[{"project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"quality_controlled":"1","volume":99,"department":[{"_id":"HeEd"}],"date_published":"2018-06-11T00:00:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","abstract":[{"lang":"eng","text":"Given a locally finite X ⊆ ℝd and a radius r ≥ 0, the k-fold cover of X and r consists of all points in ℝd that have k or more points of X within distance r. We consider two filtrations - one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k - and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in ℝd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module from Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. "}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["516"],"_id":"187","file_date_updated":"2020-07-14T12:45:19Z","doi":"10.4230/LIPIcs.SoCG.2018.34","publist_id":"7732","date_created":"2018-12-11T11:45:05Z","citation":{"chicago":"Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">https://doi.org/10.4230/LIPIcs.SoCG.2018.34</a>.","ista":"Edelsbrunner H, Osang GF. 2018. The multi-cover persistence of Euclidean balls. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 34.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. <i>The Multi-Cover Persistence of Euclidean Balls</i>. Vol. 99, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">10.4230/LIPIcs.SoCG.2018.34</a>.","ieee":"H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","ama":"Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">10.4230/LIPIcs.SoCG.2018.34</a>","short":"H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","apa":"Edelsbrunner, H., &#38; Osang, G. F. (2018). The multi-cover persistence of Euclidean balls (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">https://doi.org/10.4230/LIPIcs.SoCG.2018.34</a>"},"year":"2018","acknowledgement":"This work is partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","article_number":"34","related_material":{"record":[{"status":"public","id":"9317","relation":"later_version"},{"relation":"dissertation_contains","id":"9056","status":"public"}]},"status":"public","type":"conference","alternative_title":["LIPIcs"],"author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","first_name":"Georg F"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":528018,"access_level":"open_access","creator":"dernst","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-18T09:27:22Z","file_id":"5738","checksum":"d8c0533ad0018eb4ed1077475eb8fc18","file_name":"2018_LIPIcs_Edelsbrunner_Osang.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"11","oa_version":"Published Version","month":"06","conference":{"end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry"},"language":[{"iso":"eng"}],"title":"The multi-cover persistence of Euclidean balls","oa":1,"date_updated":"2023-09-07T13:29:00Z","scopus_import":1,"has_accepted_license":"1","intvolume":"        99"},{"_id":"188","file_date_updated":"2020-07-14T12:45:20Z","doi":"10.4230/LIPIcs.SoCG.2018.35","citation":{"apa":"Edelsbrunner, H., Virk, Z., &#38; Wagner, H. (2018). Smallest enclosing spheres and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">https://doi.org/10.4230/LIPIcs.SoCG.2018.35</a>","mla":"Edelsbrunner, Herbert, et al. <i>Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">10.4230/LIPIcs.SoCG.2018.35</a>.","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">https://doi.org/10.4230/LIPIcs.SoCG.2018.35</a>.","ista":"Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13.","short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13.","ama":"Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:35:1-35:13. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">10.4230/LIPIcs.SoCG.2018.35</a>","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13."},"publist_id":"7733","date_created":"2018-12-11T11:45:05Z","year":"2018","acknowledgement":"This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund","project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"quality_controlled":"1","volume":99,"department":[{"_id":"HeEd"}],"page":"35:1 - 35:13","date_published":"2018-06-11T00:00:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","abstract":[{"lang":"eng","text":"Smallest enclosing spheres of finite point sets are central to methods in topological data analysis. Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["000"],"language":[{"iso":"eng"}],"title":"Smallest enclosing spheres and Chernoff points in Bregman geometry","oa":1,"date_updated":"2021-01-12T06:53:48Z","has_accepted_license":"1","scopus_import":1,"intvolume":"        99","type":"conference","status":"public","alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"last_name":"Virk","first_name":"Ziga","full_name":"Virk, Ziga"},{"first_name":"Hubert","full_name":"Wagner, Hubert","last_name":"Wagner","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"5724","checksum":"7509403803b3ac1aee94bbc2ad293d21","file_name":"2018_LIPIcs_Edelsbrunner.pdf","date_created":"2018-12-17T16:31:31Z","date_updated":"2020-07-14T12:45:20Z","creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":489080}],"oa_version":"Published Version","day":"11","month":"06","conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2018-06-11","location":"Budapest, Hungary","end_date":"2018-06-14"}},{"doi":"10.1093/molbev/msy163","_id":"19","article_type":"original","year":"2018","citation":{"apa":"Palmer, A., Chait, R. P., &#38; Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>","mla":"Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11, Oxford University Press, 2018, pp. 2669–84, doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>.","chicago":"Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>.","ista":"Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684.","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","ieee":"A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.","ama":"Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. 2018;35(11):2669-2684. doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>"},"date_created":"2018-12-11T11:44:11Z","publist_id":"8036","date_published":"2018-08-28T00:00:00Z","publisher":"Oxford University Press","quality_controlled":"1","volume":35,"page":"2669 - 2684","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses."}],"external_id":{"pmid":["30169679"],"isi":["000452567200006"]},"publication_status":"published","publication":"Molecular Biology and Evolution","language":[{"iso":"eng"}],"isi":1,"intvolume":"        35","scopus_import":"1","issue":"11","article_processing_charge":"No","date_updated":"2023-10-17T11:51:06Z","oa":1,"title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","status":"public","type":"journal_article","pmid":1,"month":"08","publication_identifier":{"issn":["0737-4038"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"28","oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679","open_access":"1"}],"author":[{"last_name":"Palmer","full_name":"Palmer, Adam","first_name":"Adam"},{"last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","first_name":"Remy P","full_name":"Chait, Remy P"},{"first_name":"Roy","full_name":"Kishony, Roy","last_name":"Kishony"}]},{"language":[{"iso":"eng"}],"publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","article_processing_charge":"No","oa":1,"date_updated":"2023-09-11T13:59:54Z","title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","isi":1,"scopus_import":"1","intvolume":"       330","status":"public","type":"journal_article","pmid":1,"author":[{"last_name":"Harrison","full_name":"Harrison, Mark","first_name":"Mark"},{"full_name":"Arning, Nicolas","first_name":"Nicolas","last_name":"Arning"},{"first_name":"Lucas","full_name":"Kremer, Lucas","last_name":"Kremer"},{"first_name":"Guillem","full_name":"Ylla, Guillem","last_name":"Ylla"},{"last_name":"Belles","full_name":"Belles, Xavier","first_name":"Xavier"},{"last_name":"Bornberg Bauer","first_name":"Erich","full_name":"Bornberg Bauer, Erich"},{"orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","first_name":"Ann K","full_name":"Huylmans, Ann K"},{"first_name":"Evelien","full_name":"Jongepier, Evelien","last_name":"Jongepier"},{"last_name":"Puilachs","full_name":"Puilachs, Maria","first_name":"Maria"},{"first_name":"Stephen","full_name":"Richards, Stephen","last_name":"Richards"},{"full_name":"Schal, Coby","first_name":"Coby","last_name":"Schal"}],"month":"07","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"11","main_file_link":[{"open_access":"1","url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824"}],"oa_version":"Submitted Version","article_type":"original","_id":"190","doi":"10.1002/jez.b.22824","year":"2018","citation":{"apa":"Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer, E., … Schal, C. (2018). Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>","short":"M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer, A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.","ama":"Harrison M, Arning N, Kremer L, et al. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. 2018;330:254-264. doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>","ieee":"M. Harrison <i>et al.</i>, “Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest,” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330. Wiley, pp. 254–264, 2018.","ista":"Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 330, 254–264.","mla":"Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330, Wiley, 2018, pp. 254–64, doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>.","chicago":"Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles, Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>."},"publist_id":"7730","date_created":"2018-12-11T11:45:06Z","date_published":"2018-07-11T00:00:00Z","publisher":"Wiley","quality_controlled":"1","volume":330,"page":"254-264","department":[{"_id":"BeVi"}],"publication_status":"published","abstract":[{"lang":"eng","text":"The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control."}],"external_id":{"isi":["000443231000002"],"pmid":["29998472"]}},{"type":"journal_article","status":"public","file":[{"creator":"dernst","file_size":2413876,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"266b03f4fb8198e83141617aaa99dcab","file_id":"5714","file_name":"2018_ScientificReports_Grones.pdf","date_updated":"2020-07-14T12:45:20Z","date_created":"2018-12-17T15:38:56Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"06","oa_version":"Published Version","month":"07","author":[{"full_name":"Grones, Peter","first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Melinda F","full_name":"Abas, Melinda F","last_name":"Abas","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jakub","full_name":"Hajny, Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","orcid":"0000-0003-2140-7195"},{"first_name":"Angharad","full_name":"Jones, Angharad","last_name":"Jones"},{"first_name":"Sascha","full_name":"Waidmann, Sascha","last_name":"Waidmann"},{"full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen","last_name":"Kleine Vehn"},{"first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"publication":"Scientific Reports","language":[{"iso":"eng"}],"intvolume":"         8","scopus_import":"1","has_accepted_license":"1","isi":1,"title":"PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism","issue":"1","article_processing_charge":"No","date_updated":"2025-05-07T11:12:31Z","oa":1,"volume":8,"quality_controlled":"1","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"date_published":"2018-07-06T00:00:00Z","publisher":"Springer","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Intercellular distribution of the plant hormone auxin largely depends on the polar subcellular distribution of the plasma membrane PIN-FORMED (PIN) auxin transporters. PIN polarity switches in response to different developmental and environmental signals have been shown to redirect auxin fluxes mediating certain developmental responses. PIN phosphorylation at different sites and by different kinases is crucial for PIN function. Here we investigate the role of PIN phosphorylation during gravitropic response. Loss- and gain-of-function mutants in PINOID and related kinases but not in D6PK kinase as well as mutations mimicking constitutive dephosphorylated or phosphorylated status of two clusters of predicted phosphorylation sites partially disrupted PIN3 phosphorylation and caused defects in gravitropic bending in roots and hypocotyls. In particular, they impacted PIN3 polarity rearrangements in response to gravity and during feed-back regulation by auxin itself. Thus PIN phosphorylation, besides regulating transport activity and apical-basal targeting, is also important for the rapid polarity switches in response to environmental and endogenous signals.","lang":"eng"}],"external_id":{"isi":["000437673200053"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["581"],"publication_status":"published","doi":"10.1038/s41598-018-28188-1","_id":"191","file_date_updated":"2020-07-14T12:45:20Z","article_number":"10279","related_material":{"record":[{"status":"public","id":"8822","relation":"dissertation_contains"}]},"ec_funded":1,"date_created":"2018-12-11T11:45:06Z","publist_id":"7729","citation":{"ista":"Grones P, Abas MF, Hajny J, Jones A, Waidmann S, Kleine Vehn J, Friml J. 2018. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 8(1), 10279.","mla":"Grones, Peter, et al. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” <i>Scientific Reports</i>, vol. 8, no. 1, 10279, Springer, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-28188-1\">10.1038/s41598-018-28188-1</a>.","chicago":"Grones, Peter, Melinda F Abas, Jakub Hajny, Angharad Jones, Sascha Waidmann, Jürgen Kleine Vehn, and Jiří Friml. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” <i>Scientific Reports</i>. Springer, 2018. <a href=\"https://doi.org/10.1038/s41598-018-28188-1\">https://doi.org/10.1038/s41598-018-28188-1</a>.","short":"P. Grones, M.F. Abas, J. Hajny, A. Jones, S. Waidmann, J. Kleine Vehn, J. Friml, Scientific Reports 8 (2018).","ieee":"P. Grones <i>et al.</i>, “PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism,” <i>Scientific Reports</i>, vol. 8, no. 1. Springer, 2018.","ama":"Grones P, Abas MF, Hajny J, et al. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-28188-1\">10.1038/s41598-018-28188-1</a>","apa":"Grones, P., Abas, M. F., Hajny, J., Jones, A., Waidmann, S., Kleine Vehn, J., &#38; Friml, J. (2018). PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. <i>Scientific Reports</i>. Springer. <a href=\"https://doi.org/10.1038/s41598-018-28188-1\">https://doi.org/10.1038/s41598-018-28188-1</a>"},"year":"2018"},{"title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","oa":1,"date_updated":"2023-09-15T12:11:03Z","issue":"7","article_processing_charge":"No","scopus_import":"1","intvolume":"         4","isi":1,"language":[{"iso":"eng"}],"publication":"Nature Plants","author":[{"orcid":"0000-0002-9767-8699","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","full_name":"Fendrych, Matyas","first_name":"Matyas"},{"orcid":"0000-0003-1522-3162","last_name":"Akhmanova","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","full_name":"Akhmanova, Maria","first_name":"Maria"},{"orcid":"0000-0001-5145-4609","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","full_name":"Merrin, Jack"},{"last_name":"Glanc","full_name":"Glanc, Matous","first_name":"Matous"},{"last_name":"Hagihara","full_name":"Hagihara, Shinya","first_name":"Shinya"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"last_name":"Uchida","full_name":"Uchida, Naoyuki","first_name":"Naoyuki"},{"last_name":"Torii","first_name":"Keiko U","full_name":"Torii, Keiko U"},{"first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"day":"25","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048"}],"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"06","pmid":1,"type":"journal_article","status":"public","date_created":"2018-12-11T11:45:07Z","publist_id":"7728","citation":{"apa":"Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-018-0190-1\">https://doi.org/10.1038/s41477-018-0190-1</a>","ista":"Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459.","chicago":"Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” <i>Nature Plants</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0190-1\">https://doi.org/10.1038/s41477-018-0190-1</a>.","mla":"Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” <i>Nature Plants</i>, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:<a href=\"https://doi.org/10.1038/s41477-018-0190-1\">10.1038/s41477-018-0190-1</a>.","ama":"Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. <i>Nature Plants</i>. 2018;4(7):453-459. doi:<a href=\"https://doi.org/10.1038/s41477-018-0190-1\">10.1038/s41477-018-0190-1</a>","ieee":"M. Fendrych <i>et al.