[{"year":"2020","external_id":{"pmid":["31696764"],"isi":["000494909300001"]},"date_updated":"2023-10-17T09:01:48Z","issue":"1","oa":1,"month":"01","intvolume":"        15","date_published":"2020-01-01T00:00:00Z","article_number":"1687175","isi":1,"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054","open_access":"1"}],"doi":"10.1080/15592324.2019.1687175","publication":"Plant Signaling & Behavior","date_created":"2020-01-30T10:12:04Z","status":"public","day":"01","pmid":1,"volume":15,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"JiFr"}],"title":"Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593","last_name":"Sinclair","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A"},{"full_name":"Krämer, U.","last_name":"Krämer","first_name":"U."}],"publisher":"Taylor & Francis","publication_status":"published","_id":"7416","quality_controlled":"1","citation":{"chicago":"Sinclair, Scott A, and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis, 2020. <a href=\"https://doi.org/10.1080/15592324.2019.1687175\">https://doi.org/10.1080/15592324.2019.1687175</a>.","ama":"Sinclair SA, Krämer U. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. <i>Plant Signaling &#38; Behavior</i>. 2020;15(1). doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687175\">10.1080/15592324.2019.1687175</a>","ista":"Sinclair SA, Krämer U. 2020. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling &#38; Behavior. 15(1), 1687175.","short":"S.A. Sinclair, U. Krämer, Plant Signaling &#38; Behavior 15 (2020).","ieee":"S. A. Sinclair and U. Krämer, “Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation,” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1. Taylor &#38; Francis, 2020.","mla":"Sinclair, Scott A., and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1, 1687175, Taylor &#38; Francis, 2020, doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687175\">10.1080/15592324.2019.1687175</a>.","apa":"Sinclair, S. A., &#38; Krämer, U. (2020). Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15592324.2019.1687175\">https://doi.org/10.1080/15592324.2019.1687175</a>"},"publication_identifier":{"issn":["1559-2324"]},"type":"journal_article","scopus_import":"1","abstract":[{"text":"Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2 (MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status, and not to the local Zn status in roots. This provided evidence for shoot-to-root communication in the acclimation of plants to Zn deficiency. Zn-deficient soils limit both the yield and quality of agricultural crops and can result in clinically relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency during cultivation of the model plant Arabidopsis thaliana on agar-solidified media is difficult because trace element contaminations are present in almost all commercially available agars. Here, we demonstrate root morphological acclimations to Zn deficiency on agar-solidified medium following the effective removal of contaminants. These advancements allow reproducible phenotyping toward understanding fundamental plant responses to deficiencies of Zn and other essential trace elements.","lang":"eng"}]},{"article_number":"e1687185","date_published":"2020-01-01T00:00:00Z","intvolume":"        15","month":"01","oa":1,"issue":"1","date_updated":"2023-09-06T15:23:04Z","external_id":{"pmid":["31696770"],"isi":["000494907500001"]},"year":"2020","volume":15,"pmid":1,"day":"01","status":"public","date_created":"2020-01-30T10:14:14Z","publication":"Plant Signaling & Behavior","doi":"10.1080/15592324.2019.1687185","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012154"}],"oa_version":"Submitted Version","isi":1,"publisher":"Informa UK Limited","title":"Regulation of acetylation of plant cell wall components is complex and responds to external stimuli","author":[{"last_name":"Sinclair","orcid":"0000-0002-4566-0593","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A","full_name":"Sinclair, Scott A"},{"first_name":"S.","last_name":"Gille","full_name":"Gille, S."},{"last_name":"Pauly","first_name":"M.","full_name":"Pauly, M."},{"first_name":"U.","last_name":"Krämer","full_name":"Krämer, U."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JiFr"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"Previously, we reported that the allelic de-etiolated by zinc (dez) and trichome birefringence (tbr) mutants exhibit photomorphogenic development in the dark, which is enhanced by high Zn. TRICHOME BIREFRINGENCE-LIKE proteins had been implicated in transferring acetyl groups to various hemicelluloses. Pectin O-acetylation levels were lower in dark-grown dez seedlings than in the wild type. We observed Zn-enhanced photomorphogenesis in the dark also in the reduced wall acetylation 2 (rwa2-3) mutant, which exhibits lowered O-acetylation levels of cell wall macromolecules including pectins and xyloglucans, supporting a role for cell wall macromolecule O-acetylation in the photomorphogenic phenotypes of rwa2-3 and dez. Application of very short oligogalacturonides (vsOGs) restored skotomorphogenesis in dark-grown dez and rwa2-3. Here we demonstrate that in dez, O-acetylation of non-pectin cell wall components, notably of xyloglucan, is enhanced. Our results highlight the complexity of cell wall homeostasis and indicate against an influence of xyloglucan O-acetylation on light-dependent seedling development."}],"type":"journal_article","citation":{"mla":"Sinclair, Scott A., et al. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1, e1687185, Informa UK Limited, 2020, doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687185\">10.1080/15592324.2019.1687185</a>.","apa":"Sinclair, S. A., Gille, S., Pauly, M., &#38; Krämer, U. (2020). Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. <i>Plant Signaling &#38; Behavior</i>. Informa UK Limited. <a href=\"https://doi.org/10.1080/15592324.2019.1687185\">https://doi.org/10.1080/15592324.2019.1687185</a>","chicago":"Sinclair, Scott A, S. Gille, M. Pauly, and U. Krämer. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” <i>Plant Signaling &#38; Behavior</i>. Informa UK Limited, 2020. <a href=\"https://doi.org/10.1080/15592324.2019.1687185\">https://doi.org/10.1080/15592324.2019.1687185</a>.","short":"S.A. Sinclair, S. Gille, M. Pauly, U. Krämer, Plant Signaling &#38; Behavior 15 (2020).","ieee":"S. A. Sinclair, S. Gille, M. Pauly, and U. Krämer, “Regulation of acetylation of plant cell wall components is complex and responds to external stimuli,” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1. Informa UK Limited, 2020.","ista":"Sinclair SA, Gille S, Pauly M, Krämer U. 2020. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling &#38; Behavior. 