174 results on '"Meijer, Jeroen"'
Search Results
2. Innovative analytical methodologies for characterizing chemical exposure with a view to next-generation risk assessment
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Tkalec, Žiga, Antignac, Jean-Philippe, Bandow, Nicole, Béen, Frederic M., Belova, Lidia, Bessems, Jos, Le Bizec, Bruno, Brack, Werner, Cano-Sancho, German, Chaker, Jade, Covaci, Adrian, Creusot, Nicolas, David, Arthur, Debrauwer, Laurent, Dervilly, Gaud, Duca, Radu Corneliu, Fessard, Valérie, Grimalt, Joan O., Guerin, Thierry, Habchi, Baninia, Hecht, Helge, Hollender, Juliane, Jamin, Emilien L., Klánová, Jana, Kosjek, Tina, Krauss, Martin, Lamoree, Marja, Lavison-Bompard, Gwenaelle, Meijer, Jeroen, Moeller, Ruth, Mol, Hans, Mompelat, Sophie, Van Nieuwenhuyse, An, Oberacher, Herbert, Parinet, Julien, Van Poucke, Christof, Roškar, Robert, Togola, Anne, Trontelj, Jurij, and Price, Elliott J.
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- 2024
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3. NORMAN guidance on suspect and non-target screening in environmental monitoring
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Hollender, Juliane, Schymanski, Emma L., Ahrens, Lutz, Alygizakis, Nikiforos, Béen, Frederic, Bijlsma, Lubertus, Brunner, Andrea M., Celma, Alberto, Fildier, Aurelie, Fu, Qiuguo, Gago-Ferrero, Pablo, Gil-Solsona, Ruben, Haglund, Peter, Hansen, Martin, Kaserzon, Sarit, Kruve, Anneli, Lamoree, Marja, Margoum, Christelle, Meijer, Jeroen, Merel, Sylvain, Rauert, Cassandra, Rostkowski, Pawel, Samanipour, Saer, Schulze, Bastian, Schulze, Tobias, Singh, Randolph R., Slobodnik, Jaroslav, Steininger-Mairinger, Teresa, Thomaidis, Nikolaos S., Togola, Anne, Vorkamp, Katrin, Vulliet, Emmanuelle, Zhu, Linyan, and Krauss, Martin
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- 2023
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- View/download PDF
4. Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome
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van Dijk, Bram, Buffard, Pauline, Farr, Andrew D., Giersdorf, Franz, Meijer, Jeroen, Dutilh, Bas E., and Rainey, Paul B.
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- 2023
- Full Text
- View/download PDF
5. Interdisciplinary strategies to assess the relationship between exposure to complex chemical mixtures and thyroid hormone system disruption
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Margalef, Maria, Meijer, Jeroen, Lamoree, Marja, and Hamers, Timo
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- 2023
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6. Do cats mirror their owner? Paired exposure assessment using silicone bands to measure residential PAH exposure
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Figueiredo, Daniel M., Lô, Serigne, Krop, Esmeralda, Meijer, Jeroen, Beeltje, Henry, Lamoree, Marja H., and Vermeulen, Roel
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- 2023
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7. The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry
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Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.
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- 2022
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8. Dioxin(-like)-Related Biological Effects through Integrated Chemical-wide and Metabolome-wide Analyses
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IRAS OH Epidemiology Chemical Agents, IRAS – One Health Chemical, Zhao, Yujia, Meijer, Jeroen, Walker, Douglas I, Kim, Juni, Portengen, Lützen, Jones, Dean P, Saberi Hosnijeh, Fatemeh, Vlaanderen, Jelle, Vermeulen, Roel, IRAS OH Epidemiology Chemical Agents, IRAS – One Health Chemical, Zhao, Yujia, Meijer, Jeroen, Walker, Douglas I, Kim, Juni, Portengen, Lützen, Jones, Dean P, Saberi Hosnijeh, Fatemeh, Vlaanderen, Jelle, and Vermeulen, Roel
- Published
- 2024
9. Innovative analytical methodologies for characterizing chemical exposure with a view to next-generation risk assessment
- Author
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European Commission, 0000-0003-4518-3923, 0000-0001-5718-0733, 0000-0002-3680-4786, 0000-0003-0527-1136, 0000-0001-8189-1826, 0000-0001-9705-167X, 0000-0002-4660-274X, 0000-0002-8818-5307, 0000-0002-6421-0344, 0000-0002-0362-4244, 0000-0002-7373-7738, 0000-0002-4551-6823, 0000-0003-0087-6910, 0000-0002-3063-1853, 0000-0002-5393-1533, 0000-0002-2558-1425, Tkalec, Žiga, Antignac, Jean-Philippe, Bandow, Nicole, Béen, Frederic M., Belova, Lidia, Bessems, Jos, Le Bizec, Bruno, Brack, Werner, Cano-Sancho, German, Chaker, Jade, Covaci, Adrian, Creusot, Nicolas, David, Arthur, Debrauwer, Laurent, Dervilly, Gaud, Duca, Radu Corneliu, Fessard, Valérie, Grimalt, Joan O., Guerin, Thierry, Habchi, Baninia, Hecht, Helge, Hollender, Juliane, Jamin, Emilien L., Klánová, Jana, Kosjek, Tina, Krauss, Martin, Lamoree, Marja, Lavison-Bompard, Gwenaelle, Meijer, Jeroen, Moeller, Ruth, Mol, Hans, Mompelat, Sophie, Van Nieuwenhuyse, An, Oberacher, Herbert, Parinet, Julien, Van Poucke, Christof, Roškar, Robert, Togola, Anne, Trontelj, Jurij, Price, Elliott J., European Commission, 0000-0003-4518-3923, 0000-0001-5718-0733, 0000-0002-3680-4786, 0000-0003-0527-1136, 0000-0001-8189-1826, 0000-0001-9705-167X, 0000-0002-4660-274X, 0000-0002-8818-5307, 0000-0002-6421-0344, 0000-0002-0362-4244, 0000-0002-7373-7738, 0000-0002-4551-6823, 0000-0003-0087-6910, 0000-0002-3063-1853, 0000-0002-5393-1533, 0000-0002-2558-1425, Tkalec, Žiga, Antignac, Jean-Philippe, Bandow, Nicole, Béen, Frederic M., Belova, Lidia, Bessems, Jos, Le Bizec, Bruno, Brack, Werner, Cano-Sancho, German, Chaker, Jade, Covaci, Adrian, Creusot, Nicolas, David, Arthur, Debrauwer, Laurent, Dervilly, Gaud, Duca, Radu Corneliu, Fessard, Valérie, Grimalt, Joan O., Guerin, Thierry, Habchi, Baninia, Hecht, Helge, Hollender, Juliane, Jamin, Emilien L., Klánová, Jana, Kosjek, Tina, Krauss, Martin, Lamoree, Marja, Lavison-Bompard, Gwenaelle, Meijer, Jeroen, Moeller, Ruth, Mol, Hans, Mompelat, Sophie, Van Nieuwenhuyse, An, Oberacher, Herbert, Parinet, Julien, Van Poucke, Christof, Roškar, Robert, Togola, Anne, Trontelj, Jurij, and Price, Elliott J.