</i>, “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” <i>Nature Plants</i>, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018.","short":"M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459."},"year":"2018","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/","relation":"press_release"}]},"_id":"192","article_type":"original","doi":"10.1038/s41477-018-0190-1","publication_status":"published","external_id":{"isi":["000443221200017"],"pmid":["29942048"]},"abstract":[{"text":"The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway.","lang":"eng"}],"department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"page":"453 - 459","volume":4,"quality_controlled":"1","publisher":"Springer Nature","date_published":"2018-06-25T00:00:00Z"},{"acknowledgement":"Leonid Reyzin was supported in part by IST Austria and by US NSF grants 1012910, 1012798, and 1422965; this research was performed while he was visiting IST Austria.","year":"2018","publist_id":"7723","date_created":"2018-12-11T11:45:07Z","citation":{"apa":"Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak, K. Z., … Rybar, M. (2018). On the memory hardness of data independent password hashing functions. In <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i> (pp. 51–65). Incheon, Republic of Korea: ACM. <a href=\"https://doi.org/10.1145/3196494.3196534\">https://doi.org/10.1145/3196494.3196534</a>","mla":"Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password Hashing Functions.” <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, ACM, 2018, pp. 51–65, doi:<a href=\"https://doi.org/10.1145/3196494.3196534\">10.1145/3196494.3196534</a>.","chicago":"Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar. “On the Memory Hardness of Data Independent Password Hashing Functions.” In <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, 51–65. ACM, 2018. <a href=\"https://doi.org/10.1145/3196494.3196534\">https://doi.org/10.1145/3196494.3196534</a>.","ista":"Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password hashing functions. Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ASIACCS: Asia Conference on Computer and Communications Security , 51–65.","short":"J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak, L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65.","ama":"Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data independent password hashing functions. In: <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>. ACM; 2018:51-65. doi:<a href=\"https://doi.org/10.1145/3196494.3196534\">10.1145/3196494.3196534</a>","ieee":"J. F. Alwen <i>et al.</i>, “On the memory hardness of data independent password hashing functions,” in <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, Incheon, Republic of Korea, 2018, pp. 51–65."},"ec_funded":1,"_id":"193","doi":"10.1145/3196494.3196534","publication_status":"published","external_id":{"isi":["000516620100005"]},"abstract":[{"lang":"eng","text":"We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki'16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block'16] for analyzing the hardware costs of an iMHF."}],"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"},{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"publisher":"ACM","date_published":"2018-06-01T00:00:00Z","department":[{"_id":"KrPi"},{"_id":"HeEd"},{"_id":"VlKo"}],"page":"51 - 65","quality_controlled":"1","oa":1,"date_updated":"2023-09-13T09:13:12Z","article_processing_charge":"No","title":"On the memory hardness of data independent password hashing functions","isi":1,"scopus_import":"1","language":[{"iso":"eng"}],"publication":"Proceedings of the 2018 on Asia Conference on Computer and Communication Security","author":[{"last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F","first_name":"Joel F"},{"full_name":"Gazi, Peter","first_name":"Peter","last_name":"Gazi"},{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan"},{"id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","first_name":"Karen","full_name":"Klein, Karen"},{"first_name":"Georg F","full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z"},{"full_name":"Reyzin, Lenoid","first_name":"Lenoid","last_name":"Reyzin"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","last_name":"Rolinek","full_name":"Rolinek, Michal","first_name":"Michal"},{"last_name":"Rybar","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Rybar, Michal"}],"conference":{"end_date":"2018-06-08","location":"Incheon, Republic of Korea","start_date":"2018-06-04","name":"ASIACCS: Asia Conference on Computer and Communications Security "},"month":"06","main_file_link":[{"url":"https://eprint.iacr.org/2016/783","open_access":"1"}],"oa_version":"Submitted Version","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","type":"conference"},{"status":"public","type":"journal_article","pmid":1,"author":[{"full_name":"Liutkeviciute, Zita","first_name":"Zita","last_name":"Liutkeviciute"},{"full_name":"Gil Mansilla, Esther","first_name":"Esther","last_name":"Gil Mansilla"},{"last_name":"Eder","full_name":"Eder, Thomas","first_name":"Thomas"},{"first_name":"Barbara E","full_name":"Casillas Perez, Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","last_name":"Casillas Perez"},{"last_name":"Giulia Di Giglio","first_name":"Maria","full_name":"Giulia Di Giglio, Maria"},{"full_name":"Muratspahić, Edin","first_name":"Edin","last_name":"Muratspahić"},{"last_name":"Grebien","first_name":"Florian","full_name":"Grebien, Florian"},{"last_name":"Rattei","full_name":"Rattei, Thomas","first_name":"Thomas"},{"first_name":"Markus","full_name":"Muttenthaler, Markus","last_name":"Muttenthaler"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gruber","first_name":"Christian","full_name":"Gruber, Christian"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":" https://doi.org/10.1096/fj.201800443","open_access":"1"}],"oa_version":"Published Version","day":"29","month":"11","publication_identifier":{"issn":["08926638"]},"language":[{"iso":"eng"}],"publication":"The FASEB Journal","title":"Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity","issue":"12","article_processing_charge":"No","date_updated":"2023-09-13T09:37:32Z","oa":1,"intvolume":"        32","scopus_import":"1","isi":1,"project":[{"_id":"25E3D34E-B435-11E9-9278-68D0E5697425","name":"Individual function and social role of oxytocin-like neuropeptides in ants"}],"quality_controlled":"1","volume":32,"page":"6808-6821","department":[{"_id":"SyCr"}],"date_published":"2018-11-29T00:00:00Z","publisher":"FASEB","publication_status":"published","abstract":[{"lang":"eng","text":"Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion."}],"external_id":{"isi":["000449359700035"],"pmid":["29939785"]},"article_type":"original","_id":"194","doi":"10.1096/fj.201800443","publist_id":"7721","date_created":"2018-12-11T11:45:08Z","citation":{"short":"Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer, C. Gruber, The FASEB Journal 32 (2018) 6808–6821.","ieee":"Z. Liutkeviciute <i>et al.</i>, “Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity,” <i>The FASEB Journal</i>, vol. 32, no. 12. FASEB, pp. 6808–6821, 2018.","ama":"Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. <i>The FASEB Journal</i>. 2018;32(12):6808-6821. doi:<a href=\"https://doi.org/10.1096/fj.201800443\">10.1096/fj.201800443</a>","mla":"Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” <i>The FASEB Journal</i>, vol. 32, no. 12, FASEB, 2018, pp. 6808–21, doi:<a href=\"https://doi.org/10.1096/fj.201800443\">10.1096/fj.201800443</a>.","ista":"Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 32(12), 6808–6821.","chicago":"Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” <i>The FASEB Journal</i>. FASEB, 2018. <a href=\"https://doi.org/10.1096/fj.201800443\">https://doi.org/10.1096/fj.201800443</a>.","apa":"Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. <i>The FASEB Journal</i>. FASEB. <a href=\"https://doi.org/10.1096/fj.201800443\">https://doi.org/10.1096/fj.201800443</a>"},"year":"2018"},{"title":"Anyonic statistics of quantum impurities in two dimensions","date_updated":"2023-09-08T13:22:57Z","oa":1,"issue":"4","article_processing_charge":"No","intvolume":"        98","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"publication":"Physical Review B - Condensed Matter and Materials Physics","author":[{"full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","last_name":"Yakaboylu","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874"},{"last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"}],"arxiv":1,"day":"15","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.00308"}],"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"07","type":"journal_article","status":"public","citation":{"chicago":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">https://doi.org/10.1103/PhysRevB.98.045402</a>.","ista":"Yakaboylu E, Lemeshko M. 2018. