[{"scopus_import":"1","DOAJ_listed":"1","issue":"2","status":"public","page":"1060-1076","PlanS_conform":"1","isi":1,"date_updated":"2025-09-08T09:53:01Z","publication":"Monthly Notices of the Royal Astronomical Society","file_date_updated":"2024-10-07T09:14:03Z","date_published":"2024-10-01T00:00:00Z","OA_place":"publisher","year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["520"],"intvolume":"       534","has_accepted_license":"1","citation":{"mla":"Hatt, Emily J., et al. “Asteroseismic Signatures of Core Magnetism and Rotation in Hundreds of Low-Luminosity Red Giants.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 534, no. 2, Oxford University Press, 2024, pp. 1060–76, doi:<a href=\"https://doi.org/10.1093/mnras/stae2053\">10.1093/mnras/stae2053</a>.","short":"E.J. Hatt, J.M.J. Ong, M.B. Nielsen, W.J. Chaplin, G.R. Davies, S. Deheuvels, J. Ballot, G. Li, L.A. Bugnet, Monthly Notices of the Royal Astronomical Society 534 (2024) 1060–1076.","ieee":"E. J. Hatt <i>et al.</i>, “Asteroseismic signatures of core magnetism and rotation in hundreds of low-luminosity red giants,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 534, no. 2. Oxford University Press, pp. 1060–1076, 2024.","apa":"Hatt, E. J., Ong, J. M. J., Nielsen, M. B., Chaplin, W. J., Davies, G. R., Deheuvels, S., … Bugnet, L. A. (2024). Asteroseismic signatures of core magnetism and rotation in hundreds of low-luminosity red giants. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stae2053\">https://doi.org/10.1093/mnras/stae2053</a>","ama":"Hatt EJ, Ong JMJ, Nielsen MB, et al. Asteroseismic signatures of core magnetism and rotation in hundreds of low-luminosity red giants. <i>Monthly Notices of the Royal Astronomical Society</i>. 2024;534(2):1060-1076. doi:<a href=\"https://doi.org/10.1093/mnras/stae2053\">10.1093/mnras/stae2053</a>","ista":"Hatt EJ, Ong JMJ, Nielsen MB, Chaplin WJ, Davies GR, Deheuvels S, Ballot J, Li G, Bugnet LA. 2024. Asteroseismic signatures of core magnetism and rotation in hundreds of low-luminosity red giants. Monthly Notices of the Royal Astronomical Society. 534(2), 1060–1076.","chicago":"Hatt, Emily J., J. M.Joel Ong, Martin B. Nielsen, William J. Chaplin, Guy R. Davies, Sébastien Deheuvels, Jérôme Ballot, Gang Li, and Lisa Annabelle Bugnet. “Asteroseismic Signatures of Core Magnetism and Rotation in Hundreds of Low-Luminosity Red Giants.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/mnras/stae2053\">https://doi.org/10.1093/mnras/stae2053</a>."},"day":"01","type":"journal_article","quality_controlled":"1","_id":"18172","language":[{"iso":"eng"}],"abstract":[{"text":"Red Giant stars host solar-like oscillations which have mixed character, being sensitive to conditions both in the outer convection zone and deep within the interior. The properties of these modes are sensitive to both core rotation and magnetic fields. While asteroseismic studies of the former have been done on a large scale, studies of the latter are currently limited to tens of stars. We aim to produce the first large catalogue of both magnetic and rotational perturbations. We jointly constrain these parameters by devising an automated method for fitting the power spectra directly. We successfully apply the method to 302 low-luminosity red giants. We find a clear bimodality in core rotation rate. The primary peak is at δνrot = 0.32 μHz, and the secondary at δνrot = 0.47 μHz. Combining our results with literature values, we find that the percentage of stars rotating much more rapidly than the population average increases with evolutionary state. We measure magnetic splittings of 2σ significance in 23 stars. While the most extreme magnetic splitting values appear in stars with masses > 1.1M⊙, implying they formerly hosted a convective core, a small but statistically significant magnetic splitting is measured at lower masses. Asymmetry between the frequencies of a rotationally split multiplet has previously been used to diagnose the presence of a magnetic perturbation. We find that of the stars with a significant detection of magnetic perturbation, 43\\% do not show strong asymmetry. We find no strong evidence of correlation between the rotation and magnetic parameters.","lang":"eng"}],"external_id":{"arxiv":["2409.01157"],"isi":["001320536900011"]},"publisher":"Oxford University Press","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes","article_type":"original","department":[{"_id":"LiBu"}],"month":"10","volume":534,"author":[{"full_name":"Hatt, Emily J.","last_name":"Hatt","first_name":"Emily J."},{"full_name":"Ong, J. M.Joel","last_name":"Ong","first_name":"J. M.Joel"},{"full_name":"Nielsen, Martin B.","last_name":"Nielsen","first_name":"Martin B."},{"last_name":"Chaplin","full_name":"Chaplin, William J.","first_name":"William J."},{"full_name":"Davies, Guy R.","last_name":"Davies","first_name":"Guy R."},{"last_name":"Deheuvels","full_name":"Deheuvels, Sébastien","first_name":"Sébastien"},{"last_name":"Ballot","full_name":"Ballot, Jérôme","first_name":"Jérôme"},{"last_name":"Li","full_name":"Li, Gang","first_name":"Gang"},{"id":"d9edb345-f866-11ec-9b37-d119b5234501","first_name":"Lisa Annabelle","orcid":"0000-0003-0142-4000","last_name":"Bugnet","full_name":"Bugnet, Lisa Annabelle"}],"acknowledgement":"EJH, WJC, and GRD acknowledge the support of Science and Technology Facilities Council. MBN acknowledges support from the UK Space Agency. JMJO acknowledges support from NASA through the NASA Hubble Fellowship grant HST-HF2-51517.001, awarded by STScI (Space Telescope Science Institute), which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. The authors acknowledge use of the Blue-BEAR HPC service at the University of Birmingham. This paper includes data collected by the Kepler mission and obtained from the MAST data archive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission was provided by the NASA Science Mission Directorate. This work has made use of data from the European Space Agency (ESA) mission Gaia (https://www.cosmos.esa.int/web/gaia), processed by the Gaia Data Processing and Analysis Consortium (DPAC, https://www.cosmos.esa.int/web/gaia/dpac/consortium). Funding for the DPAC was provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement. This paper received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (CartographY GA. 804752). SD and JB acknowledge support from the Centre National d’Etudes Spatiales (CNES).","oa":1,"doi":"10.1093/mnras/stae2053","oa_version":"Published Version","OA_type":"gold","title":"Asteroseismic signatures of core magnetism and rotation in hundreds of low-luminosity red giants","date_created":"2024-10-06T22:01:11Z","arxiv":1,"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"file":[{"date_updated":"2024-10-07T09:14:03Z","file_id":"18182","creator":"dernst","relation":"main_file","checksum":"b79f3c6a5991516abbcc8d34fa4bfb5f","file_name":"2024_MonthlyNRoyalAstronSoc_Hatt.pdf","content_type":"application/pdf","success":1,"file_size":2813008,"date_created":"2024-10-07T09:14:03Z","access_level":"open_access"}],"publication_status":"published"},{"file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"file_size":15009000,"date_created":"2024-10-07T11:25:00Z","checksum":"f3874e64ef94e94b2376f00a1fee24c3","file_name":"2024_JourChemicalPhysics_Wassermair.pdf","creator":"dernst","file_id":"18185","date_updated":"2024-10-07T11:25:00Z","relation":"main_file"}],"publication_status":"published","oa_version":"Published Version","date_created":"2024-10-06T22:01:12Z","title":"Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system","arxiv":1,"publication_identifier":{"eissn":["1089-7690"]},"month":"09","department":[{"_id":"GradSch"}],"article_type":"original","volume":161,"author":[{"last_name":"Wassermair","full_name":"Wassermair, Michael","id":"23d132c4-4e98-11ef-b275-9e8d4cd8c917","first_name":"Michael"},{"last_name":"Kahl","full_name":"Kahl, Gerhard","first_name":"Gerhard"},{"first_name":"Roland","last_name":"Roth","full_name":"Roth, Roland"},{"first_name":"Andrew J.","full_name":"Archer, Andrew J.","last_name":"Archer"}],"doi":"10.1063/5.0226954","oa":1,"acknowledgement":"The computational results presented here were enabled via a generous share of CPU time, offered by the Vienna Scientific Cluster (VSC) under Project No. 71263. The authors thank Ms. Katrin Muck for her guidance related to the use of HPC. A.J.A. gratefully acknowledges support from the EPSRC under Grant No. EP/P015689/1.","pmid":1,"publisher":"AIP Publishing","article_processing_charge":"Yes (in subscription journal)","corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"28","citation":{"chicago":"Wassermair, Michael, Gerhard Kahl, Roland Roth, and Andrew J. Archer. “Fingerprints of Ordered Self-Assembled Structures in the Liquid Phase of a Hard-Core, Square-Shoulder System.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0226954\">https://doi.org/10.1063/5.0226954</a>.","ista":"Wassermair M, Kahl G, Roth R, Archer AJ. 2024. Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. The Journal of chemical physics. 