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1. Privacy-Preserving Multi-Center Differential Protein Abundance Analysis with FedProt

Author

Burankova, Yuliya, Abele, Miriam, Bakhtiari, Mohammad, von Törne, Christine, Barth, Teresa, Schweizer, Lisa, Giesbertz, Pieter, Schmidt, Johannes R., Kalkhof, Stefan, Müller-Deile, Janina, van Veelen, Peter A, Mohammed, Yassene, Hammer, Elke, Arend, Lis, Adamowicz, Klaudia, Laske, Tanja, Hartebrodt, Anne, Frisch, Tobias, Meng, Chen, Matschinske, Julian, Späth, Julian, Röttger, Richard, Schwämmle, Veit, Hauck, Stefanie M., Lichtenthaler, Stefan, Imhof, Axel, Mann, Matthias, Ludwig, Christina, Kuster, Bernhard, Baumbach, Jan, and Zolotareva, Olga

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Machine Learning
Abstract

Quantitative mass spectrometry has revolutionized proteomics by enabling simultaneous quantification of thousands of proteins. Pooling patient-derived data from multiple institutions enhances statistical power but raises significant privacy concerns. Here we introduce FedProt, the first privacy-preserving tool for collaborative differential protein abundance analysis of distributed data, which utilizes federated learning and additive secret sharing. In the absence of a multicenter patient-derived dataset for evaluation, we created two, one at five centers from LFQ E.coli experiments and one at three centers from TMT human serum. Evaluations using these datasets confirm that FedProt achieves accuracy equivalent to DEqMS applied to pooled data, with completely negligible absolute differences no greater than $\text{$4 \times 10^{-12}$}$. In contrast, -log10(p-values) computed by the most accurate meta-analysis methods diverged from the centralized analysis results by up to 25-27. FedProt is available as a web tool with detailed documentation as a FeatureCloud App., Comment: 52 pages, 16 figures, 12 tables. Last two authors listed are joint last authors

Published
2024

2. Plasma proteome association with coronary heart disease and carotid intima media thickness: results from the KORA F4 study

Author

Elhadad, Mohamed A., del C. Gómez-Alonso, Mónica, Chen, Chien-Wei, Neumeyer, Sonja, Delerue, Thomas, Rathmann, Wolfgang, Näbauer, Michael, Meisinger, Christa, Kääb, Stefan, Seissler, Jochen, Graumann, Johannes, Koenig, Wolfgang, Suhre, Karsten, Gieger, Christian, Völker, Uwe, Peters, Annette, Hammer, Elke, and Waldenberger, Melanie

Published
2024
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4. Mutation-induced LZTR1 polymerization provokes cardiac pathology in recessive Noonan syndrome

Author

Busley, Alexandra Viktoria, Gutiérrez-Gutiérrez, Óscar, Hammer, Elke, Koitka, Fabian, Mirzaiebadizi, Amin, Steinegger, Martin, Pape, Constantin, Böhmer, Linda, Schroeder, Henning, Kleinsorge, Mandy, Engler, Melanie, Cirstea, Ion Cristian, Gremer, Lothar, Willbold, Dieter, Altmüller, Janine, Marbach, Felix, Hasenfuss, Gerd, Zimmermann, Wolfram-Hubertus, Ahmadian, Mohammad Reza, Wollnik, Bernd, and Cyganek, Lukas

Published
2024
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5. #2407 Multiomics analysis of isolated zebrafish glomeruli to unravel the impact of alternative splicing in glomerular diseases

Author

Mattias, Francescapaola, primary, Kliewe, Felix, additional, Hammer, Elke, additional, Ameling, Sabine, additional, Tsoy, Olga, additional, Gress, Alexander, additional, Lio, Chit Tong, additional, Simm, Stefan, additional, Kalinina, Olga V, additional, Baumbach, Jan, additional, Völker, Uwe, additional, and Endlich, Nicole, additional

Published
2024
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6. #2450 Alternative splicing in podocytes under mechanical stress: a new perspective for the pathogenic effect of glomerular hypertension

