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  1. Article ; Online: Exploring the Limits of the Geometric Copolymerization Model

    Martin S. Engler / Kerstin Scheubert / Ulrich S. Schubert / Sebastian Böcker

    Polymers, Vol 9, Iss 3, p

    2017  Volume 101

    Abstract: The geometric copolymerization model is a recently introduced statistical Markov chain model. Here, we investigate its practicality. First, several approaches to identify the optimal model parameters from observed copolymer fingerprints are evaluated ... ...

    Abstract The geometric copolymerization model is a recently introduced statistical Markov chain model. Here, we investigate its practicality. First, several approaches to identify the optimal model parameters from observed copolymer fingerprints are evaluated using Monte Carlo simulated data. Directly optimizing the parameters is robust against noise but has impractically long running times. A compromise between robustness and running time is found by exploiting the relationship between monomer concentrations calculated by ordinary differential equations and the geometric model. Second, we investigate the applicability of the model to copolymerizations beyond living polymerization and show that the model is useful for copolymerizations involving termination and depropagation reactions.
    Keywords copolymer kinetics ; copolymer fingerprint ; Markov model ; Monte Carlo simulations ; Organic chemistry ; QD241-441
    Language English
    Publishing date 2017-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: New Statistical Models for Copolymerization

    Martin S. Engler / Kerstin Scheubert / Ulrich S. Schubert / Sebastian Böcker

    Polymers, Vol 8, Iss 6, p

    2016  Volume 240

    Abstract: For many years, copolymerization has been studied using mathematical and statistical models. Here, we present new Markov chain models for copolymerization kinetics: the Bernoulli and Geometric models. They model copolymer synthesis as a random process ... ...

    Abstract For many years, copolymerization has been studied using mathematical and statistical models. Here, we present new Markov chain models for copolymerization kinetics: the Bernoulli and Geometric models. They model copolymer synthesis as a random process and are based on a basic reaction scheme. In contrast to previous Markov chain approaches to copolymerization, both models take variable chain lengths and time-dependent monomer probabilities into account and allow for computing sequence likelihoods and copolymer fingerprints. Fingerprints can be computed from copolymer mass spectra, potentially allowing us to estimate the model parameters from measured fingerprints. We compare both models against Monte Carlo simulations. We find that computing the models is fast and memory efficient.
    Keywords copolymer kinetics ; copolymer fingerprint ; Markov model ; Organic chemistry ; QD241-441
    Language English
    Publishing date 2016-06-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Molecular Formula Identification with SIRIUS

    Kai Dührkop / Kerstin Scheubert / Sebastian Böcker

    Metabolites, Vol 3, Iss 2, Pp 506-

    2013  Volume 516

    Abstract: We present results of the SIRIUS2 submission to the 2012 CASMI contest. Only results for Category 1 (molecular formula identification) were submitted. The SIRIUS method and the parameters used are briefly described, followed by detailed analysis of the ... ...

    Abstract We present results of the SIRIUS2 submission to the 2012 CASMI contest. Only results for Category 1 (molecular formula identification) were submitted. The SIRIUS method and the parameters used are briefly described, followed by detailed analysis of the results and a discussion of cases where SIRIUS2 was unable to come up with the correct molecular formula. SIRIUS2 returns consistently high quality results, with the exception of fragmentation pattern analysis of time-of-flight data. We then discuss possibilities for further improving SIRIUS2 in the future.
    Keywords CASMI ; mass spectrometry ; small molecules ; SIRIUS ; molecular formula identification ; isotope patterns ; fragmentation patterns ; Biochemistry ; QD415-436 ; Organic chemistry ; QD241-441 ; Chemistry ; QD1-999 ; Science ; Q ; DOAJ:Biochemistry ; DOAJ:Life Sciences ; DOAJ:Biology and Life Sciences
    Language English
    Publishing date 2013-06-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Computational mass spectrometry for small-molecule fragmentation

    Hufsky, Franziska / Kerstin Scheubert / Sebastian Böcker

    Trends in analytical chemistry. 2014 Jan., v. 53

    2014  

    Abstract: The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. Computational aspects of identifying small molecules range from searching a reference spectral library to the structural ... ...