15(1), e1687185.","ama":"Sinclair SA, Gille S, Pauly M, Krämer U. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. <i>Plant Signaling &#38; Behavior</i>. 2020;15(1). doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687185\">10.1080/15592324.2019.1687185</a>"},"publication_identifier":{"issn":["1559-2324"]},"quality_controlled":"1","_id":"7417","publication_status":"published"},{"quality_controlled":"1","_id":"7426","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"type":"journal_article","file_date_updated":"2022-05-16T22:30:04Z","citation":{"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>.","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>","short":"M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020).","ista":"Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 100856.","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.","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>."},"publication_identifier":{"issn":["1751-570X"]},"publication_status":"published","project":[{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF"},{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Abstraction based verification of stability of polyhedral switched systems","author":[{"last_name":"Garcia Soto","orcid":"0000−0003−2936−5719","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","full_name":"Garcia Soto, Miriam"},{"last_name":"Prabhakar","first_name":"Pavithra","full_name":"Prabhakar, Pavithra"}],"file":[{"embargo":"2022-05-15","checksum":"560abfddb53f9fe921b6744f59f2cfaa","access_level":"open_access","relation":"main_file","creator":"dernst","file_size":818774,"content_type":"application/pdf","file_id":"8688","date_updated":"2022-05-16T22:30:04Z","date_created":"2020-10-21T13:16:45Z","file_name":"2020_NAHS_GarciaSoto.pdf"}],"publisher":"Elsevier","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"article_processing_charge":"No","day":"01","status":"public","ddc":["000"],"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2020-02-02T23:00:59Z","volume":36,"oa_version":"Submitted Version","isi":1,"publication":"Nonlinear Analysis: Hybrid Systems","doi":"10.1016/j.nahs.2020.100856","oa":1,"issue":"5","date_updated":"2023-08-17T14:32:54Z","article_number":"100856","date_published":"2020-05-01T00:00:00Z","month":"05","intvolume":"        36","year":"2020","external_id":{"isi":["000528828600003"]}},{"publisher":"Cell Press","has_accepted_license":"1","author":[{"full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan"},{"first_name":"Melinda F","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","last_name":"Abas","full_name":"Abas, Melinda F"},{"full_name":"Verstraeten, Inge","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","last_name":"Verstraeten"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous"},{"full_name":"Molnar, Gergely","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Molnar"},{"last_name":"Hajny","orcid":"0000-0003-2140-7195","first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub"},{"full_name":"Lasák, Pavel","last_name":"Lasák","first_name":"Pavel"},{"full_name":"Petřík, Ivan","first_name":"Ivan","last_name":"Petřík"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"full_name":"Pospíšil, Jiří","last_name":"Pospíšil","first_name":"Jiří"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Salicylic acid targets protein phosphatase 2A to attenuate growth in plants","file":[{"content_type":"application/pdf","file_id":"8555","creator":"dernst","file_size":5360135,"access_level":"open_access","relation":"main_file","checksum":"16f7d51fe28f91c21e4896a2028df40b","success":1,"file_name":"2020_CurrentBiology_Tan.pdf","date_created":"2020-09-22T09:51:28Z","date_updated":"2020-09-22T09:51:28Z"}],"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"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."}],"scopus_import":"1","type":"journal_article","file_date_updated":"2020-09-22T09:51:28Z","citation":{"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>","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>.","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>","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.","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.","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>."},"publication_identifier":{"issn":["09609822"]},"quality_controlled":"1","_id":"7427","publication_status":"published","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"name":"Long Term Fellowship","_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015"}],"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). ","date_published":"2020-02-03T00:00:00Z","intvolume":"        30","month":"02","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa":1,"issue":"3","date_updated":"2024-03-25T23:30:20Z","external_id":{"pmid":["31956021"],"isi":["000511287900018"]},"page":"381-395.e8","year":"2020","volume":30,"pmid":1,"status":"public","day":"03","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"date_created":"2020-02-02T23:01:00Z","publication":"Current Biology","doi":"10.1016/j.cub.2019.11.058","oa_version":"Published Version","ec_funded":1,"isi":1,"related_material":{"record":[{"id":"8822","status":"public","relation":"dissertation_contains"}]}},{"publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors","author":[{"full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lopes","first_name":"P. L.S.","full_name":"Lopes, P. L.S."},{"first_name":"Pavan","last_name":"Hosur","full_name":"Hosur, Pavan"},{"first_name":"Matthew J.","last_name":"Gilbert","full_name":"Gilbert, Matthew J."},{"first_name":"Pouyan","last_name":"Ghaemi","full_name":"Ghaemi, Pouyan"}],"article_processing_charge":"No","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"article_type":"original","publication_identifier":{"issn":["24699950"],"eissn":["24699969"]},"citation":{"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>.","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>","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>.","short":"A. Ghazaryan, P.L.S. Lopes, P. Hosur, M.J. Gilbert, P. Ghaemi, Physical Review B 101 (2020).","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.","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.","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>"},"type":"journal_article","abstract":[{"lang":"eng","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."