Author

Mattias, Francescapaola, primary, Kliewe, Felix, additional, Hammer, Elke, additional, Ameling, Sabine, additional, Tsoy, Olga, additional, Gress, Alexander, additional, Simm, Stefan, additional, Kalinina, Olga V, additional, Endlich, Karlhans, additional, Baumbach, Jan, additional, Völker, Uwe, additional, and Endlich, Nicole, additional

Published
2024
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8. Unveiling the crucial neuronal role of the proteasomal ATPase subunit genePSMC5in neurodevelopmental proteasomopathies

Author

Küry, Sébastien, primary, Stanton, Janelle E., additional, van Woerden, Geeske, additional, Hsieh, Tzung-Chien, additional, Rosenfelt, Cory, additional, Pier Scott-Boyer, Marie, additional, Most, Victoria, additional, Wang, Tianyun, additional, Papendorf, Jonas Johannes, additional, de Konink, Charlotte, additional, Deb, Wallid, additional, Vignard, Virginie, additional, Studencka-Turski, Maja, additional, Besnard, Thomas, additional, Hajdukowicz, Anna Marta, additional, Thiel, Franziska, additional, Moller, Sophie, additional, Florenceau, Laetitia, additional, Cuinat, Silvestre, additional, Marsac, Sylvain, additional, Wentzensen, Ingrid, additional, Tuttle, Annabelle, additional, Forster, Cara, additional, Striesow, Johanna, additional, Golnik, Richard, additional, Ortiz, Damara, additional, Jenkins, Laura, additional, Rosenfeld, Jill A., additional, Ziegler, Alban, additional, Houdayer, Clara, additional, Bonneau, Dominique, additional, Torti, Erin, additional, Begtrup, Amber, additional, Monaghan, Kristin G., additional, Mullegama, Sureni V., additional, Volker-Touw, C.M.L. (Nienke), additional, van Gassen, Koen L.I., additional, Oegema, Renske, additional, de Pagter, Mirjam, additional, Steindl, Katharina, additional, Rauch, Anita, additional, Ivanovski, Ivan, additional, McDonald, Kimberly, additional, Boothe, Emily, additional, Dauber, Andrew, additional, Baker, Janice, additional, Fabie, Noelle Andrea V., additional, Bernier, Raphael A., additional, Turner, Tychele N., additional, Srivastava, Siddharth, additional, Dies, Kira A., additional, Swanson, Lindsay, additional, Costin, Carrie, additional, Jobling, Rebekah K., additional, Pappas, John, additional, Rabin, Rachel, additional, Niyazov, Dmitriy, additional, Tsai, Anne Chun-Hui, additional, Kovak, Karen, additional, Beck, David B., additional, Malicdan, May Christine V, additional, Adams, David R, additional, Wolfe, Lynne, additional, Ganetzky, Rebecca D., additional, Muraresku, Colleen, additional, Babikyan, Davit, additional, Sedlacek, Zdenek, additional, Hancarova, Miroslava, additional, Timberlake, Andrew T., additional, Al Saif, Hind, additional, Schmidt, Berkley, additional, King, Kayla, additional, Hajianpour, MJ, additional, Costain, Gregory, additional, Prendergast, D'Arcy, additional, Li, Chumei, additional, Genevieve, David, additional, Vitobello, Antonio, additional, Sorlin, Arthur, additional, Philippe, Christophe, additional, Harel, Tamar, additional, Toker, Ori, additional, Sabir, Ataf, additional, Lim, Derek, additional, Hamilton, Mark, additional, Bryson, Lisa, additional, Cleary, Elaine, additional, Weber, Sacha, additional, Hoffman, Trevor L., additional, Cueto-Gonzalez, Anna Maria, additional, Tizzano, Eduardo Fidel, additional, Gomez-Andres, David, additional, Codina-Sola, Marta, additional, Ververi, Athina, additional, Pavlidou, Efterpi, additional, Lambropoulos, Alexandros, additional, Garganis, Kyriakos, additional, Rio, Marlene, additional, Levy, Jonathan, additional, Jurgensmeyer, Sarah, additional, McRae, Anne M., additional, Lessard, Mathieu K., additional, DAgostino, Maria Daniela, additional, De Bie, Isabelle, additional, Wegler, Meret, additional, Abou Jamra, Rami, additional, Kamphausen, Susanne B., additional, Bothe, Viktoria, additional, Busch, Larissa M., additional, Volker, Uwe, additional, Hammer, Elke, additional, Wende, Kristian, additional, Cogne, Benjamin, additional, Isidor, Bertrand, additional, Meiler, Jens, additional, Bosc-Rosati, Amelie, additional, Marcoux, Julien, additional, Bousquet, Marie-Pierre, additional, Poschmann, Jeremie, additional, Laumonnier, Frederic, additional, Hildebrand, Peter W., additional, Eichler, Evan E., additional, McWalter, Kirsty, additional, Krawitz, Peter M., additional, Droit, Arnaud, additional, Elgersma, Ype, additional, Grabrucker, Andreas M., additional, Bolduc, Francois, additional, Bézieau, Stéphane, additional, Ebstein, Frédéric, additional, and Krüger, Elke, additional