    Abstract The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. Computational aspects of identifying small molecules range from searching a reference spectral library to the structural elucidation of an unknown. In this review, we concentrate on five important aspects of the computational analysis. We find that novel computational methods may overcome the boundaries of spectral libraries, by searching in the more comprehensive molecular structure databases, or not requiring any databases at all.
    Keywords chemical structure ; computational methodology ; databases ; mass spectrometry
    Language English
    Dates of publication 2014-01
    Size p. 41-48.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2014041-1
    ISSN 0165-9936
    ISSN 0165-9936
    DOI 10.1016/j.trac.2013.09.008
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Significance estimation for large scale metabolomics annotations by spectral matching

    Kerstin Scheubert / Franziska Hufsky / Daniel Petras / Mingxun Wang / Louis-Félix Nothias / Kai Dührkop / Nuno Bandeira / Pieter C. Dorrestein / Sebastian Böcker

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Volume 10

    Abstract: Matching fragment spectra to reference library spectra is an important procedure for annotating small molecules in untargeted mass spectrometry based metabolomics studies. Here, the authors develop strategies to estimate false discovery rates (FDR) by ... ...

    Abstract Matching fragment spectra to reference library spectra is an important procedure for annotating small molecules in untargeted mass spectrometry based metabolomics studies. Here, the authors develop strategies to estimate false discovery rates (FDR) by empirical Bayes and target-decoy based methods which enable a user to define the scoring criteria for spectral matching.
    Keywords Science ; Q
    Language English
    Publishing date 2017-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Significance estimation for large scale metabolomics annotations by spectral matching

    Kerstin Scheubert / Franziska Hufsky / Daniel Petras / Mingxun Wang / Louis-Félix Nothias / Kai Dührkop / Nuno Bandeira / Pieter C. Dorrestein / Sebastian Böcker

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Volume 10

    Abstract: Matching fragment spectra to reference library spectra is an important procedure for annotating small molecules in untargeted mass spectrometry based metabolomics studies. Here, the authors develop strategies to estimate false discovery rates (FDR) by ... ...

    Abstract Matching fragment spectra to reference library spectra is an important procedure for annotating small molecules in untargeted mass spectrometry based metabolomics studies. Here, the authors develop strategies to estimate false discovery rates (FDR) by empirical Bayes and target-decoy based methods which enable a user to define the scoring criteria for spectral matching.
    Keywords Science ; Q
    Language English
    Publishing date 2017-11-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: Inhibition of 5-lipoxygenase as anti-inflammatory mode of action of Plectranthus zeylanicus Benth and chemical characterization of ingredients by a mass spectrometric approach

    Napagoda, Mayuri / Aleš Svatoš / Jana Gerstmeier / Kerstin Scheubert / Oliver Werz / Sandra Wesely / Sven Popella / Sybille Lorenz

    Journal of ethnopharmacology. 2014 Feb. 03, v. 151, no. 2

    2014  

    Abstract: The perennial herb Plectranthus zeylanicus Benth is extensively used in traditional medicine in Sri Lanka and South India for treating inflammatory conditions, but pharmacological features of Plectranthus zeylanicus are hardly explored in order to ... ...

    Abstract The perennial herb Plectranthus zeylanicus Benth is extensively used in traditional medicine in Sri Lanka and South India for treating inflammatory conditions, but pharmacological features of Plectranthus zeylanicus are hardly explored in order to understand and rationalize its use in ethnomedicine. As 5-lipoxygenase (5-LO) is a key enzyme in inflammatory disorders such as asthma or atherosclerosis, we investigated 5-LO inhibition by Plectranthus zeylanicus extracts and analyzed relevant constituents.We applied cell-free and cell-based assays to investigate suppression of 5-LO activity. Cell viability, radical scavenger activities, and inhibition of reactive oxygen species formation (ROS) in neutrophils were analysed to exclude unspecific cytotoxic or antioxidant effects. Constituents of the extracts were characterized by bioassay-guided fractionation and by analysis using gas or liquid chromatography coupled to mass spectrometric (Orbitrap) analysis.Extracts of Plectranthus zeylanicus prepared with n-hexane or dichloromethane potently suppressed 5-LO activity in stimulated human neutrophils (IC50=6.6 and 12μg/ml, respectively) and inhibited isolated human recombinant 5-LO (IC50=0.7 and 1.2μg/ml, respectively). In contrast, no significant radical scavenging activity or suppression of ROS formation was observed, and neutrophil viability was unaffected. Besides ubiquitously occurring ingredients, coleone P, cinncassiol A and C, and callistric acid were identified as constituents in the most active fraction.Together, potent inhibition of 5-LO activity, without concomitant anti-oxidant activity and cytotoxic effects, rationalizes the ethnopharmacological use of Plectranthus zeylanicus as anti-inflammatory remedy. Modern chromatographic/mass spectrometric analysis reveals discrete chemical structures of relevant constituents.
    Keywords antioxidant activity ; asthma ; atherosclerosis ; cell viability ; chemical structure ; cytotoxicity ; enzyme inhibition ; fractionation ; hexane ; ingredients ; liquid chromatography ; mass spectrometry ; mechanism of action ; methylene chloride ; neutrophils ; Plectranthus ; traditional medicine ; India ; Sri Lanka
    Language English
    Dates of publication 2014-0203
    Size p. 800-809.
    Publishing place Elsevier Ireland Ltd
    Document type Article
    ZDB-ID 134511-4
    ISSN 1872-7573 ; 0378-8741
    ISSN (online) 1872-7573
    ISSN 0378-8741
    DOI 10.1016/j.jep.2013.11.004
    Database NAL-Catalogue (AGRICOLA)

