[{"isi":1,"type":"journal_article","publisher":"Springer Nature","intvolume":"        93","_id":"8817","author":[{"orcid":"0000-0001-9224-7139","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini","full_name":"Shehu, Yekini"},{"full_name":"Iyiola, Olaniyi S.","last_name":"Iyiola","first_name":"Olaniyi S."},{"full_name":"Thong, Duong Viet","last_name":"Thong","first_name":"Duong Viet"},{"full_name":"Van, Nguyen Thi Cam","last_name":"Van","first_name":"Nguyen Thi Cam"}],"citation":{"ama":"Shehu Y, Iyiola OS, Thong DV, Van NTC. An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. <i>Mathematical Methods of Operations Research</i>. 2021;93(2):213-242. doi:<a href=\"https://doi.org/10.1007/s00186-020-00730-w\">10.1007/s00186-020-00730-w</a>","ista":"Shehu Y, Iyiola OS, Thong DV, Van NTC. 2021. An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. Mathematical Methods of Operations Research. 93(2), 213–242.","mla":"Shehu, Yekini, et al. “An Inertial Subgradient Extragradient Algorithm Extended to Pseudomonotone Equilibrium Problems.” <i>Mathematical Methods of Operations Research</i>, vol. 93, no. 2, Springer Nature, 2021, pp. 213–42, doi:<a href=\"https://doi.org/10.1007/s00186-020-00730-w\">10.1007/s00186-020-00730-w</a>.","ieee":"Y. Shehu, O. S. Iyiola, D. V. Thong, and N. T. C. Van, “An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems,” <i>Mathematical Methods of Operations Research</i>, vol. 93, no. 2. Springer Nature, pp. 213–242, 2021.","chicago":"Shehu, Yekini, Olaniyi S. Iyiola, Duong Viet Thong, and Nguyen Thi Cam Van. “An Inertial Subgradient Extragradient Algorithm Extended to Pseudomonotone Equilibrium Problems.” <i>Mathematical Methods of Operations Research</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00186-020-00730-w\">https://doi.org/10.1007/s00186-020-00730-w</a>.","apa":"Shehu, Y., Iyiola, O. S., Thong, D. V., &#38; Van, N. T. C. (2021). An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. <i>Mathematical Methods of Operations Research</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00186-020-00730-w\">https://doi.org/10.1007/s00186-020-00730-w</a>","short":"Y. Shehu, O.S. Iyiola, D.V. Thong, N.T.C. Van, Mathematical Methods of Operations Research 93 (2021) 213–242."},"quality_controlled":"1","scopus_import":"1","department":[{"_id":"VlKo"}],"publication_identifier":{"issn":["1432-2994"],"eissn":["1432-5217"]},"article_processing_charge":"No","date_created":"2020-11-29T23:01:18Z","acknowledgement":"The authors are grateful to the two referees and the Associate Editor for their comments and suggestions which have improved the earlier version of the paper greatly. The project of Yekini Shehu has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160).","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7"}],"publication":"Mathematical Methods of Operations Research","year":"2021","volume":93,"external_id":{"isi":["000590497300001"]},"title":"An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems","article_type":"original","page":"213-242","day":"01","language":[{"iso":"eng"}],"ec_funded":1,"date_updated":"2024-11-04T13:52:33Z","oa_version":"None","issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s00186-020-00730-w","month":"04","status":"public","date_published":"2021-04-01T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"The paper introduces an inertial extragradient subgradient method with self-adaptive step sizes for solving equilibrium problems in real Hilbert spaces. Weak convergence of the proposed method is obtained under the condition that the bifunction is pseudomonotone and Lipchitz continuous. Linear convergence is also given when the bifunction is strongly pseudomonotone and Lipchitz continuous. Numerical implementations and comparisons with other related inertial methods are given using test problems including a real-world application to Nash–Cournot oligopolistic electricity market equilibrium model."}]},{"doi":"10.1038/s41586-020-2914-4","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","status":"public","date_published":"2021-01-07T00:00:00Z","publication_status":"published","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."}],"day":"07","language":[{"iso":"eng"}],"issue":"7840","date_updated":"2025-07-10T12:01:26Z","oa_version":"None","department":[{"_id":"JoCs"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"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.","date_created":"2020-11-29T23:01:19Z","article_processing_charge":"No","year":"2021","publication":"Nature","external_id":{"pmid":["33208951"],"isi":["000591047800005"]},"title":"Coupling of hippocampal theta and ripples with pontogeniculooccipital waves","article_type":"original","volume":589,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-020-03068-9","relation":"erratum"}]},"page":"96-102","type":"journal_article","isi":1,"publisher":"Springer Nature","intvolume":"       589","author":[{"full_name":"Ramirez Villegas, Juan F","first_name":"Juan F","last_name":"Ramirez Villegas","id":"44B06F76-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Besserve","first_name":"Michel","full_name":"Besserve, Michel"},{"first_name":"Yusuke","last_name":"Murayama","full_name":"Murayama, Yusuke"},{"full_name":"Evrard, Henry C.","first_name":"Henry C.","last_name":"Evrard"},{"full_name":"Oeltermann, Axel","first_name":"Axel","last_name":"Oeltermann"},{"last_name":"Logothetis","first_name":"Nikos K.","full_name":"Logothetis, Nikos K."}],"_id":"8818","citation":{"short":"J.F. Ramirez Villegas, M. Besserve, Y. Murayama, H.C. Evrard, A. Oeltermann, N.K. Logothetis, Nature 589 (2021) 96–102.","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>","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>.","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.","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.","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>.","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>"},"quality_controlled":"1","scopus_import":"1"},{"article_processing_charge":"Yes (via OA deal)","date_created":"2020-12-01T13:39:46Z","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.","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"department":[{"_id":"JiFr"}],"volume":31,"article_type":"original","title":"Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism","external_id":{"isi":["000614361000039"],"pmid":["33157019"]},"publication":"Current Biology","year":"2021","intvolume":"        31","publisher":"Elsevier","isi":1,"type":"journal_article","quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","citation":{"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).","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>","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>.","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>.","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>"},"file_date_updated":"2021-02-04T11:37:50Z","_id":"8824","author":[{"full_name":"Marquès-Bueno, MM","first_name":"MM","last_name":"Marquès-Bueno"},{"full_name":"Armengot, L","first_name":"L","last_name":"Armengot"},{"full_name":"Noack, LC","last_name":"Noack","first_name":"LC"},{"full_name":"Bareille, J","last_name":"Bareille","first_name":"J"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia"},{"full_name":"Platre, MP","last_name":"Platre","first_name":"MP"},{"full_name":"Bayle, V","first_name":"V","last_name":"Bayle"},{"full_name":"Liu, M","first_name":"M","last_name":"Liu"},{"last_name":"Opdenacker","first_name":"D","full_name":"Opdenacker, D"},{"last_name":"Vanneste","first_name":"S","full_name":"Vanneste, S"},{"full_name":"Möller, BK","first_name":"BK","last_name":"Möller"},{"full_name":"Nimchuk, ZL","first_name":"ZL","last_name":"Nimchuk"},{"last_name":"Beeckman","first_name":"T","full_name":"Beeckman, T"},{"first_name":"AI","last_name":"Caño-Delgado","full_name":"Caño-Delgado, AI"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"last_name":"Jaillais","first_name":"Y","full_name":"Jaillais, Y"}],"month":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pmid":1,"doi":"10.1016/j.cub.2020.10.011","ddc":["570"],"publication_status":"published","abstract":[{"lang":"eng","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."