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3. STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse.

Author

Gomez-Cabrero, David, Tarazona, Sonia, Ferreirós-Vidal, Isabel, Ramirez, Ricardo, Company, Carlos, Schmidt, Andreas, Reijmers, Theo, Paul, Veronica, Marabita, Francesco, Rodríguez-Ubreva, Javier, Garcia-Gomez, Antonio, Carroll, Thomas, Cooper, Lee, Liang, Ziwei, Dharmalingam, Gopuraja, van der Kloet, Frans, Harms, Amy, Balzano-Nogueira, Leandro, Lagani, Vincenzo, Tsamardinos, Ioannis, Lappe, Michael, Maier, Dieter, Westerhuis, Johan, Hankemeier, Thomas, Imhof, Axel, Ballestar, Esteban, Mortazavi, Ali, Merkenschlager, Matthias, Tegner, Jesper, and Conesa, Ana

Subjects
Animals, B-Lymphocytes, Cell Differentiation, Cell Line, Genomics, Metabolomics, Mice, Proteomics
Abstract

Multi-omics approaches use a diversity of high-throughput technologies to profile the different molecular layers of living cells. Ideally, the integration of this information should result in comprehensive systems models of cellular physiology and regulation. However, most multi-omics projects still include a limited number of molecular assays and there have been very few multi-omic studies that evaluate dynamic processes such as cellular growth, development and adaptation. Hence, we lack formal analysis methods and comprehensive multi-omics datasets that can be leveraged to develop true multi-layered models for dynamic cellular systems. Here we present the STATegra multi-omics dataset that combines measurements from up to 10 different omics technologies applied to the same biological system, namely the well-studied mouse pre-B-cell differentiation. STATegra includes high-throughput measurements of chromatin structure, gene expression, proteomics and metabolomics, and it is complemented with single-cell data. To our knowledge, the STATegra collection is the most diverse multi-omics dataset describing a dynamic biological system.

Published
2019

6. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Author

Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc E., Funahashi, Akira, Acencio, Marcio Luis, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro G., Hiki, Yusuke, Hiroi, Noriko F., Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon L., Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Peña-Chilet, Maria, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara Sadat, Puniya, Bhanwar Lal, Naldi, Aurélien, Helikar, Tomáš, Singh, Vidisha, Fernández, Marco Fariñas, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noël, Vincent, Ponce-de-Leon, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Luna, Augustin, Piñero, Janet, Furlong, Laura I., Balaur, Irina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert, Phair, Robert, Perfetto, Livia, Matthews, Lisa, Rex, Devasahayam Arokia Balaya, Orlic-Milacic, Marija, Gomez, Luis Cristobal Monraz, De Meulder, Bertrand, Ravel, Jean Marie, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques S., Evelo, Chris T., D’Eustachio, Peter, Schreiber, Falk, Saez-Rodriguez, Julio, Dopazo, Joaquin, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc E., Funahashi, Akira, Acencio, Marcio Luis, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro G., Hiki, Yusuke, Hiroi, Noriko F., Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon L., Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Peña-Chilet, Maria, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara Sadat, Puniya, Bhanwar Lal, Naldi, Aurélien, Helikar, Tomáš, Singh, Vidisha, Fernández, Marco Fariñas, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noël, Vincent, Ponce-de-Leon, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Luna, Augustin, Piñero, Janet, Furlong, Laura I., Balaur, Irina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert, Phair, Robert, Perfetto, Livia, Matthews, Lisa, Rex, Devasahayam Arokia Balaya, Orlic-Milacic, Marija, Gomez, Luis Cristobal Monraz, De Meulder, Bertrand, Ravel, Jean Marie, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques S., Evelo, Chris T., D’Eustachio, Peter, Schreiber, Falk, Saez-Rodriguez, Julio, Dopazo, Joaquin, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Abstract

Introduction: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Methods: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors. Results: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. Discussion: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies., Peer Reviewed

Published
2024

7. NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment

Author

Afantitis, Antreas, Melagraki, Georgia, Isigonis, Panagiotis, Tsoumanis, Andreas, Varsou, Dimitra Danai, Valsami-Jones, Eugenia, Papadiamantis, Anastasios, Ellis, Laura-Jayne A., Sarimveis, Haralambos, Doganis, Philip, Karatzas, Pantelis, Tsiros, Periklis, Liampa, Irene, Lobaskin, Vladimir, Greco, Dario, Serra, Angela, Kinaret, Pia Anneli Sofia, Saarimäki, Laura Aliisa, Grafström, Roland, Kohonen, Pekka, Nymark, Penny, Willighagen, Egon, Puzyn, Tomasz, Rybinska-Fryca, Anna, Lyubartsev, Alexander, Alstrup Jensen, Keld, Brandenburg, Jan Gerit, Lofts, Stephen, Svendsen, Claus, Harrison, Samuel, Maier, Dieter, Tamm, Kaido, Jänes, Jaak, Sikk, Lauri, Dusinska, Maria, Longhin, Eleonora, Rundén-Pran, Elise, Mariussen, Espen, El Yamani, Naouale, Unger, Wolfgang, Radnik, Jörg, Tropsha, Alexander, Cohen, Yoram, Leszczynski, Jerzy, Ogilvie Hendren, Christine, Wiesner, Mark, Winkler, David, Suzuki, Noriyuki, Yoon, Tae Hyun, Choi, Jang-Sik, Sanabria, Natasha, Gulumian, Mary, and Lynch, Iseult

Published
2020
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8. The role of FAIR nanosafety data and nanoinformatics in achieving the UN Sustainable Development Goals: the NanoCommons experience

Author

Alfaro Serrano, Beatriz, primary, Gheorghe, L. Cristiana, additional, Exner, Thomas, additional, Resch, Susanne, additional, Wolf, Clemens, additional, Himly, Martin, additional, Falk, Andreas, additional, Bossa, Nathan, additional, Vazquez, Socorro, additional, Papadiamantis, Anastasios, additional, Afantitis, Antreas, additional, Melagraki, Georgia, additional, Maier, Dieter, additional, Sarimveis, Haralambos, additional, Willighagen, Egon, additional, Lobaskin, Vladimir, additional, Oldfield, Jon, additional, and Lynch, Iseult, additional

Published
2024
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9. Erratum To: COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms

Author

Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, D A B, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff‐Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Willighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Published
2021
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11. COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Author

Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, Devasahayam Arokia Balaya, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff-Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Willighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Published
2021
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12. Harmonising knowledge for safer materials via the “NanoCommons” Knowledge Base