}],"arxiv":1,"scopus_import":"1","_id":"7428","quality_controlled":"1","publication_status":"published","intvolume":"       101","month":"01","date_published":"2020-01-13T00:00:00Z","article_number":"020504","date_updated":"2024-02-28T13:11:13Z","issue":"2","oa":1,"external_id":{"arxiv":["1907.02077"],"isi":["000506843500001"]},"year":"2020","volume":101,"date_created":"2020-02-02T23:01:01Z","status":"public","day":"13","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.02077"}],"doi":"10.1103/PhysRevB.101.020504","publication":"Physical Review B","isi":1,"oa_version":"Preprint"},{"scopus_import":"1","arxiv":1,"abstract":[{"lang":"eng","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."}],"type":"journal_article","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>.","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>","short":"A. Kolchinsky, B. Corominas-Murtra, Journal of the Royal Society Interface 17 (2020).","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.","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>.","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>"},"publication_identifier":{"eissn":["17425662"]},"quality_controlled":"1","_id":"7431","publication_status":"published","publisher":"The Royal Society","author":[{"last_name":"Kolchinsky","first_name":"Artemy","full_name":"Kolchinsky, Artemy"},{"full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Decomposing information into copying versus transformation","department":[{"_id":"EdHa"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"volume":17,"pmid":1,"day":"29","status":"public","date_created":"2020-02-02T23:01:03Z","publication":"Journal of the Royal Society Interface","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.10693"}],"doi":"10.1098/rsif.2019.0623","oa_version":"Preprint","isi":1,"article_number":"0623","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. ","date_published":"2020-01-29T00:00:00Z","intvolume":"        17","month":"01","oa":1,"issue":"162","date_updated":"2023-08-17T14:31:28Z","external_id":{"arxiv":["1903.10693"],"pmid":["31964273"],"isi":["000538369800002"]},"year":"2020"},{"related_material":{"record":[{"id":"6608","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7460","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","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"},"date_created":"2020-02-06T14:56:53Z","ddc":["514"],"supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"}],"day":"10","status":"public","year":"2020","page":"155","date_updated":"2023-09-07T13:15:30Z","keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"oa":1,"month":"02","date_published":"2020-02-10T00:00:00Z","alternative_title":["ISTA Thesis"],"publication_status":"published","_id":"7460","publication_identifier":{"issn":["2663-337X"]},"citation":{"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>","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>.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","ieee":"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>","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>."},"type":"dissertation","file_date_updated":"2020-07-14T12:47:58Z","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."}],"language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"file":[{"file_name":"thesis_ist-final_noack.pdf","date_updated":"2020-07-14T12:47:58Z","date_created":"2020-02-06T14:43:54Z","creator":"koelsboe","file_size":76195184,"file_id":"7461","content_type":"application/pdf","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","access_level":"open_access","relation":"main_file"},{"creator":"koelsboe","file_size":122103715,"content_type":"application/x-zip-compressed","file_id":"7462","checksum":"7a52383c812b0be64d3826546509e5a4","relation":"source_file","access_level":"closed","description":"latex source files, figures","file_name":"latex-files.zip","date_updated":"2020-07-14T12:47:58Z","date_created":"2020-02-06T14:52:45Z"}],"author":[{"last_name":"Ölsböck","orcid":"0000-0002-4672-8297","first_name":"Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","full_name":"Ölsböck, Katharina"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"The hole system of triangulated shapes","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria"},{"has_accepted_license":"1","publisher":"Public Library of Science","title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","author":[{"full_name":"Dick, Robert A.","last_name":"Dick","first_name":"Robert A."},{"full_name":"Xu, Chaoyi","last_name":"Xu","first_name":"Chaoyi"},{"full_name":"Morado, Dustin R.","first_name":"Dustin R.","last_name":"Morado"},{"full_name":"Kravchuk, Vladyslav","first_name":"Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","last_name":"Kravchuk","orcid":"0000-0001-9523-9089"},{"full_name":"Ricana, Clifton L.","last_name":"Ricana","first_name":"Clifton L."},{"full_name":"Lyddon, Terri D.","first_name":"Terri D.","last_name":"Lyddon"},{"full_name":"Broad, Arianna M.","first_name":"Arianna M.","last_name":"Broad"},{"full_name":"Feathers, J. Ryan","last_name":"Feathers","first_name":"J. Ryan"},{"last_name":"Johnson","first_name":"Marc C.","full_name":"Johnson, Marc C."},{"first_name":"Volker M.","last_name":"Vogt","full_name":"Vogt, Volker M."},{"last_name":"Perilla","first_name":"Juan R.","full_name":"Perilla, Juan R."},{"full_name":"Briggs, John A. G.","first_name":"John A. G.","last_name":"Briggs"},{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2020_PLOSPatho_Dick.pdf","date_created":"2020-02-11T10:07:28Z","date_updated":"2020-07-14T12:47:59Z","file_id":"7484","content_type":"application/pdf","creator":"dernst","file_size":4551246,"checksum":"a297f54d1fef0efe4789ca00f37f241e","access_level":"open_access","relation":"main_file"}],"article_processing_charge":"No","department":[{"_id":"FlSc"}],"language":[{"iso":"eng"}],"article_type":"original","publication_identifier":{"issn":["1553-7374"]},"citation":{"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>.","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>","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>.","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>","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).","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.","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."