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diff --git a/bibliography.bib b/bibliography.bib index 0fea5e0..d69d4a6 100644 --- a/bibliography.bib +++ b/bibliography.bib @@ -1,3 +1,34 @@ +@article{Wang2005, + author = {Wang, Y.P. and Yan, J. and Fu, P.P. and Chou, M.W.}, + title = {Human liver microsomal reduction of pyrrolizidine alkaloid N-oxides to form the corresponding carcinogenic parent alkaloid}, + journal = {Toxicol Lett}, + year = 2005, + number = {155(3)}, + pages = {411-420}, + doi = {10.1016/j.toxlet.2004.11.010} +} + +@article{Lin1998, + author = {Lin, G. and Cui, Y.Y. and Hawes, E.M.}, + title = {Microsomal Formation of a Pyrrolic Alcohol Glutathione Conjugate of Clivorine. Firm evidence for the formation of a pyrrolic metabolite of an otonecine-type pyrrolizidine alkaloid}, + journal = {Drug Metab Dispos}, + year = 1998, + number = {26(2)}, + pages = {181-4} +} + +@article{Ruan2014, + author = {Ruan, J. and Yang, M. and Fu, P. and Ye, Y. and Lin, G.}, + year = 2014, + title = {Metabolic activation of pyrrolizidine alkaloids: Insights into the structural and enzymatic basis}, + journal = {Chem. Res. Toxicol.}, + number = 27, + pages = {1030–1039}, + doi = {10.1021/tx500071q} +} + + + @incollection{Piegorsch1991, author = {Piegorsch, W.W. and Zeiger, E.}, booktitle = {Statistical Methods in Toxicology, Lecture Notes in Medical Informatics}, @@ -9,21 +40,19 @@ } @article{Dunkel1984, -author = {Dunkel, Virginia C. and Zeiger, Errol and Brusick, David and McCoy, Elena and McGregor, Douglas and Mortelmans, Kristien and Rosenkranz, Herbert S. and Simmon, Vincent F.}, -title = {Reproducibility of microbial mutagenicity assays: I. Tests with Salmonella typhimurium and Escherichia coli using a standardized protocol}, -journal = {Environmental Mutagenesis}, -volume = {6}, -number = {S2}, -pages = {1-50}, -keywords = {mutagenicity, Salmonella, E. coli, interlaboratory reproducibility, collaborative study, standardized protocol}, -doi = {https://doi.org/10.1002/em.2860060702}, -url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/em.2860060702}, -eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/em.2860060702}, -year = {1984} + author = {Dunkel, Virginia C. and Zeiger, Errol and Brusick, David and McCoy, Elena and McGregor, Douglas and Mortelmans, Kristien and Rosenkranz, Herbert S. and Simmon, Vincent F.}, + title = {Reproducibility of microbial mutagenicity assays: I. Tests with Salmonella typhimurium and Escherichia coli using a standardized protocol}, + journal = {Environmental Mutagenesis}, + volume = {6}, + number = {S2}, + pages = {1-50}, + keywords = {mutagenicity, Salmonella, E. coli, interlaboratory reproducibility, collaborative study, standardized protocol}, + doi = {https://doi.org/10.1002/em.2860060702}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/em.2860060702}, + eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/em.2860060702}, + year = {1984} } - - @article{Kamber2009, author = {Kamber, Markus and Flückiger-Isler, Sini and Engelhardt, Günter and Jaeckh, Rudolf and Zeiger, Errol}, title = "{Comparison of the Ames II and traditional Ames test responses with respect to mutagenicity, strain specificities, need for metabolism and correlation with rodent carcinogenicity}", @@ -59,7 +88,7 @@ year = {2016}, issn = {0378-4274}, doi = {https://doi.org/10.1016/j.toxlet.2016.05.002}, url = {https://www.sciencedirect.com/science/article/pii/S0378427416300911}, -author = {Karl-Heinz Merz and Dieter Schrenk}, +author = {K.H. Merz and D. Schrenk}, keywords = {Pyrrolizidine alkaloids, Relative potency factors, Risk assessment, Toxicity}, abstract = {Pyrrolizidine alkaloids (PAs) are among the most potent natural toxins occurring in a broad spectrum of plant species from various families. Recently, findings of