammonia monooxygenases have been found on a widespread basis and in large amounts in almost all terrestrial and marine environments, indicating that ammonia oxidizing archaea (AOA) might play a major role in nitrification on Earth. However, only one pure isolate of this group from a marine environment has so far been obtained, demonstrating archaeal ammonia oxidation coupled with autotrophic growth similar to the bacterial counterparts. Here we describe the cultivation and isolation of an AOA from soil. It grows on ammonia or urea as an energy source and is capable of using higher ammonia concentrations than the marine isolate, Nitrosopumilus maritimus. Surprisingly, although it is able to grow chemolithoautotrophically, considerable growth rates of this strain are obtained only upon addition of low amounts of pyruvate or when grown in coculture with bacteria. Our findings expand the recognized metabolic spectrum of AOA and help explain controversial results obtained in the past on the activity and carbon assimilation of these globally distributed organisms.

A Mutation in VPS35, Encoding a Subunit of the Retromer Complex, Causes Late-Onset Parkinson Disease

Abstract: To identify rare causal variants in late-onset Parkinson disease (PD), we investigated an Austrian family with 16 affected individuals by exome sequencing. We found a missense mutation, c.1858G>A (p.Asp620Asn), in the VPS35 gene in all seven affected family members who are alive. By screening additional PD cases, we saw the same variant cosegregating with the disease in an autosomal-dominant mode with high but incomplete penetrance in two further families with five and ten affected members, respectively. The mean age of onset in the affected individuals was 53 years. Genotyping showed that the shared haplotype extends across 65 kilobases around VPS35. Screening the entire VPS35 coding sequence in an additional 860 cases and 1014 controls revealed six further nonsynonymous missense variants. Three were only present in cases, two were only present in controls, and one was present in cases and controls. The familial mutation p.Asp620Asn and a further variant, c.1570C>T (p.Arg524Trp), detected in a sporadic PD case were predicted to be damaging by sequence-based and molecular-dynamics analyses. VPS35 is a component of the retromer complex and mediates retrograde transport between endosomes and the trans-Golgi network, and it has recently been found to be involved in Alzheimer disease.

Domains of physical activity and all-cause mortality: systematic review and dose–response meta-analysis of cohort studies

Abstract: Background The dose–response relation between physical activity and all-cause mortality is not well defined at present. We conducted a systematic review and meta-analysis to determine the association with all-cause mortality of different domains of physical activity and of defined increases in physical activity and energy expenditure. Methods MEDLINE, Embase and the Cochrane Library were searched up to September 2010 for cohort studies examining all-cause mortality across different domains and levels of physical activity in adult general populations. We estimated combined risk ratios (RRs) associated with defined increments and recommended levels, using random-effects meta-analysis and dose–response meta-regression models. Results Data from 80 studies with 1 338 143 participants (118 121 deaths) were included. Combined RRs comparing highest with lowest activity levels were 0.65 [95% confidence interval (95% CI) 0.60–0.71] for total activity, 0.74 (95% CI 0.70–0.77) for leisure activity, 0.64 (95% CI 0.55–0.75) for activities of daily living and 0.83 (95% CI 0.71–0.97) for occupational activity. RRs per 1-h increment per week were 0.91 (95% CI 0.87–0.94) for vigorous exercise and 0.96 (95% CI 0.93–0.98) for moderate-intensity activities of daily living. RRs corresponding to 150 and 300 min/week of moderate to vigorous activity were 0.86 (95% CI 0.80–0.92) and 0.74 (95% CI 0.65–0.85), respectively. Mortality reductions were more pronounced in women. Conclusion Higher levels of total and domain-specific physical activity were associated with reduced all-cause mortality. Risk reduction per unit of time increase was largest for vigorous exercise. Moderate-intensity activities of daily living were to a lesser extent beneficial in reducing mortality.

Universal and confident phosphorylation site localization using phosphoRS.

Abstract: An algorithm for the assignment of phosphorylation sites in peptides is described. The program uses tandem mass spectrometry data in conjunction with the respective peptide sequences to calculate site probabilities for all potential phosphorylation sites. Tandem mass spectra from synthetic phosphopeptides were used for optimization of the scoring parameters employing all commonly used fragmentation techniques. Calculation of probabilities was adapted to the different fragmentation methods and to the maximum mass deviation of the analysis. The software includes a novel approach to peak extraction, required for matching experimental data to the theoretical values of all isoforms, by defining individual peak depths for the different regions of the tandem mass spectrum. Mixtures of synthetic phosphopeptides were used to validate the program by calculation of its false localization rate versus site probability cutoff characteristic. Notably, the empirical obtained precision was higher than indicated by the applied probability cutoff. In addition, the performance of the algorithm was compared to existing approaches to site localization such as Ascore. In order to assess the practical applicability of the algorithm to large data sets, phosphopeptides from a biological sample were analyzed, localizing more than 3000 nonredundant phosphorylation sites. Finally, the results obtained for the different fragmentation methods and localization tools were compared and discussed.

Nitrogen-Doped Graphene: Efficient Growth, Structure, and Electronic Properties

Abstract: A novel strategy for efficient growth of nitrogen-doped graphene (N-graphene) on a large scale from s-triazine molecules is presented. The growth process has been unveiled in situ using time-dependent photoemission. It has been established that a postannealing of N-graphene after gold intercalation causes a conversion of the N environment from pyridinic to graphitic, allowing to obtain more than 80% of all embedded nitrogen in graphitic form, which is essential for the electron doping in graphene. A band gap, a doping level of 300 meV, and a charge-carrier concentration of ∼8 × 1012 electrons per cm2, induced by 0.4 atom % of graphitic nitrogen, have been detected by angle-resolved photoemission spectroscopy, which offers great promise for implementation of this system in next generation electronic devices.