Published
2024
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9. Metabolic remodeling in cardiac hypertrophy and heart failure with reduced ejection fraction occurs independent of transcription factor EB in mice

Author

Dörmann, Niklas, primary, Hammer, Elke, additional, Struckmann, Karlotta, additional, Rüdebusch, Julia, additional, Bartels, Kirsten, additional, Wenzel, Kristin, additional, Schulz, Julia, additional, Gross, Stefan, additional, Schwanz, Stefan, additional, Martin, Elisa, additional, Fielitz, Britta, additional, Pablo Tortola, Cristina, additional, Hahn, Alexander, additional, Benkner, Alexander, additional, Völker, Uwe, additional, Felix, Stephan B., additional, and Fielitz, Jens, additional

Published
2024
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11. Genomewide meta‐analysis identifies loci associated with IGF‐I and IGFBP‐3 levels with impact on age‐related traits

Author

Teumer, Alexander, Qi, Qibin, Nethander, Maria, Aschard, Hugues, Bandinelli, Stefania, Beekman, Marian, Berndt, Sonja I, Bidlingmaier, Martin, Broer, Linda, Group, CHARGE Longevity Working, Cappola, Anne, Ceda, Gian Paolo, Chanock, Stephen, Chen, Ming‐Huei, Chen, Tai C, Chen, Yii‐Der Ida, Chung, Jonathan, Del Greco Miglianico, Fabiola, Eriksson, Joel, Ferrucci, Luigi, Friedrich, Nele, Gnewuch, Carsten, Goodarzi, Mark O, Grarup, Niels, Guo, Tingwei, Hammer, Elke, Hayes, Richard B, Hicks, Andrew A, Hofman, Albert, Houwing‐Duistermaat, Jeanine J, Hu, Frank, Hunter, David J, Husemoen, Lise L, Isaacs, Aaron, Jacobs, Kevin B, Janssen, Joop AMJL, Jansson, John‐Olov, Jehmlich, Nico, Johnson, Simon, Juul, Anders, Karlsson, Magnus, Kilpelainen, Tuomas O, Kovacs, Peter, Kraft, Peter, Li, Chao, Linneberg, Allan, Liu, Yongmei, Loos, Ruth JF, Consortium, Body Composition Genetics, Lorentzon, Mattias, Lu, Yingchang, Maggio, Marcello, Magi, Reedik, Meigs, James, Mellström, Dan, Nauck, Matthias, Newman, Anne B, Pollak, Michael N, Pramstaller, Peter P, Prokopenko, Inga, Psaty, Bruce M, Reincke, Martin, Rimm, Eric B, Rotter, Jerome I, Pierre, Aude Saint, Schurmann, Claudia, Seshadri, Sudha, Sjögren, Klara, Slagboom, P Eline, Strickler, Howard D, Stumvoll, Michael, Suh, Yousin, Sun, Qi, Zhang, Cuilin, Svensson, Johan, Tanaka, Toshiko, Tare, Archana, Tönjes, Anke, Uh, Hae‐Won, van Duijn, Cornelia M, van Heemst, Diana, Vandenput, Liesbeth, Vasan, Ramachandran S, Völker, Uwe, Willems, Sara M, Ohlsson, Claes, Wallaschofski, Henri, and Kaplan, Robert C

