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  • 1
    Language: English
    In: Physical review. E, Statistical, nonlinear, and soft matter physics, January 2011, Vol.83(1 Pt 1), pp.011113
    Description: Many physical and chemical processes, such as folding of biopolymers, are best described as dynamics on large combinatorial energy landscapes. A concise approximate description of the dynamics is obtained by partitioning the microstates of the landscape into macrostates. Since most landscapes of interest are not tractable analytically, the probabilities of transitions between macrostates need to be extracted numerically from the microscopic ones, typically by full enumeration of the state space or approximations using the Arrhenius law. Here, we propose to approximate transition probabilities by a Markov chain Monte Carlo method. For landscapes of the number partitioning problem and an RNA switch molecule, we show that the method allows for accurate probability estimates with significantly reduced computational cost.
    Keywords: Physics;
    E-ISSN: 1550-2376
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  • 2
    Language: English
    In: Annals of the Rheumatic Diseases, March, 2013, Vol.72(3), p.A72(1)
    Keywords: Arthritis -- Risk Factors ; Arthritis -- Research ; Autoantibodies -- Research ; Muscular Diseases -- Complications And Side Effects ; Muscular Diseases -- Research ; Ultrasound Imaging -- Usage
    ISSN: 0003-4967
    Source: Cengage Learning, Inc.
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  • 3
    Language: English
    In: Chemistry - A European Journal, August 24, 2015, Vol.21(35), p.12509(8)
    Description: To purchase or authenticate to the full-text of this article, please visit this link: http://onlinelibrary.wiley.com/doi/10.1002/chem.201502199/abstract Byline: Marius I. Arz, Martin Stra[sz]mann, Andreas Meyer, Gregor Schnakenburg, Olav Schiemann, Alexander C. Filippou Keywords: multiple bonds; N-heterocyclic carbenes; radical ions; silicon Abstract One-electron oxidation of the disilicon(0) compound Si.sub.2(Idipp).sub.2 (1, Idipp=1,3-bis(2,6-diisopropylphenyl)imidazolin-2-ylidene) with [Fe(C.sub.5Me.sub.5).sub.2][B(Ar.sub.F).sub.4] (Ar.sub.F=C.sub.6H.sub.3-3,5-(CF.sub.3).sub.2) affords selectively the green radical salt [Si.sub.2(Idipp).sub.2][B(Ar.sub.F).sub.4] (1-[B(Ar.sub.F).sub.4). Oxidation of the centrosymmetric 1 occurs reversibly at a low redox potential (E.sub.1/2=-1.250 V vs. Fc.sub.+/Fc), and is accompanied by considerable structural changes as shown by single-crystal X-ray structural analysis of 1-B(Ar.sub.F).sub.4. These include a shortening of the Sii[pounds sterling] Si bond, a widening of the Si-Si-C.sub.NHC angles, and a lowering of the symmetry, leading to a quite different conformation of the NHC substituents at the two inequivalent Si sites in 1.sub.+. Comparative quantum chemical calculations of 1 and 1.sub.+ indicate that electron ejection occurs from the symmetric (n.sub.+) combination of the Si lone pairs (HOMO). EPR studies of 1-B(Ar.sub.F).sub.4 in frozen solution verified the inequivalency of the two Si sites observed in the solid-state, and point in agreement with the theoretical results to an almost equal distribution of the spin density over the two Si atoms, leading to quite similar .sub.29Si hyperfine coupling tensors in 1.sub.+. EPR studies of 1-B(Ar.sub.F).sub.4 in liquid solution unraveled a topomerization with a low activation barrier that interconverts the two Si sites in 1.sub.+. Author Affiliation: Institut fur Anorganische Chemie, Rheinische Friedrich-Wilhelms-Universitat Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn (Germany) Institut fur Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universitat Bonn, Wegelerstrasse 12, 53115 Bonn (Germany) Supporting information: Additional Supporting Information may be found in the online version of this article As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. CAPTION(S): miscellaneous_information
    Keywords: Oxidation-Reduction Reactions -- Chemical Properties ; Oxidation-Reduction Reactions -- Analysis ; Heterocyclic Compounds -- Chemical Properties ; Heterocyclic Compounds -- Analysis ; Intermediates (Chemicals) -- Chemical Properties ; Intermediates (Chemicals) -- Analysis
    ISSN: 0947-6539
    E-ISSN: 15213765
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  • 4
    Language: English
    In: The Journal of Allergy and Clinical Immunology, February 2018, Vol.141(2), pp.AB191-AB191
    Description: [...]IgE anti-sRW containing sera (range 0.1 to 380 kUa/L, n=100) were used to QC the specificity of 2-lots of sRW-allergorbents manufactured with sRW, collected pre-2015 or 2016-2017 using the same collection area, time-of-year and collection method to assess global warming's impact on allergenic potency....
