[{"year":"2023","department":[{"_id":"MiLe"}],"arxiv":1,"title":"Magnetic impurity in a one-dimensional few-fermion system","publication":"SciPost Physics","day":"24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.21468/scipostphys.14.1.006","publication_identifier":{"issn":["2542-4653"]},"language":[{"iso":"eng"}],"oa":1,"keyword":["General Physics and Astronomy"],"article_type":"original","article_number":"006","date_published":"2023-01-24T00:00:00Z","intvolume":" 14","volume":14,"author":[{"last_name":"Rammelmüller","first_name":"Lukas","full_name":"Rammelmüller, Lukas"},{"first_name":"David","full_name":"Huber, David","last_name":"Huber"},{"first_name":"Matija","full_name":"Čufar, Matija","last_name":"Čufar"},{"last_name":"Brand","first_name":"Joachim","full_name":"Brand, Joachim"},{"last_name":"Hammer","first_name":"Hans-Werner","full_name":"Hammer, Hans-Werner"},{"last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem"}],"_id":"13278","issue":"1","quality_controlled":"1","file_date_updated":"2023-07-31T08:44:38Z","abstract":[{"text":"We present a numerical analysis of spin-1/2 fermions in a one-dimensional harmonic potential in the presence of a magnetic point-like impurity at the center of the trap. The model represents a few-body analogue of a magnetic impurity in the vicinity of an s-wave superconductor. Already for a few particles we find a ground-state level crossing between sectors with different fermion parities. We interpret this crossing as a few-body precursor of a quantum phase transition, which occurs when the impurity \"breaks\" a Cooper pair. This picture is further corroborated by analyzing density-density correlations in momentum space. Finally, we discuss how the system may be realized with existing cold-atoms platforms.","lang":"eng"}],"external_id":{"isi":["001000325800008"],"arxiv":["2204.01606"]},"date_created":"2023-07-24T10:48:23Z","publication_status":"published","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"relation":"main_file","date_updated":"2023-07-31T08:44:38Z","content_type":"application/pdf","file_size":1163444,"success":1,"file_name":"2023_SciPostPhysics_Rammelmueller.pdf","access_level":"open_access","date_created":"2023-07-31T08:44:38Z","checksum":"ffdb70b9ae7aa45ea4ea6096ecbd6431","creator":"dernst","file_id":"13328"}],"ddc":["530"],"isi":1,"month":"01","status":"public","date_updated":"2023-12-13T11:39:32Z","oa_version":"Published Version","citation":{"ista":"Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. 2023. Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. 14(1), 006.","ama":"Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. 2023;14(1). doi:10.21468/scipostphys.14.1.006","short":"L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, A. Volosniev, SciPost Physics 14 (2023).","mla":"Rammelmüller, Lukas, et al. “Magnetic Impurity in a One-Dimensional Few-Fermion System.” SciPost Physics, vol. 14, no. 1, 006, SciPost Foundation, 2023, doi:10.21468/scipostphys.14.1.006.","chicago":"Rammelmüller, Lukas, David Huber, Matija Čufar, Joachim Brand, Hans-Werner Hammer, and Artem Volosniev. “Magnetic Impurity in a One-Dimensional Few-Fermion System.” SciPost Physics. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.14.1.006.","ieee":"L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, and A. Volosniev, “Magnetic impurity in a one-dimensional few-fermion system,” SciPost Physics, vol. 14, no. 1. SciPost Foundation, 2023.","apa":"Rammelmüller, L., Huber, D., Čufar, M., Brand, J., Hammer, H.-W., & Volosniev, A. (2023). Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.14.1.006"},"publisher":"SciPost Foundation","has_accepted_license":"1","article_processing_charge":"No","type":"journal_article"},{"date_created":"2023-07-24T14:10:45Z","publication_status":"published","file_date_updated":"2023-08-11T14:39:17Z","abstract":[{"lang":"eng","text":"Semiconductor-superconductor hybrid systems are the harbour of many intriguing mesoscopic phenomena. This material combination leads to spatial variations of the superconducting properties, which gives rise to Andreev bound states (ABSs). Some of these states might exhibit remarkable properties that render them highly desirable for topological quantum computing. The most prominent and hunted of such states are Majorana zero modes (MZMs), quasiparticles equals to their own quasiparticles that they follow non-abelian statistics. In this thesis, we first introduce the general framework of such hybrid systems and, then, we unveil a series of mesoscopic phenomena that we discovered. Firstly, we show tunneling spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures. Then, we introduce a novel protocol which allowed the integration of tunneling spectroscopy with Coulomb spectroscopy within the same device. Employing this approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally confined states reveal charge transport phenomenology similar to the one expected for MZMs. These findings shed light on the intricate interplay between superconductivity and quantum confinement, which brought us to explore another material platform, i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce superconductivity in such system, we showed how to engineer the proximity effect and we revealed a superconducting hard gap. Finally, we created a superconducting radio frequency driven ideal diode and a generator of non-sinusoidal current-phase relations. Our results open the path for the exploration of protected superconducting qubits and more complex hybrid devices in planar Germanium, like Kitaev chains and hybrid qubit devices."}],"page":"184","author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","full_name":"Valentini, Marco","first_name":"Marco","last_name":"Valentini"}],"date_published":"2023-07-21T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","_id":"13286","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","citation":{"ama":"Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:10.15479/at:ista:13286","ista":"Valentini M. 2023. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria.","mla":"Valentini, Marco. Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13286.","short":"M. Valentini, Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium, Institute of Science and Technology Austria, 2023.","chicago":"Valentini, Marco. “Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13286.","apa":"Valentini, M. (2023). Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13286","ieee":"M. Valentini, “Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium,” Institute of Science and Technology Austria, 2023."},"type":"dissertation","file":[{"file_id":"14033","creator":"mvalenti","checksum":"666ee31c7eade89679806287c062fa14","date_created":"2023-08-11T09:27:39Z","access_level":"closed","file_name":"PhD_thesis_Valentini_final.zip","file_size":56121429,"content_type":"application/x-zip-compressed","date_updated":"2023-08-11T10:01:34Z","relation":"source_file"},{"date_updated":"2023-08-11T14:39:17Z","content_type":"application/pdf","file_size":38199711,"file_name":"PhD_thesis_Valentini_final_validated.pdf","relation":"main_file","file_id":"14035","access_level":"open_access","date_created":"2023-08-11T14:39:17Z","creator":"mvalenti","checksum":"0992f2ebef152dee8e70055350ebbb55"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"13312"},{"id":"12118","relation":"part_of_dissertation","status":"public"},{"id":"8910","relation":"part_of_dissertation","status":"public"},{"relation":"research_data","id":"12522","status":"public"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"oa_version":"Published Version","date_updated":"2024-02-21T12:35:34Z","month":"07","status":"public","ddc":["530"],"alternative_title":["ISTA Thesis"],"title":"Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"call_identifier":"H2020","grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"F8606","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","name":"Conventional and unconventional topological superconductors"}],"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"year":"2023","oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"ec_funded":1,"degree_awarded":"PhD","day":"21","supervisor":[{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios"}],"doi":"10.15479/at:ista:13286","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"oa":1,"publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772785"]},"language":[{"iso":"eng"}],"ec_funded":1,"day":"05","publication":"50th International Colloquium on Automata, Languages, and Programming","doi":"10.4230/LIPIcs.ICALP.2023.129","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LIPIcs"],"title":"Regular methods for operator precedence languages","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093.\r\nWe thank Pierre Ganty for early discussions and the anonymous reviewers for their helpful comments.\r\n","project":[{"call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"}],"arxiv":1,"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"year":"2023","article_processing_charge":"Yes","has_accepted_license":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","citation":{"ista":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. 2023. Regular methods for operator precedence languages. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 129:1--129:20.","ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator precedence languages. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023:129:1--129:20. doi:10.4230/LIPIcs.ICALP.2023.129","mla":"Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20, doi:10.4230/LIPIcs.ICALP.2023.129.","short":"T.A. Henzinger, P. Kebis, N.A. Mazzocchi, N.E. Sarac, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20.","chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Regular Methods for Operator Precedence Languages.” In 50th International Colloquium on Automata, Languages, and Programming, 261:129:1--129:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.129.","apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., & Sarac, N. E. (2023). Regular methods for operator precedence languages. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261, p. 129:1--129:20). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.129","ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods for operator precedence languages,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20."