considerable contamination of teas/herbal infusions prepared from non-PA plants have been reported. These are obviously due to cross-contamination with minor amounts of PA plants and can affect both food and herbal medicines. Another source of human exposure is honey collected from PA plants. These findings illustrate the requirement for a comprehensive risk assessment of PAs, hampered by the enormous number of different PA congeners occurring in nature. Up to now, risk assessment is based on the carcinogenicity of certain PAs after chronic application to rats using the sum of detected PAs as dose metric. Because of the well-documented large structure-dependent differences between sub-groups of PA congeners with respect to their genotoxicity and (cyto)toxicity, however, this procedure is inadequate. Here we provide an overview of recent attempts to assess the risk of PA exposure and the available literature on the toxic effects and potencies of different congeners. Based on these considerations, we have derived interim Relative Potency (REP) factors for a number of abundant PAs suggesting a factor of 1.0 for cyclic di-esters and open-chain di-esters with 7S configuration, of 0.3 for mono-esters with 7S configuration, of 0.1 for open-chain di-esters with 7R configuration and of 0.01 for mono-esters with 7R configuration. For N-oxides we suggest to apply the REP factor of the corresponding PA. We are confident that the use of these values can provide a more scientific basis for PA risk assessment until a more detailed experimental analysis of the potencies of all relevant congeners can be carried out.} } @@ -143,7 +172,7 @@ year = {2013}, issn = {0378-8741}, doi = {https://doi.org/10.1016/j.jep.2013.09.010}, url = {https://www.sciencedirect.com/science/article/pii/S0378874113006430}, -author = {Yan Hong Li and Winnie Lai Ting Kan and Na Li and Ge Lin}, +author = {Y. H. Li and W. L. T. Kan and N. Li and G. Lin}, keywords = {Pyrrolizidine alkaloids, model, Cytotoxicity, HepG2 cell}, abstract = {Ethnopharmacological relevance Pyrrolizidine alkaloids (PAs) are a group of heterocyclic phytotoxins present in a wide range of plants. The consumption of PA-containing medicinal herbs or PA-contaminated foodstuffs has long been reported to cause human hepatotoxicity. However, the degrees of hepatotoxicity of different PAs are unknown, which makes it difficult to determine a universal threshold of toxic dose of individual PAs for safe regulation of PA-containing natural products. The aim of the present study is to develop a simple and convenient in vitro model to assess the hepatotoxicity of different PAs. @@ -184,7 +213,7 @@ Using the developed in vitro model, the cytotoxicity of different PAs and the ex issn = {0278-6915}, doi = {https://doi.org/10.1016/j.fct.2019.05.040}, url = {https://www.sciencedirect.com/science/article/pii/S0278691519303072}, - author = {Jochem Louisse and Deborah Rijkers and Geert Stoopen and Wendy Jansen Holleboom and Mona Delagrange and Elise Molthof and Patrick P.J. Mulder and Ron L.A.P. Hoogenboom and Marc Audebert and Ad A.C.M. Peijnenburg}, + author = {J. Louisse and D. Rijkers and G. Stoopen and W. J. Holleboom and M. Delagrange and E. Molthof and P. P.J. Mulder and R. L.A.P. Hoogenboom and M. Audebert and A. A.C.M. Peijnenburg}, keywords = {Pyrrolizidine alkaloids (PAs), HepaRG, Genotoxicity, γH2AX assay, Relative potency factor (RPF)}, abstract = {Pyrrolizidine alkaloids (PAs) are secondary metabolites from plants that have been found in substantial amounts in herbal supplements, infusions and teas. Several PAs cause cancer in animal bioassays, mediated via a genotoxic mode of action, but for the majority of the PAs, carcinogenicity data are lacking. It is assumed in the risk assessment that all PAs have the same potency