    Keywords: Medicine
    ISSN: 0091-6749
    E-ISSN: 1097-6825
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  • 5
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 10 September 2013, Vol.110(37), pp.E3487-96
    Description: Small RNAs (sRNAs) constitute a large and heterogeneous class of bacterial gene expression regulators. Much like eukaryotic microRNAs, these sRNAs typically target multiple mRNAs through short seed pairing, thereby acting as global posttranscriptional regulators. In some bacteria, evidence for hundreds to possibly more than 1,000 different sRNAs has been obtained by transcriptome sequencing. However, the experimental identification of possible targets and, therefore, their confirmation as functional regulators of gene expression has remained laborious. Here, we present a strategy that integrates phylogenetic information to predict sRNA targets at the genomic scale and reconstructs regulatory networks upon functional enrichment and network analysis (CopraRNA, for Comparative Prediction Algorithm for sRNA Targets). Furthermore, CopraRNA precisely predicts the sRNA domains for target recognition and interaction. When applied to several model sRNAs, CopraRNA revealed additional targets and functions for the sRNAs CyaR, FnrS, RybB, RyhB, SgrS, and Spot42. Moreover, the mRNAs gdhA, lrp, marA, nagZ, ptsI, sdhA, and yobF-cspC were suggested as regulatory hubs targeted by up to seven different sRNAs. The verification of many previously undetected targets by CopraRNA, even for extensively investigated sRNAs, demonstrates its advantages and shows that CopraRNA-based analyses can compete with experimental target prediction approaches. A Web interface allows high-confidence target prediction and efficient classification of bacterial sRNAs.
    Keywords: E. Coli ; RNA–RNA Interaction ; Regulatory RNA ; RNA, Bacterial -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 6
    In: Nucleic Acids Research, 2017, Vol. 45(W1), pp.W435-W439
    Description: The IntaRNA algorithm enables fast and accurate prediction of RNA–RNA hybrids by incorporating seed constraints and interaction site accessibility. Here, we introduce IntaRNA v2, which enables enhanced parameterization as well as fully customizable control over the prediction modes and output formats. Based on up to date benchmark data, the enhanced predictive quality is shown and further improvements due to more restrictive seed constraints are highlighted. The extended web interface provides visualizations of the new minimal energy profiles for RNA–RNA interactions. These allow a detailed investigation of interaction alternatives and can reveal potential interaction site multiplicity. IntaRNA v2 is freely available (source and binary), and distributed via the conda package manager. Furthermore, it has been included into the Galaxy workflow framework and its already established web interface enables ad hoc usage.
    Keywords: Web Server Issue;
    ISSN: 0305-1048
    E-ISSN: 1362-4962
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  • 7
    Language: English
    In: Nucleic acids research, 06 September 2017, Vol.45(15), pp.8745-8757
    Description: MicroRNAs (miRNAs) are key regulators of cell-fate decisions in development and disease with a vast array of target interactions that can be investigated using computational approaches. For this study, we developed metaMIR, a combinatorial approach to identify miRNAs that co-regulate identified subsets of genes from a user-supplied list. We based metaMIR predictions on an improved dataset of human miRNA-target interactions, compiled using a machine-learning-based meta-analysis of established algorithms. Simultaneously, the inverse dataset of negative interactions not likely to occur was extracted to increase classifier performance, as measured using an expansive set of experimentally validated interactions from a variety of sources. In a second differential mode, candidate miRNAs are predicted by indicating genes to be targeted and others to be avoided to potentially increase specificity of results. As an example, we investigate the neural crest, a transient structure in vertebrate development where miRNAs play a pivotal role. Patterns of metaMIR-predicted miRNA regulation alone partially recapitulated functional relationships among genes, and separate differential analysis revealed miRNA candidates that would downregulate components implicated in cancer progression while not targeting tumour suppressors. Such an approach could aid in therapeutic application of miRNAs to reduce unintended effects. The utility is available at http://rna.informatik.uni-freiburg.de/metaMIR/.