- Abstract
The chemical burden on the environment and human population is increasing. Consequently, regulatory risk assessment must keep pace to manage, reduce, and prevent adverse impacts on human and environmental health associated with hazardous chemicals. Surveillance of chemicals of known, emerging, or potential future concern, entering the environment-food-human continuum is needed to document the reality of risks posed by chemicals on ecosystem and human health from a one health perspective, feed into early warning systems and support public policies for exposure mitigation provisions and safe and sustainable by design strategies. The use of less-conventional sampling strategies and integration of full-scan, high-resolution mass spectrometry and effect-directed analysis in environmental and human monitoring programmes have the potential to enhance the screening and identification of a wider range of chemicals of known, emerging or potential future concern. Here, we outline the key needs and recommendations identified within the European Partnership for Assessment of Risks from Chemicals (PARC) project for leveraging these innovative methodologies to support the development of next-generation chemical risk assessment.
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- 2024
10. Symbolic Reachability Analysis of B through ProB and LTSmin
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Bendisposto, Jens, Koerner, Philipp, Leuschel, Michael, Meijer, Jeroen, van de Pol, Jaco, Treharne, Helen, and Whitefield, Jorden
- Subjects
Computer Science - Software Engineering - Abstract
We present a symbolic reachability analysis approach for B that can provide a significant speedup over traditional explicit state model checking. The symbolic analysis is implemented by linking ProB to LTSmin, a high-performance language independent model checker. The link is achieved via LTSmin's PINS interface, allowing ProB to benefit from LTSmin's analysis algorithms, while only writing a few hundred lines of glue-code, along with a bridge between ProB and C using ZeroMQ. ProB supports model checking of several formal specification languages such as B, Event-B, Z and TLA. Our experiments are based on a wide variety of B-Method and Event-B models to demonstrate the efficiency of the new link. Among the tested categories are state space generation and deadlock detection; but action detection and invariant checking are also feasible in principle. In many cases we observe speedups of several orders of magnitude. We also compare the results with other approaches for improving model checking, such as partial order reduction or symmetry reduction. We thus provide a new scalable, symbolic analysis algorithm for the B-Method and Event-B, along with a platform to integrate other model checking improvements via LTSmin in the future.
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- 2016
11. Bandwidth and Wavefront Reduction for Static Variable Ordering in Symbolic Model Checking
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Meijer, Jeroen and van de Pol, Jaco
- Subjects
Computer Science - Software Engineering ,Computer Science - Logic in Computer Science - Abstract
We demonstrate the applicability of bandwidth and wavefront reduction algorithms to static variable ordering. In symbolic model checking event locality plays a major role in time and memory usage. For example, in Petri nets event locality can be captured by dependency matrices, where nonzero entries indicate whether a transition modifies a place. The quality of event locality has been expressed as a metric called (weighted) event span. The bandwidth of a matrix is a metric indicating the distance of nonzero elements to the diagonal. Wavefront is a metric indicating the degree of nonzeros on one end of the diagonal of the matrix. Bandwidth and wavefront are well studied metrics used in sparse matrix solvers. In this work we prove that span is limited by twice the bandwidth of a matrix. This observation makes bandwidth reduction algorithms useful for obtaining good variable orders. One major issue we address is that the reduction algorithms can only be applied on symmetric matrices, while the dependency matrices are asymmetric. We show that the Sloan algorithm executed on the total graph of the adjacency graph gives the best variable orders. Practically, we demonstrate that our work allows to call standard sparse matrix operations in Boost and ViennaCL, computing very good static variable orders in milliseconds. Future work is promising, because a whole new spectrum of more off-the-shelf algorithms, including metaheuristic ones, become available for variable ordering., Comment: preprint
- Published
- 2015
12. Non-targeted screening methodology to characterise human internal chemical exposure: Application to halogenated compounds in human milk
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Pourchet, Mariane, Narduzzi, Luca, Jean, Annabelle, Guiffard, Ingrid, Bichon, Emmanuelle, Cariou, Ronan, Guitton, Yann, Hutinet, Sébastien, Vlaanderen, Jelle, Meijer, Jeroen, Le Bizec, Bruno, and Antignac, Jean-Philippe
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- 2021
- Full Text
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13. Synchronous or Alternating? : LTL Black-Box Checking of Mealy Machines by Combining the LearnLib and LTSmin
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van de Pol, Jaco, Meijer, Jeroen, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Margaria, Tiziana, editor, Graf, Susanne, editor, and Larsen, Kim G., editor
- Published
- 2019
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14. Presentation of the 9th Edition of the Model Checking Contest