Author

Maier, Dieter, primary, Exner, Thomas E., additional, Papadiamantis, Anastasios G., additional, Ammar, Ammar, additional, Tsoumanis, Andreas, additional, Doganis, Philip, additional, Rouse, Ian, additional, Slater, Luke T., additional, Gkoutos, Georgios V., additional, Jeliazkova, Nina, additional, Ilgenfritz, Hilmar, additional, Ziegler, Martin, additional, Gerhard, Beatrix, additional, Kopetsky, Sebastian, additional, Joshi, Deven, additional, Walker, Lee, additional, Svendsen, Claus, additional, Sarimveis, Haralambos, additional, Lobaskin, Vladimir, additional, Himly, Martin, additional, van Rijn, Jeaphianne, additional, Winckers, Laurent, additional, Millán Acosta, Javier, additional, Willighagen, Egon, additional, Melagraki, Georgia, additional, Afantitis, Antreas, additional, and Lynch, Iseult, additional

Published
2023
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14. Metadata stewardship in nanosafety research: learning from the past, preparing for an “on-the-fly” FAIR future

Author

Exner, Thomas E., primary, Papadiamantis, Anastasios G., additional, Melagraki, Georgia, additional, Amos, Jaleesia D., additional, Bossa, Nathan, additional, Gakis, Georgios P., additional, Charitidis, Costas A., additional, Cornelis, Geert, additional, Costa, Anna L., additional, Doganis, Philip, additional, Farcal, Lucian, additional, Friedrichs, Steffi, additional, Furxhi, Irini, additional, Klaessig, Frederick C., additional, Lobaskin, Vladimir, additional, Maier, Dieter, additional, Rumble, John, additional, Sarimveis, Haralambos, additional, Suarez-Merino, Blanca, additional, Vázquez, Socorro, additional, Wiesner, Mark R., additional, Afantitis, Antreas, additional, and Lynch, Iseult, additional

Published
2023
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15. From principles to reality. FAIR implementation in the nanosafety community

Author

Dumit, Verónica I., primary, Ammar, Ammar, additional, Bakker, Martine I., additional, Bañares, Miguel A., additional, Bossa, Cecilia, additional, Costa, Anna, additional, Cowie, Hilary, additional, Drobne, Damjana, additional, Exner, Thomas E., additional, Farcal, Lucian, additional, Friedrichs, Steffi, additional, Furxhi, Irini, additional, Grafström, Roland, additional, Haase, Andrea, additional, Himly, Martin, additional, Jeliazkova, Nina, additional, Lynch, Iseult, additional, Maier, Dieter, additional, Noorlander, Cornelle W., additional, Shin, Hyun Kil, additional, Soler-Illia, Galo J.A.A., additional, Suarez-Merino, Blanca, additional, Willighagen, Egon, additional, and Nymark, Penny, additional

Published
2023
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18. Mechanisms of the Development of Allergy (MeDALL): Introducing novel concepts in allergy phenotypes

Author

Anto, Josep M., Bousquet, Jean, Akdis, Mubeccel, Auffray, Charles, Keil, Thomas, Momas, Isabelle, Postma, Dirkje S., Valenta, Rudolf, Wickman, Magnus, Cambon-Thomsen, Anne, Haahtela, Tari, Lambrecht, Bart N., Lodrup Carlsen, Karin C., Koppelman, Gerard H., Sunyer, Jordi, Zuberbier, Torsten, Annesi-Maesano, Isabelle, Arno, Albert, Bindslev-Jensen, Carsten, De Carlo, Giuseppe, Forastiere, Francesco, Heinrich, Joachim, Kowalski, Marek L., Maier, Dieter, Melén, Erik, Smit, Henriette A., Standl, Marie, Wright, John, Asarnoj, Anna, Benet, Marta, Ballardini, Natalia, Garcia-Aymerich, Judith, Gehring, Ulrike, Guerra, Stefano, Hohmann, Cynthia, Kull, Inger, Lupinek, Christian, Pinart, Mariona, Skrindo, Ingebjorg, Westman, Marit, Smagghe, Delphine, Akdis, Cezmi, Andersson, Niklas, Bachert, Claus, Ballereau, Stephane, Ballester, Ferran, Basagana, Xavier, Bedbrook, Anna, Bergstrom, Anna, von Berg, Andrea, Brunekreef, Bert, Burte, Emilie, Carlsen, Kai-Hakon, Chatzi, Leda, Coquet, Jonathan M., Curin, Mirela, Demoly, Pascal, Eller, Esben, Fantini, Maria Pia, von Hertzen, Leena, Hovland, Vergard, Jacquemin, Benedicte, Just, Jocelyne, Keller, Theresa, Kiss, Renata, Kogevinas, Manolis, Koletzko, Sibylle, Lau, Susanne, Lehmann, Irina, Lemonnier, Nicolas, Mäkelä, Mika, Mestres, Jordi, Mowinckel, Peter, Nadif, Rachel, Nawijn, Martijn C., Pellet, Johan, Pin, Isabelle, Porta, Daniela, Rancière, Fanny, Rial-Sebbag, Emmanuelle, Saeys, Yvan, Schuijs, Martijn J., Siroux, Valerie, Tischer, Christina G., Torrent, Mathies, Varraso, Raphaelle, Wenzel, Kalus, and Xu, Cheng-Jian

Published
2017
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21. Machine Learning Identifies New Predictors on Restenosis Risk after Coronary Artery Stenting in 10,004 Patients with Surveillance Angiography

Author

Güldener, Ulrich, primary, Kessler, Thorsten, additional, von Scheidt, Moritz, additional, Hawe, Johann S., additional, Gerhard, Beatrix, additional, Maier, Dieter, additional, Lachmann, Mark, additional, Laugwitz, Karl-Ludwig, additional, Cassese, Salvatore, additional, Schömig, Albert W., additional, Kastrati, Adnan, additional, and Schunkert, Heribert, additional

Published
2023
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22. From principles to reality. FAIR implementation in the nanosafety community

Author

Dumit, Verónica i., Ammar, Ammar, Bakker, Martine i., Bañares, Miguel a., Bossa, Cecilia, Costa, Anna, Cowie, Hilary, Drobne, Damjana, Exner, Thomas e., Farcal, Lucian, Friedrichs, Steffi, Furxhi, Irini, Grafström, Roland, Haase, Andrea, Himly, Martin, Jeliazkova, Nina, Lynch, Iseult, Maier, Dieter, Noorlander, Cornelle w., Shin, Hyun kil, Soler-Illia, Galo j.a.a., Suarez-Merino, Blanca, Willighagen, Egon, Nymark, Penny, Dumit, Verónica i., Ammar, Ammar, Bakker, Martine i., Bañares, Miguel a., Bossa, Cecilia, Costa, Anna, Cowie, Hilary, Drobne, Damjana, Exner, Thomas e., Farcal, Lucian, Friedrichs, Steffi, Furxhi, Irini, Grafström, Roland, Haase, Andrea, Himly, Martin, Jeliazkova, Nina, Lynch, Iseult, Maier, Dieter, Noorlander, Cornelle w., Shin, Hyun kil, Soler-Illia, Galo j.a.a., Suarez-Merino, Blanca, Willighagen, Egon, and Nymark, Penny

Abstract

Developing safe and sustainable nanomaterials-based solutions to current global challenges including clean energy, sustainable food production and water security requires access to high quality data and appropriate analysis and modelling approaches. Achieving these challenges requires increased re-use of research data to accelerate progress and support development of new materials that are safe and sustainable for energy capture and storage, nano-agriculture and environmental remediation. The principles of Findability, Accessibility, Interoperability and Reusability (FAIR) provide a roadmap to enhanced data sharing and re-use, but require consensus within the nanosafety community on metadata, ontologies and persistent identifiers (among other things) and guidance to support implementation and achieve machine-readability. Here, we highlight the main focus of the AdvancedNano GO FAIR Implementation Network in supporting the nanosafety community with implementation of FAIR to maximize data-driven safe and sustainable application of nano- and advanced materials.