},"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"}],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:59Z","type":"journal_article","_id":"7464","quality_controlled":"1","project":[{"call_identifier":"FWF","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid"}],"publication_status":"published","date_published":"2020-01-27T00:00:00Z","intvolume":"        16","month":"01","article_number":"e1008277","date_updated":"2023-10-17T12:29:34Z","oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"issue":"1","external_id":{"isi":["000510746400010"],"pmid":["31986188"]},"year":"2020","volume":16,"pmid":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_created":"2020-02-06T18:47:17Z","day":"27","status":"public","publication":"PLOS Pathogens","doi":"10.1371/journal.ppat.1008277","related_material":{"record":[{"id":"9723","relation":"research_data","status":"deleted"}]},"oa_version":"Published Version","isi":1},{"volume":293,"status":"public","day":"01","date_created":"2020-02-09T23:00:50Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"publication":"Plant Science","doi":"10.1016/j.plantsci.2020.110414","oa_version":"Published Version","ec_funded":1,"isi":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11626"}]},"article_number":"110414","date_published":"2020-04-01T00:00:00Z","intvolume":"       293","month":"04","oa":1,"issue":"4","date_updated":"2023-08-17T14:37:32Z","external_id":{"isi":["000520609800009"]},"year":"2020","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:59Z","type":"journal_article","publication_identifier":{"issn":["01689452"],"eissn":["18732259"]},"citation":{"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.","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.","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>","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>.","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>."},"quality_controlled":"1","_id":"7465","publication_status":"published","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"publisher":"Elsevier","has_accepted_license":"1","title":"Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Mazur, Ewa","first_name":"Ewa","last_name":"Mazur"},{"full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","orcid":"0000-0003-1286-7368","last_name":"Gallei"},{"full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","last_name":"Adamowski","orcid":"0000-0001-6463-5257"},{"last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","full_name":"Han, Huibin"},{"last_name":"Robert","first_name":"Hélène S.","full_name":"Robert, Hélène S."},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"file":[{"file_id":"7471","content_type":"application/pdf","file_size":3499069,"creator":"dernst","checksum":"f7f27c6a8fea985ceb9279be2204461c","access_level":"open_access","relation":"main_file","file_name":"2020_PlantScience_Mazur.pdf","date_created":"2020-02-10T08:59:36Z","date_updated":"2020-07-14T12:47:59Z"}],"department":[{"_id":"JiFr"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}]},{"publisher":"eLife Sciences Publications","has_accepted_license":"1","file":[{"date_created":"2020-02-10T08:53:16Z","date_updated":"2020-07-14T12:47:59Z","file_name":"2020_eLife_Kierdorf.pdf","checksum":"3a072be843f416c7a7d532a51dc0addb","access_level":"open_access","relation":"main_file","file_id":"7470","content_type":"application/pdf","file_size":4959933,"creator":"dernst"}],"author":[{"full_name":"Kierdorf, Katrin","first_name":"Katrin","last_name":"Kierdorf"},{"full_name":"Hersperger, Fabian","first_name":"Fabian","last_name":"Hersperger"},{"full_name":"Sharrock, Jessica","last_name":"Sharrock","first_name":"Jessica"},{"last_name":"Vincent","first_name":"Crystal M.","full_name":"Vincent, Crystal M."},{"first_name":"Pinar","last_name":"Ustaoglu","full_name":"Ustaoglu, Pinar"},{"full_name":"Dou, Jiawen","last_name":"Dou","first_name":"Jiawen"},{"id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila","orcid":"0000-0002-1819-198X","last_name":"György","full_name":"György, Attila"},{"last_name":"Groß","first_name":"Olaf","full_name":"Groß, Olaf"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"},{"first_name":"Marc S.","last_name":"Dionne","full_name":"Dionne, Marc S."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila","department":[{"_id":"DaSi"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:59Z","type":"journal_article","scopus_import":"1","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."}],"publication_identifier":{"eissn":["2050084X"]},"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>.","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.","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).","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.","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>","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>"},"quality_controlled":"1","_id":"7466","publication_status":"published","project":[{"name":"Drosophila TNFa´s Funktion in Immunzellen","_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29638"}],"article_number":"e51595","month":"01","intvolume":"         9","date_published":"2020-01-20T00:00:00Z","oa":1,"date_updated":"2023-08-17T14:36:39Z","external_id":{"isi":["000512304800001"]},"year":"2020","volume":9,"day":"20","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-02-09T23:00:51Z","ddc":["570"],"doi":"10.7554/eLife.51595","publication":"eLife","isi":1,"oa_version":"Published Version"},{"year":"2020","page":"2120-2129","external_id":{"isi":["000526598300012"]},"issue":"3","oa":1,"date_updated":"2023-08-17T14:36:16Z","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":"         3","month":"03","date_published":"2020-03-01T00:00:00Z","isi":1,"oa_version":"Submitted Version","ec_funded":1,"doi":"10.1021/acsaem.9b02137","publication":"ACS Applied Energy Materials","day":"01","status":"public","date_created":"2020-02-09T23:00:52Z","ddc":["540"],"volume":3,"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"MaIb"}],"article_processing_charge":"No","file":[{"file_name":"2020_ACSAppliedEnergyMat_Cadavid.pdf","success":1,"date_updated":"2022-08-23T08:34:17Z","date_created":"2022-08-23T08:34:17Z","creator":"dernst","file_size":6423548,"content_type":"application/pdf","file_id":"11942","relation":"main_file","access_level":"open_access","checksum":"f23be731a766a480c77c962c1380315c"}],"author":[{"full_name":"Cadavid, Doris","first_name":"Doris","last_name":"Cadavid"},{"full_name":"Ortega, Silvia","last_name":"Ortega","first_name":"Silvia"},{"last_name":"Illera","first_name":"Sergio","full_name":"Illera, Sergio"},{"full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"full_name":"Shavel, Alexey","last_name":"Shavel","first_name":"Alexey"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"full_name":"López, Antonio M.","last_name":"López","first_name":"Antonio M."},{"first_name":"Germán","last_name":"Noriega","full_name":"Noriega, Germán"},{"full_name":"Durá, Oscar Juan","first_name":"Oscar Juan","last_name":"Durá"},{"last_name":"López De La Torre","first_name":"M. A.","full_name":"López De La Torre, M. A."