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Amparore, Elvio, Berthomieu, Bernard, Ciardo, Gianfranco, Dal Zilio, Silvano, Gallà, Francesco, Hillah, Lom Messan, Hulin-Hubard, Francis, Jensen, Peter Gjøl, Jezequel, Loïg, Kordon, Fabrice, Le Botlan, Didier, Liebke, Torsten, Meijer, Jeroen, Miner, Andrew, Paviot-Adet, Emmanuel, Srba, Jiří, Thierry-Mieg, Yann, van Dijk, Tom, Wolf, Karsten, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Beyer, Dirk, editor, Huisman, Marieke, editor, and Kordon, Fabrice, editor
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- 2019
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15. Multi-core On-The-Fly Saturation
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van Dijk, Tom, Meijer, Jeroen, van de Pol, Jaco, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Vojnar, Tomáš, editor, and Zhang, Lijun, editor
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- 2019
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16. Dioxin(-like)-Related Biological Effects through Integrated Chemical-wide and Metabolome-wide Analyses
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Zhao, Yujia, primary, Meijer, Jeroen, additional, Walker, Douglas I., additional, Kim, Juni, additional, Portengen, Lützen, additional, Jones, Dean P., additional, Saberi Hosnijeh, Fatemeh, additional, Vlaanderen, Jelle, additional, and Vermeulen, Roel, additional
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- 2023
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17. Inter-laboratory mass spectrometry dataset based on passive sampling of drinking water for non-target analysis
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Schulze, Bastian, van Herwerden, Denice, Allan, Ian, Bijlsma, Lubertus, Etxebarria, Nestor, Hansen, Martin, Merel, Sylvain, Vrana, Branislav, Aalizadeh, Reza, Bajema, Bernard, Dubocq, Florian, Coppola, Gianluca, Fildier, Aurélie, Fialová, Pavla, Frøkjær, Emil, Grabic, Roman, Gago-Ferrero, Pablo, Gravert, Thorsten, Hollender, Juliane, Huynh, Nina, Jacobs, Griet, Jonkers, Tim, Kaserzon, Sarit, Lamoree, Marja, Le Roux, Julien, Mairinger, Teresa, Margoum, Christelle, Mascolo, Giuseppe, Mebold, Emmanuelle, Menger, Frank, Miège, Cécile, Meijer, Jeroen, Moilleron, Régis, Murgolo, Sapia, Peruzzo, Massimo, Pijnappels, Martijn, Reid, Malcolm, Roscioli, Claudio, Soulier, Coralie, Valsecchi, Sara, Thomaidis, Nikolaos, Vulliet, Emmanuelle, Young, Robert, and Samanipour, Saer
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- 2021
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18. MCC’2017 – The Seventh Model Checking Contest
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Kordon, Fabrice, Garavel, Hubert, Hillah, Lom Messan, Paviot-Adet, Emmanuel, Jezequel, Loïg, Hulin-Hubard, Francis, Amparore, Elvio, Beccuti, Marco, Berthomieu, Bernard, Evrard, Hugues, Jensen, Peter G., Le Botlan, Didier, Liebke, Torsten, Meijer, Jeroen, Srba, Jiří, Thierry-Mieg, Yann, van de Pol, Jaco, Wolf, Karsten, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Koutny, Maciej, editor, Kristensen, Lars Michael, editor, and Penczek, Wojciech, editor
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- 2018
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19. State-of-the-Art Model Checking for B and Event-B Using ProB and LTSmin
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Körner, Philipp, Leuschel, Michael, Meijer, Jeroen, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Furia, Carlo A., editor, and Winter, Kirsten, editor
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- 2018
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20. Sound Black-Box Checking in the LearnLib
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Meijer, Jeroen, van de Pol, Jaco, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Dutle, Aaron, editor, Muñoz, César, editor, and Narkawicz, Anthony, editor
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- 2018
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21. Adaptive Learning for Learn-Based Regression Testing
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Huistra, David, Meijer, Jeroen, van de Pol, Jaco, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Howar, Falk, editor, and Barnat, Jiří, editor
- Published
- 2018
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22. Dioxin(-like)-Related Biological Effects through Integrated Chemical-wide and Metabolome-wide Analyses.
- Author
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Zhao, Yujia, Meijer, Jeroen, Walker, Douglas I., Kim, Juni, Portengen, Lützen, Jones, Dean P., Saberi Hosnijeh, Fatemeh, Vlaanderen, Jelle, and Vermeulen, Roel
- Published
- 2024
- Full Text
- View/download PDF
23. Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities
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Meijer, Jeroen, primary, Skiadas, Petros, additional, Rainey, Paul B, additional, Hogeweg, Paulien, additional, and Dutilh, Bas E., additional
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- 2023
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24. Sound black-box checking in the LearnLib
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Meijer, Jeroen and van de Pol, Jaco
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- 2019
- Full Text
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25. Head skeleton malformations in zebrafish (Danio rerio) to assess adverse effects of mixtures of compounds
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Staal, Yvonne C. M., Meijer, Jeroen, van der Kris, Remco J. C., de Bruijn, Annamaria C., Boersma, Anke Y., Gremmer, Eric R., Zwart, Edwin P., Beekhof, Piet K., Slob, Wout, and van der Ven, Leo T. M.