}],"date_published":"2021-01-11T00:00:00Z","status":"public","day":"11","license":"https://creativecommons.org/licenses/by/4.0/","file":[{"checksum":"30b3393d841fb2b1e2b22fb42b5c8fff","file_id":"9090","date_created":"2021-02-04T11:37:50Z","file_name":"2021_CurrentBiology_MarquesBueno.pdf","file_size":3458646,"success":1,"access_level":"open_access","creator":"dernst","date_updated":"2021-02-04T11:37:50Z","relation":"main_file","content_type":"application/pdf"}],"date_updated":"2024-10-21T06:02:09Z","oa_version":"Published Version","issue":"1","oa":1,"language":[{"iso":"eng"}]},{"department":[{"_id":"GeKa"}],"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.","date_created":"2020-12-02T10:52:51Z","article_processing_charge":"No","publication_identifier":{"eissn":["2058-8437"]},"external_id":{"arxiv":["2004.08133"],"isi":["000600826100003"]},"title":"The germanium quantum information route","article_type":"original","volume":6,"year":"2021","project":[{"call_identifier":"FP7","grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires"},{"call_identifier":"FWF","grant_number":"Y00715","name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","_id":"2552F888-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"}],"publication":"Nature Reviews Materials","page":"926–943 ","type":"journal_article","isi":1,"intvolume":"         6","publisher":"Springer Nature","author":[{"full_name":"Scappucci, Giordano","first_name":"Giordano","last_name":"Scappucci"},{"full_name":"Kloeffel, Christoph","first_name":"Christoph","last_name":"Kloeffel"},{"full_name":"Zwanenburg, Floris A.","last_name":"Zwanenburg","first_name":"Floris A."},{"first_name":"Daniel","last_name":"Loss","full_name":"Loss, Daniel"},{"first_name":"Maksym","last_name":"Myronov","full_name":"Myronov, Maksym"},{"last_name":"Zhang","first_name":"Jian-Jun","full_name":"Zhang, Jian-Jun"},{"full_name":"Franceschi, Silvano De","first_name":"Silvano De","last_name":"Franceschi"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"},{"first_name":"Menno","last_name":"Veldhorst","full_name":"Veldhorst, Menno"}],"_id":"8911","scopus_import":"1","quality_controlled":"1","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>.","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>","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.","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>","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.","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>.","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."},"doi":"10.1038/s41578-020-00262-z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/2004.08133","open_access":"1"}],"date_published":"2021-10-01T00:00:00Z","status":"public","publication_status":"published","abstract":[{"lang":"eng","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. "}],"day":"01","ec_funded":1,"oa":1,"language":[{"iso":"eng"}],"oa_version":"Preprint","date_updated":"2024-10-22T09:41:03Z","arxiv":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1111/liv.14730","pmid":1,"month":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2021-01-01T00:00:00Z","status":"public","ddc":["570"],"publication_status":"published","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"}],"file":[{"checksum":"6e4f21b77ef22c854e016240974fc473","date_created":"2021-02-04T12:01:45Z","file_id":"9091","success":1,"file_name":"2021_Liver_Nardo.pdf","file_size":930414,"creator":"dernst","access_level":"open_access","date_updated":"2021-02-04T12:01:45Z","content_type":"application/pdf","relation":"main_file"}],"day":"01","oa":1,"language":[{"iso":"eng"}],"date_updated":"2025-06-12T06:33:00Z","oa_version":"Published Version","issue":"1","department":[{"_id":"CampIT"}],"article_processing_charge":"No","date_created":"2020-12-06T23:01:16Z","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_identifier":{"eissn":["1478-3231"],"issn":["1478-3223"]},"volume":41,"article_type":"original","title":"Pathophysiological mechanisms of liver injury in COVID-19","external_id":{"isi":["000594239200001"],"pmid":["33190346"]},"publication":"Liver International","year":"2021","page":"20-32","isi":1,"type":"journal_article","intvolume":"        41","publisher":"Wiley","_id":"8927","file_date_updated":"2021-02-04T12:01:45Z","author":[{"first_name":"Alexander D.","last_name":"Nardo","full_name":"Nardo, Alexander D."},{"full_name":"Schneeweiss-Gleixner, Mathias","last_name":"Schneeweiss-Gleixner","first_name":"Mathias"},{"full_name":"Bakail, May M","first_name":"May M","orcid":"0000-0002-9592-1587","last_name":"Bakail","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E"},{"full_name":"Dixon, Emmanuel D.","last_name":"Dixon","first_name":"Emmanuel D."},{"first_name":"Sigurd F.","last_name":"Lax","full_name":"Lax, Sigurd F."},{"full_name":"Trauner, Michael","first_name":"Michael","last_name":"Trauner"}],"scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","citation":{"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>.","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.","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.","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>","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>","short":"A.D. Nardo, M. Schneeweiss-Gleixner, M.M. Bakail, E.D. Dixon, S.F. Lax, M. Trauner, Liver International 41 (2021) 20–32.","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>."}},{"oa":1,"language":[{"iso":"eng"}],"date_updated":"2025-07-10T12:01:26Z","oa_version":"Published Version","issue":"2","day":"01","date_published":"2021-02-01T00:00:00Z","status":"public","publication_status":"published","abstract":[{"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.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1111/jeb.13723","month":"02","main_file_link":[{"url":"https://doi.org/10.1111/jeb.13723","open_access":"1"}],"_id":"8928","author":[{"last_name":"Arnoux","first_name":"Stéphanie","full_name":"Arnoux, Stéphanie"},{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"last_name":"Sauvage","first_name":"Christopher","full_name":"Sauvage, Christopher"}],"quality_controlled":"1","scopus_import":"1","citation":{"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>","short":"S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283.","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>.","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.","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>.","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.","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>"},"isi":1,"type":"journal_article","intvolume":"        34","publisher":"Wiley","volume":34,"title":"Genomic inference of complex domestication histories in three Solanaceae species","external_id":{"pmid":["33107098"],"isi":["000587769700001"]},"article_type":"original","publication":"Journal of Evolutionary Biology","project":[{"call_identifier":"FWF","grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425","name":"Sex chromosomes and species barriers"}],"year":"2021","page":"270-283","related_material":{"record":[{"relation":"research_data","id":"13065","status":"public"}]},"department":[{"_id":"NiBa"}],"article_processing_charge":"No","date_created":"2020-12-06T23:01:16Z","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":["1420-9101"],"issn":["1010-061X"]}},{"intvolume":"        