161(12), 124503.","ama":"Wassermair M, Kahl G, Roth R, Archer AJ. Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. <i>The Journal of chemical physics</i>. 2024;161(12). doi:<a href=\"https://doi.org/10.1063/5.0226954\">10.1063/5.0226954</a>","apa":"Wassermair, M., Kahl, G., Roth, R., &#38; Archer, A. J. (2024). Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0226954\">https://doi.org/10.1063/5.0226954</a>","ieee":"M. Wassermair, G. Kahl, R. Roth, and A. J. Archer, “Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system,” <i>The Journal of chemical physics</i>, vol. 161, no. 12. AIP Publishing, 2024.","short":"M. Wassermair, G. Kahl, R. Roth, A.J. Archer, The Journal of Chemical Physics 161 (2024).","mla":"Wassermair, Michael, et al. “Fingerprints of Ordered Self-Assembled Structures in the Liquid Phase of a Hard-Core, Square-Shoulder System.” <i>The Journal of Chemical Physics</i>, vol. 161, no. 12, 124503, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0226954\">10.1063/5.0226954</a>."},"has_accepted_license":"1","quality_controlled":"1","type":"journal_article","external_id":{"arxiv":["2409.06447"],"pmid":["39344889"],"isi":["001325268300004"]},"_id":"18174","abstract":[{"lang":"eng","text":"We investigate the phase ordering (pattern formation) of systems of two-dimensional core–shell particles using Monte Carlo (MC) computer simulations and classical density functional theory (DFT). The particles interact via a pair potential having a hard core and a repulsive square shoulder. Our simulations show that on cooling, the liquid state structure becomes increasingly characterized by long wavelength density modulations and on further cooling forms a variety of other phases, including clustered, striped, and other patterned phases. In DFT, the hard core part of the potential is treated using either fundamental measure theory or a simple local density approximation, whereas the soft shoulder is treated using the random phase approximation. The different DFTs are benchmarked using large-scale grand-canonical-MC and Gibbs-ensemble-MC simulations, demonstrating their predictive capabilities and shortcomings. We find that having the liquid state static structure factor S(k) for wavenumber k is sufficient to identify the Fourier modes governing both the liquid and solid phases. This allows us to identify from easier-to-obtain liquid state data the wavenumbers relevant to the periodic phases and to predict roughly where in the phase diagram these patterned phases arise."}],"language":[{"iso":"eng"}],"date_published":"2024-09-28T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["530"],"year":"2024","article_number":"124503 ","intvolume":"       161","isi":1,"publication":"The Journal of chemical physics","date_updated":"2025-09-08T09:55:52Z","file_date_updated":"2024-10-07T11:25:00Z","scopus_import":"1","issue":"12","status":"public"},{"year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"intvolume":"       313","article_number":"27","date_published":"2024-09-01T00:00:00Z","type":"conference","quality_controlled":"1","abstract":[{"lang":"eng","text":"Large-scale software repositories are a source of insights for software engineering. They offer an unmatched window into the software development process at scale. Their sheer number and size holds the promise of broadly applicable results. At the same time, that very size presents practical challenges for scaling tools and algorithms to millions of projects. A reasonable approach is to limit studies to representative samples of the population of interest. Broadly applicable conclusions can then be obtained by generalizing to the entire population. The contribution of this paper is a standardized experimental design methodology for choosing the inputs of studies working with large-scale repositories. We advocate for a methodology that clearly lays out what the population of interest is, how to sample it, and that fosters reproducibility. Along the way, we discourage researchers from using extrinsic attributes of projects such as stars, that measure some unclear notion of popularity."}],"_id":"18175","language":[{"iso":"eng"}],"external_id":{"isi":["001533999700027"]},"has_accepted_license":"1","citation":{"apa":"Maj, P., Muroya Lei, S., Siek, K., Di Grazia, L., &#38; Vitek, J. (2024). The fault in our stars: Designing reproducible large-scale code analysis experiments. In <i>38th European Conference on Object-Oriented Programming</i> (Vol. 313). Vienna, Austria: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ECOOP.2024.27\">https://doi.org/10.4230/LIPIcs.ECOOP.2024.27</a>","ieee":"P. Maj, S. Muroya Lei, K. Siek, L. Di Grazia, and J. Vitek, “The fault in our stars: Designing reproducible large-scale code analysis experiments,” in <i>38th European Conference on Object-Oriented Programming</i>, Vienna, Austria, 2024, vol. 313.","short":"P. Maj, S. Muroya Lei, K. Siek, L. Di Grazia, J. Vitek, in:, 38th European Conference on Object-Oriented Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Maj, Petr, et al. “The Fault in Our Stars: Designing Reproducible Large-Scale Code Analysis Experiments.” <i>38th European Conference on Object-Oriented Programming</i>, vol. 313, 27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ECOOP.2024.27\">10.4230/LIPIcs.ECOOP.2024.27</a>.","chicago":"Maj, Petr, Stefanie Muroya Lei, Konrad Siek, Luca Di Grazia, and Jan Vitek. “The Fault in Our Stars: Designing Reproducible Large-Scale Code Analysis Experiments.” In <i>38th European Conference on Object-Oriented Programming</i>, Vol. 313. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.ECOOP.2024.27\">https://doi.org/10.4230/LIPIcs.ECOOP.2024.27</a>.","ista":"Maj P, Muroya Lei S, Siek K, Di Grazia L, Vitek J. 2024. The fault in our stars: Designing reproducible large-scale code analysis experiments. 38th European Conference on Object-Oriented Programming. ECOOP: European Conference on Object-Oriented Programming, LIPIcs, vol. 313, 27.","ama":"Maj P, Muroya Lei S, Siek K, Di Grazia L, Vitek J. The fault in our stars: Designing reproducible large-scale code analysis experiments. In: <i>38th European Conference on Object-Oriented Programming</i>. Vol 313. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ECOOP.2024.27\">10.4230/LIPIcs.ECOOP.2024.27</a>"},"day":"01","status":"public","scopus_import":"1","file_date_updated":"2024-10-07T11:10:55Z","isi":1,"publication":"38th European Conference on Object-Oriented Programming","date_updated":"2025-12-02T13:48:19Z","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773416"]},"oa_version":"Published Version","date_created":"2024-10-06T22:01:12Z","alternative_title":["LIPIcs"],"title":"The fault in our stars: Designing reproducible large-scale code analysis experiments","publication_status":"published","conference":{"end_date":"2024-09-20","location":"Vienna, Austria","name":"ECOOP: European Conference on Object-Oriented Programming","start_date":"2024-09-16"},"file":[{"access_level":"open_access","file_size":1764222,"date_created":"2024-10-07T11:10:55Z","content_type":"application/pdf","success":1,"file_name":"2024_LIPICs_Maj.pdf","checksum":"2e75d305a8c817d76a0c7f136ce34f86","file_id":"18184","relation":"main_file","date_updated":"2024-10-07T11:10:55Z","creator":"dernst"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","acknowledgement":"This work was supported by the Czech Ministry of Education, Youth and Sports under\r\nprogram ERC-CZ, grant agreement LL2325, BigCode (reg. no. CZ.02.1.01/0.0/0.0/15_003/0000421). NSF grants CCF-1910850, CNS-1925644, and CCF-2139612, as well as the GACR EXPRO grant 23-07580X. We would like to thank Digital Ocean for their involuntary contribution of computational resources during the early data gathering phase of our research. We acknoweldge the reviewers of ICSE’22, and thank the reviewers of ECOOP’23 for their encouragments and for sticking around until 2024.","doi":"10.4230/LIPIcs.ECOOP.2024.27","oa":1,"month":"09","department":[{"_id":"ToHe"}],"author":[{"first_name":"Petr","last_name":"Maj","full_name":"Maj, Petr"},{"id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","first_name":"Stefanie","full_name":"Muroya Lei, Stefanie","last_name":"Muroya Lei"},{"first_name":"Konrad","last_name":"Siek","full_name":"Siek, Konrad"},{"first_name":"Luca","full_name":"Di Grazia, Luca","last_name":"Di Grazia"},{"first_name":"Jan","last_name":"Vitek","full_name":"Vitek, Jan"}],"volume":313},{"day":"25","citation":{"chicago":"Zadnik, Lenart, Marko Ljubotina, Žiga Krajnik, Enej Ilievski, and Tomaž Prosen. “Quantum Many-Body Spin Ratchets.” <i>PRX Quantum</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PRXQuantum.5.030356\">https://doi.org/10.1103/PRXQuantum.5.030356</a>.","ista":"Zadnik L, Ljubotina M, Krajnik Ž, Ilievski E, Prosen T. 2024. Quantum many-body spin ratchets. PRX Quantum. 5(3), 030356.","ama":"Zadnik L, Ljubotina M, Krajnik Ž, Ilievski E, Prosen T. Quantum many-body spin ratchets. <i>PRX Quantum</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1103/PRXQuantum.5.030356\">10.1103/PRXQuantum.5.030356</a>","apa":"Zadnik, L., Ljubotina, M., Krajnik, Ž., Ilievski, E., &#38; Prosen, T. (2024). Quantum many-body spin ratchets. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PRXQuantum.5.030356\">https://doi.org/10.1103/PRXQuantum.5.030356</a>","ieee":"L. Zadnik, M. Ljubotina, Ž. Krajnik, E. Ilievski, and T. Prosen, “Quantum many-body spin ratchets,” <i>PRX Quantum</i>, vol. 5, no. 3. American Physical Society, 2024.","short":"L. Zadnik, M. Ljubotina, Ž. Krajnik, E. Ilievski, T. Prosen, PRX Quantum 5 (2024).","mla":"Zadnik, Lenart, et al. “Quantum Many-Body Spin Ratchets.” <i>PRX Quantum</i>, vol. 5, no. 3, 030356, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PRXQuantum.5.030356\">10.1103/PRXQuantum.5.030356</a>."},"has_accepted_license":"1","quality_controlled":"1","type":"journal_article","external_id":{"arxiv":["2406.01571"],"isi":["001327172800001"]},"abstract":[{"text":"Introducing a class of SU(2) invariant quantum unitary circuits generating chiral transport, we examine the role of broken space-reflection and time-reversal symmetries on spin-transport properties. Upon adjusting parameters of local unitary gates, the dynamics can be either chaotic or integrable. The latter corresponds to a generalization of the space-time discretized (Trotterized) higher-spin quantum Heisenberg chain. We demonstrate that breaking of space-reflection symmetry results in a drift in the dynamical spin susceptibility. Remarkably, we find a universal drift velocity given by a simple formula, which, at zero average magnetization, depends only on the values of SU(2) Casimir invariants associated with local spins. In the integrable case, the drift velocity formula is confirmed analytically based on the exact solution of thermodynamic Bethe ansatz equations. Finally, by inspecting the large fluctuations of the time-integrated current between two halves of the system in stationary maximum-entropy states, we demonstrate violation of the Gallavotti-Cohen symmetry, implying that such states cannot be regarded as equilibrium ones. We show that the scaled cumulant generating function of the time-integrated current instead obeys a generalized fluctuation relation.","lang":"eng"}],"_id":"18176","language":[{"iso":"eng"}],"OA_place":"publisher","date_published":"2024-09-25T00:00:00Z","ddc":["530"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","intvolume":"         5","article_number":"030356","isi":1,"publication":"PRX Quantum","date_updated":"2025-09-08T09:55:09Z","file_date_updated":"2024-10-07T11:04:12Z","scopus_import":"1","ec_funded":1,"DOAJ_listed":"1","issue":"3","status":"public","file":[{"file_id":"18183","date_updated":"2024-10-07T11:04:12Z","relation":"main_file","creator":"dernst","checksum":"bc230631255d3bcf8bcbbc8fdbfefcf2","file_name":"2024_PRXQuantum_Zadnik.pdf","success":1,"content_type":"application/pdf","date_created":"2024-10-07T11:04:12Z","file_size":1061648,"access_level":"open_access"}],"publication_status":"published","OA_type":"gold","oa_version":"Published Version","date_created":"2024-10-06T22:01:12Z","title":"Quantum many-body spin ratchets","publication_identifier":{"eissn":["2691-3399"]},"arxiv":1,"department":[{"_id":"MaSe"}],"month":"09","article_type":"original","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"volume":5,"author":[{"last_name":"Zadnik","full_name":"Zadnik, Lenart","first_name":"Lenart"},{"id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","first_name":"Marko","orcid":"0000-0003-0038-7068","last_name":"Ljubotina","full_name":"Ljubotina, Marko"},{"first_name":"Žiga","last_name":"Krajnik","full_name":"Krajnik, Žiga"},{"first_name":"Enej","last_name":"Ilievski","full_name":"Ilievski, Enej"},{"first_name":"Tomaž","last_name":"Prosen","full_name":"Prosen, Tomaž"}],"oa":1,"doi":"10.1103/PRXQuantum.5.030356","acknowledgement":"The authors thank Denis Bernard, Jérôme Dubail, Hosho Katsura, Kareljan Schoutens, and Alberto Zorzato for stimulating discussions. This work has been supported by: Slovenian Research Agency (ARIS) under Grants No. N1-0219 (T.P., L.Z.), No. N1-0334 (T.P., L.Z.), No. N1-0243 (E.I.), and under Research Program P1-0402 (E.I., T.P., L.Z.). European Research Council (ERC) under Consolidator Grant No. 771536—NEMO (L.Z.), Advanced Grant No.\r\n101096208—QUEST (T.P., L.Z.), and Starting Grant No. 850899—NEQuM (M.L.). Simons Foundation under Simons Junior Fellowship Grant No. 1141511 (Ž.K.). M.L. acknowledges the hospitality of the Aspen Center for Physics, which is supported by National Science Foundation Grant No. PHY-2210452. Numerical simulations were performed using the ITensor library [117]. ","publisher":"American Physical Society","article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"type":"conference","quality_controlled":"1","_id":"18177","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Partially Specified Boolean Networks (PSBNs) represent a family of Boolean models resulting from possible interpretations of unknown update logics. Hybrid extension of CTL (HCTL) has the power to express complex dynamical phenomena, such as oscillations or stability. We present BNClassifier to classify Boolean Networks corresponding to a given PSBN according to criteria specified in HCTL. The implementation of the tool is fully symbolic (based on BDDs). The results are visualised using the machine-learning-based technology of decision trees."}],"external_id":{"isi":["001333144400002"]},"citation":{"short":"N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, in:, Computational Methods in Systems Biology, Springer Nature, 2024, pp. 19–26.","ieee":"N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “BNClassifier: Classifying boolean models by dynamic properties,” in <i>Computational Methods in Systems Biology</i>, 2024, vol. 14971, pp. 19–26.","mla":"Beneš, Nikola, et al. “BNClassifier: Classifying Boolean Models by Dynamic Properties.” <i>Computational Methods in Systems Biology</i>, vol. 14971, Springer Nature, 2024, pp. 19–26, doi:<a href=\"https://doi.org/10.1007/978-3-031-71671-3_2\">10.1007/978-3-031-71671-3_2</a>.","apa":"Beneš, N., Brim, L., Huvar, O., Pastva, S., &#38; Šafránek, D. (2024). BNClassifier: Classifying boolean models by dynamic properties. In <i>Computational Methods in Systems Biology</i> (Vol. 14971, pp. 19–26). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-71671-3_2\">https://doi.org/10.1007/978-3-031-71671-3_2</a>","ista":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2024. BNClassifier: Classifying boolean models by dynamic properties. Computational Methods in Systems Biology. , LNBI, vol. 14971, 19–26.","ama":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. BNClassifier: Classifying boolean models by dynamic properties. In: <i>Computational Methods in Systems Biology</i>. Vol 14971. Springer Nature; 2024:19-26. doi:<a href=\"https://doi.org/10.1007/978-3-031-71671-3_2\">10.1007/978-3-031-71671-3_2</a>","chicago":"Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek. “BNClassifier: Classifying Boolean Models by Dynamic Properties.” In <i>Computational Methods in Systems Biology</i>, 14971:19–26. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-71671-3_2\">https://doi.org/10.1007/978-3-031-71671-3_2</a>."},"day":"19","year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"     14971","date_published":"2024-09-19T00:00:00Z","isi":1,"date_updated":"2025-09-08T09:54:27Z","publication":"Computational Methods in Systems Biology","page":"19-26","status":"public","scopus_import":"1","ec_funded":1,"publication_status":"published","publication_identifier":{"isbn":["9783031716706"],"eissn":["1611-3349"],"issn":["0302-9743"]},"oa_version":"None","title":"BNClassifier: Classifying boolean models by dynamic properties","alternative_title":["LNBI"],"date_created":"2024-10-06T22:01:12Z","acknowledgement":"The work has been supported by the Czech Science Foundation grant No. GA22-10845S. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 101034413.","doi":"10.1007/978-3-031-71671-3_2","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"month":"09","department":[{"_id":"ToHe"}],"author":[{"last_name":"Beneš","full_name":"Beneš, Nikola","first_name":"Nikola"},{"first_name":"Luboš","full_name":"Brim, Luboš","last_name":"Brim"},{"full_name":"Huvar, Ondřej","last_name":"Huvar","first_name":"Ondřej"},{"last_name":"Pastva","full_name":"Pastva, Samuel","orcid":"0000-0003-1993-0331","first_name":"Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b"},{"full_name":"Šafránek, David","last_name":"Šafránek","first_name":"David"}],"volume":14971,"publisher":"Springer Nature","article_processing_charge":"No"},{"intvolume":"        20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"date_created":"2024-10-07T11:45:17Z","title":"A kicked quasicrystal","date_published":"2024-01-19T00:00:00Z","oa_version":"None","_id":"18187","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Quasicrystals are ordered but not periodic, which makes them fascinating objects at the interface between order and disorder. Experiments with ultracold atoms zoom in on this interface by driving a quasicrystal and exploring its fractal properties."