Published
2023

23. Harmonising knowledge for safer materials via the “NanoCommons” Knowledge Base

Author

Maier, Dieter, Exner, Thomas E., Papadiamantis, Anastasios G., Ammar, Ammar, Tsoumanis, Andreas, Doganis, Philip, Rouse, Ian, Slater, Luke T., Gkoutos, Georgios V., Jeliazkova, Nina, Ilgenfritz, Hilmar, Ziegler, Martin, Gerhard, Beatrix, Kopetsky, Sebastian, Joshi, Deven, Walker, Lee, Svendsen, Claus, Sarimveis, Haralambos, Lobaskin, Vladimir, Himly, Martin, van Rijn, Jeaphianne, Winckers, Laurent, Millán Acosta, Javier, Willighagen, Egon, Melagraki, Georgia, Afantitis, Antreas, Lynch, Iseult, Maier, Dieter, Exner, Thomas E., Papadiamantis, Anastasios G., Ammar, Ammar, Tsoumanis, Andreas, Doganis, Philip, Rouse, Ian, Slater, Luke T., Gkoutos, Georgios V., Jeliazkova, Nina, Ilgenfritz, Hilmar, Ziegler, Martin, Gerhard, Beatrix, Kopetsky, Sebastian, Joshi, Deven, Walker, Lee, Svendsen, Claus, Sarimveis, Haralambos, Lobaskin, Vladimir, Himly, Martin, van Rijn, Jeaphianne, Winckers, Laurent, Millán Acosta, Javier, Willighagen, Egon, Melagraki, Georgia, Afantitis, Antreas, and Lynch, Iseult

Abstract

In mediaeval Europe, the term “commons” described the way that communities managed land that was held “in common” and provided a clear set of rules for how this “common land” was used and developed by, and for, the community. Similarly, as we move towards an increasingly knowledge-based society where data is the new oil, new approaches to sharing and jointly owning publicly funded research data are needed to maximise its added value. Such common management approaches will extend the data’s useful life and facilitate its reuse for a range of additional purposes, from modelling, to meta-analysis to regulatory risk assessment as examples relevant to nanosafety data. This “commons” approach to nanosafety data and nanoinformatics infrastructure provision, co-development, and maintenance is at the heart of the “NanoCommons” project and underpins its post-funding transition to providing a basis on which other initiatives and projects can build. The present paper summarises part of the NanoCommons infrastructure called the NanoCommons Knowledge Base. It provides interoperability for nanosafety data sources and tools, on both semantic and technical levels. The NanoCommons Knowledge Base connects knowledge and provides both programmatic (via an Application Programming Interface) and a user-friendly graphical interface to enable (and democratise) access to state of the art tools for nanomaterials safety prediction, NMs design for safety and sustainability, and NMs risk assessment, as well. In addition, the standards and interfaces for interoperability, e.g., file templates to contribute data to the NanoCommons, are described, and a snapshot of the range and breadth of nanoinformatics tools and models that have already been integrated are presented Finally, we demonstrate how the NanoCommons Knowledge Base can support users in the FAIRification of their experimental workflows and how the NanoCommons Knowledge Base itself has progressed towards richer compliance with the FAIR pr

Published
2023

24. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Author

Sanofi, Instituto de Salud Carlos III, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), German Research Foundation, Ministero della Salute, European Commission, Generalitat de Catalunya, National Institutes of Health (US), Klaus Tschira Foundation, National Library of Medicine (US), Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc E., Funahashi, Akira, Acencio, Marcio Luis, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro G., Hiki, Yusuke, Hiroi, Noriko F., Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon L., Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Peña-Chilet, María, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara Sadat, Lal Puniya, Bhanwar, Naldi, Aurelien, Helikar, Tomas, Singh, Vidisha, Fariñas Fernández, Marco, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noël, Vincent, Ponce de León, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Luna, Augustin, Piñero, Janet, Furlong, Laura I., Balaur, Irina BalaurIrina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert W., Phair, Robert, Perfetto, Livia, Matthews, Lisa, Balaya Rex, Devasahayam Arokia, Orlic-Milacic, Marija, Monraz Gómez, Luis Cristóbal, De Meulder, Bertrand, Ravel, Jean Marie, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques S., Evelo, Chris T., D’Eustachio, Peter, Schreiber, Falk, Sáez-Rodríguez, Julio, Dopazo, Joaquín, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, COVID- Disease Map Community the COVID-19 Disease Map Community, Sanofi, Instituto de Salud Carlos III, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), German Research Foundation, Ministero della Salute, European Commission, Generalitat de Catalunya, National Institutes of Health (US), Klaus Tschira Foundation, National Library of Medicine (US), Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc E., Funahashi, Akira, Acencio, Marcio Luis, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro G., Hiki, Yusuke, Hiroi, Noriko F., Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon L., Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Peña-Chilet, María, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara Sadat, Lal Puniya, Bhanwar, Naldi, Aurelien, Helikar, Tomas, Singh, Vidisha, Fariñas Fernández, Marco, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noël, Vincent, Ponce de León, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Luna, Augustin, Piñero, Janet, Furlong, Laura I., Balaur, Irina BalaurIrina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert W., Phair, Robert, Perfetto, Livia, Matthews, Lisa, Balaya Rex, Devasahayam Arokia, Orlic-Milacic, Marija, Monraz Gómez, Luis Cristóbal, De Meulder, Bertrand, Ravel, Jean Marie, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques S., Evelo, Chris T., D’Eustachio, Peter, Schreiber, Falk, Sáez-Rodríguez, Julio, Dopazo, Joaquín, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, and COVID- Disease Map Community the COVID-19 Disease Map Community

Abstract

Introduction: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing., Methods: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors., Results: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19., Discussion: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.