},{"last_name":"Prades","first_name":"Joan Daniel","full_name":"Prades, Joan Daniel"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials","publisher":"American Chemical Society","has_accepted_license":"1","publication_status":"published","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","_id":"7467","type":"journal_article","file_date_updated":"2022-08-23T08:34:17Z","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."}],"scopus_import":"1","publication_identifier":{"eissn":["2574-0962"]},"citation":{"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>.","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>","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.","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.","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."}},{"article_processing_charge":"No","department":[{"_id":"JoCs"}],"language":[{"iso":"eng"}],"article_type":"original","publisher":"Elsevier","author":[{"full_name":"Käfer, Karola","last_name":"Käfer","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola"},{"full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","last_name":"Nardin","first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Blahna","id":"3EA859AE-F248-11E8-B48F-1D18A9856A87","first_name":"Karel","full_name":"Blahna, Karel"},{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Replay of behavioral sequences in the medial prefrontal cortex during rule switching","project":[{"call_identifier":"FP7","grant_number":"607616","name":"Inter-and intracellular signalling in schizophrenia","_id":"257BBB4C-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publication_identifier":{"issn":["0896-6273"]},"citation":{"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.","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.","short":"K. Käfer, M. Nardin, K. Blahna, J.L. Csicsvari, Neuron 106 (2020) P154–165.e6.","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>","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>."},"type":"journal_article","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"}],"scopus_import":"1","_id":"7472","quality_controlled":"1","external_id":{"pmid":["32032512"],"isi":["000525319300016"]},"page":"P154-165.e6","year":"2020","month":"04","intvolume":"       106","date_published":"2020-04-08T00:00:00Z","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 ).","date_updated":"2023-08-17T14:38:02Z","issue":"1","oa":1,"acknowledged_ssus":[{"_id":"M-Shop"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2020.01.015","open_access":"1"}],"doi":"10.1016/j.neuron.2020.01.015","publication":"Neuron","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/this-brain-area-helps-us-decide/","description":"News on IST Homepage"}]},"isi":1,"ec_funded":1,"oa_version":"Published Version","pmid":1,"volume":106,"date_created":"2020-02-10T15:45:48Z","status":"public","day":"08"},{"date_updated":"2024-03-25T23:30:04Z","oa":1,"intvolume":"       105","month":"03","date_published":"2020-03-18T00:00:00Z","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.","year":"2020","external_id":{"pmid":["31928842"],"isi":["000520854700008"]},"page":"992-1006","date_created":"2020-02-10T15:59:45Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["570"],"day":"18","status":"public","pmid":1,"volume":105,"related_material":{"record":[{"id":"11196","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/","description":"News on IST Homepage","relation":"press_release"}]},"isi":1,"oa_version":"Published Version","ec_funded":1,"doi":"10.1016/j.neuron.2019.12.022","publication":"Neuron","file":[{"success":1,"file_name":"2020_Neuron_BorgesMerjane.pdf","date_created":"2020-11-20T08:58:53Z","date_updated":"2020-11-20T08:58:53Z","content_type":"application/pdf","file_id":"8778","file_size":9712957,"creator":"dernst","checksum":"3582664addf26859e86ac5bec3e01416","access_level":"open_access","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices","author":[{"full_name":"Borges Merjane, Carolina","first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","orcid":"0000-0003-0005-401X"},{"full_name":"Kim, Olena","first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","last_name":"Kim"},{"full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"has_accepted_license":"1","publisher":"Elsevier","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"PeJo"}],"_id":"7473","quality_controlled":"1","publication_identifier":{"issn":["0896-6273"]},"citation":{"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>","short":"C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006.","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.","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.","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>.","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>","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>."},"type":"journal_article","file_date_updated":"2020-11-20T08:58:53Z","scopus_import":"1","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."}],"project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020"},{"_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","call_identifier":"H2020","grant_number":"708497"},{"grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","name":"Zellkommunikation in Gesundheit und Krankheit","call_identifier":"FWF","grant_number":"W01205"}],"publication_status":"published"},{"quality_controlled":"1","editor":[{"full_name":"Schlögl, Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kiss","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","first_name":"Janos","full_name":"Kiss, Janos"},{"full_name":"Elefante, Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","last_name":"Elefante"}],"_id":"7474","type":"book_editor","file_date_updated":"2020-07-14T12:47:59Z","abstract":[{"lang":"eng","text":"This booklet is a collection of abstracts presented at the AHPC conference."}],"citation":{"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>","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>.","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.","ista":"Schlögl A, Kiss J, Elefante S eds. 2020. Austrian High-Performance-Computing meeting (AHPC2020), Klosterneuburg, Austria: IST Austria, 72p.","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>."