66","publisher":"Springer Nature","type":"journal_article","isi":1,"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","citation":{"short":"J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, Discrete &#38; Computational Geometry 66 (2021) 386–434.","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>","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>.","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.","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>.","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.","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>"},"keyword":["Theoretical Computer Science","Computational Theory and Mathematics","Geometry and Topology","Discrete Mathematics and Combinatorics"],"author":[{"last_name":"Boissonnat","first_name":"Jean-Daniel","full_name":"Boissonnat, Jean-Daniel"},{"first_name":"Siargey","last_name":"Kachanovich","full_name":"Kachanovich, Siargey"},{"orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","first_name":"Mathijs","full_name":"Wintraecken, Mathijs"}],"_id":"8940","file_date_updated":"2021-08-06T09:52:29Z","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).","date_created":"2020-12-12T11:07:02Z","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"department":[{"_id":"HeEd"}],"page":"386-434","external_id":{"isi":["000597770300001"]},"article_type":"original","title":"Triangulating submanifolds: An elementary and quantified version of Whitney’s method","volume":66,"year":"2021","publication":"Discrete & Computational Geometry","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"day":"01","corr_author":"1","file":[{"checksum":"c848986091e56699dc12de85adb1e39c","date_created":"2021-08-06T09:52:29Z","file_id":"9795","success":1,"file_size":983307,"file_name":"2021_DescreteCompGeopmetry_Boissonnat.pdf","creator":"kschuh","access_level":"open_access","date_updated":"2021-08-06T09:52:29Z","content_type":"application/pdf","relation":"main_file"}],"issue":"1","date_updated":"2025-04-14T07:43:50Z","oa_version":"Published Version","ec_funded":1,"oa":1,"language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"07","doi":"10.1007/s00454-020-00250-8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"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.","lang":"eng"}],"publication_status":"published","ddc":["516"],"date_published":"2021-07-01T00:00:00Z","status":"public"},{"month":"01","main_file_link":[{"url":"https://doi.org/10.1073/pnas.2010054118","open_access":"1"}],"doi":"10.1073/pnas.2010054118","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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."}],"publication_status":"published","date_published":"2021-01-05T00:00:00Z","status":"public","day":"05","corr_author":"1","issue":"1","date_updated":"2025-05-14T10:59:29Z","oa_version":"Published Version","language":[{"iso":"eng"}],"oa":1,"date_created":"2021-01-03T23:01:23Z","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. ","article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"department":[{"_id":"MaLo"},{"_id":"MiSi"}],"article_type":"original","title":"In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1","external_id":{"isi":["000607270100018"],"pmid":["33443153"]},"volume":118,"year":"2021","project":[{"grant_number":"RGY0083/2016","_id":"2599F062-B435-11E9-9278-68D0E5697425","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","intvolume":"       118","publisher":"National Academy of Sciences","type":"journal_article","isi":1,"quality_controlled":"1","scopus_import":"1","article_number":"e2010054118","citation":{"mla":"Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>Proceedings of the National Academy of Sciences of the United States of America</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>.","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. Proceedings of the National Academy of Sciences of the United States of America. 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>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1. National Academy of Sciences, 2021.","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>Proceedings of the National Academy of Sciences of the United States of America</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, Proceedings of the National Academy of Sciences of the United States of America 118 (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>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>","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>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>."},"author":[{"last_name":"Düllberg","id":"459064DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6335-9748","first_name":"Christian F","full_name":"Düllberg, Christian F"},{"last_name":"Auer","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3580-2906","first_name":"Albert","full_name":"Auer, Albert"},{"first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","last_name":"Canigova","orcid":"0000-0002-8518-5926","full_name":"Canigova, Nikola"},{"first_name":"Katrin","last_name":"Loibl","id":"3760F32C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2429-7668","full_name":"Loibl, Katrin"},{"first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","full_name":"Loose, Martin"}],"_id":"8988"},{"ddc":["580"],"abstract":[{"lang":"eng","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."}],"publication_status":"published","date_published":"2021-01-04T00:00:00Z","status":"public","month":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1016/j.molp.2020.11.004","date_updated":"2025-07-10T12:01:28Z","oa_version":"Published Version","issue":"1","ec_funded":1,"language":[{"iso":"eng"}],"oa":1,"day":"04","file":[{"checksum":"917e60e57092f22e16beac70b1775ea6","file_id":"8995","date_created":"2021-01-07T14:03:53Z","file_size":871088,"file_name":"2020_MolecularPlant_Tan.pdf","success":1,"access_level":"open_access","creator":"dernst","date_updated":"2021-01-07T14:03:53Z","relation":"main_file","content_type":"application/pdf"}],"page":"151-165","volume":14,"title":"Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling","article_type":"original","external_id":{"isi":["000605359400014"],"pmid":["33186755"]},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"},{"name":"Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking in Arabidopsis","_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015"}],"publication":"Molecular Plant","year":"2021","article_processing_charge":"No","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).","date_created":"2021-01-03T23:01:23Z","publication_identifier":{"issn":["1674-2052"],"eissn":["1752-9867"]},"department":[{"_id":"JiFr"}],"quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","citation":{"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>","short":"S. Tan, C. Luschnig, J. Friml, Molecular Plant 14 (2021) 151–165.","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>.","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>.","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.","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.","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>"},"file_date_updated":"2021-01-07T14:03:53Z","_id":"8992","author":[{"last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","full_name":"Tan, Shutang"},{"last_name":"Luschnig","first_name":"Christian","full_name":"Luschnig, Christian"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"intvolume":"        14","publisher":"Elsevier","isi":1,"type":"journal_article"},{"day":"05","oa":1,"language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","date_updated":"2025-05-14T10:58:54Z","issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1073/pnas.2020857118","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2020857118"}],"month":"01","status":"public","date_published":"2021-01-05T00:00:00Z","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."