[{"citation":{"ista":"Edelsbrunner H, Nikitenko A, Ölsböck K, Synak P. 2020. Radius functions on Poisson–Delaunay mosaics and related complexes experimentally. Topological Data Analysis. , Abel Symposia, vol. 15, 181–218.","ieee":"H. Edelsbrunner, A. Nikitenko, K. Ölsböck, and P. Synak, “Radius functions on Poisson–Delaunay mosaics and related complexes experimentally,” in <i>Topological Data Analysis</i>, 2020, vol. 15, pp. 181–218.","apa":"Edelsbrunner, H., Nikitenko, A., Ölsböck, K., &#38; Synak, P. (2020). Radius functions on Poisson–Delaunay mosaics and related complexes experimentally. In <i>Topological Data Analysis</i> (Vol. 15, pp. 181–218). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-43408-3_8\">https://doi.org/10.1007/978-3-030-43408-3_8</a>","mla":"Edelsbrunner, Herbert, et al. “Radius Functions on Poisson–Delaunay Mosaics and Related Complexes Experimentally.” <i>Topological Data Analysis</i>, vol. 15, Springer Nature, 2020, pp. 181–218, doi:<a href=\"https://doi.org/10.1007/978-3-030-43408-3_8\">10.1007/978-3-030-43408-3_8</a>.","ama":"Edelsbrunner H, Nikitenko A, Ölsböck K, Synak P. Radius functions on Poisson–Delaunay mosaics and related complexes experimentally. In: <i>Topological Data Analysis</i>. Vol 15. Springer Nature; 2020:181-218. doi:<a href=\"https://doi.org/10.1007/978-3-030-43408-3_8\">10.1007/978-3-030-43408-3_8</a>","short":"H. Edelsbrunner, A. Nikitenko, K. Ölsböck, P. Synak, in:, Topological Data Analysis, Springer Nature, 2020, pp. 181–218.","chicago":"Edelsbrunner, Herbert, Anton Nikitenko, Katharina Ölsböck, and Peter Synak. “Radius Functions on Poisson–Delaunay Mosaics and Related Complexes Experimentally.” In <i>Topological Data Analysis</i>, 15:181–218. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-43408-3_8\">https://doi.org/10.1007/978-3-030-43408-3_8</a>."},"article_processing_charge":"No","title":"Radius functions on Poisson–Delaunay mosaics and related complexes experimentally","type":"conference","status":"public","doi":"10.1007/978-3-030-43408-3_8","intvolume":"        15","page":"181-218","_id":"8135","quality_controlled":"1","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 78818 Alpha and No 638176). It is also 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).","department":[{"_id":"HeEd"}],"has_accepted_license":"1","alternative_title":["Abel Symposia"],"oa_version":"Submitted Version","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publication_status":"published","publication_identifier":{"eissn":["21978549"],"isbn":["9783030434076"],"issn":["21932808"]},"date_updated":"2021-01-12T08:17:06Z","ddc":["510"],"publisher":"Springer Nature","file":[{"success":1,"relation":"main_file","checksum":"7b5e0de10675d787a2ddb2091370b8d8","creator":"dernst","date_created":"2020-10-08T08:56:14Z","file_id":"8628","file_size":2207071,"access_level":"open_access","file_name":"2020-B-01-PoissonExperimentalSurvey.pdf","content_type":"application/pdf","date_updated":"2020-10-08T08:56:14Z"}],"scopus_import":"1","project":[{"grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended"},{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176"},{"call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-07-19T22:00:59Z","file_date_updated":"2020-10-08T08:56:14Z","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"},{"full_name":"Nikitenko, Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko","first_name":"Anton"},{"first_name":"Katharina","last_name":"Ölsböck","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","full_name":"Ölsböck, Katharina"},{"full_name":"Synak, Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Synak"}],"date_published":"2020-06-22T00:00:00Z","volume":15,"abstract":[{"text":"Discrete Morse theory has recently lead to new developments in the theory of random geometric complexes. This article surveys the methods and results obtained with this new approach, and discusses some of its shortcomings. It uses simulations to illustrate the results and to form conjectures, getting numerical estimates for combinatorial, topological, and geometric properties of weighted and unweighted Delaunay mosaics, their dual Voronoi tessellations, and the Alpha and Wrap complexes contained in the mosaics.","lang":"eng"}],"publication":"Topological Data Analysis","year":"2020","language":[{"iso":"eng"}],"day":"22","ec_funded":1},{"quality_controlled":"1","acknowledgement":"We are grateful to David Nelson for providing published materials and extremely helpful comments, and Elizabeth Dun and Christine Beveridge for helpful discussions. The research leading to these results has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (742985). This work was also supported by the Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, the National Natural Science Foundation of China (31370309), CEITEC 2020 (LQ1601) project with financial contribution made by the Ministry of Education, Youth and Sports of the Czech Republic within special support paid from the National Program of Sustainability II funds, Australian Research Council (FT180100081), and China Postdoctoral Science Foundation (2019M660864).","department":[{"_id":"JiFr"}],"external_id":{"isi":["000550062200004"],"pmid":["32665554"]},"doi":"10.1038/s41467-020-17252-y","intvolume":"        11","license":"https://creativecommons.org/licenses/by/4.0/","_id":"8138","page":"3508","title":"Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","status":"public","article_processing_charge":"No","citation":{"mla":"Zhang, J., et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” <i>Nature Communications</i>, vol. 11, no. 1, Springer Nature, 2020, p. 3508, doi:<a href=\"https://doi.org/10.1038/s41467-020-17252-y\">10.1038/s41467-020-17252-y</a>.","apa":"Zhang, J., Mazur, E., Balla, J., Gallei, M. C., Kalousek, P., Medveďová, Z., … Friml, J. (2020). Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17252-y\">https://doi.org/10.1038/s41467-020-17252-y</a>","short":"J. Zhang, E. Mazur, J. Balla, M.C. Gallei, P. Kalousek, Z. Medveďová, Y. Li, Y. Wang, T. Prat, M.K. Vasileva, V. Reinöhl, S. Procházka, R. Halouzka, P. Tarkowski, C. Luschnig, P. Brewer, J. Friml, Nature Communications 11 (2020) 3508.","chicago":"Zhang, J, E Mazur, J Balla, Michelle C Gallei, P Kalousek, Z Medveďová, Y Li, et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17252-y\">https://doi.org/10.1038/s41467-020-17252-y</a>.","ama":"Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. <i>Nature Communications</i>. 2020;11(1):3508. doi:<a href=\"https://doi.org/10.1038/s41467-020-17252-y\">10.1038/s41467-020-17252-y</a>","ista":"Zhang J, Mazur E, Balla J, Gallei MC, Kalousek P, Medveďová Z, Li Y, Wang Y, Prat T, Vasileva MK, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig C, Brewer P, Friml J. 2020. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 11(1), 3508.","ieee":"J. Zhang <i>et al.</i>, “Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization,” <i>Nature Communications</i>, vol. 11, no. 1. Springer Nature, p. 3508, 2020."},"isi":1,"oa":1,"publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"date_updated":"2023-08-22T08:13:44Z","ddc":["580"],"month":"07","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11626"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","article_type":"original","date_created":"2020-07-21T08:58:07Z","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"}],"scopus_import":"1","pmid":1,"file":[{"date_created":"2020-07-22T08:32:55Z","creator":"dernst","relation":"main_file","file_id":"8148","file_name":"2020_NatureComm_Zhang.pdf","access_level":"open_access","file_size":1759490,"date_updated":"2020-07-22T08:32:55Z","content_type":"application/pdf","success":1}],"publisher":"Springer Nature","ec_funded":1,"publication":"Nature Communications","year":"2020","language":[{"iso":"eng"}],"day":"14","author":[{"full_name":"Zhang, J","first_name":"J","last_name":"Zhang"},{"full_name":"Mazur, E","last_name":"Mazur","first_name":"E"},{"full_name":"Balla, J","last_name":"Balla","first_name":"J"},{"orcid":"0000-0003-1286-7368","first_name":"Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C"},{"full_name":"Kalousek, P","last_name":"Kalousek","first_name":"P"},{"full_name":"Medveďová, Z","last_name":"Medveďová","first_name":"Z"},{"full_name":"Li, Y","first_name":"Y","last_name":"Li"},{"full_name":"Wang, Y","last_name":"Wang","first_name":"Y"},{"full_name":"Prat, Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","last_name":"Prat","first_name":"Tomas"},{"id":"3407EB18-F248-11E8-B48F-1D18A9856A87","full_name":"Vasileva, Mina K","first_name":"Mina K","last_name":"Vasileva"},{"full_name":"Reinöhl, V","last_name":"Reinöhl","first_name":"V"},{"full_name":"Procházka, S","last_name":"Procházka","first_name":"S"},{"full_name":"Halouzka, R","first_name":"R","last_name":"Halouzka"},{"full_name":"Tarkowski, P","last_name":"Tarkowski","first_name":"P"},{"full_name":"Luschnig, C","last_name":"Luschnig","first_name":"C"},{"full_name":"Brewer, PB","first_name":"PB","last_name":"Brewer"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"date_published":"2020-07-14T00:00:00Z","volume":11,"abstract":[{"text":"Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration.","lang":"eng"}],"file_date_updated":"2020-07-22T08:32:55Z","issue":"1"},{"article_number":"jcs248062","has_accepted_license":"1","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"date_updated":"2023-12-01T13:51:07Z","ddc":["575"],"publication_status":"published","oa":1,"related_material":{"record":[{"id":"14510","relation":"dissertation_contains","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","month":"08","status":"public","type":"journal_article","title":"Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"}],"isi":1,"citation":{"short":"A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020).","ama":"Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. <i>Journal of Cell Science</i>. 