[{"acknowledgement":"We thank O. Eschenko and M. Constantinou for providing feedback on earlier versions of this work, and J. Werner and M. Schnabel for technical support during the development of this study. This research was supported by the Max Planck Society.","publication_status":"published","status":"public","publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"doi":"10.1038/s41586-020-2914-4","issue":"7840","abstract":[{"lang":"eng","text":"The hippocampus has a major role in encoding and consolidating long-term memories, and undergoes plastic changes during sleep1. These changes require precise homeostatic control by subcortical neuromodulatory structures2. The underlying mechanisms of this phenomenon, however, remain unknown. Here, using multi-structure recordings in macaque monkeys, we show that the brainstem transiently modulates hippocampal network events through phasic pontine waves known as pontogeniculooccipital waves (PGO waves). Two physiologically distinct types of PGO wave appear to occur sequentially, selectively influencing high-frequency ripples and low-frequency theta events, respectively. The two types of PGO wave are associated with opposite hippocampal spike-field coupling, prompting periods of high neural synchrony of neural populations during periods of ripple and theta instances. The coupling between PGO waves and ripples, classically associated with distinct sleep stages, supports the notion that a global coordination mechanism of hippocampal sleep dynamics by cholinergic pontine transients may promote systems and synaptic memory consolidation as well as synaptic homeostasis."}],"_id":"8818","author":[{"first_name":"Juan F","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","last_name":"Ramirez Villegas","full_name":"Ramirez Villegas, Juan F"},{"last_name":"Besserve","full_name":"Besserve, Michel","first_name":"Michel"},{"full_name":"Murayama, Yusuke","last_name":"Murayama","first_name":"Yusuke"},{"first_name":"Henry C.","last_name":"Evrard","full_name":"Evrard, Henry C."},{"full_name":"Oeltermann, Axel","last_name":"Oeltermann","first_name":"Axel"},{"last_name":"Logothetis","full_name":"Logothetis, Nikos K.","first_name":"Nikos K."}],"title":"Coupling of hippocampal theta and ripples with pontogeniculooccipital waves","article_processing_charge":"No","volume":589,"oa_version":"None","month":"01","pmid":1,"day":"07","citation":{"mla":"Ramirez Villegas, Juan F., et al. “Coupling of Hippocampal Theta and Ripples with Pontogeniculooccipital Waves.” <i>Nature</i>, vol. 589, no. 7840, Springer Nature, 2021, pp. 96–102, doi:<a href=\"https://doi.org/10.1038/s41586-020-2914-4\">10.1038/s41586-020-2914-4</a>.","chicago":"Ramirez Villegas, Juan F, Michel Besserve, Yusuke Murayama, Henry C. Evrard, Axel Oeltermann, and Nikos K. Logothetis. “Coupling of Hippocampal Theta and Ripples with Pontogeniculooccipital Waves.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-020-2914-4\">https://doi.org/10.1038/s41586-020-2914-4</a>.","ama":"Ramirez Villegas JF, Besserve M, Murayama Y, Evrard HC, Oeltermann A, Logothetis NK. Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. <i>Nature</i>. 2021;589(7840):96-102. doi:<a href=\"https://doi.org/10.1038/s41586-020-2914-4\">10.1038/s41586-020-2914-4</a>","ista":"Ramirez Villegas JF, Besserve M, Murayama Y, Evrard HC, Oeltermann A, Logothetis NK. 2021. Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. Nature. 589(7840), 96–102.","short":"J.F. Ramirez Villegas, M. Besserve, Y. Murayama, H.C. Evrard, A. Oeltermann, N.K. Logothetis, Nature 589 (2021) 96–102.","ieee":"J. F. Ramirez Villegas, M. Besserve, Y. Murayama, H. C. Evrard, A. Oeltermann, and N. K. Logothetis, “Coupling of hippocampal theta and ripples with pontogeniculooccipital waves,” <i>Nature</i>, vol. 589, no. 7840. Springer Nature, pp. 96–102, 2021.","apa":"Ramirez Villegas, J. F., Besserve, M., Murayama, Y., Evrard, H. C., Oeltermann, A., &#38; Logothetis, N. K. (2021). Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-020-2914-4\">https://doi.org/10.1038/s41586-020-2914-4</a>"},"article_type":"original","page":"96-102","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-020-03068-9"}]},"date_updated":"2023-08-04T11:13:08Z","publication":"Nature","year":"2021","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"intvolume":"       589","publisher":"Springer Nature","scopus_import":"1","date_created":"2020-11-29T23:01:19Z","external_id":{"isi":["000591047800005"],"pmid":["33208951"]},"date_published":"2021-01-07T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JoCs"}]},{"article_type":"original","date_updated":"2023-09-05T13:03:15Z","publication":"Current Biology","year":"2021","oa":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"publisher":"Elsevier","intvolume":"        31","date_created":"2020-12-01T13:39:46Z","external_id":{"isi":["000614361000039"],"pmid":["33157019"]},"date_published":"2021-01-11T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JiFr"}],"acknowledgement":"We thank the SiCE group for discussions and comments; S. Yalovsky, B. Scheres, and the NASC/ABRC collection for providing transgenic Arabidopsis lines and plasmids; L. Kalmbach and M. Barberon for the gift of pLOK180_pFR7m34GW; A. Lacroix, J. Berger, and P. Bolland for plant care; and M. Fendrych for help with microfluidics in the J.F. lab. We acknowledge\r\nthe contribution of the SFR Biosciences (UMS3444/CNRS, US8/Inser m, ENS de Lyon, UCBL) facilities: C. Lionet, E. Chatre, and J. Brocard at LBIPLATIM-MICROSCOPY for assistance with imaging, and V. GuegenChaignon and A. Page at the Protein Science Facility (PSF) for assistance with protein purification and mass spectrometry. Y.J. was funded by ERC\r\ngrant 3363360-APPL under FP/2007–2013. Y.J. and Z.L.N. were funded by an ANR- and NSF-supported ERA-CAPS project (SICOPID: ANR-17-CAPS0003-01/NSF PGRP IOS-1841917). A.I.C.-D. is funded by an ERC consolidator grant (ERC-2015-CoG–683163) and BIO2016-78955 grant from the Spanish Ministry of Economy and Competitiveness. Exchanges between the Y.J. and T.B. laboratories were funded by Tournesol grant 35656NB. B.K.M. was\r\nfunded by the Omics@vib Marie Curie COFUND and Research Foundation Flanders for a postdoctoral fellowship.","status":"public","publication_status":"published","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"doi":"10.1016/j.cub.2020.10.011","abstract":[{"text":"Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1,  2,  3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1,  2,  3,  4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7,  8,  9,  10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface.","lang":"eng"}],"issue":"1","_id":"8824","title":"Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism","author":[{"last_name":"Marquès-Bueno","full_name":"Marquès-Bueno, MM","first_name":"MM"},{"full_name":"Armengot, L","last_name":"Armengot","first_name":"L"},{"full_name":"Noack, LC","last_name":"Noack","first_name":"LC"},{"first_name":"J","last_name":"Bareille","full_name":"Bareille, J"},{"orcid":"0000-0002-7244-7237","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia"},{"first_name":"MP","last_name":"Platre","full_name":"Platre, MP"},{"first_name":"V","last_name":"Bayle","full_name":"Bayle, V"},{"full_name":"Liu, M","last_name":"Liu","first_name":"M"},{"first_name":"D","last_name":"Opdenacker","full_name":"Opdenacker, D"},{"last_name":"Vanneste","full_name":"Vanneste, S","first_name":"S"},{"first_name":"BK","last_name":"Möller","full_name":"Möller, BK"},{"first_name":"ZL","full_name":"Nimchuk, ZL","last_name":"Nimchuk"},{"full_name":"Beeckman, T","last_name":"Beeckman","first_name":"T"},{"first_name":"AI","full_name":"Caño-Delgado, AI","last_name":"Caño-Delgado"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"Y","last_name":"Jaillais","full_name":"Jaillais, Y"}],"article_processing_charge":"Yes (via OA deal)","volume":31,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"9090","date_created":"2021-02-04T11:37:50Z","file_name":"2021_CurrentBiology_MarquesBueno.pdf","relation":"main_file","file_size":3458646,"creator":"dernst","success":1,"date_updated":"2021-02-04T11:37:50Z","access_level":"open_access","content_type":"application/pdf","checksum":"30b3393d841fb2b1e2b22fb42b5c8fff"}],"oa_version":"Published Version","month":"01","pmid":1,"file_date_updated":"2021-02-04T11:37:50Z","ddc":["570"],"citation":{"apa":"Marquès-Bueno, M., Armengot, L., Noack, L., Bareille, J., Rodriguez Solovey, L., Platre, M., … Jaillais, Y. (2021). Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2020.10.011\">https://doi.org/10.1016/j.cub.2020.10.011</a>","ieee":"M. Marquès-Bueno <i>et al.</i>, “Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism,” <i>Current Biology</i>, vol. 31, no. 1. Elsevier, 2021.","ama":"Marquès-Bueno M, Armengot L, Noack L, et al. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. <i>Current Biology</i>. 2021;31(1). doi:<a href=\"https://doi.org/10.1016/j.cub.2020.10.011\">10.1016/j.cub.2020.10.011</a>","short":"M. Marquès-Bueno, L. Armengot, L. Noack, J. Bareille, L. Rodriguez Solovey, M. Platre, V. Bayle, M. Liu, D. Opdenacker, S. Vanneste, B. Möller, Z. Nimchuk, T. Beeckman, A. Caño-Delgado, J. Friml, Y. Jaillais, Current Biology 31 (2021).","ista":"Marquès-Bueno M, Armengot L, Noack L, Bareille J, Rodriguez Solovey L, Platre M, Bayle V, Liu M, Opdenacker D, Vanneste S, Möller B, Nimchuk Z, Beeckman T, Caño-Delgado A, Friml J, Jaillais Y. 2021. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. 31(1).","mla":"Marquès-Bueno, MM, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.” <i>Current Biology</i>, vol. 31, no. 1, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.cub.2020.10.011\">10.1016/j.cub.2020.10.011</a>.","chicago":"Marquès-Bueno, MM, L Armengot, LC Noack, J Bareille, Lesia Rodriguez Solovey, MP Platre, V Bayle, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2020.10.011\">https://doi.org/10.1016/j.cub.2020.10.011</a>."},"day":"11"},{"citation":{"chicago":"Jirovec, Daniel, Andrea C Hofmann, Andrea Ballabio, Philipp M. Mutter, Giulio Tavani, Marc Botifoll, Alessandro Crippa, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” <i>Nature Materials</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41563-021-01022-2\">https://doi.org/10.1038/s41563-021-01022-2</a>.","mla":"Jirovec, Daniel, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” <i>Nature Materials</i>, vol. 20, no. 8, Springer Nature, 2021, pp. 1106–1112, doi:<a href=\"https://doi.org/10.1038/s41563-021-01022-2\">10.1038/s41563-021-01022-2</a>.","ieee":"D. Jirovec <i>et al.</i>, “A singlet triplet hole spin qubit in planar Ge,” <i>Nature Materials</i>, vol. 20, no. 8. Springer Nature, pp. 1106–1112, 2021.","apa":"Jirovec, D., Hofmann, A. C., Ballabio, A., Mutter, P. M., Tavani, G., Botifoll, M., … Katsaros, G. (2021). A singlet triplet hole spin qubit in planar Ge. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41563-021-01022-2\">https://doi.org/10.1038/s41563-021-01022-2</a>","short":"D. Jirovec, A.C. Hofmann, A. Ballabio, P.M. Mutter, G. Tavani, M. Botifoll, A. Crippa, J. Kukucka, O. Sagi, F. Martins, J. Saez Mollejo, I. Prieto Gonzalez, M. Borovkov, J. Arbiol, D. Chrastina, G. Isella, G. Katsaros, Nature Materials 20 (2021) 1106–1112.","ista":"Jirovec D, Hofmann AC, Ballabio A, Mutter PM, Tavani G, Botifoll M, Crippa A, Kukucka J, Sagi O, Martins F, Saez Mollejo J, Prieto Gonzalez I, Borovkov M, Arbiol J, Chrastina D, Isella G, Katsaros G. 2021. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 20(8), 1106–1112.","ama":"Jirovec D, Hofmann AC, Ballabio A, et al. A singlet triplet hole spin qubit in planar Ge. <i>Nature Materials</i>. 2021;20(8):1106–1112. doi:<a href=\"https://doi.org/10.1038/s41563-021-01022-2\">10.1038/s41563-021-01022-2</a>"},"day":"01","month":"08","oa_version":"Preprint","arxiv":1,"volume":20,"article_processing_charge":"No","title":"A singlet triplet hole spin qubit in planar Ge","author":[{"orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"},{"last_name":"Hofmann","full_name":"Hofmann, Andrea C","first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrea","last_name":"Ballabio","full_name":"Ballabio, Andrea"},{"first_name":"Philipp M.","full_name":"Mutter, Philipp M.","last_name":"Mutter"},{"last_name":"Tavani","full_name":"Tavani, Giulio","first_name":"Giulio"},{"first_name":"Marc","full_name":"Botifoll, Marc","last_name":"Botifoll"},{"orcid":"0000-0002-2968-611X","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","first_name":"Alessandro","full_name":"Crippa, Alessandro","last_name":"Crippa"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","full_name":"Kukucka, Josip","last_name":"Kukucka"},{"last_name":"Sagi","full_name":"Sagi, Oliver","first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425"},{"orcid":"0000-0003-2668-2401","full_name":"Martins, Frederico","last_name":"Martins","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E","first_name":"Frederico"},{"full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo","id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime"},{"orcid":"0000-0002-7370-5357","last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087","first_name":"Maksim","full_name":"Borovkov, Maksim","last_name":"Borovkov"},{"first_name":"Jordi","full_name":"Arbiol, Jordi","last_name":"Arbiol"},{"first_name":"Daniel","full_name":"Chrastina, Daniel","last_name":"Chrastina"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"_id":"8909","abstract":[{"text":"Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies.","lang":"eng"}],"issue":"8","doi":"10.1038/s41563-021-01022-2","publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"project":[{"call_identifier":"H2020","name":"Majorana bound states in Ge/SiGe heterostructures","grant_number":"844511","_id":"26A151DA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Hole spin orbit qubits in Ge quantum wells","call_identifier":"FWF","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"}],"status":"public","acknowledgement":"This research was supported by the Scientific Service Units of Institute of Science and Technology (IST) Austria through resources provided by the Miba Machine Shop and the nanofabrication facility, and was made possible with the support of the NOMIS Foundation. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreements no. 844511 and no. 75441, and by the Austrian Science Fund FWF-P 30207 project. A.B. acknowledges support from the European Union Horizon 2020 FET project microSPIRE, no. 766955. M. Botifoll and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. The Catalan Institute of Nanoscience and Nanotechnology (ICN2) is supported by the Severo Ochoa programme from the Spanish Ministery of Economy (MINECO) (grant no. SEV-2017-0706) and is funded by the Catalonian Research Centre (CERCA) Programme, Generalitat de Catalunya. Part of the present work has been performed within the framework of the Universitat Autónoma de Barcelona Materials Science PhD programme. Part of the HAADF scanning transmission electron microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon, Universidad de Zaragoza. ICN2 acknowledge support from the Spanish Superior Council of Scientific Research (CSIC) Research Platform on Quantum Technologies PTI-001. M.B. acknowledges funding from the Catalan Agency for Management of University and Research Grants (AGAUR) Generalitat de Catalunya formation of investigators (FI) PhD grant.","publication_status":"published","ec_funded":1,"department":[{"_id":"GeKa"},{"_id":"NanoFab"},{"_id":"GradSch"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000657596400001"],"arxiv":["2011.13755"]},"date_published":"2021-08-01T00:00:00Z","date_created":"2020-12-02T10:50:47Z","scopus_import":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.13755"}],"intvolume":"        20","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"oa":1,"year":"2021","publication":"Nature Materials","date_updated":"2024-03-25T23:30:14Z","related_material":{"record":[{"id":"9323","relation":"research_data","status":"public"},{"id":"10058","relation":"dissertation_contains","status":"public"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/quantum-computing-with-holes/"}]},"page":"1106–1112","article_type":"original"},{"title":"Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states","author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","full_name":"Valentini, Marco","last_name":"Valentini"},{"first_name":"Fernando","full_name":"Peñaranda, Fernando","last_name":"Peñaranda"},{"last_name":"Hofmann","full_name":"Hofmann, Andrea C","first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Brauns, Matthias","last_name":"Brauns","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"full_name":"Krogstrup, Peter","last_name":"Krogstrup","first_name":"Peter"},{"first_name":"Pablo","last_name":"San-Jose","full_name":"San-Jose, Pablo"},{"first_name":"Elsa","last_name":"Prada","full_name":"Prada, Elsa"},{"full_name":"Aguado, Ramón","last_name":"Aguado","first_name":"Ramón"},{"last_name":"Katsaros","full_name":"Katsaros, Georgios","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"}],"_id":"8910","abstract":[{"text":"A semiconducting nanowire fully wrapped by a superconducting shell has been proposed as a platform for obtaining Majorana modes at small magnetic fields. In this study, we demonstrate that the appearance of subgap states in such structures is actually governed by the junction region in tunneling spectroscopy measurements and not the full-shell nanowire itself. Short tunneling regions never show subgap states, whereas longer junctions always do. This can be understood in terms of quantum dots forming in the junction and hosting Andreev levels in the Yu-Shiba-Rusinov regime. The intricate magnetic field dependence of the Andreev levels, through both the Zeeman and Little-Parks effects, may result in robust zero-bias peaks—features that could be easily misinterpreted as originating from Majorana zero modes but are unrelated to topological superconductivity.","lang":"eng"}],"issue":"6550","doi":"10.1126/science.abf1513","publication_identifier":{"issn":["00368075"],"eissn":["10959203"]},"project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"_id":"26A151DA-B435-11E9-9278-68D0E5697425","grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures","call_identifier":"H2020"}],"publication_status":"published","acknowledgement":"The authors thank A. Higginbotham, E. J. H. Lee and F. R. Martins for helpful discussions. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility; the NOMIS Foundation and Microsoft; the European Union’s Horizon 2020 research and innovation program under the Marie SklodowskaCurie grant agreement No 844511; the FETOPEN Grant Agreement No. 828948; the European Research Commission through the grant agreement HEMs-DAM No 716655; the Spanish Ministry of Science and Innovation through Grants PGC2018-097018-B-I00, PCI2018-093026, FIS2016-80434-P (AEI/FEDER, EU), RYC2011-09345 (Ram´on y Cajal Programme), and the Mar´ıa de Maeztu Programme for Units of Excellence in R&D (CEX2018-000805-M); the CSIC Research Platform on Quantum Technologies PTI-001.","status":"public","ec_funded":1,"citation":{"mla":"Valentini, Marco, et al. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires Induced by Flux-Tunable Andreev States.” <i>Science</i>, vol. 373, no. 6550, 82–88, American Association for the Advancement of Science, 2021, doi:<a href=\"https://doi.org/10.1126/science.abf1513\">10.1126/science.abf1513</a>.","chicago":"Valentini, Marco, Fernando Peñaranda, Andrea C Hofmann, Matthias Brauns, Robert Hauschild, Peter Krogstrup, Pablo San-Jose, Elsa Prada, Ramón Aguado, and Georgios Katsaros. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires Induced by Flux-Tunable Andreev States.” <i>Science</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/science.abf1513\">https://doi.org/10.1126/science.abf1513</a>.","apa":"Valentini, M., Peñaranda, F., Hofmann, A. C., Brauns, M., Hauschild, R., Krogstrup, P., … Katsaros, G. (2021). Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abf1513\">https://doi.org/10.1126/science.abf1513</a>","ieee":"M. Valentini <i>et al.</i>, “Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states,” <i>Science</i>, vol. 373, no. 6550. American Association for the Advancement of Science, 2021.","ista":"Valentini M, Peñaranda F, Hofmann AC, Brauns M, Hauschild R, Krogstrup P, San-Jose P, Prada E, Aguado R, Katsaros G. 2021. Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. Science. 373(6550), 82–88.","ama":"Valentini M, Peñaranda F, Hofmann AC, et al. Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. <i>Science</i>. 2021;373(6550). doi:<a href=\"https://doi.org/10.1126/science.abf1513\">10.1126/science.abf1513</a>","short":"M. Valentini, F. Peñaranda, A.C. Hofmann, M. Brauns, R. Hauschild, P. Krogstrup, P. San-Jose, E. Prada, R. Aguado, G. Katsaros, Science 373 (2021)."},"day":"02","month":"07","oa_version":"Submitted Version","arxiv":1,"article_processing_charge":"No","volume":373,"oa":1,"year":"2021","publication":"Science","date_updated":"2024-02-21T12:40:09Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13286"},{"id":"9389","status":"public","relation":"research_data"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/unfinding-a-split-electron/","relation":"press_release"}]},"article_number":"82-88","article_type":"original","department":[{"_id":"GeKa"},{"_id":"Bio"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2008.02348"],"isi":["000677843100034"]},"date_published":"2021-07-02T00:00:00Z","date_created":"2020-12-02T10:51:52Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"scopus_import":"1","publisher":"American Association for the Advancement of Science","intvolume":"       373","main_file_link":[{"url":"https://arxiv.org/abs/2008.02348","open_access":"1"}],"isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}]},{"publication_status":"published","acknowledgement":"G.S., M.W.,F.A.Z acknowledge financial support from The Netherlands Organization for Scientific Research (NWO). F.Z., D.L., G.K. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under Grand Agreement Nr. 862046. G.K. acknowledges funding from FP7 ERC Starting Grant 335497, FWF Y 715-N30, FWF P-30207. S.D. acknowledges support from the European Union’s Horizon 2020 program under Grant\r\nAgreement No. 81050 and from the Agence Nationale de la Recherche through the TOPONANO and CMOSQSPIN projects. J.Z. acknowledges support from the National Key R&D Program of China (Grant No. 2016YFA0301701) and Strategic Priority Research Program of CAS (Grant No. XDB30000000). D.L. and C.K. acknowledge the Swiss National Science Foundation and NCCR QSIT.","status":"public","ec_funded":1,"publication_identifier":{"eissn":["2058-8437"]},"project":[{"grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","call_identifier":"FP7"},{"name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","call_identifier":"FWF","_id":"2552F888-B435-11E9-9278-68D0E5697425","grant_number":"Y00715"},{"name":"Hole spin orbit qubits in Ge quantum wells","call_identifier":"FWF","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","grant_number":"P30207"}],"abstract":[{"text":"In the worldwide endeavor for disruptive quantum technologies, germanium is emerging as a versatile material to realize devices capable of encoding, processing, or transmitting quantum information. These devices leverage special properties of the germanium valence-band states, commonly known as holes, such as their inherently strong spin-orbit coupling and the ability to host superconducting pairing correlations. In this Review, we initially introduce the physics of holes in low-dimensional germanium structures with key insights from a theoretical perspective. We then examine the material science progress underpinning germanium-based planar heterostructures and nanowires. We review the most significant experimental results demonstrating key building blocks for quantum technology, such as an electrically driven universal quantum gate set with spin qubits in quantum dots and superconductor-semiconductor devices for hybrid quantum systems. We conclude by identifying the most promising prospects\r\ntoward scalable quantum information processing. ","lang":"eng"}],"doi":"10.1038/s41578-020-00262-z","author":[{"last_name":"Scappucci","full_name":"Scappucci, Giordano","first_name":"Giordano"},{"full_name":"Kloeffel, Christoph","last_name":"Kloeffel","first_name":"Christoph"},{"first_name":"Floris A.","last_name":"Zwanenburg","full_name":"Zwanenburg, Floris A."},{"first_name":"Daniel","full_name":"Loss, Daniel","last_name":"Loss"},{"full_name":"Myronov, Maksym","last_name":"Myronov","first_name":"Maksym"},{"full_name":"Zhang, Jian-Jun","last_name":"Zhang","first_name":"Jian-Jun"},{"first_name":"Silvano De","full_name":"Franceschi, Silvano De","last_name":"Franceschi"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X"},{"last_name":"Veldhorst","full_name":"Veldhorst, Menno","first_name":"Menno"}],"title":"The germanium quantum information route","_id":"8911","volume":6,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","day":"01","citation":{"chicago":"Scappucci, Giordano, Christoph Kloeffel, Floris A. Zwanenburg, Daniel Loss, Maksym Myronov, Jian-Jun Zhang, Silvano De Franceschi, Georgios Katsaros, and Menno Veldhorst. “The Germanium Quantum Information Route.” <i>Nature Reviews Materials</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41578-020-00262-z\">https://doi.org/10.1038/s41578-020-00262-z</a>.","mla":"Scappucci, Giordano, et al. “The Germanium Quantum Information Route.” <i>Nature Reviews Materials</i>, vol. 6, Springer Nature, 2021, pp. 926–943, doi:<a href=\"https://doi.org/10.1038/s41578-020-00262-z\">10.1038/s41578-020-00262-z</a>.","ama":"Scappucci G, Kloeffel C, Zwanenburg FA, et al. The germanium quantum information route. <i>Nature Reviews Materials</i>. 2021;6:926–943. doi:<a href=\"https://doi.org/10.1038/s41578-020-00262-z\">10.1038/s41578-020-00262-z</a>","ista":"Scappucci G, Kloeffel C, Zwanenburg FA, Loss D, Myronov M, Zhang J-J, Franceschi SD, Katsaros G, Veldhorst M. 2021. The germanium quantum information route. Nature Reviews Materials. 6, 926–943.","short":"G. Scappucci, C. Kloeffel, F.A. Zwanenburg, D. Loss, M. Myronov, J.-J. Zhang, S.D. Franceschi, G. Katsaros, M. Veldhorst, Nature Reviews Materials 6 (2021) 926–943.","ieee":"G. Scappucci <i>et al.</i>, “The germanium quantum information route,” <i>Nature Reviews Materials</i>, vol. 6. Springer Nature, pp. 926–943, 2021.","apa":"Scappucci, G., Kloeffel, C., Zwanenburg, F. A., Loss, D., Myronov, M., Zhang, J.-J., … Veldhorst, M. (2021). The germanium quantum information route. <i>Nature Reviews Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41578-020-00262-z\">https://doi.org/10.1038/s41578-020-00262-z</a>"},"month":"10","article_type":"original","page":"926–943 ","publication":"Nature Reviews Materials","date_updated":"2024-03-07T14:48:57Z","year":"2021","oa":1,"isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.08133"}],"intvolume":"         6","publisher":"Springer Nature","date_published":"2021-10-01T00:00:00Z","external_id":{"isi":["000600826100003"],"arxiv":["2004.08133"]},"scopus_import":"1","date_created":"2020-12-02T10:52:51Z","department":[{"_id":"GeKa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"publication":"Expert Systems with Applications","date_updated":"2023-08-04T11:19:00Z","article_number":"114203","article_type":"original","oa":1,"year":"2021","publisher":"Elsevier","intvolume":"       167","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","department":[{"_id":"ToHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-04-01T00:00:00Z","external_id":{"isi":["000640531100038"]},"date_created":"2020-12-02T13:34:25Z","scopus_import":"1","publication_identifier":{"issn":["09574174"]},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"status":"public","acknowledgement":"This work was supported by The Scientific and Technological Research Council of Turkey (TUBITAK) [grant number 114E569]. This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). We would like to thank the authors of (Roman & Szykula, 2015) for providing their heuristics implementations, which we used to compare our SynchroP implementation as given in Table 11.","publication_status":"published","title":"Boosting expensive synchronizing heuristics","author":[{"full_name":"Sarac, Naci E","last_name":"Sarac","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E"},{"first_name":"Ömer Faruk","last_name":"Altun","full_name":"Altun, Ömer Faruk"},{"first_name":"Kamil Tolga","full_name":"Atam, Kamil Tolga","last_name":"Atam"},{"full_name":"Karahoda, Sertac","last_name":"Karahoda","first_name":"Sertac"},{"last_name":"Kaya","full_name":"Kaya, Kamer","first_name":"Kamer"},{"first_name":"Hüsnü","full_name":"Yenigün, Hüsnü","last_name":"Yenigün"}],"_id":"8912","abstract":[{"lang":"eng","text":"For automata, synchronization, the problem of bringing an automaton to a particular state regardless of its initial state, is important. It has several applications in practice and is related to a fifty-year-old conjecture on the length of the shortest synchronizing word. Although using shorter words increases the effectiveness in practice, finding a shortest one (which is not necessarily unique) is NP-hard. For this reason, there exist various heuristics in the literature. However, high-quality heuristics such as SynchroP producing relatively shorter sequences are very expensive and can take hours when the automaton has tens of thousands of states. The SynchroP heuristic has been frequently used as a benchmark to evaluate the performance of the new heuristics. In this work, we first improve the runtime of SynchroP and its variants by using algorithmic techniques. We then focus on adapting SynchroP for many-core architectures,\r\nand overall, we obtain more than 1000× speedup on GPUs compared to naive sequential implementation that has been frequently used as a benchmark to evaluate new heuristics in the literature. We also propose two SynchroP variants and evaluate their performance."}],"issue":"4","doi":"10.1016/j.eswa.2020.114203","file":[{"access_level":"open_access","checksum":"600c2f81bc898a725bcfa7cf26ff4fed","content_type":"application/pdf","date_updated":"2020-12-02T13:33:51Z","file_name":"synchroPaperRevised.pdf","relation":"main_file","file_size":634967,"creator":"esarac","file_id":"8913","date_created":"2020-12-02T13:33:51Z"}],"has_accepted_license":"1","volume":167,"article_processing_charge":"No","citation":{"chicago":"Sarac, Naci E, Ömer Faruk Altun, Kamil Tolga Atam, Sertac Karahoda, Kamer Kaya, and Hüsnü Yenigün. “Boosting Expensive Synchronizing Heuristics.” <i>Expert Systems with Applications</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">https://doi.org/10.1016/j.eswa.2020.114203</a>.","mla":"Sarac, Naci E., et al. “Boosting Expensive Synchronizing Heuristics.” <i>Expert Systems with Applications</i>, vol. 167, no. 4, 114203, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">10.1016/j.eswa.2020.114203</a>.","ista":"Sarac NE, Altun ÖF, Atam KT, Karahoda S, Kaya K, Yenigün H. 2021. Boosting expensive synchronizing heuristics. Expert Systems with Applications. 167(4), 114203.","ama":"Sarac NE, Altun ÖF, Atam KT, Karahoda S, Kaya K, Yenigün H. Boosting expensive synchronizing heuristics. <i>Expert Systems with Applications</i>. 2021;167(4). doi:<a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">10.1016/j.eswa.2020.114203</a>","short":"N.E. Sarac, Ö.F. Altun, K.T. Atam, S. Karahoda, K. Kaya, H. Yenigün, Expert Systems with Applications 167 (2021).","ieee":"N. E. Sarac, Ö. F. Altun, K. T. Atam, S. Karahoda, K. Kaya, and H. Yenigün, “Boosting expensive synchronizing heuristics,” <i>Expert Systems with Applications</i>, vol. 167, no. 4. Elsevier, 2021.","apa":"Sarac, N. E., Altun, Ö. F., Atam, K. T., Karahoda, S., Kaya, K., &#38; Yenigün, H. (2021). Boosting expensive synchronizing heuristics. <i>Expert Systems with Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">https://doi.org/10.1016/j.eswa.2020.114203</a>"},"day":"01","month":"04","ddc":["000"],"file_date_updated":"2020-12-02T13:33:51Z","oa_version":"Submitted Version"},{"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"intvolume":"        41","publisher":"Wiley","scopus_import":"1","date_created":"2020-12-06T23:01:16Z","date_published":"2021-01-01T00:00:00Z","external_id":{"isi":["000594239200001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"CampIT"}],"article_type":"original","page":"20-32","date_updated":"2023-08-04T11:19:51Z","publication":"Liver International","year":"2021","oa":1,"article_processing_charge":"No","volume":41,"has_accepted_license":"1","file":[{"date_created":"2021-02-04T12:01:45Z","file_id":"9091","date_updated":"2021-02-04T12:01:45Z","success":1,"content_type":"application/pdf","checksum":"6e4f21b77ef22c854e016240974fc473","access_level":"open_access","creator":"dernst","relation":"main_file","file_size":930414,"file_name":"2021_Liver_Nardo.