}],"publication_status":"published","quality_controlled":"1","type":"journal_article","day":"19","citation":{"ama":"Leonard J. A kicked quasicrystal. <i>Nature Physics</i>. 2024;20(3):351-352. doi:<a href=\"https://doi.org/10.1038/s41567-023-02357-0\">10.1038/s41567-023-02357-0</a>","ista":"Leonard J. 2024. A kicked quasicrystal. Nature Physics. 20(3), 351–352.","chicago":"Leonard, Julian. “A Kicked Quasicrystal.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-023-02357-0\">https://doi.org/10.1038/s41567-023-02357-0</a>.","mla":"Leonard, Julian. “A Kicked Quasicrystal.” <i>Nature Physics</i>, vol. 20, no. 3, Springer Nature, 2024, pp. 351–52, doi:<a href=\"https://doi.org/10.1038/s41567-023-02357-0\">10.1038/s41567-023-02357-0</a>.","ieee":"J. Leonard, “A kicked quasicrystal,” <i>Nature Physics</i>, vol. 20, no. 3. Springer Nature, pp. 351–352, 2024.","short":"J. Leonard, Nature Physics 20 (2024) 351–352.","apa":"Leonard, J. (2024). A kicked quasicrystal. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02357-0\">https://doi.org/10.1038/s41567-023-02357-0</a>"},"article_processing_charge":"No","page":"351-352","status":"public","publisher":"Springer Nature","extern":"1","issue":"3","scopus_import":"1","doi":"10.1038/s41567-023-02357-0","author":[{"last_name":"Leonard","full_name":"Leonard, Julian","orcid":"0000-0003-3696-6870","first_name":"Julian","id":"b75b3f45-7995-11ef-9bfd-9a9cd02c3577"}],"volume":20,"date_updated":"2024-10-14T07:54:20Z","publication":"Nature Physics","month":"01","article_type":"letter_note"},{"publication_status":"published","oa_version":"Published Version","title":"Bayesian optimization for robust state preparation in quantum many-body systems","date_created":"2024-10-07T11:45:56Z","publication_identifier":{"issn":["2521-327X"]},"arxiv":1,"month":"06","article_type":"original","author":[{"first_name":"Tizian","full_name":"Blatz, Tizian","last_name":"Blatz"},{"full_name":"Kwan, Joyce","last_name":"Kwan","first_name":"Joyce"},{"id":"b75b3f45-7995-11ef-9bfd-9a9cd02c3577","first_name":"Julian","full_name":"Leonard, Julian","last_name":"Leonard"},{"last_name":"Bohrdt","full_name":"Bohrdt, Annabelle","first_name":"Annabelle"}],"volume":8,"oa":1,"doi":"10.22331/q-2024-06-27-1388","extern":"1","publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","article_processing_charge":"Yes","day":"27","citation":{"chicago":"Blatz, Tizian, Joyce Kwan, Julian Leonard, and Annabelle Bohrdt. “Bayesian Optimization for Robust State Preparation in Quantum Many-Body Systems.” <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2024. <a href=\"https://doi.org/10.22331/q-2024-06-27-1388\">https://doi.org/10.22331/q-2024-06-27-1388</a>.","ama":"Blatz T, Kwan J, Leonard J, Bohrdt A. Bayesian optimization for robust state preparation in quantum many-body systems. <i>Quantum</i>. 2024;8. doi:<a href=\"https://doi.org/10.22331/q-2024-06-27-1388\">10.22331/q-2024-06-27-1388</a>","ista":"Blatz T, Kwan J, Leonard J, Bohrdt A. 2024. Bayesian optimization for robust state preparation in quantum many-body systems. Quantum. 8, 1388.","apa":"Blatz, T., Kwan, J., Leonard, J., &#38; Bohrdt, A. (2024). Bayesian optimization for robust state preparation in quantum many-body systems. <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. <a href=\"https://doi.org/10.22331/q-2024-06-27-1388\">https://doi.org/10.22331/q-2024-06-27-1388</a>","mla":"Blatz, Tizian, et al. “Bayesian Optimization for Robust State Preparation in Quantum Many-Body Systems.” <i>Quantum</i>, vol. 8, 1388, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2024, doi:<a href=\"https://doi.org/10.22331/q-2024-06-27-1388\">10.22331/q-2024-06-27-1388</a>.","ieee":"T. Blatz, J. Kwan, J. Leonard, and A. Bohrdt, “Bayesian optimization for robust state preparation in quantum many-body systems,” <i>Quantum</i>, vol. 8. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2024.","short":"T. Blatz, J. Kwan, J. Leonard, A. Bohrdt, Quantum 8 (2024)."},"quality_controlled":"1","type":"journal_article","external_id":{"arxiv":["2312.09253"]},"_id":"18188","abstract":[{"text":"New generations of ultracold-atom experiments are continually raising the demand for efficient solutions to optimal control problems. Here, we apply Bayesian optimization to improve a state-preparation protocol recently implemented in an ultracold-atom system to realize a two-particle fractional quantum Hall state. Compared to manual ramp design, we demonstrate the superior performance of our optimization approach in a numerical simulation – resulting in a protocol that is 10x faster at the same fidelity, even when taking into account experimentally realistic levels of disorder in the system. We extensively analyze and discuss questions of robustness and the relationship between numerical simulation and experimental realization, and how to make the best use of the surrogate model trained during optimization. We find that numerical simulation can be expected to substantially reduce the number of experiments that need to be performed with even the most basic transfer learning techniques. The proposed protocol and workflow will pave the way toward the realization of more complex many-body quantum states in experiments.","lang":"eng"}],"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.22331/q-2024-06-27-1388","open_access":"1"}],"date_published":"2024-06-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","article_number":"1388","intvolume":"         8","date_updated":"2024-10-08T11:15:55Z","publication":"Quantum","scopus_import":"1","status":"public"},{"article_processing_charge":"No","status":"public","extern":"1","doi":"10.48550/arXiv.2404.07481","oa":1,"publication":"arXiv","date_updated":"2024-10-08T11:28:26Z","author":[{"first_name":"Sooshin","full_name":"Kim, Sooshin","last_name":"Kim"},{"last_name":"Lukin","full_name":"Lukin, Alexander","first_name":"Alexander"},{"first_name":"Matthew","full_name":"Rispoli, Matthew","last_name":"Rispoli"},{"first_name":"M. Eric","full_name":"Tai, M. Eric","last_name":"Tai"},{"last_name":"Kaufman","full_name":"Kaufman, Adam M.","first_name":"Adam M."},{"first_name":"Perrin","last_name":"Segura","full_name":"Segura, Perrin"},{"last_name":"Li","full_name":"Li, Yanfei","first_name":"Yanfei"},{"first_name":"Joyce","last_name":"Kwan","full_name":"Kwan, Joyce"},{"id":"b75b3f45-7995-11ef-9bfd-9a9cd02c3577","first_name":"Julian","last_name":"Leonard","full_name":"Leonard, Julian"},{"full_name":"Brice Bakkali-Hassani, Brice Bakkali-Hassani","last_name":"Brice Bakkali-Hassani","first_name":"Brice Bakkali-Hassani"},{"first_name":"Markus","full_name":"Greiner, Markus","last_name":"Greiner"}],"month":"04","article_number":"2404.07481","arxiv":1,"year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-04-11T00:00:00Z","title":"Adiabatic state preparation in a quantum Ising spin chain","date_created":"2024-10-08T11:25:52Z","oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2404.07481","open_access":"1"}],"_id":"18202","abstract":[{"text":"We report on adiabatic state preparation in the one-dimensional quantum Ising\r\nmodel using ultracold bosons in a tilted optical lattice. We prepare many-body\r\nground states of controllable system sizes and observe enhanced fluctuations\r\naround the transition between paramagnetic and antiferromagnetic states,\r\nmarking the precursor of quantum critical behavior. Furthermore, we find\r\nevidence for superpositions of domain walls and study their effect on the\r\nmany-body ground state by measuring the populations of each spin configuration\r\nacross the transition. These results shed new light on the effect of boundary\r\nconditions in finite-size quantum systems.","lang":"eng"}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["2404.07481"]},"type":"preprint","publication_status":"submitted","citation":{"apa":"Kim, S., Lukin, A., Rispoli, M., Tai, M. E., Kaufman, A. M., Segura, P., … Greiner, M. (n.d.). Adiabatic state preparation in a quantum Ising spin chain. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2404.07481\">https://doi.org/10.48550/arXiv.2404.07481</a>","short":"S. Kim, A. Lukin, M. Rispoli, M.E. Tai, A.M. Kaufman, P. Segura, Y. Li, J. Kwan, J. Leonard, B.B.-H. Brice Bakkali-Hassani, M. Greiner, ArXiv (n.d.).","ieee":"S. Kim <i>et al.</i>, “Adiabatic state preparation in a quantum Ising spin chain,” <i>arXiv</i>. .","mla":"Kim, Sooshin, et al. “Adiabatic State Preparation in a Quantum Ising Spin Chain.” <i>ArXiv</i>, 2404.07481, doi:<a href=\"https://doi.org/10.48550/arXiv.2404.07481\">10.48550/arXiv.2404.07481</a>.","chicago":"Kim, Sooshin, Alexander Lukin, Matthew Rispoli, M. Eric Tai, Adam M. Kaufman, Perrin Segura, Yanfei Li, et al. “Adiabatic State Preparation in a Quantum Ising Spin Chain.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2404.07481\">https://doi.org/10.48550/arXiv.2404.07481</a>.","ista":"Kim S, Lukin A, Rispoli M, Tai ME, Kaufman AM, Segura P, Li Y, Kwan J, Leonard J, Brice Bakkali-Hassani BB-H, Greiner M. Adiabatic state preparation in a quantum Ising spin chain. arXiv, 2404.07481.","ama":"Kim S, Lukin A, Rispoli M, et al. Adiabatic state preparation in a quantum Ising spin chain. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2404.07481\">10.48550/arXiv.2404.07481</a>"},"day":"11"},{"scopus_import":"1","status":"public","date_updated":"2024-10-09T10:08:08Z","publication":"Scientific Data","date_published":"2024-07-17T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41597-024-03595-4"}],"intvolume":"        11","article_number":"783","year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"chicago":"Rosenberg, Aviv A., Ailie Marx, and Alex M. Bronstein. “A Dataset of Alternately Located Segments in Protein Crystal Structures.” <i>Scientific Data</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41597-024-03595-4\">https://doi.org/10.1038/s41597-024-03595-4</a>.","ama":"Rosenberg AA, Marx A, Bronstein AM. A dataset of alternately located segments in protein crystal structures. <i>Scientific Data</i>. 2024;11. doi:<a href=\"https://doi.org/10.1038/s41597-024-03595-4\">10.1038/s41597-024-03595-4</a>","ista":"Rosenberg AA, Marx A, Bronstein AM. 2024. A dataset of alternately located segments in protein crystal structures. Scientific Data. 11, 783.","apa":"Rosenberg, A. A., Marx, A., &#38; Bronstein, A. M. (2024). A dataset of alternately located segments in protein crystal structures. <i>Scientific Data</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41597-024-03595-4\">https://doi.org/10.1038/s41597-024-03595-4</a>","mla":"Rosenberg, Aviv A., et al. “A Dataset of Alternately Located Segments in Protein Crystal Structures.” <i>Scientific Data</i>, vol. 11, 783, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41597-024-03595-4\">10.1038/s41597-024-03595-4</a>.","short":"A.A. Rosenberg, A. Marx, A.M. Bronstein, Scientific Data 11 (2024).","ieee":"A. A. Rosenberg, A. Marx, and A. M. Bronstein, “A dataset of alternately located segments in protein crystal structures,” <i>Scientific Data</i>, vol. 11. Springer Nature, 2024."},"day":"17","_id":"18203","abstract":[{"text":"Protein Data Bank (PDB) files list the relative spatial location of atoms in a protein structure as the final output of the process of fitting and refining to experimentally determined electron density measurements. Where experimental evidence exists for multiple conformations, atoms are modelled in alternate locations. Programs reading PDB files commonly ignore these alternate conformations by default leaving users oblivious to the presence of alternate conformations in the structures they analyze. This has led to underappreciation of their prevalence, under characterisation of their features and limited the accessibility to this high-resolution data representing structural ensembles. We have trawled PDB files to extract structural features of residues with alternately located atoms. The output includes the distance between alternate conformations and identifies the location of these segments within the protein chain and in proximity of all other atoms within a defined radius. This dataset should be of use in efforts to predict multiple structures from a single sequence and support studies investigating protein flexibility and the association with protein function.","lang":"eng"}],"language":[{"iso":"eng"}],"external_id":{"pmid":["39019896"]},"type":"journal_article","quality_controlled":"1","extern":"1","pmid":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","publisher":"Springer Nature","author":[{"full_name":"Rosenberg, Aviv A.","last_name":"Rosenberg","first_name":"Aviv A."},{"first_name":"Ailie","last_name":"Marx","full_name":"Marx, Ailie"},{"last_name":"Bronstein","full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730","first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6"}],"volume":11,"article_type":"original","month":"07","doi":"10.1038/s41597-024-03595-4","oa":1,"title":"A dataset of alternately located segments in protein crystal structures","date_created":"2024-10-08T11:50:30Z","oa_version":"Published Version","publication_identifier":{"issn":["2052-4463"]},"publication_status":"published"},{"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"_id":"18204","abstract":[{"lang":"eng","text":"Non-linear dynamical systems describe numerous real-world phenomena, ranging from the weather, to financial markets and disease progression. Individual systems may share substantial common information, for example patients’ anatomy. Lately, deep-learning has emerged as a leading method for data-driven modeling of non-linear dynamical systems. Yet, despite recent breakthroughs, prior works largely ignored the existence of shared information between different systems. However, such cases are quite common, for example, in medicine: we may wish to have a patient-specific model for some disease, but the data collected from a single patient is usually too small to train a deep-learning model. Hence, we must properly utilize data gathered from other patients. Here, we explicitly consider such cases by jointly modeling multiple systems. We show that the current single-system models consistently fail when trying to learn simultaneously from multiple systems. We suggest a framework for jointly approximating the Koopman operators of multiple systems, while intrinsically exploiting common information. We demonstrate how we can adapt to a new system using order-of-magnitude less new data and show the superiority of our model over competing methods, in terms of both forecasting ability and statistical fidelity, across chaotic, cardiac, and climate systems."}],"citation":{"mla":"Elul, Yonatan, et al. “Data-Driven Modeling of Interrelated Dynamical Systems.” <i>Communications Physics</i>, vol. 7, 141, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s42005-024-01626-5\">10.1038/s42005-024-01626-5</a>.","short":"Y. Elul, E. Rozenberg, A. Boyarski, Y. Yaniv, A. Schuster, A.M. Bronstein, Communications Physics 7 (2024).","ieee":"Y. Elul, E. Rozenberg, A. Boyarski, Y. Yaniv, A. Schuster, and A. M. Bronstein, “Data-driven modeling of interrelated dynamical systems,” <i>Communications Physics</i>, vol. 7. Springer Nature, 2024.","apa":"Elul, Y., Rozenberg, E., Boyarski, A., Yaniv, Y., Schuster, A., &#38; Bronstein, A. M. (2024). Data-driven modeling of interrelated dynamical systems. <i>Communications Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42005-024-01626-5\">https://doi.org/10.1038/s42005-024-01626-5</a>","ama":"Elul Y, Rozenberg E, Boyarski A, Yaniv Y, Schuster A, Bronstein AM. Data-driven modeling of interrelated dynamical systems. <i>Communications Physics</i>. 2024;7. doi:<a href=\"https://doi.org/10.1038/s42005-024-01626-5\">10.1038/s42005-024-01626-5</a>","ista":"Elul Y, Rozenberg E, Boyarski A, Yaniv Y, Schuster A, Bronstein AM. 2024. Data-driven modeling of interrelated dynamical systems. Communications Physics. 7, 141.","chicago":"Elul, Yonatan, Eyal Rozenberg, Amit Boyarski, Yael Yaniv, Assaf Schuster, and Alex M. Bronstein. “Data-Driven Modeling of Interrelated Dynamical Systems.” <i>Communications Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s42005-024-01626-5\">https://doi.org/10.1038/s42005-024-01626-5</a>."},"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","article_number":"141","intvolume":"         7","main_file_link":[{"url":"https://doi.org/10.1038/s42005-024-01626-5","open_access":"1"}],"date_published":"2024-05-01T00:00:00Z","publication":"Communications Physics","date_updated":"2024-10-09T10:12:11Z","status":"public","scopus_import":"1","publication_status":"published","publication_identifier":{"issn":["2399-3650"]},"oa_version":"Published Version","title":"Data-driven modeling of interrelated dynamical systems","date_created":"2024-10-08T12:45:35Z","doi":"10.1038/s42005-024-01626-5","oa":1,"month":"05","article_type":"original","author":[{"first_name":"Yonatan","full_name":"Elul, Yonatan","last_name":"Elul"},{"full_name":"Rozenberg, Eyal","last_name":"Rozenberg","first_name":"Eyal"},{"full_name":"Boyarski, Amit","last_name":"Boyarski","first_name":"Amit"},{"first_name":"Yael","last_name":"Yaniv","full_name":"Yaniv, Yael"},{"full_name":"Schuster, Assaf","last_name":"Schuster","first_name":"Assaf"},{"id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander","orcid":"0000-0001-9699-8730","last_name":"Bronstein","full_name":"Bronstein, Alexander"}],"volume":7,"publisher":"Springer Nature","article_processing_charge":"Yes","extern":"1"},{"doi":"10.1364/oe.515445","oa":1,"article_type":"original","month":"03","volume":32,"author":[{"first_name":"Omri","last_name":"Wengrowicz","full_name":"Wengrowicz, Omri"},{"full_name":"Bronstein, Alexander","last_name":"Bronstein","orcid":"0000-0001-9699-8730","first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6"},{"last_name":"Cohen","full_name":"Cohen, Oren","first_name":"Oren"}],"publisher":"Optica Publishing Group","article_processing_charge":"Yes (in subscription