Published
2023

25. Exposure to air pollution and development of asthma and rhinoconjunctivitis throughout childhood and adolescence: a population-based birth cohort study

Author

Gehring, Ulrike, Wijga, Alet H, Hoek, Gerard, Bellander, Tom, Berdel, Dietrich, Brüske, Irene, Fuertes, Elaine, Gruzieva, Olena, Heinrich, Joachim, Hoffmann, Barbara, de Jongste, Johan C, Klümper, Claudia, Koppelman, Gerard H, Korek, Michal, Krämer, Ursula, Maier, Dieter, Melén, Erik, Pershagen, Göran, Postma, Dirkje S, Standl, Marie, von Berg, Andrea, Anto, Josep M, Bousquet, Jean, Keil, Thomas, Smit, Henriette A, and Brunekreef, Bert

Published
2015
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29. Mixture Risk Assessment of Complex Real-Life Mixtures—The PANORAMIX Project

Author

Escher, Beate I., primary, Lamoree, Marja, additional, Antignac, Jean-Philippe, additional, Scholze, Martin, additional, Herzler, Matthias, additional, Hamers, Timo, additional, Jensen, Tina Kold, additional, Audebert, Marc, additional, Busquet, Francois, additional, Maier, Dieter, additional, Oelgeschläger, Michael, additional, Valente, Maria João, additional, Boye, Henriette, additional, Schmeisser, Sebastian, additional, Dervilly, Gaud, additional, Piumatti, Matteo, additional, Motteau, Soléne, additional, König, Maria, additional, Renko, Kostja, additional, Margalef, Maria, additional, Cariou, Ronan, additional, Ma, Yanying, additional, Treschow, Andreas Frederik, additional, Kortenkamp, Andreas, additional, and Vinggaard, Anne Marie, additional

Published
2022
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31. Mixture Risk Assessment of Complex Real-Life Mixtures—The PANORAMIX Project

Author

Escher, Beate I., Lamoree, Marja, Antignac, Jean-Philippe, Scholze, Martin, Herzler, Matthias, Hamers, Timo, Jensen, Tina Kold, Audebert, Marc, Busquet, Francois, Maier, Dieter, Oelgeschläger, Michael, Valente, Maria João, Boye, Henriette, Schmeisser, Sebastian, Dervilly, Gaud, Piumatti, Matteo, Motteau, Soléne, König, Maria, Renko, Kostja, Margalef, Maria, Cariou, Ronan, Ma, Yanying, Treschow, Andreas Frederik, Kortenkamp, Andreas, Vinggaard, Anne Marie, Escher, Beate I., Lamoree, Marja, Antignac, Jean-Philippe, Scholze, Martin, Herzler, Matthias, Hamers, Timo, Jensen, Tina Kold, Audebert, Marc, Busquet, Francois, Maier, Dieter, Oelgeschläger, Michael, Valente, Maria João, Boye, Henriette, Schmeisser, Sebastian, Dervilly, Gaud, Piumatti, Matteo, Motteau, Soléne, König, Maria, Renko, Kostja, Margalef, Maria, Cariou, Ronan, Ma, Yanying, Treschow, Andreas Frederik, Kortenkamp, Andreas, and Vinggaard, Anne Marie

Abstract

Humans are involuntarily exposed to hundreds of chemicals that either contaminate our environment and food or are added intentionally to our daily products. These complex mixtures of chemicals may pose a risk to human health. One of the goals of the European Union’s Green Deal and zero-pollution ambition for a toxic-free environment is to tackle the existent gaps in chemical mixture risk assessment by providing scientific grounds that support the implementation of adequate regulatory measures within the EU. We suggest dealing with this challenge by: (1) characterising ‘real-life’ chemical mixtures and determining to what extent they are transferred from the environment to humans via food and water, and from the mother to the foetus; (2) establishing a high-throughput whole-mixture-based in vitro strategy for screening of real-life complex mixtures of organic chemicals extracted from humans using integrated chemical profiling (suspect screening) together with effect-directed analysis; (3) evaluating which human blood levels of chemical mixtures might be of concern for children’s development; and (4) developing a web-based, ready-to-use interface that integrates hazard and exposure data to enable component-based mixture risk estimation. These concepts form the basis of the Green Deal project PANORAMIX, whose ultimate goal is to progress mixture risk assessment of chemicals.

Published
2022

32. Differential Outcomes Following 4 Weeks of Aclidinium/Formoterol in Patients with COPD: A Reanalysis of the ACTIVATE Study

Author

Koopman,Maud, Franssen,Frits ME, Gaffron,Swetlana, Watz,Henrik, Troosters,Thierry, Garcia-Aymerich,Judith, Paggiaro,Pierluigi, Molins,Eduard, Moya,Miguel, van Burk,Lindy, Maier,Dieter, Garcia Gil,Esther, Wouters,Emiel FM, Vanfleteren,Lowie EGW, Spruit,Martijn A, Koopman,Maud, Franssen,Frits ME, Gaffron,Swetlana, Watz,Henrik, Troosters,Thierry, Garcia-Aymerich,Judith, Paggiaro,Pierluigi, Molins,Eduard, Moya,Miguel, van Burk,Lindy, Maier,Dieter, Garcia Gil,Esther, Wouters,Emiel FM, Vanfleteren,Lowie EGW, and Spruit,Martijn A

Abstract

Maud Koopman,1– 3 Frits ME Franssen,1– 3 Swetlana Gaffron,4 Henrik Watz,5 Thierry Troosters,6,7 Judith Garcia-Aymerich,8– 10 Pierluigi Paggiaro,11 Eduard Molins,12 Miguel Moya,12 Lindy van Burk,13 Dieter Maier,14 Esther Garcia Gil,12 Emiel FM Wouters,1,3,15 Lowie EGW Vanfleteren,16 Martijn A Spruit1– 3 1Department of Research and Development, CIRO+, Center of Expertise for Chronic Organ Failure, Horn, the Netherlands; 2NUTRIM, School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht, the Netherlands; 3Department of Respiratory Medicine, Maastricht University Medical Center (MUMC+), Maastricht, the Netherlands; 4Viscovery Software GmbH, Vienna, Austria; 5Pulmonary Research Institute at LungenClinic Grosshansdorf, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany; 6Department of Rehabilitation Sciences, KU Leuven – University of Leuven, Leuven, Belgium; 7Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium; 8Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain; 9Universitat Pompeu Fabra (UPF), Barcelona, Spain; 10CIBER Epidemiología y Salud Publica (CIBERESP), Madrid, Spain; 11Department of Surgery, Medicine, Molecular Biology and Critical Care, University of Pisa, Pisa, Italy; 12AstraZeneca, Barcelona, Spain; 13AstraZeneca, Den Haag, the Netherlands; 14Biomax Informatics AB, Planegg, 82152, Germany; 15Ludwig Boltzmann Institute for Lung Health, Vienna, Austria; 16COPD Center, Sahlgrenska University Hospital, Institute of Medicine, University of Gothenburg, Gothenburg, SwedenCorrespondence: Maud Koopman, CIRO+, Center of Expertise for Chronic Organ Failure, Hornerheide 1, Horn, 6085 NM, the Netherlands, Email maudkoopman@gmail.comRationale: It is difficult to predict the effects of long-acting bronchodilators (LABD) on lung function, exercise capacity and physical activity in patients with ch