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- 2018
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26. Contingent evolution of alternative metabolic network topologies determines whether cross-feeding evolves
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Meijer, Jeroen, van Dijk, Bram, and Hogeweg, Paulien
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- 2020
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27. Identifying antimicrobials and their metabolites in wastewater and surface water with effect-directed analysis
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Jonkers, Tim J.H., primary, Keizers, Peter H.J., additional, Béen, Frederic, additional, Meijer, Jeroen, additional, Houtman, Corine J., additional, Al Gharib, Imane, additional, Molenaar, Douwe, additional, Hamers, Timo, additional, and Lamoree, Marja H., additional
- Published
- 2023
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28. Bandwidth and Wavefront Reduction for Static Variable Ordering in Symbolic Reachability Analysis
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Meijer, Jeroen, van de Pol, Jaco, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Rayadurgam, Sanjai, editor, and Tkachuk, Oksana, editor
- Published
- 2016
- Full Text
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29. Do cats mirror their owner?: Paired exposure assessment using silicone bands to measure residential PAH exposure
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IRAS OH Epidemiology Chemical Agents, IRAS OH Epidemiology Microbial Agents, Figueiredo, Daniel M, Lô, Serigne, Krop, Esmeralda, Meijer, Jeroen, Beeltje, Henry, Lamoree, Marja H, Vermeulen, Roel, IRAS OH Epidemiology Chemical Agents, IRAS OH Epidemiology Microbial Agents, Figueiredo, Daniel M, Lô, Serigne, Krop, Esmeralda, Meijer, Jeroen, Beeltje, Henry, Lamoree, Marja H, and Vermeulen, Roel
- Published
- 2023
30. Towards evolutionary predictions : current promises and challenges
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Wortel, Meike T., Agashe, Deepa, Bailey, Susan F., Bank, Claudia, Bisschop, Karen, Blankers, Thomas, Cairns, Johannes, Colizzi, Enrico Sandro, Cusseddu, Davide, Desai, Michael M., van Dijk, Bram, Egas, Martijn, Ellers, Jacintha, Groot, Astrid T., Heckel, David G., Johnson, Marcelle L., Kraaijeveld, Ken, Krug, Joachim, Laan, Liedewij, Lässig, Michael, Lind, Peter A, Meijer, Jeroen, Noble, Luke M., Okasha, Samir, Rainey, Paul B., Rozen, Daniel E., Shitut, Shraddha, Tans, Sander J., Tenaillon, Olivier, Teotónio, Henrique, de Visser, J. Arjan G. M., Visser, Marcel E., Vroomans, Renske M. A., Werner, Gijsbert D. A., Wertheim, Bregje, Pennings, Pleuni S., Wortel, Meike T., Agashe, Deepa, Bailey, Susan F., Bank, Claudia, Bisschop, Karen, Blankers, Thomas, Cairns, Johannes, Colizzi, Enrico Sandro, Cusseddu, Davide, Desai, Michael M., van Dijk, Bram, Egas, Martijn, Ellers, Jacintha, Groot, Astrid T., Heckel, David G., Johnson, Marcelle L., Kraaijeveld, Ken, Krug, Joachim, Laan, Liedewij, Lässig, Michael, Lind, Peter A, Meijer, Jeroen, Noble, Luke M., Okasha, Samir, Rainey, Paul B., Rozen, Daniel E., Shitut, Shraddha, Tans, Sander J., Tenaillon, Olivier, Teotónio, Henrique, de Visser, J. Arjan G. M., Visser, Marcel E., Vroomans, Renske M. A., Werner, Gijsbert D. A., Wertheim, Bregje, and Pennings, Pleuni S.
- Abstract
Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.
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- 2023
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31. Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome
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Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Sub Bioinformatics, van Dijk, Bram, Buffard, Pauline, Farr, Andrew D, Giersdorf, Franz, Meijer, Jeroen, Dutilh, Bas E, Rainey, Paul B, Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Sub Bioinformatics, van Dijk, Bram, Buffard, Pauline, Farr, Andrew D, Giersdorf, Franz, Meijer, Jeroen, Dutilh, Bas E, and Rainey, Paul B
- Published
- 2023
32. NORMAN guidance on suspect and non-target screening in environmental monitoring
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0000-0002-4660-274X, 0000-0001-6868-8145, 0000-0002-5430-6764, 0000-0002-5727-4999, 0000-0001-5910-3248, 0000-0001-7005-8775, 0000-0002-2801-1751, 0000-0001-9763-8737, 0000-0002-3805-4122, 0000-0002-4227-5948, 0000-0002-5987-0399, 0000-0002-4269-1036, 0000-0003-2293-7913, 0000-0002-4663-8742, 0000-0002-6744-1279, 0000-0001-9725-3351, 0000-0002-7373-7738, 0000-0002-7386-4454, 0000-0002-4551-6823, 0000-0002-9587-2981, 0000-0002-2543-9023, 0000-0001-9778-4283, 0000-0001-8270-6979, 0000-0003-4641-8659, 0000-0002-9744-8914, 0000-0003-4500-3400, 0000-0003-2622-6318, 0000-0001-7809-1529, 0000-0002-4624-4735, 0000-0002-5393-1533, 0000-0002-1131-5687, 0000-0002-6325-1531, 0000-0003-2036-1447, 0000-0002-0362-4244, Hollender, Juliane, Schymanski, Emma L., Ahrens, Lutz, Alygizakis, Nikiforos, Béen, Frederic, Bijlsma, Lubertus, Brunner, Andrea M., Celma, Alberto, Fildier, Aurelie, Fu, Qiuguo, Gago-Ferrero, Pablo, Gil-Solsona, Rubén, Haglund, Peter, Hansen, Martin, Kaserzon, Sarit, Kruve, Anneli, Lamoree, Marja, Margoum, Christelle, Meijer, Jeroen, Merel, Sylvain, Rauert, Cassandra, Rostkowski, Pawel, Samanipour, Saer, Schulze, Bastian, Schulze, Tobias, Singh, Randolph R., Slobodnik, Jaroslav, Steininger-Mairinger, Teresa, Thomaidis, Nikolaos S., Togola, Anne, Vorkamp, Katrin, Vulliet, Emmanuelle, Zhu, Linyan, Krauss, Martin, 0000-0002-4660-274X, 0000-0001-6868-8145, 0000-0002-5430-6764, 0000-0002-5727-4999, 0000-0001-5910-3248, 0000-0001-7005-8775, 0000-0002-2801-1751, 0000-0001-9763-8737, 0000-0002-3805-4122, 0000-0002-4227-5948, 0000-0002-5987-0399, 0000-0002-4269-1036, 0000-0003-2293-7913, 0000-0002-4663-8742, 0000-0002-6744-1279, 0000-0001-9725-3351, 0000-0002-7373-7738, 0000-0002-7386-4454, 0000-0002-4551-6823, 0000-0002-9587-2981, 0000-0002-2543-9023, 0000-0001-9778-4283, 0000-0001-8270-6979, 0000-0003-4641-8659, 0000-0002-9744-8914, 0000-0003-4500-3400, 0000-0003-2622-6318, 0000-0001-7809-1529, 0000-0002-4624-4735, 0000-0002-5393-1533, 0000-0002-1131-5687, 0000-0002-6325-1531, 0000-0003-2036-1447, 0000-0002-0362-4244, Hollender, Juliane, Schymanski, Emma L., Ahrens, Lutz, Alygizakis, Nikiforos, Béen, Frederic, Bijlsma, Lubertus, Brunner, Andrea M., Celma, Alberto, Fildier, Aurelie, Fu, Qiuguo, Gago-Ferrero, Pablo, Gil-Solsona, Rubén, Haglund, Peter, Hansen, Martin, Kaserzon, Sarit, Kruve, Anneli, Lamoree, Marja, Margoum, Christelle, Meijer, Jeroen, Merel, Sylvain, Rauert, Cassandra, Rostkowski, Pawel, Samanipour, Saer, Schulze, Bastian, Schulze, Tobias, Singh, Randolph R., Slobodnik, Jaroslav, Steininger-Mairinger, Teresa, Thomaidis, Nikolaos S., Togola, Anne, Vorkamp, Katrin, Vulliet, Emmanuelle, Zhu, Linyan, and Krauss, Martin
