[{"_id":"505","type":"journal_article","issue":"2","publication":"Green Chemistry","citation":{"ama":"Greimel K, Perz V, Koren K, et al. Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. <i>Green Chemistry</i>. 2013;15(2):381-388. doi:<a href=\"https://doi.org/10.1039/c2gc36666e\">10.1039/c2gc36666e</a>","ista":"Greimel K, Perz V, Koren K, Feola R, Temel A, Sohar C, Herrero Acero E, Klimant I, Guebitz G. 2013. Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. 15(2), 381–388.","ieee":"K. Greimel <i>et al.</i>, “Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins,” <i>Green Chemistry</i>, vol. 15, no. 2. Royal Society of Chemistry, pp. 381–388, 2013.","mla":"Greimel, Katrin, et al. “Banning Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.” <i>Green Chemistry</i>, vol. 15, no. 2, Royal Society of Chemistry, 2013, pp. 381–88, doi:<a href=\"https://doi.org/10.1039/c2gc36666e\">10.1039/c2gc36666e</a>.","apa":"Greimel, K., Perz, V., Koren, K., Feola, R., Temel, A., Sohar, C., … Guebitz, G. (2013). Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. <i>Green Chemistry</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c2gc36666e\">https://doi.org/10.1039/c2gc36666e</a>","short":"K. Greimel, V. Perz, K. Koren, R. Feola, A. Temel, C. Sohar, E. Herrero Acero, I. Klimant, G. Guebitz, Green Chemistry 15 (2013) 381–388.","chicago":"Greimel, Katrin, Veronika Perz, Klaus Koren, Roland Feola, Armin Temel, Christian Sohar, Enrique Herrero Acero, Ingo Klimant, and Georg Guebitz. “Banning Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.” <i>Green Chemistry</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c2gc36666e\">https://doi.org/10.1039/c2gc36666e</a>."},"doi":"10.1039/c2gc36666e","oa_version":"None","date_created":"2018-12-11T11:46:51Z","quality_controlled":"1","department":[{"_id":"HaJa"}],"acknowledgement":"This study was performed within the Austrian Centre of Indus-\r\ntrial Biotechnology ACIB and the COST Action 868. This work\r\nhas been supported by the Federal Ministry of Economy,\r\nFamily and Youth (BMWFJ), the Federal Ministry of Tra\r\nffi\r\nc,\r\nInnovation and Technology (bmvit), the Styrian Business\r\nPromotion Agency SFG, the Standortagentur Tirol and ZIT\r\n–\r\nTechnology  Agency  of  the  City  of  Vienna  through  the\r\nCOMET-Funding Program managed by the Austrian Research\r\nPromotion Agency FFG. Dr Massimiliano Cardinale (Institute of\r\nEnvironmental Biotechnology, TU Graz) is gratefully acknowl-\r\nedged for technical support with the CLSM measurements.","author":[{"last_name":"Greimel","first_name":"Katrin","full_name":"Greimel, Katrin"},{"first_name":"Veronika","last_name":"Perz","full_name":"Perz, Veronika"},{"first_name":"Klaus","id":"382FBD6A-F248-11E8-B48F-1D18A9856A87","last_name":"Koren","full_name":"Koren, Klaus"},{"last_name":"Feola","first_name":"Roland","full_name":"Feola, Roland"},{"full_name":"Temel, Armin","first_name":"Armin","last_name":"Temel"},{"first_name":"Christian","last_name":"Sohar","full_name":"Sohar, Christian"},{"full_name":"Herrero Acero, Enrique","last_name":"Herrero Acero","first_name":"Enrique"},{"full_name":"Klimant, Ingo","first_name":"Ingo","last_name":"Klimant"},{"full_name":"Guebitz, Georg","first_name":"Georg","last_name":"Guebitz"}],"language":[{"iso":"eng"}],"day":"01","year":"2013","status":"public","intvolume":"        15","title":"Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins","volume":15,"scopus_import":1,"page":"381 - 388","month":"02","date_published":"2013-02-01T00:00:00Z","abstract":[{"text":"Alkyd resins are polyesters containing unsaturated fatty acids that are used as binding agents in paints and coatings. Chemical drying of these polyesters is based on heavy metal catalyzed cross-linking of the unsaturated fatty acid moieties. Among the heavy-metal catalysts, cobalt complexes are the most effective, yet they have been proven to be carcinogenic. Therefore, strategies to replace the cobalt-based catalyst by environmentally friendlier and less toxic alternatives are under development. Here, we demonstrate for the first time that a laccase-mediator system can effectively replace the heavy-metal catalyst and cross-link alkyd resins. Interestingly, the biocatalytic reaction does not only work in aqueous media, but also in a solid film, where enzyme diffusion is limited. Within the catalytic cycle, the mediator oxidizes the alkyd resin and is regenerated by the laccase, which is uniformly distributed within the drying film as evidenced by confocal laser scanning microscopy. During gradual build-up of molecular weight, there is a concomitant decrease of the oxygen content in the film. A new optical sensor to follow oxygen consumption during the cross-linking reaction was developed and validated with state of the art techniques. A remarkable feature is the low sample amount required, which allows faster screening of new catalysts.","lang":"eng"}],"publisher":"Royal Society of Chemistry","publist_id":"7313","date_updated":"2021-01-12T08:01:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published"},{"publisher":"American Society of Plant Biologists","date_updated":"2021-01-12T08:01:12Z","publist_id":"7312","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2013-08-01T00:00:00Z","month":"08","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784592/"}],"status":"public","title":"Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis","volume":25,"day":"01","department":[{"_id":"JiFr"}],"author":[{"first_name":"Soo","last_name":"Kim","full_name":"Kim, Soo"},{"last_name":"Xu","first_name":"Zheng","full_name":"Xu, Zheng"},{"full_name":"Song, Kyungyoung","first_name":"Kyungyoung","last_name":"Song"},{"last_name":"Kim","first_name":"Dae","full_name":"Kim, Dae"},{"full_name":"Kang, Hyangju","first_name":"Hyangju","last_name":"Kang"},{"full_name":"Reichardt, Ilka","last_name":"Reichardt","first_name":"Ilka"},{"full_name":"Sohn, Eun","first_name":"Eun","last_name":"Sohn"},{"last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Juergens, Gerd","last_name":"Juergens","first_name":"Gerd"},{"last_name":"Hwang","first_name":"Inhwan","full_name":"Hwang, Inhwan"}],"type":"journal_article","_id":"507","issue":"8","publication":"Plant Cell","date_created":"2018-12-11T11:46:52Z","oa_version":"Submitted Version","oa":1,"abstract":[{"text":"Fertilization in flowering plants requires the temporal and spatial coordination of many developmental processes, including pollen production, anther dehiscence, ovule production, and pollen tube elongation. However, it remains elusive as to how this coordination occurs during reproduction. Here, we present evidence that endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays multiple defects in pollen production and viability, as well as elongation of staminal filaments and pollen tubes, all of which are pivotal processes needed for fertilization. Of these abnormalities, the defects in elongation of staminal filaments and pollen tubes were partially rescued by exogenous auxin. Moreover, DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl) pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments. Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent endocytosis plays a crucial role in coordinating the multiple developmental aspects of male reproductive organs by modulating cellular auxin level through the regulation of the amount and polarity of PINs.","lang":"eng"}],"external_id":{"pmid":["23975898"]},"page":"2970 - 2985","pmid":1,"intvolume":"        25","language":[{"iso":"eng"}],"year":"2013","citation":{"ama":"Kim S, Xu Z, Song K, et al. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. <i>Plant Cell</i>. 2013;25(8):2970-2985. doi:<a href=\"https://doi.org/10.1105/tpc.113.114264\">10.1105/tpc.113.114264</a>","apa":"Kim, S., Xu, Z., Song, K., Kim, D., Kang, H., Reichardt, I., … Hwang, I. (2013). Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114264\">https://doi.org/10.1105/tpc.113.114264</a>","chicago":"Kim, Soo, Zheng Xu, Kyungyoung Song, Dae Kim, Hyangju Kang, Ilka Reichardt, Eun Sohn, Jiří Friml, Gerd Juergens, and Inhwan Hwang. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114264\">https://doi.org/10.1105/tpc.113.114264</a>.","short":"S. Kim, Z. Xu, K. Song, D. Kim, H. Kang, I. Reichardt, E. Sohn, J. Friml, G. Juergens, I. Hwang, Plant Cell 25 (2013) 2970–2985.","ista":"Kim S, Xu Z, Song K, Kim D, Kang H, Reichardt I, Sohn E, Friml J, Juergens G, Hwang I. 2013. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. Plant Cell. 25(8), 2970–2985.","ieee":"S. Kim <i>et al.</i>, “Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis,” <i>Plant Cell</i>, vol. 25, no. 8. American Society of Plant Biologists, pp. 2970–2985, 2013.","mla":"Kim, Soo, et al. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” <i>Plant Cell</i>, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2970–85, doi:<a href=\"https://doi.org/10.1105/tpc.113.114264\">10.1105/tpc.113.114264</a>."},"doi":"10.1105/tpc.113.114264","quality_controlled":"1"},{"citation":{"ama":"Tarazona Santos E, Machado M, Magalhães W, et al. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. <i>Molecular Biology and Evolution</i>. 