Published
2022

33. Differential Outcomes Following 4 Weeks of Aclidinium/Formoterol in Patients with COPD: A Reanalysis of the ACTIVATE Study

Author

Koopman, Maud, primary, Franssen, Frits ME, additional, Gaffron, Swetlana, additional, Watz, Henrik, additional, Troosters, Thierry, additional, Garcia-Aymerich, Judith, additional, Paggiaro, Pierluigi, additional, Molins, Eduard, additional, Moya, Miguel, additional, van Burk, Lindy, additional, Maier, Dieter, additional, Garcia Gil, Esther, additional, Wouters, Emiel FM, additional, Vanfleteren, Lowie EGW, additional, and Spruit, Martijn A, additional

Published
2022
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34. Additional file 2 of Combining gene expression analysis of gastric cancer cell lines and tumor specimens to identify biomarkers for anti-HER therapies���the role of HAS2, SHB and HBEGF

Author

Ebert, Karolin, Haffner, Ivonne, Zwingenberger, Gwen, Keller, Simone, Raim��ndez, Elba, Geffers, Robert, Wirtz, Ralph, Barbaria, Elena, Hollerieth, Vanessa, Arnold, Rouven, Walch, Axel, Hasenauer, Jan, Maier, Dieter, Lordick, Florian, and Luber, Birgit

Subjects
Data_FILES
Abstract

Additional file 2

Published
2022
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35. If you want to go far go together - Collaborative research supported by NanoCommons transnational access

Author

Lynch, Iseult, Exner, Thomas, Svendsen, Claus, Furxhi, Irini, Maier, Dieter, Simeone, Felice, Sarimveis, Haralambos, Doganis, Philip, Afantitis, Antreas, and Himly, Martin

Abstract

OnTuesday, 9th Nov 2021, the NanoCommons team, in a joint initiative with the NanoSafety Cluster, offered an online webinar on the use of their Nanoinformatics data services & toolsaccessible via the NanoCommons Infrastructure and Knowledge Base (NC KB). Hosts: Christine Balmer, UKCEH, UK, Beatriz Alfaro-Serrano, BNN, AT, Martin Himly, PLUS, AT, Chair of NanoSafety Cluster WG-A on Education, Training, and Communication The H2020 research e-infrastructure projectNanoCommonsis fostering collaborative research by trying to bring the nanosafety community together to work hands-on on the establishment of ways to make data and software platforms, developed in the different projects, to talk to each other. In order to give this a major push, we organised a workshop where, first, different organisations, that have already applied for Transnational Access (TA) projects with NanoCommons, reported about their experiences. This was followed by presentations on how the learnings from these projects resulted in collaboration and interoperability concepts, which could be extended to span across different tools and platforms, and on the upcoming training activities of NanoCommons and other possible follow-ups to this workshop. This workshop showcased how NanoCommons could support all of you, individually and as a group, as independent data harmoniser, platform harmoniser (e.g. through joint APIs, containerisation solutions, etc.) and overall data/metadata consultant not creating new tools or replacing existing solutions but to bring all these closer together so that they can be combined into integrated workflows. This could be based on common metadata and data standards, linking of data warehouses, workflow tools (KNIME, Jupyter) and deployment options to combine different services with complementary features. This could also be supplemented by ways of collaborative dissemination of the results from the projects and knowledge sharing like common service catalogues, training and knowledge platforms and the shared usage of applications like electronic lab notebooks. These are just some first thought-starters but of course we are open to hearing your needs and even more important things you could / would like to bring in. Attached here you find the pdf of the entire webinar slide set. The webinar recording is amongst others available online at the NanoCommons YouTube channel, for a direct link to the recordings of this event click here. Furthermore, you find additional information on related trainings at the NanoCommons Infrastructure, in the NanoCommons Customer Guidance Handbook, and at the ELIXIR TeSS channel of NanoCommons.

Published
2021
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36. Genetic and Molecular Interactions between H Δ CT , a Novel Allele of the Notch Antagonist Hairless, and the Histone Chaperone Asf1 in Drosophila melanogaster.

Author

Maier, Dieter, Bauer, Milena, Boger, Mike, Sanchez Jimenez, Anna, Yuan, Zhenyu, Fechner, Johannes, Scharpf, Janika, Kovall, Rhett A., Preiss, Anette, and Nagel, Anja C.

Subjects
*MOLECULAR interactions, *DROSOPHILA melanogaster, *NOTCH genes, *NOTCH signaling pathway, *GENETIC regulation, *ALLELES
Abstract

Cellular differentiation relies on the highly conserved Notch signaling pathway. Notch activity induces gene expression changes that are highly sensitive to chromatin landscape. We address Notch gene regulation using Drosophila as a model, focusing on the genetic and molecular interactions between the Notch antagonist Hairless and the histone chaperone Asf1. Earlier work implied that Asf1 promotes the silencing of Notch target genes via Hairless (H). Here, we generate a novel HΔCT allele by genome engineering. Phenotypically, HΔCT behaves as a Hairless gain of function allele in several developmental contexts, indicating that the conserved CT domain of H has an attenuator role under native biological contexts. Using several independent methods to assay protein–protein interactions, we define the sequences of the CT domain that are involved in Hairless–Asf1 binding. Based on previous models, where Asf1 promotes Notch repression via Hairless, a loss of Asf1 binding should reduce Hairless repressive activity. However, tissue-specific Asf1 overexpression phenotypes are increased, not rescued, in the HΔCT background. Counterintuitively, Hairless protein binding mitigates the repressive activity of Asf1 in the context of eye development. These findings highlight the complex connections of Notch repressors and chromatin modulators during Notch target-gene regulation and open the avenue for further investigations. [ABSTRACT FROM AUTHOR]

Published
2023
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37. Recovery from COVID-19: a sprint or marathon? 24-week follow-up data of online long COVID-19 peer support groups

Author

Vaes, Anouk W., primary, Goërtz, Yvonne M.J., additional, Van Herck, Maarten, additional, Machado, Felipe V.C., additional, Meys, Roy, additional, Delbressine, Jeannet M., additional, Houben-Wilke, Sarah, additional, Gaffron, Swetlana, additional, Maier, Dieter, additional, Burtin, Chris, additional, Posthuma, Rein, additional, Van Loon, Nicole P.H., additional, Franssen, Frits M.E., additional, Hajian, Bita, additional, Simons, Sami O., additional, Van Boven, Job F.M., additional, Klok, Frederikus A., additional, Spaetgens, Bartholomeus P.A., additional, Pinxt, Claire M.H., additional, Liu, Limmie Y.L., additional, Wesseling, Geertjan, additional, Spies, Yvonne, additional, Vijlbrief, Herman, additional, Van 'T Hul, Alex J., additional, Janssen, Daisy J.A., additional, and Spruit, Martijn A., additional