2020;133(15). doi:<a href=\"https://doi.org/10.1242/jcs.248062\">10.1242/jcs.248062</a>","chicago":"Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan, G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” <i>Journal of Cell Science</i>. The Company of Biologists, 2020. <a href=\"https://doi.org/10.1242/jcs.248062\">https://doi.org/10.1242/jcs.248062</a>.","apa":"Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek, S., &#38; Friml, J. (2020). Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.248062\">https://doi.org/10.1242/jcs.248062</a>","mla":"Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” <i>Journal of Cell Science</i>, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020, doi:<a href=\"https://doi.org/10.1242/jcs.248062\">10.1242/jcs.248062</a>.","ista":"Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15), jcs248062.","ieee":"A. J. Johnson <i>et al.</i>, “Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis,” <i>Journal of Cell Science</i>, vol. 133, no. 15. The Company of Biologists, 2020."},"article_processing_charge":"No","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"quality_controlled":"1","acknowledgement":"This paper is dedicated to the memory of Christien Merrifield. He pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship inspired the development of all\r\nthe analysis methods presented here. His joy in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP plants used in this manuscript. We further thank the\r\nScientific Service Units at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility for access to equipment. ","intvolume":"       133","_id":"8139","external_id":{"isi":["000561047900021"],"pmid":["32616560"]},"doi":"10.1242/jcs.248062","date_published":"2020-08-06T00:00:00Z","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples."}],"volume":133,"author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","first_name":"Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843"},{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","first_name":"Nataliia","last_name":"Gnyliukh"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315"},{"full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","last_name":"Narasimhan","orcid":"0000-0002-8600-0671"},{"full_name":"Vert, G","first_name":"G","last_name":"Vert"},{"full_name":"Bednarek, SY","last_name":"Bednarek","first_name":"SY"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"issue":"15","file_date_updated":"2021-08-08T22:30:03Z","ec_funded":1,"year":"2020","language":[{"iso":"eng"}],"day":"06","publication":"Journal of Cell Science","scopus_import":"1","pmid":1,"file":[{"embargo":"2021-08-07","date_created":"2020-11-26T17:12:51Z","creator":"ajohnson","checksum":"2d11f79a0b4e0a380fb002b933da331a","relation":"main_file","file_id":"8815","file_name":"2020 - Johnson - JSC - plant CME toolbox.pdf","access_level":"open_access","file_size":15150403,"date_updated":"2021-08-08T22:30:03Z","content_type":"application/pdf"}],"publisher":"The Company of Biologists","project":[{"call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-07-21T08:58:19Z","article_type":"original"},{"day":"01","year":"2020","language":[{"iso":"eng"}],"publication":"The Embo Journal","abstract":[{"text":"Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells.","lang":"eng"}],"volume":39,"date_published":"2020-09-01T00:00:00Z","author":[{"orcid":"0000-0001-9179-6099","first_name":"Juan C","last_name":"Montesinos López","full_name":"Montesinos López, Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abuzeineh, A","first_name":"A","last_name":"Abuzeineh"},{"last_name":"Kopf","first_name":"Aglaja","orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","full_name":"Kopf, Aglaja"},{"full_name":"Juanes Garcia, Alba","id":"40F05888-F248-11E8-B48F-1D18A9856A87","last_name":"Juanes Garcia","first_name":"Alba","orcid":"0000-0002-1009-9652"},{"full_name":"Ötvös, Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","last_name":"Ötvös","first_name":"Krisztina","orcid":"0000-0002-5503-4983"},{"full_name":"Petrášek, J","first_name":"J","last_name":"Petrášek"},{"orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"issue":"17","file_date_updated":"2020-12-02T09:13:23Z","article_type":"original","date_created":"2020-07-21T09:08:38Z","project":[{"grant_number":"ALTF710-2016","_id":"253E54C8-B435-11E9-9278-68D0E5697425","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants"},{"call_identifier":"FWF","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","file":[{"success":1,"content_type":"application/pdf","date_updated":"2020-12-02T09:13:23Z","file_size":3497156,"access_level":"open_access","file_name":"2020_EMBO_Montesinos.pdf","file_id":"8827","checksum":"43d2b36598708e6ab05c69074e191d57","relation":"main_file","date_created":"2020-12-02T09:13:23Z","creator":"dernst"}],"publisher":"Embo Press","pmid":1,"ddc":["580"],"date_updated":"2023-09-05T13:05:47Z","publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"oa":1,"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","month":"09","article_number":"e104238","has_accepted_license":"1","department":[{"_id":"MiSi"},{"_id":"EvBe"}],"acknowledgement":"We thank Takashi Aoyama, David Alabadi, and Bert De Rybel for sharing material, Jiří Friml, Maciek Adamowski, and Katerina Schwarzerová for inspiring discussions, and Martine De Cock for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by the Bioimaging Facility (BIF), especially to Robert Hauschild; and the Life Science Facility (LSF). J.C.M. is the recipient of a EMBO Long‐Term Fellowship (ALTF number 710‐2016). This work was supported with MEYS CR, project no.CZ.02.1.01/0.0/0.0/16_019/0000738 to J.P., and by the Austrian Science Fund (FWF01_I1774S) to E.B.","quality_controlled":"1","_id":"8142","intvolume":"        39","doi":"10.15252/embj.2019104238","external_id":{"isi":["000548311800001"],"pmid":["32667089"]},"type":"journal_article","status":"public","title":"Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"citation":{"ista":"Montesinos López JC, Abuzeineh A, Kopf A, Juanes Garcia A, Ötvös K, Petrášek J, Sixt MK, Benková E. 2020. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. 39(17), e104238.","ieee":"J. C. Montesinos López <i>et al.</i>, “Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage,” <i>The Embo Journal</i>, vol. 39, no. 17. Embo Press, 2020.","chicago":"Montesinos López, Juan C, A Abuzeineh, Aglaja Kopf, Alba Juanes Garcia, Krisztina Ötvös, J Petrášek, Michael K Sixt, and Eva Benková. “Phytohormone Cytokinin Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated Stage.” <i>The Embo Journal</i>. Embo Press, 2020. <a href=\"https://doi.org/10.15252/embj.2019104238\">https://doi.org/10.15252/embj.2019104238</a>.","short":"J.C. Montesinos López, A. Abuzeineh, A. Kopf, A. Juanes Garcia, K. Ötvös, J. Petrášek, M.K. Sixt, E. Benková, The Embo Journal 39 (2020).","ama":"Montesinos López JC, Abuzeineh A, Kopf A, et al. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. <i>The Embo Journal</i>. 2020;39(17). doi:<a href=\"https://doi.org/10.15252/embj.2019104238\">10.15252/embj.2019104238</a>","apa":"Montesinos López, J. C., Abuzeineh, A., Kopf, A., Juanes Garcia, A., Ötvös, K., Petrášek, J., … Benková, E. (2020). Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. <i>The Embo Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2019104238\">https://doi.org/10.15252/embj.2019104238</a>","mla":"Montesinos López, Juan C., et al. “Phytohormone Cytokinin Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated Stage.” <i>The Embo Journal</i>, vol. 39, no. 17, e104238, Embo Press, 2020, doi:<a href=\"https://doi.org/10.15252/embj.2019104238\">10.15252/embj.2019104238</a>."},"article_processing_charge":"Yes (via OA deal)"},{"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"oa":1,"publication_status":"published","date_updated":"2023-09-07T13:13:27Z","ddc":["530","570"],"publication_identifier":{"issn":["2663-337X"]},"month":"07","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","id":"7675","relation":"part_of_dissertation"},{"status":"public","id":"7569","relation":"part_of_dissertation"},{"status":"public","id":"7652","relation":"part_of_dissertation"}]},"title":"Gene regulation across scales – how biophysical constraints shape evolution","type":"dissertation","status":"public","citation":{"mla":"Grah, Rok. <i>Gene Regulation across Scales – How Biophysical Constraints Shape Evolution</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8155\">10.15479/AT:ISTA:8155</a>.","apa":"Grah, R. (2020). <i>Gene regulation across scales – how biophysical constraints shape evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8155\">https://doi.org/10.15479/AT:ISTA:8155</a>","short":"R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.","ama":"Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8155\">10.15479/AT:ISTA:8155</a>","chicago":"Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8155\">https://doi.org/10.15479/AT:ISTA:8155</a>.","ieee":"R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020.","ista":"Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria."},"article_processing_charge":"No","acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","degree_awarded":"PhD","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"doi":"10.15479/AT:ISTA:8155","_id":"8155","page":"310","author":[{"first_name":"Rok","last_name":"Grah","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.\r\nIn the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are\r\nhard to evolve or maintain. ","lang":"eng"}],"date_published":"2020-07-24T00:00:00Z","file_date_updated":"2020-07-30T13:04:55Z","day":"24","year":"2020","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"publisher":"Institute of Science and Technology Austria","file":[{"success":1,"access_level":"open_access","file_size":16638998,"file_name":"Thesis_RokGrah_200727_convertedNew.pdf","content_type":"application/pdf","date_updated":"2020-07-27T12:00:07Z","relation":"main_file","date_created":"2020-07-27T12:00:07Z","creator":"rgrah","file_id":"8176"},{"file_id":"8177","relation":"main_file","creator":"rgrah","date_created":"2020-07-27T12:02:23Z","content_type":"application/zip","date_updated":"2020-07-30T13:04:55Z","file_size":347459978,"access_level":"closed","file_name":"Thesis_new.zip"}],"date_created":"2020-07-23T09:51:28Z","project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}]},{"day":"24","year":"2020","language":[{"iso":"eng"}],"author":[{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","full_name":"Avvakumov, Sergey","last_name":"Avvakumov","first_name":"Sergey"}],"abstract":[{"text":"We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry.","lang":"eng"}],"date_published":"2020-07-24T00:00:00Z","file_date_updated":"2020-07-27T12:46:53Z","date_created":"2020-07-23T09:51:29Z","supervisor":[{"orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_id":"8178","relation":"source_file","creator":"savvakum","date_created":"2020-07-27T12:44:51Z","content_type":"application/zip","date_updated":"2020-07-27T12:44:51Z","access_level":"closed","file_size":1061740,"file_name":"source.zip"},{"relation":"main_file","date_created":"2020-07-27T12:46:53Z","creator":"savvakum","file_id":"8179","access_level":"open_access","file_size":1336501,"file_name":"thesis_pdfa.pdf","content_type":"application/pdf","date_updated":"2020-07-27T12:46:53Z","success":1}],"publisher":"Institute of Science and Technology Austria","oa":1,"publication_status":"published","ddc":["514"],"date_updated":"2023-12-18T10:51:01Z","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","month":"07","related_material":{"record":[{"id":"8182","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"8183","status":"public"},{"status":"public","id":"8185","relation":"part_of_dissertation"},{"status":"public","id":"8184","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6355","status":"public"},{"id":"75","relation":"part_of_dissertation","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","department":[{"_id":"UlWa"}],"doi":"10.15479/AT:ISTA:8156","_id":"8156","page":"119","title":"Topological methods in geometry and discrete mathematics","type":"dissertation","status":"public","article_processing_charge":"No","citation":{"mla":"Avvakumov, Sergey. <i>Topological Methods in Geometry and Discrete Mathematics</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8156\">10.15479/AT:ISTA:8156</a>.","apa":"Avvakumov, S. (2020). <i>Topological methods in geometry and discrete mathematics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8156\">https://doi.org/10.15479/AT:ISTA:8156</a>","short":"S. Avvakumov, Topological Methods in Geometry and Discrete Mathematics, Institute of Science and Technology Austria, 2020.","chicago":"Avvakumov, Sergey. “Topological Methods in Geometry and Discrete Mathematics.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8156\">https://doi.org/10.15479/AT:ISTA:8156</a>.","ama":"Avvakumov S. Topological methods in geometry and discrete mathematics. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8156\">10.15479/AT:ISTA:8156</a>","ista":"Avvakumov S. 2020. Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria.","ieee":"S. Avvakumov, “Topological methods in geometry and discrete mathematics,” Institute of Science and Technology Austria, 2020."}},{"date_published":"2020-09-23T00:00:00Z","volume":107,"abstract":[{"lang":"eng","text":"In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity."}],"author":[{"last_name":"Laukoter","first_name":"Susanne","orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pauler","first_name":"Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian"},{"orcid":"0000-0002-8483-8753","last_name":"Beattie","first_name":"Robert J","full_name":"Beattie, Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","first_name":"Nicole","last_name":"Amberg"},{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H","last_name":"Hansen","first_name":"Andi H"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen"},{"full_name":"Penz, Thomas","last_name":"Penz","first_name":"Thomas"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph","orcid":"0000-0001-6091-3088"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"issue":"6","file_date_updated":"2020-12-02T09:26:46Z","ec_funded":1,"year":"2020","language":[{"iso":"eng"}],"day":"23","publication":"Neuron","scopus_import":"1","file":[{"success":1,"date_updated":"2020-12-02T09:26:46Z","content_type":"application/pdf","file_name":"2020_Neuron_Laukoter.pdf","access_level":"open_access","file_size":8911830,"file_id":"8828","date_created":"2020-12-02T09:26:46Z","creator":"dernst","relation":"main_file","checksum":"7becdc16a6317304304631087ae7dd7f"}],"publisher":"Elsevier","article_type":"original","date_created":"2020-07-23T16:03:12Z","project":[{"name":"Molecular Mechanisms of Radial Neuronal Migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812"},{"name":"Role of Eed in neural stem cell lineage progression","_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031","call_identifier":"FWF"},{"grant_number":"M02416","call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425"},{"_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","grant_number":"LS13-002"},{"grant_number":"RGP0053/2014","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425"},{"grant_number":"618444","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020"}],"has_accepted_license":"1","publication_identifier":{"issn":["0896-6273"]},"ddc":["570"],"date_updated":"2023-08-22T08:20:11Z","publication_status":"published","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/cells-react-differently-to-genomic-imprinting/"}]},"month":"09","oa_version":"Published Version","type":"journal_article","status":"public","title":"Cell-type specificity of genomic imprinting in cerebral cortex","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"isi":1,"article_processing_charge":"No","citation":{"ieee":"S. Laukoter <i>et al.</i>, “Cell-type specificity of genomic imprinting in cerebral cortex,” <i>Neuron</i>, vol. 107, no. 6. Elsevier, p. 1160–1179.e9, 2020.","ista":"Laukoter S, Pauler F, Beattie RJ, Amberg N, Hansen AH, Streicher C, Penz T, Bock C, Hippenmeyer S. 2020. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 107(6), 1160–1179.e9.","apa":"Laukoter, S., Pauler, F., Beattie, R. J., Amberg, N., Hansen, A. H., Streicher, C., … Hippenmeyer, S. (2020). Cell-type specificity of genomic imprinting in cerebral cortex. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.06.031\">https://doi.org/10.1016/j.neuron.2020.06.031</a>","mla":"Laukoter, Susanne, et al. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” <i>Neuron</i>, vol. 107, no. 6, Elsevier, 2020, p. 1160–1179.e9, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.06.031\">10.1016/j.neuron.2020.06.031</a>.","short":"S. Laukoter, F. Pauler, R.J. Beattie, N. Amberg, A.H. Hansen, C. Streicher, T. Penz, C. Bock, S. Hippenmeyer, Neuron 107 (2020) 1160–1179.e9.","ama":"Laukoter S, Pauler F, Beattie RJ, et al. Cell-type specificity of genomic imprinting in cerebral cortex. <i>Neuron</i>. 2020;107(6):1160-1179.e9. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.06.031\">10.1016/j.neuron.2020.06.031</a>","chicago":"Laukoter, Susanne, Florian Pauler, Robert J Beattie, Nicole Amberg, Andi H Hansen, Carmen Streicher, Thomas Penz, Christoph Bock, and Simon Hippenmeyer. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2020.06.031\">https://doi.org/10.1016/j.neuron.2020.06.031</a>."},"department":[{"_id":"SiHi"}],"quality_controlled":"1","acknowledgement":"We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), and A. Seitz and P. Moll (Lexogen GmbH) for technical support; G. Arque, S. Resch, C. Igler, C. Dotter, C. Yahya, Q. Hudson, and D. Andergassen for initial experiments and/or assistance; D. Barlow, O. Bell, and all members of the Hippenmeyer lab for discussion; and N. Barton, B. Vicoso, M. Sixt, and L. Luo for comments on earlier versions of the manuscript. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facilities (BIF), Life Science Facilities (LSF), and Preclinical Facilities (PCF). A.H.H. is a recipient of a DOC fellowship (24812) of the Austrian Academy of Sciences. N.A. received support from the FWF Firnberg-Programm (T 1031). R.B. received support from the FWF Meitner-Programm (M 2416). This work was also supported by IST Austria institutional funds; a NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; a program grant from the Human Frontiers Science Program (RGP0053/2014) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H.","intvolume":"       107","_id":"8162","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","page":"1160-1179.e9","external_id":{"isi":["000579698700006"]},"doi":"10.1016/j.neuron.2020.06.031"},{"quality_controlled":"1","acknowledgement":"The authors are greatly indebted to Dror Atariah, Günther Rote and John Sullivan for discussion and suggestions. The authors also thank Jean-Daniel Boissonnat, Ramsay Dyer, David de Laat and Rien van de Weijgaert for discussion. This work has been supported in part by the European Union’s Seventh Framework Programme for Research of the\r\nEuropean Commission, under FET-Open grant number 255827 (CGL Computational Geometry Learning) and ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions), the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement number 754411,and the Austrian Science Fund (FWF): Z00342 N31.","department":[{"_id":"HeEd"}],"external_id":{"isi":["000570978400005"]},"doi":"10.1556/012.2020.57.2.1454","intvolume":"        57","page":"193-199","license":"https://creativecommons.org/licenses/by-nc/4.0/","_id":"8163","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"title":"Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes","status":"public","type":"journal_article","article_processing_charge":"No","citation":{"apa":"Vegter, G., &#38; Wintraecken, M. (2020). Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. <i>Studia Scientiarum Mathematicarum Hungarica</i>. Akadémiai Kiadó. <a href=\"https://doi.org/10.1556/012.2020.57.2.1454\">https://doi.org/10.1556/012.2020.57.2.1454</a>","mla":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” <i>Studia Scientiarum Mathematicarum Hungarica</i>, vol. 57, no. 2, Akadémiai Kiadó, 2020, pp. 193–99, doi:<a href=\"https://doi.org/10.1556/012.2020.57.2.1454\">10.1556/012.2020.57.2.1454</a>.","ama":"Vegter G, Wintraecken M. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. <i>Studia Scientiarum Mathematicarum Hungarica</i>. 2020;57(2):193-199. doi:<a href=\"https://doi.org/10.1556/012.2020.57.2.1454\">10.1556/012.2020.57.2.1454</a>","chicago":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” <i>Studia Scientiarum Mathematicarum Hungarica</i>. Akadémiai Kiadó, 2020. <a href=\"https://doi.org/10.1556/012.2020.57.2.1454\">https://doi.org/10.1556/012.2020.57.2.1454</a>.","short":"G. Vegter, M. Wintraecken, Studia Scientiarum Mathematicarum Hungarica 57 (2020) 193–199.","ieee":"G. Vegter and M. Wintraecken, “Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes,” <i>Studia Scientiarum Mathematicarum Hungarica</i>, vol. 57, no. 2. Akadémiai Kiadó, pp. 193–199, 2020.","ista":"Vegter G, Wintraecken M. 2020. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 57(2), 193–199."},"isi":1,"oa":1,"publication_status":"published","publication_identifier":{"issn":["0081-6906"],"eissn":["1588-2896"]},"ddc":["510"],"date_updated":"2023-10-10T13:05:27Z","month":"07","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","article_type":"original","date_created":"2020-07-24T07:09:18Z","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"call_identifier":"FWF","grant_number":"Z00342","name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","publisher":"Akadémiai Kiadó","file":[{"date_created":"2020-07-24T07:09:06Z","creator":"mwintrae","relation":"main_file","file_id":"8164","file_name":"57-2-05_4214-1454Vegter-Wintraecken_OpenAccess_CC-BY-NC.pdf","access_level":"open_access","file_size":1476072,"date_updated":"2020-07-24T07:09:06Z","content_type":"application/pdf"}],"ec_funded":1,"publication":"Studia Scientiarum Mathematicarum Hungarica","year":"2020","language":[{"iso":"eng"}],"day":"24","author":[{"first_name":"Gert","last_name":"Vegter","full_name":"Vegter, Gert"},{"full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","first_name":"Mathijs","orcid":"0000-0002-7472-2220"}],"date_published":"2020-07-24T00:00:00Z","abstract":[{"lang":"eng","text":"Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces."}],"volume":57,"file_date_updated":"2020-07-24T07:09:06Z","issue":"2"},{"status":"public","type":"journal_article","title":"The evolution of strong reproductive isolation between sympatric intertidal snails","isi":1,"article_processing_charge":"No","citation":{"mla":"Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806, 20190545, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rstb.2019.0545\">10.1098/rstb.2019.0545</a>.","apa":"Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T., Johannesson, K., &#38; Butlin, R. K. (2020). The evolution of strong reproductive isolation between sympatric intertidal snails. <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2019.0545\">https://doi.org/10.1098/rstb.2019.0545</a>","short":"S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson, R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ama":"Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive isolation between sympatric intertidal snails. <i>Philosophical Transactions of the Royal Society Series B: Biological Sciences</i>. 2020;375(1806). doi:<a href=\"https://doi.org/10.1098/rstb.2019.0545\">10.1098/rstb.2019.0545</a>","chicago":"Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres, Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rstb.2019.0545\">https://doi.org/10.1098/rstb.2019.0545</a>.","ista":"Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190545.","ieee":"S. Stankowski <i>et al.</i>, “The evolution of strong reproductive isolation between sympatric intertidal snails,” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806. The Royal Society, 2020."},"department":[{"_id":"NiBa"}],"quality_controlled":"1","acknowledgement":"Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin Garlovsky and Hernan Morales for advice and/or useful discussion during the project. Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton participated in the collection and processing of samples. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and an anonymous reviewer provided comments that improved the manuscript.","intvolume":"       375","_id":"8167","external_id":{"isi":["000552662100014"],"pmid":["32654639"]},"doi":"10.1098/rstb.2019.0545","article_number":"20190545","publication_identifier":{"eissn":["1471-2970"]},"date_updated":"2023-08-22T08:22:13Z","oa":1,"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"07","oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1098/rstb.2019.0545","open_access":"1"}],"pmid":1,"publisher":"The Royal Society","article_type":"original","date_created":"2020-07-26T22:01:01Z","date_published":"2020-07-12T00:00:00Z","volume":375,"abstract":[{"lang":"eng","text":"The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions."}],"author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean"},{"orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zagrodzka, Zuzanna B.","first_name":"Zuzanna B.","last_name":"Zagrodzka"},{"last_name":"Eyres","first_name":"Isobel","full_name":"Eyres, Isobel"},{"last_name":"Broquet","first_name":"Thomas","full_name":"Broquet, Thomas"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"issue":"1806","year":"2020","language":[{"iso":"eng"}],"day":"12","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences"},{"publication_status":"published","oa":1,"publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"date_updated":"2023-08-22T08:21:31Z","month":"07","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"20190528","quality_controlled":"1","department":[{"_id":"NiBa"}],"external_id":{"isi":["000552662100001"],"pmid":["32654637"]},"doi":"10.1098/rstb.2019.0528","intvolume":"       375","_id":"8168","title":"Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers","status":"public","type":"journal_article","article_processing_charge":"No","citation":{"ieee":"J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers,” <i>Philosophical Transactions of the Royal Society. Series B: Biological sciences</i>, vol. 375, no. 1806. The Royal Society, 2020.","ista":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological sciences. 375(1806), 20190528.","short":"J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ama":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. <i>Philosophical Transactions of the Royal Society Series B: Biological sciences</i>. 2020;375(1806). doi:<a href=\"https://doi.org/10.1098/rstb.2019.0528\">10.1098/rstb.2019.0528</a>","chicago":"Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rstb.2019.0528\">https://doi.org/10.1098/rstb.2019.0528</a>.","mla":"Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806, 20190528, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rstb.2019.0528\">10.1098/rstb.2019.0528</a>.","apa":"Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., &#38; Westram, A. M. (2020). Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2019.0528\">https://doi.org/10.1098/rstb.2019.0528</a>"},"isi":1,"ec_funded":1,"publication":"Philosophical Transactions of the Royal Society. Series B: Biological sciences","year":"2020","language":[{"iso":"eng"}],"day":"12","author":[{"first_name":"Jonna","last_name":"Kulmuni","full_name":"Kulmuni, Jonna"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"last_name":"Lucek","first_name":"Kay","full_name":"Lucek, Kay"},{"first_name":"Vincent","last_name":"Savolainen","full_name":"Savolainen, Vincent"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969"}],"date_published":"2020-07-12T00:00:00Z","abstract":[{"lang":"eng","text":"Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed."}],"volume":375,"issue":"1806","article_type":"original","project":[{"grant_number":"797747","call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-07-26T22:01:01Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rstb.2019.0528"}],"pmid":1,"publisher":"The Royal Society"},{"author":[{"last_name":"Chatterley","first_name":"Adam S.","full_name":"Chatterley, Adam S."},{"last_name":"Christiansen","first_name":"Lars","full_name":"Christiansen, Lars"},{"first_name":"Constant A.","last_name":"Schouder","full_name":"Schouder, Constant A."},{"full_name":"Jørgensen, Anders V.","first_name":"Anders V.","last_name":"Jørgensen"},{"last_name":"Shepperson","first_name":"Benjamin","full_name":"Shepperson, Benjamin"},{"id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","full_name":"Cherepanov, Igor","last_name":"Cherepanov","first_name":"Igor"},{"full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","first_name":"Giacomo","last_name":"Bighin"},{"full_name":"Zillich, Robert E.","first_name":"Robert E.","last_name":"Zillich"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"last_name":"Stapelfeldt","first_name":"Henrik","full_name":"Stapelfeldt, Henrik"}],"date_published":"2020-07-03T00:00:00Z","abstract":[{"text":"Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function\r\nof time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct\r\npeaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and\r\ncentrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For\r\nCS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the\r\ngas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in\r\ndetail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in\r\nhelium droplets introduced here should apply to a range of molecules and complexes.","lang":"eng"}],"volume":125,"issue":"1","ec_funded":1,"publication":"Physical Review Letters","language":[{"iso":"eng"}],"year":"2020","day":"03","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2006.02694"}],"publisher":"American Physical Society","date_created":"2020-07-26T22:01:02Z","project":[{"call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020"},{"grant_number":"M02641","call_identifier":"FWF","name":"A path-integral approach to composite impurities","_id":"26986C82-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"article_type":"original","article_number":"013001","arxiv":1,"publication_status":"published","oa":1,"publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"date_updated":"2024-08-07T07:16:52Z","month":"07","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains","type":"journal_article","status":"public","article_processing_charge":"No","citation":{"ista":"Chatterley AS, Christiansen L, Schouder CA, Jørgensen AV, Shepperson B, Cherepanov I, Bighin G, Zillich RE, Lemeshko M, Stapelfeldt H. 2020. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 125(1), 013001.","ieee":"A. S. Chatterley <i>et al.</i>, “Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains,” <i>Physical Review Letters</i>, vol. 125, no. 1. American Physical Society, 2020.","chicago":"Chatterley, Adam S., Lars Christiansen, Constant A. Schouder, Anders V. Jørgensen, Benjamin Shepperson, Igor Cherepanov, Giacomo Bighin, Robert E. Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” <i>Physical Review Letters</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">https://doi.org/10.1103/PhysRevLett.125.013001</a>.","ama":"Chatterley AS, Christiansen L, Schouder CA, et al. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. <i>Physical Review Letters</i>. 2020;125(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">10.1103/PhysRevLett.125.013001</a>","short":"A.S. Chatterley, L. Christiansen, C.A. Schouder, A.V. Jørgensen, B. Shepperson, I. Cherepanov, G. Bighin, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 125 (2020).","apa":"Chatterley, A. S., Christiansen, L., Schouder, C. A., Jørgensen, A. V., Shepperson, B., Cherepanov, I., … Stapelfeldt, H. (2020). Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">https://doi.org/10.1103/PhysRevLett.125.013001</a>","mla":"Chatterley, Adam S., et al. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” <i>Physical Review Letters</i>, vol. 125, no. 1, 013001, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">10.1103/PhysRevLett.125.013001</a>."},"isi":1,"quality_controlled":"1","acknowledgement":"H. S. acknowledges support from the European Research Council-AdG (Project No. 320459, DropletControl)\r\nand from The Villum Foundation through a Villum Investigator Grant No. 25886. M. L. acknowledges support\r\nby the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council\r\n(ERC) Starting Grant No. 801770 (ANGULON). G. B. acknowledges support from the Austrian Science Fund\r\n(FWF), under Project No. M2641-N27. I. C. acknowledges support by the European Union’s Horizon 2020 research and\r\ninnovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Computational resources for\r\nthe PIMC simulations were provided by the division for scientific computing at the Johannes Kepler University.","department":[{"_id":"MiLe"}],"external_id":{"arxiv":["2006.02694"],"isi":["000544526900006"]},"doi":"10.1103/PhysRevLett.125.013001","intvolume":"       125","_id":"8170"},{"file_date_updated":"2020-08-24T15:43:52Z","has_accepted_license":"1","date_published":"2020-08-24T00:00:00Z","author":[{"orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"}],"day":"24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","month":"08","date_updated":"2021-01-11T15:29:08Z","oa":1,"file":[{"success":1,"file_id":"8290","creator":"rhauschild","date_created":"2020-08-24T15:43:49Z","checksum":"878c60885ce30afb59a884dd5eef451c","relation":"main_file","date_updated":"2020-08-24T15:43:49Z","content_type":"text/plain","file_name":"centriolesDistance.m","file_size":6577,"access_level":"open_access"},{"content_type":"text/plain","date_updated":"2020-08-24T15:43:52Z","access_level":"open_access","file_size":2680,"file_name":"goTracking.m","file_id":"8291","relation":"main_file","checksum":"5a93ac7be2b66b28e4bd8b113ee6aade","creator":"rhauschild","date_created":"2020-08-24T15:43:52Z","success":1}],"publisher":"IST Austria","citation":{"apa":"Hauschild, R. (2020). Amplified centrosomes in dendritic cells promote immune cell effector functions. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">https://doi.org/10.15479/AT:ISTA:8181</a>","mla":"Hauschild, Robert. <i>Amplified Centrosomes in Dendritic Cells Promote Immune Cell Effector Functions</i>. IST Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>.","chicago":"Hauschild, Robert. “Amplified Centrosomes in Dendritic Cells Promote Immune Cell Effector Functions.” IST Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">https://doi.org/10.15479/AT:ISTA:8181</a>.","short":"R. Hauschild, (2020).","ama":"Hauschild R. Amplified centrosomes in dendritic cells promote immune cell effector functions. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>","ieee":"R. Hauschild, “Amplified centrosomes in dendritic cells promote immune cell effector functions.” IST Austria, 2020.","ista":"Hauschild R. 2020. Amplified centrosomes in dendritic cells promote immune cell effector functions, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>."},"status":"public","type":"software","title":"Amplified centrosomes in dendritic cells promote immune cell effector functions","tmp":{"name":"The 3-Clause BSD License","legal_code_url":"https://opensource.org/licenses/BSD-3-Clause","short":"3-Clause BSD"},"license":"https://opensource.org/licenses/BSD-3-Clause","_id":"8181","date_created":"2020-07-28T16:24:37Z","doi":"10.15479/AT:ISTA:8181","department":[{"_id":"Bio"}]},{"_id":"8186","page":"7498-7507","external_id":{"arxiv":["2004.04180"]},"doi":"10.1109/CVPR42600.2020.00752","department":[{"_id":"ChLa"}],"quality_controlled":"1","citation":{"ieee":"P. M. Henderson, V. Tsiminaki, and C. Lampert, “Leveraging 2D data to learn textured 3D mesh generation,” in <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Virtual, 2020, pp. 7498–7507.","ista":"Henderson PM, Tsiminaki V, Lampert C. 2020. Leveraging 2D data to learn textured 3D mesh generation. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 7498–7507.","apa":"Henderson, P. M., Tsiminaki, V., &#38; Lampert, C. (2020). Leveraging 2D data to learn textured 3D mesh generation. In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 7498–7507). Virtual: IEEE. <a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">https://doi.org/10.1109/CVPR42600.2020.00752</a>","mla":"Henderson, Paul M., et al. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2020, pp. 7498–507, doi:<a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">10.1109/CVPR42600.2020.00752</a>.","chicago":"Henderson, Paul M, Vagia Tsiminaki, and Christoph Lampert. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 7498–7507. IEEE, 2020. <a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">https://doi.org/10.1109/CVPR42600.2020.00752</a>.","short":"P.M. Henderson, V. Tsiminaki, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–7507.","ama":"Henderson PM, Tsiminaki V, Lampert C. Leveraging 2D data to learn textured 3D mesh generation. In: <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2020:7498-7507. doi:<a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">10.1109/CVPR42600.2020.00752</a>"},"article_processing_charge":"No","type":"conference","status":"public","title":"Leveraging 2D data to learn textured 3D mesh generation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","oa_version":"Submitted Version","publication_identifier":{"eissn":["2575-7075"],"eisbn":["9781728171685"]},"ddc":["004"],"date_updated":"2023-10-17T07:37:11Z","conference":{"end_date":"2020-06-19","name":"CVPR: Conference on Computer Vision and Pattern Recognition","start_date":"2020-06-14","location":"Virtual"},"oa":1,"publication_status":"published","arxiv":1,"has_accepted_license":"1","date_created":"2020-07-31T16:53:49Z","main_file_link":[{"open_access":"1","url":"https://openaccess.thecvf.com/content_CVPR_2020/papers/Henderson_Leveraging_2D_Data_to_Learn_Textured_3D_Mesh_Generation_CVPR_2020_paper.pdf"}],"file":[{"file_name":"paper.pdf","access_level":"open_access","file_size":10262773,"date_updated":"2020-07-31T16:57:12Z","content_type":"application/pdf","creator":"phenders","date_created":"2020-07-31T16:57:12Z","relation":"main_file","file_id":"8187","success":1}],"publisher":"IEEE","scopus_import":"1","language":[{"iso":"eng"}],"year":"2020","day":"01","publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","file_date_updated":"2020-07-31T16:57:12Z","date_published":"2020-07-01T00:00:00Z","abstract":[{"text":"Numerous methods have been proposed for probabilistic generative modelling of\r\n3D objects. However, none of these is able to produce textured objects, which\r\nrenders them of limited use for practical tasks. In this work, we present the\r\nfirst generative model of textured 3D meshes. Training such a model would\r\ntraditionally require a large dataset of textured meshes, but unfortunately,\r\nexisting datasets of meshes lack detailed textures. We instead propose a new\r\ntraining methodology that allows learning from collections of 2D images without\r\nany 3D information. To do so, we train our model to explain a distribution of\r\nimages by modelling each image as a 3D foreground object placed in front of a\r\n2D background. Thus, it learns to generate meshes that when rendered, produce\r\nimages similar to those in its training set.\r\n  A well-known problem when generating meshes with deep networks is the\r\nemergence of self-intersections, which are problematic for many use-cases. As a\r\nsecond contribution we therefore introduce a new generation process for 3D\r\nmeshes that guarantees no self-intersections arise, based on the physical\r\nintuition that faces should push one another out of the way as they move.\r\n  We conduct extensive experiments on our approach, reporting quantitative and\r\nqualitative results on both synthetic data and natural images. These show our\r\nmethod successfully learns to generate plausible and diverse textured 3D\r\nsamples for five challenging object classes.","lang":"eng"}],"author":[{"full_name":"Henderson, Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425","first_name":"Paul M","last_name":"Henderson","orcid":"0000-0002-5198-7445"},{"full_name":"Tsiminaki, Vagia","first_name":"Vagia","last_name":"Tsiminaki"},{"orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}]},{"language":[{"iso":"eng"}],"year":"2020","day":"07","publication":"34th Conference on Neural Information Processing Systems","date_published":"2020-07-07T00:00:00Z","volume":33,"abstract":[{"text":"A natural approach to generative modeling of videos is to represent them as a composition of moving objects. Recent works model a set of 2D sprites over a slowly-varying background, but without considering the underlying 3D scene that\r\ngives rise to them. We instead propose to model a video as the view seen while moving through a scene with multiple 3D objects and a 3D background. Our model is trained from monocular videos without any supervision, yet learns to\r\ngenerate coherent 3D scenes containing several moving objects. We conduct detailed experiments on two datasets, going beyond the visual complexity supported by state-of-the-art generative approaches. We evaluate our method on\r\ndepth-prediction and 3D object detection---tasks which cannot be addressed by those earlier works---and show it out-performs them even on 2D instance segmentation and tracking.","lang":"eng"}],"author":[{"orcid":"0000-0002-5198-7445","first_name":"Paul M","last_name":"Henderson","full_name":"Henderson, Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-07-31T16:59:19Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.06705"}],"publisher":"Curran Associates","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"07","publication_identifier":{"isbn":["9781713829546"]},"date_updated":"2023-04-25T09:49:58Z","conference":{"location":"Vancouver, Canada","start_date":"2020-12-06","end_date":"2020-12-12","name":"NeurIPS: Neural Information Processing Systems"},"publication_status":"published","oa":1,"arxiv":1,"intvolume":"        33","_id":"8188","page":"3106–3117","external_id":{"arxiv":["2007.06705"]},"department":[{"_id":"ChLa"}],"quality_controlled":"1","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources\r\nprovided by Scientific Computing (SciComp). PH is employed part-time by Blackford Analysis, but\r\nthey did not support this project in any way.","acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"mla":"Henderson, Paul M., and Christoph Lampert. “Unsupervised Object-Centric Video Generation and Decomposition in 3D.” <i>34th Conference on Neural Information Processing Systems</i>, vol. 33, Curran Associates, 2020, pp. 3106–3117.","apa":"Henderson, P. M., &#38; Lampert, C. (2020). Unsupervised object-centric video generation and decomposition in 3D. In <i>34th Conference on Neural Information Processing Systems</i> (Vol. 33, pp. 3106–3117). Vancouver, Canada: Curran Associates.","short":"P.M. Henderson, C. Lampert, in:, 34th Conference on Neural Information Processing Systems, Curran Associates, 2020, pp. 3106–3117.","ama":"Henderson PM, Lampert C. Unsupervised object-centric video generation and decomposition in 3D. In: <i>34th Conference on Neural Information Processing Systems</i>. Vol 33. Curran Associates; 2020:3106–3117.","chicago":"Henderson, Paul M, and Christoph Lampert. “Unsupervised Object-Centric Video Generation and Decomposition in 3D.” In <i>34th Conference on Neural Information Processing Systems</i>, 33:3106–3117. Curran Associates, 2020.","ieee":"P. M. Henderson and C. Lampert, “Unsupervised object-centric video generation and decomposition in 3D,” in <i>34th Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2020, vol. 33, pp. 3106–3117.","ista":"Henderson PM, Lampert C. 2020. Unsupervised object-centric video generation and decomposition in 3D. 34th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 33, 3106–3117."},"article_processing_charge":"No","type":"conference","status":"public","title":"Unsupervised object-centric video generation and decomposition in 3D"},{"doi":"10.1083/jcb.202007029","external_id":{"isi":["000573631000004"]},"_id":"8190","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","intvolume":"       219","department":[{"_id":"MiSi"}],"citation":{"ista":"Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029.","ieee":"M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,” <i>The Journal of Cell Biology</i>, vol. 219, no. 8. Rockefeller University Press, 2020.","mla":"Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” <i>The Journal of Cell Biology</i>, vol. 219, no. 8, e202007029, Rockefeller University Press, 2020, doi:<a href=\"https://doi.org/10.1083/jcb.202007029\">10.1083/jcb.202007029</a>.","apa":"Sixt, M. K., &#38; Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology in context. <i>The Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202007029\">https://doi.org/10.1083/jcb.202007029</a>","short":"M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020).","ama":"Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. <i>The Journal of Cell Biology</i>. 2020;219(8). doi:<a href=\"https://doi.org/10.1083/jcb.202007029\">10.1083/jcb.202007029</a>","chicago":"Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” <i>The Journal of Cell Biology</i>. Rockefeller University Press, 2020. <a href=\"https://doi.org/10.1083/jcb.202007029\">https://doi.org/10.1083/jcb.202007029</a>."