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","month":"01","ddc":["570"],"file_date_updated":"2021-02-04T12:01:45Z","day":"01","citation":{"chicago":"Nardo, Alexander D., Mathias Schneeweiss-Gleixner, May M Bakail, Emmanuel D. Dixon, Sigurd F. Lax, and Michael Trauner. “Pathophysiological Mechanisms of Liver Injury in COVID-19.” <i>Liver International</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/liv.14730\">https://doi.org/10.1111/liv.14730</a>.","mla":"Nardo, Alexander D., et al. “Pathophysiological Mechanisms of Liver Injury in COVID-19.” <i>Liver International</i>, vol. 41, no. 1, Wiley, 2021, pp. 20–32, doi:<a href=\"https://doi.org/10.1111/liv.14730\">10.1111/liv.14730</a>.","ama":"Nardo AD, Schneeweiss-Gleixner M, Bakail MM, Dixon ED, Lax SF, Trauner M. Pathophysiological mechanisms of liver injury in COVID-19. <i>Liver International</i>. 2021;41(1):20-32. doi:<a href=\"https://doi.org/10.1111/liv.14730\">10.1111/liv.14730</a>","ista":"Nardo AD, Schneeweiss-Gleixner M, Bakail MM, Dixon ED, Lax SF, Trauner M. 2021. Pathophysiological mechanisms of liver injury in COVID-19. Liver International. 41(1), 20–32.","short":"A.D. Nardo, M. Schneeweiss-Gleixner, M.M. Bakail, E.D. Dixon, S.F. Lax, M. Trauner, Liver International 41 (2021) 20–32.","ieee":"A. D. Nardo, M. Schneeweiss-Gleixner, M. M. Bakail, E. D. Dixon, S. F. Lax, and M. Trauner, “Pathophysiological mechanisms of liver injury in COVID-19,” <i>Liver International</i>, vol. 41, no. 1. Wiley, pp. 20–32, 2021.","apa":"Nardo, A. D., Schneeweiss-Gleixner, M., Bakail, M. M., Dixon, E. D., Lax, S. F., &#38; Trauner, M. (2021). Pathophysiological mechanisms of liver injury in COVID-19. <i>Liver International</i>. Wiley. <a href=\"https://doi.org/10.1111/liv.14730\">https://doi.org/10.1111/liv.14730</a>"},"status":"public","acknowledgement":"This work was supported by grant F7310‐B21 from the Austrian Science Foundation (to MT). We thank Jelena Remetic, Claudia D. Fuchs, Veronika Mlitz and Daniel Steinacher, for their valuable input and discussion. Figure 1 and Figure 2 have been created with BioRender.com.","publication_status":"published","publication_identifier":{"eissn":["14783231"],"issn":["14783223"]},"doi":"10.1111/liv.14730","issue":"1","abstract":[{"text":"The recent outbreak of coronavirus disease 2019 (COVID‐19), caused by the Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) has resulted in a world‐wide pandemic. Disseminated lung injury with the development of acute respiratory distress syndrome (ARDS) is the main cause of mortality in COVID‐19. Although liver failure does not seem to occur in the absence of pre‐existing liver disease, hepatic involvement in COVID‐19 may correlate with overall disease severity and serve as a prognostic factor for the development of ARDS. The spectrum of liver injury in COVID‐19 may range from direct infection by SARS‐CoV‐2, indirect involvement by systemic inflammation, hypoxic changes, iatrogenic causes such as drugs and ventilation to exacerbation of underlying liver disease. This concise review discusses the potential pathophysiological mechanisms for SARS‐CoV‐2 hepatic tropism as well as acute and possibly long‐term liver injury in COVID‐19.","lang":"eng"}],"_id":"8927","author":[{"first_name":"Alexander D.","full_name":"Nardo, Alexander D.","last_name":"Nardo"},{"first_name":"Mathias","full_name":"Schneeweiss-Gleixner, Mathias","last_name":"Schneeweiss-Gleixner"},{"orcid":"0000-0002-9592-1587","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M","full_name":"Bakail, May M","last_name":"Bakail"},{"first_name":"Emmanuel D.","full_name":"Dixon, Emmanuel D.","last_name":"Dixon"},{"first_name":"Sigurd F.","last_name":"Lax","full_name":"Lax, Sigurd F."},{"first_name":"Michael","last_name":"Trauner","full_name":"Trauner, Michael"}],"title":"Pathophysiological mechanisms of liver injury in COVID-19"},{"abstract":[{"lang":"eng","text":"Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available."}],"issue":"2","doi":"10.1111/jeb.13723","title":"Genomic inference of complex domestication histories in three Solanaceae species","author":[{"first_name":"Stéphanie","full_name":"Arnoux, Stéphanie","last_name":"Arnoux"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"last_name":"Sauvage","full_name":"Sauvage, Christopher","first_name":"Christopher"}],"_id":"8928","publication_status":"published","status":"public","acknowledgement":"This work was supported by the EU Marie Curie Career Integration grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant Breeding division of INRA, in partnership with Gautier Semences. CF was supported by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding (University of Torino), the Biotechnology Department (University of Verona), the CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC ) for managing and providing the genetic resources, to Marie‐Christine Daunay and Alain Palloix (INRA UR1052) for assistance in choosing the biological material used, to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France) for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques Lagnel (INRA UR1052) for their Bioinformatics assistance.","publication_identifier":{"eissn":["14209101"],"issn":["1010061X"]},"project":[{"grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosomes and species barriers"}],"oa_version":"Published Version","citation":{"chicago":"Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>.","mla":"Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2, Wiley, 2021, pp. 270–83, doi:<a href=\"https://doi.org/10.1111/jeb.13723\">10.1111/jeb.13723</a>.","ama":"Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication histories in three Solanaceae species. <i>Journal of Evolutionary Biology</i>. 2021;34(2):270-283. doi:<a href=\"https://doi.org/10.1111/jeb.13723\">10.1111/jeb.13723</a>","ista":"Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2), 270–283.","short":"S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283.","apa":"Arnoux, S., Fraisse, C., &#38; Sauvage, C. (2021). Genomic inference of complex domestication histories in three Solanaceae species. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication histories in three Solanaceae species,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2. Wiley, pp. 270–283, 2021."},"day":"01","month":"02","pmid":1,"volume":34,"article_processing_charge":"No","year":"2021","oa":1,"related_material":{"record":[{"id":"13065","status":"public","relation":"research_data"}]},"page":"270-283","article_type":"original","publication":"Journal of Evolutionary Biology","date_updated":"2023-08-04T11:19:26Z","date_published":"2021-02-01T00:00:00Z","external_id":{"pmid":["33107098"],"isi":["000587769700001"]},"date_created":"2020-12-06T23:01:16Z","scopus_import":"1","department":[{"_id":"NiBa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"Wiley","intvolume":"        34","main_file_link":[{"url":"https://doi.org/10.1111/jeb.13723","open_access":"1"}]},{"article_processing_charge":"Yes (via OA deal)","volume":303,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2021_PlantScience_Gelova.pdf","file_size":12563728,"creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"a7f2562bdca62d67dfa88e271b62a629","content_type":"application/pdf","success":1,"date_updated":"2021-02-04T07:49:25Z","file_id":"9083","date_created":"2021-02-04T07:49:25Z"}],"oa_version":"Published Version","ddc":["580"],"file_date_updated":"2021-02-04T07:49:25Z","month":"02","pmid":1,"citation":{"mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>, vol. 303, 110750, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>.","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>.","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>","ieee":"Z. Gelová <i>et al.</i>, “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” <i>Plant Science</i>, vol. 303. Elsevier, 2021.","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. 2021;303. doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>"},"day":"01","ec_funded":1,"publication_status":"published","acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","status":"public","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["0168-9452"]},"doi":"10.1016/j.plantsci.2020.110750","abstract":[{"lang":"eng","text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy."}],"_id":"8931","title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","author":[{"orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana","full_name":"Gelová, Zuzana","last_name":"Gelová"},{"orcid":"0000-0003-1286-7368","last_name":"Gallei","full_name":"Gallei, Michelle C","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pernisová, Markéta","last_name":"Pernisová","first_name":"Markéta"},{"last_name":"Brunoud","full_name":"Brunoud, Géraldine","first_name":"Géraldine"},{"last_name":"Zhang","full_name":"Zhang, Xixi","first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","full_name":"Glanc, Matous","last_name":"Glanc","orcid":"0000-0003-0619-7783"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","full_name":"Li, Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X"},{"last_name":"Michalko","full_name":"Michalko, Jaroslav","first_name":"Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zlata","full_name":"Pavlovicova, Zlata","last_name":"Pavlovicova"},{"last_name":"Verstraeten","full_name":"Verstraeten, Inge","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328"},{"first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","full_name":"Han, Huibin"},{"orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"first_name":"Milada","last_name":"Čovanová","full_name":"Čovanová, Milada"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","full_name":"Hörmayer, Lukas","last_name":"Hörmayer","orcid":"0000-0001-8295-2926"},{"last_name":"Fendrych","full_name":"Fendrych, Matyas","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699"},{"first_name":"Tongda","full_name":"Xu, Tongda","last_name":"Xu"},{"first_name":"Teva","last_name":"Vernoux","full_name":"Vernoux, Teva"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"publisher":"Elsevier","intvolume":"       303","date_created":"2020-12-09T14:48:28Z","scopus_import":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_published":"2021-02-01T00:00:00Z","external_id":{"isi":["000614154500001"],"pmid":["33487339"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"},{"_id":"Bio"}],"article_number":"110750","article_type":"original","related_material":{"record":[{"id":"11626","status":"public","relation":"dissertation_contains"},{"id":"10083","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-10-29T10:22:43Z","publication":"Plant Science","keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"year":"2021","oa":1},{"doi":"10.15479/AT:ISTA:8934","abstract":[{"lang":"eng","text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades."}],"_id":"8934","author":[{"last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"}],"title":"Parameterized and algebro-geometric advances in static program analysis","supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","status":"public","publication_status":"published","project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","license":"https://creativecommons.org/publicdomain/zero/1.0/","month":"01","file_date_updated":"2021-12-23T23:30:04Z","ddc":["005"],"day":"01","citation":{"ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>","short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","apa":"Goharshady, A. K. (2021). <i>Parameterized and algebro-geometric advances in static program analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>.","mla":"Goharshady, Amir Kafshdar. <i>Parameterized and Algebro-Geometric Advances in Static Program Analysis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>."},"article_processing_charge":"No","has_accepted_license":"1","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"file":[{"file_id":"8969","date_created":"2020-12-22T20:08:44Z","date_updated":"2021-12-23T23:30:04Z","access_level":"open_access","checksum":"d1b9db3725aed34dadd81274aeb9426c","content_type":"application/pdf","embargo":"2021-12-22","file_name":"Thesis-pdfa.pdf","creator":"akafshda","file_size":5251507,"relation":"main_file"},{"date_created":"2020-12-22T20:08:50Z","file_id":"8970","embargo_to":"open_access","date_updated":"2021-03-04T23:30:04Z","content_type":"application/zip","checksum":"1661df7b393e6866d2460eba3c905130","access_level":"closed","relation":"source_file","creator":"akafshda","file_size":10636756,"file_name":"source.zip"}],"degree_awarded":"PhD","year":"2021","alternative_title":["ISTA Thesis"],"oa":1,"page":"278","related_material":{"record":[{"id":"1386","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"1437"},{"relation":"part_of_dissertation","status":"public","id":"639"},{"id":"6918","relation":"part_of_dissertation","status":"public"},{"id":"6490","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"7158"},{"id":"6009","relation":"part_of_dissertation","status":"public"},{"id":"949","relation":"part_of_dissertation","status":"public"},{"id":"311","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7810"},{"relation":"part_of_dissertation","status":"public","id":"8089"},{"status":"public","relation":"part_of_dissertation","id":"8728"},{"status":"public","relation":"part_of_dissertation","id":"5977"},{"id":"6056","relation":"part_of_dissertation","status":"public"},{"id":"6175","relation":"part_of_dissertation","status":"public"},{"id":"6340","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"6378"},{"id":"6380","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"66"},{"id":"6780","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"7014"}]},"date_updated":"2025-06-02T08:53:47Z","date_created":"2020-12-10T12:17:07Z","date_published":"2021-01-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria"},{"day":"01","citation":{"chicago":"Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-020-00250-8\">https://doi.org/10.1007/s00454-020-00250-8</a>.","mla":"Boissonnat, Jean-Daniel, et al. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” <i>Discrete &#38; Computational Geometry</i>, vol. 66, no. 1, Springer Nature, 2021, pp. 386–434, doi:<a href=\"https://doi.org/10.1007/s00454-020-00250-8\">10.1007/s00454-020-00250-8</a>.","apa":"Boissonnat, J.-D., Kachanovich, S., &#38; Wintraecken, M. (2021). Triangulating submanifolds: An elementary and quantified version of Whitney’s method. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00250-8\">https://doi.org/10.1007/s00454-020-00250-8</a>","ieee":"J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Triangulating submanifolds: An elementary and quantified version of Whitney’s method,” <i>Discrete &#38; Computational Geometry</i>, vol. 66, no. 1. Springer Nature, pp. 386–434, 2021.","ama":"Boissonnat J-D, Kachanovich S, Wintraecken M. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. <i>Discrete &#38; Computational Geometry</i>. 2021;66(1):386-434. doi:<a href=\"https://doi.org/10.1007/s00454-020-00250-8\">10.1007/s00454-020-00250-8</a>","short":"J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, Discrete &#38; Computational Geometry 66 (2021) 386–434.","ista":"Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete &#38; Computational Geometry. 66(1), 386–434."},"file_date_updated":"2021-08-06T09:52:29Z","ddc":["516"],"month":"07","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"c848986091e56699dc12de85adb1e39c","success":1,"date_updated":"2021-08-06T09:52:29Z","file_name":"2021_DescreteCompGeopmetry_Boissonnat.pdf","relation":"main_file","file_size":983307,"creator":"kschuh","file_id":"9795","date_created":"2021-08-06T09:52:29Z"}],"has_accepted_license":"1","volume":66,"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat","first_name":"Jean-Daniel"},{"first_name":"Siargey","last_name":"Kachanovich","full_name":"Kachanovich, Siargey"},{"last_name":"Wintraecken","full_name":"Wintraecken, Mathijs","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220"}],"title":"Triangulating submanifolds: An elementary and quantified version of Whitney’s method","_id":"8940","issue":"1","abstract":[{"lang":"eng","text":"We quantise Whitney’s construction to prove the existence of a triangulation for any C^2 manifold, so that we get an algorithm with explicit bounds. We also give a new elementary proof, which is completely geometric."}],"doi":"10.1007/s00454-020-00250-8","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","status":"public","acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement Number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. Open access funding provided by the Institute of Science and Technology (IST Austria).","ec_funded":1,"department":[{"_id":"HeEd"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000597770300001"]},"date_published":"2021-07-01T00:00:00Z","date_created":"2020-12-12T11:07:02Z","intvolume":"        66","publisher":"Springer Nature","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","oa":1,"year":"2021","keyword":["Theoretical Computer Science","Computational Theory and Mathematics","Geometry and Topology","Discrete Mathematics and Combinatorics"],"publication":"Discrete & Computational Geometry","date_updated":"2023-09-05T15:02:40Z","article_type":"original","page":"386-434"},{"abstract":[{"text":"During development, a single cell is transformed into a highly complex organism through progressive cell division, specification and rearrangement. An important prerequisite for the emergence of patterns within the developing organism is to establish asymmetries at various scales, ranging from individual cells to the entire embryo, eventually giving rise to the different body structures. This becomes especially apparent during gastrulation, when the earliest major lineage restriction events lead to the formation of the different germ layers. Traditionally, the unfolding of the developmental program from symmetry breaking to germ layer formation has been studied by dissecting the contributions of different signaling pathways and cellular rearrangements in the in vivo context of intact embryos. Recent efforts, using the intrinsic capacity of embryonic stem cells to self-assemble and generate embryo-like structures de novo, have opened new avenues for understanding the many ways by which an embryo can be built and the influence of extrinsic factors therein. Here, we discuss and compare divergent and conserved strategies leading to germ layer formation in embryos as compared to in vitro systems, their upstream molecular cascades and the role of extrinsic factors in this process.","lang":"eng"}],"doi":"10.1016/j.ydbio.2020.12.014","title":"Reassembling gastrulation","author":[{"full_name":"Schauer, Alexandra","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra","orcid":"0000-0001-7659-9142"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"_id":"8966","acknowledgement":"We thank Nicoletta Petridou, Diana Pinheiro, Cornelia Schwayer and Stefania Tavano for feedback on the manuscript. Research in the Heisenberg lab is supported by an ERC Advanced Grant (MECSPEC 742573) to C.-P.H. A.S. is a recipient of a DOC Fellowship of the Austrian Academy of Science.","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["0012-1606"]},"project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","citation":{"apa":"Schauer, A., &#38; Heisenberg, C.-P. J. (2021). Reassembling gastrulation. <i>Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">https://doi.org/10.1016/j.ydbio.2020.12.014</a>","ieee":"A. Schauer and C.-P. J. Heisenberg, “Reassembling gastrulation,” <i>Developmental Biology</i>, vol. 474. Elsevier, pp. 71–81, 2021.","ista":"Schauer A, Heisenberg C-PJ. 2021. Reassembling gastrulation. Developmental Biology. 474, 71–81.","ama":"Schauer A, Heisenberg C-PJ. Reassembling gastrulation. <i>Developmental Biology</i>. 2021;474:71-81. doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">10.1016/j.ydbio.2020.12.014</a>","short":"A. Schauer, C.-P.J. Heisenberg, Developmental Biology 474 (2021) 71–81.","chicago":"Schauer, Alexandra, and Carl-Philipp J Heisenberg. “Reassembling Gastrulation.” <i>Developmental Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">https://doi.org/10.1016/j.ydbio.2020.12.014</a>.","mla":"Schauer, Alexandra, and Carl-Philipp J. Heisenberg. “Reassembling Gastrulation.” <i>Developmental Biology</i>, vol. 474, Elsevier, 2021, pp. 71–81, doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">10.1016/j.ydbio.2020.12.014</a>."