    Keywords: Algorithms ; Gene Regulatory Networks ; Computational Biology -- Methods ; Micrornas -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 8
    Language: English
    In: Chemistry - A European Journal, Nov 23, 2015, Vol.21(48), p.17184(7)
    Description: To purchase or authenticate to the full-text of this article, please visit this link: http://onlinelibrary.wiley.com/doi/10.1002/chem.201503300/abstract Byline: Joel Torres-Alacan, Ujjal Das, Boris Wezisla, Martin Stra[sz]mann, Alexander C. Filippou, Peter Vohringer Keywords: metallacycles; metathesis; photochemistry; time-resolved vibrational spectroscopy; transition-metal complexes Abstract Flash photolysis combined with step-scan and rapid-scan Fourier-transform infrared spectroscopy was carried out to explore the photochemistry of a puckered, quasi-square pyramidal ferracyclobutadiene, [Fe{I*.sub.2-C.sub.3(NEt.sub.2).sub.3}(CO).sub.3]BF.sub.4 ([1]BF.sub.4), that features three additional carbonyl ligands in the metal coordination sphere. In liquid solution at room temperature, an excitation with I'=355 nm light resulted in the loss of one CO ligand, which is cleaved from a basal metal-coordination site. Within the time resolution of the experiment, a solvent molecule promptly refills the resultant vacancy at the coordinatively unsaturated metal center. In the weakly interacting liquid, dichloromethane, the counterion of the complex is subsequently able to substitute the solvent in the coordination sphere of the iron center, thereby forming as a stable product a neutral dicarbonyl tetrafluoroborato iron(0) species containing a four-membered ferracycle. Author Affiliation: Institut fur Physikalische und Theoretische Chemie, der Rheinischen Friedrich-Wilhelms-Universitat, Wegelerstrasse 12, 53115 Bonn (Germany) Institut fur Anorganische Chemie, der Rheinischen Friedrich-Wilhelms-Universitat, Gerhard-Domagk-Strasse 1, 53121 Bonn (Germany) Supporting information: Additional Supporting Information may be found in the online version of this article As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. CAPTION(S): miscellaneous_information
    Keywords: Chlorinated Solvents ; Infrared Spectroscopy ; Photolysis
    ISSN: 0947-6539
    E-ISSN: 15213765
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  • 9
    Language: English
    In: Taxation, July 14, 2011, Vol.168(4312), p.14-17
    Keywords: Tax Incentives -- Management ; Small Business -- Investments ; Investments -- Taxation
    ISSN: 0040-0149
    Source: Cengage Learning, Inc.
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  • 10
    Article
    Article
    De Gruyter
    In: Bio-Algorithms and Med-Systems, 2014, Vol.10(4), pp.213-225
    Description: Lattice protein models are well-studied abstractions of globular proteins. By discretizing the structure space and simplifying the energy model over regular proteins, they enable detailed studies of protein structure formation and evolution. However, even in the simplest lattice protein models, the prediction of optimal structures is computationally difficult. Therefore, often, heuristic approaches are applied to find such conformations. Commonly, heuristic methods find only locally optimal solutions. Nevertheless, there exist methods that guarantee to predict globally optimal structures. Currently, only one such exact approach is publicly available, namely the constraint-based protein structure prediction method and variants. Here, we review exact approaches and derived methods. We discuss fundamental concepts like hydrophobic core construction and their use in optimal structure prediction, as well as possible applications like combinations of different energy models.
    Keywords: Cpsp ; Hp-Model ; Lattice Protein ; Optimal Structure ; Protein Structure Prediction
    ISSN: 1895-9091
    E-ISSN: 1896-530X
    Source: Walter de Gruyter GmbH
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