- Abstract
Increasing production and use of chemicals and awareness of their impact on ecosystems and humans has led to large interest for broadening the knowledge on the chemical status of the environment and human health by suspect and non-target screening (NTS). To facilitate effective implementation of NTS in scientific, commercial and governmental laboratories, as well as acceptance by managers, regulators and risk assessors, more harmonisation in NTS is required. To address this, NORMAN Association members involved in NTS activities have prepared this guidance document, based on the current state of knowledge. The document is intended to provide guidance on performing high quality NTS studies and data interpretation while increasing awareness of the promise but also pitfalls and challenges associated with these techniques. Guidance is provided for all steps; from sampling and sample preparation to analysis by chromatography (liquid and gas—LC and GC) coupled via various ionisation techniques to high-resolution tandem mass spectrometry (HRMS/MS), through to data evaluation and reporting in the context of NTS. Although most experience within the NORMAN network still involves water analysis of polar compounds using LC–HRMS/MS, other matrices (sediment, soil, biota, dust, air) and instrumentation (GC, ion mobility) are covered, reflecting the rapid development and extension of the field. Due to the ongoing developments, the different questions addressed with NTS and manifold techniques in use, NORMAN members feel that no standard operation process can be provided at this stage. However, appropriate analytical methods, data processing techniques and databases commonly compiled in NTS workflows are introduced, their limitations are discussed and recommendations for different cases are provided. Proper quality assurance, quantification without reference standards and reporting results with clear confidence of identification assignment complete the guidance together with a gloss
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- 2023
33. Trusting the hand that feeds: microbes evolve to anticipate a serial transfer protocol as individuals or collectives
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van Dijk, Bram, Meijer, Jeroen, Cuypers, Thomas D., and Hogeweg, Paulien
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- 2019
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34. Synchronous or Alternating?
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van de Pol, Jaco, primary and Meijer, Jeroen, additional
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- 2019
- Full Text
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35. Multi-core On-The-Fly Saturation
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van Dijk, Tom, primary, Meijer, Jeroen, additional, and van de Pol, Jaco, additional
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- 2019
- Full Text
- View/download PDF
36. Presentation of the 9th Edition of the Model Checking Contest
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Amparore, Elvio, primary, Berthomieu, Bernard, additional, Ciardo, Gianfranco, additional, Dal Zilio, Silvano, additional, Gallà, Francesco, additional, Hillah, Lom Messan, additional, Hulin-Hubard, Francis, additional, Jensen, Peter Gjøl, additional, Jezequel, Loïg, additional, Kordon, Fabrice, additional, Le Botlan, Didier, additional, Liebke, Torsten, additional, Meijer, Jeroen, additional, Miner, Andrew, additional, Paviot-Adet, Emmanuel, additional, Srba, Jiří, additional, Thierry-Mieg, Yann, additional, van Dijk, Tom, additional, and Wolf, Karsten, additional
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- 2019
- Full Text
- View/download PDF
37. LTSmin: High-Performance Language-Independent Model Checking
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Kant, Gijs, Laarman, Alfons, Meijer, Jeroen, van de Pol, Jaco, Blom, Stefan, van Dijk, Tom, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Baier, Christel, editor, and Tinelli, Cesare, editor
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- 2015
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38. Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome
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Dijk, Bram van, primary, Farr, Andrew, additional, Buffard, Pauline, additional, Giersdorf, Franz, additional, Meijer, Jeroen, additional, Dutilh, Bas E., additional, and Rainey, Paul B, additional
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- 2023
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39. Adaptive Learning for Learn-Based Regression Testing
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Huistra, David, primary, Meijer, Jeroen, additional, and van de Pol, Jaco, additional
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- 2018
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40. MCC’2017 – The Seventh Model Checking Contest
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Kordon, Fabrice, primary, Garavel, Hubert, additional, Hillah, Lom Messan, additional, Paviot-Adet, Emmanuel, additional, Jezequel, Loïg, additional, Hulin-Hubard, Francis, additional, Amparore, Elvio, additional, Beccuti, Marco, additional, Berthomieu, Bernard, additional, Evrard, Hugues, additional, Jensen, Peter G., additional, Le Botlan, Didier, additional, Liebke, Torsten, additional, Meijer, Jeroen, additional, Srba, Jiří, additional, Thierry-Mieg, Yann, additional, van de Pol, Jaco, additional, and Wolf, Karsten, additional