2013;30(9):2157-2167. doi:<a href=\"https://doi.org/10.1093/molbev/mst119\">10.1093/molbev/mst119</a>","chicago":"Tarazona Santos, Eduardo, Moara Machado, Wagner Magalhães, Renee Chen, Fernanda Lyon, Laurie Burdett, Andrew Crenshaw, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/molbev/mst119\">https://doi.org/10.1093/molbev/mst119</a>.","short":"E. Tarazona Santos, M. Machado, W. Magalhães, R. Chen, F. Lyon, L. Burdett, A. Crenshaw, C. Fabbri, L. Pereira, L. Pinto, R.A. Fernandes Redondo, B. Sestanovich, M. Yeager, S. Chanock, Molecular Biology and Evolution 30 (2013) 2157–2167.","apa":"Tarazona Santos, E., Machado, M., Magalhães, W., Chen, R., Lyon, F., Burdett, L., … Chanock, S. (2013). Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/mst119\">https://doi.org/10.1093/molbev/mst119</a>","mla":"Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” <i>Molecular Biology and Evolution</i>, vol. 30, no. 9, Oxford University Press, 2013, pp. 2157–67, doi:<a href=\"https://doi.org/10.1093/molbev/mst119\">10.1093/molbev/mst119</a>.","ista":"Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M, Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 30(9), 2157–2167.","ieee":"E. Tarazona Santos <i>et al.</i>, “Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” <i>Molecular Biology and Evolution</i>, vol. 30, no. 9. Oxford University Press, pp. 2157–2167, 2013."},"doi":"10.1093/molbev/mst119","quality_controlled":"1","year":"2013","language":[{"iso":"eng"}],"pmid":1,"intvolume":"        30","page":"2157 - 2167","external_id":{"pmid":["23821607"]},"oa":1,"abstract":[{"text":"The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. Using evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggests that this region may have a function in host-pathogen interactions. On the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2, and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the pattern of CYBA diversity is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other complex diseases.","lang":"eng"}],"oa_version":"Submitted Version","date_created":"2018-12-11T11:46:52Z","issue":"9","_id":"508","type":"journal_article","publication":"Molecular Biology and Evolution","author":[{"full_name":"Tarazona Santos, Eduardo","first_name":"Eduardo","last_name":"Tarazona Santos"},{"full_name":"Machado, Moara","first_name":"Moara","last_name":"Machado"},{"first_name":"Wagner","last_name":"Magalhães","full_name":"Magalhães, Wagner"},{"full_name":"Chen, Renee","last_name":"Chen","first_name":"Renee"},{"last_name":"Lyon","first_name":"Fernanda","full_name":"Lyon, Fernanda"},{"last_name":"Burdett","first_name":"Laurie","full_name":"Burdett, Laurie"},{"full_name":"Crenshaw, Andrew","last_name":"Crenshaw","first_name":"Andrew"},{"full_name":"Fabbri, Cristina","first_name":"Cristina","last_name":"Fabbri"},{"full_name":"Pereira, Latife","first_name":"Latife","last_name":"Pereira"},{"last_name":"Pinto","first_name":"Laelia","full_name":"Pinto, Laelia"},{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793","full_name":"Fernandes Redondo, Rodrigo A"},{"first_name":"Ben","last_name":"Sestanovich","full_name":"Sestanovich, Ben"},{"last_name":"Yeager","first_name":"Meredith","full_name":"Yeager, Meredith"},{"full_name":"Chanock, Stephen","first_name":"Stephen","last_name":"Chanock"}],"department":[{"_id":"JoBo"}],"day":"01","title":"Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications","volume":30,"status":"public","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/"}],"scopus_import":1,"month":"09","date_published":"2013-09-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Oxford University Press","publist_id":"7310","date_updated":"2021-01-12T08:01:12Z"},{"oa":1,"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) regulates many aspects of plant development, including hormone signaling and responses to environmental stresses. Despite the importance of this process, the machinery that regulates CME in plants is largely unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the formation of clathrin-coated vesicles at the plasma membrane (PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana, the biochemistry and functionality of the complex is still uncharacterized. Here, we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification and found that one of the large AP-2 subunits, AP2A1, localized at the PM and interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2. Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis is evolutionarily conserved and that AP-2 functions in receptormediated endocytosis. "}],"external_id":{"pmid":["23975899"]},"page":"2986 - 2997","pmid":1,"intvolume":"        25","language":[{"iso":"eng"}],"year":"2013","doi":"10.1105/tpc.113.114058","citation":{"chicago":"Di Rubbo, Simone, Niloufer Irani, Soo Kim, Zheng Xu, Astrid Gadeyne, Wim Dejonghe, Isabelle Vanhoutte, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114058\">https://doi.org/10.1105/tpc.113.114058</a>.","short":"S. Di Rubbo, N. Irani, S. Kim, Z. Xu, A. Gadeyne, W. Dejonghe, I. Vanhoutte, G. Persiau, D. Eeckhout, S. Simon, K. Song, J. Kleine Vehn, J. Friml, G. De Jaeger, D. Van Damme, I. Hwang, E. Russinova, Plant Cell 25 (2013) 2986–2997.","apa":"Di Rubbo, S., Irani, N., Kim, S., Xu, Z., Gadeyne, A., Dejonghe, W., … Russinova, E. (2013). The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114058\">https://doi.org/10.1105/tpc.113.114058</a>","mla":"Di Rubbo, Simone, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” <i>Plant Cell</i>, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2986–97, doi:<a href=\"https://doi.org/10.1105/tpc.113.114058\">10.1105/tpc.113.114058</a>.","ista":"Di Rubbo S, Irani N, Kim S, Xu Z, Gadeyne A, Dejonghe W, Vanhoutte I, Persiau G, Eeckhout D, Simon S, Song K, Kleine Vehn J, Friml J, De Jaeger G, Van Damme D, Hwang I, Russinova E. 2013. The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. 25(8), 2986–2997.","ieee":"S. Di Rubbo <i>et al.</i>, “The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis,” <i>Plant Cell</i>, vol. 25, no. 8. American Society of Plant Biologists, pp. 2986–2997, 2013.","ama":"Di Rubbo S, Irani N, Kim S, et al. The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. <i>Plant Cell</i>. 2013;25(8):2986-2997. doi:<a href=\"https://doi.org/10.1105/tpc.113.114058\">10.1105/tpc.113.114058</a>"},"quality_controlled":"1","publisher":"American Society of Plant Biologists","date_updated":"2021-01-12T08:01:13Z","publist_id":"7311","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2013-08-01T00:00:00Z","month":"08","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784593/","open_access":"1"}],"status":"public","title":"The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis","volume":25,"day":"01","department":[{"_id":"JiFr"}],"author":[{"full_name":"Di Rubbo, Simone","first_name":"Simone","last_name":"Di Rubbo"},{"full_name":"Irani, Niloufer","last_name":"Irani","first_name":"Niloufer"},{"first_name":"Soo","last_name":"Kim","full_name":"Kim, Soo"},{"full_name":"Xu, Zheng","first_name":"Zheng","last_name":"Xu"},{"last_name":"Gadeyne","first_name":"Astrid","full_name":"Gadeyne, Astrid"},{"full_name":"Dejonghe, Wim","last_name":"Dejonghe","first_name":"Wim"},{"first_name":"Isabelle","last_name":"Vanhoutte","full_name":"Vanhoutte, Isabelle"},{"full_name":"Persiau, Geert","last_name":"Persiau","first_name":"Geert"},{"last_name":"Eeckhout","first_name":"Dominique","full_name":"Eeckhout, Dominique"},{"last_name":"Simon","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741"},{"last_name":"Song","first_name":"Kyungyoung","full_name":"Song, Kyungyoung"},{"full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen","last_name":"Kleine Vehn"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Geert","last_name":"De Jaeger","full_name":"De Jaeger, Geert"},{"full_name":"Van Damme, Daniël","first_name":"Daniël","last_name":"Van Damme"},{"last_name":"Hwang","first_name":"Inhwan","full_name":"Hwang, Inhwan"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"}],"issue":"8","_id":"509","type":"journal_article","publication":"Plant Cell","date_created":"2018-12-11T11:46:52Z","oa_version":"Submitted Version"},{"status":"public","volume":25,"title":"Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid","day":"01","department":[{"_id":"JiFr"}],"author":[{"last_name":"Pěnčík","first_name":"Aleš","full_name":"Pěnčík, Aleš"},{"first_name":"Biljana","last_name":"Simonovik","full_name":"Simonovik, Biljana"},{"last_name":"Petersson","first_name":"Sara","full_name":"Petersson, Sara"},{"first_name":"Eva","last_name":"Henyková","full_name":"Henyková, Eva"},{"first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741"},{"full_name":"Greenham, Kathleen","last_name":"Greenham","first_name":"Kathleen"},{"first_name":"Yi","last_name":"Zhang","full_name":"Zhang, Yi"},{"full_name":"Kowalczyk, Mariusz","last_name":"Kowalczyk","first_name":"Mariusz"},{"first_name":"Mark","last_name":"Estelle","full_name":"Estelle, Mark"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"last_name":"Sandberg","first_name":"Göran","full_name":"Sandberg, Göran"},{"full_name":"Ljung, Karin","first_name":"Karin","last_name":"Ljung"}],"type":"journal_article","_id":"511","issue":"10","publication":"Plant Cell","date_created":"2018-12-11T11:46:53Z","oa_version":"Published Version","publisher":"American Society of Plant Biologists","publist_id":"7309","date_updated":"2021-01-12T08:01:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","month":"10","date_published":"2013-10-01T00:00:00Z","scopus_import":1,"main_file_link":[{"url":"www.doi.org/10.1105/tpc.113.114421","open_access":"1"}],"pmid":1,"intvolume":"        25","language":[{"iso":"eng"}],"year":"2013","citation":{"apa":"Pěnčík, A., Simonovik, B., Petersson, S., Henyková, E., Simon, S., Greenham, K., … Ljung, K. (2013). Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114421\">https://doi.org/10.1105/tpc.113.114421</a>","chicago":"Pěnčík, Aleš, Biljana Simonovik, Sara Petersson, Eva Henyková, Sibu Simon, Kathleen Greenham, Yi Zhang, et al. “Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic Acid.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114421\">https://doi.org/10.1105/tpc.113.114421</a>.","short":"A. Pěnčík, B. Simonovik, S. Petersson, E. Henyková, S. Simon, K. Greenham, Y. Zhang, M. Kowalczyk, M. Estelle, E. Zažímalová, O. Novák, G. Sandberg, K. Ljung, Plant Cell 25 (2013) 3858–3870.","ista":"Pěnčík A, Simonovik B, Petersson S, Henyková E, Simon S, Greenham K, Zhang Y, Kowalczyk M, Estelle M, Zažímalová E, Novák O, Sandberg G, Ljung K. 2013. Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell. 25(10), 3858–3870.","ieee":"A. Pěnčík <i>et al.</i>, “Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid,” <i>Plant Cell</i>, vol. 25, no. 10. American Society of Plant Biologists, pp. 3858–3870, 2013.","mla":"Pěnčík, Aleš, et al. “Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic Acid.” <i>Plant Cell</i>, vol. 25, no. 10, American Society of Plant Biologists, 2013, pp. 3858–70, doi:<a href=\"https://doi.org/10.1105/tpc.113.114421\">10.1105/tpc.113.114421</a>.","ama":"Pěnčík A, Simonovik B, Petersson S, et al. Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. <i>Plant Cell</i>. 2013;25(10):3858-3870. doi:<a href=\"https://doi.org/10.1105/tpc.113.114421\">10.1105/tpc.113.114421</a>"},"doi":"10.1105/tpc.113.114421","quality_controlled":"1","oa":1,"abstract":[{"text":"The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant growth and development. Its nonuniform distribution between cells and tissues underlies the spatiotemporal coordination of many developmental events and responses to environmental stimuli. The regulation of auxin gradients and the formation of auxin maxima/minima most likely involve the regulation of both metabolic and transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana root tissues. OxIAA had little biological activity and was formed rapidly and irreversibly in response to increases in auxin levels. We further showed that there is cell type-specific regulation of oxIAA levels in the Arabidopsis root apex. We propose that oxIAA is an important element in the regulation of output from auxin gradients and, therefore, in the regulation of auxin homeostasis and response mechanisms.","lang":"eng"}],"external_id":{"pmid":["24163311"]},"page":"3858 - 3870"},{"file":[{"checksum":"9c4fbe793af4bb22b3fe50cc677a39bf","file_size":3257692,"creator":"system","date_updated":"2020-07-14T12:46:36Z","file_id":"4644","date_created":"2018-12-12T10:07:46Z","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-936-v1+1_2008_Barton_A_map.pdf","relation":"main_file"}],"ddc":["581"],"oa":1,"abstract":[{"text":"In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin‐responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue‐specific transcriptional regulation of cell‐identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin‐response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome‐level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development.","lang":"eng"}],"doi":"10.1038/msb.2013.40","citation":{"ama":"Bargmann B, Vanneste S, Krouk G, et al. A map of cell type‐specific auxin responses. <i>Molecular Systems Biology</i>. 2013;9(1). doi:<a href=\"https://doi.org/10.1038/msb.2013.40\">10.1038/msb.2013.40</a>","apa":"Bargmann, B., Vanneste, S., Krouk, G., Nawy, T., Efroni, I., Shani, E., … Birnbaum, K. (2013). A map of cell type‐specific auxin responses. <i>Molecular Systems Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/msb.2013.40\">https://doi.org/10.1038/msb.2013.40</a>","short":"B. Bargmann, S. Vanneste, G. Krouk, T. Nawy, I. Efroni, E. Shani, G. Choe, J. Friml, D. Bergmann, M. Estelle, K. Birnbaum, Molecular Systems Biology 9 (2013).","chicago":"Bargmann, Bastiaan, Steffen Vanneste, Gabriel Krouk, Tal Nawy, Idan Efroni, Eilon Shani, Goh Choe, et al. “A Map of Cell Type‐specific Auxin Responses.” <i>Molecular Systems Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/msb.2013.40\">https://doi.org/10.1038/msb.2013.40</a>.","ista":"Bargmann B, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml J, Bergmann D, Estelle M, Birnbaum K. 2013. A map of cell type‐specific auxin responses. Molecular Systems Biology. 9(1), 688.","ieee":"B. Bargmann <i>et al.</i>, “A map of cell type‐specific auxin responses,” <i>Molecular Systems Biology</i>, vol. 9, no. 1. Nature Publishing Group, 2013.","mla":"Bargmann, Bastiaan, et al. “A Map of Cell Type‐specific Auxin Responses.” <i>Molecular Systems Biology</i>, vol. 9, no. 1, 688, Nature Publishing Group, 2013, doi:<a href=\"https://doi.org/10.1038/msb.2013.40\">10.1038/msb.2013.40</a>."},"quality_controlled":"1","language":[{"iso":"eng"}],"year":"2013","intvolume":"         9","has_accepted_license":"1","scopus_import":1,"date_published":"2013-09-10T00:00:00Z","month":"09","publisher":"Nature Publishing Group","date_updated":"2021-01-12T08:01:17Z","publist_id":"7303","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","article_processing_charge":"No","_id":"516","issue":"1","type":"journal_article","file_date_updated":"2020-07-14T12:46:36Z","publication":"Molecular Systems Biology","date_created":"2018-12-11T11:46:55Z","oa_version":"Published Version","pubrep_id":"936","department":[{"_id":"JiFr"}],"author":[{"first_name":"Bastiaan","last_name":"Bargmann","full_name":"Bargmann, Bastiaan"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"full_name":"Krouk, Gabriel","first_name":"Gabriel","last_name":"Krouk"},{"full_name":"Nawy, Tal","first_name":"Tal","last_name":"Nawy"},{"full_name":"Efroni, Idan","last_name":"Efroni","first_name":"Idan"},{"full_name":"Shani, Eilon","first_name":"Eilon","last_name":"Shani"},{"last_name":"Choe","first_name":"Goh","full_name":"Choe, Goh"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"full_name":"Bergmann, Dominique","first_name":"Dominique","last_name":"Bergmann"},{"last_name":"Estelle","first_name":"Mark","full_name":"Estelle, Mark"},{"first_name":"Kenneth","last_name":"Birnbaum","full_name":"Birnbaum, Kenneth"}],"day":"10","article_number":"688","status":"public","title":"A map of cell type‐specific auxin responses","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"volume":9},{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:01:22Z","publist_id":"7300","publisher":"Elsevier","abstract":[{"text":"Podoplanin, a mucin-like plasma membrane protein, is expressed by lymphatic endothelial cells and responsible for separation of blood and lymphatic circulation through activation of platelets. Here we show that podoplanin is also expressed by thymic fibroblastic reticular cells (tFRC), a novel thymic medulla stroma cell type associated with thymic conduits, and involved in development of natural regulatory T cells (nTreg). Young mice deficient in podoplanin lack nTreg owing to retardation of CD4+CD25+ thymocytes in the cortex and missing differentiation of Foxp3+ thymocytes in the medulla. This might be due to CCL21 that delocalizes upon deletion of the CCL21-binding podoplanin from medullar tFRC to cortex areas. The animals do not remain devoid of nTreg but generate them delayed within the first month resulting in Th2-biased hypergammaglobulinemia but not in the death-causing autoimmune phenotype of Foxp3-deficient Scurfy mice.","lang":"eng"}],"date_published":"2013-07-01T00:00:00Z","month":"07","scopus_import":1,"page":"31 - 41","volume":154,"title":"Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells","status":"public","intvolume":"       154","day":"01","year":"2013","language":[{"iso":"eng"}],"author":[{"last_name":"Fuertbauer","first_name":"Elke","full_name":"Fuertbauer, Elke"},{"full_name":"Zaujec, Jan","first_name":"Jan","last_name":"Zaujec"},{"last_name":"Uhrin","first_name":"Pavel","full_name":"Uhrin, Pavel"},{"last_name":"Raab","first_name":"Ingrid","full_name":"Raab, Ingrid"},{"first_name":"Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","last_name":"Weber","full_name":"Weber, Michele"},{"first_name":"Helga","last_name":"Schachner","full_name":"Schachner, Helga"},{"full_name":"Bauer, Miroslav","last_name":"Bauer","first_name":"Miroslav"},{"full_name":"Schütz, Gerhard","first_name":"Gerhard","last_name":"Schütz"},{"last_name":"Binder","first_name":"Bernd","full_name":"Binder, Bernd"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kerjaschki","first_name":"Dontscho","full_name":"Kerjaschki, Dontscho"},{"full_name":"Stockinger, Hannes","last_name":"Stockinger","first_name":"Hannes"}],"department":[{"_id":"MiSi"}],"quality_controlled":"1","date_created":"2018-12-11T11:46:57Z","oa_version":"None","doi":"10.1016/j.imlet.2013.07.007","citation":{"ama":"Fuertbauer E, Zaujec J, Uhrin P, et al. Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. <i>Immunology Letters</i>. 2013;154(1-2):31-41. doi:<a href=\"https://doi.org/10.1016/j.imlet.2013.07.007\">10.1016/j.imlet.2013.07.007</a>","mla":"Fuertbauer, Elke, et al. “Thymic Medullar Conduits-Associated Podoplanin Promotes Natural Regulatory T Cells.” <i>Immunology Letters</i>, vol. 154, no. 1–2, Elsevier, 2013, pp. 31–41, doi:<a href=\"https://doi.org/10.1016/j.imlet.2013.07.007\">10.1016/j.imlet.2013.07.007</a>.","ieee":"E. Fuertbauer <i>et al.</i>, “Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells,” <i>Immunology Letters</i>, vol. 154, no. 1–2. Elsevier, pp. 31–41, 2013.","ista":"Fuertbauer E, Zaujec J, Uhrin P, Raab I, Weber M, Schachner H, Bauer M, Schütz G, Binder B, Sixt MK, Kerjaschki D, Stockinger H. 2013. Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. Immunology Letters. 154(1–2), 31–41.","short":"E. Fuertbauer, J. Zaujec, P. Uhrin, I. Raab, M. Weber, H. Schachner, M. Bauer, G. Schütz, B. Binder, M.K. Sixt, D. Kerjaschki, H. Stockinger, Immunology Letters 154 (2013) 31–41.","chicago":"Fuertbauer, Elke, Jan Zaujec, Pavel Uhrin, Ingrid Raab, Michele Weber, Helga Schachner, Miroslav Bauer, et al. “Thymic Medullar Conduits-Associated Podoplanin Promotes Natural Regulatory T Cells.” <i>Immunology Letters</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.imlet.2013.07.007\">https://doi.org/10.1016/j.imlet.2013.07.007</a>.","apa":"Fuertbauer, E., Zaujec, J., Uhrin, P., Raab, I., Weber, M., Schachner, H., … Stockinger, H. (2013). Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. <i>Immunology Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.imlet.2013.07.007\">https://doi.org/10.1016/j.imlet.2013.07.007</a>"},"publication":"Immunology Letters","_id":"522","issue":"1-2","type":"journal_article"},{"quality_controlled":"1","ec_funded":1,"date_created":"2018-12-11T11:46:58Z","oa_version":"None","citation":{"ista":"Wabnik KT, Robert H, Smith R, Friml J. 2013. Modeling framework for the establishment of the apical-basal embryonic axis in plants. Current Biology. 23(24), 2513–2518.","ieee":"K. T. Wabnik, H. Robert, R. Smith, and J. Friml, “Modeling framework for the establishment of the apical-basal embryonic axis in plants,” <i>Current Biology</i>, vol. 23, no. 24. Cell Press, pp. 2513–2518, 2013.","mla":"Wabnik, Krzysztof T., et al. “Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.” <i>Current Biology</i>, vol. 23, no. 24, Cell Press, 2013, pp. 2513–18, doi:<a href=\"https://doi.org/10.1016/j.cub.2013.10.038\">10.1016/j.cub.2013.10.038</a>.","apa":"Wabnik, K. T., Robert, H., Smith, R., &#38; Friml, J. (2013). Modeling framework for the establishment of the apical-basal embryonic axis in plants. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2013.10.038\">https://doi.org/10.1016/j.cub.2013.10.038</a>","chicago":"Wabnik, Krzysztof T, Hélène Robert, Richard Smith, and Jiří Friml. “Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2013.10.038\">https://doi.org/10.1016/j.cub.2013.10.038</a>.","short":"K.T. Wabnik, H. Robert, R. Smith, J. Friml, Current Biology 23 (2013) 2513–2518.","ama":"Wabnik KT, Robert H, Smith R, Friml J. Modeling framework for the establishment of the apical-basal embryonic axis in plants. <i>Current Biology</i>. 2013;23(24):2513-2518. doi:<a href=\"https://doi.org/10.1016/j.cub.2013.10.038\">10.1016/j.cub.2013.10.038</a>"},"doi":"10.1016/j.cub.2013.10.038","project":[{"name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7"}],"publication":"Current Biology","_id":"527","type":"journal_article","issue":"24","author":[{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560"},{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène"},{"full_name":"Smith, Richard","last_name":"Smith","first_name":"Richard"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"day":"16","year":"2013","language":[{"iso":"eng"}],"volume":23,"title":"Modeling framework for the establishment of the apical-basal embryonic axis in plants","status":"public","intvolume":"        23","page":"2513 - 2518","scopus_import":1,"abstract":[{"lang":"eng","text":"The apical-basal axis of the early plant embryo determines the body plan of the adult organism. To establish a polarized embryonic axis, plants evolved a unique mechanism that involves directional, cell-to-cell transport of the growth regulator auxin. Auxin transport relies on PIN auxin transporters [1], whose polar subcellular localization determines the flow directionality. PIN-mediated auxin transport mediates the spatial and temporal activity of the auxin response machinery [2-7] that contributes to embryo patterning processes, including establishment of the apical (shoot) and basal (root) embryo poles [8]. However, little is known of upstream mechanisms guiding the (re)polarization of auxin fluxes during embryogenesis [9]. Here, we developed a model of plant embryogenesis that correctly generates emergent cell polarities and auxin-mediated sequential initiation of apical-basal axis of plant embryo. The model relies on two precisely localized auxin sources and a feedback between auxin and the polar, subcellular PIN transporter localization. Simulations reproduced PIN polarity and auxin distribution, as well as previously unknown polarization events during early embryogenesis. The spectrum of validated model predictions suggests that our model corresponds to a minimal mechanistic framework for initiation and orientation of the apical-basal axis to guide both embryonic and postembryonic plant development."}],"month":"12","date_published":"2013-12-16T00:00:00Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:01:24Z","publist_id":"7292","publisher":"Cell Press"},{"citation":{"apa":"Robert, H., Grones, P., Stepanova, A., Robles, L., Lokerse, A., Alonso, J., … Friml, J. (2013). Local auxin sources orient the apical basal axis in arabidopsis embryos. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2013.09.039\">https://doi.org/10.1016/j.cub.2013.09.039</a>","chicago":"Robert, Hélène, Peter Grones, Anna Stepanova, Linda Robles, Annemarie Lokerse, Jose Alonso, Dolf Weijers, and Jiří Friml. “Local Auxin Sources Orient the Apical Basal Axis in Arabidopsis Embryos.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2013.09.039\">https://doi.org/10.1016/j.cub.2013.09.039</a>.","short":"H. Robert, P. Grones, A. Stepanova, L. Robles, A. Lokerse, J. Alonso, D. Weijers, J. Friml, Current Biology 23 (2013) 2506–2512.","ista":"Robert H, Grones P, Stepanova A, Robles L, Lokerse A, Alonso J, Weijers D, Friml J. 2013. Local auxin sources orient the apical basal axis in arabidopsis embryos. Current Biology. 23(24), 2506–2512.","ieee":"H. Robert <i>et al.</i>, “Local auxin sources orient the apical basal axis in arabidopsis embryos,” <i>Current Biology</i>, vol. 23, no. 24. Cell Press, pp. 2506–2512, 2013.","mla":"Robert, Hélène, et al. “Local Auxin Sources Orient the Apical Basal Axis in Arabidopsis Embryos.” <i>Current Biology</i>, vol. 23, no. 24, Cell Press, 2013, pp. 2506–12, doi:<a href=\"https://doi.org/10.1016/j.cub.2013.09.039\">10.1016/j.cub.2013.09.039</a>.","ama":"Robert H, Grones P, Stepanova A, et al. Local auxin sources orient the apical basal axis in arabidopsis embryos. <i>Current Biology</i>. 2013;23(24):2506-2512. doi:<a href=\"https://doi.org/10.1016/j.cub.2013.09.039\">10.1016/j.cub.2013.09.039</a>"},"doi":"10.1016/j.cub.2013.09.039","project":[{"call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"quality_controlled":"1","oa_version":"None","date_created":"2018-12-11T11:46:59Z","issue":"24","_id":"528","type":"journal_article","publication":"Current Biology","author":[{"full_name":"Robert, Hélène","last_name":"Robert","first_name":"Hélène"},{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Grones","full_name":"Grones, Peter"},{"full_name":"Stepanova, Anna","last_name":"Stepanova","first_name":"Anna"},{"last_name":"Robles","first_name":"Linda","full_name":"Robles, Linda"},{"first_name":"Annemarie","last_name":"Lokerse","full_name":"Lokerse, Annemarie"},{"last_name":"Alonso","first_name":"Jose","full_name":"Alonso, Jose"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"department":[{"_id":"JiFr"}],"year":"2013","day":"16","language":[{"iso":"eng"}],"title":"Local auxin sources orient the apical basal axis in arabidopsis embryos","volume":23,"status":"public","intvolume":"        23","page":"2506 - 2512","scopus_import":1,"abstract":[{"lang":"eng","text":"Establishment of the embryonic axis foreshadows the main body axis of adults both in plants and in animals, but underlying mechanisms are considered distinct. Plants utilize directional, cell-to-cell transport of the growth hormone auxin [1, 2] to generate an asymmetric auxin response that specifies the embryonic apical-basal axis [3-6]. The auxin flow directionality depends on the polarized subcellular localization of PIN-FORMED (PIN) auxin transporters [7, 8]. It remains unknown which mechanisms and spatial cues guide cell polarization and axis orientation in early embryos. Herein, we provide conceptually novel insights into the formation of embryonic axis in Arabidopsis by identifying a crucial role of localized tryptophan-dependent auxin biosynthesis [9-12]. Local auxin production at the base of young embryos and the accompanying PIN7-mediated auxin flow toward the proembryo are required for the apical auxin response maximum and the specification of apical embryonic structures. Later in embryogenesis, the precisely timed onset of localized apical auxin biosynthesis mediates PIN1 polarization, basal auxin response maximum, and specification of the root pole. Thus, the tight spatiotemporal control of distinct local auxin sources provides a necessary, non-cell-autonomous trigger for the coordinated cell polarization and subsequent apical-basal axis orientation during embryogenesis and, presumably, also for other polarization events during postembryonic plant life [13, 14]."