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 98(4), 045402.","mla":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 98, no. 4, 045402, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">10.1103/PhysRevB.98.045402</a>.","short":"E. Yakaboylu, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 98 (2018).","ama":"Yakaboylu E, Lemeshko M. Anyonic statistics of quantum impurities in two dimensions. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2018;98(4). doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">10.1103/PhysRevB.98.045402</a>","ieee":"E. Yakaboylu and M. Lemeshko, “Anyonic statistics of quantum impurities in two dimensions,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 98, no. 4. American Physical Society, 2018.","apa":"Yakaboylu, E., &#38; Lemeshko, M. (2018). Anyonic statistics of quantum impurities in two dimensions. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">https://doi.org/10.1103/PhysRevB.98.045402</a>"},"date_created":"2018-12-11T11:45:08Z","year":"2018","ec_funded":1,"article_number":"045402","_id":"195","doi":"10.1103/PhysRevB.98.045402","publication_status":"published","external_id":{"isi":["000436939100007"],"arxiv":["1712.00308"]},"abstract":[{"text":"We demonstrate that identical impurities immersed in a two-dimensional many-particle bath can be viewed as flux-tube-charged-particle composites described by fractional statistics. In particular, we find that the bath manifests itself as an external magnetic flux tube with respect to the impurities, and hence the time-reversal symmetry is broken for the effective Hamiltonian describing the impurities. The emerging flux tube acts as a statistical gauge field after a certain critical coupling. This critical coupling corresponds to the intersection point between the quasiparticle state and the phonon wing, where the angular momentum is transferred from the impurity to the bath. This amounts to a novel configuration with emerging anyons. The proposed setup paves the way to realizing anyons using electrons interacting with superfluid helium or lattice phonons, as well as using atomic impurities in ultracold gases.","lang":"eng"}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment"}],"department":[{"_id":"MiLe"}],"volume":98,"quality_controlled":"1","publisher":"American Physical Society","date_published":"2018-07-15T00:00:00Z"},{"pubrep_id":"1021","oa":1,"date_updated":"2023-09-07T12:51:46Z","article_processing_charge":"No","title":"Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images","has_accepted_license":"1","language":[{"iso":"eng"}],"author":[{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","full_name":"Kolesnikov, Alexander","first_name":"Alexander"}],"month":"05","publication_identifier":{"issn":["2663-337X"]},"day":"25","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2018-12-12T10:14:57Z","date_updated":"2020-07-14T12:45:22Z","file_name":"IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf","file_id":"5113","checksum":"bc678e02468d8ebc39dc7267dfb0a1c4","content_type":"application/pdf","file_size":12918758,"access_level":"open_access","relation":"main_file","creator":"system"},{"file_name":"2018_Thesis_Kolesnikov_source.zip","checksum":"bc66973b086da5a043f1162dcfb1fde4","file_id":"6225","date_created":"2019-04-05T09:34:49Z","date_updated":"2020-07-14T12:45:22Z","creator":"dernst","file_size":55973760,"content_type":"application/zip","access_level":"closed","relation":"source_file"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","status":"public","acknowledgement":"I also gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research.","year":"2018","citation":{"apa":"Kolesnikov, A. (2018). <i>Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">https://doi.org/10.15479/AT:ISTA:th_1021</a>","short":"A. Kolesnikov, Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images, Institute of Science and Technology Austria, 2018.","ama":"Kolesnikov A. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">10.15479/AT:ISTA:th_1021</a>","ieee":"A. Kolesnikov, “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images,” Institute of Science and Technology Austria, 2018.","ista":"Kolesnikov A. 2018. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria.","mla":"Kolesnikov, Alexander. <i>Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">10.15479/AT:ISTA:th_1021</a>.","chicago":"Kolesnikov, Alexander. “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">https://doi.org/10.15479/AT:ISTA:th_1021</a>."},"publist_id":"7718","date_created":"2018-12-11T11:45:09Z","ec_funded":1,"degree_awarded":"PhD","file_date_updated":"2020-07-14T12:45:22Z","_id":"197","doi":"10.15479/AT:ISTA:th_1021","publication_status":"published","ddc":["004"],"abstract":[{"text":"Modern computer vision systems heavily rely on statistical machine learning models, which typically require large amounts of labeled data to be learned reliably. Moreover, very recently computer vision research widely adopted techniques for representation learning, which further increase the demand for labeled data. However, for many important practical problems there is relatively small amount of labeled data available, so it is problematic to leverage full potential of the representation learning methods. One way to overcome this obstacle is to invest substantial resources into producing large labelled datasets. Unfortunately, this can be prohibitively expensive in practice. In this thesis we focus on the alternative way of tackling the aforementioned issue. We concentrate on methods, which make use of weakly-labeled or even unlabeled data. Specifically, the first half of the thesis is dedicated to the semantic image segmentation task. We develop a technique, which achieves competitive segmentation performance and only requires annotations in a form of global image-level labels instead of dense segmentation masks. Subsequently, we present a new methodology, which further improves segmentation performance by leveraging tiny additional feedback from a human annotator. By using our methods practitioners can greatly reduce the amount of data annotation effort, which is required to learn modern image segmentation models. In the second half of the thesis we focus on methods for learning from unlabeled visual data. We study a family of autoregressive models for modeling structure of natural images and discuss potential applications of these models. Moreover, we conduct in-depth study of one of these applications, where we develop the state-of-the-art model for the probabilistic image colorization task.","lang":"eng"}],"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2018-05-25T00:00:00Z","department":[{"_id":"ChLa"}],"page":"113"},{"related_material":{"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4028971"}],"record":[{"relation":"research_data","id":"9814","status":"public"}]},"article_number":"20180073","ec_funded":1,"date_created":"2018-12-11T11:45:09Z","citation":{"mla":"Ibsen-Jensen, Rasmus, et al. “Language Acquisition with Communication between Learners.” <i>Journal of the Royal Society Interface</i>, vol. 15, no. 140, 20180073, The Royal Society, 2018, doi:<a href=\"https://doi.org/10.1098/rsif.2018.0073\">10.1098/rsif.2018.0073</a>.","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2018. Language acquisition with communication between learners. Journal of the Royal Society Interface. 15(140), 20180073.","chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Language Acquisition with Communication between Learners.” <i>Journal of the Royal Society Interface</i>. The Royal Society, 2018. <a href=\"https://doi.org/10.1098/rsif.2018.0073\">https://doi.org/10.1098/rsif.2018.0073</a>.","ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Language acquisition with communication between learners. <i>Journal of the Royal Society Interface</i>. 