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Clinical Research, Aging, 2.1 Biological and endogenous factors, Aetiology, Metabolic and endocrine, Cardiovascular, Adult, Female, Gene Expression Regulation, Genome-Wide Association Study, Humans, Insulin-Like Growth Factor Binding Protein 3, Insulin-Like Growth Factor I, Male, Metabolome, Quantitative Trait Loci, Quantitative Trait, Heritable, Regulatory Sequences, Nucleic Acid, aging, genomewide association study, growth hormone axis, IGF-I, IGFBP-3, longevity, CHARGE Longevity Working Group, Body Composition Genetics Consortium, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

The growth hormone/insulin-like growth factor (IGF) axis can be manipulated in animal models to promote longevity, and IGF-related proteins including IGF-I and IGF-binding protein-3 (IGFBP-3) have also been implicated in risk of human diseases including cardiovascular diseases, diabetes, and cancer. Through genomewide association study of up to 30 884 adults of European ancestry from 21 studies, we confirmed and extended the list of previously identified loci associated with circulating IGF-I and IGFBP-3 concentrations (IGF1, IGFBP3, GCKR, TNS3, GHSR, FOXO3, ASXL2, NUBP2/IGFALS, SORCS2, and CELSR2). Significant sex interactions, which were characterized by different genotype-phenotype associations between men and women, were found only for associations of IGFBP-3 concentrations with SNPs at the loci IGFBP3 and SORCS2. Analyses of SNPs, gene expression, and protein levels suggested that interplay between IGFBP3 and genes within the NUBP2 locus (IGFALS and HAGH) may affect circulating IGF-I and IGFBP-3 concentrations. The IGF-I-decreasing allele of SNP rs934073, which is an eQTL of ASXL2, was associated with lower adiposity and higher likelihood of survival beyond 90 years. The known longevity-associated variant rs2153960 (FOXO3) was observed to be a genomewide significant SNP for IGF-I concentrations. Bioinformatics analysis suggested enrichment of putative regulatory elements among these IGF-I- and IGFBP-3-associated loci, particularly of rs646776 at CELSR2. In conclusion, this study identified several loci associated with circulating IGF-I and IGFBP-3 concentrations and provides clues to the potential role of the IGF axis in mediating effects of known (FOXO3) and novel (ASXL2) longevity-associated loci.

Published
2016

20. MassSpecPreppy—An end‐to‐end solution for automated protein concentration determination and flexible sample digestion for proteomics applications

Author

Reder, Alexander, primary, Hentschker, Christian, additional, Steil, Leif, additional, Gesell Salazar, Manuela, additional, Hammer, Elke, additional, Dhople, Vishnu M., additional, Sura, Thomas, additional, Lissner, Ulrike, additional, Wolfgramm, Hannes, additional, Dittmar, Denise, additional, Harms, Marco, additional, Surmann, Kristin, additional, Völker, Uwe, additional, and Michalik, Stephan, additional

Published
2023
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21. Plasma Proteome Association with Coronary Heart Disease and Carotid Intima Media Thickness: results from the KORA F4 study

Author

Elhadad, Mohamed A., primary, Gómez-Alonso, Monica del C., additional, Chen, Chien-Wei, additional, Neumeyer, Sonja, additional, Delerue, Thomas, additional, Rathmann, Wolfgang, additional, Näbauer, Michael, additional, Meisinger, Christa, additional, Kääb, Stefan, additional, Seissler, Jochen, additional, Graumann, Johannes, additional, Koenig, Wolfgang, additional, Suhre, Karsten, additional, Gieger, Christian, additional, Völker, Uwe, additional, Peters, Annette, additional, Hammer, Elke, additional, and Waldenberger, Melanie, additional