},"publication_identifier":{"isbn":["978-3-99078-004-6"]},"publication_status":"published","place":"Klosterneuburg, Austria","file":[{"file_name":"BOOKLET_AHPC2020.final.pdf","date_created":"2020-02-19T06:53:38Z","date_updated":"2020-07-14T12:47:59Z","file_size":90899507,"creator":"schloegl","file_id":"7504","content_type":"application/pdf","relation":"main_file","checksum":"49798edb9e57bbd6be18362d1d7b18a9","access_level":"open_access"}],"title":"Austrian High-Performance-Computing meeting (AHPC2020)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IST Austria","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"ScienComp"}],"article_processing_charge":"No","status":"public","day":"19","date_created":"2020-02-11T07:59:04Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"oa_version":"Published Version","doi":"10.15479/AT:ISTA:7474","oa":1,"date_updated":"2023-05-16T07:48:28Z","month":"02","date_published":"2020-02-19T00:00:00Z","year":"2020","conference":{"location":"Klosterneuburg, Austria","end_date":"2020-02-21","start_date":"2020-02-19","name":"AHPC: Austrian High-Performance-Computing Meeting"},"page":"72"},{"intvolume":"       124","month":"01","date_published":"2020-01-24T00:00:00Z","article_number":"036802","date_updated":"2021-01-12T08:13:48Z","issue":"3","oa":1,"external_id":{"arxiv":["1905.05505"]},"year":"2020","volume":124,"date_created":"2020-02-11T08:50:02Z","status":"public","day":"24","main_file_link":[{"url":"https://arxiv.org/abs/1905.05505","open_access":"1"}],"doi":"10.1103/physrevlett.124.036802","publication":"Physical Review Letters","oa_version":"Preprint","publisher":"APS","title":"Conductance-matrix symmetries of a three-terminal hybrid device","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ménard, G. C.","first_name":"G. C.","last_name":"Ménard"},{"full_name":"Anselmetti, G. L. R.","last_name":"Anselmetti","first_name":"G. L. R."},{"last_name":"Martinez","first_name":"E. A.","full_name":"Martinez, E. A."},{"full_name":"Puglia, D.","last_name":"Puglia","first_name":"D."},{"full_name":"Malinowski, F. K.","last_name":"Malinowski","first_name":"F. K."},{"full_name":"Lee, J. S.","first_name":"J. S.","last_name":"Lee"},{"full_name":"Choi, S.","last_name":"Choi","first_name":"S."},{"full_name":"Pendharkar, M.","last_name":"Pendharkar","first_name":"M."},{"last_name":"Palmstrøm","first_name":"C. J.","full_name":"Palmstrøm, C. J."},{"full_name":"Flensberg, K.","first_name":"K.","last_name":"Flensberg"},{"full_name":"Marcus, C. M.","first_name":"C. M.","last_name":"Marcus"},{"full_name":"Casparis, L.","first_name":"L.","last_name":"Casparis"},{"full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original","citation":{"apa":"Ménard, G. C., Anselmetti, G. L. R., Martinez, E. A., Puglia, D., Malinowski, F. K., Lee, J. S., … Higginbotham, A. P. (2020). Conductance-matrix symmetries of a three-terminal hybrid device. <i>Physical Review Letters</i>. APS. <a href=\"https://doi.org/10.1103/physrevlett.124.036802\">https://doi.org/10.1103/physrevlett.124.036802</a>","mla":"Ménard, G. C., et al. “Conductance-Matrix Symmetries of a Three-Terminal Hybrid Device.” <i>Physical Review Letters</i>, vol. 124, no. 3, 036802, APS, 2020, doi:<a href=\"https://doi.org/10.1103/physrevlett.124.036802\">10.1103/physrevlett.124.036802</a>.","short":"G.C. Ménard, G.L.R. Anselmetti, E.A. Martinez, D. Puglia, F.K. Malinowski, J.S. Lee, S. Choi, M. Pendharkar, C.J. Palmstrøm, K. Flensberg, C.M. Marcus, L. Casparis, A.P. Higginbotham, Physical Review Letters 124 (2020).","ista":"Ménard GC, Anselmetti GLR, Martinez EA, Puglia D, Malinowski FK, Lee JS, Choi S, Pendharkar M, Palmstrøm CJ, Flensberg K, Marcus CM, Casparis L, Higginbotham AP. 2020. Conductance-matrix symmetries of a three-terminal hybrid device. Physical Review Letters. 124(3), 036802.","ieee":"G. C. Ménard <i>et al.</i>, “Conductance-matrix symmetries of a three-terminal hybrid device,” <i>Physical Review Letters</i>, vol. 124, no. 3. APS, 2020.","ama":"Ménard GC, Anselmetti GLR, Martinez EA, et al. Conductance-matrix symmetries of a three-terminal hybrid device. <i>Physical Review Letters</i>. 2020;124(3). doi:<a href=\"https://doi.org/10.1103/physrevlett.124.036802\">10.1103/physrevlett.124.036802</a>","chicago":"Ménard, G. C., G. L. R. Anselmetti, E. A. Martinez, D. Puglia, F. K. Malinowski, J. S. Lee, S. Choi, et al. “Conductance-Matrix Symmetries of a Three-Terminal Hybrid Device.” <i>Physical Review Letters</i>. APS, 2020. <a href=\"https://doi.org/10.1103/physrevlett.124.036802\">https://doi.org/10.1103/physrevlett.124.036802</a>."},"publication_identifier":{"issn":["0031-9007","1079-7114"]},"extern":"1","type":"journal_article","arxiv":1,"abstract":[{"lang":"eng","text":"We present conductance-matrix measurements of a three-terminal superconductor-semiconductor hybrid device consisting of two normal leads and one superconducting lead. Using a symmetry decomposition of the conductance, we find that antisymmetric components of pairs of local and nonlocal conductances qualitatively match at energies below the superconducting gap, and we compare this finding with symmetry relations based on a noninteracting scattering matrix approach. Further, the local charge character of Andreev bound states is extracted from the symmetry-decomposed conductance data and is found to be similar at both ends of the device and tunable with gate voltage. Finally, we measure the conductance matrix as a function of magnetic field and identify correlated splittings in low-energy features, demonstrating how conductance-matrix measurements can complement traditional single-probe measurements in the search for Majorana zero modes."}],"_id":"7477","quality_controlled":"1","publication_status":"published"},{"oa_version":"Preprint","publication":"Physical Review Letters","doi":"10.1103/physrevlett.124.036801","main_file_link":[{"url":"https://arxiv.org/abs/1905.05438","open_access":"1"}],"date_created":"2020-02-11T08:55:40Z","status":"public","day":"24","volume":124,"year":"2020","external_id":{"arxiv":["1905.05438"]},"date_updated":"2021-01-12T08:13:48Z","oa":1,"issue":"3","date_published":"2020-01-24T00:00:00Z","intvolume":"       124","month":"01","article_number":"036801","publication_status":"published","_id":"7478","quality_controlled":"1","publication_identifier":{"issn":["0031-9007","1079-7114"]},"extern":"1","citation":{"mla":"Danon, Jeroen, et al. “Nonlocal Conductance Spectroscopy of Andreev Bound States: Symmetry Relations and BCS Charges.” <i>Physical Review Letters</i>, vol. 124, no. 3, 036801, APS, 2020, doi:<a href=\"https://doi.org/10.1103/physrevlett.124.036801\">10.1103/physrevlett.124.036801</a>.","apa":"Danon, J., Hellenes, A. B., Hansen, E. B., Casparis, L., Higginbotham, A. P., &#38; Flensberg, K. (2020). Nonlocal conductance spectroscopy of Andreev bound states: Symmetry relations and BCS charges. <i>Physical Review Letters</i>. APS. <a href=\"https://doi.org/10.1103/physrevlett.124.036801\">https://doi.org/10.1103/physrevlett.124.036801</a>","chicago":"Danon, Jeroen, Anna Birk Hellenes, Esben Bork Hansen, Lucas Casparis, Andrew P Higginbotham, and Karsten Flensberg. “Nonlocal Conductance Spectroscopy of Andreev Bound States: Symmetry Relations and BCS Charges.” <i>Physical Review Letters</i>. APS, 2020. <a href=\"https://doi.org/10.1103/physrevlett.124.036801\">https://doi.org/10.1103/physrevlett.124.036801</a>.","ama":"Danon J, Hellenes AB, Hansen EB, Casparis L, Higginbotham AP, Flensberg K. Nonlocal conductance spectroscopy of Andreev bound states: Symmetry relations and BCS charges. <i>Physical Review Letters</i>. 