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

Abstract: Recent statistical analyses suggest that sequencing of pooled samples provides a cost effective approach to determine genome-wide population genetic parameters. Here we introduce PoPoolation, a toolbox specifically designed for the population genetic analysis of sequence data from pooled individuals. PoPoolation calculates estimates of θWatterson, θπ, and Tajima's D that account for the bias introduced by pooling and sequencing errors, as well as divergence between species. Results of genome-wide analyses can be graphically displayed in a sliding window plot. PoPoolation is written in Perl and R and it builds on commonly used data formats. Its source code can be downloaded from http://code.google.com/p/popoolation/. Furthermore, we evaluate the influence of mapping algorithms, sequencing errors, and read coverage on the accuracy of population genetic parameter estimates from pooled data.

21st century climate change threatens mountain flora unequally across Europe

Abstract: Continental-scale assessments of 21st century global impacts of climate change on biodiversity have forecasted range contractions for many species. These coarse resolution studies are, however, of limited relevance for projecting risks to biodiversity in mountain systems, where pronounced microclimatic variation could allow species to persist locally, and are ill-suited for assessment of species-specific threat in particular regions. Here, we assess the impacts of climate change on 2632 plant species across all major European mountain ranges, using high-resolution (ca. 100 m) species samples and data expressing four future climate scenarios. Projected habitat loss is greater for species distributed at higher elevations; depending on the climate scenario, we find 36-55% of alpine species, 31-51% of subalpine species and 19-46% of montane species lose more than 80% of their suitable habitat by 2070-2100. While our high-resolution analyses consistently indicate marked levels of threat to cold-adapted mountain florae across Europe, they also reveal unequal distribution of this threat across the various mountain ranges. Impacts on florae from regions projected to undergo increased warming accompanied by decreased precipitation, such as the Pyrenees and the Eastern Austrian Alps, will likely be greater than on florae in regions where the increase in temperature is less pronounced and rainfall increases concomitantly, such as in the Norwegian Scandes and the Scottish Highlands. This suggests that change in precipitation, not only warming, plays an important role in determining the potential impacts of climate change on vegetation.

Time-dependent variational principle for quantum lattices.

Abstract: We develop a new algorithm based on the time-dependent variational principle applied to matrix product states to efficiently simulate the real- and imaginary-time dynamics for infinite one-dimensional quantum lattices. This procedure (i) is argued to be optimal, (ii) does not rely on the Trotter decomposition and thus has no Trotter error, (iii) preserves all symmetries and conservation laws, and (iv) has low computational complexity. The algorithm is illustrated by using both an imaginary-time and a real-time example.

Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

Abstract: “Barcode-tagged” PCR primers used for multiplex amplicon sequencing generate a thus-far-overlooked amplification bias that produces variable terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing data from the same environmental DNA template. We propose a simple two-step PCR approach that increases reproducibility and consistently recovers higher genetic diversity in pyrosequencing libraries.

Patchy colloids: state of the art and perspectives

Abstract: Recently, an increasing experimental effort has been devoted to the synthesis of complex colloidal particles with chemically or physically patterned surfaces and possible specific shapes that are far from spherical. These new colloidal particles with anisotropic interactions are commonly named patchy particles. In this Perspective article, we focus on patchy systems characterized by spherical neutral particles with patchy surfaces. We summarize most of the patchy particle models that have been developed so far and describe how their basic features are connected to the physical systems they are meant to investigate. Patchy models consider particles as hard or soft spheres carrying a finite and small number of attractive sites arranged in precise geometries on the particle's surface. The anisotropy of the interaction and the limited valence in bonding are the salient features determining the collective behavior of such systems. By tuning the number, the interaction parameters and the local arrangements of the patches, it is possible to investigate a wide range of physical phenomena, from different self-assembly processes of proteins, polymers and patchy colloids to the dynamical arrest of gel-like structures. We also draw attention to charged patchy systems: colloidal patchy particles as well as proteins are likely charged, hence the description of the presence of heterogeneously distributed charges on the particle surface is a promising perspective for future investigations.

Nomenclature of the tourmaline-supergroup minerals

Abstract: A nomenclature for tourmaline-supergroup minerals is based on chemical systematics using the generalized tourmaline structural formula: XY3 Z6(T6O18)(BO3)3V3W where the common ions at each site are X = Na1+, Ca2+, K1+ and vacancy; Y = Fe2+, Mg2+, Al3+, Li1+, Fe3+ and Cr3+; Z = Al3+, Fe3+, Mg2+ and Cr3+; T = Si4+, Al3+ and B3+; B = B3+; V = OH1- and O2-; and W = OH1-, F1- and O2-. Most compositional variability occurs at the X, Y, Z, W and V sites.

Inspiral-merger-ringdown waveforms for black-hole binaries with nonprecessing spins

Abstract: We present the first analytical inspiral-merger-ringdown gravitational waveforms from binary black holes (BBHs) with nonprecessing spins, that is based on a description of the late-inspiral, merger and ringdown in full general relativity. By matching a post-Newtonian description of the inspiral to a set of numerical-relativity simulations, we obtain a waveform family with a conveniently small number of physical parameters. These waveforms will allow us to detect a larger parameter space of BBH coalescence, including a considerable fraction of precessing binaries in the comparable-mass regime, thus significantly improving the expected detection rates.

Analyticity of periodic traveling free surface water waves with vorticity

Abstract: We prove that the prole of a periodic traveling wave propagating at the surface of water above a at bed in a ow with a real analytic vorticity must be real analytic, provided the wave speed exceeds the horizontal uid velocity throughout the ow. The real analyticity of each streamline be