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- 2018
- Full Text
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41. Towards evolutionary predictions: Current promises and challenges
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Wortel, Meike T., primary, Agashe, Deepa, additional, Bailey, Susan F., additional, Bank, Claudia, additional, Bisschop, Karen, additional, Blankers, Thomas, additional, Cairns, Johannes, additional, Colizzi, Enrico Sandro, additional, Cusseddu, Davide, additional, Desai, Michael M., additional, van Dijk, Bram, additional, Egas, Martijn, additional, Ellers, Jacintha, additional, Groot, Astrid T., additional, Heckel, David G., additional, Johnson, Marcelle L., additional, Kraaijeveld, Ken, additional, Krug, Joachim, additional, Laan, Liedewij, additional, Lässig, Michael, additional, Lind, Peter A., additional, Meijer, Jeroen, additional, Noble, Luke M., additional, Okasha, Samir, additional, Rainey, Paul B., additional, Rozen, Daniel E., additional, Shitut, Shraddha, additional, Tans, Sander J., additional, Tenaillon, Olivier, additional, Teotónio, Henrique, additional, de Visser, J. Arjan G. M., additional, Visser, Marcel E., additional, Vroomans, Renske M. A., additional, Werner, Gijsbert D. A., additional, Wertheim, Bregje, additional, and Pennings, Pleuni S., additional
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- 2022
- Full Text
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42. The NORMAN Suspect List Exchange (NORMAN-SLE): Facilitating European and Worldwide Collaboration on Suspect Screening in High Resolution Mass Spectrometry
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Taha, Hiba Mohammed, primary, Aalizadeh, Reza, additional, Alygizakis, Nikiforos, additional, Antignac, Jean-Philippe, additional, Arp, Hans Peter H., additional, Bade, Richard, additional, Baker, Nancy, additional, Belova, Lidia, additional, Bijlsma, Lubertus, additional, Bolton, Evan E., additional, Brack, Werner, additional, Celma, Alberto, additional, Chen, Wen-Ling, additional, Cheng, Tiejun, additional, Chirsir, Parviel, additional, Čirka, Ľuboš, additional, D’Agostino, Lisa, additional, Feunang, Yannick Djoumbou, additional, Dulio, Valeria, additional, Fischer, Stellan, additional, Gago-Ferrero, Pablo, additional, Galani, Aikaterini, additional, Geueke, Birgit, additional, Głowacka, Natalia, additional, Glüge, Juliane, additional, Groh, Ksenia, additional, Grosse, Sylvia, additional, Haglund, Peter, additional, Hakkinen, Pertti J., additional, Hale, Sarah E., additional, Hernández, Félix, additional, Janssen, Elisabeth M.-L., additional, Jonkers, Tim, additional, Kiefer, Karin, additional, Kirchner, Michal, additional, Koschorreck, Jan, additional, Krauss, Martin, additional, Krier, Jessy, additional, Lamoree, Marja H., additional, Letzel, Marion, additional, Letzel, Thomas, additional, Li, Qingliang, additional, Little, James, additional, Liu, Yanna, additional, Lunderberg, David M., additional, Martin, Jonathan W., additional, McEachran, Andrew D., additional, McLean, John A., additional, Meier, Christiane, additional, Meijer, Jeroen, additional, Menger, Frank, additional, Merino, Carla, additional, Muncke, Jane, additional, Muschket, Matthias, additional, Neumann, Michael, additional, Neveu, Vanessa, additional, Ng, Kelsey, additional, Oberacher, Herbert, additional, O'Brien, Jake, additional, Oswald, Peter, additional, Oswaldova, Martina, additional, Picache, Jaqueline A., additional, Postigo, Cristina, additional, Ramírez, Noelia, additional, Reemtsma, Thorsten, additional, Renaud, Justin, additional, Rostkowski, Pawel, additional, Rüdel, Heinz, additional, Salek, Reza, additional, Samanipour, Saer, additional, Scheringer, Martin, additional, Schliebner, Ivo, additional, Schulz, Wolfgang, additional, Schulze, Tobias, additional, Sengl, Manfred, additional, Shoemaker, Benjamin A., additional, Sims, Kerry, additional, Singer, Heinz, additional, Singh, Randolph R., additional, Sumarah, Mark, additional, Thiessen, Paul A., additional, Thomas, Kevin V., additional, Torres, Sonia, additional, Trier, Xenia, additional, Wezel, Annemarie P. van, additional, Vermeulen, Roel C. H., additional, Vlaanderen, Jelle J., additional, Ohe, Peter C. von der, additional, Wang, Zhanyun, additional, Williams, Antony J., additional, Willighagen, Egon L., additional, Wishart, David S., additional, Zhang, Jian, additional, Thomaidis, Nikolaos S., additional, Hollender, Juliane, additional, Slobodnik, Jaroslav, additional, and Schymanski, Emma L., additional
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- 2022
- Full Text
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43. High-Performance Data Processing Workflow Incorporating Effect-Directed Analysis for Feature Prioritization in Suspect and Nontarget Screening
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IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, Jonkers, Tim J H, Meijer, Jeroen, Vlaanderen, Jelle J, Vermeulen, Roel C H, Houtman, Corine J, Hamers, Timo, Lamoree, Marja H, IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, Jonkers, Tim J H, Meijer, Jeroen, Vlaanderen, Jelle J, Vermeulen, Roel C H, Houtman, Corine J, Hamers, Timo, and Lamoree, Marja H
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- 2022
44. The NORMAN Suspect List Exchange (NORMAN-SLE) : facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry
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Taha, Hiba Mohammed, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A., Feunang, Yannick Djoumbou, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L., Taha, Hiba Mohammed, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A., Feunang, Yannick Djoumbou, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.