},"type":"conference","file":[{"relation":"main_file","file_name":"icalp23.pdf","success":1,"file_size":859379,"content_type":"application/pdf","date_updated":"2023-07-24T15:11:05Z","creator":"esarac","checksum":"5d4c8932ef3450615a53b9bb15d92eb2","date_created":"2023-07-24T15:11:05Z","access_level":"open_access","file_id":"13293"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","date_updated":"2023-07-31T08:38:38Z","status":"public","month":"07","ddc":["000"],"publication_status":"published","external_id":{"arxiv":["2305.03447"]},"date_created":"2023-07-24T15:11:41Z","abstract":[{"lang":"eng","text":"The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time."}],"file_date_updated":"2023-07-24T15:11:05Z","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger"},{"last_name":"Kebis","full_name":"Kebis, Pavol","first_name":"Pavol"},{"last_name":"Mazzocchi","id":"b26baa86-3308-11ec-87b0-8990f34baa85","full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien"},{"first_name":"Naci E","full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac"}],"volume":261,"page":"129:1--129:20","intvolume":" 261","date_published":"2023-07-05T00:00:00Z","conference":{"start_date":"2023-07-10","end_date":"2023-07-14","name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Paderborn, Germany"},"quality_controlled":"1","_id":"13292"},{"page":"358–382","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Karimi","full_name":"Karimi, Mahyar","first_name":"Mahyar","id":"f1dedef5-2f78-11ee-989a-c4c97bccf506","orcid":"0009-0005-0820-1696"},{"last_name":"Kueffner","full_name":"Kueffner, Konstantin","first_name":"Konstantin","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","orcid":"0000-0001-8974-2542"},{"orcid":"0000-0001-9864-7475","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","first_name":"Kaushik","full_name":"Mallik, Kaushik","last_name":"Mallik"}],"volume":13965,"intvolume":" 13965","conference":{"start_date":"2023-07-17","location":"Paris, France","end_date":"2023-07-22","name":"CAV: Computer Aided Verification"},"date_published":"2023-07-18T00:00:00Z","quality_controlled":"1","_id":"13310","date_created":"2023-07-25T18:32:40Z","external_id":{"arxiv":["2305.15979"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Machine-learned systems are in widespread use for making decisions about humans, and it is important that they are fair, i.e., not biased against individuals based on sensitive attributes. We present runtime verification of algorithmic fairness for systems whose models are unknown, but are assumed to have a Markov chain structure. We introduce a specification language that can model many common algorithmic fairness properties, such as demographic parity, equal opportunity, and social burden. We build monitors that observe a long sequence of events as generated by a given system, and output, after each observation, a quantitative estimate of how fair or biased the system was on that run until that point in time. The estimate is proven to be correct modulo a variable error bound and a given confidence level, where the error bound gets tighter as the observed sequence gets longer. Our monitors are of two types, and use, respectively, frequentist and Bayesian statistical inference techniques. While the frequentist monitors compute estimates that are objectively correct with respect to the ground truth, the Bayesian monitors compute estimates that are correct subject to a given prior belief about the system’s model. Using a prototype implementation, we show how we can monitor if a bank is fair in giving loans to applicants from different social backgrounds, and if a college is fair in admitting students while maintaining a reasonable financial burden on the society. Although they exhibit different theoretical complexities in certain cases, in our experiments, both frequentist and Bayesian monitors took less than a millisecond to update their verdicts after each observation."}],"file_date_updated":"2023-07-31T08:11:20Z","file":[{"relation":"main_file","file_name":"2023_LNCS_CAV_HenzingerT.pdf","file_size":647760,"success":1,"date_updated":"2023-07-31T08:11:20Z","content_type":"application/pdf","checksum":"ccaf94bf7d658ba012c016e11869b54c","creator":"dernst","date_created":"2023-07-31T08:11:20Z","access_level":"open_access","file_id":"13327"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","date_updated":"2023-09-05T15:14:00Z","month":"07","status":"public","ddc":["000"],"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","publisher":"Springer Nature","citation":{"apa":"Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Monitoring algorithmic fairness. In Computer Aided Verification (Vol. 13965, pp. 358–382). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37703-7_17","ieee":"T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Monitoring algorithmic fairness,” in Computer Aided Verification, Paris, France, 2023, vol. 13965, pp. 358–382.","chicago":"Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Monitoring Algorithmic Fairness.” In Computer Aided Verification, 13965:358–382. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37703-7_17.","mla":"Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness.” Computer Aided Verification, vol. 13965, Springer Nature, 2023, pp. 358–382, doi:10.1007/978-3-031-37703-7_17.","short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification, Springer Nature, 2023, pp. 358–382.","ista":"Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Monitoring algorithmic fairness. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13965, 358–382.","ama":"Henzinger TA, Karimi M, Kueffner K, Mallik K. Monitoring algorithmic fairness. In: Computer Aided Verification. Vol 13965. Springer Nature; 2023:358–382. doi:10.1007/978-3-031-37703-7_17"},"type":"conference","acknowledgement":"This work is supported by the European Research Council under Grant No.: ERC-2020-AdG101020093.","project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"arxiv":1,"year":"2023","alternative_title":["LNCS"],"title":"Monitoring algorithmic fairness","day":"18","publication":"Computer Aided Verification","doi":"10.1007/978-3-031-37703-7_17","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783031377020"],"eissn":["1611-3349"],"eisbn":["9783031377037"],"issn":["0302-9743"]},"ec_funded":1},{"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"acknowledgement":"The authors acknowledge Alexander Brinkmann, Alessandro Crippa, Andrew Higginbotham, Andrea Iorio, Giordano\r\nScappucci and Christian Schonenberger for helpful discussions. We thank Marcel Verheijen for the support in the\r\nTEM analysis. This research and related results were made\r\npossible with the support of the NOMIS Foundation. It was\r\nsupported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the\r\nnanofabrication facility, the European Union’s Horizon 2020\r\nresearch and innovation programme under Grant Agreement\r\nNo 862046, the HORIZON-RIA 101069515 project and the\r\nFWF Projects #P-32235, #P-36507 and #F-8606. R.S.S.\r\nacknowledges Spanish CM “Talento Program” Project No.\r\n2022-T1/IND-24070.","project":[{"call_identifier":"H2020","grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","name":"Towards scalable hut wire quantum devices","call_identifier":"FWF"},{"grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","name":"Conventional and unconventional topological superconductors","grant_number":"F8606"},{"name":"Protected states of quantum matter","_id":"bd5b4ec5-d553-11ed-ba76-a6eedb083344"}],"department":[{"_id":"GeKa"},{"_id":"M-Shop"}],"arxiv":1,"year":"2023","title":"Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.07109","open_access":"1"}],"day":"13","publication":"arXiv","doi":"10.48550/arXiv.2306.07109","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"keyword":["Mesoscale and Nanoscale Physics"],"language":[{"iso":"eng"}],"article_number":"2306.07109","ec_funded":1,"author":[{"last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","full_name":"Valentini, Marco"},{"last_name":"Sagi","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver","first_name":"Oliver"},{"last_name":"Baghumyan","first_name":"Levon","full_name":"Baghumyan, Levon"},{"last_name":"Gijsel","full_name":"Gijsel, Thijs de","first_name":"Thijs de"},{"first_name":"Jason","id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87","full_name":"Jung, Jason","last_name":"Jung"},{"last_name":"Calcaterra","full_name":"Calcaterra, Stefano","first_name":"Stefano"},{"full_name":"Ballabio, Andrea","first_name":"Andrea","last_name":"Ballabio"},{"first_name":"Juan Aguilera","full_name":"Servin, Juan Aguilera","last_name":"Servin"},{"last_name":"Aggarwal","full_name":"Aggarwal, Kushagra","first_name":"Kushagra","orcid":"0000-0001-9985-9293","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb"},{"first_name":"Marian","full_name":"Janik, Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87","last_name":"Janik"},{"last_name":"Adletzberger","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Adletzberger, Thomas"},{"full_name":"Souto, Rubén Seoane","first_name":"Rubén Seoane","last_name":"Souto"},{"last_name":"Leijnse","full_name":"Leijnse, Martin","first_name":"Martin"},{"last_name":"Danon","full_name":"Danon, Jeroen","first_name":"Jeroen"},{"last_name":"Schrade","first_name":"Constantin","full_name":"Schrade, Constantin"},{"last_name":"Bakkers","full_name":"Bakkers, Erik","first_name":"Erik"},{"full_name":"Chrastina, Daniel","first_name":"Daniel","last_name":"Chrastina"},{"first_name":"Giovanni","full_name":"Isella, Giovanni","last_name":"Isella"},{"last_name":"Katsaros","full_name":"Katsaros, Georgios","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"}],"date_published":"2023-06-13T00:00:00Z","_id":"13312","date_created":"2023-07-26T11:17:20Z","external_id":{"arxiv":["2306.07109"]},"publication_status":"submitted","abstract":[{"text":"Superconductor/semiconductor hybrid devices have attracted increasing\r\ninterest in the past years. Superconducting electronics aims to complement\r\nsemiconductor technology, while hybrid architectures are at the forefront of\r\nnew ideas such as topological superconductivity and protected qubits. In this\r\nwork, we engineer the induced superconductivity in two-dimensional germanium\r\nhole gas by varying the distance between the quantum well and the aluminum. We\r\ndemonstrate a hard superconducting gap and realize an electrically and flux\r\ntunable superconducting diode using a superconducting quantum interference\r\ndevice (SQUID). This allows to tune the current phase relation (CPR), to a\r\nregime where single Cooper pair tunneling is suppressed, creating a $ \\sin\r\n\\left( 2 \\varphi \\right)$ CPR. Shapiro experiments complement this\r\ninterpretation and the microwave drive allows to create a diode with $ \\approx\r\n100 \\%$ efficiency. The reported results open up the path towards monolithic\r\nintegration of spin qubit devices, microwave resonators and (protected)\r\nsuperconducting qubits on a silicon technology compatible platform.","lang":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"13286","status":"public"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Preprint","date_updated":"2024-02-07T07:52:32Z","status":"public","month":"06","ddc":["530"],"article_processing_charge":"No","citation":{"short":"M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.A. Servin, K. Aggarwal, M. Janik, T. Adletzberger, R.S. Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).","mla":"Valentini, Marco, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, 2306.07109, doi:10.48550/arXiv.2306.07109.","ista":"Valentini M, Sagi O, Baghumyan L, Gijsel T de, Jung J, Calcaterra S, Ballabio A, Servin JA, Aggarwal K, Janik M, Adletzberger T, Souto RS, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv, 2306.07109.","ama":"Valentini M, Sagi O, Baghumyan L, et al. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. doi:10.48550/arXiv.2306.07109","apa":"Valentini, M., Sagi, O., Baghumyan, L., Gijsel, T. de, Jung, J., Calcaterra, S., … Katsaros, G. (n.d.). Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. https://doi.org/10.48550/arXiv.2306.07109","ieee":"M. Valentini et al., “Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas,” arXiv. .","chicago":"Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2306.07109."},"type":"preprint"},{"article_processing_charge":"Yes (in subscription journal)","citation":{"ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. Nature Physics. 2023;19:1916-1926. doi:10.1038/s41567-023-02218-w","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments. Nature Physics. 19, 1916–1926.","mla":"Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:10.1038/s41567-023-02218-w.","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, Nature Physics 19 (2023) 1916–1926.","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02218-w.","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02218-w","ieee":"Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments,” Nature Physics, vol. 19. Springer Nature, pp. 1916–1926, 2023."},"publisher":"Springer Nature","has_accepted_license":"1","type":"journal_article","related_material":{"record":[{"id":"13116","relation":"research_data","status":"public"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_name":"2023_NaturePhysics_Dunajova.pdf","content_type":"application/pdf","date_updated":"2024-01-30T14:28:30Z","success":1,"file_size":22471673,"relation":"main_file","file_id":"14916","creator":"dernst","checksum":"bc7673ca07d37309013a86166577b2f7","access_level":"open_access","date_created":"2024-01-30T14:28:30Z"}],"date_updated":"2024-02-21T12:19:08Z","oa_version":"Published Version","ddc":["530"],"month":"12","status":"public","date_created":"2023-07-27T14:44:45Z","publication_status":"published","external_id":{"pmid":["38075437"]},"abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division."}],"file_date_updated":"2024-01-30T14:28:30Z","scopus_import":"1","date_published":"2023-12-01T00:00:00Z","intvolume":" 19","volume":19,"page":"1916-1926","author":[{"last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","full_name":"Dunajova, Zuzana","first_name":"Zuzana"},{"full_name":"Prats Mateu, Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87","first_name":"Batirtze","last_name":"Prats Mateu"},{"last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 "},{"last_name":"Lim","full_name":"Lim, Keesiang","first_name":"Keesiang"},{"last_name":"Brandis","id":"21d64d35-f128-11eb-9611-b8bcca7a12fd","full_name":"Brandis, Dörte","first_name":"Dörte"},{"first_name":"Philipp","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","last_name":"Velicky"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl"},{"last_name":"Wong","first_name":"Richard W.","full_name":"Wong, Richard W."},{"last_name":"Elgeti","first_name":"Jens","full_name":"Elgeti, Jens"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B"},{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724"}],"quality_controlled":"1","_id":"13314","oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"article_type":"original","ec_funded":1,"publication":"Nature Physics","day":"01","doi":"10.1038/s41567-023-02218-w","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Chiral and nematic phases of flexible active filaments","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"pmid":1,"project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020"},{"grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"grant_number":"26360","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments"}],"acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF).","year":"2023","department":[{"_id":"JoDa"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"GradSch"}]},{"title":"Fundamental limits in structured principal component analysis and how to reach them","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"acknowledgement":"J.B. was funded by the European Union (ERC, CHORAL, project number 101039794). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. M.M. was supported by the 2019 Lopez-Loreta Prize. We would like to thank the reviewers for the insightful comments and, in particular, for suggesting the BAMP-inspired denoisers leading to AMP-AP.","year":"2023","department":[{"_id":"MaMo"}],"pmid":1,"article_number":"e2302028120","article_type":"original","oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1091-6490"]},"doi":"10.1073/pnas.2302028120","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"25","scopus_import":"1","date_created":"2023-07-30T22:01:02Z","external_id":{"pmid":["37463204"]},"publication_status":"published","file_date_updated":"2023-07-31T07:30:48Z","abstract":[{"lang":"eng","text":"How do statistical dependencies in measurement noise influence high-dimensional inference? To answer this, we study the paradigmatic spiked matrix model of principal components analysis (PCA), where a rank-one matrix is corrupted by additive noise. We go beyond the usual independence assumption on the noise entries, by drawing the noise from a low-order polynomial orthogonal matrix ensemble. The resulting noise correlations make the setting relevant for applications but analytically challenging. We provide characterization of the Bayes optimal limits of inference in this model. If the spike is rotation invariant, we show that standard spectral PCA is optimal. However, for more general priors, both PCA and the existing approximate message-passing algorithm (AMP) fall short of achieving the information-theoretic limits, which we compute using the replica method from statistical physics. We thus propose an AMP, inspired by the theory of adaptive Thouless–Anderson–Palmer equations, which is empirically observed to saturate the conjectured theoretical limit. This AMP comes with a rigorous state evolution analysis tracking its performance. Although we focus on specific noise distributions, our methodology can be generalized to a wide class of trace matrix ensembles at the cost of more involved expressions. Finally, despite the seemingly strong assumption of rotation-invariant noise, our theory empirically predicts algorithmic performance on real data, pointing at strong universality properties."}],"issue":"30","quality_controlled":"1","_id":"13315","intvolume":" 120","date_published":"2023-07-25T00:00:00Z","volume":120,"author":[{"first_name":"Jean","full_name":"Barbier, Jean","last_name":"Barbier"},{"full_name":"Camilli, Francesco","first_name":"Francesco","last_name":"Camilli"},{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli"},{"last_name":"Sáenz","full_name":"Sáenz, Manuel","first_name":"Manuel"}],"type":"journal_article","article_processing_charge":"Yes (in subscription journal)","citation":{"apa":"Barbier, J., Camilli, F., Mondelli, M., & Sáenz, M. (2023). Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2302028120","ieee":"J. Barbier, F. Camilli, M. Mondelli, and M. Sáenz, “Fundamental limits in structured principal component analysis and how to reach them,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 30. National Academy of Sciences, 2023.","chicago":"Barbier, Jean, Francesco Camilli, Marco Mondelli, and Manuel Sáenz. “Fundamental Limits in Structured Principal Component Analysis and How to Reach Them.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2302028120.","mla":"Barbier, Jean, et al. “Fundamental Limits in Structured Principal Component Analysis and How to Reach Them.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 30, e2302028120, National Academy of Sciences, 2023, doi:10.1073/pnas.2302028120.","short":"J. Barbier, F. Camilli, M. Mondelli, M. Sáenz, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","ista":"Barbier J, Camilli F, Mondelli M, Sáenz M. 2023. Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. 120(30), e2302028120.","ama":"Barbier J, Camilli F, Mondelli M, Sáenz M. Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(30). doi:10.1073/pnas.2302028120"},"publisher":"National Academy of Sciences","has_accepted_license":"1","date_updated":"2024-09-10T13:03:18Z","oa_version":"Published Version","ddc":["000"],"month":"07","status":"public","related_material":{"link":[{"url":"https://github.com/fcamilli95/Structured-PCA-","relation":"software"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"relation":"main_file","file_name":"2023_PNAS_Barbier.pdf","date_updated":"2023-07-31T07:30:48Z","content_type":"application/pdf","success":1,"file_size":995933,"checksum":"1fc06228afdb3aa80cf8e7766bcf9dc5","creator":"dernst","access_level":"open_access","date_created":"2023-07-31T07:30:48Z","file_id":"13323"}]},{"date_updated":"2023-12-13T11:37:36Z","oa_version":"Published Version","isi":1,"ddc":["570"],"month":"07","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"checksum":"2af111a00cf5e3a956f7f0fd13199b15","creator":"dernst","date_created":"2023-07-31T07:43:00Z","access_level":"open_access","file_id":"13324","relation":"main_file","file_name":"2023_eLife_Toshima.pdf","file_size":11980913,"success":1,"content_type":"application/pdf","date_updated":"2023-07-31T07:43:00Z"}],"type":"journal_article","article_processing_charge":"Yes","citation":{"ama":"Toshima JY, Tsukahara A, Nagano M, et al. The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. eLife. 