}],"publication_status":"published","isi":1,"type":"journal_article","publisher":"National Academy of Sciences","intvolume":"       118","_id":"8993","author":[{"last_name":"Abas","first_name":"Lindy","full_name":"Abas, Lindy"},{"last_name":"Kolb","first_name":"Martina","full_name":"Kolb, Martina"},{"full_name":"Stadlmann, Johannes","first_name":"Johannes","last_name":"Stadlmann"},{"first_name":"Dorina P.","last_name":"Janacek","full_name":"Janacek, Dorina P."},{"first_name":"Kristina","orcid":"0000-0003-1581-881X","last_name":"Lukic","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","full_name":"Lukic, Kristina"},{"full_name":"Schwechheimer, Claus","first_name":"Claus","last_name":"Schwechheimer"},{"first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","full_name":"Sazanov, Leonid A"},{"last_name":"Mach","first_name":"Lukas","full_name":"Mach, Lukas"},{"full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Hammes, Ulrich Z.","first_name":"Ulrich Z.","last_name":"Hammes"}],"citation":{"ama":"Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2020857118\">10.1073/pnas.2020857118</a>","ieee":"L. Abas <i>et al.</i>, “Naphthylphthalamic acid associates with and inhibits PIN auxin transporters,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1. National Academy of Sciences, 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. Proceedings of the National Academy of Sciences of the United States of America. 118(1), e2020857118.","mla":"Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” <i>Proceedings of the National Academy of Sciences of the United States of America</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>.","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>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2020857118\">https://doi.org/10.1073/pnas.2020857118</a>.","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>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2020857118\">https://doi.org/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, Proceedings of the National Academy of Sciences of the United States of America 118 (2021)."},"article_number":"e2020857118","quality_controlled":"1","scopus_import":"1","department":[{"_id":"JiFr"},{"_id":"LeSa"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_processing_charge":"No","date_created":"2021-01-03T23:01:23Z","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.","publication":"Proceedings of the National Academy of Sciences of the United States of America","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"year":"2021","volume":118,"article_type":"original","external_id":{"isi":["000607270100073"],"pmid":["33443187"]},"title":"Naphthylphthalamic acid associates with and inhibits PIN auxin transporters","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.2102232118"}]}},{"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"01","doi":"10.1371/journal.pcbi.1008529","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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."}],"publication_status":"published","ddc":["570"],"status":"public","date_published":"2021-01-07T00:00:00Z","day":"07","file":[{"success":1,"file_size":3690053,"file_name":"2021_PlosComBio_Kavcic.pdf","checksum":"e29f2b42651bef8e034781de8781ffac","date_created":"2021-02-04T12:30:48Z","file_id":"9092","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_updated":"2021-02-04T12:30:48Z"}],"date_updated":"2025-06-12T06:33:18Z","oa_version":"Published Version","language":[{"iso":"eng"}],"oa":1,"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.). ","date_created":"2021-01-08T07:16:18Z","article_processing_charge":"Yes","department":[{"_id":"GaTk"}],"related_material":{"record":[{"relation":"research_data","id":"8930","status":"public"},{"id":"7673","status":"public","relation":"earlier_version"}]},"year":"2021","project":[{"call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions"},{"grant_number":"P28844-B27","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"publication":"PLOS Computational Biology","external_id":{"isi":["000608045000010"],"pmid":["33411759"]},"title":"Minimal biophysical model of combined antibiotic action","article_type":"original","volume":17,"publisher":"Public Library of Science","intvolume":"        17","type":"journal_article","isi":1,"citation":{"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>.","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>","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>","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.","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>."},"keyword":["Modelling and Simulation","Genetics","Molecular Biology","Antibiotics","Drug interactions"],"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","article_number":"e1008529","author":[{"full_name":"Kavcic, Bor","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","orcid":"0000-0001-6041-254X"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"},{"full_name":"Bollenbach, Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Tobias"}],"file_date_updated":"2021-02-04T12:30:48Z","_id":"8997"},{"date_published":"2021-01-01T00:00:00Z","status":"public","abstract":[{"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. ","lang":"eng"}],"publication_status":"published","ddc":["530"],"doi":"10.3390/e23010058","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"01","oa":1,"language":[{"iso":"eng"}],"issue":"1","date_updated":"2023-08-07T13:31:07Z","oa_version":"Published Version","file":[{"checksum":"3ba3dd8b7eecff713b72c5e9ba30d626","file_id":"9003","date_created":"2021-01-11T07:50:32Z","file_size":9456389,"file_name":"2021_Entropy_Avila.pdf","success":1,"access_level":"open_access","creator":"dernst","date_updated":"2021-01-11T07:50:32Z","relation":"main_file","content_type":"application/pdf"}],"day":"01","title":"Second-order phase transition in counter-rotating taylor-couette flow experiment","external_id":{"isi":["000610135400001"],"pmid":["33396499"]},"article_type":"original","volume":23,"year":"2021","publication":"Entropy","department":[{"_id":"BjHo"}],"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","date_created":"2021-01-10T23:01:17Z","article_processing_charge":"No","publication_identifier":{"eissn":["1099-4300"]},"author":[{"full_name":"Avila, Kerstin","first_name":"Kerstin","last_name":"Avila","id":"fcf74381-53e1-11eb-a6dc-b0e2acf78757"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn"}],"_id":"8999","file_date_updated":"2021-01-11T07:50:32Z","has_accepted_license":"1","article_number":"58","scopus_import":"1","quality_controlled":"1","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>.","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.","ista":"Avila K, Hof B. 2021. Second-order phase transition in counter-rotating taylor-couette flow experiment. Entropy. 23(1), 58.","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).","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>","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>."},"type":"journal_article","isi":1,"intvolume":"        23","publisher":"MDPI"},{"isi":1,"type":"journal_article","intvolume":"        67","publisher":"IEEE","_id":"9002","author":[{"full_name":"Fazeli, Arman","first_name":"Arman","last_name":"Fazeli"},{"last_name":"Hassani","first_name":"Hamed","full_name":"Hassani, Hamed"},{"full_name":"Mondelli, Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco"},{"first_name":"Alexander","last_name":"Vardy","full_name":"Vardy, Alexander"}],"scopus_import":"1","quality_controlled":"1","citation":{"short":"A. Fazeli, H. Hassani, M. Mondelli, A. Vardy, IEEE Transactions on Information Theory 67 (2021) 5693–5710.","apa":"Fazeli, A., Hassani, H., Mondelli, M., &#38; Vardy, A. (2021). Binary linear codes with optimal scaling: Polar codes with large kernels. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2020.3038806\">https://doi.org/10.1109/TIT.2020.3038806</a>","chicago":"Fazeli, Arman, Hamed Hassani, Marco Mondelli, and Alexander Vardy. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2021. <a href=\"https://doi.org/10.1109/TIT.2020.3038806\">https://doi.org/10.1109/TIT.2020.3038806</a>.","ista":"Fazeli A, Hassani H, Mondelli M, Vardy A. 2021. Binary linear codes with optimal scaling: Polar codes with large kernels. IEEE Transactions on Information Theory. 67(9), 5693–5710.","mla":"Fazeli, Arman, et al. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” <i>IEEE Transactions on Information Theory</i>, vol. 67, no. 9, IEEE, 2021, pp. 5693–710, doi:<a href=\"https://doi.org/10.1109/TIT.2020.3038806\">10.1109/TIT.2020.3038806</a>.","ieee":"A. Fazeli, H. Hassani, M. Mondelli, and A. Vardy, “Binary linear codes with optimal scaling: Polar codes with large kernels,” <i>IEEE Transactions on Information Theory</i>, vol. 67, no. 9. IEEE, pp. 5693–5710, 2021.","ama":"Fazeli A, Hassani H, Mondelli M, Vardy A. Binary linear codes with optimal scaling: Polar codes with large kernels. <i>IEEE Transactions on Information Theory</i>. 2021;67(9):5693-5710. doi:<a href=\"https://doi.org/10.1109/TIT.2020.3038806\">10.1109/TIT.2020.3038806</a>"},"department":[{"_id":"MaMo"}],"article_processing_charge":"No","date_created":"2021-01-10T23:01:18Z","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"volume":67,"title":"Binary linear codes with optimal scaling: Polar codes with large kernels","article_type":"original","external_id":{"isi":["000690440100007"],"arxiv":["1711.01339"]},"publication":"IEEE Transactions on Information Theory","year":"2021","page":"5693-5710","OA_place":"repository","related_material":{"record":[{"id":"6665","status":"public","relation":"earlier_version"}]},"day":"01","language":[{"iso":"eng"}],"oa":1,"date_updated":"2025-09-10T09:59:12Z","oa_version":"Preprint","issue":"9","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1109/TIT.2020.3038806","OA_type":"green","month":"09","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1711.01339","open_access":"1"}],"date_published":"2021-09-01T00:00:00Z","status":"public","abstract":[{"text":" We prove that, for the binary erasure channel (BEC), the polar-coding paradigm gives rise to codes that not only approach the Shannon limit but do so under the best possible scaling of their block length as a function of the gap to capacity. This result exhibits the first known family of binary codes that attain both optimal scaling and quasi-linear complexity of encoding and decoding. Our proof is based on the construction and analysis of binary polar codes with large kernels. When communicating reliably at rates within ε>0 of capacity, the code length n often scales as O(1/εμ), where the constant μ is called the scaling exponent. It is known that the optimal scaling exponent is μ=2, and it is achieved by random linear codes. The scaling exponent of conventional polar codes (based on the 2×2 kernel) on the BEC is μ=3.63. This falls far short of the optimal scaling guaranteed by random codes. Our main contribution is a rigorous proof of the following result: for the BEC, there exist ℓ×ℓ binary kernels, such that polar codes constructed from these kernels achieve scaling exponent μ(ℓ) that tends to the optimal value of 2 as ℓ grows. We furthermore characterize precisely how large ℓ needs to be as a function of the gap between μ(ℓ) and 2. The resulting binary codes maintain the recursive structure of conventional polar codes, and thereby achieve construction complexity O(n) and encoding/decoding complexity O(nlogn).","lang":"eng"}],"publication_status":"published"},{"publication_identifier":{"eissn":["1573-675X"],"issn":["1360-8185"]},"acknowledgement":"This work was supported by National Institute of Health grants R01 EY030123, P30 EY016665, and T32 GM081061, an unrestricted research grant from Research to Prevent Blindness, Inc., and the Frederick A. Davis Endowment from the Department of Ophthalmology and Visual Sciences at the University of Wisconsin-Madison.","date_created":"2021-01-17T23:01:11Z","article_processing_charge":"No","department":[{"_id":"SaSi"}],"page":"132-145","year":"2021","publication":"Apoptosis","external_id":{"pmid":["33426618"],"isi":["000606722600001"]},"title":"Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis","article_type":"original","volume":26,"publisher":"Springer Nature","intvolume":"        26","type":"journal_article","isi":1,"citation":{"chicago":"Grosser, Joshua A., Margaret E Maes, and Robert W. Nickells. “Characteristics of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.” <i>Apoptosis</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s10495-020-01654-w\">https://doi.org/10.1007/s10495-020-01654-w</a>.","short":"J.A. Grosser, M.E. Maes, R.W. Nickells, Apoptosis 26 (2021) 132–145.","apa":"Grosser, J. A., Maes, M. E., &#38; Nickells, R. W. (2021). Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. <i>Apoptosis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10495-020-01654-w\">https://doi.org/10.1007/s10495-020-01654-w</a>","ama":"Grosser JA, Maes ME, Nickells RW. Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. <i>Apoptosis</i>. 2021;26(2):132-145. doi:<a href=\"https://doi.org/10.1007/s10495-020-01654-w\">10.1007/s10495-020-01654-w</a>","mla":"Grosser, Joshua A., et al. “Characteristics of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.” <i>Apoptosis</i>, vol. 26, no. 2, Springer Nature, 2021, pp. 132–45, doi:<a href=\"https://doi.org/10.1007/s10495-020-01654-w\">10.1007/s10495-020-01654-w</a>.","ieee":"J. A. Grosser, M. E. Maes, and R. W. Nickells, “Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis,” <i>Apoptosis</i>, vol. 26, no. 2. Springer Nature, pp. 132–145, 2021.","ista":"Grosser JA, Maes ME, Nickells RW. 2021. Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. Apoptosis. 26(2), 132–145."},"scopus_import":"1","quality_controlled":"1","author":[{"first_name":"Joshua A.","last_name":"Grosser","full_name":"Grosser, Joshua A."},{"first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E"},{"full_name":"Nickells, Robert W.","first_name":"Robert W.","last_name":"Nickells"}],"_id":"9009","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082518/","open_access":"1"}],"month":"02","pmid":1,"doi":"10.1007/s10495-020-01654-w","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Recent advancements in live cell imaging technologies have identified the phenomenon of intracellular propagation of late apoptotic events, such as cytochrome c release and caspase activation. The mechanism, prevalence, and speed of apoptosis propagation remain unclear. Additionally, no studies have demonstrated propagation of the pro-apoptotic protein, BAX. To evaluate the role of BAX in intracellular apoptotic propagation, we used high speed live-cell imaging to visualize fluorescently tagged-BAX recruitment to mitochondria in four immortalized cell lines. We show that propagation of mitochondrial BAX recruitment occurs in parallel to cytochrome c and SMAC/Diablo release and is affected by cellular morphology, such that cells with processes are more likely to exhibit propagation. The initiation of propagation events is most prevalent in the distal tips of processes, while the rate of propagation is influenced by the 2-dimensional width of the process. Propagation was rarely observed in the cell soma, which exhibited near synchronous recruitment of BAX. Propagation velocity is not affected by mitochondrial volume in segments of processes, but is negatively affected by mitochondrial density. There was no evidence of a propagating wave of increased levels of intracellular calcium ions. Alternatively, we did observe a uniform increase in superoxide build-up in cellular mitochondria, which was released as a propagating wave simultaneously with the propagating recruitment of BAX to the mitochondrial outer membrane."