[{"publication_status":"published","doi":"10.1016/j.nahs.2020.100856","date_published":"2020-05-01T00:00:00Z","oa_version":"Submitted Version","ddc":["000"],"file_date_updated":"2022-05-16T22:30:04Z","scopus_import":"1","intvolume":"        36","citation":{"chicago":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.nahs.2020.100856\">https://doi.org/10.1016/j.nahs.2020.100856</a>.","apa":"Garcia Soto, M., &#38; Prabhakar, P. (2020). Abstraction based verification of stability of polyhedral switched systems. <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nahs.2020.100856\">https://doi.org/10.1016/j.nahs.2020.100856</a>","mla":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 36, no. 5, 100856, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.nahs.2020.100856\">10.1016/j.nahs.2020.100856</a>.","ista":"Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 100856.","ama":"Garcia Soto M, Prabhakar P. Abstraction based verification of stability of polyhedral switched systems. <i>Nonlinear Analysis: Hybrid Systems</i>. 2020;36(5). doi:<a href=\"https://doi.org/10.1016/j.nahs.2020.100856\">10.1016/j.nahs.2020.100856</a>","ieee":"M. Garcia Soto and P. Prabhakar, “Abstraction based verification of stability of polyhedral switched systems,” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 36, no. 5. Elsevier, 2020.","short":"M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020)."},"year":"2020","date_updated":"2023-08-17T14:32:54Z","abstract":[{"lang":"eng","text":"This paper presents a novel abstraction technique for analyzing Lyapunov and asymptotic stability of polyhedral switched systems. A polyhedral switched system is a hybrid system in which the continuous dynamics is specified by polyhedral differential inclusions, the invariants and guards are specified by polyhedral sets and the switching between the modes do not involve reset of variables. A finite state weighted graph abstracting the polyhedral switched system is constructed from a finite partition of the state–space, such that the satisfaction of certain graph conditions, such as the absence of cycles with product of weights on the edges greater than (or equal) to 1, implies the stability of the system. However, the graph is in general conservative and hence, the violation of the graph conditions does not imply instability. If the analysis fails to establish stability due to the conservativeness in the approximation, a counterexample (cycle with product of edge weights greater than or equal to 1) indicating a potential reason for the failure is returned. Further, a more precise approximation of the switched system can be constructed by considering a finer partition of the state–space in the construction of the finite weighted graph. We present experimental results on analyzing stability of switched systems using the above method."}],"issue":"5","_id":"7426","article_number":"100856","oa":1,"publication_identifier":{"issn":["1751-570X"]},"status":"public","month":"05","date_created":"2020-02-02T23:00:59Z","publication":"Nonlinear Analysis: Hybrid Systems","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"type":"journal_article","article_type":"original","article_processing_charge":"No","external_id":{"isi":["000528828600003"]},"volume":36,"quality_controlled":"1","day":"01","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"file":[{"creator":"dernst","checksum":"560abfddb53f9fe921b6744f59f2cfaa","file_id":"8688","access_level":"open_access","date_updated":"2022-05-16T22:30:04Z","file_name":"2020_NAHS_GarciaSoto.pdf","date_created":"2020-10-21T13:16:45Z","relation":"main_file","content_type":"application/pdf","file_size":818774,"embargo":"2022-05-15"}],"project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"author":[{"full_name":"Garcia Soto, Miriam","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","last_name":"Garcia Soto","first_name":"Miriam","orcid":"0000−0003−2936−5719"},{"full_name":"Prabhakar, Pavithra","first_name":"Pavithra","last_name":"Prabhakar"}],"isi":1,"title":"Abstraction based verification of stability of polyhedral switched systems","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/"},{"scopus_import":"1","file_date_updated":"2020-09-22T09:51:28Z","ddc":["580"],"citation":{"mla":"Tan, Shutang, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” <i>Current Biology</i>, vol. 30, no. 3, Cell Press, 2020, p. 381–395.e8, doi:<a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">10.1016/j.cub.2019.11.058</a>.","ista":"Tan S, Abas MF, Verstraeten I, Glanc M, Molnar G, Hajny J, Lasák P, Petřík I, Russinova E, Petrášek J, Novák O, Pospíšil J, Friml J. 2020. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 30(3), 381–395.e8.","apa":"Tan, S., Abas, M. F., Verstraeten, I., Glanc, M., Molnar, G., Hajny, J., … Friml, J. (2020). Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">https://doi.org/10.1016/j.cub.2019.11.058</a>","chicago":"Tan, Shutang, Melinda F Abas, Inge Verstraeten, Matous Glanc, Gergely Molnar, Jakub Hajny, Pavel Lasák, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” <i>Current Biology</i>. Cell Press, 2020. <a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">https://doi.org/10.1016/j.cub.2019.11.058</a>.","short":"S. Tan, M.F. Abas, I. Verstraeten, M. Glanc, G. Molnar, J. Hajny, P. Lasák, I. Petřík, E. Russinova, J. Petrášek, O. Novák, J. Pospíšil, J. Friml, Current Biology 30 (2020) 381–395.e8.","ieee":"S. Tan <i>et al.</i>, “Salicylic acid targets protein phosphatase 2A to attenuate growth in plants,” <i>Current Biology</i>, vol. 30, no. 3. Cell Press, p. 381–395.e8, 2020.","ama":"Tan S, Abas MF, Verstraeten I, et al. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. <i>Current Biology</i>. 2020;30(3):381-395.e8. doi:<a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">10.1016/j.cub.2019.11.058</a>"},"intvolume":"        30","publication_status":"published","doi":"10.1016/j.cub.2019.11.058","oa_version":"Published Version","date_published":"2020-02-03T00:00:00Z","status":"public","oa":1,"publication_identifier":{"issn":["09609822"]},"month":"02","ec_funded":1,"date_updated":"2024-03-25T23:30:20Z","issue":"3","abstract":[{"lang":"eng","text":"Plants, like other multicellular organisms, survive through a delicate balance between growth and defense against pathogens. Salicylic acid (SA) is a major defense signal in plants, and the perception mechanism as well as downstream signaling activating the immune response are known. Here, we identify a parallel SA signaling that mediates growth attenuation. SA directly binds to A subunits of protein phosphatase 2A (PP2A), inhibiting activity of this complex. Among PP2A targets, the PIN2 auxin transporter is hyperphosphorylated in response to SA, leading to changed activity of this important growth regulator. Accordingly, auxin transport and auxin-mediated root development, including growth, gravitropic response, and lateral root organogenesis, are inhibited. This study reveals how SA, besides activating immunity, concomitantly attenuates growth through crosstalk with the auxin distribution network. Further analysis of this dual role of SA and characterization of additional SA-regulated PP2A targets will provide further insights into mechanisms maintaining a balance between growth and defense."}],"year":"2020","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"_id":"7427","article_processing_charge":"No","article_type":"original","external_id":{"pmid":["31956021"],"isi":["000511287900018"]},"quality_controlled":"1","volume":30,"related_material":{"record":[{"id":"8822","status":"public","relation":"dissertation_contains"}]},"has_accepted_license":"1","date_created":"2020-02-02T23:01:00Z","page":"381-395.e8","publication":"Current Biology","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publisher":"Cell Press","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Salicylic acid targets protein phosphatase 2A to attenuate growth in plants","license":"https://creativecommons.org/licenses/by/4.0/","acknowledgement":"We thank Shigeyuki Betsuyaku (University of Tsukuba), Alison Delong (Brown University), Xinnian Dong (Duke University), Dolf Weijers (Wageningen University), Yuelin Zhang (UBC), and Martine Pastuglia (Institut Jean-Pierre Bourgin) for sharing published materials; Jana Riederer for help with cantharidin physiological analysis; David Domjan for help with cloning pET28a-PIN2HL; Qing Lu for help with DARTS; Hana Kozubı´kova´ for technical support on SA derivative synthesis; Zuzana Vondra´ kova´ for technical support with tobacco cells; Lucia Strader (Washington University), Bert De Rybel (Ghent University), Bartel Vanholme (Ghent University), and Lukas Mach (BOKU) for helpful discussions; and bioimaging and life science facilities of IST Austria for continuous support. We gratefully acknowledge the Nottingham Arabidopsis Stock Center (NASC) for providing T-DNA insertional mutants. The DSC and SPR instruments were provided by the EQ-BOKU VIBT GmbH and the BOKU Core Facility for Biomolecular and Cellular Analysis, with help of Irene Schaffner. The research leading to these results has received funding from the European Union’s Horizon 2020 program (ERC grant agreement no. 742985 to J.F.) and the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. S.T. was supported by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). O.N. was supported by the Ministry of Education, Youth and Sports of the Czech Republic (European Regional Development Fund-Project ‘‘Centre for Experimental Plant Biology’’ no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Pospısil was supported by European Regional Development Fund Project ‘‘Centre for Experimental Plant Biology’’\r\n(no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Petrasek was supported by EU Operational Programme Prague-Competitiveness (no. CZ.2.16/3.1.00/21519). ","pmid":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"03","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015","name":"Long Term Fellowship"}],"author":[{"first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","full_name":"Tan, Shutang"},{"full_name":"Abas, Melinda F","first_name":"Melinda F","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","last_name":"Abas"},{"full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous"},{"full_name":"Molnar, Gergely","first_name":"Gergely","last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hajny, Jakub","first_name":"Jakub","orcid":"0000-0003-2140-7195","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pavel","last_name":"Lasák","full_name":"Lasák, Pavel"},{"last_name":"Petřík","first_name":"Ivan","full_name":"Petřík, Ivan"},{"first_name":"Eugenia","last_name":"Russinova","full_name":"Russinova, Eugenia"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"full_name":"Pospíšil, Jiří","first_name":"Jiří","last_name":"Pospíšil"},{"full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"file":[{"content_type":"application/pdf","relation":"main_file","success":1,"file_size":5360135,"file_id":"8555","creator":"dernst","checksum":"16f7d51fe28f91c21e4896a2028df40b","access_level":"open_access","date_updated":"2020-09-22T09:51:28Z","file_name":"2020_CurrentBiology_Tan.pdf","date_created":"2020-09-22T09:51:28Z"}]},{"article_processing_charge":"No","article_type":"original","external_id":{"arxiv":["1907.02077"],"isi":["000506843500001"]},"volume":101,"quality_controlled":"1","date_created":"2020-02-02T23:01:01Z","publication":"Physical Review B","language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"type":"journal_article","title":"Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"13","author":[{"full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg"},{"full_name":"Lopes, P. L.S.","first_name":"P. L.S.","last_name":"Lopes"},{"full_name":"Hosur, Pavan","first_name":"Pavan","last_name":"Hosur"},{"first_name":"Matthew J.","last_name":"Gilbert","full_name":"Gilbert, Matthew J."