},"day":"01","file_date_updated":"2021-08-11T10:28:06Z","ddc":["570"],"month":"06","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","volume":474,"file":[{"content_type":"application/pdf","checksum":"fa2a5731fd16ab171b029f32f031c440","access_level":"open_access","date_updated":"2021-08-11T10:28:06Z","success":1,"relation":"main_file","file_size":1440321,"creator":"kschuh","file_name":"2021_DevBiology_Schauer.pdf","date_created":"2021-08-11T10:28:06Z","file_id":"9880"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"year":"2021","keyword":["Developmental Biology","Cell Biology","Molecular Biology"],"oa":1,"related_material":{"record":[{"id":"12891","status":"public","relation":"dissertation_contains"}]},"page":"71-81","article_type":"original","publication":"Developmental Biology","date_updated":"2023-08-07T13:30:01Z","date_published":"2021-06-01T00:00:00Z","external_id":{"isi":["000639461800008"]},"date_created":"2020-12-22T09:53:34Z","scopus_import":"1","department":[{"_id":"CaHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"Elsevier","intvolume":"       474"},{"publisher":"National Academy of Sciences","intvolume":"       118","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2010054118"}],"isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"MaLo"},{"_id":"MiSi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-01-05T00:00:00Z","external_id":{"pmid":["33443153"],"isi":["000607270100018"]},"date_created":"2021-01-03T23:01:23Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"scopus_import":"1","publication":"PNAS","date_updated":"2023-08-04T11:20:46Z","article_number":"e2010054118","article_type":"original","oa":1,"year":"2021","volume":118,"article_processing_charge":"No","citation":{"chicago":"Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>PNAS</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>.","mla":"Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>PNAS</i>, vol. 118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>.","ama":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>PNAS</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>","short":"C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, PNAS 118 (2021).","ista":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. PNAS. 118(1), e2010054118.","ieee":"C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1,” <i>PNAS</i>, vol. 118, no. 1. National Academy of Sciences, 2021.","apa":"Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., &#38; Loose, M. (2021). In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>"},"day":"05","month":"01","pmid":1,"oa_version":"Published Version","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"project":[{"_id":"2599F062-B435-11E9-9278-68D0E5697425","grant_number":"RGY0083/2016","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"publication_status":"published","acknowledgement":"We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky, Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging facility, the life science facility, and Armel Nicolas from the mass spec facility at the Institute of Science and Technology (IST) Austria for technical support. C.D. acknowledges funding from the IST fellowship program; this work was supported by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. ","status":"public","title":"In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1","author":[{"first_name":"Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87","last_name":"Düllberg","full_name":"Düllberg, Christian F","orcid":"0000-0001-6335-9748"},{"orcid":"0000-0002-3580-2906","first_name":"Albert","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","last_name":"Auer","full_name":"Auer, Albert"},{"last_name":"Canigova","full_name":"Canigova, Nikola","first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8518-5926"},{"first_name":"Katrin","id":"3760F32C-F248-11E8-B48F-1D18A9856A87","last_name":"Loibl","full_name":"Loibl, Katrin","orcid":"0000-0002-2429-7668"},{"orcid":"0000-0001-7309-9724","last_name":"Loose","full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"_id":"8988","abstract":[{"lang":"eng","text":"The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching."}],"issue":"1","doi":"10.1073/pnas.2010054118"},{"doi":"10.1016/j.molp.2020.11.004","abstract":[{"text":"The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational modification, regulating physiological and developmental auxin output at all levels. In this review, we comprehensively discuss earlier and recent advances in our understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases participating in auxin action. We provide insights into the mechanisms by which reversible protein phosphorylation defines developmental auxin responses, discuss current challenges, and provide our perspectives on future directions involving the integration of the control of protein phosphorylation into the molecular auxin network.","lang":"eng"}],"issue":"1","_id":"8992","title":"Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling","author":[{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"This work was supported by the European Union’s Horizon 2020 Program (ERC grant agreement no. 742985 to J.F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). C.L. is supported by the Austrian Science Fund (FWF; P 31493).","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Long Term Fellowship"}],"publication_identifier":{"eissn":["17529867"],"issn":["16742052"]},"oa_version":"Published Version","file_date_updated":"2021-01-07T14:03:53Z","ddc":["580"],"pmid":1,"month":"01","citation":{"mla":"Tan, Shutang, et al. “Pho-View of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.” <i>Molecular Plant</i>, vol. 14, no. 1, Elsevier, 2021, pp. 151–65, doi:<a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">10.1016/j.molp.2020.11.004</a>.","chicago":"Tan, Shutang, Christian Luschnig, and Jiří Friml. “Pho-View of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.” <i>Molecular Plant</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">https://doi.org/10.1016/j.molp.2020.11.004</a>.","ama":"Tan S, Luschnig C, Friml J. Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. <i>Molecular Plant</i>. 2021;14(1):151-165. doi:<a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">10.1016/j.molp.2020.11.004</a>","ista":"Tan S, Luschnig C, Friml J. 2021. Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. Molecular Plant. 14(1), 151–165.","short":"S. Tan, C. Luschnig, J. Friml, Molecular Plant 14 (2021) 151–165.","apa":"Tan, S., Luschnig, C., &#38; Friml, J. (2021). Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">https://doi.org/10.1016/j.molp.2020.11.004</a>","ieee":"S. Tan, C. Luschnig, and J. Friml, “Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling,” <i>Molecular Plant</i>, vol. 14, no. 1. Elsevier, pp. 151–165, 2021."},"day":"04","volume":14,"article_processing_charge":"No","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","creator":"dernst","file_size":871088,"file_name":"2020_MolecularPlant_Tan.pdf","content_type":"application/pdf","checksum":"917e60e57092f22e16beac70b1775ea6","access_level":"open_access","date_updated":"2021-01-07T14:03:53Z","success":1,"date_created":"2021-01-07T14:03:53Z","file_id":"8995"}],"year":"2021","oa":1,"page":"151-165","article_type":"original","date_updated":"2023-08-04T11:21:13Z","publication":"Molecular Plant","date_created":"2021-01-03T23:01:23Z","scopus_import":"1","date_published":"2021-01-04T00:00:00Z","external_id":{"pmid":["33186755"],"isi":["000605359400014"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"publisher":"Elsevier","intvolume":"        14"},{"volume":118,"article_processing_charge":"No","oa_version":"Published Version","month":"01","pmid":1,"day":"05","citation":{"ama":"Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. <i>PNAS</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2020857118\">10.1073/pnas.2020857118</a>","short":"L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer, L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, PNAS 118 (2021).","ista":"Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. 118(1), e2020857118.","apa":"Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer, C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2020857118\">https://doi.org/10.1073/pnas.2020857118</a>","ieee":"L. Abas <i>et al.</i>, “Naphthylphthalamic acid associates with and inhibits PIN auxin transporters,” <i>PNAS</i>, vol. 118, no. 1. National Academy of Sciences, 2021.","chicago":"Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” <i>PNAS</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2020857118\">https://doi.org/10.1073/pnas.2020857118</a>.","mla":"Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” <i>PNAS</i>, vol. 118, no. 1, e2020857118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2020857118\">10.1073/pnas.2020857118</a>."},"ec_funded":1,"acknowledgement":"This work was supported by Austrian Science Fund Grant FWF P21533-B20 (to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing access to mass spectrometry instruments at the Vienna BioCenter Core Facilities. We thank PNAS reviewers for the many comments and suggestions that helped to improve this manuscript.","status":"public","publication_status":"published","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"doi":"10.1073/pnas.2020857118","issue":"1","abstract":[{"lang":"eng","text":"N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism."}],"_id":"8993","author":[{"last_name":"Abas","full_name":"Abas, Lindy","first_name":"Lindy"},{"last_name":"Kolb","full_name":"Kolb, Martina","first_name":"Martina"},{"full_name":"Stadlmann, Johannes","last_name":"Stadlmann","first_name":"Johannes"},{"first_name":"Dorina P.","last_name":"Janacek","full_name":"Janacek, Dorina P."},{"orcid":"0000-0003-1581-881X","last_name":"Lukic","full_name":"Lukic, Kristina","first_name":"Kristina","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schwechheimer","full_name":"Schwechheimer, Claus","first_name":"Claus"},{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"},{"first_name":"Lukas","full_name":"Mach, Lukas","last_name":"Mach"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"Ulrich Z.","full_name":"Hammes, Ulrich Z.","last_name":"Hammes"}],"title":"Naphthylphthalamic acid associates with and inhibits PIN auxin transporters","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"intvolume":"       118","main_file_link":[{"url":"https://doi.org/10.1073/pnas.2020857118","open_access":"1"}],"publisher":"National Academy of Sciences","scopus_import":"1","date_created":"2021-01-03T23:01:23Z","external_id":{"pmid":["33443187"],"isi":["000607270100073"]},"date_published":"2021-01-05T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"},{"_id":"LeSa"}],"article_type":"original","article_number":"e2020857118","related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.2102232118","relation":"erratum"}]},"date_updated":"2023-08-07T13:29:23Z","publication":"PNAS","year":"2021","oa":1},{"month":"01","file_date_updated":"2021-02-04T12:30:48Z","ddc":["570"],"day":"07","citation":{"apa":"Kavcic, B., Tkačik, G., &#38; Bollenbach, M. T. (2021). Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” <i>PLOS Computational Biology</i>, vol. 17. Public Library of Science, 2021.","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 17, e1008529.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).","ama":"Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. 2021;17. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>.","mla":"Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>, vol. 17, e1008529, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>."},"oa_version":"Published Version","file":[{"date_created":"2021-02-04T12:30:48Z","file_id":"9092","date_updated":"2021-02-04T12:30:48Z","success":1,"checksum":"e29f2b42651bef8e034781de8781ffac","content_type":"application/pdf","access_level":"open_access","file_size":3690053,"creator":"dernst","relation":"main_file","file_name":"2021_PlosComBio_Kavcic.