}],"publication_status":"published","status":"public","date_published":"2021-02-01T00:00:00Z","day":"01","issue":"2","date_updated":"2023-08-07T13:32:40Z","oa_version":"Submitted Version","oa":1,"language":[{"iso":"eng"}]},{"intvolume":"        23","publisher":"MDPI","isi":1,"type":"journal_article","article_number":"e23010125","scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","citation":{"short":"T. Gulden, A. Kamenev, Entropy 23 (2021).","apa":"Gulden, T., &#38; Kamenev, A. (2021). Dynamics of ion channels via non-hermitian quantum mechanics. <i>Entropy</i>. MDPI. <a href=\"https://doi.org/10.3390/e23010125\">https://doi.org/10.3390/e23010125</a>","chicago":"Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian Quantum Mechanics.” <i>Entropy</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/e23010125\">https://doi.org/10.3390/e23010125</a>.","mla":"Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian Quantum Mechanics.” <i>Entropy</i>, vol. 23, no. 1, e23010125, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/e23010125\">10.3390/e23010125</a>.","ista":"Gulden T, Kamenev A. 2021. Dynamics of ion channels via non-hermitian quantum mechanics. Entropy. 23(1), e23010125.","ieee":"T. Gulden and A. Kamenev, “Dynamics of ion channels via non-hermitian quantum mechanics,” <i>Entropy</i>, vol. 23, no. 1. MDPI, 2021.","ama":"Gulden T, Kamenev A. Dynamics of ion channels via non-hermitian quantum mechanics. <i>Entropy</i>. 2021;23(1). doi:<a href=\"https://doi.org/10.3390/e23010125\">10.3390/e23010125</a>"},"_id":"9020","file_date_updated":"2021-01-19T11:11:14Z","author":[{"full_name":"Gulden, Tobias","first_name":"Tobias","orcid":"0000-0001-6814-7541","id":"1083E038-9F73-11E9-A4B5-532AE6697425","last_name":"Gulden"},{"full_name":"Kamenev, Alex","last_name":"Kamenev","first_name":"Alex"}],"article_processing_charge":"Yes","acknowledgement":"A.K. was supported by NSF grants DMR-2037654. T.G. acknowledges funding from the Institute of Science and Technology (IST) Austria, and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411.\r\nWe are indebted to Boris Shklovskii for introducing us to the problem, and Alexander Gorsky and Peter Koroteev for introducing us to the Picard-Fuchs methods. A very special thanks goes to Michael Janas for several years of excellent collaboration on these topics. TG thanks Michael Kreshchuk for introduction to the exact WKB method and great collaboration on related projects. Figure 3 and Figure 4 are reproduced from Reference [25] with friendly permission by the Russian Academy of Sciences. Figure 2, Figure 4, Figure 5, Figure 6, and Figure 8 are reproduced from Reference [26] with friendly permission by IOP Publishing.","date_created":"2021-01-19T11:12:06Z","publication_identifier":{"eissn":["1099-4300"]},"department":[{"_id":"MaSe"}],"volume":23,"external_id":{"arxiv":["2012.01390"],"pmid":["33477903"],"isi":["000610122000001"]},"title":"Dynamics of ion channels via non-hermitian quantum mechanics","article_type":"original","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication":"Entropy","year":"2021","day":"19","file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2021-01-19T11:11:14Z","creator":"tgulden","access_level":"open_access","file_size":981285,"file_name":"Final published paper.pdf","date_created":"2021-01-19T11:11:14Z","file_id":"9021","checksum":"6cd0e706156827c45c740534bd32c179"}],"date_updated":"2025-06-12T06:33:38Z","oa_version":"Published Version","issue":"1","arxiv":1,"ec_funded":1,"oa":1,"language":[{"iso":"eng"}],"month":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.3390/e23010125","pmid":1,"ddc":["530"],"publication_status":"published","abstract":[{"lang":"eng","text":"We study dynamics and thermodynamics of ion transport in narrow, water-filled channels, considered as effective 1D Coulomb systems. The long range nature of the inter-ion interactions comes about due to the dielectric constants mismatch between the water and the surrounding medium, confining the electric filed to stay mostly within the water-filled channel. Statistical mechanics of such Coulomb systems is dominated by entropic effects which may be accurately accounted for by mapping onto an effective quantum mechanics. In presence of multivalent ions the corresponding quantum mechanics appears to be non-Hermitian. In this review we discuss a framework for semiclassical calculations for the effective non-Hermitian Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line to closed cycles on a complex Riemann surfaces where direct calculations are not attainable. We circumvent this issue by applying tools from algebraic topology, such as the Picard-Fuchs equation. We discuss how its solutions relate to the thermodynamics and correlation functions of multivalent solutions within narrow, water-filled channels. "}],"date_published":"2021-01-19T00:00:00Z","status":"public"},{"main_file_link":[{"url":"https://arxiv.org/abs/1910.10447","open_access":"1"}],"month":"03","doi":"10.1016/j.aim.2021.107595","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"In this short note, we prove that the square root of the quantum Jensen-Shannon divergence is a true metric on the cone of positive matrices, and hence in particular on the quantum state space.","lang":"eng"}],"publication_status":"published","status":"public","date_published":"2021-03-26T00:00:00Z","day":"26","arxiv":1,"issue":"3","oa_version":"Preprint","date_updated":"2025-04-14T07:50:40Z","oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0001-8708"]},"acknowledgement":"D. Virosztek was supported by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 846294, and partially supported by the Hungarian National Research, Development and Innovation Office (NKFIH) via grants no. K124152, and no. KH129601.","date_created":"2021-01-22T17:55:17Z","article_processing_charge":"No","department":[{"_id":"LaEr"}],"year":"2021","publication":"Advances in Mathematics","project":[{"call_identifier":"H2020","grant_number":"846294","name":"Geometric study of Wasserstein spaces and free probability","_id":"26A455A6-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000619676100035"],"arxiv":["1910.10447"]},"article_type":"original","title":"The metric property of the quantum Jensen-Shannon divergence","volume":380,"publisher":"Elsevier","intvolume":"       380","type":"journal_article","isi":1,"citation":{"chicago":"Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.” <i>Advances in Mathematics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.aim.2021.107595\">https://doi.org/10.1016/j.aim.2021.107595</a>.","apa":"Virosztek, D. (2021). The metric property of the quantum Jensen-Shannon divergence. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2021.107595\">https://doi.org/10.1016/j.aim.2021.107595</a>","short":"D. Virosztek, Advances in Mathematics 380 (2021).","ama":"Virosztek D. The metric property of the quantum Jensen-Shannon divergence. <i>Advances in Mathematics</i>. 2021;380(3). doi:<a href=\"https://doi.org/10.1016/j.aim.2021.107595\">10.1016/j.aim.2021.107595</a>","ieee":"D. Virosztek, “The metric property of the quantum Jensen-Shannon divergence,” <i>Advances in Mathematics</i>, vol. 380, no. 3. Elsevier, 2021.","ista":"Virosztek D. 2021. The metric property of the quantum Jensen-Shannon divergence. Advances in Mathematics. 380(3), 107595.","mla":"Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.” <i>Advances in Mathematics</i>, vol. 380, no. 3, 107595, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.aim.2021.107595\">10.1016/j.aim.2021.107595</a>."