},{"full_name":"Ghaemi, Pouyan","first_name":"Pouyan","last_name":"Ghaemi"}],"isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1907.02077","open_access":"1"}],"scopus_import":"1","citation":{"chicago":"Ghazaryan, Areg, P. L.S. Lopes, Pavan Hosur, Matthew J. Gilbert, and Pouyan Ghaemi. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">https://doi.org/10.1103/PhysRevB.101.020504</a>.","apa":"Ghazaryan, A., Lopes, P. L. S., Hosur, P., Gilbert, M. J., &#38; Ghaemi, P. (2020). Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">https://doi.org/10.1103/PhysRevB.101.020504</a>","mla":"Ghazaryan, Areg, et al. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” <i>Physical Review B</i>, vol. 101, no. 2, 020504, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">10.1103/PhysRevB.101.020504</a>.","ista":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. 2020. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 101(2), 020504.","ama":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. <i>Physical Review B</i>. 2020;101(2). doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">10.1103/PhysRevB.101.020504</a>","ieee":"A. Ghazaryan, P. L. S. Lopes, P. Hosur, M. J. Gilbert, and P. Ghaemi, “Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors,” <i>Physical Review B</i>, vol. 101, no. 2. American Physical Society, 2020.","short":"A. Ghazaryan, P.L.S. Lopes, P. Hosur, M.J. Gilbert, P. Ghaemi, Physical Review B 101 (2020)."},"intvolume":"       101","publication_status":"published","doi":"10.1103/PhysRevB.101.020504","date_published":"2020-01-13T00:00:00Z","oa_version":"Preprint","oa":1,"publication_identifier":{"eissn":["24699969"],"issn":["24699950"]},"status":"public","month":"01","year":"2020","date_updated":"2024-02-28T13:11:13Z","arxiv":1,"issue":"2","abstract":[{"text":"In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices which are distinguished by the presence or absence of zero-energy states in their core. To understand their origin, we examine the interplay of Zeeman coupling and superconducting pairings in three-dimensional metals with band inversion. Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known to localize the states at the ends of the vortices on the surface. On the other hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions, but leads to delocalized zero-energy Majorana modes which extend through the vortex. In contrast, the finite-energy vortex modes remain localized at the vortex ends even when the pairing is of orbital-triplet form. Phenomenologically, this manifests as an observed disappearance of zero-bias peaks within the cores of topological vortices upon an increase of the applied magnetic field. The presence of magnetic impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to such Zeeman-induced delocalization of Majorana modes in a fraction of vortices that capture a large enough number of magnetic impurities. Our results provide an explanation for the dichotomy between topological and nontopological vortices recently observed in FeTe(1−x)Sex.","lang":"eng"}],"_id":"7428","article_number":"020504"},{"publication":"Journal of the Royal Society Interface","date_created":"2020-02-02T23:01:03Z","type":"journal_article","department":[{"_id":"EdHa"}],"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","volume":17,"quality_controlled":"1","external_id":{"isi":["000538369800002"],"arxiv":["1903.10693"],"pmid":["31964273"]},"pmid":1,"acknowledgement":"AK was supported by Grant No. FQXi-RFP-1622 from the FQXi foundation, and Grant No. CHE-1648973 from the U.S.\r\nNational Science Foundation. AK would like to thank the Santa Fe Institute for supporting this research. The authors\r\nthank Jordi Fortuny, Rudolf Hanel, Joshua Garland, and Blai Vidiella for helpful discussions, as well as the anonymous\r\nreviewers for their insightful suggestions. ","day":"29","author":[{"full_name":"Kolchinsky, Artemy","first_name":"Artemy","last_name":"Kolchinsky"},{"orcid":"0000-0001-9806-5643","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat"}],"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"The Royal Society","title":"Decomposing information into copying versus transformation","doi":"10.1098/rsif.2019.0623","publication_status":"published","oa_version":"Preprint","date_published":"2020-01-29T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1903.10693","open_access":"1"}],"scopus_import":"1","intvolume":"        17","citation":{"chicago":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” <i>Journal of the Royal Society Interface</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rsif.2019.0623\">https://doi.org/10.1098/rsif.2019.0623</a>.","apa":"Kolchinsky, A., &#38; Corominas-Murtra, B. (2020). Decomposing information into copying versus transformation. <i>Journal of the Royal Society Interface</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsif.2019.0623\">https://doi.org/10.1098/rsif.2019.0623</a>","ista":"Kolchinsky A, Corominas-Murtra B. 2020. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 17(162), 0623.","mla":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 162, 0623, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rsif.2019.0623\">10.1098/rsif.2019.0623</a>.","ama":"Kolchinsky A, Corominas-Murtra B. Decomposing information into copying versus transformation. <i>Journal of the Royal Society Interface</i>. 2020;17(162). doi:<a href=\"https://doi.org/10.1098/rsif.2019.0623\">10.1098/rsif.2019.0623</a>","ieee":"A. Kolchinsky and B. Corominas-Murtra, “Decomposing information into copying versus transformation,” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 162. The Royal Society, 2020.","short":"A. Kolchinsky, B. Corominas-Murtra, Journal of the Royal Society Interface 17 (2020)."},"issue":"162","arxiv":1,"abstract":[{"text":"In many real-world systems, information can be transmitted in two qualitatively different ways: by copying or by transformation. Copying occurs when messages are transmitted without modification, e.g. when an offspring receives an unaltered copy of a gene from its parent. Transformation occurs when messages are modified systematically during transmission, e.g. when mutational biases occur during genetic replication. Standard information-theoretic measures do not distinguish these two modes of information transfer, although they may reflect different mechanisms and have different functional consequences. Starting from a few simple axioms, we derive a decomposition of mutual information into the information transmitted by copying versus the information transmitted by transformation. We begin with a decomposition that applies when the source and destination of the channel have the same set of messages and a notion of message identity exists. We then generalize our decomposition to other kinds of channels, which can involve different source and destination sets and broader notions of similarity. In addition, we show that copy information can be interpreted as the minimal work needed by a physical copying process, which is relevant for understanding the physics of replication. We use the proposed decomposition to explore a model of amino acid substitution rates. Our results apply to any system in which the fidelity of copying, rather than simple predictability, is of critical relevance.","lang":"eng"}],"date_updated":"2023-08-17T14:31:28Z","year":"2020","article_number":"0623","_id":"7431","status":"public","publication_identifier":{"eissn":["17425662"]},"oa":1,"month":"01"},{"date_published":"2020-02-10T00:00:00Z","oa_version":"Published Version","doi":"10.15479/AT:ISTA:7460","publication_status":"published","citation":{"short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7460\">10.15479/AT:ISTA:7460</a>","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","apa":"Ölsböck, K. (2020). <i>The hole system of triangulated shapes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7460\">https://doi.org/10.15479/AT:ISTA:7460</a>","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","mla":"Ölsböck, Katharina. <i>The Hole System of Triangulated Shapes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7460\">10.15479/AT:ISTA:7460</a>.","chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7460\">https://doi.org/10.15479/AT:ISTA:7460</a>."},"ddc":["514"],"file_date_updated":"2020-07-14T12:47:58Z","_id":"7460","year":"2020","abstract":[{"lang":"eng","text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries."}],"date_updated":"2023-09-07T13:15:30Z","month":"02","publication_identifier":{"issn":["2663-337X"]},"oa":1,"status":"public","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"type":"dissertation","page":"155","date_created":"2020-02-06T14:56:53Z","has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6608"}]},"keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"article_processing_charge":"No","file":[{"checksum":"1df9f8c530b443c0e63a3f2e4fde412e","creator":"koelsboe","file_id":"7461","access_level":"open_access","date_updated":"2020-07-14T12:47:58Z","file_name":"thesis_ist-final_noack.pdf","date_created":"2020-02-06T14:43:54Z","content_type":"application/pdf","relation":"main_file","file_size":76195184},{"access_level":"closed","checksum":"7a52383c812b0be64d3826546509e5a4","file_id":"7462","creator":"koelsboe","date_created":"2020-02-06T14:52:45Z","file_name":"latex-files.zip","date_updated":"2020-07-14T12:47:58Z","file_size":122103715,"content_type":"application/x-zip-compressed","description":"latex source files, figures","relation":"source_file"}],"author":[{"orcid":"0000-0002-4672-8297","first_name":"Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","last_name":"Ölsböck","full_name":"Ölsböck, Katharina"}],"day":"10","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","supervisor":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"title":"The hole system of triangulated shapes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria"},{"acknowledged_ssus":[{"_id":"ScienComp"}],"article_number":"e1008277","_id":"7464","abstract":[{"text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.","lang":"eng"}],"issue":"1","date_updated":"2023-10-17T12:29:34Z","year":"2020","month":"01","status":"public","publication_identifier":{"issn":["1553-7374"]},"oa":1,"oa_version":"Published Version","date_published":"2020-01-27T00:00:00Z","doi":"10.1371/journal.ppat.1008277","publication_status":"published","intvolume":"        16","citation":{"short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020).","ieee":"R. A. Dick <i>et al.</i>, “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” <i>PLOS Pathogens</i>, vol. 16, no. 1. Public Library of Science, 2020.","ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. <i>PLOS Pathogens</i>. 2020;16(1). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1008277\">10.1371/journal.ppat.1008277</a>","chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” <i>PLOS Pathogens</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.ppat.1008277\">https://doi.org/10.1371/journal.ppat.1008277</a>.","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. <i>PLOS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1008277\">https://doi.org/10.1371/journal.ppat.1008277</a>","mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” <i>PLOS Pathogens</i>, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1008277\">10.1371/journal.ppat.1008277</a>."},"scopus_import":"1","file_date_updated":"2020-07-14T12:47:59Z","ddc":["570"],"author":[{"first_name":"Robert A.","last_name":"Dick","full_name":"Dick, Robert A."