- Abstract
Background: The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide. Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov
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- 2022
- Full Text
- View/download PDF
45. The NORMAN Suspect List Exchange (NORMAN-SLE): Facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry
- Author
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IRAS OH Epidemiology Chemical Agents, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H, Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E, Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A, Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J, Hale, Sarah E, Hernandez, Felix, Janssen, Elisabeth M-L, Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H, Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M, Martin, Jonathan W, McEachran, Andrew D, McLean, John A, Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A, Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M, Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A, Sims, Kerry, Singer, Heinz, Singh, Randolph R, Sumarah, Mark, Thiessen, Paul A, Thomas, Kevin V, Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P, Vermeulen, Roel C H, Vlaanderen, Jelle J, von der Ohe, Peter C, Wang, Zhanyun, Williams, Antony J, Willighagen, Egon L, Wishart, David S, Zhang, Jian, Thomaidis, Nikolaos S, Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L, IRAS OH Epidemiology Chemical Agents, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H, Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E, Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A, Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J, Hale, Sarah E, Hernandez, Felix, Janssen, Elisabeth M-L, Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H, Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M, Martin, Jonathan W, McEachran, Andrew D, McLean, John A, Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A, Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M, Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A, Sims, Kerry, Singer, Heinz, Singh, Randolph R, Sumarah, Mark, Thiessen, Paul A, Thomas, Kevin V, Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P, Vermeulen, Roel C H, Vlaanderen, Jelle J, von der Ohe, Peter C, Wang, Zhanyun, Williams, Antony J, Willighagen, Egon L, Wishart, David S, Zhang, Jian, Thomaidis, Nikolaos S, Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L
- Published
- 2022
46. The NORMAN Suspect List Exchange (NORMAN-SLE):facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry
- Author
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Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C.H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L., Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C.H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.
- Abstract
Background: The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide. Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.
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- 2022
47. Towards evolutionary predictions: Current promises and challenges
- Author
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Wortel, Meike T. (author), Agashe, Deepa (author), Bailey, Susan F. (author), Bank, Claudia (author), Bisschop, Karen (author), Blankers, Thomas (author), Laan, L. (author), Meijer, Jeroen (author), Tans, S.J. (author), Wortel, Meike T. (author), Agashe, Deepa (author), Bailey, Susan F. (author), Bank, Claudia (author), Bisschop, Karen (author), Blankers, Thomas (author), Laan, L. (author), Meijer, Jeroen (author), and Tans, S.J. (author)
- Abstract
Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions., BN/Bionanoscience, BN/Liedewij Laan Lab
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- 2022
- Full Text
- View/download PDF
48. The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry
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Ministerio de Ciencia e Innovación (España), European Commission, 0000-0001-7820-4335, 0000-0001-9167-9060, 0000-0002-5727-4999, 0000-0001-9512-9314, 0000-0002-0747-8838, 0000-0003-2724-9183, 0000-0002-8351-9435, 0000-0001-7147-384X, 0000-0001-7005-8775, 0000-0002-5959-6190, 0000-0001-9269-6524, 0000-0001-9763-8737, 0000-0001-5143-0543, 0000-0002-4486-3356, 0000-0002-9932-8609, 0000-0001-9351-6855, 0000-0002-9734-324X, 0000-0001-7850-184X, 0000-0002-9436-9954, 0000-0002-5987-0399, 0000-0003-1112-6867, 0000-0002-0749-3982, 0000-0002-1740-9422, 0000-0003-1997-2750, 0000-0002-3778-4721, 0000-0003-2293-7913, 0000-0002-8295-9738, 0000-0002-7743-9199, 0000-0003-1268-3083, 0000-0002-5475-6730, 0000-0002-6415-6173, 0000-0002-6917-3431, 0000-0002-1043-3278, 0000-0002-0362-4244, 0000-0001-6986-5545, 0000-0002-7373-7738, 0000-0003-1008-8790, 0000-0002-6453-236X, 0000-0001-7893-9876, 0000-0002-4439-9194, 0000-0001-6265-4294, 0000-0003-1423-330X, 0000-0001-8918-6419, 0000-0003-3126-5186, 0000-0002-4551-6823, 0000-0002-1808-8835, 0000-0002-8793-5516, 0000-0002-6942-0594, 0000-0001-6672-8414, 0000-0002-2558-4431, 0000-0002-8501-7789, 0000-0003-2396-2993, 0000-0002-0963-8268, 0000-0001-9336-9656, 0000-0003-3088-9771, 0000-0002-1948-9243, 0000-0002-7344-7044, 0000-0002-9251-0790, 0000-0003-1606-0764, 0000-0001-6974-0224, 0000-0001-9778-4283, 0000-0002-4175-4787, 0000-0001-8604-1732, 0000-0001-8270-6979, 0000-0002-0809-7826, 0000-0002-1553-3868, 0000-0002-9744-8914, 0000-0002-1356-285X, 0000-0001-6273-4083, 0000-0002-8542-3699, 0000-0003-4500-3400, 0000-0003-0977-1656, 0000-0002-1992-2086, 0000-0002-2155-100X, 0000-0001-8881-0793, 0000-0001-6067-8321, 0000-0002-6875-957X, 0000-0003-4082-8163, 0000-0001-7350-8962, 0000-0001-9914-7659, 0000-0002-2668-4821, 0000-0001-7542-0286, 