},"article_processing_charge":"No","isi":1,"title":"Zena Werb (1945-2020): Cell biology in context","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"type":"journal_article","status":"public","oa_version":"Published Version","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"date_updated":"2023-10-17T10:04:49Z","ddc":["570"],"publication_identifier":{"eissn":["1540-8140"]},"has_accepted_license":"1","article_number":"e202007029","date_created":"2020-08-02T22:00:57Z","article_type":"letter_note","file":[{"file_id":"8200","date_created":"2020-08-04T13:11:52Z","creator":"dernst","relation":"main_file","checksum":"30016d778d266b8e17d01094917873b8","date_updated":"2021-02-02T23:30:03Z","content_type":"application/pdf","file_name":"2020_JCB_Sixt.pdf","access_level":"open_access","file_size":830725,"embargo":"2021-02-01"}],"publisher":"Rockefeller University Press","scopus_import":"1","publication":"The Journal of Cell Biology","day":"22","year":"2020","language":[{"iso":"eng"}],"file_date_updated":"2021-02-02T23:30:03Z","issue":"8","author":[{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179"},{"full_name":"Huttenlocher, Anna","last_name":"Huttenlocher","first_name":"Anna"}],"volume":219,"date_published":"2020-07-22T00:00:00Z"},{"external_id":{"isi":["000884318000002"]},"doi":"10.1007/978-3-030-51074-9_2","intvolume":"     12166","_id":"8194","page":"13-31","quality_controlled":"1","department":[{"_id":"ToHe"}],"article_processing_charge":"No","citation":{"ista":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. 2020. An SMT theory of fixed-point arithmetic. Automated Reasoning. IJCAR: International Joint Conference on Automated Reasoning, LNCS, vol. 12166, 13–31.","ieee":"M. Baranowski, S. He, M. Lechner, T. S. Nguyen, and Z. Rakamarić, “An SMT theory of fixed-point arithmetic,” in <i>Automated Reasoning</i>, Paris, France, 2020, vol. 12166, pp. 13–31.","short":"M. Baranowski, S. He, M. Lechner, T.S. Nguyen, Z. Rakamarić, in:, Automated Reasoning, Springer Nature, 2020, pp. 13–31.","chicago":"Baranowski, Marek, Shaobo He, Mathias Lechner, Thanh Son Nguyen, and Zvonimir Rakamarić. “An SMT Theory of Fixed-Point Arithmetic.” In <i>Automated Reasoning</i>, 12166:13–31. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">https://doi.org/10.1007/978-3-030-51074-9_2</a>.","ama":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. An SMT theory of fixed-point arithmetic. In: <i>Automated Reasoning</i>. Vol 12166. Springer Nature; 2020:13-31. doi:<a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">10.1007/978-3-030-51074-9_2</a>","mla":"Baranowski, Marek, et al. “An SMT Theory of Fixed-Point Arithmetic.” <i>Automated Reasoning</i>, vol. 12166, Springer Nature, 2020, pp. 13–31, doi:<a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">10.1007/978-3-030-51074-9_2</a>.","apa":"Baranowski, M., He, S., Lechner, M., Nguyen, T. S., &#38; Rakamarić, Z. (2020). An SMT theory of fixed-point arithmetic. In <i>Automated Reasoning</i> (Vol. 12166, pp. 13–31). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">https://doi.org/10.1007/978-3-030-51074-9_2</a>"},"isi":1,"title":"An SMT theory of fixed-point arithmetic","status":"public","type":"conference","oa_version":"Published Version","month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","conference":{"end_date":"2020-07-04","name":"IJCAR: International Joint Conference on Automated Reasoning","start_date":"2020-07-01","location":"Paris, France"},"publication_status":"published","oa":1,"publication_identifier":{"issn":["03029743"],"eissn":["16113349"],"isbn":["9783030510732"]},"date_updated":"2023-08-22T08:27:25Z","alternative_title":["LNCS"],"project":[{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"}],"date_created":"2020-08-02T22:00:59Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-030-51074-9_2"}],"publisher":"Springer Nature","scopus_import":"1","publication":"Automated Reasoning","language":[{"iso":"eng"}],"year":"2020","day":"24","author":[{"full_name":"Baranowski, Marek","last_name":"Baranowski","first_name":"Marek"},{"first_name":"Shaobo","last_name":"He","full_name":"He, Shaobo"},{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner"},{"full_name":"Nguyen, Thanh Son","first_name":"Thanh Son","last_name":"Nguyen"},{"full_name":"Rakamarić, Zvonimir","first_name":"Zvonimir","last_name":"Rakamarić"}],"date_published":"2020-06-24T00:00:00Z","abstract":[{"lang":"eng","text":"Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks."}],"volume":12166},{"project":[{"call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-08-03T11:45:35Z","scopus_import":"1","publisher":"Springer Nature","file":[{"file_id":"8201","date_created":"2020-08-06T08:14:54Z","creator":"dernst","relation":"main_file","date_updated":"2020-08-06T08:14:54Z","content_type":"application/pdf","file_name":"2020_LNCS_Kragl.pdf","file_size":804237,"access_level":"open_access","success":1}],"year":"2020","language":[{"iso":"eng"}],"day":"14","publication":"Computer Aided Verification","date_published":"2020-07-14T00:00:00Z","abstract":[{"text":"This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier.","lang":"eng"}],"volume":12224,"author":[{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl","first_name":"Bernhard"},{"first_name":"Shaz","last_name":"Qadeer","full_name":"Qadeer, Shaz"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-08-06T08:14:54Z","department":[{"_id":"ToHe"}],"quality_controlled":"1","acknowledgement":"Bernhard Kragl and Thomas A. Henzinger were supported by\r\nthe Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","intvolume":"     12224","_id":"8195","page":"275-298","external_id":{"isi":["000695276000014"]},"doi":"10.1007/978-3-030-53288-8_14","type":"conference","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Refinement for structured concurrent programs","isi":1,"citation":{"ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Refinement for structured concurrent programs,” in <i>Computer Aided Verification</i>, 2020, vol. 12224, pp. 275–298.","ista":"Kragl B, Qadeer S, Henzinger TA. 2020. Refinement for structured concurrent programs. Computer Aided Verification. , LNCS, vol. 12224, 275–298.","ama":"Kragl B, Qadeer S, Henzinger TA. Refinement for structured concurrent programs. In: <i>Computer Aided Verification</i>. Vol 12224. Springer Nature; 2020:275-298. doi:<a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">10.1007/978-3-030-53288-8_14</a>","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Computer Aided Verification, Springer Nature, 2020, pp. 275–298.","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Refinement for Structured Concurrent Programs.” In <i>Computer Aided Verification</i>, 12224:275–98. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">https://doi.org/10.1007/978-3-030-53288-8_14</a>.","mla":"Kragl, Bernhard, et al. “Refinement for Structured Concurrent Programs.” <i>Computer Aided Verification</i>, vol. 12224, Springer Nature, 2020, pp. 275–98, doi:<a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">10.1007/978-3-030-53288-8_14</a>.","apa":"Kragl, B., Qadeer, S., &#38; Henzinger, T. A. (2020). Refinement for structured concurrent programs. In <i>Computer Aided Verification</i> (Vol. 12224, pp. 275–298). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">https://doi.org/10.1007/978-3-030-53288-8_14</a>"},"article_processing_charge":"No","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030532871"],"issn":["0302-9743"],"eisbn":["9783030532888"]},"date_updated":"2023-09-07T13:18:00Z","ddc":["000"],"oa":1,"publication_status":"published","related_material":{"record":[{"status":"public","id":"8332","relation":"dissertation_contains"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","month":"07","alternative_title":["LNCS"],"has_accepted_license":"1"},{"publication_identifier":{"issn":["2542-4653"]},"date_updated":"2023-08-22T08:28:24Z","ddc":["530"],"oa":1,"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","month":"07","article_number":"015","has_accepted_license":"1","department":[{"_id":"MaSe"}],"quality_controlled":"1","acknowledgement":"N.L., T.G. and E.B. acknowledge support from the European Research Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme (Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411. N.L. acknowledges support from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence (I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12). M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC) under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B. acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft","intvolume":"         9","_id":"8199","external_id":{"isi":["000557362300008"]},"doi":"10.21468/scipostphys.9.1.015","type":"journal_article","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps","isi":1,"citation":{"chicago":"Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” <i>SciPost Physics</i>. SciPost Foundation, 2020. <a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">https://doi.org/10.21468/scipostphys.9.1.015</a>.","short":"T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020).","ama":"Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. <i>SciPost Physics</i>. 2020;9. doi:<a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">10.21468/scipostphys.9.1.015</a>","apa":"Gulden, T., Berg, E., Rudner, M. S., &#38; Lindner, N. (2020). Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">https://doi.org/10.21468/scipostphys.9.1.015</a>","mla":"Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” <i>SciPost Physics</i>, vol. 9, 015, SciPost Foundation, 2020, doi:<a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">10.21468/scipostphys.9.1.015</a>.","ista":"Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 9, 015.","ieee":"T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps,” <i>SciPost Physics</i>, vol. 9. SciPost Foundation, 2020."