},{"full_name":"Xu, Chaoyi","last_name":"Xu","first_name":"Chaoyi"},{"full_name":"Morado, Dustin R.","first_name":"Dustin R.","last_name":"Morado"},{"last_name":"Kravchuk","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","first_name":"Vladyslav","orcid":"0000-0001-9523-9089","full_name":"Kravchuk, Vladyslav"},{"full_name":"Ricana, Clifton L.","last_name":"Ricana","first_name":"Clifton L."},{"first_name":"Terri D.","last_name":"Lyddon","full_name":"Lyddon, Terri D."},{"full_name":"Broad, Arianna M.","last_name":"Broad","first_name":"Arianna M."},{"first_name":"J. Ryan","last_name":"Feathers","full_name":"Feathers, J. Ryan"},{"first_name":"Marc C.","last_name":"Johnson","full_name":"Johnson, Marc C."},{"full_name":"Vogt, Volker M.","last_name":"Vogt","first_name":"Volker M."},{"full_name":"Perilla, Juan R.","last_name":"Perilla","first_name":"Juan R."},{"last_name":"Briggs","first_name":"John A. G.","full_name":"Briggs, John A. G."},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian KM"}],"isi":1,"project":[{"call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445"}],"file":[{"file_size":4551246,"content_type":"application/pdf","relation":"main_file","date_created":"2020-02-11T10:07:28Z","date_updated":"2020-07-14T12:47:59Z","file_name":"2020_PLOSPatho_Dick.pdf","access_level":"open_access","file_id":"7484","checksum":"a297f54d1fef0efe4789ca00f37f241e","creator":"dernst"}],"pmid":1,"day":"27","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","type":"journal_article","department":[{"_id":"FlSc"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"PLOS Pathogens","date_created":"2020-02-06T18:47:17Z","volume":16,"quality_controlled":"1","external_id":{"pmid":["31986188"],"isi":["000510746400010"]},"related_material":{"record":[{"status":"deleted","relation":"research_data","id":"9723"}]},"article_type":"original","article_processing_charge":"No"},{"external_id":{"isi":["000520609800009"]},"quality_controlled":"1","volume":293,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11626"}]},"article_type":"original","article_processing_charge":"No","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"has_accepted_license":"1","date_created":"2020-02-09T23:00:50Z","publication":"Plant Science","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"author":[{"full_name":"Mazur, Ewa","first_name":"Ewa","last_name":"Mazur"},{"full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368"},{"last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek"},{"full_name":"Han, Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"},{"full_name":"Robert, Hélène S.","first_name":"Hélène S.","last_name":"Robert"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří"}],"isi":1,"file":[{"date_created":"2020-02-10T08:59:36Z","file_name":"2020_PlantScience_Mazur.pdf","date_updated":"2020-07-14T12:47:59Z","access_level":"open_access","file_id":"7471","checksum":"f7f27c6a8fea985ceb9279be2204461c","creator":"dernst","file_size":3499069,"relation":"main_file","content_type":"application/pdf"}],"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. 2020. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. Plant Science. 293(4), 110414.","apa":"Mazur, E., Gallei, M. C., Adamowski, M., Han, H., Robert, H. S., &#38; Friml, J. (2020). Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">https://doi.org/10.1016/j.plantsci.2020.110414</a>","mla":"Mazur, Ewa, et al. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” <i>Plant Science</i>, vol. 293, no. 4, 110414, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">10.1016/j.plantsci.2020.110414</a>.","chicago":"Mazur, Ewa, Michelle C Gallei, Maciek Adamowski, Huibin Han, Hélène S. Robert, and Jiří Friml. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” <i>Plant Science</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">https://doi.org/10.1016/j.plantsci.2020.110414</a>.","short":"E. Mazur, M.C. Gallei, M. Adamowski, H. Han, H.S. Robert, J. Friml, Plant Science 293 (2020).","ieee":"E. Mazur, M. C. Gallei, M. Adamowski, H. Han, H. S. Robert, and J. Friml, “Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis,” <i>Plant Science</i>, vol. 293, no. 4. Elsevier, 2020.","ama":"Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. <i>Plant Science</i>. 2020;293(4). doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">10.1016/j.plantsci.2020.110414</a>"},"intvolume":"       293","file_date_updated":"2020-07-14T12:47:59Z","scopus_import":"1","ddc":["580"],"oa_version":"Published Version","date_published":"2020-04-01T00:00:00Z","publication_status":"published","doi":"10.1016/j.plantsci.2020.110414","month":"04","ec_funded":1,"status":"public","oa":1,"publication_identifier":{"issn":["01689452"],"eissn":["18732259"]},"article_number":"110414","_id":"7465","date_updated":"2023-08-17T14:37:32Z","issue":"4","abstract":[{"lang":"eng","text":"The flexible development of plants is characterized by a high capacity for post-embryonic organ formation and tissue regeneration, processes, which require tightly regulated intercellular communication and coordinated tissue (re-)polarization. The phytohormone auxin, the main driver for these processes, is able to establish polarized auxin transport channels, which are characterized by the expression and polar, subcellular localization of the PIN1 auxin transport proteins. These channels are demarcating the position of future vascular strands necessary for organ formation and tissue regeneration. Major progress has been made in the last years to understand how PINs can change their polarity in different contexts and thus guide auxin flow through the plant. However, it still remains elusive how auxin mediates the establishment of auxin conducting channels and the formation of vascular tissue and which cellular processes are involved. By the means of sophisticated regeneration experiments combined with local auxin applications in Arabidopsis thaliana inflorescence stems we show that (i) PIN subcellular dynamics, (ii) PIN internalization by clathrin-mediated trafficking and (iii) an intact actin cytoskeleton required for post-endocytic trafficking are indispensable for auxin channel formation, de novo vascular formation and vascular regeneration after wounding. These observations provide novel insights into cellular mechanism of coordinated tissue polarization during auxin canalization."}],"year":"2020"},{"publication_identifier":{"eissn":["2050084X"]},"oa":1,"status":"public","month":"01","year":"2020","date_updated":"2023-08-17T14:36:39Z","abstract":[{"lang":"eng","text":"Unpaired ligands are secreted signals that act via a GP130-like receptor, domeless, to activate JAK/STAT signalling in Drosophila. Like many mammalian cytokines, unpaireds can be activated by infection and other stresses and can promote insulin resistance in target tissues. However, the importance of this effect in non-inflammatory physiology is unknown. Here, we identify a requirement for unpaired-JAK signalling as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show basal JAK-STAT signalling activity in the absence of any immune challenge. Plasmatocytes (Drosophila macrophages) are an important source of this tonic signal. Loss of the dome receptor on adult muscles significantly reduces lifespan and causes local and systemic metabolic pathology. These pathologies result from hyperactivation of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine signal that must be received in muscle to control AKT activity and metabolic homeostasis."}],"_id":"7466","article_number":"e51595","ddc":["570"],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:59Z","citation":{"chicago":"Kierdorf, Katrin, Fabian Hersperger, Jessica Sharrock, Crystal M. Vincent, Pinar Ustaoglu, Jiawen Dou, Attila György, Olaf Groß, Daria E Siekhaus, and Marc S. Dionne. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.51595\">https://doi.org/10.7554/eLife.51595</a>.","mla":"Kierdorf, Katrin, et al. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” <i>ELife</i>, vol. 9, e51595, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.51595\">10.7554/eLife.51595</a>.","apa":"Kierdorf, K., Hersperger, F., Sharrock, J., Vincent, C. M., Ustaoglu, P., Dou, J., … Dionne, M. S. (2020). Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.51595\">https://doi.org/10.7554/eLife.51595</a>","ista":"Kierdorf K, Hersperger F, Sharrock J, Vincent CM, Ustaoglu P, Dou J, György A, Groß O, Siekhaus DE, Dionne MS. 2020. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. eLife. 9, e51595.","short":"K. Kierdorf, F. Hersperger, J. Sharrock, C.M. Vincent, P. Ustaoglu, J. Dou, A. György, O. Groß, D.E. Siekhaus, M.S. Dionne, ELife 9 (2020).","ama":"Kierdorf K, Hersperger F, Sharrock J, et al. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.51595\">10.7554/eLife.51595</a>","ieee":"K. Kierdorf <i>et al.</i>, “Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020."},"intvolume":"         9","publication_status":"published","doi":"10.7554/eLife.51595","date_published":"2020-01-20T00:00:00Z","oa_version":"Published Version","title":"Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila","publisher":"eLife Sciences Publications","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"20","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2020-07-14T12:47:59Z","file_name":"2020_eLife_Kierdorf.pdf","date_created":"2020-02-10T08:53:16Z","file_id":"7470","checksum":"3a072be843f416c7a7d532a51dc0addb","creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":4959933}],"project":[{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638","call_identifier":"FWF","name":"Drosophila TNFa´s Funktion in Immunzellen"}],"isi":1,"author":[{"last_name":"Kierdorf","first_name":"Katrin","full_name":"Kierdorf, Katrin"},{"last_name":"Hersperger","first_name":"Fabian","full_name":"Hersperger, Fabian"},{"full_name":"Sharrock, Jessica","last_name":"Sharrock","first_name":"Jessica"},{"last_name":"Vincent","first_name":"Crystal M.","full_name":"Vincent, Crystal M."},{"full_name":"Ustaoglu, Pinar","first_name":"Pinar","last_name":"Ustaoglu"},{"last_name":"Dou","first_name":"Jiawen","full_name":"Dou, Jiawen"},{"first_name":"Attila","orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György","full_name":"György, Attila"},{"full_name":"Groß, Olaf","first_name":"Olaf","last_name":"Groß"},{"first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"},{"full_name":"Dionne, Marc S.","first_name":"Marc S.","last_name":"Dionne"}],"article_type":"original","article_processing_charge":"No","external_id":{"isi":["000512304800001"]},"quality_controlled":"1","volume":9,"date_created":"2020-02-09T23:00:51Z","publication":"eLife","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"DaSi"}],"type":"journal_article"},{"intvolume":"         3","citation":{"ista":"Cadavid D, Ortega S, Illera S, Liu Y, Ibáñez M, Shavel A, Zhang Y, Li M, López AM, Noriega G, Durá OJ, López De La Torre MA, Prades JD, Cabot A. 2020. Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. ACS Applied Energy Materials. 3(3), 2120–2129.","mla":"Cadavid, Doris, et al. “Influence of the Ligand Stripping on the Transport Properties of Nanoparticle-Based PbSe Nanomaterials.” <i>ACS Applied Energy Materials</i>, vol. 3, no. 3, American Chemical Society, 2020, pp. 2120–29, doi:<a href=\"https://doi.org/10.1021/acsaem.9b02137\">10.1021/acsaem.9b02137</a>.","apa":"Cadavid, D., Ortega, S., Illera, S., Liu, Y., Ibáñez, M., Shavel, A., … Cabot, A. (2020). Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. <i>ACS Applied Energy Materials</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsaem.9b02137\">https://doi.org/10.1021/acsaem.9b02137</a>","chicago":"Cadavid, Doris, Silvia Ortega, Sergio Illera, Yu Liu, Maria Ibáñez, Alexey Shavel, Yu Zhang, et al. “Influence of the Ligand Stripping on the Transport Properties of Nanoparticle-Based PbSe Nanomaterials.” <i>ACS Applied Energy Materials</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acsaem.9b02137\">https://doi.org/10.1021/acsaem.9b02137</a>.","short":"D. Cadavid, S. Ortega, S. Illera, Y. Liu, M. Ibáñez, A. Shavel, Y. Zhang, M. Li, A.M. López, G. Noriega, O.J. Durá, M.A. López De La Torre, J.D. Prades, A. Cabot, ACS Applied Energy Materials 3 (2020) 2120–2129.","ama":"Cadavid D, Ortega S, Illera S, et al. Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. <i>ACS Applied Energy Materials</i>. 2020;3(3):2120-2129. doi:<a href=\"https://doi.org/10.1021/acsaem.9b02137\">10.1021/acsaem.9b02137</a>","ieee":"D. Cadavid <i>et al.</i>, “Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials,” <i>ACS Applied Energy Materials</i>, vol. 3, no. 3. American Chemical Society, pp. 2120–2129, 2020."},"ddc":["540"],"scopus_import":"1","file_date_updated":"2022-08-23T08:34:17Z","date_published":"2020-03-01T00:00:00Z","oa_version":"Submitted Version","doi":"10.1021/acsaem.9b02137","publication_status":"published","ec_funded":1,"month":"03","oa":1,"publication_identifier":{"eissn":["2574-0962"]},"status":"public","_id":"7467","year":"2020","abstract":[{"lang":"eng","text":"Nanomaterials produced from the bottom-up assembly of nanocrystals may incorporate ∼1020–1021 cm–3 not fully coordinated surface atoms, i.e., ∼1020–1021 cm–3 potential donor or acceptor states that can strongly affect transport properties. Therefore, to exploit the full potential of nanocrystal building blocks to produce functional nanomaterials and thin films, a proper control of their surface chemistry is required. Here, we analyze how the ligand stripping procedure influences the charge and heat transport properties of sintered PbSe nanomaterials produced from the bottom-up assembly of colloidal PbSe nanocrystals. First, we show that the removal of the native organic ligands by thermal decomposition in an inert atmosphere leaves relatively large amounts of carbon at the crystal interfaces. This carbon blocks crystal growth during consolidation and at the same time hampers charge and heat transport through the final nanomaterial. Second, we demonstrate that, by stripping ligands from the nanocrystal surface before consolidation, nanomaterials with larger crystal domains, lower porosity, and higher charge carrier concentrations are obtained, thus resulting in nanomaterials with higher electrical and thermal conductivities. In addition, the ligand displacement leaves the nanocrystal surface unprotected, facilitating oxidation and chalcogen evaporation. The influence of the ligand displacement on the nanomaterial charge transport properties is rationalized here using a two-band model based on the standard Boltzmann transport equation with the relaxation time approximation. Finally, we present an application of the produced functional nanomaterials by modeling, fabricating, and testing a simple PbSe-based thermoelectric device with a ring geometry."}],"issue":"3","date_updated":"2023-08-17T14:36:16Z","quality_controlled":"1","volume":3,"external_id":{"isi":["000526598300012"]},"article_processing_charge":"No","article_type":"original","department":[{"_id":"MaIb"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"ACS Applied Energy Materials","date_created":"2020-02-09T23:00:52Z","page":"2120-2129","has_accepted_license":"1","title":"Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Chemical Society","file":[{"file_size":6423548,"success":1,"relation":"main_file","content_type":"application/pdf","date_created":"2022-08-23T08:34:17Z","file_name":"2020_ACSAppliedEnergyMat_Cadavid.pdf","date_updated":"2022-08-23T08:34:17Z","access_level":"open_access","file_id":"11942","creator":"dernst","checksum":"f23be731a766a480c77c962c1380315c"}],"isi":1,"author":[{"last_name":"Cadavid","first_name":"Doris","full_name":"Cadavid, Doris"},{"last_name":"Ortega","first_name":"Silvia","full_name":"Ortega, Silvia"},{"last_name":"Illera","first_name":"Sergio","full_name":"Illera, Sergio"},{"id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","orcid":"0000-0001-7313-6740","first_name":"Yu","full_name":"Liu, Yu"},{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"first_name":"Alexey","last_name":"Shavel","full_name":"Shavel, Alexey"},{"first_name":"Yu","last_name":"Zhang","full_name":"Zhang, Yu"},{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"full_name":"López, Antonio M.","last_name":"López","first_name":"Antonio M."},{"last_name":"Noriega","first_name":"Germán","full_name":"Noriega, Germán"},{"full_name":"Durá, Oscar Juan","last_name":"Durá","first_name":"Oscar Juan"},{"full_name":"López De La Torre, M. A.","first_name":"M. A.","last_name":"López De La Torre"},{"full_name":"Prades, Joan Daniel","last_name":"Prades","first_name":"Joan Daniel"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"day":"01","acknowledgement":"This work was supported by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP (ENE2016-77798-C4-3-R) and the Generalitat de Catalunya through the project 2017SGR1246. D.C. acknowledges support from Universidad Nacional de Colombia. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 754411. M.I. acknowledges financial support from IST Austria."},{"intvolume":"       106","citation":{"short":"K. Käfer, M. Nardin, K. Blahna, J.L. Csicsvari, Neuron 106 (2020) P154–165.e6.","ama":"Käfer K, Nardin M, Blahna K, Csicsvari JL. Replay of behavioral sequences in the medial prefrontal cortex during rule switching. <i>Neuron</i>. 2020;106(1):P154-165.e6. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">10.1016/j.neuron.2020.01.015</a>","ieee":"K. Käfer, M. Nardin, K. Blahna, and J. L. Csicsvari, “Replay of behavioral sequences in the medial prefrontal cortex during rule switching,” <i>Neuron</i>, vol. 106, no. 1. Elsevier, p. P154–165.e6, 2020.","chicago":"Käfer, Karola, Michele Nardin, Karel Blahna, and Jozsef L Csicsvari. “Replay of Behavioral Sequences in the Medial Prefrontal Cortex during Rule Switching.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">https://doi.org/10.1016/j.neuron.2020.01.015</a>.","apa":"Käfer, K., Nardin, M., Blahna, K., &#38; Csicsvari, J. L. (2020). Replay of behavioral sequences in the medial prefrontal cortex during rule switching. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">https://doi.org/10.1016/j.neuron.2020.01.015</a>","ista":"Käfer K, Nardin M, Blahna K, Csicsvari JL. 2020. Replay of behavioral sequences in the medial prefrontal cortex during rule switching. Neuron. 106(1), P154–165.e6.","mla":"Käfer, Karola, et al. “Replay of Behavioral Sequences in the Medial Prefrontal Cortex during Rule Switching.” <i>Neuron</i>, vol. 106, no. 1, Elsevier, 2020, p. P154–165.e6, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">10.1016/j.neuron.2020.01.015</a>."},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2020.01.015"}],"oa_version":"Published Version","date_published":"2020-04-08T00:00:00Z","doi":"10.1016/j.neuron.2020.01.015","publication_status":"published","month":"04","ec_funded":1,"status":"public","oa":1,"publication_identifier":{"issn":["0896-6273"]},"acknowledged_ssus":[{"_id":"M-Shop"}],"_id":"7472","issue":"1","abstract":[{"text":"Temporally organized reactivation of experiences during awake immobility periods is thought to underlie cognitive processes like planning and evaluation. While replay of trajectories is well established for the hippocampus, it is unclear whether the medial prefrontal cortex (mPFC) can reactivate sequential behavioral experiences in the awake state to support task execution. We simultaneously recorded from hippocampal and mPFC principal neurons in rats performing a mPFC-dependent rule-switching task on a plus maze. We found that mPFC neuronal activity encoded relative positions between the start and goal. During awake immobility periods, the mPFC replayed temporally organized sequences of these generalized positions, resembling entire spatial trajectories. The occurrence of mPFC trajectory replay positively correlated with rule-switching performance. However, hippocampal and mPFC trajectory replay occurred independently, indicating different functions. These results demonstrate that the mPFC can replay ordered activity patterns representing generalized locations and suggest that mPFC replay might have a role in flexible behavior.","lang":"eng"}],"date_updated":"2023-08-17T14:38:02Z","year":"2020","quality_controlled":"1","volume":106,"external_id":{"isi":["000525319300016"],"pmid":["32032512"]},"related_material":{"link":[{"url":"https://ist.ac.at/en/news/this-brain-area-helps-us-decide/","description":"News on IST Homepage","relation":"press_release"}]},"article_processing_charge":"No","article_type":"original","type":"journal_article","department":[{"_id":"JoCs"}],"language":[{"iso":"eng"}],"publication":"Neuron","date_created":"2020-02-10T15:45:48Z","page":"P154-165.e6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","title":"Replay of behavioral sequences in the medial prefrontal cortex during rule switching","isi":1,"author":[{"first_name":"Karola","last_name":"Käfer","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","full_name":"Käfer, Karola"},{"full_name":"Nardin, Michele","first_name":"Michele","orcid":"0000-0001-8849-6570","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karel","last_name":"Blahna","id":"3EA859AE-F248-11E8-B48F-1D18A9856A87","full_name":"Blahna, Karel"},{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","orcid":"0000-0002-5193-4036"}],"project":[{"name":"Inter-and intracellular signalling in schizophrenia","call_identifier":"FP7","grant_number":"607616","_id":"257BBB4C-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"We thank Todor Asenov and Thomas Menner from the Machine Shop for the drive design and production, Hugo Malagon-Vina for assistance in maze automatization, Jago Wallenschus for taking the images of the histology, and Federico Stella and Juan Felipe Ramirez-Villegas for comments on an earlier version of the manuscript. This work was supported by the EU-FP7 MC-ITN IN-SENS (grant 607616 ).","pmid":1,"day":"08"},{"date_published":"2020-03-18T00:00:00Z","oa_version":"Published Version","doi":"10.1016/j.neuron.2019.12.022","publication_status":"published","intvolume":"       105","citation":{"short":"C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006.","ieee":"C. Borges Merjane, O. Kim, and P. M. Jonas, “Functional electron microscopy (‘Flash and Freeze’) of identified cortical synapses in acute brain slices,” <i>Neuron</i>, vol. 105. Elsevier, pp. 992–1006, 2020.","ama":"Borges Merjane C, Kim O, Jonas PM. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. <i>Neuron</i>. 2020;105:992-1006. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">10.1016/j.neuron.2019.12.022</a>","mla":"Borges Merjane, Carolina, et al. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” <i>Neuron</i>, vol. 105, Elsevier, 2020, pp. 992–1006, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">10.1016/j.neuron.2019.12.022</a>.","apa":"Borges Merjane, C., Kim, O., &#38; Jonas, P. M. (2020). Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">https://doi.org/10.1016/j.neuron.2019.12.022</a>","ista":"Borges Merjane C, Kim O, Jonas PM. 2020. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 105, 992–1006.","chicago":"Borges Merjane, Carolina, Olena Kim, and Peter M Jonas. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">https://doi.org/10.1016/j.neuron.2019.12.022</a>."