},"keyword":["General Mathematics"],"scopus_import":"1","article_number":"107595","quality_controlled":"1","author":[{"full_name":"Virosztek, Daniel","orcid":"0000-0003-1109-5511","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","last_name":"Virosztek","first_name":"Daniel"}],"_id":"9036"},{"isi":1,"type":"journal_article","publisher":"London Mathematical Society","intvolume":"        53","file_date_updated":"2021-08-06T09:59:45Z","_id":"9037","author":[{"full_name":"Ivanov, Grigory","first_name":"Grigory","last_name":"Ivanov","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"}],"citation":{"ama":"Ivanov G. No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. <i>Bulletin of the London Mathematical Society</i>. 2021;53(2):631-641. doi:<a href=\"https://doi.org/10.1112/blms.12449\">10.1112/blms.12449</a>","ieee":"G. Ivanov, “No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p,” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2. London Mathematical Society, pp. 631–641, 2021.","mla":"Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach Spaces of Type P.” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2, London Mathematical Society, 2021, pp. 631–41, doi:<a href=\"https://doi.org/10.1112/blms.12449\">10.1112/blms.12449</a>.","ista":"Ivanov G. 2021. No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. Bulletin of the London Mathematical Society. 53(2), 631–641.","chicago":"Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach Spaces of Type P.” <i>Bulletin of the London Mathematical Society</i>. London Mathematical Society, 2021. <a href=\"https://doi.org/10.1112/blms.12449\">https://doi.org/10.1112/blms.12449</a>.","short":"G. Ivanov, Bulletin of the London Mathematical Society 53 (2021) 631–641.","apa":"Ivanov, G. (2021). No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. <i>Bulletin of the London Mathematical Society</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/blms.12449\">https://doi.org/10.1112/blms.12449</a>"},"quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","department":[{"_id":"UlWa"}],"publication_identifier":{"issn":["0024-6093"],"eissn":["1469-2120"]},"article_processing_charge":"Yes (via OA deal)","acknowledgement":"I wish to thank Imre Bárány for bringing the problem to my attention. I am grateful to Marton Naszódi and Igor Tsiutsiurupa for useful remarks and help with the text.\r\nThe author acknowledges the financial support from the Ministry of Educational and Science of the Russian Federation in the framework of MegaGrant no 075‐15‐2019‐1926.","date_created":"2021-01-24T23:01:08Z","publication":"Bulletin of the London Mathematical Society","year":"2021","volume":53,"external_id":{"isi":["000607265100001"],"arxiv":["1912.08561"]},"title":"No-dimension Tverberg's theorem and its corollaries in Banach spaces of type p","article_type":"original","page":"631-641","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"kschuh","date_updated":"2021-08-06T09:59:45Z","file_size":194550,"file_name":"2021_BLMS_Ivanov.pdf","success":1,"checksum":"e6ceaa6470d835eb4c211cbdd38fdfd1","file_id":"9796","date_created":"2021-08-06T09:59:45Z"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","day":"01","language":[{"iso":"eng"}],"oa":1,"arxiv":1,"date_updated":"2025-07-10T12:01:31Z","oa_version":"Published Version","issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1112/blms.12449","month":"04","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"status":"public","date_published":"2021-04-01T00:00:00Z","ddc":["510"],"abstract":[{"lang":"eng","text":"We continue our study of ‘no‐dimension’ analogues of basic theorems in combinatorial and convex geometry in Banach spaces. We generalize some results of the paper (Adiprasito, Bárány and Mustafa, ‘Theorems of Carathéodory, Helly, and Tverberg without dimension’, Proceedings of the Thirtieth Annual ACM‐SIAM Symposium on Discrete Algorithms (Society for Industrial and Applied Mathematics, San Diego, California, 2019) 2350–2360) and prove no‐dimension versions of the colored Tverberg theorem, the selection lemma and the weak  𝜀 ‐net theorem in Banach spaces of type  𝑝>1 . To prove these results, we use the original ideas of Adiprasito, Bárány and Mustafa for the Euclidean case, our no‐dimension version of the Radon theorem and slightly modified version of the celebrated Maurey lemma."}],"publication_status":"published"},{"file":[{"file_name":"2021_PlosPathogens_Roemhild.pdf","file_size":570066,"success":1,"checksum":"d745d7f8fcbb9b95fea16a36f94dee31","file_id":"9070","date_created":"2021-02-03T12:13:03Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2021-02-03T12:13:03Z"}],"day":"14","oa":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","date_updated":"2025-07-10T12:01:33Z","issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1371/journal.ppat.1009172","month":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","date_published":"2021-01-14T00:00:00Z","ddc":["570"],"publication_status":"published","isi":1,"type":"journal_article","publisher":"Public Library of Science","intvolume":"        17","file_date_updated":"2021-02-03T12:13:03Z","_id":"9046","author":[{"full_name":"Römhild, Roderich","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","last_name":"Römhild","orcid":"0000-0001-9480-5261","first_name":"Roderich"},{"last_name":"Andersson","first_name":"Dan I.","full_name":"Andersson, Dan I."}],"citation":{"chicago":"Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.” <i>PLoS Pathogens</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.ppat.1009172\">https://doi.org/10.1371/journal.ppat.1009172</a>.","apa":"Römhild, R., &#38; Andersson, D. I. (2021). Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. <i>PLoS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1009172\">https://doi.org/10.1371/journal.ppat.1009172</a>","short":"R. Römhild, D.I. Andersson, PLoS Pathogens 17 (2021).","ama":"Römhild R, Andersson DI. Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. <i>PLoS Pathogens</i>. 2021;17(1). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1009172\">10.1371/journal.ppat.1009172</a>","ieee":"R. Römhild and D. I. Andersson, “Mechanisms and therapeutic potential of collateral sensitivity to antibiotics,” <i>PLoS Pathogens</i>, vol. 17, no. 1. Public Library of Science, 2021.","mla":"Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.” <i>PLoS Pathogens</i>, vol. 17, no. 1, e1009172, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1009172\">10.1371/journal.ppat.1009172</a>.","ista":"Römhild R, Andersson DI. 2021. Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. PLoS Pathogens. 17(1), e1009172."},"scopus_import":"1","quality_controlled":"1","article_number":"e1009172","has_accepted_license":"1","department":[{"_id":"CaGu"}],"publication_identifier":{"eissn":["1553-7374"],"issn":["1553-7366"]},"article_processing_charge":"No","acknowledgement":"Our work was supported by the Swedish Research Council (grant 2017-01527) to DIA","date_created":"2021-01-31T23:01:21Z","publication":"PLoS Pathogens","year":"2021","volume":17,"external_id":{"isi":["000610190400007"],"pmid":["33444399"]},"title":"Mechanisms and therapeutic potential of collateral sensitivity to antibiotics","article_type":"original"},{"article_processing_charge":"No","acknowledgement":"M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305, IIS-1741162, and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council of Canada (NSERC) and by Huawei. The authors would like to thank the anonymous reviewers for their comments that helped improving the quality of the manuscript.","date_created":"2021-01-31T23:01:21Z","publication_identifier":{"issn":["1536-1276"],"eissn":["1558-2248"]},"department":[{"_id":"MaMo"}],"page":"18-27","related_material":{"record":[{"relation":"earlier_version","id":"8536","status":"public"}]},"volume":20,"external_id":{"isi":["000607808800002"],"arxiv":["1909.04892"]},"article_type":"original","title":"Sublinear latency for simplified successive cancellation decoding of polar codes","publication":"IEEE Transactions on Wireless Communications","year":"2021","intvolume":"        20","publisher":"IEEE","isi":1,"type":"journal_article","quality_controlled":"1","scopus_import":"1","citation":{"ama":"Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. Sublinear latency for simplified successive cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. 