2018;15(140). doi:<a href=\"https://doi.org/10.1098/rsif.2018.0073\">10.1098/rsif.2018.0073</a>","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Language acquisition with communication between learners,” <i>Journal of the Royal Society Interface</i>, vol. 15, no. 140. The Royal Society, 2018.","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, Journal of the Royal Society Interface 15 (2018).","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2018). Language acquisition with communication between learners. <i>Journal of the Royal Society Interface</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsif.2018.0073\">https://doi.org/10.1098/rsif.2018.0073</a>"},"publist_id":"7715","year":"2018","doi":"10.1098/rsif.2018.0073","article_type":"original","_id":"198","file_date_updated":"2020-07-14T12:45:22Z","abstract":[{"lang":"eng","text":"We consider a class of students learning a language from a teacher. The situation can be interpreted as a group of child learners receiving input from the linguistic environment. The teacher provides sample sentences. The students try to learn the grammar from the teacher. In addition to just listening to the teacher, the students can also communicate with each other. The students hold hypotheses about the grammar and change them if they receive counter evidence. The process stops when all students have converged to the correct grammar. We study how the time to convergence depends on the structure of the classroom by introducing and evaluating various complexity measures. We find that structured communication between students, although potentially introducing confusion, can greatly reduce some of the complexity measures. Our theory can also be interpreted as applying to the scientific process, where nature is the teacher and the scientists are the students."}],"external_id":{"isi":["000428576200023"],"pmid":["29593089"]},"ddc":["000"],"publication_status":"published","volume":15,"quality_controlled":"1","department":[{"_id":"KrCh"}],"date_published":"2018-03-01T00:00:00Z","publisher":"The Royal Society","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"has_accepted_license":"1","intvolume":"        15","scopus_import":"1","isi":1,"title":"Language acquisition with communication between learners","article_processing_charge":"No","issue":"140","oa":1,"date_updated":"2023-10-18T06:36:00Z","publication":"Journal of the Royal Society Interface","language":[{"iso":"eng"}],"file":[{"date_created":"2019-02-12T07:54:37Z","date_updated":"2020-07-14T12:45:22Z","file_name":"2018_RS_IbsenJensen.pdf","file_id":"5955","checksum":"444e1a9d98eb0e780671be82b13025f3","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":219837,"creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Submitted Version","publication_identifier":{"eissn":["1742-5662"]},"month":"03","author":[{"first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389"},{"first_name":"Josef","full_name":"Tkadlec, Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"status":"public","type":"journal_article","pmid":1},{"isi":1,"scopus_import":"1","has_accepted_license":"1","intvolume":"         9","date_updated":"2023-09-19T10:15:31Z","oa":1,"article_processing_charge":"No","issue":"6","title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","publication":"Genes","language":[{"iso":"eng"}],"month":"06","oa_version":"Published Version","day":"12","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_id":"5905","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","file_name":"2018_Genes_Ma.pdf","date_updated":"2020-07-14T12:45:22Z","date_created":"2019-02-01T07:52:28Z","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_size":3985796,"access_level":"open_access"}],"author":[{"last_name":"Ma","first_name":"Wen","full_name":"Ma, Wen"},{"last_name":"Veltsos","full_name":"Veltsos, Paris","first_name":"Paris"},{"full_name":"Toups, Melissa A","first_name":"Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380"},{"last_name":"Rodrigues","full_name":"Rodrigues, Nicolas","first_name":"Nicolas"},{"last_name":"Sermier","first_name":"Roberto","full_name":"Sermier, Roberto"},{"first_name":"Daniel","full_name":"Jeffries, Daniel","last_name":"Jeffries"},{"last_name":"Perrin","first_name":"Nicolas","full_name":"Perrin, Nicolas"}],"status":"public","type":"journal_article","article_number":"294","year":"2018","citation":{"ieee":"W. Ma <i>et al.</i>, “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” <i>Genes</i>, vol. 9, no. 6. MDPI AG, 2018.","ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. <i>Genes</i>. 2018;9(6). doi:<a href=\"https://doi.org/10.3390/genes9060294\">10.3390/genes9060294</a>","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294.","mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” <i>Genes</i>, vol. 9, no. 6, 294, MDPI AG, 2018, doi:<a href=\"https://doi.org/10.3390/genes9060294\">10.3390/genes9060294</a>.","chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” <i>Genes</i>. MDPI AG, 2018. <a href=\"https://doi.org/10.3390/genes9060294\">https://doi.org/10.3390/genes9060294</a>.","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., &#38; Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. <i>Genes</i>. MDPI AG. <a href=\"https://doi.org/10.3390/genes9060294\">https://doi.org/10.3390/genes9060294</a>"},"publist_id":"7714","date_created":"2018-12-11T11:45:09Z","doi":"10.3390/genes9060294","file_date_updated":"2020-07-14T12:45:22Z","_id":"199","ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000436494200026"]},"abstract":[{"text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes.","lang":"eng"}],"publication_status":"published","publisher":"MDPI AG","date_published":"2018-06-12T00:00:00Z","department":[{"_id":"BeVi"}],"volume":9,"quality_controlled":"1"},{"doi":"10.1073/pnas.1810565115","_id":"2","ec_funded":1,"related_material":{"record":[{"id":"10293","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/no-cooperation-without-open-communication/","description":"News on IST Homepage","relation":"press_release"}]},"year":"2018","citation":{"chicago":"Hilbe, Christian, Laura Schmid, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1810565115\">https://doi.org/10.1073/pnas.1810565115</a>.","mla":"Hilbe, Christian, et al. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” <i>PNAS</i>, vol. 115, no. 48, National Academy of Sciences, 2018, pp. 12241–46, doi:<a href=\"https://doi.org/10.1073/pnas.1810565115\">10.1073/pnas.1810565115</a>.","ista":"Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. 2018. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 115(48), 12241–12246.","ama":"Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. Indirect reciprocity with private, noisy, and incomplete information. <i>PNAS</i>. 2018;115(48):12241-12246. doi:<a href=\"https://doi.org/10.1073/pnas.1810565115\">10.1073/pnas.1810565115</a>","ieee":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, and M. Nowak, “Indirect reciprocity with private, noisy, and incomplete information,” <i>PNAS</i>, vol. 115, no. 48. National Academy of Sciences, pp. 12241–12246, 2018.","short":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, M. Nowak, PNAS 115 (2018) 12241–12246.","apa":"Hilbe, C., Schmid, L., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2018). Indirect reciprocity with private, noisy, and incomplete information. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1810565115\">https://doi.org/10.1073/pnas.1810565115</a>"},"date_created":"2018-12-11T11:44:05Z","publisher":"National Academy of Sciences","date_published":"2018-11-27T00:00:00Z","department":[{"_id":"KrCh"}],"page":"12241-12246","quality_controlled":"1","volume":115,"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000451351000063"],"pmid":["30429320"]},"abstract":[{"lang":"eng","text":"Indirect reciprocity explores how humans act when their reputation is at stake, and which social norms they use to assess the actions of others. A crucial question in indirect reciprocity is which social norms can maintain stable cooperation in a society. Past research has highlighted eight such norms, called “leading-eight” strategies. This past research, however, is based on the assumption that all relevant information about other population members is publicly available and that everyone agrees on who is good or bad. Instead, here we explore the reputation dynamics when information is private and noisy. We show that under these conditions, most leading-eight strategies fail to evolve. Those leading-eight strategies that do evolve are unable to sustain full cooperation.Indirect reciprocity is a mechanism for cooperation based on shared moral systems and individual reputations. It assumes that members of a community routinely observe and assess each other and that they use this information to decide who is good or bad, and who deserves cooperation. When information is transmitted publicly, such that all community members agree on each other’s reputation, previous research has highlighted eight crucial moral systems. These “leading-eight” strategies can maintain cooperation and resist invasion by defectors. However, in real populations individuals often hold their own private views of others. Once two individuals disagree about their opinion of some third party, they may also see its subsequent actions in a different light. Their opinions may further diverge over time. Herein, we explore indirect reciprocity when information transmission is private and noisy. We find that in the presence of perception errors, most leading-eight strategies cease to be stable. Even if a leading-eight strategy evolves, cooperation rates may drop considerably when errors are common. Our research highlights the role of reliable information and synchronized reputations to maintain stable moral systems."}],"publication_status":"published","publication":"PNAS","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","intvolume":"       115","oa":1,"date_updated":"2025-07-14T09:10:09Z","article_processing_charge":"No","issue":"48","title":"Indirect reciprocity with private, noisy, and incomplete information","pmid":1,"type":"journal_article","status":"public","month":"11","day":"27","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30429320"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","full_name":"Hilbe, Christian"},{"first_name":"Laura","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329","last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkadlec, Josef","first_name":"Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}]},{"status":"public","type":"journal_article","file":[{"date_created":"2018-12-17T14:52:57Z","date_updated":"2020-07-14T12:45:23Z","file_id":"5712","file_name":"2018_BMCGenomics_Higareda.pdf","checksum":"a56516e734dab589dc7f3e1915973b4d","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":4629784,"creator":"dernst"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"03","oa_version":"Published Version","month":"11","publication_identifier":{"issn":["1471-2164"]},"author":[{"first_name":"Juan","full_name":"Higareda Almaraz, Juan","last_name":"Higareda Almaraz"},{"full_name":"Karbiener, Michael","first_name":"Michael","last_name":"Karbiener"},{"last_name":"Giroud","first_name":"Maude","full_name":"Giroud, Maude"},{"last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian"},{"first_name":"Teresa","full_name":"Gerhalter, Teresa","last_name":"Gerhalter"},{"first_name":"Stephan","full_name":"Herzig, Stephan","last_name":"Herzig"},{"first_name":"Marcel","full_name":"Scheideler, Marcel","last_name":"Scheideler"}],"publication":"BMC Genomics","language":[{"iso":"eng"}],"intvolume":"        19","has_accepted_license":"1","scopus_import":"1","isi":1,"title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","article_processing_charge":"No","issue":"1","date_updated":"2023-09-13T09:10:47Z","oa":1,"volume":19,"quality_controlled":"1","department":[{"_id":"SiHi"}],"date_published":"2018-11-03T00:00:00Z","publisher":"BioMed Central","abstract":[{"lang":"eng","text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function."}],"external_id":{"isi":["000450976700002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"publication_status":"published","doi":"10.1186/s12864-018-5173-0","_id":"20","article_type":"original","file_date_updated":"2020-07-14T12:45:23Z","related_material":{"record":[{"status":"public","id":"9807","relation":"research_data"},{"status":"public","relation":"research_data","id":"9808"}]},"publist_id":"8035","citation":{"ieee":"J. Higareda Almaraz <i>et al.</i>, “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” <i>BMC Genomics</i>, vol. 19, no. 1. BioMed Central, 2018.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. <i>BMC Genomics</i>. 2018;19(1). doi:<a href=\"https://doi.org/10.1186/s12864-018-5173-0\">10.1186/s12864-018-5173-0</a>","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” <i>BMC Genomics</i>, vol. 19, no. 1, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s12864-018-5173-0\">10.1186/s12864-018-5173-0</a>.","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” <i>BMC Genomics</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s12864-018-5173-0\">https://doi.org/10.1186/s12864-018-5173-0</a>.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1).","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., &#38; Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12864-018-5173-0\">https://doi.org/10.1186/s12864-018-5173-0</a>"},"date_created":"2018-12-11T11:44:12Z","year":"2018","acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19)."},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","date_published":"2018-02-21T00:00:00Z","supervisor":[{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"publisher":"Institute of Science and Technology Austria","page":"146","department":[{"_id":"NiBa"}],"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"ddc":["576"],"abstract":[{"text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm.","lang":"eng"}],"publication_status":"published","doi":"10.15479/AT:ISTA:th_963","_id":"200","file_date_updated":"2020-07-14T12:45:23Z","degree_awarded":"PhD","related_material":{"record":[{"id":"563","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"1074"}]},"year":"2018","date_created":"2018-12-11T11:45:10Z","citation":{"ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">10.15479/AT:ISTA:th_963</a>","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">https://doi.org/10.15479/AT:ISTA:th_963</a>.","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","mla":"Ringbauer, Harald. <i>Inferring Recent Demography from Spatial Genetic Structure</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">10.15479/AT:ISTA:th_963</a>.","apa":"Ringbauer, H. (2018). <i>Inferring recent demography from spatial genetic structure</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">https://doi.org/10.15479/AT:ISTA:th_963</a>"},"publist_id":"7713","type":"dissertation","status":"public","alternative_title":["ISTA Thesis"],"month":"02","publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2018-12-12T10:14:55Z","date_updated":"2020-07-14T12:45:23Z","checksum":"8cc534d2b528ae017acf80874cce48c9","file_id":"5111","file_name":"IST-2018-963-v1+1_thesis.pdf","access_level":"open_access","relation":"main_file","file_size":5792935,"content_type":"application/pdf","creator":"system"},{"creator":"dernst","content_type":"application/zip","file_size":113365,"relation":"source_file","access_level":"closed","checksum":"6af18d7e5a7e2728ceda2f41ee24f628","file_id":"6224","file_name":"2018_thesis_ringbauer_source.zip","date_updated":"2020-07-14T12:45:23Z","date_created":"2019-04-05T09:30:12Z"}],"oa_version":"Published Version","day":"21","author":[{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer","orcid":"0000-0002-4884-9682","full_name":"Ringbauer, Harald","first_name":"Harald"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","pubrep_id":"963","oa":1,"date_updated":"2025-05-28T11:57:06Z","title":"Inferring recent demography from spatial genetic structure"},{"department":[{"_id":"HeEd"}],"page":"171","supervisor":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"}],"date_published":"2018-06-11T00:00:00Z","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"We describe arrangements of three-dimensional spheres from a geometrical and topological point of view. Real data (fitting this setup) often consist of soft spheres which show certain degree of deformation while strongly packing against each other. In this context, we answer the following questions: If we model a soft packing of spheres by hard spheres that are allowed to overlap, can we measure the volume in the overlapped areas? Can we be more specific about the overlap volume, i.e. quantify how much volume is there covered exactly twice, three times, or k times? What would be a good optimization criteria that rule the arrangement of soft spheres while making a good use of the available space? Fixing a particular