2023;12. doi:10.7554/eLife.84850","ista":"Toshima JY, Tsukahara A, Nagano M, Tojima T, Siekhaus DE, Nakano A, Toshima J. 2023. The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. eLife. 12, e84850.","short":"J.Y. Toshima, A. Tsukahara, M. Nagano, T. Tojima, D.E. Siekhaus, A. Nakano, J. Toshima, ELife 12 (2023).","mla":"Toshima, Junko Y., et al. “The Yeast Endocytic Early/Sorting Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.” ELife, vol. 12, e84850, eLife Sciences Publications, 2023, doi:10.7554/eLife.84850.","chicago":"Toshima, Junko Y., Ayana Tsukahara, Makoto Nagano, Takuro Tojima, Daria E Siekhaus, Akihiko Nakano, and Jiro Toshima. “The Yeast Endocytic Early/Sorting Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.” ELife. eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.84850.","ieee":"J. Y. Toshima et al., “The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network,” eLife, vol. 12. eLife Sciences Publications, 2023.","apa":"Toshima, J. Y., Tsukahara, A., Nagano, M., Tojima, T., Siekhaus, D. E., Nakano, A., & Toshima, J. (2023). The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.84850"},"has_accepted_license":"1","publisher":"eLife Sciences Publications","quality_controlled":"1","_id":"13316","intvolume":" 12","date_published":"2023-07-21T00:00:00Z","author":[{"first_name":"Junko Y.","full_name":"Toshima, Junko Y.","last_name":"Toshima"},{"last_name":"Tsukahara","first_name":"Ayana","full_name":"Tsukahara, Ayana"},{"first_name":"Makoto","full_name":"Nagano, Makoto","last_name":"Nagano"},{"full_name":"Tojima, Takuro","first_name":"Takuro","last_name":"Tojima"},{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus"},{"full_name":"Nakano, Akihiko","first_name":"Akihiko","last_name":"Nakano"},{"first_name":"Jiro","full_name":"Toshima, Jiro","last_name":"Toshima"}],"volume":12,"scopus_import":"1","publication_status":"published","external_id":{"isi":["001035372800001"],"pmid":["37477116"]},"date_created":"2023-07-30T22:01:02Z","abstract":[{"text":"Although budding yeast has been extensively used as a model organism for studying organelle functions and intracellular vesicle trafficking, whether it possesses an independent endocytic early/sorting compartment that sorts endocytic cargos to the endo-lysosomal pathway or the recycling pathway has long been unclear. The structure and properties of the endocytic early/sorting compartment differ significantly between organisms; in plant cells, the trans-Golgi network (TGN) serves this role, whereas in mammalian cells a separate intracellular structure performs this function. The yeast syntaxin homolog Tlg2p, widely localizing to the TGN and endosomal compartments, is presumed to act as a Q-SNARE for endocytic vesicles, but which compartment is the direct target for endocytic vesicles remained unanswered. Here we demonstrate by high-speed and high-resolution 4D imaging of fluorescently labeled endocytic cargos that the Tlg2p-residing compartment within the TGN functions as the early/sorting compartment. After arriving here, endocytic cargos are recycled to the plasma membrane or transported to the yeast Rab5-residing endosomal compartment through the pathway requiring the clathrin adaptors GGAs. Interestingly, Gga2p predominantly localizes at the Tlg2p-residing compartment, and the deletion of GGAs has little effect on another TGN region where Sec7p is present but suppresses dynamics of the Tlg2-residing early/sorting compartment, indicating that the Tlg2p- and Sec7p-residing regions are discrete entities in the mutant. Thus, the Tlg2p-residing region seems to serve as an early/sorting compartment and function independently of the Sec7p-residing region within the TGN.","lang":"eng"}],"file_date_updated":"2023-07-31T07:43:00Z","doi":"10.7554/eLife.84850","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"eLife","day":"21","article_number":"e84850","article_type":"original","oa":1,"publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"acknowledgement":"This work was supported by JSPS KAKENHI grant #18K062291, and the Takeda Science Foundation to JYT., as well as JSPS KAKENHI grant #19K065710, the Takeda Science Foundation, and Life Science Foundation of Japan to JT.","year":"2023","department":[{"_id":"DaSi"}],"pmid":1,"title":"The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network"},{"date_created":"2023-07-30T22:01:02Z","external_id":{"arxiv":["2304.04213"],"isi":["001035677200002"]},"publication_status":"published","file_date_updated":"2023-07-31T07:49:31Z","abstract":[{"lang":"eng","text":"We prove the Eigenstate Thermalisation Hypothesis (ETH) for local observables in a typical translation invariant system of quantum spins with L-body interactions, where L is the number of spins. This mathematically verifies the observation first made by Santos and Rigol (Phys Rev E 82(3):031130, 2010, https://doi.org/10.1103/PhysRevE.82.031130) that the ETH may hold for systems with additional translational symmetries for a naturally restricted class of observables. We also present numerical support for the same phenomenon for Hamiltonians with local interaction."}],"scopus_import":"1","date_published":"2023-07-21T00:00:00Z","intvolume":" 190","author":[{"first_name":"Shoki","full_name":"Sugimoto, Shoki","last_name":"Sugimoto"},{"last_name":"Henheik","full_name":"Henheik, Sven Joscha","orcid":"0000-0003-1106-327X","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","first_name":"Sven Joscha"},{"id":"1949f904-edfb-11eb-afb5-e2dfddabb93b","first_name":"Volodymyr","full_name":"Riabov, Volodymyr","last_name":"Riabov"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","last_name":"Erdös"}],"volume":190,"quality_controlled":"1","issue":"7","_id":"13317","article_processing_charge":"Yes (in subscription journal)","citation":{"short":"S. Sugimoto, S.J. Henheik, V. Riabov, L. Erdös, Journal of Statistical Physics 190 (2023).","mla":"Sugimoto, Shoki, et al. “Eigenstate Thermalisation Hypothesis for Translation Invariant Spin Systems.” Journal of Statistical Physics, vol. 190, no. 7, 128, Springer Nature, 2023, doi:10.1007/s10955-023-03132-4.","ama":"Sugimoto S, Henheik SJ, Riabov V, Erdös L. Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. 2023;190(7). doi:10.1007/s10955-023-03132-4","ista":"Sugimoto S, Henheik SJ, Riabov V, Erdös L. 2023. Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. 190(7), 128.","apa":"Sugimoto, S., Henheik, S. J., Riabov, V., & Erdös, L. (2023). Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-023-03132-4","ieee":"S. Sugimoto, S. J. Henheik, V. Riabov, and L. Erdös, “Eigenstate thermalisation hypothesis for translation invariant spin systems,” Journal of Statistical Physics, vol. 190, no. 7. Springer Nature, 2023.","chicago":"Sugimoto, Shoki, Sven Joscha Henheik, Volodymyr Riabov, and László Erdös. “Eigenstate Thermalisation Hypothesis for Translation Invariant Spin Systems.” Journal of Statistical Physics. Springer Nature, 2023. https://doi.org/10.1007/s10955-023-03132-4."},"has_accepted_license":"1","publisher":"Springer Nature","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"date_updated":"2023-07-31T07:49:31Z","content_type":"application/pdf","success":1,"file_size":612755,"file_name":"2023_JourStatPhysics_Sugimoto.pdf","relation":"main_file","file_id":"13325","access_level":"open_access","date_created":"2023-07-31T07:49:31Z","checksum":"c2ef6b2aecfee1ad6d03fab620507c2c","creator":"dernst"}],"date_updated":"2023-12-13T11:38:44Z","oa_version":"Published Version","ddc":["510","530"],"isi":1,"status":"public","month":"07","title":"Eigenstate thermalisation hypothesis for translation invariant spin systems","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","call_identifier":"H2020"}],"acknowledgement":"LE, JH, and VR were supported by ERC Advanced Grant “RMTBeyond” No. 101020331. SS was supported by KAKENHI Grant Number JP22J14935 from the Japan Society for the Promotion of Science (JSPS) and Forefront Physics and Mathematics Program to Drive Transformation (FoPM), a World-leading Innovative Graduate Study (WINGS) Program, the University of Tokyo.\r\nOpen access funding provided by The University of Tokyo.","year":"2023","department":[{"_id":"LaEr"}],"arxiv":1,"oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-4715"],"eissn":["1572-9613"]},"article_number":"128","ec_funded":1,"article_type":"original","publication":"Journal of Statistical Physics","day":"21","doi":"10.1007/s10955-023-03132-4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"quality_controlled":"1","_id":"13318","author":[{"first_name":"Alexander","full_name":"Volberg, Alexander","last_name":"Volberg"},{"full_name":"Zhang, Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","first_name":"Haonan","last_name":"Zhang"}],"date_published":"2023-07-24T00:00:00Z","scopus_import":"1","date_created":"2023-07-30T22:01:03Z","external_id":{"arxiv":["2210.14468"],"isi":["001035665500001"]},"publication_status":"epub_ahead","abstract":[{"lang":"eng","text":"Bohnenblust–Hille inequalities for Boolean cubes have been proven with dimension-free constants that grow subexponentially in the degree (Defant et al. in Math Ann 374(1):653–680, 2019). Such inequalities have found great applications in learning low-degree Boolean functions (Eskenazis and Ivanisvili in Proceedings of the 54th annual ACM SIGACT symposium on theory of computing, pp 203–207, 2022). Motivated by learning quantum observables, a qubit analogue of Bohnenblust–Hille inequality for Boolean cubes was recently conjectured in Rouzé et al. (Quantum Talagrand, KKL and Friedgut’s theorems and the learnability of quantum Boolean functions, 2022. arXiv preprint arXiv:2209.07279). The conjecture was resolved in Huang et al. (Learning to predict arbitrary quantum processes, 2022. arXiv preprint arXiv:2210.14894). In this paper, we give a new proof of these Bohnenblust–Hille inequalities for qubit system with constants that are dimension-free and of exponential growth in the degree. As a consequence, we obtain a junta theorem for low-degree polynomials. Using similar ideas, we also study learning problems of low degree quantum observables and Bohr’s radius phenomenon on quantum Boolean cubes."