}],"date_published":"2013-12-16T00:00:00Z","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Cell Press","publist_id":"7291","date_updated":"2021-01-12T08:01:25Z"},{"page":"6453 - 6458","date_published":"2013-04-16T00:00:00Z","month":"04","abstract":[{"text":"Sex chromosomes originate from autosomes. The accumulation of sexually antagonistic mutations on protosex chromosomes selects for a loss of recombination and sets in motion the evolutionary processes generating heteromorphic sex chromosomes. Recombination suppression and differentiation are generally viewed as the default path of sex chromosome evolution, and the occurrence of old, homomorphic sex chromosomes, such as those of ratite birds, has remained a mystery. Here, we analyze the genome and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes on the sex chromosome are shared between the Z and W. Surprisingly, however, levels of gene expression are generally sex-biased for all sex-linked genes relative to autosomes, including those in the pseudoautosomal region, and the male-bias increases after gonad formation. This expression bias suggests that the emu sex chromosomes have become masculinized, even in the absence of ZW differentiation. Thus, birds may have taken different evolutionary solutions to minimize the deleterious effects imposed by sexually antagonistic mutations: some lineages eliminate recombination along the protosex chromosomes to physically restrict sexually antagonistic alleles to one sex, whereas ratites evolved sex-biased expression to confine the product of a sexually antagonistic allele to the sex it benefits. This difference in conflict resolution may explain the preservation of recombining, homomorphic sex chromosomes in other lineages and illustrates the importance of sexually antagonistic mutations driving the evolution of sex chromosomes. ","lang":"eng"}],"publisher":"National Academy of Sciences","publist_id":"4964","date_updated":"2021-01-12T06:55:08Z","publication_status":"published","issue":"16","_id":"2074","type":"journal_article","extern":1,"publication":"PNAS","doi":"10.1073/pnas.1217027110","citation":{"short":"B. Vicoso, V. Kaiser, D. Bachtrog, PNAS 110 (2013) 6453–6458.","chicago":"Vicoso, Beatriz, Vera Kaiser, and Doris Bachtrog. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1217027110\">https://doi.org/10.1073/pnas.1217027110</a>.","apa":"Vicoso, B., Kaiser, V., &#38; Bachtrog, D. (2013). Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1217027110\">https://doi.org/10.1073/pnas.1217027110</a>","mla":"Vicoso, Beatriz, et al. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” <i>PNAS</i>, vol. 110, no. 16, National Academy of Sciences, 2013, pp. 6453–58, doi:<a href=\"https://doi.org/10.1073/pnas.1217027110\">10.1073/pnas.1217027110</a>.","ista":"Vicoso B, Kaiser V, Bachtrog D. 2013. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PNAS. 110(16), 6453–6458.","ieee":"B. Vicoso, V. Kaiser, and D. Bachtrog, “Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution,” <i>PNAS</i>, vol. 110, no. 16. National Academy of Sciences, pp. 6453–6458, 2013.","ama":"Vicoso B, Kaiser V, Bachtrog D. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. <i>PNAS</i>. 2013;110(16):6453-6458. doi:<a href=\"https://doi.org/10.1073/pnas.1217027110\">10.1073/pnas.1217027110</a>"},"quality_controlled":0,"date_created":"2018-12-11T11:55:33Z","author":[{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Beatriz Vicoso"},{"full_name":"Kaiser, Vera B","last_name":"Kaiser","first_name":"Vera"},{"first_name":"Doris","last_name":"Bachtrog","full_name":"Bachtrog, Doris"}],"day":"16","year":"2013","status":"public","intvolume":"       110","volume":110,"title":"Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution"},{"quality_controlled":0,"date_created":"2018-12-11T11:55:34Z","citation":{"ama":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. <i>PLoS Biology</i>. 2013;11(8). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001643\">10.1371/journal.pbio.1001643</a>","chicago":"Vicoso, Beatriz, Jr Emerson, Yulia Zektser, Shivani Mahajan, and Doris Bachtrog. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” <i>PLoS Biology</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pbio.1001643\">https://doi.org/10.1371/journal.pbio.1001643</a>.","short":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, D. Bachtrog, PLoS Biology 11 (2013).","apa":"Vicoso, B., Emerson, J., Zektser, Y., Mahajan, S., &#38; Bachtrog, D. (2013). Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1001643\">https://doi.org/10.1371/journal.pbio.1001643</a>","mla":"Vicoso, Beatriz, et al. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” <i>PLoS Biology</i>, vol. 11, no. 8, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001643\">10.1371/journal.pbio.1001643</a>.","ieee":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, and D. Bachtrog, “Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation,” <i>PLoS Biology</i>, vol. 11, no. 8. Public Library of Science, 2013.","ista":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. 2013. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. PLoS Biology. 11(8)."},"doi":"10.1371/journal.pbio.1001643","publication":"PLoS Biology","extern":1,"_id":"2076","type":"journal_article","issue":"8","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Beatriz Vicoso"},{"full_name":"Emerson, Jr J.","last_name":"Emerson","first_name":"Jr"},{"first_name":"Yulia","last_name":"Zektser","full_name":"Zektser, Yulia"},{"full_name":"Mahajan, Shivani","first_name":"Shivani","last_name":"Mahajan"},{"first_name":"Doris","last_name":"Bachtrog","full_name":"Bachtrog, Doris"}],"acknowledgement":"Funded by NIH grants (R01GM076007 and R01GM093182) and a Packard Fellowship to DB.","year":"2013","day":"27","volume":11,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation","intvolume":"        11","status":"public","abstract":[{"lang":"eng","text":"Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution.\n"}],"month":"08","date_published":"2013-08-27T00:00:00Z","publication_status":"published","date_updated":"2021-01-12T06:55:09Z","publist_id":"4962","publisher":"Public Library of Science"},{"date_published":"2013-07-01T00:00:00Z","month":"07","abstract":[{"lang":"eng","text":"We present a method for fabrication-oriented design of actuated deformable characters that allows a user to automatically create physical replicas of digitally designed characters using rapid manufacturing technologies. Given a deformable character and a set of target poses as input, our method computes a small set of actuators along with their locations on the surface and optimizes the internal material distribution such that the resulting character exhibits the desired deformation behavior. We approach this problem with a dedicated algorithm that combines finite-element analysis, sparse regularization, and constrained optimization. We validate our pipeline on a set of two- and three-dimensional example characters and present results in simulation and physically-fabricated prototypes."}],"publist_id":"4926","date_updated":"2021-01-12T06:55:21Z","publisher":"ACM","publication_status":"published","publication":"ACM Transactions on Graphics","extern":1,"_id":"2107","type":"journal_article","issue":"4","quality_controlled":0,"date_created":"2018-12-11T11:55:45Z","citation":{"apa":"Skouras, M., Thomaszewski, B., Coros, S., Bickel, B., &#38; Groß, M. (2013). Computational design of actuated deformable characters. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461979\">https://doi.org/10.1145/2461912.2461979</a>","chicago":"Skouras, Mélina, Bernhard Thomaszewski, Stelian Coros, Bernd Bickel, and Markus Groß. “Computational Design of Actuated Deformable Characters.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461979\">https://doi.org/10.1145/2461912.2461979</a>.","short":"M. Skouras, B. Thomaszewski, S. Coros, B. Bickel, M. Groß, ACM Transactions on Graphics 32 (2013).","ista":"Skouras M, Thomaszewski B, Coros S, Bickel B, Groß M. 2013. Computational design of actuated deformable characters. ACM Transactions on Graphics. 32(4).","ieee":"M. Skouras, B. Thomaszewski, S. Coros, B. Bickel, and M. Groß, “Computational design of actuated deformable characters,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","mla":"Skouras, Mélina, et al. “Computational Design of Actuated Deformable Characters.