},"ddc":["570"],"scopus_import":"1","file_date_updated":"2020-11-20T08:58:53Z","_id":"7473","year":"2020","abstract":[{"lang":"eng","text":"How structural and functional properties of synapses relate to each other is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms of synaptic transmission, and electron microscopy (EM) has provided insight into morphological properties of synapses. Here we describe an enhanced method for functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure freezing. We demonstrate that the improved method can be applied to intact networks in acute brain slices and organotypic slice cultures from mice. As a proof of concept, we probed vesicle pool changes during synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked vesicle pool and the functionally defined readily releasable pool and provide evidence of fast endocytosis at this synapse. Functional EM with acute slices and slice cultures has the potential to reveal the structural and functional mechanisms of transmission in intact, genetically perturbed, and disease-affected synapses."}],"date_updated":"2024-03-25T23:30:04Z","ec_funded":1,"month":"03","oa":1,"publication_identifier":{"issn":["0896-6273"]},"status":"public","department":[{"_id":"PeJo"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Neuron","page":"992-1006","date_created":"2020-02-10T15:59:45Z","has_accepted_license":"1","related_material":{"record":[{"id":"11196","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/","description":"News on IST Homepage","relation":"press_release"}]},"volume":105,"quality_controlled":"1","external_id":{"isi":["000520854700008"],"pmid":["31928842"]},"article_type":"original","article_processing_charge":"No","file":[{"access_level":"open_access","creator":"dernst","file_id":"8778","checksum":"3582664addf26859e86ac5bec3e01416","date_created":"2020-11-20T08:58:53Z","date_updated":"2020-11-20T08:58:53Z","file_name":"2020_Neuron_BorgesMerjane.pdf","success":1,"file_size":9712957,"content_type":"application/pdf","relation":"main_file"}],"author":[{"id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","orcid":"0000-0003-0005-401X","first_name":"Carolina","full_name":"Borges Merjane, Carolina"},{"full_name":"Kim, Olena","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M"}],"isi":1,"project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","grant_number":"708497","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","call_identifier":"H2020"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"},{"call_identifier":"FWF","name":"Zellkommunikation in Gesundheit und Krankheit","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","grant_number":"W01205"}],"day":"18","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"acknowledgement":"This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement No. 692692 and Marie Sklodowska-Curie 708497) and from Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27 Wittgenstein award and DK W1205-B09). We thank Johann Danzl and Ryuichi Shigemoto for critically reading the manuscript; Walter Kaufmann, Daniel Gutl, and Vanessa Zheden for extensive EM training, advice, and experimental assistance; Benjamin Suter for substantial help with light stimulation, ImageJ plugins for analysis, and manuscript editing; Florian Marr and Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; Julia König and Paul Wurzinger (Leica Microsystems) for helpful technical discussions; and Taija Makinen for providing the Prox1-CreERT2 mouse line.","pmid":1,"title":"Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier"},{"publisher":"IST Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Austrian High-Performance-Computing meeting (AHPC2020)","file":[{"relation":"main_file","content_type":"application/pdf","file_size":90899507,"date_updated":"2020-07-14T12:47:59Z","file_name":"BOOKLET_AHPC2020.final.pdf","date_created":"2020-02-19T06:53:38Z","creator":"schloegl","file_id":"7504","checksum":"49798edb9e57bbd6be18362d1d7b18a9","access_level":"open_access"}],"day":"19","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"editor":[{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl"},{"full_name":"Kiss, Janos","first_name":"Janos","last_name":"Kiss","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","full_name":"Elefante, Stefano"}],"quality_controlled":"1","article_processing_charge":"No","type":"book_editor","language":[{"iso":"eng"}],"department":[{"_id":"ScienComp"}],"has_accepted_license":"1","date_created":"2020-02-11T07:59:04Z","page":"72","month":"02","status":"public","publication_identifier":{"isbn":["978-3-99078-004-6"]},"oa":1,"place":"Klosterneuburg, Austria","_id":"7474","date_updated":"2023-05-16T07:48:28Z","abstract":[{"lang":"eng","text":"This booklet is a collection of abstracts presented at the AHPC conference."}],"year":"2020","citation":{"ama":"Schlögl A, Kiss J, Elefante S, eds. <i>Austrian High-Performance-Computing Meeting (AHPC2020)</i>. Klosterneuburg, Austria: IST Austria; 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7474\">10.15479/AT:ISTA:7474</a>","ieee":"A. Schlögl, J. Kiss, and S. Elefante, Eds., <i>Austrian High-Performance-Computing meeting (AHPC2020)</i>. Klosterneuburg, Austria: IST Austria, 2020.","short":"A. Schlögl, J. Kiss, S. Elefante, eds., Austrian High-Performance-Computing Meeting (AHPC2020), IST Austria, Klosterneuburg, Austria, 2020.","chicago":"Schlögl, Alois, Janos Kiss, and Stefano Elefante, eds. <i>Austrian High-Performance-Computing Meeting (AHPC2020)</i>. Klosterneuburg, Austria: IST Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7474\">https://doi.org/10.15479/AT:ISTA:7474</a>.","mla":"Schlögl, Alois, et al., editors. <i>Austrian High-Performance-Computing Meeting (AHPC2020)</i>. IST Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7474\">10.15479/AT:ISTA:7474</a>.","apa":"Schlögl, A., Kiss, J., &#38; Elefante, S. (Eds.). (2020). <i>Austrian High-Performance-Computing meeting (AHPC2020)</i>. Presented at the AHPC: Austrian High-Performance-Computing Meeting, Klosterneuburg, Austria: IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7474\">https://doi.org/10.15479/AT:ISTA:7474</a>","ista":"Schlögl A, Kiss J, Elefante S eds. 2020. Austrian High-Performance-Computing meeting (AHPC2020), Klosterneuburg, Austria: IST Austria, 72p."},"file_date_updated":"2020-07-14T12:47:59Z","ddc":["000"],"oa_version":"Published Version","date_published":"2020-02-19T00:00:00Z","conference":{"location":"Klosterneuburg, Austria","end_date":"2020-02-21","name":"AHPC: Austrian High-Performance-Computing Meeting","start_date":"2020-02-19"},"publication_status":"published","doi":"10.15479/AT:ISTA:7474"},{"citation":{"short":"M. Phuong, C. Lampert, in:, 8th International Conference on Learning Representations, 2020.","ama":"Phuong M, Lampert C. Functional vs. parametric equivalence of ReLU networks. In: <i>8th International Conference on Learning Representations</i>. ; 2020.","ieee":"M. Phuong and C. Lampert, “Functional vs. parametric equivalence of ReLU networks,” in <i>8th International Conference on Learning Representations</i>, Online, 2020.","apa":"Phuong, M., &#38; Lampert, C. (2020). Functional vs. parametric equivalence of ReLU networks. In <i>8th International Conference on Learning Representations</i>. Online.","ista":"Phuong M, Lampert C. 2020. Functional vs. parametric equivalence of ReLU networks. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","mla":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” <i>8th International Conference on Learning Representations</i>, 2020.","chicago":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” In <i>8th International Conference on Learning Representations</i>, 2020."},"quality_controlled":"1","related_material":{"link":[{"relation":"supplementary_material","url":"https://iclr.cc/virtual_2020/poster_Bylx-TNKvH.html"}],"record":[{"id":"9418","relation":"dissertation_contains","status":"public"}]},"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:59Z","ddc":["000"],"oa_version":"Published Version","type":"conference","department":[{"_id":"ChLa"}],"date_published":"2020-04-26T00:00:00Z","language":[{"iso":"eng"}],"conference":{"location":"Online","end_date":"2020-04-30","name":"ICLR: International Conference on Learning Representations","start_date":"2020-04-27"},"publication_status":"published","has_accepted_license":"1","publication":"8th International Conference on Learning Representations","date_created":"2020-02-11T09:07:37Z","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa":1,"title":"Functional vs. parametric equivalence of ReLU networks","author":[{"first_name":"Phuong","last_name":"Bui Thi Mai","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","full_name":"Bui Thi Mai, Phuong"},{"full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"}],"_id":"7481","file":[{"date_created":"2020-02-11T09:07:27Z","date_updated":"2020-07-14T12:47:59Z","file_name":"main.pdf","access_level":"open_access","file_id":"7482","checksum":"8d372ea5defd8cb8fdc430111ed754a9","creator":"bphuong","file_size":405469,"content_type":"application/pdf","relation":"main_file"}],"abstract":[{"lang":"eng","text":"We address the following question:  How redundant is the parameterisation of ReLU networks? Specifically, we consider transformations of the weight space which leave the function implemented by the network intact.  Two such transformations are known for feed-forward architectures:  permutation of neurons within a layer, and positive scaling of all incoming weights of a neuron coupled with inverse scaling of its outgoing weights. In this work, we show for architectures with non-increasing widths that permutation and scaling are in fact the only function-preserving weight transformations.  For any eligible architecture we give an explicit construction of a neural network such that any other network that implements the same function can be obtained from the original one by the application of permutations and rescaling.  The proof relies on a geometric understanding of boundaries between linear regions of ReLU networks, and we hope the developed mathematical tools are of independent interest."}],"date_updated":"2023-09-07T13:29:50Z","year":"2020","day":"26"},{"related_material":{"link":[{"url":"https://doi.org/10.1038/s41598-020-80651-0","relation":"erratum"}]},"external_id":{"pmid":["32042057"],"isi":["000560694800012"]},"volume":10,"quality_controlled":"1","article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"department":[{"_id":"CaBe"}],"type":"journal_article","date_created":"2020-02-16T23:00:49Z","publication":"Scientific reports","has_accepted_license":"1","title":"Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"2020_ScientificReport_Lopez.pdf","date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-18T07:43:21Z","creator":"dernst","checksum":"c780bd87476a9c9e12668ff66de3dc96","file_id":"7495","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":4703751}],"author":[{"last_name":"López De La Oliva","first_name":"Amada R.","full_name":"López De La Oliva, Amada R."},{"full_name":"Campos-Sandoval, José A.","last_name":"Campos-Sandoval","first_name":"José A."},{"last_name":"Gómez-García","first_name":"María C.","full_name":"Gómez-García, María C."},{"last_name":"Cardona","first_name":"Carolina","full_name":"Cardona, Carolina"},{"last_name":"Martín-Rufián","first_name":"Mercedes","full_name":"Martín-Rufián, Mercedes"},{"full_name":"Sialana, Fernando J.","last_name":"Sialana","first_name":"Fernando J."