as riddelliine, which is considered to be one of the most potent carcinogenic PAs in rats. This may overestimate the risks, since many PAs are expected to have lower potencies. In this study we determined the concentration-dependent genotoxicity of 37 PAs representing different chemical classes using the γH2AX in cell western assay in HepaRG human liver cells. Based on these in vitro data, PAs were grouped into different potency classes. The group with the highest potency consists particularly of open diester PAs and cyclic diester PAs (including riddelliine). The group of the least potent or non-active PAs includes the monoester PAs, non-esterified necine bases, PA N-oxides, and the unsaturated PA trachelanthamine. This study reveals differences in in vitro genotoxic potencies of PAs, supporting that the assumption that all PAs have a similar potency as riddelliine is rather conservative.} } @@ -198,7 +227,7 @@ Using the developed in vitro model, the cytotoxicity of different PAs and the ex issn = {0278-6915}, doi = {https://doi.org/10.1016/j.fct.2018.08.003}, url = {https://www.sciencedirect.com/science/article/pii/S027869151830512X}, - author = {Ashley Allemang and Catherine Mahony and Cathy Lester and Stefan Pfuhler}, + author = {A. Allemang and C. Mahony and C. Lester and S. Pfuhler}, keywords = {Pyrrolizidine alkaloids, HepaRG, Genetic toxicology, Micronucleus test, Relative potency factor, Risk assessment}, abstract = {Plant-based 1,2-unsaturated Pyrrolizidine Alkaloids (PAs) can be found as contaminants in foods like teas, herbs and honey. PAs are responsible for liver genotoxicity/carcinogenicity following metabolic activation, making them a relevant concern for safety assessment. Current regulatory risk assessments take a precautionary approach and assume all PAs are as potent as the known most potent representatives: lasiocarpine and riddelliine. Our study investigated whether genotoxicity potency differed as a consequence of structural differences, assessing micronuclei in vitro in HepaRG cells which express metabolising enzymes at levels similar to primary human hepatocytes. Benchmark Dose (BMD) analysis was used to calculate the critical effect dose for 15 PAs representing 6 structural classes. When BMD confidence intervals were used to rank PAs, lasiocarpine was the most potent PA and plotted distinctly from all other PAs examined. PA-N-oxides were least potent, notably less potent than their corresponding parent PA's. The observed genotoxic potency compared favorably with existing in vitro data when metabolic competency was considered. Although further consideration of biokinetics will be needed to develop a robust understanding of relative potencies for a realistic risk assessment of PA mixtures, these data facilitate understanding of their genotoxic potencies and affirm that not all PAs are created equal.} } @@ -211,7 +240,7 @@ Using the developed in vitro model, the cytotoxicity of different PAs and the ex issn = {1383-5718}, doi = {https://doi.org/10.1016/j.mrgentox.2020.503305}, url = {https://www.sciencedirect.com/science/article/pii/S1383571820301765}, - author = {Naji Said Aboud Hadi and Ezgi Eyluel Bankoglu and Lea Schott and Eva Leopoldsberger and Vanessa Ramge and Olaf Kelber and Hartwig Sievers and Helga Stopper}, + author = {N. S. A. Hadi and E. E. Bankoglu and L. Schott and E. Leopoldsberger and V. Ramge and O. Kelber and H. Sievers and H. Stopper}, keywords = {Pyrrolizidine alkaloids, Genomic damage, Micronuclei, Crosslink comet assay, HepG2 cells, Huh6 cells}, abstract = {Introduction Pyrrolizidine alkaloids (PAs) are found in many plant species as secondary metabolites which affect humans via contaminated food sources, herbal medicines and dietary supplements. Hundreds of compounds belonging to PAs have been identified. PAs undergo hepatic metabolism, after which they can induce hepatotoxicity and carcinogenicity. Many aspects of their mechanism of carcinogenicity are still unclear and it is important for human risk assessment to investigate this class of compounds further. @@ -244,7 +273,7 @@ The widely available human hepatoma cell lines HepG2 and Huh6 were suitable for } @article{Weininger1989, - author = {David Weininger and Arthur Weininger and Joseph L. Weininger}, + author = {D. Weininger and A. Weininger and J. L. Weininger}, title = {SMILES. 