ALBERT

Description: : Many existing databases annotate experimentally characterized single nucleotide polymorphisms (SNPs). Each non-synonymous SNP (nsSNP) changes one amino acid in the gene product (single amino acid substitution;SAAS). This change can either affect protein function or be neutral in that respect. Most polymorphisms lack experimental annotation of their functional impact. Here, we introduce SNPdbe—SNP database of effects, with predictions of computationally annotated functional impacts of SNPs. Database entries represent nsSNPs in dbSNP and 1000 Genomes collection, as well as variants from UniProt and PMD. SAASs come from 〉2600 organisms; ‘human’ being the most prevalent. The impact of each SAAS on protein function is predicted using the SNAP and SIFT algorithms and augmented with experimentally derived function/structure information and disease associations from PMD, OMIM and UniProt. SNPdbe is consistently updated and easily augmented with new sources of information. The database is available as an MySQL dump and via a web front end that allows searches with any combination of organism names, sequences and mutation IDs. Availability: http://www.rostlab.org/services/snpdbe Contact: schaefer@rostlab.org ; snpdbe@rostlab.org

Description: [1]  The North Atlantic Oscillation (NAO) index is a frequently used measure for the mean winter conditions in northern Europe. A positive, high index is associated with strong westerlies and anomalous warm temperatures. The effects on sea ice conditions in the Baltic Sea are twofold. Warm temperatures prevent sea ice formation. If ice is present nevertheless, the strong winds can promote the formation of ice ridges which hinders ship traffic. We use an ocean-sea ice model to investigate the NAO impact on the ridged ice area fraction in the Baltic during 1962–2007. Our simulations indicate that in the northern Bothnian Bay a high NAO index is related to an anomalous accumulation of ridges while in the rest of the Baltic Sea the relationship is contrary. The NAO explains only 20–25% of the ridged ice fraction interannual variability which indicates the systems complexity. However, we find high skill with local correlations around 0.8 for annually averaged ridged ice fraction reconstructed from multilinear regression using winter averaged wind extremes, surface air temperature, and sea surface temperature (SST). This suggests that the amount of ridged ice in late winter can be derived from these routinely measured quantities. In large parts of the basin, it is sufficient to use the atmospheric parameters as a predictor while in the eastern Bothnian Bay and southern Gulf of Finland the SST is required to reconstruct the bulk of the ridged ice fraction.

Description: From Russia in the east to Sweden, Denmark, and Germany in the west, reaching south to the tips of the Czech Republic, Slovakia, and Ukraine, the Baltic Sea watershed drains nearly 20% of Europe (see Figure 1). In the highly populated south, the temperate climate hosts intensive agriculture and industry. In the north, the landscape is boreal and rural. In the Baltic Sea itself, complex bathymetry and stratification patterns as well as extended hypoxic and anoxic deep waters add to the diversity. Yet in recent history, the differences across the Baltic Sea region have been more than physical: In the mid-20th century, the watershed was split in two.

Description: SUMMARY We present an algorithm for automated S -phase arrival time determination of local, regional and teleseismic events based on autoregressive (AR) prediction of the waveform. The waveforms of the horizontal components are predicted using a scalar AR model for multicomponent recordings. The AR coefficients are estimated in a short moving window using a least-squares approach minimizing the forward prediction error. Synthetic tests with single-component data show that the least-squares approach yields similar or even better results than the Yule–Walker and Burg’s algorithms. We discuss the choice of the AR model and show that the corresponding prediction error of the AR model, applied to both horizontal components, is sufficient to detect instantaneous changes in amplitude, frequency, phase and polarization. The rms prediction error of both horizontal components defines the characteristic function, to which an algorithm for the estimation of the arrival time is applied. The proposed algorithm also accounts for automatic quality assessment of the estimated S -onset times. Four quality criteria are used to define the weight of the automatically estimated S -arrival time. They are based on two different estimations of the slope of the characteristic function and on two signal-to-noise ratios (SNRs). The proposed algorithm is applied to a large data set recorded by a dense regional seismic network in the southern Aegean. The data set contains recordings of local and regional crustal as well as intermediate deep earthquakes. The reliability and the robustness of the picking algorithm is tested by comparing more than 2600 manual S readings, serving as reference picks, with the corresponding automatically derived S -onset times. We find an average deviation from the reference picks of 0.5 s ± 0.8 s. If only excellent automatic picks are considered, the average difference from the reference picks is reduced to −0.057 s ± 0.12 s. The proposed automatic quality weighting scheme yields similar weights for the individual S onsets as the ones set by the analysts. The presented algorithm works reliably and robust even when applied to a data set with heterogeneous SNRs. Furthermore, the proposed method may be suitable for the implementation in an earthquake early-warning system as additional, accurate S -wave arrival time estimates stabilize the location, especially the determination of the event depth.