2020;124(3). doi:<a href=\"https://doi.org/10.1103/physrevlett.124.036801\">10.1103/physrevlett.124.036801</a>","short":"J. Danon, A.B. Hellenes, E.B. Hansen, L. Casparis, A.P. Higginbotham, K. Flensberg, Physical Review Letters 124 (2020).","ista":"Danon J, Hellenes AB, Hansen EB, Casparis L, Higginbotham AP, Flensberg K. 2020. Nonlocal conductance spectroscopy of Andreev bound states: Symmetry relations and BCS charges. Physical Review Letters. 124(3), 036801.","ieee":"J. Danon, A. B. Hellenes, E. B. Hansen, L. Casparis, A. P. Higginbotham, and K. Flensberg, “Nonlocal conductance spectroscopy of Andreev bound states: Symmetry relations and BCS charges,” <i>Physical Review Letters</i>, vol. 124, no. 3. APS, 2020."},"abstract":[{"text":"Two-terminal conductance spectroscopy of superconducting devices is a common tool for probing Andreev and Majorana bound states. Here, we study theoretically a three-terminal setup, with two normal leads coupled to a grounded superconducting terminal. Using a single-electron scattering matrix, we derive the subgap conductance matrix for the normal leads and discuss its symmetries. In particular, we show that the local and the nonlocal elements of the conductance matrix have pairwise identical antisymmetric components. Moreover, we find that the nonlocal elements are directly related to the local BCS charges of the bound states close to the normal probes and we show how the BCS charge of overlapping Majorana bound states can be extracted from experiments.","lang":"eng"}],"arxiv":1,"type":"journal_article","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jeroen","last_name":"Danon","full_name":"Danon, Jeroen"},{"last_name":"Hellenes","first_name":"Anna Birk","full_name":"Hellenes, Anna Birk"},{"first_name":"Esben Bork","last_name":"Hansen","full_name":"Hansen, Esben Bork"},{"full_name":"Casparis, Lucas","first_name":"Lucas","last_name":"Casparis"},{"full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham"},{"first_name":"Karsten","last_name":"Flensberg","full_name":"Flensberg, Karsten"}],"title":"Nonlocal conductance spectroscopy of Andreev bound states: Symmetry relations and BCS charges","publisher":"APS"},{"citation":{"apa":"Phuong, M., &#38; Lampert, C. (2020). Functional vs. parametric equivalence of ReLU networks. In <i>8th International Conference on Learning Representations</i>. Online.","mla":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” <i>8th International Conference on Learning Representations</i>, 2020.","ama":"Phuong M, Lampert C. Functional vs. parametric equivalence of ReLU networks. In: <i>8th International Conference on Learning Representations</i>. ; 2020.","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.","short":"M. Phuong, C. Lampert, in:, 8th International Conference on Learning Representations, 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.","chicago":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” In <i>8th International Conference on Learning Representations</i>, 2020."},"type":"conference","file_date_updated":"2020-07-14T12:47:59Z","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."}],"ddc":["000"],"_id":"7481","date_created":"2020-02-11T09:07:37Z","quality_controlled":"1","status":"public","day":"26","publication_status":"published","publication":"8th International Conference on Learning Representations","related_material":{"link":[{"url":"https://iclr.cc/virtual_2020/poster_Bylx-TNKvH.html","relation":"supplementary_material"}],"record":[{"relation":"dissertation_contains","status":"public","id":"9418"}]},"oa_version":"Published Version","month":"04","has_accepted_license":"1","date_published":"2020-04-26T00:00:00Z","date_updated":"2023-09-07T13:29:50Z","file":[{"file_id":"7482","content_type":"application/pdf","creator":"bphuong","file_size":405469,"relation":"main_file","access_level":"open_access","checksum":"8d372ea5defd8cb8fdc430111ed754a9","file_name":"main.pdf","date_created":"2020-02-11T09:07:27Z","date_updated":"2020-07-14T12:47:59Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Functional vs. parametric equivalence of ReLU networks","oa":1,"author":[{"full_name":"Bui Thi Mai, Phuong","last_name":"Bui Thi Mai","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"article_processing_charge":"No","department":[{"_id":"ChLa"}],"conference":{"location":"Online","end_date":"2020-04-30","start_date":"2020-04-27","name":"ICLR: International Conference on Learning Representations"},"language":[{"iso":"eng"}],"year":"2020"},{"status":"public","day":"10","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-02-16T23:00:49Z","ddc":["570"],"volume":10,"pmid":1,"oa_version":"Published Version","isi":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41598-020-80651-0"}]},"publication":"Scientific reports","doi":"10.1038/s41598-020-58264-4","oa":1,"issue":"1","date_updated":"2023-08-18T06:35:13Z","article_number":"2259","date_published":"2020-02-10T00:00:00Z","intvolume":"        10","month":"02","year":"2020","external_id":{"isi":["000560694800012"],"pmid":["32042057"]},"quality_controlled":"1","_id":"7487","scopus_import":"1","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"}],"type":"journal_article","file_date_updated":"2020-07-14T12:47:59Z","citation":{"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>.","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.","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.","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>","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>.","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>"},"publication_identifier":{"eissn":["20452322"]},"publication_status":"published","title":"Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation","author":[{"first_name":"Amada R.","last_name":"López De La Oliva","full_name":"López De La Oliva, Amada R."},{"full_name":"Campos-Sandoval, José A.","first_name":"José A.","last_name":"Campos-Sandoval"},{"last_name":"Gómez-García","first_name":"María C.","full_name":"Gómez-García, María C."