2. Algorithm for generation of unique SMILES notation}, journal = {J. Chem. Inf. Comput. Sci.}, year = 1989, @@ -263,7 +292,7 @@ The widely available human hepatoma cell lines HepG2 and Huh6 were suitable for } @article{Schoening2017, - author = {Verena Schöning and Felix Hammann and Mark Peinl and Jürgen Drewe}, + author = {V. Schöning and F. Hammann and M. Peinl and J. Drewe}, title = {Editor's Highlight: Identification of Any Structure-Specific Hepatotoxic Potential of Different Pyrrolizidine Alkaloids Using Random Forests and Artificial Neural Networks}, journal = {Toxicol. Sci.}, year = 2017, @@ -273,7 +302,7 @@ The widely available human hepatoma cell lines HepG2 and Huh6 were suitable for } @book{Mattocks1986, - author = {Mattocks, AR}, + author = {Mattocks, A.R.}, title = {Chemistry and Toxicology of Pyrrolizidine Alkaloids}, year = 1986, publisher = {Academic Press}, @@ -289,7 +318,7 @@ The widely available human hepatoma cell lines HepG2 and Huh6 were suitable for } @article{Helma2018, - author = { Christoph Helma and David Vorgrimmler and Denis Gebele and Martin Gütlein and Barbara Engeli and Jürg Zarn and Benoit Schilter and Elena Lo Piparo}, + author = { C. Helma and D. Vorgrimmler and D. Gebele and M. Gütlein and B. Engeli and J. Zarn and B. Schilter and E. Lo Piparo}, title = "Modeling Chronic Toxicity: A comparison of experimental variability with {(Q)SAR}/read-across predictions", year = 2018, journal = {Frontiers in Pharmacology}, @@ -331,7 +360,7 @@ eprint = { } @article{Hansen2009, - author = {Hansen, Katja and Mika, Sebastian and Schroeter, Timon and Sutter, Andreas and ter Laak, Antonius and Steger-Hartmann, Thomas and Heinrich, Nikolaus and Müller, Klaus-Robert}, + author = {Hansen, K. and Mika, S. and Schroeter, T. and Sutter, A. and ter Laak, A. and Steger-Hartmann, T. and Heinrich, N. and Müller, K. R.}, title = {Benchmark Data Set for in Silico Prediction of Ames Mutagenicity}, journal = {Journal of Chemical Information and Modeling}, volume = {49}, @@ -355,8 +384,8 @@ eprint = { } @Article{Bender2004, - author = "Andreas Bender and Hamse Y. Mussa and Robert C. - Glen and Stephan Reiling", + author = "A. Bender and H. Y. Mussa and R. C. + Glen and S. Reiling", title = "Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier", @@ -375,7 +404,7 @@ eprint = { @article{OBoyle2011a, abstract = {{BACKGROUND: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats.RESULTS: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.CONCLUSIONS: Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.}}, added-at = {2019-03-11T21:00:05.000+0100}, - author = {O'Boyle, Noel and Banck, Michael and James, Craig and Morley, Chris and Vandermeersch, Tim and Hutchison, Geoffrey}, + author = {O'Boyle, N. and Banck, M. and James, C. and Morley, C. and Vandermeersch, T. and Hutchison, G.}, biburl = {https://www.bibsonomy.org/bibtex/27ab2699fef73132efcfa6853c3031bf0/fairybasslet}, booktitle = {Journal of Cheminformatics}, citeulike-article-id = {9866193}, @@ -432,7 +461,7 @@ eprint = { } @Article{doi:10.1021/ci00057a005, - author = "David Weininger", + author = "D. Weininger", title = "SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules", journal = "Journal of Chemical Information and Computer |