Published
2023
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22. Excessive sodium chloride ingestion promotes inflammation and kidney fibrosis in aging mice

Author

Bernhardt, Anja, primary, Krause, Anna, additional, Reichardt, Charlotte, additional, Steffen, Hannes, additional, Isermann, Berend, additional, Völker, Uwe, additional, Hammer, Elke, additional, Geffers, Robert, additional, Philipsen, Lars, additional, Dhjamandi, Kristin, additional, Ahmad, Sohail, additional, Brandt, Sabine, additional, Lindquist, Jonathan A., additional, and Mertens, Peter R., additional

Published
2023
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23. Global Protein Profiling in Processed Immunohistochemistry Tissue Sections

Author

Venz, Simone, primary, von Bohlen und Halbach, Viola, additional, Hentschker, Christian, additional, Junker, Heike, additional, Kuss, Andreas Walter, additional, Sura, Thomas, additional, Krüger, Elke, additional, Völker, Uwe, additional, von Bohlen und Halbach, Oliver, additional, Jensen, Lars Riff, additional, and Hammer, Elke, additional

Published
2023
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25. PSMC3 proteasome subunit variants are associated with neurodevelopmental delay and type I interferon production

Author

Ebstein, Frédéric, primary, Küry, Sébastien, additional, Most, Victoria, additional, Rosenfelt, Cory, additional, Scott-Boyer, Marie-Pier, additional, van Woerden, Geeske M., additional, Besnard, Thomas, additional, Papendorf, Jonas Johannes, additional, Studencka-Turski, Maja, additional, Wang, Tianyun, additional, Hsieh, Tzung-Chien, additional, Golnik, Richard, additional, Baldridge, Dustin, additional, Forster, Cara, additional, de Konink, Charlotte, additional, Teurlings, Selina M.W., additional, Vignard, Virginie, additional, van Jaarsveld, Richard H., additional, Ades, Lesley, additional, Cogné, Benjamin, additional, Mignot, Cyril, additional, Deb, Wallid, additional, Jongmans, Marjolijn C.J., additional, Cole, F. Sessions, additional, van den Boogaard, Marie-José H., additional, Wambach, Jennifer A., additional, Wegner, Daniel J., additional, Yang, Sandra, additional, Hannig, Vickie, additional, Brault, Jennifer Ann, additional, Zadeh, Neda, additional, Bennetts, Bruce, additional, Keren, Boris, additional, Gélineau, Anne-Claire, additional, Powis, Zöe, additional, Towne, Meghan, additional, Bachman, Kristine, additional, Seeley, Andrea, additional, Beck, Anita E., additional, Morrison, Jennifer, additional, Westman, Rachel, additional, Averill, Kelly, additional, Brunet, Theresa, additional, Haasters, Judith, additional, Carter, Melissa T., additional, Osmond, Matthew, additional, Wheeler, Patricia G., additional, Forzano, Francesca, additional, Mohammed, Shehla, additional, Trakadis, Yannis, additional, Accogli, Andrea, additional, Harrison, Rachel, additional, Guo, Yiran, additional, Hakonarson, Hakon, additional, Rondeau, Sophie, additional, Baujat, Geneviève, additional, Barcia, Giulia, additional, Feichtinger, René Günther, additional, Mayr, Johannes Adalbert, additional, Preisel, Martin, additional, Laumonnier, Frédéric, additional, Kallinich, Tilmann, additional, Knaus, Alexej, additional, Isidor, Bertrand, additional, Krawitz, Peter, additional, Völker, Uwe, additional, Hammer, Elke, additional, Droit, Arnaud, additional, Eichler, Evan E., additional, Elgersma, Ype, additional, Hildebrand, Peter W., additional, Bolduc, François, additional, Krüger, Elke, additional, and Bézieau, Stéphane, additional

Published
2023
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30. LZTR1 polymerization provokes cardiac pathology in recessive Noonan syndrome