journal)","pmid":1,"extern":"1","publication_status":"published","publication_identifier":{"issn":["1094-4087"]},"oa_version":"Published Version","date_created":"2024-10-08T12:46:01Z","title":"Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography","publication":"Optics Express","date_updated":"2024-10-09T10:26:44Z","page":"8791-8803","status":"public","scopus_import":"1","issue":"6","type":"journal_article","quality_controlled":"1","_id":"18205","language":[{"iso":"eng"}],"abstract":[{"text":"We explore numerically an unsupervised, physics-informed, deep learning-based reconstruction technique for time-resolved imaging by multiplexed ptychography. In our method, the untrained deep learning model replaces the iterative algorithm’s update step, yielding superior reconstructions of multiple dynamic object frames compared to conventional methodologies. More precisely, we demonstrate improvements in image quality and resolution, while reducing sensitivity to the number of recorded frames, the mutual orthogonality of different probe modes, overlap between neighboring probe beams and the cutoff frequency of the ptychographic microscope – properties that are generally of paramount importance for ptychographic reconstruction algorithms.","lang":"eng"}],"external_id":{"pmid":["38571128"]},"day":"11","citation":{"chicago":"Wengrowicz, Omri, Alex M. Bronstein, and Oren Cohen. “Unsupervised Physics-Informed Deep Learning-Based Reconstruction for Time-Resolved Imaging by Multiplexed Ptychography.” <i>Optics Express</i>. Optica Publishing Group, 2024. <a href=\"https://doi.org/10.1364/oe.515445\">https://doi.org/10.1364/oe.515445</a>.","ista":"Wengrowicz O, Bronstein AM, Cohen O. 2024. Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography. Optics Express. 32(6), 8791–8803.","ama":"Wengrowicz O, Bronstein AM, Cohen O. Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography. <i>Optics Express</i>. 2024;32(6):8791-8803. doi:<a href=\"https://doi.org/10.1364/oe.515445\">10.1364/oe.515445</a>","apa":"Wengrowicz, O., Bronstein, A. M., &#38; Cohen, O. (2024). Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography. <i>Optics Express</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/oe.515445\">https://doi.org/10.1364/oe.515445</a>","ieee":"O. Wengrowicz, A. M. Bronstein, and O. Cohen, “Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography,” <i>Optics Express</i>, vol. 32, no. 6. Optica Publishing Group, pp. 8791–8803, 2024.","short":"O. Wengrowicz, A.M. Bronstein, O. Cohen, Optics Express 32 (2024) 8791–8803.","mla":"Wengrowicz, Omri, et al. “Unsupervised Physics-Informed Deep Learning-Based Reconstruction for Time-Resolved Imaging by Multiplexed Ptychography.” <i>Optics Express</i>, vol. 32, no. 6, Optica Publishing Group, 2024, pp. 8791–803, doi:<a href=\"https://doi.org/10.1364/oe.515445\">10.1364/oe.515445</a>."},"year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        32","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1364/OE.515445"}],"date_published":"2024-03-11T00:00:00Z"},{"scopus_import":"1","extern":"1","publisher":"Springer Nature","page":"160-171","status":"public","article_processing_charge":"No","month":"08","date_updated":"2024-10-09T10:33:39Z","publication":"First International Conference on Artificial Intelligence in Healthcare","author":[{"first_name":"Gilad","full_name":"Rave, Gilad","last_name":"Rave"},{"last_name":"Fordham","full_name":"Fordham, Daniel E.","first_name":"Daniel E."},{"orcid":"0000-0001-9699-8730","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander","full_name":"Bronstein, Alexander","last_name":"Bronstein"},{"full_name":"Silver, David H.","last_name":"Silver","first_name":"David H."}],"volume":14976,"doi":"10.1007/978-3-031-67285-9_12","oa_version":"None","date_published":"2024-08-15T00:00:00Z","alternative_title":["LNCS"],"title":"Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications","date_created":"2024-10-08T12:46:23Z","year":"2024","publication_identifier":{"isbn":["9783031672842"],"eisbn":["9783031672859"],"eissn":["1611-3349"],"issn":["0302-9743"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"     14976","day":"15","citation":{"apa":"Rave, G., Fordham, D. E., Bronstein, A. M., &#38; Silver, D. H. (2024). Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. In <i>First International Conference on Artificial Intelligence in Healthcare</i> (Vol. 14976, pp. 160–171). Swansea, United Kingdom: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-67285-9_12\">https://doi.org/10.1007/978-3-031-67285-9_12</a>","short":"G. Rave, D.E. Fordham, A.M. Bronstein, D.H. Silver, in:, First International Conference on Artificial Intelligence in Healthcare, Springer Nature, 2024, pp. 160–171.","ieee":"G. Rave, D. E. Fordham, A. M. Bronstein, and D. H. Silver, “Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications,” in <i>First International Conference on Artificial Intelligence in Healthcare</i>, Swansea, United Kingdom, 2024, vol. 14976, pp. 160–171.","mla":"Rave, Gilad, et al. “Enhancing Predictive Accuracy in Embryo Implantation: The Bonna Algorithm and Its Clinical Implications.” <i>First International Conference on Artificial Intelligence in Healthcare</i>, vol. 14976, Springer Nature, 2024, pp. 160–71, doi:<a href=\"https://doi.org/10.1007/978-3-031-67285-9_12\">10.1007/978-3-031-67285-9_12</a>.","chicago":"Rave, Gilad, Daniel E. Fordham, Alex M. Bronstein, and David H. Silver. “Enhancing Predictive Accuracy in Embryo Implantation: The Bonna Algorithm and Its Clinical Implications.” In <i>First International Conference on Artificial Intelligence in Healthcare</i>, 14976:160–71. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-67285-9_12\">https://doi.org/10.1007/978-3-031-67285-9_12</a>.","ista":"Rave G, Fordham DE, Bronstein AM, Silver DH. 2024. Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. First International Conference on Artificial Intelligence in Healthcare. AIiH: Artificial Intelligence in Healthcare, LNCS, vol. 14976, 160–171.","ama":"Rave G, Fordham DE, Bronstein AM, Silver DH. Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. In: <i>First International Conference on Artificial Intelligence in Healthcare</i>. Vol 14976. Springer Nature; 2024:160-171. doi:<a href=\"https://doi.org/10.1007/978-3-031-67285-9_12\">10.1007/978-3-031-67285-9_12</a>"},"type":"conference","quality_controlled":"1","publication_status":"published","conference":{"start_date":"2024-09-04","name":"AIiH: Artificial Intelligence in Healthcare","location":"Swansea, United Kingdom","end_date":"2024-09-06"},"abstract":[{"text":"In the context of in vitro fertilization (IVF), selecting embryos for transfer is critical in determining pregnancy outcomes, with implantation as the essential first milestone for a successful pregnancy. This study introduces the Bonna algorithm, an advanced deep-learning framework engineered to predict embryo implantation probabilities. The algorithm employs a sophisticated integration of machine-learning techniques, utilizing MobileNetV2 for pixel and context embedding, a custom Pix2Pix model for precise segmentation, and a Vision Transformer for additional depth in embedding. MobileNetV2 was chosen for its robust feature extraction capabilities, focusing on textures and edges. The custom Pix2Pix model is adapted for precise segmentation of significant biological features such as the zona pellucida and blastocyst cavity. The Vision Transformer adds a global perspective, capturing complex patterns not apparent in local image segments. Tested on a dataset of images of human blastocysts collected from Ukraine, Israel, and Spain, the Bonna algorithm was rigorously validated through 10-fold cross-validation to ensure its robustness and reliability. It demonstrates superior performance with a mean area under the receiver operating characteristic curve (AUC) of 0.754, significantly outperforming existing models. The study not only advances predictive accuracy in embryo selection but also highlights the algorithm’s clinical applicability due to reliable confidence reporting.","lang":"eng"}],"_id":"18206","language":[{"iso":"eng"}]},{"date_published":"2024-10-02T00:00:00Z","OA_place":"publisher","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1523/JNEUROSCI.1238-24.2024"}],"intvolume":"        44","article_number":"e1238242024","year":"2024","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"ieee":"P. Kratsios, N. Zampieri, R. Carrillo, K. Mizumoto, L. B. Sweeney, and P. Philippidou, “Molecular and cellular mechanisms of motor circuit development,” <i>The Journal of Neuroscience</i>, vol. 44, no. 40. Society for Neuroscience, 2024.","short":"P. Kratsios, N. Zampieri, R. Carrillo, K. Mizumoto, L.B. Sweeney, P. Philippidou, The Journal of Neuroscience 44 (2024).","mla":"Kratsios, Paschalis, et al. “Molecular and Cellular Mechanisms of Motor Circuit Development.” <i>The Journal of Neuroscience</i>, vol. 44, no. 40, e1238242024, Society for Neuroscience, 2024, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1238-24.2024\">10.1523/JNEUROSCI.1238-24.2024</a>.","apa":"Kratsios, P., Zampieri, N., Carrillo, R., Mizumoto, K., Sweeney, L. B., &#38; Philippidou, P. (2024). Molecular and cellular mechanisms of motor circuit development. <i>The Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1238-24.2024\">https://doi.org/10.1523/JNEUROSCI.1238-24.2024</a>","ista":"Kratsios P, Zampieri N, Carrillo R, Mizumoto K, Sweeney LB, Philippidou P. 2024. Molecular and cellular mechanisms of motor circuit development. The Journal of Neuroscience. 