criterion, what would be the optimal sphere configuration? The first result of this thesis are short formulas for the computation of volumes covered by at least k of the balls. The formulas exploit information contained in the order-k Voronoi diagrams and its closely related Level-k complex. The used complexes lead to a natural generalization into poset diagrams, a theoretical formalism that contains the order-k and degree-k diagrams as special cases. In parallel, we define different criteria to determine what could be considered an optimal arrangement from a geometrical point of view. Fixing a criterion, we find optimal soft packing configurations in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools from computational topology on real physical data, to show the potentials of higher-order diagrams in the description of melting crystals. The results of the experiments leaves us with an open window to apply the theories developed in this thesis in real applications.","lang":"eng"}],"ddc":["514","516"],"publication_status":"published","doi":"10.15479/AT:ISTA:th_1026","_id":"201","file_date_updated":"2020-07-14T12:45:24Z","degree_awarded":"PhD","publist_id":"7712","date_created":"2018-12-11T11:45:10Z","citation":{"apa":"Iglesias Ham, M. (2018). <i>Multiple covers with balls</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1026\">https://doi.org/10.15479/AT:ISTA:th_1026</a>","ama":"Iglesias Ham M. Multiple covers with balls. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1026\">10.15479/AT:ISTA:th_1026</a>","ieee":"M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology Austria, 2018.","short":"M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology Austria, 2018.","chicago":"Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1026\">https://doi.org/10.15479/AT:ISTA:th_1026</a>.","mla":"Iglesias Ham, Mabel. <i>Multiple Covers with Balls</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1026\">10.15479/AT:ISTA:th_1026</a>.","ista":"Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and Technology Austria."},"year":"2018","type":"dissertation","status":"public","alternative_title":["ISTA Thesis"],"file":[{"file_name":"IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip","checksum":"dd699303623e96d1478a6ae07210dd05","file_id":"5918","date_updated":"2020-07-14T12:45:24Z","date_created":"2019-02-05T07:43:31Z","creator":"kschuh","access_level":"closed","relation":"source_file","content_type":"application/zip","file_size":11827713},{"file_size":4783846,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"kschuh","date_created":"2019-02-05T07:43:45Z","date_updated":"2020-07-14T12:45:24Z","file_id":"5919","checksum":"ba163849a190d2b41d66fef0e4983294","file_name":"IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","day":"11","publication_identifier":{"issn":["2663-337X"]},"month":"06","author":[{"last_name":"Iglesias Ham","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel","full_name":"Iglesias Ham, Mabel"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","title":"Multiple covers with balls","article_processing_charge":"No","date_updated":"2023-09-07T12:25:32Z","oa":1,"pubrep_id":"1026"},{"article_number":"e183","year":"2018","publist_id":"5061","date_created":"2018-12-11T11:55:13Z","citation":{"apa":"Raskutti, G., &#38; Uhler, C. (2018). Learning directed acyclic graphs based on sparsest permutations. <i>STAT</i>. Wiley. <a href=\"https://doi.org/10.1002/sta4.183\">https://doi.org/10.1002/sta4.183</a>","short":"G. Raskutti, C. Uhler, STAT 7 (2018).","ama":"Raskutti G, Uhler C. Learning directed acyclic graphs based on sparsest permutations. <i>STAT</i>. 2018;7(1). doi:<a href=\"https://doi.org/10.1002/sta4.183\">10.1002/sta4.183</a>","ieee":"G. Raskutti and C. Uhler, “Learning directed acyclic graphs based on sparsest permutations,” <i>STAT</i>, vol. 7, no. 1. Wiley, 2018.","mla":"Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based on Sparsest Permutations.” <i>STAT</i>, vol. 7, no. 1, e183, Wiley, 2018, doi:<a href=\"https://doi.org/10.1002/sta4.183\">10.1002/sta4.183</a>.","ista":"Raskutti G, Uhler C. 2018. Learning directed acyclic graphs based on sparsest permutations. STAT. 7(1), e183.","chicago":"Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based on Sparsest Permutations.” <i>STAT</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/sta4.183\">https://doi.org/10.1002/sta4.183</a>."},"doi":"10.1002/sta4.183","_id":"2015","article_type":"original","external_id":{"arxiv":["1307.0366"]},"abstract":[{"text":"We consider the problem of learning a Bayesian network or directed acyclic graph model from observational data. A number of constraint‐based, score‐based and hybrid algorithms have been developed for this purpose. Statistical consistency guarantees of these algorithms rely on the faithfulness assumption, which has been shown to be restrictive especially for graphs with cycles in the skeleton. We here propose the sparsest permutation (SP) algorithm, showing that learning Bayesian networks is possible under strictly weaker assumptions than faithfulness. This comes at a computational price, thereby indicating a statistical‐computational trade‐off for causal inference algorithms. In the Gaussian noiseless setting, we prove that the SP algorithm boils down to finding the permutation of the variables with the sparsest Cholesky decomposition of the inverse covariance matrix, which is equivalent to ℓ0‐penalized maximum likelihood estimation. We end with a simulation study showing that in line with the proven stronger consistency guarantees, and the SP algorithm compares favourably to standard causal inference algorithms in terms of accuracy for a given sample size.","lang":"eng"}],"publication_status":"published","publisher":"Wiley","date_published":"2018-04-17T00:00:00Z","extern":"1","quality_controlled":"1","volume":7,"intvolume":"         7","oa":1,"date_updated":"2021-01-12T06:54:44Z","issue":"1","article_processing_charge":"No","title":"Learning directed acyclic graphs based on sparsest permutations","publication":"STAT","language":[{"iso":"eng"}],"month":"04","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.0366"}],"day":"17","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Raskutti","full_name":"Raskutti, Garvesh","first_name":"Garvesh"},{"first_name":"Caroline","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"}],"arxiv":1,"status":"public","type":"journal_article"},{"doi":"10.1073/pnas.1806565115","_id":"203","ec_funded":1,"citation":{"ieee":"M. Abbas <i>et al.</i>, “Auxin methylation is required for differential growth in Arabidopsis,” <i>PNAS</i>, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018.","ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. <i>PNAS</i>. 2018;115(26):6864-6869. doi:<a href=\"https://doi.org/10.1073/pnas.1806565115\">10.1073/pnas.1806565115</a>","short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869.","mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” <i>PNAS</i>, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:<a href=\"https://doi.org/10.1073/pnas.1806565115\">10.1073/pnas.1806565115</a>.","ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.","chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1806565115\">https://doi.org/10.1073/pnas.1806565115</a>.","apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1806565115\">https://doi.org/10.1073/pnas.1806565115</a>"},"publist_id":"7710","date_created":"2018-12-11T11:45:11Z","year":"2018","page":"6864-6869","department":[{"_id":"JiFr"}],"quality_controlled":"1","volume":115,"publisher":"National Academy of Sciences","date_published":"2018-06-26T00:00:00Z","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000436245000096"]},"abstract":[{"lang":"eng","text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses."}],"publication_status":"published","publication":"PNAS","language":[{"iso":"eng"}],"intvolume":"       115","scopus_import":"1","isi":1,"title":"Auxin methylation is required for differential growth in Arabidopsis","date_updated":"2025-05-07T11:12:32Z","oa":1,"issue":"26","article_processing_charge":"No","status":"public","type":"journal_article","main_file_link":[{"url":"http://eprints.nottingham.ac.uk/52388/","open_access":"1"}],"oa_version":"None","day":"26","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"06","author":[{"full_name":"Abbas, Mohamad","first_name":"Mohamad","last_name":"Abbas","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hernández, García J","first_name":"García J","last_name":"Hernández"},{"first_name":"Stephan","full_name":"Pollmann, Stephan","last_name":"Pollmann"},{"full_name":"Samodelov, Sophia L","first_name":"Sophia L","last_name":"Samodelov"},{"full_name":"Kolb, Martina","first_name":"Martina","last_name":"Kolb"},{"first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hammes, Ulrich Z","first_name":"Ulrich Z","last_name":"Hammes"},{"first_name":"Matias D","full_name":"Zurbriggen, Matias D","last_name":"Zurbriggen"},{"last_name":"Blázquez","first_name":"Miguel","full_name":"Blázquez, Miguel"},{"last_name":"Alabadí","first_name":"David","full_name":"Alabadí, David"}]},{"author":[{"last_name":"Samanta","first_name":"Dipak","full_name":"Samanta, Dipak"},{"first_name":"Daria","full_name":"Galaktionova, Daria","last_name":"Galaktionova"},{"last_name":"Gemen","full_name":"Gemen, Julius","first_name":"Julius"},{"first_name":"Linda J. W.","full_name":"Shimon, Linda J. W.","last_name":"Shimon"},{"last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael","first_name":"Yael"},{"last_name":"Avram","first_name":"Liat","full_name":"Avram, Liat"},{"first_name":"Petr","full_name":"Král, Petr","last_name":"Král"},{"first_name":"Rafal","full_name":"Klajn, Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"month":"02","publication_identifier":{"eissn":["2041-1723"]},"day":"13","main_file_link":[{"url":"https://doi.org/10.1038/s41467-017-02715-6","open_access":"1"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"status":"public","type":"journal_article","date_updated":"2023-08-07T10:54:05Z","oa":1,"article_processing_charge":"No","title":"Reversible chromism of spiropyran in the cavity of a flexible coordination cage","intvolume":"         9","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Nature Communications","publication_status":"published","external_id":{"pmid":["29440687"]},"abstract":[{"text":"Confining molecules to volumes only slightly larger than the molecules themselves can profoundly alter their properties. Molecular switches—entities that can be toggled between two or more forms upon exposure to an external stimulus—often require conformational freedom to isomerize. Therefore, placing these switches in confined spaces can render them non-operational. To preserve the switchability of these species under confinement, we work with a water-soluble coordination cage that is flexible enough to adapt its shape to the conformation of the encapsulated guest. We show that owing to its flexibility, the cage is not only capable of accommodating—and solubilizing in water—several light-responsive spiropyran-based molecular switches, but, more importantly, it also provides an environment suitable for the efficient, reversible photoisomerization of the bound guests. Our findings pave the way towards studying various molecular switching processes in confined environments.","lang":"eng"}],"publisher":"Springer Nature","date_published":"2018-02-13T00:00:00Z","extern":"1","volume":9,"quality_controlled":"1","year":"2018","date_created":"2023-08-01T09:39:32Z","citation":{"short":"D. Samanta, D. Galaktionova, J. Gemen, L.J.W. Shimon, Y. Diskin-Posner, L. Avram, P. Král, R. Klajn, Nature Communications 9 (2018).","ieee":"D. Samanta <i>et al.</i>, “Reversible chromism of spiropyran in the cavity of a flexible coordination cage,” <i>Nature Communications</i>, vol. 9. Springer Nature, 2018.","ama":"Samanta D, Galaktionova D, Gemen J, et al. Reversible chromism of spiropyran in the cavity of a flexible coordination cage. <i>Nature Communications</i>. 2018;9. doi:<a href=\"https://doi.org/10.1038/s41467-017-02715-6\">10.1038/s41467-017-02715-6</a>","chicago":"Samanta, Dipak, Daria Galaktionova, Julius Gemen, Linda J. W. Shimon, Yael Diskin-Posner, Liat Avram, Petr Král, and Rafal Klajn. “Reversible Chromism of Spiropyran in the Cavity of a Flexible Coordination Cage.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-017-02715-6\">https://doi.org/10.1038/s41467-017-02715-6</a>.","ista":"Samanta D, Galaktionova D, Gemen J, Shimon LJW, Diskin-Posner Y, Avram L, Král P, Klajn R. 2018. Reversible chromism of spiropyran in the cavity of a flexible coordination cage. Nature Communications. 9, 641.","mla":"Samanta, Dipak, et al. “Reversible Chromism of Spiropyran in the Cavity of a Flexible Coordination Cage.” <i>Nature Communications</i>, vol. 9, 641, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-017-02715-6\">10.1038/s41467-017-02715-6</a>.","apa":"Samanta, D., Galaktionova, D., Gemen, J., Shimon, L. J. W., Diskin-Posner, Y., Avram, L., … Klajn, R. (2018). Reversible chromism of spiropyran in the cavity of a flexible coordination cage. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-017-02715-6\">https://doi.org/10.1038/s41467-017-02715-6</a>"},"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-018-03701-2","relation":"erratum"}]},"article_number":"641","article_type":"original","_id":"13374","doi":"10.1038/s41467-017-02715-6"},{"article_type":"original","_id":"13375","doi":"10.1002/adma.201706750","year":"2018","keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"date_created":"2023-08-01T09:39:46Z","citation":{"apa":"De, S., &#38; Klajn, R. (2018). Dissipative self-assembly driven by the consumption of chemical fuels. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.201706750\">https://doi.org/10.1002/adma.201706750</a>","short":"S. De, R. Klajn, Advanced Materials 30 (2018).","ama":"De S, Klajn R. Dissipative self-assembly driven by the consumption of chemical fuels. <i>Advanced Materials</i>. 2018;30(41). doi:<a href=\"https://doi.org/10.1002/adma.201706750\">10.1002/adma.201706750</a>","ieee":"S. De and R. Klajn, “Dissipative self-assembly driven by the consumption of chemical fuels,” <i>Advanced Materials</i>, vol. 30, no. 41. Wiley, 2018.","chicago":"De, Soumen, and Rafal Klajn. “Dissipative Self-Assembly Driven by the Consumption of Chemical Fuels.” <i>Advanced Materials</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/adma.201706750\">https://doi.org/10.1002/adma.201706750</a>.","mla":"De, Soumen, and Rafal Klajn. “Dissipative Self-Assembly Driven by the Consumption of Chemical Fuels.” <i>Advanced Materials</i>, vol. 30, no. 41, 1706750, Wiley, 2018, doi:<a href=\"https://doi.org/10.1002/adma.201706750\">10.1002/adma.201706750</a>.","ista":"De S, Klajn R. 2018. Dissipative self-assembly driven by the consumption of chemical fuels. Advanced Materials. 30(41), 1706750."},"article_number":"1706750","date_published":"2018-10-11T00:00:00Z","publisher":"Wiley","volume":30,"quality_controlled":"1","extern":"1","publication_status":"published","abstract":[{"text":"Dissipative self-assembly leads to structures and materials that exist away from equilibrium by continuously exchanging energy and materials with the external environment. Although this mode of self-assembly is ubiquitous in nature, where it gives rise to functions such as signal processing, motility, self-healing, self-replication, and ultimately life, examples of dissipative self-assembly processes in man-made systems are few and far between. Herein, recent progress in developing diverse synthetic dissipative self-assembly systems is discussed. The systems reported thus far can be categorized into three classes, in which: i) the fuel chemically modifies the building blocks, thus triggering their self-assembly, ii) the fuel acts as a template interacting with the building blocks noncovalently, and iii) transient states are induced by the addition of two mutually exclusive stimuli. These early studies give rise to materials that would be difficult to obtain otherwise, including hydrogels with programmable lifetimes, vesicular nanoreactors, and membranes exhibiting transient conductivity.","lang":"eng"}],"external_id":{"pmid":["29520846"]},"language":[{"iso":"eng"}],"publication":"Advanced Materials","article_processing_charge":"No","issue":"41","date_updated":"2023-08-07T10:56:26Z","title":"Dissipative self-assembly driven by the consumption of chemical fuels","scopus_import":"1","intvolume":"        30","status":"public","type":"journal_article","pmid":1,"author":[{"full_name":"De, Soumen","first_name":"Soumen","last_name":"De"},{"first_name":"Rafal","full_name":"Klajn, Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"month":"10","publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","day":"11"}]