},{"last_name":"Cardona","first_name":"Carolina","full_name":"Cardona, Carolina"},{"full_name":"Martín-Rufián, Mercedes","last_name":"Martín-Rufián","first_name":"Mercedes"},{"full_name":"Sialana, Fernando J.","first_name":"Fernando J.","last_name":"Sialana"},{"full_name":"Castilla, Laura","first_name":"Laura","last_name":"Castilla"},{"full_name":"Bae, Narkhyun","last_name":"Bae","id":"3A5F7CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Narkhyun"},{"last_name":"Lobo","first_name":"Carolina","full_name":"Lobo, Carolina"},{"last_name":"Peñalver","first_name":"Ana","full_name":"Peñalver, Ana"},{"first_name":"Marina","last_name":"García-Frutos","full_name":"García-Frutos, Marina"},{"full_name":"Carro, David","last_name":"Carro","first_name":"David"},{"first_name":"Victoria","last_name":"Enrique","full_name":"Enrique, Victoria"},{"full_name":"Paz, José C.","first_name":"José C.","last_name":"Paz"},{"full_name":"Mirmira, Raghavendra G.","last_name":"Mirmira","first_name":"Raghavendra G."},{"first_name":"Antonia","last_name":"Gutiérrez","full_name":"Gutiérrez, Antonia"},{"last_name":"Alonso","first_name":"Francisco J.","full_name":"Alonso, Francisco J."},{"last_name":"Segura","first_name":"Juan A.","full_name":"Segura, Juan A."},{"last_name":"Matés","first_name":"José M.","full_name":"Matés, José M."},{"full_name":"Lubec, Gert","first_name":"Gert","last_name":"Lubec"},{"full_name":"Márquez, Javier","first_name":"Javier","last_name":"Márquez"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"checksum":"c780bd87476a9c9e12668ff66de3dc96","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7495","file_size":4703751,"creator":"dernst","date_created":"2020-02-18T07:43:21Z","date_updated":"2020-07-14T12:47:59Z","file_name":"2020_ScientificReport_Lopez.pdf"}],"publisher":"Springer Nature","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"CaBe"}],"article_processing_charge":"No"},{"article_processing_charge":"No","department":[{"_id":"GaNo"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"MDPI","file":[{"file_name":"2020_IntMolecSciences_Latorre.pdf","date_created":"2020-02-18T07:49:22Z","date_updated":"2020-07-14T12:47:59Z","content_type":"application/pdf","file_id":"7496","file_size":4271234,"creator":"dernst","relation":"main_file","checksum":"0e6658c4fe329d55d4d9bef01c5b15d0","access_level":"open_access"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Latorre-Pellicer, Ana","first_name":"Ana","last_name":"Latorre-Pellicer"},{"first_name":"Ángela","last_name":"Ascaso","full_name":"Ascaso, Ángela"},{"full_name":"Trujillano, Laura","first_name":"Laura","last_name":"Trujillano"},{"last_name":"Gil-Salvador","first_name":"Marta","full_name":"Gil-Salvador, Marta"},{"full_name":"Arnedo, Maria","last_name":"Arnedo","first_name":"Maria"},{"full_name":"Lucia-Campos, Cristina","first_name":"Cristina","last_name":"Lucia-Campos"},{"full_name":"Antoñanzas-Pérez, Rebeca","first_name":"Rebeca","last_name":"Antoñanzas-Pérez"},{"last_name":"Marcos-Alcalde","first_name":"Iñigo","full_name":"Marcos-Alcalde, Iñigo"},{"full_name":"Parenti, Ilaria","last_name":"Parenti","id":"D93538B0-5B71-11E9-AC62-02EBE5697425","first_name":"Ilaria"},{"first_name":"Gloria","last_name":"Bueno-Lozano","full_name":"Bueno-Lozano, Gloria"},{"last_name":"Musio","first_name":"Antonio","full_name":"Musio, Antonio"},{"full_name":"Puisac, Beatriz","last_name":"Puisac","first_name":"Beatriz"},{"full_name":"Kaiser, Frank J.","first_name":"Frank J.","last_name":"Kaiser"},{"last_name":"Ramos","first_name":"Feliciano J.","full_name":"Ramos, Feliciano J."},{"first_name":"Paulino","last_name":"Gómez-Puertas","full_name":"Gómez-Puertas, Paulino"},{"full_name":"Pié, Juan","last_name":"Pié","first_name":"Juan"}],"title":"Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes","publication_status":"published","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"citation":{"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>.","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>","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.","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).","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.","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>"},"type":"journal_article","file_date_updated":"2020-07-14T12:47:59Z","scopus_import":"1","abstract":[{"lang":"eng","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."}],"_id":"7488","quality_controlled":"1","external_id":{"isi":["000522551606028"]},"year":"2020","month":"02","intvolume":"        21","date_published":"2020-02-04T00:00:00Z","article_number":"1042","date_updated":"2023-08-18T06:35:41Z","issue":"3","oa":1,"doi":"10.3390/ijms21031042","publication":"International Journal of Molecular Sciences","isi":1,"oa_version":"Published Version","volume":21,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_created":"2020-02-16T23:00:49Z","status":"public","day":"04"},{"date_updated":"2023-09-07T13:30:45Z","oa":1,"intvolume":"       236","month":"05","date_published":"2020-05-01T00:00:00Z","year":"2020","external_id":{"isi":["000511060200001"]},"page":"967-1087","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-02-16T23:00:50Z","ddc":["530","532"],"day":"01","status":"public","volume":236,"related_material":{"record":[{"id":"10007","status":"public","relation":"dissertation_contains"}]},"isi":1,"oa_version":"Published Version","ec_funded":1,"doi":"10.1007/s00205-019-01486-2","publication":"Archive for Rational Mechanics and Analysis","file":[{"success":1,"file_name":"2020_ArchRatMechAn_Fischer.pdf","date_updated":"2020-11-20T09:14:22Z","date_created":"2020-11-20T09:14:22Z","content_type":"application/pdf","file_id":"8779","creator":"dernst","file_size":1897571,"checksum":"f107e21b58f5930876f47144be37cf6c","relation":"main_file","access_level":"open_access"}],"title":"Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","full_name":"Fischer, Julian L"},{"full_name":"Hensel, Sebastian","last_name":"Hensel","orcid":"0000-0001-7252-8072","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"}],"has_accepted_license":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"JuFi"}],"_id":"7489","quality_controlled":"1","publication_identifier":{"issn":["00039527"],"eissn":["14320673"]},"citation":{"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>","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>.","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>","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.","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.","short":"J.L. Fischer, S. Hensel, Archive for Rational Mechanics and Analysis 236 (2020) 967–1087.","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>."},"file_date_updated":"2020-11-20T09:14:22Z","type":"journal_article","scopus_import":"1","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."}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publication_status":"published"}]