44(40), e1238242024.","ama":"Kratsios P, Zampieri N, Carrillo R, Mizumoto K, Sweeney LB, Philippidou P. Molecular and cellular mechanisms of motor circuit development. <i>The Journal of Neuroscience</i>. 2024;44(40). doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1238-24.2024\">10.1523/JNEUROSCI.1238-24.2024</a>","chicago":"Kratsios, Paschalis, Niccolò Zampieri, Robert Carrillo, Kota Mizumoto, Lora B. Sweeney, and Polyxeni Philippidou. “Molecular and Cellular Mechanisms of Motor Circuit Development.” <i>The Journal of Neuroscience</i>. Society for Neuroscience, 2024. <a href=\"https://doi.org/10.1523/JNEUROSCI.1238-24.2024\">https://doi.org/10.1523/JNEUROSCI.1238-24.2024</a>."},"day":"02","language":[{"iso":"eng"}],"_id":"18305","abstract":[{"text":"Motor circuits represent the main output of the central nervous system and produce dynamic behaviors ranging from relatively simple rhythmic activities like swimming in fish and breathing in mammals to highly sophisticated dexterous movements in humans. Despite decades of research, the development and function of motor circuits remain poorly understood. Breakthroughs in the field recently provided new tools and tractable model systems that set the stage to discover the molecular mechanisms and circuit logic underlying motor control. Here, we describe recent advances from both vertebrate (mouse, frog) and invertebrate (nematode, fruit fly) systems on cellular and molecular mechanisms that enable motor circuits to develop and function and highlight conserved and divergent mechanisms necessary for motor circuit development.","lang":"eng"}],"external_id":{"pmid":["39358025"],"isi":["001335212200016"]},"type":"journal_article","quality_controlled":"1","issue":"40","scopus_import":"1","status":"public","publication":"The Journal of Neuroscience","date_updated":"2026-01-05T14:01:26Z","isi":1,"date_created":"2024-10-13T22:01:49Z","title":"Molecular and cellular mechanisms of motor circuit development","oa_version":"Published Version","OA_type":"hybrid","publication_identifier":{"eissn":["1529-2401"]},"publication_status":"published","pmid":1,"article_processing_charge":"No","publisher":"Society for Neuroscience","volume":44,"author":[{"first_name":"Paschalis","last_name":"Kratsios","full_name":"Kratsios, Paschalis"},{"first_name":"Niccolò","last_name":"Zampieri","full_name":"Zampieri, Niccolò"},{"first_name":"Robert","full_name":"Carrillo, Robert","last_name":"Carrillo"},{"first_name":"Kota","last_name":"Mizumoto","full_name":"Mizumoto, Kota"},{"full_name":"Sweeney, Lora Beatrice Jaeger","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","orcid":"0000-0001-9242-5601"},{"first_name":"Polyxeni","full_name":"Philippidou, Polyxeni","last_name":"Philippidou"}],"article_type":"original","project":[{"_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","grant_number":"101041551","name":"Development and Evolution of Tetrapod Motor Circuits"}],"month":"10","department":[{"_id":"LoSw"}],"OA_embargo":"6 months","acknowledgement":"Work in the authors’ labs is funded by the Helmholtz Association (N.Z.), National Institute of Neurological Disorders and Stroke (NINDS) R01NS116365 (P.K.), NINDS R01NS123439 and National Science Foundation IOS-2048080 (R.C.), NINDS R01NS114510 (P.P.), Natural Sciences and Engineering Research Council of Canada RGPIN-2021-03154 (K.M.) and Horizon Europe European Research Council Starting Grant Number 101041551 (L.B.S.). P.P. is the Weidenthal Family Designated Professor in Career Development.","oa":1,"doi":"10.1523/JNEUROSCI.1238-24.2024"},{"publication_identifier":{"issn":["2041-8205"],"eissn":["2041-8213"]},"arxiv":1,"title":"Redshifted sodium transient near exoplanet transit","date_created":"2024-10-13T22:01:49Z","OA_type":"gold","oa_version":"Published Version","publication_status":"published","file":[{"file_size":1249747,"date_created":"2024-10-21T11:05:11Z","content_type":"application/pdf","success":1,"access_level":"open_access","creator":"dernst","relation":"main_file","file_id":"18456","date_updated":"2024-10-21T11:05:11Z","file_name":"2024_AstrophysicalJourn_Oza.pdf","checksum":"23eea2a6a0519694a84998957ad7b7fb"}],"article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"IOP Publishing","oa":1,"doi":"10.3847/2041-8213/ad6b29","acknowledgement":"The research described in this Letter was carried out in part at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics Space Administration, © 2024. California Institute of Technology. Government sponsorship acknowledged. A.V.O. and J.V.S. thank M. Lendl for constraints and discussions on the mass of WASP-49 A b. S.G.S acknowledges the support from FCT through Investigador FCT contract nr. CEECIND/00826/2018 and POPH/FSE (EC).","volume":973,"author":[{"last_name":"Oza","full_name":"Oza, Apurva V.","first_name":"Apurva V."},{"full_name":"Seidel, Julia V.","last_name":"Seidel","first_name":"Julia V."},{"last_name":"Hoeijmakers","full_name":"Hoeijmakers, H. Jens","first_name":"H. Jens"},{"full_name":"Unni, Athira","last_name":"Unni","first_name":"Athira"},{"first_name":"Aurora Y.","full_name":"Kesseli, Aurora Y.","last_name":"Kesseli"},{"first_name":"Carl A.","last_name":"Schmidt","full_name":"Schmidt, Carl A."},{"full_name":"Sivarani, Thirupathi","last_name":"Sivarani","first_name":"Thirupathi"},{"first_name":"Aaron","last_name":"Bello-Arufe","full_name":"Bello-Arufe, Aaron"},{"first_name":"Andrea","full_name":"Gebek, Andrea","last_name":"Gebek"},{"first_name":"Moritz","full_name":"Meyer Zu Westram, Moritz","last_name":"Meyer Zu Westram"},{"last_name":"Sousa","full_name":"Sousa, Sérgio G.","first_name":"Sérgio G."},{"last_name":"Lopes","full_name":"Lopes, Rosaly M.C.","first_name":"Rosaly M.C."},{"first_name":"Renyu","full_name":"Hu, Renyu","last_name":"Hu"},{"first_name":"Katherine","full_name":"De Kleer, Katherine","last_name":"De Kleer"},{"first_name":"Chloe","full_name":"Fisher, Chloe","last_name":"Fisher"},{"full_name":"Charnoz, Sébastien","last_name":"Charnoz","first_name":"Sébastien"},{"last_name":"Baker","full_name":"Baker, Ashley D.","first_name":"Ashley D."},{"first_name":"Samuel P.","last_name":"Halverson","full_name":"Halverson, Samuel P."},{"first_name":"Nick M.","full_name":"Schneider, Nick M.","last_name":"Schneider"},{"last_name":"Psaridi","full_name":"Psaridi, Angelica","first_name":"Angelica"},{"last_name":"Wyttenbach","full_name":"Wyttenbach, Aurélien","first_name":"Aurélien"},{"full_name":"Torres Rodriguez, Santiago","last_name":"Torres Rodriguez","orcid":"0000-0002-3150-8988","first_name":"Santiago","id":"a8df4360-4328-11ee-8f1a-e502d0c83fc2"},{"first_name":"Ishita","full_name":"Bhatnagar, Ishita","last_name":"Bhatnagar"},{"first_name":"Robert E.","last_name":"Johnson","full_name":"Johnson, Robert E."}],"department":[{"_id":"LiBu"}],"month":"10","article_type":"original","intvolume":"       973","article_number":"L53","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["520"],"year":"2024","OA_place":"publisher","date_published":"2024-10-01T00:00:00Z","external_id":{"isi":["001322169500001"],"arxiv":["2409.19844"]},"language":[{"iso":"eng"}],"_id":"18306","abstract":[{"text":"Neutral sodium (Na i) is an alkali metal with a favorable absorption cross section such that tenuous gases are easily illuminated at select transiting exoplanet systems. We examine both the time-averaged and time-series alkali spectral flux individually, over 4 nights at a hot Saturn system on a ∼2.8 day orbit about a Sun-like star WASP-49 A. Very Large Telescope/ESPRESSO observations are analyzed, providing new constraints. We recover the previously confirmed residual sodium flux uniquely when averaged, whereas night-to-night Na i varies by more than an order of magnitude. On HARPS/3.6 m Epoch II, we report a Doppler redshift at vΓ,NaD = + 9.7 ± 1.6 km s−1 with respect to the planet's rest frame. Upon examining the lightcurves, we confirm night-to-night variability, on the order of ∼1%–4% in NaD, rarely coinciding with exoplanet transit, not readily explained by stellar activity, starspots, tellurics, or the interstellar medium. Coincident with the ∼+10 km s−1 Doppler redshift, we detect a transient sodium absorption event dFNaD/F⋆ = 3.6% ± 1% at a relative difference of ΔFNaD(t) ∼ 4.4% ± 1%, lasting ΔtNaD ≳ 40 minutes. Since exoplanetary alkali signatures are blueshifted due to the natural vector of radiation pressure, estimated here at roughly ∼−5.7 km s−1, the radial velocity is rather at +15.4 km s−1, far larger than any known exoplanet system. Given that the redshift magnitude vΓ is in between the Roche limit and dynamically stable satellite orbits, the transient sodium may be a putative indication of a natural satellite orbiting WASP-49 A b.","lang":"eng"}],"quality_controlled":"1","type":"journal_article","citation":{"ista":"Oza AV, Seidel JV, Hoeijmakers HJ, Unni A, Kesseli AY, Schmidt CA, Sivarani T, Bello-Arufe A, Gebek A, Meyer Zu Westram M, Sousa SG, Lopes RMC, Hu R, De Kleer K, Fisher C, Charnoz S, Baker AD, Halverson SP, Schneider NM, Psaridi A, Wyttenbach A, Torres Rodriguez S, Bhatnagar I, Johnson RE. 2024. Redshifted sodium transient near exoplanet transit. Astrophysical Journal Letters. 