Published
2021
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39. Determination of Molecular Weight Distributions from Rheological Data: An Application to Polystyrene, Polymethylmethacrylate and Isotactic Polypropylene

Author

Thimm Wolfgang, Friedrich Christian, Maier Dieter, Marth Michael, and Honerkamp Josef

Subjects
double reptation, determination of molecular weight distribution, mixing rule, ill-posed inverse problems in rheology, Materials of engineering and construction. Mechanics of materials, TA401-492
Abstract

Based on a recently introduced generalized mixing rule, which contains the results of the reptation and double reptation model as special cases, it is possible to determine the molecular weight distribution (MWD) from rheological data. By evaluating data from bimodal PS-mixtures Maier et al. (1998) have shown how the MWD can be estimated from the relaxation shear modulus, G(t), using an inversion method. Thimm et al. (1999) derived an analytical relation between the relaxation time spectrum and the MWD, which is able to reproduce the result of Maier et al. (1998) with less computational effort. In this article we compare both methods by evaluating data from three different series of polymer mixtures: Polystyrene (PS), Polymethylmethacrylate (PMMA) and isotactic Polypropylene (iPP). We compare the MWD obtained from rheological data with results from size exclusion chromatography (SEC) and discuss differences.

Published
1999
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40. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta-Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G., Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E., Shoemaker, Jason E., Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, Devasahayam Arokia Balaya, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic-Milacic, Marija, Senff Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean-Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W., Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Vega, Carlos, Groues, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban-Medina, Marina, Peña-Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C., Augé, Franck, Beckmann, Jacques S., Hasenauer, Jan, Wolkenhauer, Olaf, Wilighagen, Egon L., Pico, Alexander R., Evelo, Chris T., Gillespie, Marc E., Stein, Lincoln D., Hermjakob, Henning, D'Eustachio, Peter, Saez-Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta-Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G., Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E., Shoemaker, Jason E., Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, Devasahayam Arokia Balaya, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic-Milacic, Marija, Senff Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean-Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W., Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Vega, Carlos, Groues, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban-Medina, Marina, Peña-Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C., Augé, Franck, Beckmann, Jacques S., Hasenauer, Jan, Wolkenhauer, Olaf, Wilighagen, Egon L., Pico, Alexander R., Evelo, Chris T., Gillespie, Marc E., Stein, Lincoln D., Hermjakob, Henning, D'Eustachio, Peter, Saez-Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Abstract

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

Published
2021

41. COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Author

Fonds National de la Recherche Luxembourg, European Commission, Federal Ministry of Education and Research (Germany), Ministry of Science, Research and Art Baden-Württemberg, German Center for Infection Research, Netherlands Organisation for Health Research and Development, National Institutes of Health (US), European Molecular Biology Laboratory, Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta-Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Schreiber, Falk, Montagud, Arnau, Ponce de León, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G., Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Orlic-Milacic, Marija, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Senff Ribeiro, Andrea, Ackerman, Emily E., Shoemaker, Jason E., Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yagmu, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Rothfels, Karen, Eijssen, Lars, Ehrhart, Friederike, Arokia Balaya Rex, Devasahayam, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Shamovsky, Veronic, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean-Marie, Fraser, Rupsha, Ortseifen, Vera, Soliman, Sylvain, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Valdeolivas, Alberto, Hu, Xiaoming, Overall, Rupert W., Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Vega, Carlos, Groues, Valentin, Vázquez, Miguel, Porras, Pablo, Esteban-Medina, Marina, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, Waard, Anita de, Turei, Denes, Luna, Augustín, Babur, Ozgun, Peña-Chilet, María, Rian, Kinza, Helikar, Tomas, Lal Puniya, Bhanwar, Modos, Dezso, Treveil, Agatha, Olbe, Marton, Fobo, Gisela, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurelien, Naldi, Aurelien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C., Montrone, Corinna, Auge, Franck, Beckmann, Jacques S., Hasenauer, Jan, Wolkenhauer, Olaf, Wilighagen, Egon L ., Pico, Alexander R., Evelo, Chris T., Gillespie, Marc E., Stein, Lincoln D., Hermjakob, Henning, Brauner, Barbara, D’Eustachio, Peter, Sáez-Rodríguez, Julio, Dopazo, Joaquín, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Gupta, Shailendra Kumar, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Fonds National de la Recherche Luxembourg, European Commission, Federal Ministry of Education and Research (Germany), Ministry of Science, Research and Art Baden-Württemberg, German Center for Infection Research, Netherlands Organisation for Health Research and Development, National Institutes of Health (US), European Molecular Biology Laboratory, Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta-Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Schreiber, Falk, Montagud, Arnau, Ponce de León, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G., Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Orlic-Milacic, Marija, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Senff Ribeiro, Andrea, Ackerman, Emily E., Shoemaker, Jason E., Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yagmu, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Rothfels, Karen, Eijssen, Lars, Ehrhart, Friederike, Arokia Balaya Rex, Devasahayam, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Shamovsky, Veronic, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean-Marie, Fraser, Rupsha, Ortseifen, Vera, Soliman, Sylvain, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Valdeolivas, Alberto, Hu, Xiaoming, Overall, Rupert W., Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Vega, Carlos, Groues, Valentin, Vázquez, Miguel, Porras, Pablo, Esteban-Medina, Marina, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, Waard, Anita de, Turei, Denes, Luna, Augustín, Babur, Ozgun, Peña-Chilet, María, Rian, Kinza, Helikar, Tomas, Lal Puniya, Bhanwar, Modos, Dezso, Treveil, Agatha, Olbe, Marton, Fobo, Gisela, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurelien, Naldi, Aurelien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C., Montrone, Corinna, Auge, Franck, Beckmann, Jacques S., Hasenauer, Jan, Wolkenhauer, Olaf, Wilighagen, Egon L ., Pico, Alexander R., Evelo, Chris T., Gillespie, Marc E., Stein, Lincoln D., Hermjakob, Henning, Brauner, Barbara, D’Eustachio, Peter, Sáez-Rodríguez, Julio, Dopazo, Joaquín, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Gupta, Shailendra Kumar, Scheel, Julia, Borlinghaus, Hanna, and Czauderna, Tobias

Abstract

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

Published
2021

44. HER2 Expression, Test Deviations, and Their Impact on Survival in Metastatic Gastric Cancer: Results From the Prospective Multicenter VARIANZ Study