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461979\">10.1145/2461912.2461979</a>.","ama":"Skouras M, Thomaszewski B, Coros S, Bickel B, Groß M. Computational design of actuated deformable characters. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461979\">10.1145/2461912.2461979</a>"},"doi":"10.1145/2461912.2461979","acknowledgement":"This work was partly funded by the NCCR Co-Me of the Swiss NSF","author":[{"first_name":"Mélina","last_name":"Skouras","full_name":"Skouras, Mélina"},{"full_name":"Thomaszewski, Bernhard","first_name":"Bernhard","last_name":"Thomaszewski"},{"full_name":"Coros, Stelian","first_name":"Stelian","last_name":"Coros"},{"orcid":"0000-0001-6511-9385","full_name":"Bernd Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel"},{"full_name":"Groß, Markus S","first_name":"Markus","last_name":"Groß"}],"year":"2013","day":"01","status":"public","intvolume":"        32","title":"Computational design of actuated deformable characters","volume":32},{"author":[{"first_name":"Stelian","last_name":"Coros","full_name":"Coros, Stelian"},{"full_name":"Thomaszewski, Bernhard","last_name":"Thomaszewski","first_name":"Bernhard"},{"full_name":"Noris, Gioacchino","last_name":"Noris","first_name":"Gioacchino"},{"last_name":"Sueda","first_name":"Shinjiro","full_name":"Sueda, Shinjiro"},{"last_name":"Forberg","first_name":"Moira","full_name":"Forberg, Moira"},{"full_name":"Sumner, Robert W","first_name":"Robert","last_name":"Sumner"},{"full_name":"Matusik, Wojciech","first_name":"Wojciech","last_name":"Matusik"},{"full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel"}],"publication":"ACM Transactions on Graphics","extern":1,"_id":"2108","type":"journal_article","issue":"4","date_created":"2018-12-11T11:55:46Z","quality_controlled":0,"citation":{"ama":"Coros S, Thomaszewski B, Noris G, et al. Computational design of mechanical characters. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461953\">10.1145/2461912.2461953</a>","mla":"Coros, Stelian, et al. “Computational Design of Mechanical Characters.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461953\">10.1145/2461912.2461953</a>.","ieee":"S. Coros <i>et al.</i>, “Computational design of mechanical characters,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","ista":"Coros S, Thomaszewski B, Noris G, Sueda S, Forberg M, Sumner R, Matusik W, Bickel B. 2013. Computational design of mechanical characters. ACM Transactions on Graphics. 32(4).","short":"S. Coros, B. Thomaszewski, G. Noris, S. Sueda, M. Forberg, R. Sumner, W. Matusik, B. Bickel, ACM Transactions on Graphics 32 (2013).","chicago":"Coros, Stelian, Bernhard Thomaszewski, Gioacchino Noris, Shinjiro Sueda, Moira Forberg, Robert Sumner, Wojciech Matusik, and Bernd Bickel. “Computational Design of Mechanical Characters.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461953\">https://doi.org/10.1145/2461912.2461953</a>.","apa":"Coros, S., Thomaszewski, B., Noris, G., Sueda, S., Forberg, M., Sumner, R., … Bickel, B. (2013). Computational design of mechanical characters. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461953\">https://doi.org/10.1145/2461912.2461953</a>"},"doi":"10.1145/2461912.2461953","status":"public","intvolume":"        32","title":"Computational design of mechanical characters","volume":32,"year":"2013","day":"01","publist_id":"4927","date_updated":"2021-01-12T06:55:21Z","publisher":"ACM","publication_status":"published","date_published":"2013-07-01T00:00:00Z","month":"07","abstract":[{"text":"We present an interactive design system that allows non-expert users to create animated mechanical characters. Given an articulated character as input, the user iteratively creates an animation by sketching motion curves indicating how different parts of the character should move. For each motion curve, our framework creates an optimized mechanism that reproduces it as closely as possible. The resulting mechanisms are attached to the character and then connected to each other using gear trains, which are created in a semi-automated fashion. The mechanical assemblies generated with our system can be driven with a single input driver, such as a hand-operated crank or an electric motor, and they can be fabricated using rapid prototyping devices. We demonstrate the versatility of our approach by designing a wide range of mechanical characters, several of which we manufactured using 3D printing. While our pipeline is designed for characters driven by planar mechanisms, significant parts of it extend directly to non-planar mechanisms, allowing us to create characters with compelling 3D motions. ","lang":"eng"}]},{"author":[{"last_name":"Hildebrand","first_name":"Kristian","full_name":"Hildebrand, Kristian"},{"orcid":"0000-0001-6511-9385","full_name":"Bernd Bickel","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"last_name":"Alexa","first_name":"Marc","full_name":"Alexa, Marc"}],"type":"journal_article","_id":"2109","issue":"6","extern":1,"publication":"Computers and Graphics (Pergamon)","citation":{"ama":"Hildebrand K, Bickel B, Alexa M. Orthogonal slicing for additive manufacturing. <i>Computers and Graphics (Pergamon)</i>. 2013;37(6):669-675. doi:<a href=\"https://doi.org/10.1016/j.cag.2013.05.011\">10.1016/j.cag.2013.05.011</a>","ieee":"K. Hildebrand, B. Bickel, and M. Alexa, “Orthogonal slicing for additive manufacturing,” <i>Computers and Graphics (Pergamon)</i>, vol. 37, no. 6. Elsevier, pp. 669–675, 2013.","ista":"Hildebrand K, Bickel B, Alexa M. 2013. Orthogonal slicing for additive manufacturing. Computers and Graphics (Pergamon). 37(6), 669–675.","mla":"Hildebrand, Kristian, et al. “Orthogonal Slicing for Additive Manufacturing.” <i>Computers and Graphics (Pergamon)</i>, vol. 37, no. 6, Elsevier, 2013, pp. 669–75, doi:<a href=\"https://doi.org/10.1016/j.cag.2013.05.011\">10.1016/j.cag.2013.05.011</a>.","apa":"Hildebrand, K., Bickel, B., &#38; Alexa, M. (2013). Orthogonal slicing for additive manufacturing. <i>Computers and Graphics (Pergamon)</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cag.2013.05.011\">https://doi.org/10.1016/j.cag.2013.05.011</a>","short":"K. Hildebrand, B. Bickel, M. Alexa, Computers and Graphics (Pergamon) 37 (2013) 669–675.","chicago":"Hildebrand, Kristian, Bernd Bickel, and Marc Alexa. “Orthogonal Slicing for Additive Manufacturing.” <i>Computers and Graphics (Pergamon)</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cag.2013.05.011\">https://doi.org/10.1016/j.cag.2013.05.011</a>."},"doi":"10.1016/j.cag.2013.05.011","quality_controlled":0,"date_created":"2018-12-11T11:55:46Z","status":"public","intvolume":"        37","title":"Orthogonal slicing for additive manufacturing","volume":37,"day":"01","year":"2013","page":"669 - 675","publisher":"Elsevier","date_updated":"2021-01-12T06:55:22Z","publist_id":"4924","publication_status":"published","date_published":"2013-10-01T00:00:00Z","month":"10","abstract":[{"lang":"eng","text":"Most additive manufacturing technologies work by layering, i.e. slicing the shape and then generating each slice independently. This introduces an anisotropy into the process, often as different accuracies in the tangential and normal directions, but also in terms of other parameters such as build speed or tensile strength and strain. We model this as an anisotropic cubic element. Our approach then finds a compromise between modeling each part of the shape individually in the best possible direction and using one direction for the whole shape part. In particular, we compute an orthogonal basis and consider only the three basis vectors as slice normals (i.e. fabrication directions). Then we optimize a decomposition of the shape along this basis so that each part can be consistently sliced along one of the basis vectors. In simulation, we show that this approach is superior to slicing the whole shape in one direction, only. It also has clear benefits if the shape is larger than the build volume of the available equipment."}]},{"date_updated":"2021-01-12T06:55:22Z","publist_id":"4925","publisher":"ACM","publication_status":"published","date_published":"2013-07-01T00:00:00Z","month":"07","abstract":[{"text":"We present a method for practical physical reproduction and design of homogeneous materials with desired subsurface scattering. Our process uses a collection of different pigments that can be suspended in a clear base material. Our goal is to determine pigment concentrations that best reproduce the appearance and subsurface scattering of a given target material. In order to achieve this task we first fabricate a collection of material samples composed of known mixtures of the available pigments with the base material. We then acquire their reflectance profiles using a custom-built measurement device. We use the same device to measure the reflectance profile of a target material. Based on the database of mappings from pigment concentrations to reflectance profiles, we use an optimization process to compute the concentration of pigments to best replicate the target material appearance. We demonstrate the practicality of our method by reproducing a variety of different translucent materials. We also present a tool that allows the user to explore the range of achievable appearances for a given set of pigments. ","lang":"eng"}],"author":[{"first_name":"Marios","last_name":"Papas","full_name":"Papas, Marios"},{"first_name":"Christian","last_name":"Regg","full_name":"Regg, Christian"},{"last_name":"Jarosz","first_name":"Wojciech","full_name":"Jarosz, Wojciech"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bernd Bickel"},{"last_name":"Jackson","first_name":"Philip","full_name":"Jackson, Philip V"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"full_name":"Marschner, Steve","first_name":"Steve","last_name":"Marschner"},{"full_name":"Groß, Markus S","last_name":"Groß","first_name":"Markus"}],"publication":"ACM Transactions on Graphics","extern":1,"_id":"2110","issue":"4","type":"journal_article","quality_controlled":0,"date_created":"2018-12-11T11:55:46Z","doi":"10.1145/2461912.2461974","citation":{"ama":"Papas M, Regg C, Jarosz W, et al. Fabricating translucent materials using continuous pigment mixtures. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461974\">10.1145/2461912.2461974</a>","short":"M. Papas, C. Regg, W. Jarosz, B. Bickel, P. Jackson, W. Matusik, S. Marschner, M. Groß, ACM Transactions on Graphics 32 (2013).","chicago":"Papas, Marios, Christian Regg, Wojciech Jarosz, Bernd Bickel, Philip Jackson, Wojciech Matusik, Steve Marschner, and Markus Groß. “Fabricating Translucent Materials Using Continuous Pigment Mixtures.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461974\">https://doi.org/10.1145/2461912.2461974</a>.","apa":"Papas, M., Regg, C., Jarosz, W., Bickel, B., Jackson, P., Matusik, W., … Groß, M. (2013). Fabricating translucent materials using continuous pigment mixtures. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461974\">https://doi.org/10.1145/2461912.2461974</a>","mla":"Papas, Marios, et al. “Fabricating Translucent Materials Using Continuous Pigment Mixtures.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461974\">10.1145/2461912.2461974</a>.","ieee":"M. Papas <i>et al.</i>, “Fabricating translucent materials using continuous pigment mixtures,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","ista":"Papas M, Regg C, Jarosz W, Bickel B, Jackson P, Matusik W, Marschner S, Groß M. 2013. Fabricating translucent materials using continuous pigment mixtures. ACM Transactions on Graphics. 32(4)."},"status":"public","intvolume":"        32","volume":32,"title":"Fabricating translucent materials using continuous pigment mixtures","year":"2013","day":"01"},{"month":"11","date_published":"2013-11-01T00:00:00Z","abstract":[{"text":"Animated animatronic figures are a unique way to give physical presence to a character. However, their movement and expressions are often limited due to mechanical constraints. In this paper, we propose a complete process for augmenting physical avatars using projector-based illumination, significantly increasing their expressiveness. Given an input animation, the system decomposes the motion into low-frequency motion that can be physically reproduced by the animatronic head and high-frequency details that are added using projected shading. At the core is a spatio-temporal optimization process that compresses the motion in gradient space, ensuring faithful motion replay while respecting the physical limitations of the system. We also propose a complete multi-camera and projection system, including a novel defocused projection and subsurface scattering compensation scheme. The result of our system is a highly expressive physical avatar that features facial details and motion otherwise unattainable due to physical constraints.","lang":"eng"}],"publisher":"ACM","publist_id":"4922","date_updated":"2021-01-12T06:55:23Z","publication_status":"published","_id":"2111","type":"journal_article","issue":"6","extern":1,"publication":"ACM Transactions on Graphics","doi":"10.1145/2508363.2508416","citation":{"ama":"Bermano A, Bruschweiler P, Grundhöfer A, Iwai D, Bickel B, Groß M. Augmenting physical avatars using projector-based illumination. <i>ACM Transactions on Graphics</i>. 2013;32(6). doi:<a href=\"https://doi.org/10.1145/2508363.2508416\">10.1145/2508363.2508416</a>","ista":"Bermano A, Bruschweiler P, Grundhöfer A, Iwai D, Bickel B, Groß M. 2013. Augmenting physical avatars using projector-based illumination. ACM Transactions on Graphics. 32(6).","ieee":"A. Bermano, P. Bruschweiler, A. Grundhöfer, D. Iwai, B. Bickel, and M. Groß, “Augmenting physical avatars using projector-based illumination,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 6. ACM, 2013.","mla":"Bermano, Amit, et al. “Augmenting Physical Avatars Using Projector-Based Illumination.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 6, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2508363.2508416\">10.1145/2508363.2508416</a>.","apa":"Bermano, A., Bruschweiler, P., Grundhöfer, A., Iwai, D., Bickel, B., &#38; Groß, M. (2013). Augmenting physical avatars using projector-based illumination. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2508363.2508416\">https://doi.org/10.1145/2508363.2508416</a>","short":"A. Bermano, P. Bruschweiler, A. Grundhöfer, D. Iwai, B. Bickel, M. Groß, ACM Transactions on Graphics 32 (2013).","chicago":"Bermano, Amit, Philipp Bruschweiler, Anselm Grundhöfer, Daisuke Iwai, Bernd Bickel, and Markus Groß. “Augmenting Physical Avatars Using Projector-Based Illumination.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2508363.2508416\">https://doi.org/10.1145/2508363.2508416</a>."},"quality_controlled":0,"date_created":"2018-12-11T11:55:47Z","author":[{"last_name":"Bermano","first_name":"Amit","full_name":"Bermano, Amit H"},{"first_name":"Philipp","last_name":"Bruschweiler","full_name":"Bruschweiler, Philipp"},{"last_name":"Grundhöfer","first_name":"Anselm","full_name":"Grundhöfer, Anselm"},{"first_name":"Daisuke","last_name":"Iwai","full_name":"Iwai, Daisuke"},{"full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"},{"first_name":"Markus","last_name":"Groß","full_name":"Groß, Markus S"}],"day":"01","year":"2013","intvolume":"        32","status":"public","volume":32,"title":"Augmenting physical avatars using projector-based illumination"},{"date_created":"2018-12-11T11:55:47Z","quality_controlled":0,"doi":"10.1145/2508363.2508389 ","citation":{"ama":"Miguel E, Tamstorf R, Bradley D, et al. Modeling and estimation of internal friction in cloth. <i>ACM Transactions on Graphics</i>. 2013;32(6). doi:<a href=\"https://doi.org/10.1145/2508363.2508389 \">10.1145/2508363.2508389 </a>","short":"E. Miguel, R. Tamstorf, D. Bradley, S. Schvartzman, B. Thomaszewski, B. Bickel, W. Matusik, S. Marschner, M. Otaduy, ACM Transactions on Graphics 32 (2013).","chicago":"Miguel, Eder, Rasmus Tamstorf, Derek Bradley, Sara Schvartzman, Bernhard Thomaszewski, Bernd Bickel, Wojciech Matusik, Steve Marschner, and Miguel Otaduy. “Modeling and Estimation of Internal Friction in Cloth.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2508363.2508389 \">https://doi.org/10.1145/2508363.2508389 </a>.","apa":"Miguel, E., Tamstorf, R., Bradley, D., Schvartzman, S., Thomaszewski, B., Bickel, B., … Otaduy, M. (2013). Modeling and estimation of internal friction in cloth. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2508363.2508389 \">https://doi.org/10.1145/2508363.2508389 </a>","mla":"Miguel, Eder, et al. “Modeling and Estimation of Internal Friction in Cloth.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 6, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2508363.2508389 \">10.1145/2508363.2508389 </a>.","ieee":"E. Miguel <i>et al.</i>, “Modeling and estimation of internal friction in cloth,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 6. ACM, 2013.","ista":"Miguel E, Tamstorf R, Bradley D, Schvartzman S, Thomaszewski B, Bickel B, Matusik W, Marschner S, Otaduy M. 2013. Modeling and estimation of internal friction in cloth. ACM Transactions on Graphics. 32(6)."},"publication":"ACM Transactions on Graphics","extern":1,"type":"journal_article","_id":"2112","issue":"6","author":[{"full_name":"Miguel, Eder","last_name":"Miguel","first_name":"Eder"},{"first_name":"Rasmus","last_name":"Tamstorf","full_name":"Tamstorf, Rasmus"},{"full_name":"Bradley, Derek J","first_name":"Derek","last_name":"Bradley"},{"full_name":"Schvartzman, Sara C","last_name":"Schvartzman","first_name":"Sara"},{"first_name":"Bernhard","last_name":"Thomaszewski","full_name":"Thomaszewski, Bernhard"},{"last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385"},{"first_name":"Wojciech","last_name":"Matusik","full_name":"Matusik, Wojciech"},{"first_name":"Steve","last_name":"Marschner","full_name":"Marschner, Steve"},{"full_name":"Otaduy, Miguel A","first_name":"Miguel","last_name":"Otaduy"}],"acknowledgement":"This work was supported in part by the European Research Council (ERC-2011-StG-280135 Animetrics) and the Spanish Ministry of Economy (TIN2012-35840).","day":"01","year":"2013","title":"Modeling and estimation of internal friction in cloth","volume":32,"status":"public","intvolume":"        32","abstract":[{"lang":"eng","text":"Force-deformation measurements of cloth exhibit significant hysteresis, and many researchers have identified internal friction as the source of this effect. However, it has not been incorporated into computer animation models of cloth. In this paper, we propose a model of internal friction based on an augmented reparameterization of Dahl's model, and we show that this model provides a good match to several important features of cloth hysteresis even with a minimal set of parameters. We also propose novel parameter estimation procedures that are based on simple and inexpensive setups and need only sparse data, as opposed to the complex hardware and dense data acquisition of previous methods. Finally, we provide an algorithm for the efficient simulation of internal friction, and we demonstrate it on simulation examples that show disparate behavior with and without internal friction."