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes","volume":17,"has_accepted_license":"1","_id":"8997","author":[{"orcid":"0000-0001-6041-254X","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","full_name":"Kavcic, Bor"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"orcid":"0000-0003-4398-476X","last_name":"Bollenbach","full_name":"Bollenbach, Tobias","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"title":"Minimal biophysical model of combined antibiotic action","doi":"10.1371/journal.pcbi.1008529","abstract":[{"lang":"eng","text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems."}],"project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"publication_identifier":{"issn":["1553-7358"]},"acknowledgement":"This work was supported in part by Tum stipend of Knafelj foundation (to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). ","status":"public","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"GaTk"}],"date_created":"2021-01-08T07:16:18Z","date_published":"2021-01-07T00:00:00Z","external_id":{"isi":["000608045000010"]},"intvolume":"        17","publisher":"Public Library of Science","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"oa":1,"keyword":["Modelling and Simulation","Genetics","Molecular Biology","Antibiotics","Drug interactions"],"year":"2021","date_updated":"2024-02-21T12:41:41Z","publication":"PLOS Computational Biology","article_type":"original","article_number":"e1008529","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"7673"},{"relation":"research_data","status":"public","id":"8930"}]}},{"_id":"8999","author":[{"id":"fcf74381-53e1-11eb-a6dc-b0e2acf78757","first_name":"Kerstin","full_name":"Avila, Kerstin","last_name":"Avila"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754"}],"title":"Second-order phase transition in counter-rotating taylor-couette flow experiment","doi":"10.3390/e23010058","issue":"1","abstract":[{"lang":"eng","text":"In many basic shear flows, such as pipe, Couette, and channel flow, turbulence does not\r\narise from an instability of the laminar state, and both dynamical states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number) the fraction of fluid in laminar motion increases while turbulence recedes and eventually the entire flow relaminarizes. The first step towards understanding the nature of this transition is to determine if the phase change is of either first or second order. In the former case, the turbulent fraction would drop discontinuously to zero as the Reynolds number decreases while in the latter the process would be continuous. For Couette flow, the flow between two parallel plates, earlier studies suggest a discontinuous scenario. In the present study we realize a Couette flow between two concentric cylinders which allows studies to be carried out in large aspect ratios and for extensive observation times. The presented measurements show that the transition in this circular Couette geometry is continuous suggesting that former studies were limited by finite size effects. A further characterization of this transition, in particular its relation to the directed percolation universality class, requires even larger system sizes than presently available. "}],"publication_identifier":{"eissn":["1099-4300"]},"status":"public","publication_status":"published","acknowledgement":"This research was funded by the Central Research Development Fund of the University of\r\nBremen grant number ZF04B /2019/FB04 Avila_Kerstin (“Independent Project for Postdocs”). Shreyas Jalikop is acknowledged for recording some of the lifetime measurements\r\n","ddc":["530"],"file_date_updated":"2021-01-11T07:50:32Z","pmid":1,"month":"01","day":"01","citation":{"mla":"Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating Taylor-Couette Flow Experiment.” <i>Entropy</i>, vol. 23, no. 1, 58, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/e23010058\">10.3390/e23010058</a>.","chicago":"Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating Taylor-Couette Flow Experiment.” <i>Entropy</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/e23010058\">https://doi.org/10.3390/e23010058</a>.","ama":"Avila K, Hof B. Second-order phase transition in counter-rotating taylor-couette flow experiment. <i>Entropy</i>. 2021;23(1). doi:<a href=\"https://doi.org/10.3390/e23010058\">10.3390/e23010058</a>","short":"K. Avila, B. Hof, Entropy 23 (2021).","ista":"Avila K, Hof B. 2021. Second-order phase transition in counter-rotating taylor-couette flow experiment. Entropy. 23(1), 58.","ieee":"K. Avila and B. Hof, “Second-order phase transition in counter-rotating taylor-couette flow experiment,” <i>Entropy</i>, vol. 23, no. 1. MDPI, 2021.","apa":"Avila, K., &#38; Hof, B. (2021). Second-order phase transition in counter-rotating taylor-couette flow experiment. <i>Entropy</i>. MDPI. <a href=\"https://doi.org/10.3390/e23010058\">https://doi.org/10.3390/e23010058</a>"},"oa_version":"Published Version","file":[{"file_id":"9003","date_created":"2021-01-11T07:50:32Z","success":1,"date_updated":"2021-01-11T07:50:32Z","access_level":"open_access","content_type":"application/pdf","checksum":"3ba3dd8b7eecff713b72c5e9ba30d626","file_name":"2021_Entropy_Avila.pdf","creator":"dernst","relation":"main_file","file_size":9456389}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":23,"article_processing_charge":"No","has_accepted_license":"1","oa":1,"year":"2021","date_updated":"2023-08-07T13:31:07Z","publication":"Entropy","article_type":"original","article_number":"58","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BjHo"}],"scopus_import":"1","date_created":"2021-01-10T23:01:17Z","date_published":"2021-01-01T00:00:00Z","external_id":{"isi":["000610135400001"],"pmid":["33396499"]},"intvolume":"        23","publisher":"MDPI","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1},{"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"publisher":"Wiley","main_file_link":[{"url":"https://arxiv.org/abs/1910.10435","open_access":"1"}],"intvolume":"        53","date_created":"2019-10-24T08:04:09Z","scopus_import":"1","external_id":{"arxiv":["1910.10435"],"isi":["000594805800001"]},"date_published":"2021-04-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"TaHa"}],"page":"560-574","article_type":"original","date_updated":"2023-08-04T10:43:39Z","publication":"Bulletin of the London Mathematical Society","year":"2021","oa":1,"volume":53,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","month":"04","citation":{"chicago":"Rychlewicz, Kamil P. “The Positivity of Local Equivariant Hirzebruch Class for Toric Varieties.” <i>Bulletin of the London Mathematical Society</i>. Wiley, 2021. <a href=\"https://doi.org/10.1112/blms.12442\">https://doi.org/10.1112/blms.12442</a>.","mla":"Rychlewicz, Kamil P. “The Positivity of Local Equivariant Hirzebruch Class for Toric Varieties.” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2, Wiley, 2021, pp. 560–74, doi:<a href=\"https://doi.org/10.1112/blms.12442\">10.1112/blms.12442</a>.","ista":"Rychlewicz KP. 2021. The positivity of local equivariant Hirzebruch class for toric varieties. Bulletin of the London Mathematical Society. 53(2), 560–574.","short":"K.P. Rychlewicz, Bulletin of the London Mathematical Society 53 (2021) 560–574.","ama":"Rychlewicz KP. The positivity of local equivariant Hirzebruch class for toric varieties. <i>Bulletin of the London Mathematical Society</i>. 2021;53(2):560-574. doi:<a href=\"https://doi.org/10.1112/blms.12442\">10.1112/blms.12442</a>","apa":"Rychlewicz, K. P. (2021). The positivity of local equivariant Hirzebruch class for toric varieties. <i>Bulletin of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/blms.12442\">https://doi.org/10.1112/blms.12442</a>","ieee":"K. P. Rychlewicz, “The positivity of local equivariant Hirzebruch class for toric varieties,” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2. Wiley, pp. 560–574, 2021."},"day":"01","publication_status":"published","status":"public","publication_identifier":{"eissn":["1469-2120"],"issn":["0024-6093"]},"doi":"10.1112/blms.12442","abstract":[{"lang":"eng","text":"The central object of investigation of this paper is the Hirzebruch class, a deformation of the Todd class, given by Hirzebruch (for smooth varieties). The generalization for singular varieties is due to Brasselet–Schürmann–Yokura. Following the work of Weber, we investigate its equivariant version for (possibly singular) toric varieties. The local decomposition of the Hirzebruch class to the fixed points of the torus action and a formula for the local class in terms of the defining fan are recalled. After this review part, we prove the positivity of local Hirzebruch classes for all toric varieties, thus proving false the alleged counterexample given by Weber."}],"issue":"2","_id":"6965","title":"The positivity of local equivariant Hirzebruch class for toric varieties","author":[{"first_name":"Kamil P","id":"85A07246-A8BF-11E9-B4FA-D9E3E5697425","last_name":"Rychlewicz","full_name":"Rychlewicz, Kamil P"}]},{"article_processing_charge":"Yes","volume":24,"oa_version":"Published Version","day":"23","citation":{"chicago":"Samarasinghe, Ranmal A., Osvaldo Miranda, Jessie E. Buth, Simon Mitchell, Isabella Ferando, Momoko Watanabe, Arinnae Kurdian, et al. <i>Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids</i>. Vol. 24. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41593-021-00906-5\">https://doi.org/10.1038/s41593-021-00906-5</a>.","mla":"Samarasinghe, Ranmal A., et al. <i>Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids</i>. Vol. 24, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41593-021-00906-5\">10.1038/s41593-021-00906-5</a>.","short":"R.A. Samarasinghe, O. Miranda, J.E. Buth, S. Mitchell, I. Ferando, M. Watanabe, A. Kurdian, P. Golshani, K. Plath, W.E. Lowry, J.M. Parent, I. Mody, B.G. Novitch, Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids, Springer Nature, 2021.","ama":"Samarasinghe RA, Miranda O, Buth JE, et al. <i>Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids</i>. Vol 24. Springer Nature; 2021. doi:<a href=\"https://doi.org/10.1038/s41593-021-00906-5\">10.1038/s41593-021-00906-5</a>","ista":"Samarasinghe RA, Miranda O, Buth JE, Mitchell S, Ferando I, Watanabe M, Kurdian A, Golshani P, Plath K, Lowry WE, Parent JM, Mody I, Novitch BG. 2021. Identification of neural oscillations and epileptiform changes in human brain organoids, Springer Nature, 32p.","apa":"Samarasinghe, R. A., Miranda, O., Buth, J. E., Mitchell, S., Ferando, I., Watanabe, M., … Novitch, B. G. (2021). <i>Identification of neural oscillations and epileptiform changes in human brain organoids</i> (Vol. 24). Springer Nature. <a href=\"https://doi.org/10.1038/s41593-021-00906-5\">https://doi.org/10.1038/s41593-021-00906-5</a>","ieee":"R. A. Samarasinghe <i>et al.