Author

Busley, Alexandra Viktoria, primary, Gutiérrez-Gutiérrez, Óscar, additional, Hammer, Elke, additional, Steinegger, Martin, additional, Böhmer, Linda, additional, Schroeder, Henning, additional, Kleinsorge, Mandy, additional, Altmüller, Janine, additional, Marbach, Felix, additional, Hasenfuss, Gerd, additional, Zimmermann, Wolfram-Hubertus, additional, Wollnik, Bernd, additional, and Cyganek, Lukas, additional

Published
2023
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33. BCL11B depletion induces the development of highly cytotoxic innate T cells out of IL-15 stimulated peripheral blood αβ CD8+ T cells

Author

Forkel, Hannes, primary, Grabarczyk, Piotr, additional, Depke, Maren, additional, Troschke-Meurer, Sascha, additional, Simm, Stefan, additional, Hammer, Elke, additional, Michalik, Stephan, additional, Hentschker, Christian, additional, Corleis, Björn, additional, Loyal, Lucie, additional, Zumpe, Maxi, additional, Siebert, Nikolai, additional, Dorhoi, Anca, additional, Thiel, Andreas, additional, Lode, Holger, additional, Völker, Uwe, additional, and Schmidt, Christian A., additional

Published
2022
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37. ACTN2 Mutant Causes Proteopathy in Human iPSC-Derived Cardiomyocytes

Author

Zech, Antonia T. L., primary, Prondzynski, Maksymilian, additional, Singh, Sonia R., additional, Pietsch, Niels, additional, Orthey, Ellen, additional, Alizoti, Erda, additional, Busch, Josefine, additional, Madsen, Alexandra, additional, Behrens, Charlotta S., additional, Meyer-Jens, Moritz, additional, Mearini, Giulia, additional, Lemoine, Marc D., additional, Krämer, Elisabeth, additional, Mosqueira, Diogo, additional, Virdi, Sanamjeet, additional, Indenbirken, Daniela, additional, Depke, Maren, additional, Salazar, Manuela Gesell, additional, Völker, Uwe, additional, Braren, Ingke, additional, Pu, William T., additional, Eschenhagen, Thomas, additional, Hammer, Elke, additional, Schlossarek, Saskia, additional, and Carrier, Lucie, additional

Published
2022
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39. Riociguat attenuates the changes in left ventricular proteome and microRNA profile after experimental aortic stenosis in mice

Author

Benkner, Alexander, primary, Rüdebusch, Julia, additional, Nath, Neetika, additional, Hammer, Elke, additional, Grube, Karina, additional, Gross, Stefan, additional, Dhople, Vishnu M., additional, Eckstein, Gertrud, additional, Meitinger, Thomas, additional, Kaderali, Lars, additional, Völker, Uwe, additional, Fielitz, Jens, additional, and Felix, Stephan B., additional

Published
2022
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50. Testicular growth and spermatogenesis: new goals for pubertal hormone replacement in boys with hypogonadotropic hypogonadism? ‐a multicentre prospective study of hCG/rFSH treatment outcomes during adolescence‐

Author

Rohayem, Julia, Hauffa, Berthold P., Zacharin, Margaret, Kliesch, Sabine, Zitzmann, Michael, Wüsthof, Achim, Tittel, Bettina, Tittel, Bettina, Morlot, Michel, Vorhoff, Walburga, MüllerRossberg, Elke, MüllerRossberg, Elke, Wagner, Verena, Wagner, Verena, Wagner, Verena, Konrad, Katja, Salzgeber, Kirsten, FrickeOtto, Susanne, Wölfle, Joachim, Willig, Peter, Karges, Beate, Lankes, Erwin, Droste, Michael, RichterUnruh, Annette, Liesenkötter, KlausPeter, Hübner, Angela, Zichner, Stefanie, Welzel, Maik, Dunstheimer, Desiree, Potelajew, Ulrike, Heger, Sabine, Hammer, Elke, Oevering, Rudolf, Schmidt, Silke, and Nieschlag, Eberhard

Published
2017
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