}],"date_published":"2013-11-01T00:00:00Z","month":"11","publication_status":"published","publist_id":"4923","date_updated":"2021-01-12T06:55:23Z","publisher":"ACM"},{"publisher":"IEEE","date_updated":"2021-01-12T06:55:23Z","publist_id":"4920","publication_status":"published","month":"09","date_published":"2013-09-23T00:00:00Z","abstract":[{"lang":"eng","text":"A new method fabricates custom surface reflectance and spatially varying bidirectional reflectance distribution functions (svBRDFs). Researchers optimize a microgeometry for a range of normal distribution functions and simulate the resulting surface's effective reflectance. Using the simulation's results, they reproduce an input svBRDF's appearance by distributing the microgeometry on the printed material's surface. This method lets people print svBRDFs on planar samples with current 3D printing technology, even with a limited set of printing materials. It extends naturally to printing svBRDFs on arbitrary shapes."}],"page":"48 - 57","status":"public","intvolume":"        33","title":"3D printing spatially varying BRDFs","volume":33,"day":"23","year":"2013","author":[{"full_name":"Rouiller, Olivier","first_name":"Olivier","last_name":"Rouiller"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bernd Bickel"},{"full_name":"Kautz, Jan","first_name":"Jan","last_name":"Kautz"},{"full_name":"Matusik, Wojciech","first_name":"Wojciech","last_name":"Matusik"},{"last_name":"Alexa","first_name":"Marc","full_name":"Alexa, Marc"}],"_id":"2113","issue":"6","type":"journal_article","extern":1,"publication":"IEEE Computer Graphics and Applications","doi":"10.1109/MCG.2013.82 ","citation":{"ama":"Rouiller O, Bickel B, Kautz J, Matusik W, Alexa M. 3D printing spatially varying BRDFs. <i>IEEE Computer Graphics and Applications</i>. 2013;33(6):48-57. doi:<a href=\"https://doi.org/10.1109/MCG.2013.82 \">10.1109/MCG.2013.82 </a>","apa":"Rouiller, O., Bickel, B., Kautz, J., Matusik, W., &#38; Alexa, M. (2013). 3D printing spatially varying BRDFs. <i>IEEE Computer Graphics and Applications</i>. IEEE. <a href=\"https://doi.org/10.1109/MCG.2013.82 \">https://doi.org/10.1109/MCG.2013.82 </a>","short":"O. Rouiller, B. Bickel, J. Kautz, W. Matusik, M. Alexa, IEEE Computer Graphics and Applications 33 (2013) 48–57.","chicago":"Rouiller, Olivier, Bernd Bickel, Jan Kautz, Wojciech Matusik, and Marc Alexa. “3D Printing Spatially Varying BRDFs.” <i>IEEE Computer Graphics and Applications</i>. IEEE, 2013. <a href=\"https://doi.org/10.1109/MCG.2013.82 \">https://doi.org/10.1109/MCG.2013.82 </a>.","ieee":"O. Rouiller, B. Bickel, J. Kautz, W. Matusik, and M. Alexa, “3D printing spatially varying BRDFs,” <i>IEEE Computer Graphics and Applications</i>, vol. 33, no. 6. IEEE, pp. 48–57, 2013.","ista":"Rouiller O, Bickel B, Kautz J, Matusik W, Alexa M. 2013. 3D printing spatially varying BRDFs. IEEE Computer Graphics and Applications. 33(6), 48–57.","mla":"Rouiller, Olivier, et al. “3D Printing Spatially Varying BRDFs.” <i>IEEE Computer Graphics and Applications</i>, vol. 33, no. 6, IEEE, 2013, pp. 48–57, doi:<a href=\"https://doi.org/10.1109/MCG.2013.82 \">10.1109/MCG.2013.82 </a>."},"quality_controlled":0,"date_created":"2018-12-11T11:55:47Z"},{"abstract":[{"lang":"eng","text":"3D printing is considered a disruptive technology with a potentially tremendous socioeconomic impact. The three articles in this special issue illustrate how novel computer graphics approaches are advancing such digital fabrication."}],"month":"12","date_published":"2013-12-01T00:00:00Z","publication_status":"published","date_updated":"2021-01-12T06:55:24Z","publist_id":"4921","publisher":"IEEE","page":"24 - 25","year":"2013","day":"01","title":"Computational aspects of fabrication: Modeling, design and 3d printing","volume":33,"status":"public","intvolume":"        33","date_created":"2018-12-11T11:55:48Z","quality_controlled":0,"doi":"10.1109/MCG.2013.89","citation":{"ama":"Bickel B, Alexa M. Computational aspects of fabrication: Modeling, design and 3d printing. <i>IEEE Computer Graphics and Applications</i>. 2013;33(6):24-25. doi:<a href=\"https://doi.org/10.1109/MCG.2013.89\">10.1109/MCG.2013.89</a>","mla":"Bickel, Bernd, and Marc Alexa. “Computational Aspects of Fabrication: Modeling, Design and 3d Printing.” <i>IEEE Computer Graphics and Applications</i>, vol. 33, no. 6, IEEE, 2013, pp. 24–25, doi:<a href=\"https://doi.org/10.1109/MCG.2013.89\">10.1109/MCG.2013.89</a>.","ieee":"B. Bickel and M. Alexa, “Computational aspects of fabrication: Modeling, design and 3d printing,” <i>IEEE Computer Graphics and Applications</i>, vol. 33, no. 6. IEEE, pp. 24–25, 2013.","ista":"Bickel B, Alexa M. 2013. Computational aspects of fabrication: Modeling, design and 3d printing. IEEE Computer Graphics and Applications. 33(6), 24–25.","short":"B. Bickel, M. Alexa, IEEE Computer Graphics and Applications 33 (2013) 24–25.","chicago":"Bickel, Bernd, and Marc Alexa. “Computational Aspects of Fabrication: Modeling, Design and 3d Printing.” <i>IEEE Computer Graphics and Applications</i>. IEEE, 2013. <a href=\"https://doi.org/10.1109/MCG.2013.89\">https://doi.org/10.1109/MCG.2013.89</a>.","apa":"Bickel, B., &#38; Alexa, M. (2013). Computational aspects of fabrication: Modeling, design and 3d printing. <i>IEEE Computer Graphics and Applications</i>. IEEE. <a href=\"https://doi.org/10.1109/MCG.2013.89\">https://doi.org/10.1109/MCG.2013.89</a>"},"publication":"IEEE Computer Graphics and Applications","extern":1,"_id":"2114","type":"journal_article","issue":"6","author":[{"orcid":"0000-0001-6511-9385","full_name":"Bernd Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"},{"first_name":"Marc","last_name":"Alexa","full_name":"Alexa, Marc"}]},{"intvolume":"        18","status":"public","title":"Poisson stochastic integration in Banach spaces","volume":18,"year":"2013","day":"18","acknowledgement":"The first and third named authors were supported by VICI subsidy 639.033.604 of the Netherlands Organisation for Scientific Research (NWO). The first and second named authors were supported by the German Research Foundation in the Collaborative Research C","author":[{"full_name":"Dirksen, Sjoerd","first_name":"Sjoerd","last_name":"Dirksen"},{"orcid":"0000-0002-0845-1338","full_name":"Jan Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Maas"},{"last_name":"Van Neerven","first_name":"Jan","full_name":"van Neerven, Jan M"}],"publication":"Electronic Journal of Probability","extern":1,"type":"journal_article","_id":"2117","date_created":"2018-12-11T11:55:49Z","quality_controlled":0,"citation":{"ama":"Dirksen S, Maas J, Van Neerven J. Poisson stochastic integration in Banach spaces. <i>Electronic Journal of Probability</i>. 2013;18. doi:<a href=\"https://doi.org/10.1214/EJP.v18-2945 \">10.1214/EJP.v18-2945 </a>","apa":"Dirksen, S., Maas, J., &#38; Van Neerven, J. (2013). Poisson stochastic integration in Banach spaces. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/EJP.v18-2945 \">https://doi.org/10.1214/EJP.v18-2945 </a>","chicago":"Dirksen, Sjoerd, Jan Maas, and Jan Van Neerven. “Poisson Stochastic Integration in Banach Spaces.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2013. <a href=\"https://doi.org/10.1214/EJP.v18-2945 \">https://doi.org/10.1214/EJP.v18-2945 </a>.","short":"S. Dirksen, J. Maas, J. Van Neerven, Electronic Journal of Probability 18 (2013).","ieee":"S. Dirksen, J. Maas, and J. Van Neerven, “Poisson stochastic integration in Banach spaces,” <i>Electronic Journal of Probability</i>, vol. 18. Institute of Mathematical Statistics, 2013.","ista":"Dirksen S, Maas J, Van Neerven J. 2013. Poisson stochastic integration in Banach spaces. Electronic Journal of Probability. 18.","mla":"Dirksen, Sjoerd, et al. “Poisson Stochastic Integration in Banach Spaces.” <i>Electronic Journal of Probability</i>, vol. 18, Institute of Mathematical Statistics, 2013, doi:<a href=\"https://doi.org/10.1214/EJP.v18-2945 \">10.1214/EJP.v18-2945 </a>."},"doi":"10.1214/EJP.v18-2945 ","date_updated":"2021-01-12T06:55:24Z","publist_id":"4917","publisher":"Institute of Mathematical Statistics","publication_status":"published","month":"11","date_published":"2013-11-18T00:00:00Z","abstract":[{"text":"We prove new upper and lower bounds for Banach space-valued stochastic integrals with respect to a compensated Poisson random measure. Our estimates apply to Banach spaces with non-trivial martingale (co)type and extend various results in the literature. We also develop a Malliavin framework to interpret Poisson stochastic integrals as vector-valued Skorohod integrals, and prove a Clark-Ocone representation formula.","lang":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.7901 "}]}]