},{"last_name":"Castilla","first_name":"Laura","full_name":"Castilla, Laura"},{"last_name":"Bae","id":"3A5F7CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Narkhyun","full_name":"Bae, Narkhyun"},{"first_name":"Carolina","last_name":"Lobo","full_name":"Lobo, Carolina"},{"last_name":"Peñalver","first_name":"Ana","full_name":"Peñalver, Ana"},{"last_name":"García-Frutos","first_name":"Marina","full_name":"García-Frutos, Marina"},{"full_name":"Carro, David","first_name":"David","last_name":"Carro"},{"full_name":"Enrique, Victoria","first_name":"Victoria","last_name":"Enrique"},{"full_name":"Paz, José C.","first_name":"José C.","last_name":"Paz"},{"full_name":"Mirmira, Raghavendra G.","first_name":"Raghavendra G.","last_name":"Mirmira"},{"first_name":"Antonia","last_name":"Gutiérrez","full_name":"Gutiérrez, Antonia"},{"full_name":"Alonso, Francisco J.","last_name":"Alonso","first_name":"Francisco J."},{"full_name":"Segura, Juan A.","first_name":"Juan A.","last_name":"Segura"},{"full_name":"Matés, José M.","first_name":"José M.","last_name":"Matés"},{"last_name":"Lubec","first_name":"Gert","full_name":"Lubec, Gert"},{"first_name":"Javier","last_name":"Márquez","full_name":"Márquez, Javier"}],"isi":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"10","pmid":1,"citation":{"short":"A.R. López De La Oliva, J.A. Campos-Sandoval, M.C. Gómez-García, C. Cardona, M. Martín-Rufián, F.J. Sialana, L. Castilla, N. Bae, C. Lobo, A. Peñalver, M. García-Frutos, D. Carro, V. Enrique, J.C. Paz, R.G. Mirmira, A. Gutiérrez, F.J. Alonso, J.A. Segura, J.M. Matés, G. Lubec, J. Márquez, Scientific Reports 10 (2020).","ama":"López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, et al. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. <i>Scientific reports</i>. 2020;10(1). doi:<a href=\"https://doi.org/10.1038/s41598-020-58264-4\">10.1038/s41598-020-58264-4</a>","ieee":"A. R. López De La Oliva <i>et al.</i>, “Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation,” <i>Scientific reports</i>, vol. 10, no. 1. Springer Nature, 2020.","apa":"López De La Oliva, A. R., Campos-Sandoval, J. A., Gómez-García, M. C., Cardona, C., Martín-Rufián, M., Sialana, F. J., … Márquez, J. (2020). Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-020-58264-4\">https://doi.org/10.1038/s41598-020-58264-4</a>","ista":"López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, Cardona C, Martín-Rufián M, Sialana FJ, Castilla L, Bae N, Lobo C, Peñalver A, García-Frutos M, Carro D, Enrique V, Paz JC, Mirmira RG, Gutiérrez A, Alonso FJ, Segura JA, Matés JM, Lubec G, Márquez J. 2020. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific reports. 10(1), 2259.","mla":"López De La Oliva, Amada R., et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” <i>Scientific Reports</i>, vol. 10, no. 1, 2259, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41598-020-58264-4\">10.1038/s41598-020-58264-4</a>.","chicago":"López De La Oliva, Amada R., José A. Campos-Sandoval, María C. Gómez-García, Carolina Cardona, Mercedes Martín-Rufián, Fernando J. Sialana, Laura Castilla, et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” <i>Scientific Reports</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41598-020-58264-4\">https://doi.org/10.1038/s41598-020-58264-4</a>."},"intvolume":"        10","ddc":["570"],"file_date_updated":"2020-07-14T12:47:59Z","scopus_import":"1","date_published":"2020-02-10T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1038/s41598-020-58264-4","month":"02","oa":1,"publication_identifier":{"eissn":["20452322"]},"status":"public","_id":"7487","article_number":"2259","year":"2020","date_updated":"2023-08-18T06:35:13Z","abstract":[{"text":"Glutaminase (GA) catalyzes the first step in mitochondrial glutaminolysis playing a key role in cancer metabolic reprogramming. Humans express two types of GA isoforms: GLS and GLS2. GLS isozymes have been consistently related to cell proliferation, but the role of GLS2 in cancer remains poorly understood. GLS2 is repressed in many tumor cells and a better understanding of its function in tumorigenesis may further the development of new therapeutic approaches. We analyzed GLS2 expression in HCC, GBM and neuroblastoma cells, as well as in monkey COS-7 cells. We studied GLS2 expression after induction of differentiation with phorbol ester (PMA) and transduction with the full-length cDNA of GLS2. In parallel, we investigated cell cycle progression and levels of p53, p21 and c-Myc proteins. Using the baculovirus system, human GLS2 protein was overexpressed, purified and analyzed for posttranslational modifications employing a proteomics LC-MS/MS platform. We have demonstrated a dual targeting of GLS2 in human cancer cells. Immunocytochemistry and subcellular fractionation gave consistent results demonstrating nuclear and mitochondrial locations, with the latter being predominant. Nuclear targeting was confirmed in cancer cells overexpressing c-Myc- and GFP-tagged GLS2 proteins. We assessed the subnuclear location finding a widespread distribution of GLS2 in the nucleoplasm without clear overlapping with specific nuclear substructures. GLS2 expression and nuclear accrual notably increased by treatment of SH-SY5Y cells with PMA and it correlated with cell cycle arrest at G2/M, upregulation of tumor suppressor p53 and p21 protein. A similar response was obtained by overexpression of GLS2 in T98G glioma cells, including downregulation of oncogene c-Myc. Furthermore, human GLS2 was identified as being hypusinated by MS analysis, a posttranslational modification which may be relevant for its nuclear targeting and/or function. Our studies provide evidence for a tumor suppressor role of GLS2 in certain types of cancer. The data imply that GLS2 can be regarded as a highly mobile and multilocalizing protein translocated to both mitochondria and nuclei. Upregulation of GLS2 in cancer cells induced an antiproliferative response with cell cycle arrest at the G2/M phase.","lang":"eng"}],"issue":"1"},{"oa":1,"publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"status":"public","month":"02","year":"2020","abstract":[{"text":"Characteristic or classic phenotype of Cornelia de Lange syndrome (CdLS) is associated with a recognisable facial pattern. However, the heterogeneity in causal genes and the presence of overlapping syndromes have made it increasingly difficult to diagnose only by clinical features. DeepGestalt technology, and its app Face2Gene, is having a growing impact on the diagnosis and management of genetic diseases by analysing the features of affected individuals. Here, we performed a phenotypic study on a cohort of 49 individuals harbouring causative variants in known CdLS genes in order to evaluate Face2Gene utility and sensitivity in the clinical diagnosis of CdLS. Based on the profile images of patients, a diagnosis of CdLS was within the top five predicted syndromes for 97.9% of our cases and even listed as first prediction for 83.7%. The age of patients did not seem to affect the prediction accuracy, whereas our results indicate a correlation between the clinical score and affected genes. Furthermore, each gene presents a different pattern recognition that may be used to develop new neural networks with the goal of separating different genetic subtypes in CdLS. Overall, we conclude that computer-assisted image analysis based on deep learning could support the clinical diagnosis of CdLS.","lang":"eng"}],"issue":"3","date_updated":"2023-08-18T06:35:41Z","_id":"7488","article_number":"1042","ddc":["570"],"file_date_updated":"2020-07-14T12:47:59Z","scopus_import":"1","intvolume":"        21","citation":{"apa":"Latorre-Pellicer, A., Ascaso, Á., Trujillano, L., Gil-Salvador, M., Arnedo, M., Lucia-Campos, C., … Pié, J. (2020). Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms21031042\">https://doi.org/10.3390/ijms21031042</a>","mla":"Latorre-Pellicer, Ana, et al. “Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes.” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 3, 1042, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ijms21031042\">10.3390/ijms21031042</a>.","ista":"Latorre-Pellicer A, Ascaso Á, Trujillano L, Gil-Salvador M, Arnedo M, Lucia-Campos C, Antoñanzas-Pérez R, Marcos-Alcalde I, Parenti I, Bueno-Lozano G, Musio A, Puisac B, Kaiser FJ, Ramos FJ, Gómez-Puertas P, Pié J. 2020. Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. International Journal of Molecular Sciences. 21(3), 1042.","chicago":"Latorre-Pellicer, Ana, Ángela Ascaso, Laura Trujillano, Marta Gil-Salvador, Maria Arnedo, Cristina Lucia-Campos, Rebeca Antoñanzas-Pérez, et al. “Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes.” <i>International Journal of Molecular Sciences</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ijms21031042\">https://doi.org/10.3390/ijms21031042</a>.","ieee":"A. Latorre-Pellicer <i>et al.</i>, “Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes,” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 3. MDPI, 2020.","ama":"Latorre-Pellicer A, Ascaso Á, Trujillano L, et al. Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. <i>International Journal of Molecular Sciences</i>. 2020;21(3). doi:<a href=\"https://doi.org/10.3390/ijms21031042\">10.3390/ijms21031042</a>","short":"A. Latorre-Pellicer, Á. Ascaso, L. Trujillano, M. Gil-Salvador, M. Arnedo, C. Lucia-Campos, R. Antoñanzas-Pérez, I. Marcos-Alcalde, I. Parenti, G. Bueno-Lozano, A. Musio, B. Puisac, F.J. Kaiser, F.J. Ramos, P. Gómez-Puertas, J. Pié, International Journal of Molecular Sciences 21 (2020)."},"doi":"10.3390/ijms21031042","publication_status":"published","date_published":"2020-02-04T00:00:00Z","oa_version":"Published Version","title":"Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"MDPI","day":"04","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2020-07-14T12:47:59Z","file_name":"2020_IntMolecSciences_Latorre.pdf","date_created":"2020-02-18T07:49:22Z","creator":"dernst","checksum":"0e6658c4fe329d55d4d9bef01c5b15d0","file_id":"7496","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":4271234}],"author":[{"full_name":"Latorre-Pellicer, Ana","last_name":"Latorre-Pellicer","first_name":"Ana"},{"full_name":"Ascaso, Ángela","last_name":"Ascaso","first_name":"Ángela"},{"full_name":"Trujillano, Laura","first_name":"Laura","last_name":"Trujillano"},{"full_name":"Gil-Salvador, Marta","last_name":"Gil-Salvador","first_name":"Marta"},{"last_name":"Arnedo","first_name":"Maria","full_name":"Arnedo, Maria"},{"full_name":"Lucia-Campos, Cristina","first_name":"Cristina","last_name":"Lucia-Campos"},{"first_name":"Rebeca","last_name":"Antoñanzas-Pérez","full_name":"Antoñanzas-Pérez, Rebeca"},{"first_name":"Iñigo","last_name":"Marcos-Alcalde","full_name":"Marcos-Alcalde, Iñigo"},{"first_name":"Ilaria","last_name":"Parenti","id":"D93538B0-5B71-11E9-AC62-02EBE5697425","full_name":"Parenti, Ilaria"},{"first_name":"Gloria","last_name":"Bueno-Lozano","full_name":"Bueno-Lozano, Gloria"},{"full_name":"Musio, Antonio","last_name":"Musio","first_name":"Antonio"},{"full_name":"Puisac, Beatriz","first_name":"Beatriz","last_name":"Puisac"},{"full_name":"Kaiser, Frank J.","first_name":"Frank J.","last_name":"Kaiser"},{"first_name":"Feliciano J.","last_name":"Ramos","full_name":"Ramos, Feliciano J."