2021;20(1):18-27. doi:<a href=\"https://doi.org/10.1109/TWC.2020.3022922\">10.1109/TWC.2020.3022922</a>","ista":"Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. 2021. Sublinear latency for simplified successive cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. 20(1), 18–27.","mla":"Mondelli, Marco, et al. “Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>, vol. 20, no. 1, IEEE, 2021, pp. 18–27, doi:<a href=\"https://doi.org/10.1109/TWC.2020.3022922\">10.1109/TWC.2020.3022922</a>.","ieee":"M. Mondelli, S. A. Hashemi, J. M. Cioffi, and A. Goldsmith, “Sublinear latency for simplified successive cancellation decoding of polar codes,” <i>IEEE Transactions on Wireless Communications</i>, vol. 20, no. 1. IEEE, pp. 18–27, 2021.","chicago":"Mondelli, Marco, Seyyed Ali Hashemi, John M. Cioffi, and Andrea Goldsmith. “Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>. IEEE, 2021. <a href=\"https://doi.org/10.1109/TWC.2020.3022922\">https://doi.org/10.1109/TWC.2020.3022922</a>.","apa":"Mondelli, M., Hashemi, S. A., Cioffi, J. M., &#38; Goldsmith, A. (2021). Sublinear latency for simplified successive cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. IEEE. <a href=\"https://doi.org/10.1109/TWC.2020.3022922\">https://doi.org/10.1109/TWC.2020.3022922</a>","short":"M. Mondelli, S.A. Hashemi, J.M. Cioffi, A. Goldsmith, IEEE Transactions on Wireless Communications 20 (2021) 18–27."},"_id":"9047","author":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","orcid":"0000-0002-3242-7020","first_name":"Marco","full_name":"Mondelli, Marco"},{"full_name":"Hashemi, Seyyed Ali","first_name":"Seyyed Ali","last_name":"Hashemi"},{"full_name":"Cioffi, John M.","last_name":"Cioffi","first_name":"John M."},{"first_name":"Andrea","last_name":"Goldsmith","full_name":"Goldsmith, Andrea"}],"month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1909.04892","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1109/TWC.2020.3022922","abstract":[{"text":"This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N1−1/μ) , where N is the block length and μ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 or 1.","lang":"eng"}],"publication_status":"published","date_published":"2021-01-01T00:00:00Z","status":"public","day":"01","corr_author":"1","date_updated":"2025-09-10T10:27:04Z","oa_version":"Preprint","issue":"1","arxiv":1,"oa":1,"language":[{"iso":"eng"}]},{"file":[{"access_level":"open_access","creator":"dernst","date_updated":"2021-02-03T12:47:04Z","relation":"main_file","content_type":"application/pdf","checksum":"d9acbc502390ed7a97e631d23ae19ecd","file_id":"9074","date_created":"2021-02-03T12:47:04Z","file_name":"2021_PhysicalRevLett_DeNicola.pdf","file_size":398075,"success":1}],"day":"29","oa":1,"language":[{"iso":"eng"}],"ec_funded":1,"arxiv":1,"issue":"4","oa_version":"Published Version","date_updated":"2025-04-14T07:43:50Z","doi":"10.1103/physrevlett.126.040602","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"01","status":"public","date_published":"2021-01-29T00:00:00Z","publication_status":"published","abstract":[{"text":"The analogy between an equilibrium partition function and the return probability in many-body unitary dynamics has led to the concept of dynamical quantum phase transition (DQPT). DQPTs are defined by nonanalyticities in the return amplitude and are present in many models. In some cases, DQPTs can be related to equilibrium concepts, such as order parameters, yet their universal description is an open question. In this Letter, we provide first steps toward a classification of DQPTs by using a matrix product state description of unitary dynamics in the thermodynamic limit. This allows us to distinguish the two limiting cases of “precession” and “entanglement” DQPTs, which are illustrated using an analytical description in the quantum Ising model. While precession DQPTs are characterized by a large entanglement gap and are semiclassical in their nature, entanglement DQPTs occur near avoided crossings in the entanglement spectrum and can be distinguished by a complex pattern of nonlocal correlations. We demonstrate the existence of precession and entanglement DQPTs beyond Ising models, discuss observables that can distinguish them, and relate their interplay to complex DQPT phenomenology.","lang":"eng"}],"ddc":["530"],"type":"journal_article","isi":1,"publisher":"American Physical Society","intvolume":"       126","author":[{"full_name":"De Nicola, Stefano","first_name":"Stefano","orcid":"0000-0002-4842-6671","id":"42832B76-F248-11E8-B48F-1D18A9856A87","last_name":"De Nicola"},{"full_name":"Michailidis, Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","orcid":"0000-0002-8443-1064","first_name":"Alexios"},{"full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"}],"_id":"9048","file_date_updated":"2021-02-03T12:47:04Z","citation":{"chicago":"De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement View of Dynamical Quantum Phase Transitions.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.126.040602\">https://doi.org/10.1103/physrevlett.126.040602</a>.","apa":"De Nicola, S., Michailidis, A., &#38; Serbyn, M. (2021). Entanglement view of dynamical quantum phase transitions. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.126.040602\">https://doi.org/10.1103/physrevlett.126.040602</a>","short":"S. De Nicola, A. Michailidis, M. Serbyn, Physical Review Letters 126 (2021).","ama":"De Nicola S, Michailidis A, Serbyn M. Entanglement view of dynamical quantum phase transitions. <i>Physical Review Letters</i>. 2021;126(4). doi:<a href=\"https://doi.org/10.1103/physrevlett.126.040602\">10.1103/physrevlett.126.040602</a>","mla":"De Nicola, Stefano, et al. “Entanglement View of Dynamical Quantum Phase Transitions.” <i>Physical Review Letters</i>, vol. 126, no. 4, 040602, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.126.040602\">10.1103/physrevlett.126.040602</a>.","ieee":"S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement view of dynamical quantum phase transitions,” <i>Physical Review Letters</i>, vol. 126, no. 4. American Physical Society, 2021.","ista":"De Nicola S, Michailidis A, Serbyn M. 2021. Entanglement view of dynamical quantum phase transitions. Physical Review Letters. 126(4), 040602."},"keyword":["General Physics and Astronomy"],"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","article_number":"040602","department":[{"_id":"MaSe"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"date_created":"2021-02-01T09:20:00Z","acknowledgement":"S. D. N. acknowledges funding from the Institute of Science and Technology (IST) Austria and from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. A. M. and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 Research and\r\nInnovation Programme (Grant Agreement No. 850899).","article_processing_charge":"Yes","year":"2021","publication":"Physical Review Letters","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"article_type":"original","external_id":{"isi":["000613148200001"],"arxiv":["2008.04894"]},"title":"Entanglement view of dynamical quantum phase transitions","volume":126}]