</i>, <i>Identification of neural oscillations and epileptiform changes in human brain organoids</i>, vol. 24. Springer Nature, 2021."},"pmid":1,"month":"08","status":"public","publication_status":"published","acknowledgement":"We thank S. Butler, T. Carmichael and members of the laboratory of B.G.N. for helpful discussions and comments on the manuscript; N. Vishlaghi and F. Turcios-Hernandez for technical assistance, and J. Lee, S.-K. Lee, H. Shinagawa and K. Yoshikawa for valuable reagents. We also thank the UCLA Eli and Edythe Broad Stem Cell Research Center (BSCRC) and Intellectual and Developmental Disabilities Research Center microscopy cores for access to imaging facilities. This work was supported by grants from the California Institute for Regenerative Medicine (CIRM) (DISC1-08819 to B.G.N.), the National Institute of Health (R01NS089817, R01DA051897 and P50HD103557 to B.G.N.; K08NS119747 to R.A.S.; K99HD096105 to M.W.; R01MH123922, R01MH121521 and P50HD103557 to M.J.G.; R01GM099134 to K.P.; R01NS103788 to W.E.L.; R01NS088571 to J.M.P.; R01NS030549 and R01AG050474 to I.M.), and research awards from the UCLA Jonsson Comprehensive Cancer Center and BSCRC Ablon Scholars Program (to B.G.N.), the BSCRC Innovation Program (to B.G.N., K.P. and W.E.L.), the UCLA BSCRC Steffy Brain Aging Research Fund (to B.G.N. and W.E.L.) and the UCLA Clinical and Translational Science Institute (to B.G.N.), Paul Allen Family Foundation Frontiers Group (to K.P. and W.E.L.), the March of Dimes Foundation (to W.E.L.) and the Simons Foundation Autism Research Initiative Bridge to Independence Program (to R.A.S. and M.J.G.). R.A.S. was also supported by the UCLA/NINDS Translational Neuroscience Training Grant (R25NS065723), a Research and Training Fellowship from the American Epilepsy Society, a Taking Flight Award from CURE Epilepsy and a Clinician Scientist training award from the UCLA BSCRC. J.E.B. was supported by the UCLA BSCRC Rose Hills Foundation Graduate Scholarship Training Program. M.W. was supported by postdoctoral training awards provided by the UCLA BSCRC and the Uehara Memorial Foundation. O.A.M. and A.K. were supported in part by the UCLA-California State University Northridge CIRM-Bridges training program (EDUC2-08411). We also acknowledge the support of the IDDRC Cells, Circuits and Systems Analysis, Microscopy and Genetics and Genomics Cores of the Semel Institute of Neuroscience at UCLA, which are supported by the NICHD (U54HD087101 and P50HD10355701). We lastly acknowledge support from a Quantitative and Computational Biosciences Collaboratory Postdoctoral Fellowship to S.M. and the Quantitative and Computational Biosciences Collaboratory community, directed by M. Pellegrini.","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"abstract":[{"text":"Human brain organoids represent a powerful tool for the study of human neurological diseases particularly those that impact brain growth and structure. However, many neurological diseases lack obvious anatomical abnormalities, yet significantly impact neural network functions, raising the question of whether organoids possess sufficient neural network architecture and complexity to model these conditions. Here, we explore the network level functions of brain organoids using calcium sensor imaging and extracellular recording approaches that together reveal the existence of complex oscillatory network behaviors reminiscent of intact brain preparations. We further demonstrate strikingly abnormal epileptiform network activity in organoids derived from a Rett Syndrome patient despite only modest anatomical differences from isogenically matched controls, and rescue with an unconventional neuromodulatory drug Pifithrin-α. Together, these findings provide an essential foundation for the utilization of human brain organoids to study intact and disordered human brain network formation and illustrate their utility in therapeutic discovery.","lang":"eng"}],"doi":"10.1038/s41593-021-00906-5","author":[{"first_name":"Ranmal A.","full_name":"Samarasinghe, Ranmal A.","last_name":"Samarasinghe"},{"full_name":"Miranda, Osvaldo","last_name":"Miranda","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","first_name":"Osvaldo","orcid":"0000-0001-6618-6889"},{"last_name":"Buth","full_name":"Buth, Jessie E.","first_name":"Jessie E."},{"full_name":"Mitchell, Simon","last_name":"Mitchell","first_name":"Simon"},{"first_name":"Isabella","full_name":"Ferando, Isabella","last_name":"Ferando"},{"full_name":"Watanabe, Momoko","last_name":"Watanabe","first_name":"Momoko"},{"first_name":"Arinnae","full_name":"Kurdian, Arinnae","last_name":"Kurdian"},{"first_name":"Peyman","last_name":"Golshani","full_name":"Golshani, Peyman"},{"first_name":"Kathrin","full_name":"Plath, Kathrin","last_name":"Plath"},{"last_name":"Lowry","full_name":"Lowry, William E.","first_name":"William E."},{"first_name":"Jack M.","full_name":"Parent, Jack M.","last_name":"Parent"},{"first_name":"Istvan","last_name":"Mody","full_name":"Mody, Istvan"},{"first_name":"Bennett G.","full_name":"Novitch, Bennett G.","last_name":"Novitch"}],"title":"Identification of neural oscillations and epileptiform changes in human brain organoids","_id":"6995","isi":1,"type":"technical_report","language":[{"iso":"eng"}],"intvolume":"        24","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41593-021-00906-5"}],"publisher":"Springer Nature","external_id":{"pmid":["34426698 "],"isi":["000687516300001"]},"date_published":"2021-08-23T00:00:00Z","date_created":"2019-11-10T11:23:58Z","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"32","date_updated":"2023-08-04T10:49:44Z","alternative_title":["Nature Neuroscience"],"year":"2021","oa":1},{"publication_identifier":{"issn":["0925-2312"],"eissn":["1872-8286"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"status":"public","publication_status":"published","acknowledgement":"LdA would like to acknowledge the financial support from MIUR-PRIN2017 WZFTZP and VALERE:VAnviteLli pEr la RicErca 2019. FL acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 754411. HJH would like to thank the Agencies CAPES and FUNCAP for financial support.","ec_funded":1,"title":"Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches","author":[{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio","full_name":"Lombardi, Fabrizio","last_name":"Lombardi","orcid":"0000-0003-2623-5249"},{"first_name":"Oren","last_name":"Shriki","full_name":"Shriki, Oren"},{"first_name":"Hans J","full_name":"Herrmann, Hans J","last_name":"Herrmann"},{"first_name":"Lucilla","last_name":"de Arcangelis","full_name":"de Arcangelis, Lucilla"}],"_id":"7463","abstract":[{"lang":"eng","text":"Resting-state brain activity is characterized by the presence of neuronal avalanches showing absence of characteristic size. Such evidence has been interpreted in the context of criticality and associated with the normal functioning of the brain. A distinctive attribute of systems at criticality is the presence of long-range correlations. Thus, to verify the hypothesis that the brain operates close to a critical point and consequently assess deviations from criticality for diagnostic purposes, it is of primary importance to robustly and reliably characterize correlations in resting-state brain activity. Recent works focused on the analysis of narrow-band electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude envelope, showing evidence of long-range temporal correlations (LRTC) in neural oscillations. However, brain activity is a broadband phenomenon, and a significant piece of information useful to precisely discriminate between normal (critical) and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal cortical dynamics. Here we propose to characterize the temporal correlations in the broadband brain activity through the lens of neuronal avalanches. To this end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding neuronal avalanche sequences, and study their temporal correlations. We demonstrate that the broadband resting-state brain activity consistently exhibits long-range power-law correlations in both EEG and MEG recordings, with similar values of the scaling exponents. Importantly, although we observe that the avalanche size distribution depends on scale parameters, scaling exponents characterizing long-range correlations are quite robust. In particular, they are independent of the temporal binning (scale of analysis), indicating that our analysis captures intrinsic characteristics of the underlying dynamics. Because neuronal avalanches constitute a fundamental feature of neural systems with universal characteristics, the proposed approach may serve as a general, systems- and experiment-independent procedure to infer the existence of underlying long-range correlations in extended neural systems, and identify pathological behaviors in the complex spatio-temporal interplay of cortical rhythms."}],"doi":"10.1016/j.neucom.2020.05.126","article_processing_charge":"No","volume":461,"citation":{"mla":"Lombardi, Fabrizio, et al. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” <i>Neurocomputing</i>, vol. 461, Elsevier, 2021, pp. 657–66, doi:<a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">10.1016/j.neucom.2020.05.126</a>.","chicago":"Lombardi, Fabrizio, Oren Shriki, Hans J Herrmann, and Lucilla de Arcangelis. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” <i>Neurocomputing</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">https://doi.org/10.1016/j.neucom.2020.05.126</a>.","apa":"Lombardi, F., Shriki, O., Herrmann, H. J., &#38; de Arcangelis, L. (2021). Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. <i>Neurocomputing</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">https://doi.org/10.1016/j.neucom.2020.05.126</a>","ieee":"F. Lombardi, O. Shriki, H. J. Herrmann, and L. de Arcangelis, “Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches,” <i>Neurocomputing</i>, vol. 461. Elsevier, pp. 657–666, 2021.","short":"F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461 (2021) 657–666.","ama":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. <i>Neurocomputing</i>. 2021;461:657-666. doi:<a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">10.1016/j.neucom.2020.05.126</a>","ista":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. 2021. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. Neurocomputing. 461, 657–666."},"day":"13","month":"05","oa_version":"Preprint","publication":"Neurocomputing","date_updated":"2023-08-04T10:46:29Z","page":"657-666","article_type":"original","oa":1,"year":"2021","publisher":"Elsevier","intvolume":"       461","main_file_link":[{"url":"https://doi.org/10.1101/2020.02.03.930966","open_access":"1"}],"isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-05-13T00:00:00Z","external_id":{"isi":["000704086300015"]},"date_created":"2020-02-06T16:09:14Z","scopus_import":"1"}]