},"article_processing_charge":"No","ec_funded":1,"language":[{"iso":"eng"}],"year":"2020","day":"29","publication":"SciPost Physics","date_published":"2020-07-29T00:00:00Z","volume":9,"abstract":[{"text":"We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist.","lang":"eng"}],"author":[{"full_name":"Gulden, Tobias","id":"1083E038-9F73-11E9-A4B5-532AE6697425","first_name":"Tobias","last_name":"Gulden","orcid":"0000-0001-6814-7541"},{"full_name":"Berg, Erez","last_name":"Berg","first_name":"Erez"},{"full_name":"Rudner, Mark Spencer","last_name":"Rudner","first_name":"Mark Spencer"},{"last_name":"Lindner","first_name":"Netanel","full_name":"Lindner, Netanel"}],"file_date_updated":"2020-08-06T08:56:06Z","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"date_created":"2020-08-04T13:04:15Z","article_type":"original","scopus_import":"1","publisher":"SciPost Foundation","file":[{"relation":"main_file","creator":"dernst","date_created":"2020-08-06T08:56:06Z","file_id":"8202","file_size":531137,"access_level":"open_access","file_name":"2020_SciPostPhys_Gulden.pdf","content_type":"application/pdf","date_updated":"2020-08-06T08:56:06Z","success":1}]},{"file":[{"access_level":"open_access","file_size":3308906,"file_name":"2020_NanoLetters_Katsaros.pdf","content_type":"application/pdf","date_updated":"2020-08-06T09:35:37Z","relation":"main_file","date_created":"2020-08-06T09:35:37Z","creator":"dernst","file_id":"8204","success":1}],"publisher":"American Chemical Society","pmid":1,"scopus_import":"1","article_type":"original","project":[{"grant_number":"P32235","call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"862046","call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"}],"date_created":"2020-08-06T09:25:04Z","issue":"7","file_date_updated":"2020-08-06T09:35:37Z","volume":20,"abstract":[{"lang":"eng","text":"Using inelastic cotunneling spectroscopy we observe a zero field splitting within the spin triplet manifold of Ge hut wire quantum dots. The states with spin ±1 in the confinement direction are energetically favored by up to 55 μeV compared to the spin 0 triplet state because of the strong spin–orbit coupling. The reported effect should be observable in a broad class of strongly confined hole quantum-dot systems and might need to be considered when operating hole spin qubits."}],"date_published":"2020-06-01T00:00:00Z","author":[{"orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kukucka","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip"},{"first_name":"Lada","last_name":"Vukušić","orcid":"0000-0003-2424-8636","full_name":"Vukušić, Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Watzinger","first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes"},{"full_name":"Gao, Fei","last_name":"Gao","first_name":"Fei"},{"full_name":"Wang, Ting","orcid":"0000-0002-4619-9575","first_name":"Ting","last_name":"Wang"},{"full_name":"Zhang, Jian-Jun","first_name":"Jian-Jun","last_name":"Zhang"},{"full_name":"Held, Karsten","last_name":"Held","first_name":"Karsten"}],"day":"01","language":[{"iso":"eng"}],"year":"2020","publication":"Nano Letters","ec_funded":1,"isi":1,"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"citation":{"ista":"Katsaros G, Kukucka J, Vukušić L, Watzinger H, Gao F, Wang T, Zhang J-J, Held K. 2020. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 20(7), 5201–5206.","ieee":"G. Katsaros <i>et al.</i>, “Zero field splitting of heavy-hole states in quantum dots,” <i>Nano Letters</i>, vol. 20, no. 7. American Chemical Society, pp. 5201–5206, 2020.","apa":"Katsaros, G., Kukucka, J., Vukušić, L., Watzinger, H., Gao, F., Wang, T., … Held, K. (2020). Zero field splitting of heavy-hole states in quantum dots. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">https://doi.org/10.1021/acs.nanolett.0c01466</a>","mla":"Katsaros, Georgios, et al. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” <i>Nano Letters</i>, vol. 20, no. 7, American Chemical Society, 2020, pp. 5201–06, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">10.1021/acs.nanolett.0c01466</a>.","short":"G. Katsaros, J. Kukucka, L. Vukušić, H. Watzinger, F. Gao, T. Wang, J.-J. Zhang, K. Held, Nano Letters 20 (2020) 5201–5206.","chicago":"Katsaros, Georgios, Josip Kukucka, Lada Vukušić, Hannes Watzinger, Fei Gao, Ting Wang, Jian-Jun Zhang, and Karsten Held. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” <i>Nano Letters</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">https://doi.org/10.1021/acs.nanolett.0c01466</a>.","ama":"Katsaros G, Kukucka J, Vukušić L, et al. Zero field splitting of heavy-hole states in quantum dots. <i>Nano Letters</i>. 2020;20(7):5201-5206. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">10.1021/acs.nanolett.0c01466</a>"},"article_processing_charge":"Yes (via OA deal)","status":"public","type":"journal_article","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Zero field splitting of heavy-hole states in quantum dots","_id":"8203","page":"5201-5206","intvolume":"        20","doi":"10.1021/acs.nanolett.0c01466","external_id":{"pmid":["32479090"],"isi":["000548893200066"]},"department":[{"_id":"GeKa"}],"acknowledgement":"We acknowledge G. Burkard, V. N. Golovach, C. Kloeffel, D.Loss, P. Rabl, and M. Rancič ́ for helpful discussions. We\r\nfurther acknowledge T. Adletzberger, J. Aguilera, T. Asenov, S. Bagiante, T. Menner, L. Shafeek, P. Taus, P. Traunmüller, and D. Waldhausl for their invaluable assistance. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, by the FWF-P 32235 project, by the National Key R&D Program of China (2016YFA0301701, 2016YFA0300600), and by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 862046. All data of this publication are available at 10.15479/AT:ISTA:7689.","quality_controlled":"1","has_accepted_license":"1","related_material":{"record":[{"id":"7689","relation":"research_data","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","month":"06","ddc":["530"],"date_updated":"2024-02-21T12:44:01Z","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"oa":1,"publication_status":"published"},{"year":"2020","language":[{"iso":"eng"}],"day":"21","publication":"Proceedings of the National Academy of Sciences of the United States of America","ec_funded":1,"issue":"29","file_date_updated":"2020-08-10T06:50:28Z","date_published":"2020-07-21T00:00:00Z","volume":117,"abstract":[{"text":"Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings.","lang":"eng"}],"author":[{"last_name":"Corominas-Murtra","first_name":"Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","full_name":"Corominas-Murtra, Bernat"},{"full_name":"Scheele, Colinda L.G.J.","first_name":"Colinda L.G.J.","last_name":"Scheele"},{"first_name":"Kasumi","last_name":"Kishi","full_name":"Kishi, Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ellenbroek, Saskia I.J.","first_name":"Saskia I.J.","last_name":"Ellenbroek"},{"first_name":"Benjamin D.","last_name":"Simons","full_name":"Simons, Benjamin D."},{"last_name":"Van Rheenen","first_name":"Jacco","full_name":"Van Rheenen, Jacco"},{"first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","project":[{"call_identifier":"H2020","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis"}],"date_created":"2020-08-09T22:00:52Z","pmid":1,"file":[{"file_size":1111604,"access_level":"open_access","file_name":"2020_PNAS_Corominas.pdf","content_type":"application/pdf","date_updated":"2020-08-10T06:50:28Z","relation":"main_file","creator":"dernst","date_created":"2020-08-10T06:50:28Z","file_id":"8223","success":1}],"publisher":"National Academy of Sciences","scopus_import":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/order-from-noise/","relation":"press_release"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","month":"07","publication_identifier":{"eissn":["10916490"]},"ddc":["570"],"date_updated":"2023-08-22T08:29:30Z","publication_status":"published","oa":1,"has_accepted_license":"1","intvolume":"       117","_id":"8220","page":"16969-16975","external_id":{"isi":["000553292900014"],"pmid":["32611816"]},"doi":"10.1073/pnas.1921205117","department":[{"_id":"EdHa"}],"quality_controlled":"1","acknowledgement":"We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z.","isi":1,"article_processing_charge":"No","citation":{"apa":"Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., &#38; Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1921205117\">https://doi.org/10.1073/pnas.1921205117</a>","mla":"Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:<a href=\"https://doi.org/10.1073/pnas.1921205117\">10.1073/pnas.1921205117</a>.","short":"B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975.","ama":"Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(29):16969-16975. doi:<a href=\"https://doi.org/10.1073/pnas.1921205117\">10.1073/pnas.1921205117</a>","chicago":"Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1921205117\">https://doi.org/10.1073/pnas.1921205117</a>.","ista":"Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975.","ieee":"B. Corominas-Murtra <i>et al.</i>, “Stem cell lineage survival as a noisy competition for niche access,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020."},"status":"public","type":"journal_article","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Stem cell lineage survival as a noisy competition for niche access"}]