},{"last_name":"Gómez-Puertas","first_name":"Paulino","full_name":"Gómez-Puertas, Paulino"},{"last_name":"Pié","first_name":"Juan","full_name":"Pié, Juan"}],"isi":1,"article_type":"original","article_processing_charge":"No","quality_controlled":"1","volume":21,"external_id":{"isi":["000522551606028"]},"publication":"International Journal of Molecular Sciences","date_created":"2020-02-16T23:00:49Z","has_accepted_license":"1","department":[{"_id":"GaNo"}],"language":[{"iso":"eng"}],"type":"journal_article"},{"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"author":[{"full_name":"Fischer, Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L"},{"orcid":"0000-0001-7252-8072","first_name":"Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","last_name":"Hensel","full_name":"Hensel, Sebastian"}],"isi":1,"file":[{"relation":"main_file","content_type":"application/pdf","success":1,"file_size":1897571,"date_updated":"2020-11-20T09:14:22Z","file_name":"2020_ArchRatMechAn_Fischer.pdf","date_created":"2020-11-20T09:14:22Z","creator":"dernst","checksum":"f107e21b58f5930876f47144be37cf6c","file_id":"8779","access_level":"open_access"}],"publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension","has_accepted_license":"1","page":"967-1087","date_created":"2020-02-16T23:00:50Z","publication":"Archive for Rational Mechanics and Analysis","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JuFi"}],"article_processing_charge":"Yes (via OA deal)","article_type":"original","external_id":{"isi":["000511060200001"]},"quality_controlled":"1","volume":236,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10007"}]},"date_updated":"2023-09-07T13:30:45Z","abstract":[{"lang":"eng","text":"In the present work, we consider the evolution of two fluids separated by a sharp interface in the presence of surface tension—like, for example, the evolution of oil bubbles in water. Our main result is a weak–strong uniqueness principle for the corresponding free boundary problem for the incompressible Navier–Stokes equation: as long as a strong solution exists, any varifold solution must coincide with it. In particular, in the absence of physical singularities, the concept of varifold solutions—whose global in time existence has been shown by Abels (Interfaces Free Bound 9(1):31–65, 2007) for general initial data—does not introduce a mechanism for non-uniqueness. The key ingredient of our approach is the construction of a relative entropy functional capable of controlling the interface error. If the viscosities of the two fluids do not coincide, even for classical (strong) solutions the gradient of the velocity field becomes discontinuous at the interface, introducing the need for a careful additional adaption of the relative entropy."}],"year":"2020","_id":"7489","status":"public","publication_identifier":{"eissn":["14320673"],"issn":["00039527"]},"oa":1,"month":"05","ec_funded":1,"publication_status":"published","doi":"10.1007/s00205-019-01486-2","oa_version":"Published Version","date_published":"2020-05-01T00:00:00Z","scopus_import":"1","file_date_updated":"2020-11-20T09:14:22Z","ddc":["530","532"],"intvolume":"       236","citation":{"chicago":"Fischer, Julian L, and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00205-019-01486-2\">https://doi.org/10.1007/s00205-019-01486-2</a>.","ista":"Fischer JL, Hensel S. 2020. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. 236, 967–1087.","mla":"Fischer, Julian L., and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 236, Springer Nature, 2020, pp. 967–1087, doi:<a href=\"https://doi.org/10.1007/s00205-019-01486-2\">10.1007/s00205-019-01486-2</a>.","apa":"Fischer, J. L., &#38; Hensel, S. (2020). Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-019-01486-2\">https://doi.org/10.1007/s00205-019-01486-2</a>","short":"J.L. Fischer, S. Hensel, Archive for Rational Mechanics and Analysis 236 (2020) 967–1087.","ieee":"J. L. Fischer and S. Hensel, “Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 236. Springer Nature, pp. 967–1087, 2020.","ama":"Fischer JL, Hensel S. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. <i>Archive for Rational Mechanics and Analysis</i>. 2020;236:967-1087. doi:<a href=\"https://doi.org/10.1007/s00205-019-01486-2\">10.1007/s00205-019-01486-2</a>"}},{"title":"Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants","publisher":"eLife Sciences Publications","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"23","pmid":1,"file":[{"file_size":7247468,"relation":"main_file","content_type":"application/pdf","date_created":"2020-02-18T07:21:16Z","date_updated":"2020-07-14T12:47:59Z","file_name":"2020_eLife_Narasimhan.pdf","access_level":"open_access","file_id":"7494","checksum":"2052daa4be5019534f3a42f200a09f32","creator":"dernst"}],"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"author":[{"first_name":"Madhumitha","orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Prizak, Roshan","last_name":"Prizak","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan"},{"full_name":"Kaufmann, Walter","first_name":"Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tan, Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang"},{"full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"isi":1,"article_type":"original","article_processing_charge":"No","external_id":{"isi":["000514104100001"],"pmid":["31971511"]},"volume":9,"quality_controlled":"1","date_created":"2020-02-16T23:00:50Z","publication":"eLife","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"},{"_id":"GaTk"},{"_id":"EM-Fac"},{"_id":"SyCr"}],"type":"journal_article","oa":1,"publication_identifier":{"eissn":["2050-084X"]},"status":"public","ec_funded":1,"month":"01","year":"2020","date_updated":"2023-08-18T06:33:07Z","abstract":[{"lang":"eng","text":"In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the plasma membrane but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes."}],"_id":"7490","article_number":"e52067","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"ddc":["570","580"],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:59Z","intvolume":"         9","citation":{"chicago":"Narasimhan, Madhumitha, Alexander J Johnson, Roshan Prizak, Walter Kaufmann, Shutang Tan, Barbara E Casillas Perez, and Jiří Friml. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.52067\">https://doi.org/10.7554/eLife.52067</a>.","apa":"Narasimhan, M., Johnson, A. J., Prizak, R., Kaufmann, W., Tan, S., Casillas Perez, B. E., &#38; Friml, J. (2020). Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.52067\">https://doi.org/10.7554/eLife.52067</a>","ista":"Narasimhan M, Johnson AJ, Prizak R, Kaufmann W, Tan S, Casillas Perez BE, Friml J. 2020. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife. 9, e52067.","mla":"Narasimhan, Madhumitha, et al. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” <i>ELife</i>, vol. 9, e52067, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.52067\">10.7554/eLife.52067</a>.","ieee":"M. Narasimhan <i>et al.</i>, “Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","ama":"Narasimhan M, Johnson AJ, Prizak R, et al. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.52067\">10.7554/eLife.52067</a>","short":"M. Narasimhan, A.J. Johnson, R. Prizak, W. Kaufmann, S. Tan, B.E. Casillas Perez, J. Friml, ELife 9 (2020)."},"publication_status":"published","doi":"10.7554/eLife.52067","date_published":"2020-01-23T00:00:00Z","oa_version":"Published Version"},{"status":"public","publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"oa":1,"month":"09","abstract":[{"text":"Endophytic fungi can be beneficial to plant growth. However, the molecular mechanisms underlying colonization of Acremonium spp. remain unclear. In this study, a novel endophytic Acremonium strain was isolated from the buds of Panax notoginseng and named Acremonium sp. D212. The Acremonium sp. D212 could colonize the roots of P. notoginseng, enhance the resistance of P. notoginseng to root rot disease, and promote root growth and saponin biosynthesis in P. notoginseng. Acremonium sp. D212 could secrete indole‐3‐acetic acid (IAA) and jasmonic acid (JA), and inoculation with the fungus increased the endogenous levels of IAA and JA in P. notoginseng. Colonization of the Acremonium sp. D212 in the roots of the rice line Nipponbare was dependent on the concentration of methyl jasmonate (MeJA) (2 to 15 μM) and 1‐naphthalenacetic acid (NAA) (10 to 20 μM). Moreover, the roots of the JA signalling‐defective coi1‐18 mutant were colonized by Acremonium sp. D212 to a lesser degree than those of the wild‐type Nipponbare and miR393b‐overexpressing lines, and the colonization was rescued by MeJA but not by NAA. It suggests that the cross‐talk between JA signalling and the auxin biosynthetic pathway plays a crucial role in the colonization of Acremonium sp. D212 in host plants.","lang":"eng"}],"issue":"9","date_updated":"2023-08-18T06:44:16Z","year":"2020","_id":"7497","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1111/jipb.12905","open_access":"1"}],"citation":{"short":"L. Han, X. Zhou, Y. Zhao, S. Zhu, L. Wu, Y. He, X. Ping, X. Lu, W. Huang, J. Qian, L. Zhang, X. Jiang, D. Zhu, C. Luo, S. Li, Q. Dong, Q. Fu, K. Deng, X. Wang, L. Wang, S. Peng, J. Wu, W. Li, J. Friml, Y. Zhu, X. He, Y. Du, Journal of Integrative Plant Biology 62 (2020) 1433–1451.","ama":"Han L, Zhou X, Zhao Y, et al. Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. <i>Journal of Integrative Plant Biology</i>. 2020;62(9):1433-1451. doi:<a href=\"https://doi.org/10.1111/jipb.12905\">10.1111/jipb.12905</a>","ieee":"L. Han <i>et al.</i>, “Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid,” <i>Journal of Integrative Plant Biology</i>, vol. 62, no. 9. Wiley, pp. 1433–1451, 2020.","ista":"Han L, Zhou X, Zhao Y, Zhu S, Wu L, He Y, Ping X, Lu X, Huang W, Qian J, Zhang L, Jiang X, Zhu D, Luo C, Li S, Dong Q, Fu Q, Deng K, Wang X, Wang L, Peng S, Wu J, Li W, Friml J, Zhu Y, He X, Du Y. 2020. Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. Journal of Integrative Plant Biology. 62(9), 1433–1451.","mla":"Han, L., et al. “Colonization of Endophyte Acremonium Sp. D212 in Panax Notoginseng and Rice Mediated by Auxin and Jasmonic Acid.” <i>Journal of Integrative Plant Biology</i>, vol. 62, no. 9, Wiley, 2020, pp. 1433–51, doi:<a href=\"https://doi.org/10.1111/jipb.12905\">10.1111/jipb.12905</a>.","apa":"Han, L., Zhou, X., Zhao, Y., Zhu, S., Wu, L., He, Y., … Du, Y. (2020). Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.12905\">https://doi.org/10.1111/jipb.12905</a>","chicago":"Han, L, X Zhou, Y Zhao, S Zhu, L Wu, Y He, X Ping, et al. “Colonization of Endophyte Acremonium Sp. D212 in Panax Notoginseng and Rice Mediated by Auxin and Jasmonic Acid.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/jipb.12905\">https://doi.org/10.1111/jipb.12905</a>."