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  8. Article: Munronia pinnata (Wall.) Theob.: Unveiling phytochemistry and dual inhibition of 5-lipoxygenase and microsomal prostaglandin E2 synthase (mPGES)-1

    Napagoda, Mayuri / Aleš Svatoš / Andreas Koeberle / Jana Gerstmeier / Kerstin Scheubert / Oliver Werz / Sandra Wesely / Sebastian Böcker / Sven Popella / Sybille Lorenz

    Journal of ethnopharmacology. 2014 Feb. 03, v. 151, no. 2

    2014  

    Abstract: Preparations from Munronia pinnata (Wall.) Theob. are extensively used in traditional medicine in Sri Lanka for the treatment of inflammatory conditions. However, neither the pharmacological features nor the phytochemistry of this plant are explored in ... ...

    Abstract Preparations from Munronia pinnata (Wall.) Theob. are extensively used in traditional medicine in Sri Lanka for the treatment of inflammatory conditions. However, neither the pharmacological features nor the phytochemistry of this plant are explored in order to understand and rationalize the reported ethnobotanical significance. As 5-lipoxygenase (5-LO) and microsomal prostaglandin E2 synthase (mPGES)-1 are crucial enzymes in inflammatory disorders, we evaluated their inhibition by M. pinnata extracts and studied the chemical profile of the plant for the identification of relevant constituents.Cell-free and cell-based assays were employed in order to investigate the suppression of 5-LO and mPGES-1 activity. Cell viability, radical scavenger activities, and inhibition of reactive oxygen species formation (ROS) in neutrophils were studied to assess cytotoxic and antioxidant effects. Gas and liquid chromatography coupled to mass spectrometric analysis enabled the characterization of secondary metabolites.The n-hexane extract of M. pinnata efficiently suppressed 5-LO activity in stimulated human neutrophils (IC50 =8.7μg/ml) and potently inhibited isolated human recombinant 5-LO (IC50 =0.48μg/ml) and mPGES-1 (IC50 =1.0μg/ml). In contrast, no significant radical scavenging activity or suppression of ROS formation was observed, and neutrophil viability was unaffected. The phytochemistry of the plant was unveiled for the first time and phytosterols, fatty acids, sesquiterpenes and several other types of secondary metabolites were identified.Together, potent inhibition of 5-LO and mPGES-1 activity, without concomitant antioxidant activity and cytotoxic effects, rationalizes the ethnopharmacological use of M. pinnata as anti-inflammatory remedy. Detailed chromatographic/mass spectrometric analysis reveals discrete chemical structures of relevant constituents.
    Keywords antioxidant activity ; cell viability ; chemical structure ; cytotoxicity ; enzyme inhibition ; ethnobotany ; fatty acids ; hexane ; inhibitory concentration 50 ; liquid chromatography ; mass spectrometry ; neutrophils ; phytosterols ; prostaglandin-E synthase ; secondary metabolites ; sesquiterpenoids ; traditional medicine ; Sri Lanka
    Language English
    Dates of publication 2014-0203
    Size p. 882-890.
    Publishing place Elsevier Ireland Ltd
    Document type Article
    ZDB-ID 134511-4
    ISSN 1872-7573 ; 0378-8741
    ISSN (online) 1872-7573
    ISSN 0378-8741
    DOI 10.1016/j.jep.2013.11.052
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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