}],"oa_version":"Published Version","date_updated":"2023-12-13T11:36:20Z","status":"public","month":"07","isi":1,"type":"journal_article","article_processing_charge":"No","publisher":"Springer Nature","citation":{"chicago":"Volberg, Alexander, and Haonan Zhang. “Noncommutative Bohnenblust–Hille Inequalities.” Mathematische Annalen. Springer Nature, 2023. https://doi.org/10.1007/s00208-023-02680-0.","apa":"Volberg, A., & Zhang, H. (2023). Noncommutative Bohnenblust–Hille inequalities. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-023-02680-0","ieee":"A. Volberg and H. Zhang, “Noncommutative Bohnenblust–Hille inequalities,” Mathematische Annalen. Springer Nature, 2023.","ista":"Volberg A, Zhang H. 2023. Noncommutative Bohnenblust–Hille inequalities. Mathematische Annalen.","ama":"Volberg A, Zhang H. Noncommutative Bohnenblust–Hille inequalities. Mathematische Annalen. 2023. doi:10.1007/s00208-023-02680-0","mla":"Volberg, Alexander, and Haonan Zhang. “Noncommutative Bohnenblust–Hille Inequalities.” Mathematische Annalen, Springer Nature, 2023, doi:10.1007/s00208-023-02680-0.","short":"A. Volberg, H. Zhang, Mathematische Annalen (2023)."},"acknowledgement":"The research of A.V. is supported by NSF DMS-1900286, DMS-2154402 and by Hausdorff Center for Mathematics. H.Z. is supported by the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. This work is partially supported by NSF DMS-1929284 while both authors were in residence at the Institute for Computational and Experimental Research in Mathematics in Providence, RI, during the Harmonic Analysis and Convexity program.","project":[{"grant_number":"M03337","name":"Curvature-dimension in noncommutative analysis","_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6"}],"arxiv":1,"department":[{"_id":"JaMa"}],"year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00208-023-02680-0"}],"title":"Noncommutative Bohnenblust–Hille inequalities","doi":"10.1007/s00208-023-02680-0","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"24","publication":"Mathematische Annalen","article_type":"original","oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0025-5831"],"eissn":["1432-1807"]}},{"doi":"10.1007/s00220-023-04795-6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","publication":"Communications in Mathematical Physics","article_type":"original","oa":1,"publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"language":[{"iso":"eng"}],"acknowledgement":"The authors are grateful to Martijn Caspers for helpful comments on a preliminary version of this manuscript. M. V. was supported by the NWO Vidi grant VI.Vidi.192.018 ‘Non-commutative harmonic analysis and rigidity of operator algebras’. M. W. was funded by the Austrian Science Fund (FWF) under the Esprit Programme [ESP 156]. For the purpose of Open Access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. Open access funding provided by Austrian Science Fund (FWF).","project":[{"grant_number":"ESP156_N","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833","name":"Gradient flow techniques for quantum Markov semigroups"}],"department":[{"_id":"JaMa"}],"arxiv":1,"year":"2023","title":"Derivations and KMS-symmetric quantum Markov semigroups","oa_version":"Published Version","date_updated":"2024-01-30T12:16:32Z","month":"10","status":"public","ddc":["510"],"isi":1,"file":[{"relation":"main_file","file_name":"2023_CommMathPhysics_Vernooij.pdf","content_type":"application/pdf","date_updated":"2024-01-30T12:15:11Z","file_size":481209,"success":1,"creator":"dernst","checksum":"cca204e81891270216a0c84eb8bcd398","access_level":"open_access","date_created":"2024-01-30T12:15:11Z","file_id":"14905"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature","has_accepted_license":"1","citation":{"short":"M. Vernooij, M. Wirth, Communications in Mathematical Physics 403 (2023) 381–416.","mla":"Vernooij, Matthijs, and Melchior Wirth. “Derivations and KMS-Symmetric Quantum Markov Semigroups.” Communications in Mathematical Physics, vol. 403, Springer Nature, 2023, pp. 381–416, doi:10.1007/s00220-023-04795-6.","ama":"Vernooij M, Wirth M. Derivations and KMS-symmetric quantum Markov semigroups. Communications in Mathematical Physics. 2023;403:381-416. doi:10.1007/s00220-023-04795-6","ista":"Vernooij M, Wirth M. 2023. Derivations and KMS-symmetric quantum Markov semigroups. Communications in Mathematical Physics. 403, 381–416.","ieee":"M. Vernooij and M. Wirth, “Derivations and KMS-symmetric quantum Markov semigroups,” Communications in Mathematical Physics, vol. 403. Springer Nature, pp. 381–416, 2023.","apa":"Vernooij, M., & Wirth, M. (2023). Derivations and KMS-symmetric quantum Markov semigroups. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-023-04795-6","chicago":"Vernooij, Matthijs, and Melchior Wirth. “Derivations and KMS-Symmetric Quantum Markov Semigroups.” Communications in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s00220-023-04795-6."},"quality_controlled":"1","_id":"13319","page":"381-416","volume":403,"author":[{"first_name":"Matthijs","full_name":"Vernooij, Matthijs","last_name":"Vernooij"},{"last_name":"Wirth","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","full_name":"Wirth, Melchior","orcid":"0000-0002-0519-4241","first_name":"Melchior"}],"intvolume":" 403","date_published":"2023-10-01T00:00:00Z","scopus_import":"1","date_created":"2023-07-30T22:01:03Z","publication_status":"published","external_id":{"arxiv":["2303.15949"],"isi":["001033655400002"]},"file_date_updated":"2024-01-30T12:15:11Z","abstract":[{"text":"We prove that the generator of the L2 implementation of a KMS-symmetric quantum Markov semigroup can be expressed as the square of a derivation with values in a Hilbert bimodule, extending earlier results by Cipriani and Sauvageot for tracially symmetric semigroups and the second-named author for GNS-symmetric semigroups. This result hinges on the introduction of a new completely positive map on the algebra of bounded operators on the GNS Hilbert space. This transformation maps symmetric Markov operators to symmetric Markov operators and is essential to obtain the required inner product on the Hilbert bimodule.","lang":"eng"}]},{"oa_version":"Preprint","date_updated":"2024-09-10T13:03:19Z","status":"public","month":"05","isi":1,"type":"conference","article_processing_charge":"No","publisher":"Institute of Electrical and Electronics Engineers","citation":{"chicago":"Xu, Yizhou, Tian Qi Hou, Shan Suo Liang, and Marco Mondelli. “Approximate Message Passing for Multi-Layer Estimation in Rotationally Invariant Models.” In 2023 IEEE Information Theory Workshop, 294–98. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/ITW55543.2023.10160238.","apa":"Xu, Y., Hou, T. Q., Liang, S. S., & Mondelli, M. (2023). Approximate message passing for multi-layer estimation in rotationally invariant models. In 2023 IEEE Information Theory Workshop (pp. 294–298). Saint-Malo, France: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/ITW55543.2023.10160238","ieee":"Y. Xu, T. Q. Hou, S. S. Liang, and M. Mondelli, “Approximate message passing for multi-layer estimation in rotationally invariant models,” in 2023 IEEE Information Theory Workshop, Saint-Malo, France, 2023, pp. 294–298.","ama":"Xu Y, Hou TQ, Liang SS, Mondelli M. Approximate message passing for multi-layer estimation in rotationally invariant models. In: 2023 IEEE Information Theory Workshop. Institute of Electrical and Electronics Engineers; 2023:294-298. doi:10.1109/ITW55543.2023.10160238","ista":"Xu Y, Hou TQ, Liang SS, Mondelli M. 2023. Approximate message passing for multi-layer estimation in rotationally invariant models. 2023 IEEE Information Theory Workshop. ITW: Information Theory Workshop, 294–298.","mla":"Xu, Yizhou, et al. “Approximate Message Passing for Multi-Layer Estimation in Rotationally Invariant Models.” 2023 IEEE Information Theory Workshop, Institute of Electrical and Electronics Engineers, 2023, pp. 294–98, doi:10.1109/ITW55543.2023.10160238.","short":"Y. Xu, T.Q. Hou, S.S. Liang, M. Mondelli, in:, 2023 IEEE Information Theory Workshop, Institute of Electrical and Electronics Engineers, 2023, pp. 294–298."},"quality_controlled":"1","_id":"13321","page":"294-298","author":[{"last_name":"Xu","full_name":"Xu, Yizhou","first_name":"Yizhou"},{"last_name":"Hou","first_name":"Tian Qi","full_name":"Hou, Tian Qi"},{"last_name":"Liang","full_name":"Liang, Shan Suo","first_name":"Shan Suo"},{"orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","full_name":"Mondelli, Marco","last_name":"Mondelli"}],"conference":{"location":"Saint-Malo, France","end_date":"2023-04-28","name":"ITW: Information Theory Workshop","start_date":"2023-04-23"},"date_published":"2023-05-01T00:00:00Z","scopus_import":"1","date_created":"2023-07-30T22:01:04Z","external_id":{"isi":["001031733100053"],"arxiv":["2212.01572"]},"publication_status":"published","abstract":[{"text":"We consider the problem of reconstructing the signal and the hidden variables from observations coming from a multi-layer network with rotationally invariant weight matrices. The multi-layer structure models inference from deep generative priors, and the rotational invariance imposed on the weights generalizes the i.i.d. Gaussian assumption by allowing for a complex correlation structure, which is typical in applications. In this work, we present a new class of approximate message passing (AMP) algorithms and give a state evolution recursion which precisely characterizes their performance in the large system limit. In contrast with the existing multi-layer VAMP (ML-VAMP) approach, our proposed AMP – dubbed multilayer rotationally invariant generalized AMP (ML-RI-GAMP) – provides a natural generalization beyond Gaussian designs, in the sense that it recovers the existing Gaussian AMP as a special case. Furthermore, ML-RI-GAMP exhibits a significantly lower complexity than ML-VAMP, as the computationally intensive singular value decomposition is replaced by an estimation of the moments of the design matrices. Finally, our numerical results show that this complexity gain comes at little to no cost in the performance of the algorithm.","lang":"eng"}],"doi":"10.1109/ITW55543.2023.10160238","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","publication":"2023 IEEE Information Theory Workshop","oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2475-4218"],"isbn":["9798350301496"]},"acknowledgement":"Marco Mondelli was partially supported by the 2019 Lopez-Loreta prize.","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"arxiv":1,"department":[{"_id":"MaMo"}],"year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.01572"}],"title":"Approximate message passing for multi-layer estimation in rotationally invariant models"},{"date_created":"2023-07-31T10:20:55Z","publication_status":"published","abstract":[{"lang":"eng","text":"The extension of extremal combinatorics to the setting of exterior algebra is a work\r\nin progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms.\r\n"}],"file_date_updated":"2023-08-03T15:28:55Z","date_published":"2023-07-31T00:00:00Z","author":[{"last_name":"Köse","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb","full_name":"Köse, Seyda","first_name":"Seyda"}],"page":"26","_id":"13331","article_processing_charge":"No","citation":{"ista":"Köse S. 2023. Exterior algebra and combinatorics. Institute of Science and Technology Austria.","ama":"Köse S. Exterior algebra and combinatorics. 2023. doi:10.15479/at:ista:13331","mla":"Köse, Seyda. Exterior Algebra and Combinatorics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13331.","short":"S. Köse, Exterior Algebra and Combinatorics, Institute of Science and Technology Austria, 2023.","chicago":"Köse, Seyda. “Exterior Algebra and Combinatorics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13331.","ieee":"S. Köse, “Exterior algebra and combinatorics,” Institute of Science and Technology Austria, 2023.","apa":"Köse, S. (2023). Exterior algebra and combinatorics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13331"},"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","type":"dissertation","related_material":{"record":[{"status":"public","id":"12680","relation":"part_of_dissertation"}]},"file":[{"file_id":"13333","access_level":"closed","date_created":"2023-07-31T10:16:32Z","creator":"skoese","checksum":"96ee518d796d02af71395622c45de03c","date_updated":"2023-07-31T10:16:32Z","content_type":"application/x-zip-compressed","file_size":28684,"file_name":"Exterior Algebra and Combinatorics.zip","relation":"source_file"},{"file_id":"13480","access_level":"open_access","date_created":"2023-08-03T15:28:55Z","creator":"skoese","checksum":"f610f4713f88bc477de576aaa46b114e","content_type":"application/pdf","date_updated":"2023-08-03T15:28:55Z","success":1,"file_size":4953418,"file_name":"thesis-pdfa.pdf","relation":"main_file"}],"date_updated":"2023-10-04T11:54:56Z","oa_version":"Published Version","ddc":["510","516"],"month":"07","status":"public","alternative_title":["ISTA Master's Thesis"],"title":"Exterior algebra and combinatorics","year":"2023","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2791-4585"]},"degree_awarded":"MS","day":"31","supervisor":[{"full_name":"Wagner, Uli","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"doi":"10.15479/at:ista:13331","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"date_created":"2023-07-31T11:30:46Z","title":"kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8059564"}],"author":[{"last_name":"Kleshnina","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","full_name":"Kleshnina, Maria","first_name":"Maria"}],"date_published":"2023-06-20T00:00:00Z","department":[{"_id":"KrCh"}],"year":"2023","_id":"13336","article_processing_charge":"No","oa":1,"publisher":"Zenodo","citation":{"short":"M. Kleshnina, (2023).","mla":"Kleshnina, Maria. Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games. Zenodo, 2023, doi:10.5281/ZENODO.8059564.","ama":"Kleshnina M. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. 2023. doi:10.5281/ZENODO.8059564","ista":"Kleshnina M. 2023. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games, Zenodo, 10.5281/ZENODO.8059564.","ieee":"M. Kleshnina, “kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games.” Zenodo, 2023.","apa":"Kleshnina, M. (2023). kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. Zenodo. https://doi.org/10.5281/ZENODO.8059564","chicago":"Kleshnina, Maria. “Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8059564."},"type":"research_data_reference","day":"20","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"13258"}]},"oa_version":"Published Version","doi":"10.5281/ZENODO.8059564","date_updated":"2025-07-14T09:09:53Z","status":"public","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"]},{"scopus_import":"1","date_created":"2023-08-01T08:26:15Z","publication_status":"published","abstract":[{"lang":"eng","text":"Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E-to-Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E-azobenzenes to the Z state. In this way, the host–photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation."}],"quality_controlled":"1","issue":"6664","_id":"13340","intvolume":" 381","date_published":"2023-09-22T00:00:00Z","page":"1357-1363","volume":381,"author":[{"last_name":"Gemen","full_name":"Gemen, Julius","first_name":"Julius"},{"last_name":"Church","full_name":"Church, Jonathan R.","first_name":"Jonathan R."},{"first_name":"Tero-Petri","full_name":"Ruoko, Tero-Petri","last_name":"Ruoko"},{"full_name":"Durandin, Nikita","first_name":"Nikita","last_name":"Durandin"},{"full_name":"Białek, Michał J.","first_name":"Michał J.","last_name":"Białek"},{"full_name":"Weissenfels, Maren","first_name":"Maren","last_name":"Weissenfels"},{"last_name":"Feller","first_name":"Moran","full_name":"Feller, Moran"},{"last_name":"Kazes","first_name":"Miri","full_name":"Kazes, Miri"},{"last_name":"Borin","first_name":"Veniamin A.","full_name":"Borin, Veniamin A."},{"full_name":"Odaybat, Magdalena","first_name":"Magdalena","last_name":"Odaybat"},{"last_name":"Kalepu","first_name":"Rishir","full_name":"Kalepu, Rishir"},{"last_name":"Diskin-Posner","first_name":"Yael","full_name":"Diskin-Posner, Yael"},{"first_name":"Dan","full_name":"Oron, Dan","last_name":"Oron"},{"full_name":"Fuchter, Matthew J.","first_name":"Matthew J.","last_name":"Fuchter"},{"last_name":"Priimagi","first_name":"Arri","full_name":"Priimagi, Arri"},{"full_name":"Schapiro, Igor","first_name":"Igor","last_name":"Schapiro"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","full_name":"Klajn, Rafal","last_name":"Klajn"}],"type":"journal_article","article_processing_charge":"No","citation":{"chicago":"Gemen, Julius, Jonathan R. Church, Tero-Petri Ruoko, Nikita Durandin, Michał J. Białek, Maren Weissenfels, Moran Feller, et al. “Disequilibrating Azoarenes by Visible-Light Sensitization under Confinement.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adh9059.","ieee":"J. Gemen et al., “Disequilibrating azoarenes by visible-light sensitization under confinement,” Science, vol. 381, no. 6664. American Association for the Advancement of Science, pp. 1357–1363, 2023.","apa":"Gemen, J., Church, J. R., Ruoko, T.-P., Durandin, N., Białek, M. J., Weissenfels, M., … Klajn, R. (2023). Disequilibrating azoarenes by visible-light sensitization under confinement. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adh9059","ista":"Gemen J, Church JR, Ruoko T-P, Durandin N, Białek MJ, Weissenfels M, Feller M, Kazes M, Borin VA, Odaybat M, Kalepu R, Diskin-Posner Y, Oron D, Fuchter MJ, Priimagi A, Schapiro I, Klajn R. 2023. Disequilibrating azoarenes by visible-light sensitization under confinement. Science. 381(6664), 1357–1363.","ama":"Gemen J, Church JR, Ruoko T-P, et al. Disequilibrating azoarenes by visible-light sensitization under confinement. Science. 2023;381(6664):1357-1363. doi:10.1126/science.adh9059","mla":"Gemen, Julius, et al. “Disequilibrating Azoarenes by Visible-Light Sensitization under Confinement.” Science, vol. 381, no. 6664, American Association for the Advancement of Science, 2023, pp. 1357–63, doi:10.1126/science.adh9059.","short":"J. Gemen, J.R. Church, T.-P. Ruoko, N. Durandin, M.J. Białek, M. Weissenfels, M. Feller, M. Kazes, V.A. Borin, M. Odaybat, R. Kalepu, Y. Diskin-Posner, D. Oron, M.J. Fuchter, A. Priimagi, I. Schapiro, R. Klajn, Science 381 (2023) 1357–1363."},"publisher":"American Association for the Advancement of Science","date_updated":"2023-10-03T08:11:26Z","oa_version":"Preprint","status":"public","month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv-2023-gq2h0"}],"title":"Disequilibrating azoarenes by visible-light sensitization under confinement","acknowledgement":"We acknowledge funding from the European Union’s Horizon 2020 Research and Innovation Program [European Research Council grants 820008 (Ra.K.) and 101045223 (A.P.) and Marie Skłodowska-Curie grants 812868 (J.G.) and 101022777 (T.-P.R.)], the Academy of Finland [Center of Excellence Programme LIBER grant 346107 (A.P.), Flagship Programme PREIN grant 320165 (A.P.), and Postdoctoral Researcher grant 340103 (T.-P.R.)], Zuckerman STEM Leadership Program Fellowship (J.R.C.), President’s PhD Scholarship (M.O.), and the EPSRC [Established Career Fellowship grant EP/R00188X/1 (M.J.F.)].","year":"2023","department":[{"_id":"RaKl"}],"article_type":"original","oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"]},"doi":"10.1126/science.adh9059","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Science","day":"22"},{"publication_status":"published","external_id":{"isi":["000966611000003"],"arxiv":["2006.02356"],"oaworkID":["w3033938593"]},"date_created":"2020-10-19T14:28:50Z","abstract":[{"text":"It is known that the Brauer--Manin obstruction to the Hasse principle is vacuous for smooth Fano hypersurfaces of dimension at least 3 over any number field. Moreover, for such varieties it follows from a general conjecture of Colliot-Thélène that the Brauer--Manin obstruction to the Hasse principle should be the only one, so that the Hasse principle is expected to hold. Working over the field of rational numbers and ordering Fano hypersurfaces of fixed degree and dimension by height, we prove that almost every such hypersurface satisfies the Hasse principle provided that the dimension is at least 3. This proves a conjecture of Poonen and Voloch in every case except for cubic surfaces.","lang":"eng"}],"page":"1115-1203","volume":197,"author":[{"last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","first_name":"Timothy D"},{"full_name":"Boudec, Pierre Le","first_name":"Pierre Le","last_name":"Boudec"},{"last_name":"Sawin","first_name":"Will","full_name":"Sawin, Will"}],"date_published":"2023-05-01T00:00:00Z","intvolume":" 197","quality_controlled":"1","issue":"3","_id":"8682","article_processing_charge":"No","publisher":"Princeton University","citation":{"short":"T.D. Browning, P.L. Boudec, W. Sawin, Annals of Mathematics 197 (2023) 1115–1203.","mla":"Browning, Timothy D., et al. “The Hasse Principle for Random Fano Hypersurfaces.” Annals of Mathematics, vol. 197, no. 3, Princeton University, 2023, pp. 1115–203, doi:10.4007/annals.2023.197.3.3.","ama":"Browning TD, Boudec PL, Sawin W. The Hasse principle for random Fano hypersurfaces. Annals of Mathematics. 