},"intvolume":"        62","doi":"10.1111/jipb.12905","publication_status":"published","oa_version":"Published Version","date_published":"2020-09-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Wiley","title":"Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid","pmid":1,"acknowledgement":"We thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for providing generous support with the IAA and JA measurements. We thank Professor Guohua Xu (Nanjing Agricultural University) for generously providing the Nipponbare rice expressing DR5::GUS. We thank Professor Muyuan Zhu (Zhejiang University) for generously providing a rice line expressing 35S::miR393b. We thank Professor Yinong Yang (Pennsylvania State University) for generously providing the rice line coi1-18. This work was supported by grants from the National Natural Science Foundation of China (31660501, 31460453, 31860064 and 31470382), the Major Special Program for Scientific Research, Education Department of Yunnan Province (ZD2015005), the Project sponsored by SRF for ROCS, SEM ([2013] 1792), the Major Science and Technique Programs in Yunnan Province (2016ZF001), the Key Projects of the Applied Basic Research Plan of Yunnan Province (2017FA018), the National Key R&D Program of China (2018YFD0201100) and the China Agriculture Research System (CARS-21).","day":"01","isi":1,"author":[{"first_name":"L","last_name":"Han","full_name":"Han, L"},{"full_name":"Zhou, X","last_name":"Zhou","first_name":"X"},{"full_name":"Zhao, Y","last_name":"Zhao","first_name":"Y"},{"full_name":"Zhu, S","first_name":"S","last_name":"Zhu"},{"first_name":"L","last_name":"Wu","full_name":"Wu, L"},{"full_name":"He, Y","first_name":"Y","last_name":"He"},{"full_name":"Ping, X","first_name":"X","last_name":"Ping"},{"full_name":"Lu, X","first_name":"X","last_name":"Lu"},{"first_name":"W","last_name":"Huang","full_name":"Huang, W"},{"first_name":"J","last_name":"Qian","full_name":"Qian, J"},{"first_name":"L","last_name":"Zhang","full_name":"Zhang, L"},{"first_name":"X","last_name":"Jiang","full_name":"Jiang, X"},{"last_name":"Zhu","first_name":"D","full_name":"Zhu, D"},{"last_name":"Luo","first_name":"C","full_name":"Luo, C"},{"first_name":"S","last_name":"Li","full_name":"Li, S"},{"full_name":"Dong, Q","last_name":"Dong","first_name":"Q"},{"last_name":"Fu","first_name":"Q","full_name":"Fu, Q"},{"full_name":"Deng, K","last_name":"Deng","first_name":"K"},{"full_name":"Wang, X","last_name":"Wang","first_name":"X"},{"first_name":"L","last_name":"Wang","full_name":"Wang, L"},{"first_name":"S","last_name":"Peng","full_name":"Peng, S"},{"full_name":"Wu, J","first_name":"J","last_name":"Wu"},{"first_name":"W","last_name":"Li","full_name":"Li, W"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Zhu, Y","first_name":"Y","last_name":"Zhu"},{"last_name":"He","first_name":"X","full_name":"He, X"},{"last_name":"Du","first_name":"Y","full_name":"Du, Y"}],"article_processing_charge":"No","article_type":"original","volume":62,"quality_controlled":"1","external_id":{"isi":["000515803000001"],"pmid":["31912615"]},"publication":"Journal of Integrative Plant Biology","page":"1433-1451","date_created":"2020-02-18T10:02:25Z","type":"journal_article","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}]},{"title":"Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis","publisher":"Wiley","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2020-11-20T09:32:10Z","date_updated":"2020-11-20T09:32:10Z","file_name":"2020_NewPhytologist_Mazur.pdf","access_level":"open_access","file_id":"8781","checksum":"17de728b0205979feb95ce663ba918c2","creator":"dernst","success":1,"file_size":2106888,"relation":"main_file","content_type":"application/pdf"}],"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"Cell surface receptor complexes for PIN polarity and auxin-mediated development","grant_number":"25239","_id":"2699E3D2-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Mazur, E","last_name":"Mazur","first_name":"E"},{"first_name":"Ivan","last_name":"Kulik","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","full_name":"Kulik, Ivan"},{"first_name":"Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","full_name":"Hajny, Jakub"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"isi":1,"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"acknowledgement":"We thank Mark Estelle, José M. Alonso and the Arabidopsis Stock Centre for providing seeds. We acknowledge the core facility CELLIM of CEITEC supported by the MEYS CR (LM2015062 Czech‐BioImaging) and Plant Sciences Core Facility of CEITEC Masaryk University for help in generating essential data. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement no. 742985) and the Czech Science Foundation GAČR (GA13‐40637S and GA18‐26981S) to JF. JH is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology. The authors declare no competing interests.","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8822"}]},"external_id":{"isi":["000514939700001"],"pmid":["31971254"]},"volume":226,"quality_controlled":"1","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"type":"journal_article","page":"1375-1383","date_created":"2020-02-18T10:03:47Z","publication":"New Phytologist","has_accepted_license":"1","ec_funded":1,"month":"06","oa":1,"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"status":"public","_id":"7500","year":"2020","date_updated":"2024-03-25T23:30:21Z","abstract":[{"text":"Plant survival depends on vascular tissues, which originate in a self‐organizing manner as strands of cells co‐directionally transporting the plant hormone auxin. The latter phenomenon (also known as auxin canalization) is classically hypothesized to be regulated by auxin itself via the effect of this hormone on the polarity of its own intercellular transport. Correlative observations supported this concept, but molecular insights remain limited.\r\nIn the current study, we established an experimental system based on the model Arabidopsis thaliana, which exhibits auxin transport channels and formation of vasculature strands in response to local auxin application.\r\nOur methodology permits the genetic analysis of auxin canalization under controllable experimental conditions. By utilizing this opportunity, we confirmed the dependence of auxin canalization on a PIN‐dependent auxin transport and nuclear, TIR1/AFB‐mediated auxin signaling. We also show that leaf venation and auxin‐mediated PIN repolarization in the root require TIR1/AFB signaling.\r\nFurther studies based on this experimental system are likely to yield better understanding of the mechanisms underlying auxin transport polarization in other developmental contexts.","lang":"eng"}],"issue":"5","intvolume":"       226","citation":{"mla":"Mazur, E., et al. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” <i>New Phytologist</i>, vol. 226, no. 5, Wiley, 2020, pp. 1375–83, doi:<a href=\"https://doi.org/10.1111/nph.16446\">10.1111/nph.16446</a>.","apa":"Mazur, E., Kulik, I., Hajny, J., &#38; Friml, J. (2020). Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16446\">https://doi.org/10.1111/nph.16446</a>","ista":"Mazur E, Kulik I, Hajny J, Friml J. 2020. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 226(5), 1375–1383.","chicago":"Mazur, E, Ivan Kulik, Jakub Hajny, and Jiří Friml. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” <i>New Phytologist</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/nph.16446\">https://doi.org/10.1111/nph.16446</a>.","short":"E. Mazur, I. Kulik, J. Hajny, J. Friml, New Phytologist 226 (2020) 1375–1383.","ama":"Mazur E, Kulik I, Hajny J, Friml J. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. <i>New Phytologist</i>. 2020;226(5):1375-1383. doi:<a href=\"https://doi.org/10.1111/nph.16446\">10.1111/nph.16446</a>","ieee":"E. Mazur, I. Kulik, J. Hajny, and J. Friml, “Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis,” <i>New Phytologist</i>, vol. 226, no. 5. Wiley, pp. 1375–1383, 2020."},"ddc":["580"],"file_date_updated":"2020-11-20T09:32:10Z","date_published":"2020-06-01T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1111/nph.16446"},{"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)"},"day":"24","acknowledgement":"We thank Christoph Lampert and Nikolaus Mayer for fruitful discussions. This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award) and the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie grant agreement No. 754411.","file":[{"access_level":"open_access","checksum":"80642fa0b6cd7da95dcd87d63789ad5e","file_id":"8540","creator":"dernst","date_created":"2020-09-21T07:12:32Z","file_name":"2020_ECAI_Henzinger.pdf","date_updated":"2020-09-21T07:12:32Z","success":1,"file_size":1692214,"relation":"main_file","content_type":"application/pdf"}],"isi":1,"author":[{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Lukina, Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","last_name":"Lukina","first_name":"Anna"},{"full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"title":"Outside the box: Abstraction-based monitoring of neural networks","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"IOS Press","license":"https://creativecommons.org/licenses/by-nc/4.0/","alternative_title":["Frontiers in Artificial Intelligence and Applications"],"publication":"24th European Conference on Artificial Intelligence","date_created":"2020-02-21T16:44:03Z","page":"2433-2440","has_accepted_license":"1","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"type":"conference","article_processing_charge":"No","quality_controlled":"1","volume":325,"external_id":{"arxiv":["1911.09032"],"isi":["000650971303002"]},"year":"2020","abstract":[{"text":"Neural networks have demonstrated unmatched performance in a range of classification tasks. Despite numerous efforts of the research community, novelty detection remains one of the significant limitations of neural networks. The ability to identify previously unseen inputs as novel is crucial for our understanding of the decisions made by neural networks. At runtime, inputs not falling into any of the categories learned during training cannot be classified correctly by the neural network. Existing approaches treat the neural network as a black box and try to detect novel inputs based on the confidence of the output predictions. However, neural networks are not trained to reduce their confidence for novel inputs, which limits the effectiveness of these approaches. We propose a framework to monitor a neural network by observing the hidden layers. We employ a common abstraction from program analysis - boxes - to identify novel behaviors in the monitored layers, i.e., inputs that cause behaviors outside the box. For each neuron, the boxes range over the values seen in training. The framework is efficient and flexible to achieve a desired trade-off between raising false warnings and detecting novel inputs. We illustrate the performance and the robustness to variability in the unknown classes on popular image-classification benchmarks.","lang":"eng"}],"arxiv":1,"date_updated":"2023-08-18T06:38:16Z","_id":"7505","oa":1,"status":"public","ec_funded":1,"month":"02","doi":"10.3233/FAIA200375","conference":{"end_date":"2020-09-08","location":"Santiago de Compostela, Spain","start_date":"2020-08-29","name":"ECAI: European Conference on Artificial Intelligence"},"publication_status":"published","date_published":"2020-02-24T00:00:00Z","oa_version":"Published Version","ddc":["000"],"file_date_updated":"2020-09-21T07:12:32Z","intvolume":"       325","citation":{"mla":"Henzinger, Thomas A., et al. “Outside the Box: Abstraction-Based Monitoring of Neural Networks.” <i>24th European Conference on Artificial Intelligence</i>, vol. 325, IOS Press, 2020, pp. 2433–40, doi:<a href=\"https://doi.org/10.3233/FAIA200375\">10.3233/FAIA200375</a>.","apa":"Henzinger, T. A., Lukina, A., &#38; Schilling, C. (2020). Outside the box: Abstraction-based monitoring of neural networks. In <i>24th European Conference on Artificial Intelligence</i> (Vol. 325, pp. 2433–2440). Santiago de Compostela, Spain: IOS Press. <a href=\"https://doi.org/10.3233/FAIA200375\">https://doi.org/10.3233/FAIA200375</a>","ista":"Henzinger TA, Lukina A, Schilling C. 2020. Outside the box: Abstraction-based monitoring of neural networks. 24th European Conference on Artificial Intelligence. ECAI: European Conference on Artificial Intelligence, Frontiers in Artificial Intelligence and Applications, vol. 325, 2433–2440.","chicago":"Henzinger, Thomas A, Anna Lukina, and Christian Schilling. “Outside the Box: Abstraction-Based Monitoring of Neural Networks.” In <i>24th European Conference on Artificial Intelligence</i>, 325:2433–40. IOS Press, 2020. <a href=\"https://doi.org/10.3233/FAIA200375\">https://doi.org/10.3233/FAIA200375</a>.","ieee":"T. A. Henzinger, A. Lukina, and C. Schilling, “Outside the box: Abstraction-based monitoring of neural networks,” in <i>24th European Conference on Artificial Intelligence</i>, Santiago de Compostela, Spain, 2020, vol. 325, pp. 2433–2440.","ama":"Henzinger TA, Lukina A, Schilling C. Outside the box: Abstraction-based monitoring of neural networks. In: <i>24th European Conference on Artificial Intelligence</i>. Vol 325. IOS Press; 2020:2433-2440. doi:<a href=\"https://doi.org/10.3233/FAIA200375\">10.3233/FAIA200375</a>","short":"T.A. Henzinger, A. Lukina, C. Schilling, in:, 24th European Conference on Artificial Intelligence, IOS Press, 2020, pp. 2433–2440."}}]