0000-0002-3207-2434, 0000-0002-6192-4632, 0000-0002-4624-4735, 0000-0002-4660-274X, 0000-0003-2622-6318, 0000-0001-6868-8145, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramírez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L., Ministerio de Ciencia e Innovación (España), European Commission, 0000-0001-7820-4335, 0000-0001-9167-9060, 0000-0002-5727-4999, 0000-0001-9512-9314, 0000-0002-0747-8838, 0000-0003-2724-9183, 0000-0002-8351-9435, 0000-0001-7147-384X, 0000-0001-7005-8775, 0000-0002-5959-6190, 0000-0001-9269-6524, 0000-0001-9763-8737, 0000-0001-5143-0543, 0000-0002-4486-3356, 0000-0002-9932-8609, 0000-0001-9351-6855, 0000-0002-9734-324X, 0000-0001-7850-184X, 0000-0002-9436-9954, 0000-0002-5987-0399, 0000-0003-1112-6867, 0000-0002-0749-3982, 0000-0002-1740-9422, 0000-0003-1997-2750, 0000-0002-3778-4721, 0000-0003-2293-7913, 0000-0002-8295-9738, 0000-0002-7743-9199, 0000-0003-1268-3083, 0000-0002-5475-6730, 0000-0002-6415-6173, 0000-0002-6917-3431, 0000-0002-1043-3278, 0000-0002-0362-4244, 0000-0001-6986-5545, 0000-0002-7373-7738, 0000-0003-1008-8790, 0000-0002-6453-236X, 0000-0001-7893-9876, 0000-0002-4439-9194, 0000-0001-6265-4294, 0000-0003-1423-330X, 0000-0001-8918-6419, 0000-0003-3126-5186, 0000-0002-4551-6823, 0000-0002-1808-8835, 0000-0002-8793-5516, 0000-0002-6942-0594, 0000-0001-6672-8414, 0000-0002-2558-4431, 0000-0002-8501-7789, 0000-0003-2396-2993, 0000-0002-0963-8268, 0000-0001-9336-9656, 0000-0003-3088-9771, 0000-0002-1948-9243, 0000-0002-7344-7044, 0000-0002-9251-0790, 0000-0003-1606-0764, 0000-0001-6974-0224, 0000-0001-9778-4283, 0000-0002-4175-4787, 0000-0001-8604-1732, 0000-0001-8270-6979, 0000-0002-0809-7826, 0000-0002-1553-3868, 0000-0002-9744-8914, 0000-0002-1356-285X, 0000-0001-6273-4083, 0000-0002-8542-3699, 0000-0003-4500-3400, 0000-0003-0977-1656, 0000-0002-1992-2086, 0000-0002-2155-100X, 0000-0001-8881-0793, 0000-0001-6067-8321, 0000-0002-6875-957X, 0000-0003-4082-8163, 0000-0001-7350-8962, 0000-0001-9914-7659, 0000-0002-2668-4821, 0000-0001-7542-0286, 0000-0002-3207-2434, 0000-0002-6192-4632, 0000-0002-4624-4735, 0000-0002-4660-274X, 0000-0003-2622-6318, 0000-0001-6868-8145, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramírez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.
- Abstract
The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for "suspect screening" lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide.
- Published
- 2022
49. High-Performance Data Processing Workflow Incorporating Effect-Directed Analysis for Feature Prioritization in Suspect and Nontarget Screening
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Jonkers, Tim J H, Meijer, Jeroen, Vlaanderen, Jelle J, Vermeulen, Roel C H, Houtman, Corine J, Hamers, Timo, Lamoree, Marja H, IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, E&H: Environmental Chemistry and Toxicology, AIMMS, E&H: Environmental Health and Toxicology, IRAS OH Epidemiology Chemical Agents, and dIRAS RA-2
- Subjects
Chemistry(all) ,TTR-binding ,General Chemistry ,effect-directed analysis ,Gas Chromatography-Mass Spectrometry ,Mass Spectrometry ,Article ,Workflow ,bioassay ,antibiotic ,Toxicity Tests ,Humans ,Environmental Chemistry ,Biological Assay ,suspect and nontarget screening ,environment - Abstract
Effect-directed analysis (EDA) aims at the detection of bioactive chemicals of emerging concern (CECs) by combining toxicity testing and high-resolution mass spectrometry (HRMS). However, consolidation of toxicological and chemical analysis techniques to identify bioactive CECs remains challenging and laborious. In this study, we incorporate state-of-the-art identification approaches in EDA and propose a robust workflow for the high-throughput screening of CECs in environmental and human samples. Three different sample types were extracted and chemically analyzed using a single high-performance liquid chromatography HRMS method. Chemical features were annotated by suspect screening with several reference databases. Annotation quality was assessed using an automated scoring system. In parallel, the extracts were fractionated into 80 micro-fractions each covering a couple of seconds from the chromatogram run and tested for bioactivity in two bioassays. The EDA workflow prioritized and identified chemical features related to bioactive fractions with varying levels of confidence. Confidence levels were improved with the in silico software tools MetFrag and the retention time indices platform. The toxicological and chemical data quality was comparable between the use of single and multiple technical replicates. The proposed workflow incorporating EDA for feature prioritization in suspect and nontarget screening paves the way for the routine identification of CECs in a high-throughput manner., A comprehensive workflow was developed that incorporates effect-directed analysis in suspect and nontarget screening for feature prioritization, allowing for the high-throughput identification of bioactive chemicals of emerging concern.
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- 2022
50. Additional file 2 of The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry
- Author
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Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.
- Subjects
Pharmacology ,Ecology ,39999 Chemical Sciences not elsewhere classified ,FOS: Chemical sciences ,FOS: Biological sciences ,Computational Biology ,Marine Biology ,Biochemistry ,Molecular Biology ,Biotechnology ,Cancer - Abstract
Additional file 2: Overview of the NORMAN-SLE website (DOCX format) as of 30 May 2022 [82].
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- 2022
- Full Text
- View/download PDF
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