2023;197(3):1115-1203. doi:10.4007/annals.2023.197.3.3","ista":"Browning TD, Boudec PL, Sawin W. 2023. The Hasse principle for random Fano hypersurfaces. Annals of Mathematics. 197(3), 1115–1203.","apa":"Browning, T. D., Boudec, P. L., & Sawin, W. (2023). The Hasse principle for random Fano hypersurfaces. Annals of Mathematics. Princeton University. https://doi.org/10.4007/annals.2023.197.3.3","ieee":"T. D. Browning, P. L. Boudec, and W. Sawin, “The Hasse principle for random Fano hypersurfaces,” Annals of Mathematics, vol. 197, no. 3. Princeton University, pp. 1115–1203, 2023.","chicago":"Browning, Timothy D, Pierre Le Boudec, and Will Sawin. “The Hasse Principle for Random Fano Hypersurfaces.” Annals of Mathematics. Princeton University, 2023. https://doi.org/10.4007/annals.2023.197.3.3."},"type":"journal_article","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/when-is-necessary-sufficient/","relation":"press_release"}]},"oa_version":"Preprint","date_updated":"2025-08-11T11:59:49Z","month":"05","status":"public","isi":1,"title":"The Hasse principle for random Fano hypersurfaces","main_file_link":[{"url":"https://arxiv.org/abs/2006.02356","open_access":"1"}],"arxiv":1,"department":[{"_id":"TiBr"}],"year":"2023","oa":1,"publication_identifier":{"issn":["0003-486X"]},"language":[{"iso":"eng"}],"article_type":"original","day":"01","publication":"Annals of Mathematics","doi":"10.4007/annals.2023.197.3.3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"year":"2023","department":[{"_id":"TiBr"}],"arxiv":1,"acknowledgement":"This work was supported by the German Academic Exchange Service. Parts of this article were prepared at the Institut de Mathémathiques de Jussieu—Paris Rive Gauche. I wish to thank Antoine Chambert-Loir for his remarks and the institute for its hospitality, as well as the anonymous referee for several useful remarks and suggestions for improvements.","title":"Integral points of bounded height on a log Fano threefold","main_file_link":[{"url":"https://arxiv.org/abs/1901.08503","open_access":"1"}],"publication":"International Mathematics Research Notices","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1093/imrn/rnac048","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"oa":1,"article_type":"original","intvolume":" 2023","date_published":"2023-04-01T00:00:00Z","page":"6780-6808","author":[{"id":"560601DA-8D36-11E9-A136-7AC1E5697425","first_name":"Florian Alexander","full_name":"Wilsch, Florian Alexander","orcid":"0000-0001-7302-8256","last_name":"Wilsch"}],"volume":2023,"_id":"9034","quality_controlled":"1","issue":"8","abstract":[{"text":"We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors.","lang":"eng"}],"publication_status":"published","date_created":"2021-01-22T09:31:09Z","external_id":{"arxiv":["1901.08503"],"isi":["000773116000001"]},"isi":1,"month":"04","status":"public","date_updated":"2023-08-01T12:23:55Z","oa_version":"Preprint","citation":{"ama":"Wilsch FA. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023;2023(8):6780-6808. doi:10.1093/imrn/rnac048","ista":"Wilsch FA. 2023. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023(8), 6780–6808.","short":"F.A. Wilsch, International Mathematics Research Notices 2023 (2023) 6780–6808.","mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices, vol. 2023, no. 8, Oxford Academic, 2023, pp. 6780–808, doi:10.1093/imrn/rnac048.","chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices. Oxford Academic, 2023. https://doi.org/10.1093/imrn/rnac048.","ieee":"F. A. Wilsch, “Integral points of bounded height on a log Fano threefold,” International Mathematics Research Notices, vol. 2023, no. 8. Oxford Academic, pp. 6780–6808, 2023.","apa":"Wilsch, F. A. (2023). Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. Oxford Academic. https://doi.org/10.1093/imrn/rnac048"},"publisher":"Oxford Academic","article_processing_charge":"No","type":"journal_article"},{"ddc":["570"],"isi":1,"status":"public","month":"04","date_updated":"2024-01-16T09:29:35Z","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"success":1,"file_size":7931643,"content_type":"application/pdf","date_updated":"2024-01-16T09:26:52Z","file_name":"2023_Cells_Cheung.pdf","relation":"main_file","file_id":"14808","date_created":"2024-01-16T09:26:52Z","access_level":"open_access","checksum":"6798cd75d8857976fbc58a43fd173d68","creator":"dernst"}],"type":"journal_article","citation":{"ieee":"G. T. Cheung et al., “Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses,” Cells, vol. 12, no. 8. MDPI, 2023.","apa":"Cheung, G. T., Chever, O., Rollenhagen, A., Quenech’du, N., Ezan, P., Lübke, J. H. R., & Rouach, N. (2023). Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. MDPI. https://doi.org/10.3390/cells12081133","chicago":"Cheung, Giselle T, Oana Chever, Astrid Rollenhagen, Nicole Quenech’du, Pascal Ezan, Joachim H. R. Lübke, and Nathalie Rouach. “Astroglial Connexin 43 Regulates Synaptic Vesicle Release at Hippocampal Synapses.” Cells. MDPI, 2023. https://doi.org/10.3390/cells12081133.","short":"G.T. Cheung, O. Chever, A. Rollenhagen, N. Quenech’du, P. Ezan, J.H.R. Lübke, N. Rouach, Cells 12 (2023).","mla":"Cheung, Giselle T., et al. “Astroglial Connexin 43 Regulates Synaptic Vesicle Release at Hippocampal Synapses.” Cells, vol. 12, no. 8, 1133, MDPI, 2023, doi:10.3390/cells12081133.","ista":"Cheung GT, Chever O, Rollenhagen A, Quenech’du N, Ezan P, Lübke JHR, Rouach N. 2023. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. 12(8), 1133.","ama":"Cheung GT, Chever O, Rollenhagen A, et al. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. 2023;12(8). doi:10.3390/cells12081133"},"publisher":"MDPI","has_accepted_license":"1","article_processing_charge":"Yes","_id":"14783","issue":"8","quality_controlled":"1","intvolume":" 12","date_published":"2023-04-11T00:00:00Z","volume":12,"author":[{"last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","first_name":"Giselle T","orcid":"0000-0001-8457-2572"},{"last_name":"Chever","first_name":"Oana","full_name":"Chever, Oana"},{"full_name":"Rollenhagen, Astrid","first_name":"Astrid","last_name":"Rollenhagen"},{"first_name":"Nicole","full_name":"Quenech’du, Nicole","last_name":"Quenech’du"},{"last_name":"Ezan","first_name":"Pascal","full_name":"Ezan, Pascal"},{"first_name":"Joachim H. R.","full_name":"Lübke, Joachim H. R.","last_name":"Lübke"},{"full_name":"Rouach, Nathalie","first_name":"Nathalie","last_name":"Rouach"}],"abstract":[{"lang":"eng","text":"Connexin 43, an astroglial gap junction protein, is enriched in perisynaptic astroglial processes and plays major roles in synaptic transmission. We have previously found that astroglial Cx43 controls synaptic glutamate levels and allows for activity-dependent glutamine release to sustain physiological synaptic transmissions and cognitiogns. However, whether Cx43 is important for the release of synaptic vesicles, which is a critical component of synaptic efficacy, remains unanswered. Here, using transgenic mice with a glial conditional knockout of Cx43 (Cx43−/−), we investigate whether and how astrocytes regulate the release of synaptic vesicles from hippocampal synapses. We report that CA1 pyramidal neurons and their synapses develop normally in the absence of astroglial Cx43. However, a significant impairment in synaptic vesicle distribution and release dynamics were observed. In particular, the FM1-43 assays performed using two-photon live imaging and combined with multi-electrode array stimulation in acute hippocampal slices, revealed a slower rate of synaptic vesicle release in Cx43−/− mice. Furthermore, paired-pulse recordings showed that synaptic vesicle release probability was also reduced and is dependent on glutamine supply via Cx43 hemichannel (HC). Taken together, we have uncovered a role for Cx43 in regulating presynaptic functions by controlling the rate and probability of synaptic vesicle release. Our findings further highlight the significance of astroglial Cx43 in synaptic transmission and efficacy."}],"file_date_updated":"2024-01-16T09:26:52Z","external_id":{"pmid":["37190042"],"isi":["000977445700001"]},"publication_status":"published","date_created":"2024-01-10T09:46:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.3390/cells12081133","publication":"Cells","day":"11","article_type":"original","article_number":"1133","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2073-4409"]},"keyword":["General Medicine"],"oa":1,"year":"2023","department":[{"_id":"SiHi"}],"acknowledgement":"This research was funded by grants from the European Research Council (Consolidator grant #683154) and European Union’s Horizon 2020 research and innovation program (Marie Sklodowska-Curie Innovative Training Networks, grant #722053, EU-GliaPhD) to N.R., as well as from FP7-PEOPLE Marie Curie Intra-European Fellowship for career development (grant #622289) to G.C. We thank Elena Dossi, Grégory Ghézali, and Jérémie Teillon for support with setting up the MEA system for the two-photon microscope. We would also like to thank Tayfun Palaz for their technical assistance with the EM preparations.","pmid":1,"title":"Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses"},{"status":"public","month":"08","isi":1,"ddc":["570"],"oa_version":"Published Version","date_updated":"2024-01-16T09:38:58Z","file":[{"relation":"main_file","file_size":1596639,"success":1,"date_updated":"2024-01-16T09:35:28Z","content_type":"application/pdf","file_name":"2023_ScienceAdvances_GallardoDodd.pdf","date_created":"2024-01-16T09:35:28Z","access_level":"open_access","checksum":"b9072e20e2d5d9d34d2c53319bafee41","creator":"dernst","file_id":"14809"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","publisher":"American Association for the Advancement of Science","has_accepted_license":"1","citation":{"ieee":"C. J. Gallardo-Dodd et al., “Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells,” Science Advances, vol. 9, no. 34. American Association for the Advancement of Science, 2023.","apa":"Gallardo-Dodd, C. J., Oertlin, C., Record, J., Galvani, R. G., Sommerauer, C., Kuznetsov, N. V., … Westerberg, L. S. (2023). Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adg1610","chicago":"Gallardo-Dodd, Carlos J., Christian Oertlin, Julien Record, Rômulo G. Galvani, Christian Sommerauer, Nikolai V. Kuznetsov, Evangelos Doukoumopoulos, et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.adg1610.","short":"C.J. Gallardo-Dodd, C. Oertlin, J. Record, R.G. Galvani, C. Sommerauer, N.V. Kuznetsov, E. Doukoumopoulos, L. Ali, M.M.S. Oliveira, C. Seitz, M. Percipalle, T. Nikić, A.A. Sadova, S.M. Shulgina, V.A. Shmarov, O.V. Kutko, D.D. Vlasova, K.D. Orlova, M.P. Rykova, J. Andersson, P. Percipalle, C. Kutter, S.A. Ponomarev, L.S. Westerberg, Science Advances 9 (2023).","mla":"Gallardo-Dodd, Carlos J., et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” Science Advances, vol. 9, no. 34, adg1610, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.adg1610.","ista":"Gallardo-Dodd CJ, Oertlin C, Record J, Galvani RG, Sommerauer C, Kuznetsov NV, Doukoumopoulos E, Ali L, Oliveira MMS, Seitz C, Percipalle M, Nikić T, Sadova AA, Shulgina SM, Shmarov VA, Kutko OV, Vlasova DD, Orlova KD, Rykova MP, Andersson J, Percipalle P, Kutter C, Ponomarev SA, Westerberg LS. 2023. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. 9(34), adg1610.","ama":"Gallardo-Dodd CJ, Oertlin C, Record J, et al. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. 2023;9(34). doi:10.1126/sciadv.adg1610"},"article_processing_charge":"Yes","_id":"14784","quality_controlled":"1","issue":"34","author":[{"last_name":"Gallardo-Dodd","full_name":"Gallardo-Dodd, Carlos J.","first_name":"Carlos J."},{"full_name":"Oertlin, Christian","first_name":"Christian","last_name":"Oertlin"},{"last_name":"Record","full_name":"Record, Julien","first_name":"Julien"},{"full_name":"Galvani, Rômulo G.","first_name":"Rômulo G.","last_name":"Galvani"},{"first_name":"Christian","full_name":"Sommerauer, Christian","last_name":"Sommerauer"},{"full_name":"Kuznetsov, Nikolai V.","first_name":"Nikolai V.","last_name":"Kuznetsov"},{"first_name":"Evangelos","full_name":"Doukoumopoulos, Evangelos","last_name":"Doukoumopoulos"},{"first_name":"Liaqat","full_name":"Ali, Liaqat","last_name":"Ali"},{"full_name":"Oliveira, Mariana M. S.","first_name":"Mariana M. S.","last_name":"Oliveira"},{"last_name":"Seitz","first_name":"Christina","full_name":"Seitz, Christina"},{"last_name":"Percipalle","first_name":"Mathias","full_name":"Percipalle, Mathias","id":"45adb726-eb97-11eb-a6c2-c7c3d3caabe9"},{"last_name":"Nikić","first_name":"Tijana","full_name":"Nikić, Tijana"},{"full_name":"Sadova, Anastasia A.","first_name":"Anastasia A.","last_name":"Sadova"},{"full_name":"Shulgina, Sofia M.","first_name":"Sofia M.","last_name":"Shulgina"},{"last_name":"Shmarov","first_name":"Vjacheslav A.","full_name":"Shmarov, Vjacheslav A."},{"last_name":"Kutko","first_name":"Olga V.","full_name":"Kutko, Olga V."},{"last_name":"Vlasova","full_name":"Vlasova, Daria D.","first_name":"Daria D."},{"last_name":"Orlova","first_name":"Kseniya D.","full_name":"Orlova, Kseniya D."},{"last_name":"Rykova","full_name":"Rykova, Marina P.","first_name":"Marina P."},{"first_name":"John","full_name":"Andersson, John","last_name":"Andersson"},{"last_name":"Percipalle","first_name":"Piergiorgio","full_name":"Percipalle, Piergiorgio"},{"last_name":"Kutter","first_name":"Claudia","full_name":"Kutter, Claudia"},{"first_name":"Sergey A.","full_name":"Ponomarev, Sergey A.","last_name":"Ponomarev"},{"first_name":"Lisa S.","full_name":"Westerberg, Lisa S.","last_name":"Westerberg"}],"volume":9,"date_published":"2023-08-25T00:00:00Z","intvolume":" 9","file_date_updated":"2024-01-16T09:35:28Z","abstract":[{"lang":"eng","text":"The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity."}],"external_id":{"pmid":["37624890"],"isi":["001054596800007"]},"publication_status":"published","date_created":"2024-01-10T09:48:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1126/sciadv.adg1610","day":"25","publication":"Science Advances","article_type":"original","article_number":"adg1610","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2375-2548"]},"keyword":["Multidisciplinary"],"oa":1,"department":[{"_id":"FlSc"}],"year":"2023","acknowledgement":"This work was supported by a postdoctoral fellowship from the Swedish Society for Medical Research to J.R., a CAPES-STINT joint grant to R.G.G. and L.S.W., a PhD fellowship from Karolinska Institutet (KID) to E.D., a PhD fellowship from Fundação para a Ciência e a Tecnologia and European Social Fund to M.M.S.O., the program of fundamental research (theme 65.1) of the Institute for Biomedical Problems of the Russian Academy of Sciences (IBMP RAS) to A.A.S., S.M.S., V.A.S., O.V.K., D.D.V., K.D.O., M.P.R., and S.A.P., the Tamkeen under the NYU Abu Dhabi Research Institute Award to the NYUAD Center for Genomics and Systems Biology (ADHPG-CGSB) to P.P., the Knut and Alice Wallenberg foundation to C.K., the Swedish National Space Agency to N.V.K. and L.S.W., Swedish Research Council, Gösta Fraenckel Foundation, and Karolinska Institutet to L.S.W.","pmid":1,"title":"Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells"},{"external_id":{"isi":["001080203100001"],"pmid":["37794696"]},"date_created":"2024-01-10T10:41:07Z","publication_status":"published","file_date_updated":"2024-01-16T09:42:10Z","abstract":[{"text":"Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this species is supported by horizontal transfer remains understudied. Here, we show that the small cryptic plasmid DNA is transferred in the population exclusively by natural transformation, where the transfer frequency of plasmid‐encoded genes is similar to that of chromosome‐encoded genes. Establishing a system to follow gene transfer, we compared the transfer frequency of genes encoded in cryptic plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations of two Synechocystis sp. PCC 6803 labtypes (termed Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake in the Sevilla labtype ranged among the lowest detected transfer rates in our experiments. Our study indicates that horizontal DNA transfer via natural transformation is frequent in the evolution of small cryptic plasmids that reside in naturally competent organisms. Furthermore, we suggest that the contribution of natural transformation to cryptic plasmid persistence in Synechocystis is limited.","lang":"eng"}],"date_published":"2023-12-01T00:00:00Z","intvolume":" 15","volume":15,"page":"656-668","author":[{"last_name":"Nies","full_name":"Nies, Fabian","first_name":"Fabian"},{"first_name":"Tanita","full_name":"Wein, Tanita","last_name":"Wein"},{"last_name":"Hanke","first_name":"Dustin M.","full_name":"Hanke, Dustin M."},{"id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","first_name":"Benjamin L","orcid":"0000-0002-3461-5391","full_name":"Springstein, Benjamin L","last_name":"Springstein"},{"last_name":"Alcorta","full_name":"Alcorta, Jaime","first_name":"Jaime"},{"full_name":"Taubenheim, Claudia","first_name":"Claudia","last_name":"Taubenheim"},{"last_name":"Dagan","full_name":"Dagan, Tal","first_name":"Tal"}],"quality_controlled":"1","issue":"6","_id":"14785","article_processing_charge":"Yes (in subscription journal)","citation":{"ama":"Nies F, Wein T, Hanke DM, et al. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. 2023;15(6):656-668. doi:10.1111/1758-2229.13203","ista":"Nies F, Wein T, Hanke DM, Springstein BL, Alcorta J, Taubenheim C, Dagan T. 2023. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. 15(6), 656–668.","mla":"Nies, Fabian, et al. “Role of Natural Transformation in the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” Environmental Microbiology Reports, vol. 15, no. 6, Wiley, 2023, pp. 656–68, doi:10.1111/1758-2229.13203.","short":"F. Nies, T. Wein, D.M. Hanke, B.L. Springstein, J. Alcorta, C. Taubenheim, T. Dagan, Environmental Microbiology Reports 15 (2023) 656–668.","chicago":"Nies, Fabian, Tanita Wein, Dustin M. Hanke, Benjamin L Springstein, Jaime Alcorta, Claudia Taubenheim, and Tal Dagan. “Role of Natural Transformation in the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” Environmental Microbiology Reports. Wiley, 2023. https://doi.org/10.1111/1758-2229.13203.","ieee":"F. Nies et al., “Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803,” Environmental Microbiology Reports, vol. 15, no. 6. Wiley, pp. 656–668, 2023.","apa":"Nies, F., Wein, T., Hanke, D. M., Springstein, B. L., Alcorta, J., Taubenheim, C., & Dagan, T. (2023). Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. Wiley. https://doi.org/10.1111/1758-2229.13203"},"has_accepted_license":"1","publisher":"Wiley","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_id":"14810","access_level":"open_access","date_created":"2024-01-16T09:42:10Z","creator":"dernst","checksum":"d09ebb68fee61f4e2e09ec286c9cf1d3","content_type":"application/pdf","date_updated":"2024-01-16T09:42:10Z","file_size":1518350,"success":1,"file_name":"2023_EnvirMicroBiolReports_Nies.pdf","relation":"main_file"}],"date_updated":"2024-01-16T09:46:12Z","oa_version":"Published Version","isi":1,"ddc":["570"],"month":"12","status":"public","title":"Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803","pmid":1,"acknowledgement":"We thank the lab of Francisco Javier Florencio Bel-lido, Sevilla, Spain for supplying theSynechocystislabtype Sevilla used in this work and the lab of MartinHagemann, Rostock, Germany for supplying the pIGAplasmidusedinthiswork.WethankNilsHülterforfruitful discussions. We thank Fenna Stücker forgraphical illustrations and Katrin Schumann, FennaStücker, and Lidusha Manivannan for technicalsupport.\r\nChilean National Agency for Research andDevelopment (ANID), Grant/Award Number:21191763; DeutscheForschungsgemeinschaft, Grant/AwardNumbers: 456882089, RTG2501; EuropeanResearch Council (ERC), Grant/AwardNumber: 101043835","year":"2023","department":[{"_id":"MaLo"}],"oa":1,"keyword":["Agricultural and Biological Sciences (miscellaneous)","Ecology","Evolution","Behavior and Systematics"],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1758-2229"]},"article_type":"original","publication":"Environmental Microbiology Reports","day":"01","doi":"10.1111/1758-2229.13203","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]