Author

Haffner, Ivonne, primary, Schierle, Katrin, additional, Raimúndez, Elba, additional, Geier, Birgitta, additional, Maier, Dieter, additional, Hasenauer, Jan, additional, Luber, Birgit, additional, Walch, Axel, additional, Kolbe, Katharina, additional, Riera Knorrenschild, Jorge, additional, Kretzschmar, Albrecht, additional, Rau, Beate, additional, Fischer von Weikersthal, Ludwig, additional, Ahlborn, Miriam, additional, Siegler, Gabriele, additional, Fuxius, Stefan, additional, Decker, Thomas, additional, Wittekind, Christian, additional, and Lordick, Florian, additional

Published
2021
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45. Recovery from COVID-19: a sprint or marathon? 6-month follow-up data from online long COVID-19 support group members

Author

Vaes, Anouk W., primary, Goërtz, Yvonne M.J., additional, Van Herck, Maarten, additional, Machado, Felipe V.C., additional, Meys, Roy, additional, Delbressine, Jeannet M., additional, Houben-Wilke, Sarah, additional, Gaffron, Swetlana, additional, Maier, Dieter, additional, Burtin, Chris, additional, Posthuma, Rein, additional, van Loon, Nicole P.H., additional, Franssen, Frits M.E., additional, Hajian, Bita, additional, Simons, Sami O., additional, van Boven, Job F.M., additional, Klok, Frederikus A., additional, Spaetgens, Bart, additional, Pinxt, Claire M.H., additional, Liu, Limmie Y.L., additional, Wesseling, Geertjan, additional, Spies, Yvonne, additional, Vijlbrief, Herman, additional, van ’t Hul, Alex J., additional, Janssen, Daisy J.A., additional, and Spruit, Martijn A., additional

Published
2021
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46. Associations between air pollution and pediatric eczema, rhinoconjunctivitis and asthma: A meta-analysis of European birth cohorts

Author

Fuertes, Elaine, Sunyer, Jordi, Gehring, Ulrike, Porta, Daniela, Forastiere, Francesco, Cesaroni, Giulia, Vrijheid, Martine, Guxens, Mònica, Annesi-Maesano, Isabella, Slama, Rémy, Maier, Dieter, Kogevinas, Manolis, Bousquet, Jean, Chatzi, Leda, Lertxundi, Aitana, Basterrechea, Mikel, Esplugues, Ana, Ferrero, Amparo, Wright, John, Mason, Dan, McEachan, Rosie, Garcia-Aymerich, Judith, Jacquemin, Bénédicte, IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, Child and Adolescent Psychiatry / Psychology, Instituto de Salud Global - Institute For Global Health [Barcelona] (ISGlobal), National Heart and Lung Institute [London] (NHLI), Imperial College London-Royal Brompton and Harefield NHS Foundation Trust, CIBER de Epidemiología y Salud Pública (CIBERESP), Universitat Pompeu Fabra [Barcelona] (UPF), Institute for Risk Assessment Sciences, Utrecht University [Utrecht], Lazio Regional Health Service [Rome], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Biomax Informatics AG, Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Arnaud de Villeneuve [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), University of Crete [Heraklion] (UOC), University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), ISGlobal, Centre de Recerca en Epidemiologia Ambiental (CREAL), Vieillissement et Maladies chroniques : approches épidémiologique et de santé publique (VIMA), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM), École des Hautes Études en Santé Publique [EHESP] (EHESP), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), 211250, European Community’s Seventh Framework Program, European Project: 261357,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,MEDALL(2010), European Project: 211250,EC:FP7:ENV,FP7-ENV-2007-1,ESCAPE(2008), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Université d'Angers (UA)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )

Subjects
010504 meteorology & atmospheric sciences, Air pollution exposure, Air pollution, Eczema, cross-sectional studies, 010501 environmental sciences, medicine.disease_cause, 01 natural sciences, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Rhinoconjunctivitis, Environmental health, Air Pollution, medicine, Air Pollutants/toxicity, Humans, [SDV.IMM.ALL]Life Sciences [q-bio]/Immunology/Allergology, Adverse effect, Child, lcsh:Environmental sciences, 0105 earth and related environmental sciences, General Environmental Science, Asthma, Rhinitis, lcsh:GE1-350, Pediatric, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, [SDV.MHEP.PED]Life Sciences [q-bio]/Human health and pathology/Pediatrics, Air Pollutants, Odds ratio, Environmental Exposure, medicine.disease, Conjunctivitis, Confidence interval, 3. Good health, Europe, 13. Climate action, Meta-analysis, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Particulate Matter, Conjunctivitis/epidemiology, Birth cohort, Environmental Sciences
Abstract

Background: Uncertainly continues to exist regarding the role of air pollution on pediatric asthma and allergic conditions, especially as air pollution levels have started to decrease in recent decades. Objective: We examined associations of long-term air pollution levels at the home address with pediatric eczema, rhinoconjunctivitis and asthma prevalences in five birth cohorts (BIB, EDEN, GASPII, RHEA and INMA) from seven areas in five European countries. Methods: Current eczema, rhinoconjunctivitis and asthma were assessed in children aged four (N = 6527) and eight years (N = 2489). A multi-morbidity outcome (≥2 conditions versus none) was also defined. Individual outdoor levels of nitrogen dioxide (NO2), nitrogen oxides, mass of particulate matter with an aerodynamic diameter

Published
2020
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47. Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?

Author

Lynch, Iseult, Anreas Afantitis, Exner, Thomas, Himley, Martin, Lobaskin, Vladimir, Doganis, Phillip, Maier, Dieter, Sanabria, Natasha, Rybinska-Fryca, Anna, Gromelski, Maciej, Puzyn, Tomasz, Willighagen, Egon, Johnston, Blair, Gulumian, Mary, Matzke, Marianne, Etxabe, Amaia Green, Bossa, Nathan, Serra, Angela, Liampa, Irene, Harper, Stacey, Tämm, Kaido, Jensen, Alexander CØ, Kohonen, Pekka, Slater, Luke, Tsoumanis, Andreas, Greco, Dario, Winkler, David, Haralambos Sarimveis, and Melagraki, Georgia

Subjects
FOS: Nanotechnology, 100708 Nanomaterials
Abstract

Chemoinformatics has developed efficient ways of representing chemical structures for small molecules as simple text strings, simplified molecular-input line-entry system (SMILES) and the IUPAC International Chemical Identifier (InChI), which are machine-readable. In particular, InChIs have been extended to encode formalized representations of mixtures and reactions, and work is ongoing to represent polymers and other macromolecules in this way. The next frontier is encoding the multi-component structures of nanomaterials (NMs) in a machine-readable format to enable linking of datasets for nanoinformatics and regulatory applications. A workshop organized by the H2020 research infrastructure NanoCommons and the nanoinformatics project NanoSolveIT analysed issues involved in developing an InChI for NMs (NInChI). The layers needed to captureNMstructures include but are not limited to: core composition (possibly multi-layered); surface topography; surface coatings or functionalization; doping with other chemicals; and representation of impurities. NM distributions (size, shape, composition, surface properties, etc.), types of chemical linkages connecting surface functionalization and coating molecules to the core, and various crystallographic forms exhibited by NMs also need to be considered. Six case studies were conducted to elucidate requirements for unambiguous description of NMs. The suggested NInChI layers are intended to stimulate further analysis that will lead to the first version of a “nano” extension to the InChI standard.