Description: The formation of epicormic sprouts on the boles of trees is a phenomenon that has, until recently, been poorly understood. Renewed interest in the topic in the last two decades has led to significant advances in our knowledge of the subject, especially in regard to bud anatomy, morphology and ontogeny. There exists, however, no comprehensive synthesis of results from different disciplines across genera and geographical areas; this review seeks to fill that void and provide a comprehensive framework capable of guiding future research. A tree's potential for producing epicormic branches is dependent on the number of buds that are produced on a growing shoot, the development of those buds and associated meristems over time and the factors that promote sprout formation or bud death. Based on the descriptions of a limited number of researched species, we were able to describe four different developmental strategies for epicormics based on characteristics of meristem development. Control over epicormic bud dormancy is complex, but it is clear that the traditional view of auxin-mediated dormancy release is incomplete. Genetic control over epicormic development is yet to be empirically proven. Future research should focus on clarifying these physiological and genetic controls of epicormic bud development as well as developing more robust methods for tracking epicormics in ecological and silvicultural studies.

Description: Default logic was introduced by Reiter in 1980. In 1992, Gottlob classified the complexity of the extension existence problem for propositional default logic as $${\Sigma }_{2}^{\hbox{ p }}$$ -complete, and the complexity of the credulous and skeptical reasoning problem as $${\Sigma }_{2}^{\hbox{ p }}$$ -complete, respectively $${\Pi }_{2}^{\hbox{ p }}$$ -complete. Additionally, he investigated restrictions on the default rules, i.e. semi-normal default rules. Selman used in 1992 a similar approach with disjunction-free and unary default rules. In this article, we systematically restrict the set of allowed propositional connectives. We give a complete complexity classification for all sets of Boolean functions in the meaning of Post's lattice for all three common decision problems for propositional default logic. We show that the complexity is a hexachotomy ( $${\Sigma }_{2}^{\hbox{ p }}$$ -, $${\Delta }_{2}^{\hbox{ p }}$$ -, NP-, P-, NL-complete, trivial) for the extension existence problem, while for the credulous and skeptical reasoning problem we obtain similar classifications without trivial cases.

Description: Motivation: The precise identification of functionally and structurally important residues of a protein is still an open problem, and state-of-the-art classifiers predict only one or at most two different categories. Result: We have implemented the classifier CLIPS-4D, which predicts in a mutually exclusively manner a role in catalysis, ligand-binding or protein stability for each residue-position of a protein. Each prediction is assigned a P -value, which enables the statistical assessment and the selection of predictions with similar quality. CLIPS-4D requires as input a multiple sequence alignment and a 3D structure of one protein in PDB format. A comparison with existing methods confirmed state-of-the-art prediction quality, even though CLIPS-4D classifies more specifically than other methods. CLIPS-4D was implemented as a multiclass support vector machine, which exploits seven sequence-based and two structure-based features, each of which was shown to contribute to classification quality. The classification of ligand-binding sites profited most from the 3D features, which were the assessment of the solvent accessible surface area and the identification of surface pockets. In contrast, five additionally tested 3D features did not increase the classification performance achieved with evolutionary signals deduced from the multiple sequence alignment. Availability: CLIPS-4D is available as a web-service at http://www-bioinf.uni-regensburg.de . Contact: rainer.merkl@ur.de Supplementary information: Supplementary data are available at Bioinformatics online.