Published
2020
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49. Associations between air pollution and pediatric eczema, rhinoconjunctivitis and asthma: A meta-analysis of European birth cohorts

Author

IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, Fuertes, Elaine, Sunyer, Jordi, Gehring, Ulrike, Porta, Daniela, Forastiere, Francesco, Cesaroni, Giulia, Vrijheid, Martine, Guxens, Mònica, Annesi-Maesano, Isabella, Slama, Rémy, Maier, Dieter, Kogevinas, Manolis, Bousquet, Jean, Chatzi, Leda, Lertxundi, Aitana, Basterrechea, Mikel, Esplugues, Ana, Ferrero, Amparo, Wright, John, Mason, Dan, McEachan, Rosie, Garcia-Aymerich, Judith, Jacquemin, Bénédicte, IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, Fuertes, Elaine, Sunyer, Jordi, Gehring, Ulrike, Porta, Daniela, Forastiere, Francesco, Cesaroni, Giulia, Vrijheid, Martine, Guxens, Mònica, Annesi-Maesano, Isabella, Slama, Rémy, Maier, Dieter, Kogevinas, Manolis, Bousquet, Jean, Chatzi, Leda, Lertxundi, Aitana, Basterrechea, Mikel, Esplugues, Ana, Ferrero, Amparo, Wright, John, Mason, Dan, McEachan, Rosie, Garcia-Aymerich, Judith, and Jacquemin, Bénédicte

Published
2020

50. Obesity is associated with shorter telomeres in 8 year-old children

Author

Fuertes, Elaine, Sunyer, Jordi, Gehring, Ulrike, Porta, Daniela, Forastiere, Francesco, Cesaroni, Giulia, Guxens, Mònica, Annesi-Maesano, Isabella, Maier, Dieter, Kogevinas, Manolis, Bousquet, Jean, Lertxundi, Aitana, Basterrechea, Mikel, Esplugues, Ana, Ferrero, Amparo, Mason, Dan, Garcia-Aymerich, Judith, Jacquemin, Bénédicte, Clemente, Diana, Maitre, Lea, Bustamante, Mariona, Chatzi, Leda, Roumeliotaki, Theano, Fossati, Serena, Grazuleviciene, Regina, Gützkow, Kristine, Lepeule, Johanna, Martens, Dries, Mceachan, Rosie, Meltzer, Helle, Petraviciene, Inga, Slama, Rémy, Tamayo-Uria, Ibon, Urquiza, Jose, Vafeiadi, Marina, Wright, John, Nawrot, Tim, Vrijheid, Martine, Institut National de la Santé et de la Recherche Médicale (INSERM), Université Grenoble Alpes (UGA), Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), European Project, Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Universitaire [Grenoble] (CHU)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Slama, Remy/0000-0002-8980-8529, lepeule, johanna/0000-0001-8907-197X, Fossati, Serena/0000-0002-7484-5837, Tamayo Uria, and Ibon/0000-0002-8183-7106

Subjects
Male, 0301 basic medicine, Aging, BLOOD, Epidemiology, [SDV]Life Sciences [q-bio], Eczema, lcsh:Medicine, Body Mass Index, MESH: Skinfold Thickness, Cohort Studies, 0302 clinical medicine, MESH: Pregnancy, Pregnancy, MESH: Risk Factors, MESH: Child, LENGTH, Medicine, MESH: Obesity, MESH: Aging, 030212 general & internal medicine, OXIDATIVE STRESS, lcsh:Science, Child, MESH: Cohort Studies, Telomere Shortening, Adiposity, 2. Zero hunger, Pediatric, Multidisciplinary, Telomere, Circumference, Multidisciplinary Sciences, MOTHER, Skinfold Thickness, Skinfold thickness, Cohort effect, CARDIOVASCULAR-DISEASE, MESH: Waist Circumference, Science & Technology - Other Topics, Female, SMOKING, Waist Circumference, Birth cohort, Adult, Waist, Air pollution, Predictive markers, Article, Fat mass, MESH: Body Mass Index, 03 medical and health sciences, AGE, INFLAMMATION, Rhinoconjunctivitis, MESH: Telomere Shortening, Humans, Obesity, Retrospective Studies, MESH: Adiposity, Science & Technology, MESH: Humans, business.industry, MORTALITY, lcsh:R, MESH: Adult, MESH: Retrospective Studies, medicine.disease, Asthma, MESH: Male, 030104 developmental biology, Risk factors, COHORT PROFILE, MESH: Biomarkers, lcsh:Q, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, MESH: Telomere, Body mass index, MESH: Female, Biomarkers, Demography
Abstract

Telomere length is considered a biomarker of biological aging. Shorter telomeres and obesity have both been associated with age-related diseases. To evaluate the association between various indices of obesity with leukocyte telomere length (LTL) in childhood, data from 1,396 mother-child pairs of the multi-centre European birth cohort study HELIX were used. Maternal pre-pregnancy body mass index (BMI) and 4 adiposity markers in children at age 8 (6-11) years were assessed: BMI, fat mass, waist circumference, and skinfold thickness. Relative LTL was obtained. Associations of LTL with each adiposity marker were calculated using linear mixed models with a random cohort effect. For each 1 kg/ m 2 increment in maternal pre-pregnancy BMI, the child's LTL was 0.23% shorter (95%CI: 0.01,0.46%). Each unit increase in child BMI z-score was associated with 1.21% (95%CI: 0.30,2.11%) shorter LTL. Inverse associations were observed between waist circumference and LTL (-0.96% per z-score unit; 95%CI: -2.06,0.16%), and skinfold thickness and LTL (-0.10% per z-score unit; 95%CI: -0.23,0.02%). In conclusion, this large multicentric study suggests that higher child adiposity indicators are associated with short telomeres in children, and that associations are stronger for child BMI than for maternal pre-pregnancy BMI. This work was supported by the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement no 308333 - the HELIX project. INMA data collection was supported by grant C/from the Instituto de Salud Carlos III. This project has received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No 774548. Tim S. Nawrot was funded by the EU Program "Ideas" (ERC-2012-StG 310898). ISGlobal is a member of the CERCA Programme, Generalitat de Catalunya. We are grateful to all the participating families in the six countries who took part in this study. Vrijheid, M (reprint author), Inst Global Hlth Barcelona, ISGlobal, C Doctor Aiguader 88, Barcelona 08003, Spain, Univ Pompeu Fabra, Placa Merce 10, Barcelona 08002, Spain, CIBER Epidemiol & Salud Publ CIBERESP, Ave Monforte de Lemos 3-5, Madrid, Spain. martine.vrijheid@isglobal.org

Published
2019
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