973(2), L53.","ama":"Oza AV, Seidel JV, Hoeijmakers HJ, et al. Redshifted sodium transient near exoplanet transit. <i>Astrophysical Journal Letters</i>. 2024;973(2). doi:<a href=\"https://doi.org/10.3847/2041-8213/ad6b29\">10.3847/2041-8213/ad6b29</a>","chicago":"Oza, Apurva V., Julia V. Seidel, H. Jens Hoeijmakers, Athira Unni, Aurora Y. Kesseli, Carl A. Schmidt, Thirupathi Sivarani, et al. “Redshifted Sodium Transient near Exoplanet Transit.” <i>Astrophysical Journal Letters</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/2041-8213/ad6b29\">https://doi.org/10.3847/2041-8213/ad6b29</a>.","ieee":"A. V. Oza <i>et al.</i>, “Redshifted sodium transient near exoplanet transit,” <i>Astrophysical Journal Letters</i>, vol. 973, no. 2. IOP Publishing, 2024.","short":"A.V. Oza, J.V. Seidel, H.J. Hoeijmakers, A. Unni, A.Y. Kesseli, C.A. Schmidt, T. Sivarani, A. Bello-Arufe, A. Gebek, M. Meyer Zu Westram, S.G. Sousa, R.M.C. Lopes, R. Hu, K. De Kleer, C. Fisher, S. Charnoz, A.D. Baker, S.P. Halverson, N.M. Schneider, A. Psaridi, A. Wyttenbach, S. Torres Rodriguez, I. Bhatnagar, R.E. Johnson, Astrophysical Journal Letters 973 (2024).","mla":"Oza, Apurva V., et al. “Redshifted Sodium Transient near Exoplanet Transit.” <i>Astrophysical Journal Letters</i>, vol. 973, no. 2, L53, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/2041-8213/ad6b29\">10.3847/2041-8213/ad6b29</a>.","apa":"Oza, A. V., Seidel, J. V., Hoeijmakers, H. J., Unni, A., Kesseli, A. Y., Schmidt, C. A., … Johnson, R. E. (2024). Redshifted sodium transient near exoplanet transit. <i>Astrophysical Journal Letters</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/2041-8213/ad6b29\">https://doi.org/10.3847/2041-8213/ad6b29</a>"},"day":"01","has_accepted_license":"1","status":"public","DOAJ_listed":"1","issue":"2","scopus_import":"1","file_date_updated":"2024-10-21T11:05:11Z","date_updated":"2025-09-08T14:18:18Z","publication":"Astrophysical Journal Letters","isi":1},{"scopus_import":"1","ec_funded":1,"status":"public","isi":1,"date_updated":"2025-12-02T13:49:11Z","publication":"32nd Annual European Symposium on Algorithms","file_date_updated":"2024-10-21T09:41:48Z","OA_place":"publisher","date_published":"2024-09-23T00:00:00Z","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","intvolume":"       308","article_number":"100","citation":{"chicago":"La Tour, Max Dupré, Monika Henzinger, and David Saulpic. “Fully Dynamic K-Means Coreset in near-Optimal Update Time.” In <i>32nd Annual European Symposium on Algorithms</i>, Vol. 308. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2024.100\">https://doi.org/10.4230/LIPIcs.ESA.2024.100</a>.","ista":"La Tour MD, Henzinger M, Saulpic D. 2024. Fully dynamic k-means coreset in near-optimal update time. 32nd Annual European Symposium on Algorithms. ESA: European Symposium on Algorithms, LIPIcs, vol. 308, 100.","ama":"La Tour MD, Henzinger M, Saulpic D. Fully dynamic k-means coreset in near-optimal update time. In: <i>32nd Annual European Symposium on Algorithms</i>. Vol 308. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2024.100\">10.4230/LIPIcs.ESA.2024.100</a>","apa":"La Tour, M. D., Henzinger, M., &#38; Saulpic, D. (2024). Fully dynamic k-means coreset in near-optimal update time. In <i>32nd Annual European Symposium on Algorithms</i> (Vol. 308). London, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2024.100\">https://doi.org/10.4230/LIPIcs.ESA.2024.100</a>","ieee":"M. D. La Tour, M. Henzinger, and D. Saulpic, “Fully dynamic k-means coreset in near-optimal update time,” in <i>32nd Annual European Symposium on Algorithms</i>, London, United Kingdom, 2024, vol. 308.","short":"M.D. La Tour, M. Henzinger, D. Saulpic, in:, 32nd Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"La Tour, Max Dupré, et al. “Fully Dynamic K-Means Coreset in near-Optimal Update Time.” <i>32nd Annual European Symposium on Algorithms</i>, vol. 308, 100, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2024.100\">10.4230/LIPIcs.ESA.2024.100</a>."},"day":"23","has_accepted_license":"1","quality_controlled":"1","type":"conference","external_id":{"isi":["001545622400100"],"arxiv":["2406.19926"]},"_id":"18308","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We study in this paper the problem of maintaining a solution to k-median and k-means clustering in a fully dynamic setting. To do so, we present an algorithm to efficiently maintain a coreset, a compressed version of the dataset, that allows easy computation of a clustering solution at query time. Our coreset algorithm has near-optimal update time of Õ(k) in general metric spaces, which reduces to Õ(d) in the Euclidean space ℝ^d. The query time is O(k²) in general metrics, and O(kd) in ℝ^d. To maintain a constant-factor approximation for k-median and k-means clustering in Euclidean space, this directly leads to an algorithm with update time Õ(d), and query time Õ(kd + k²). To maintain a O(polylog k)-approximation, the query time is reduced to Õ(kd)."}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_processing_charge":"Yes","corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"MoHe"}],"month":"09","project":[{"name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020"},{"name":"Efficient algorithms","grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer"},{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"volume":308,"author":[{"last_name":"La Tour","full_name":"La Tour, Max Dupré","first_name":"Max Dupré"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"last_name":"Saulpic","full_name":"Saulpic, David","first_name":"David","id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964"}],"oa":1,"doi":"10.4230/LIPIcs.ESA.2024.100","acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct Grant agreement No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/Z422, grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nDavid Saulpic: Work partially done while at ISTA. Received funding from the European Union’s\r\nHorizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 101034413. This work was partially funded by the grant ANR-19-CE48-0016 from the French National Research Agency (ANR).","OA_type":"gold","oa_version":"Published Version","title":"Fully dynamic k-means coreset in near-optimal update time","alternative_title":["LIPIcs"],"date_created":"2024-10-13T22:01:50Z","arxiv":1,"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773386"]},"file":[{"creator":"dernst","relation":"main_file","file_id":"18454","date_updated":"2024-10-21T09:41:48Z","file_name":"2024_LIPICs_DuprelaTour.pdf","checksum":"8e8c0b13049f11bb0133dfac22e32718","file_size":873561,"date_created":"2024-10-21T09:41:48Z","success":1,"content_type":"application/pdf","access_level":"open_access"}],"conference":{"name":"ESA: European Symposium on Algorithms","start_date":"2024-09-02","end_date":"2024-09-04","location":"London, United Kingdom"},"publication_status":"published"},{"alternative_title":["LIPIcs"],"title":"Connectivity oracles for predictable vertex failures","date_created":"2024-10-13T22:01:50Z","oa_version":"Published Version","OA_type":"gold","publication_identifier":{"isbn":["9783959773386"],"issn":["1868-8969"]},"arxiv":1,"file":[{"date_updated":"2024-10-21T10:03:48Z","file_id":"18455","relation":"main_file","creator":"dernst","checksum":"ab1f2f9161549a8763eda15db40e022c","file_name":"2024_LIPICs_Hu.pdf","success":1,"content_type":"application/pdf","file_size":853914,"date_created":"2024-10-21T10:03:48Z","access_level":"open_access"}],"publication_status":"published","conference":{"end_date":"2024-09-04","location":"London, United Kingdom","name":"ESA: European Symposium on Algorithms","start_date":"2024-09-02"},"corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"first_name":"Bingbing","full_name":"Hu, Bingbing","last_name":"Hu"},{"id":"4c7f9625-dbbc-11ee-9d86-bdcc2db5a949","first_name":"Evangelos","last_name":"Kosinas","full_name":"Kosinas, Evangelos"},{"first_name":"Adam","last_name":"Polak","full_name":"Polak, Adam"}],"volume":308,"department":[{"_id":"MoHe"}],"month":"09","acknowledgement":"Part of this work was done when Evangelos Kosinas was at University of Ioannina and Adam Polak was at Max Planck Institute of Informatics.\r\n","doi":"10.4230/LIPIcs.ESA.2024.72","oa":1,"date_published":"2024-09-01T00:00:00Z","OA_place":"publisher","intvolume":"       308","article_number":"72","year":"2024","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","day":"01","citation":{"chicago":"Hu, Bingbing, Evangelos Kosinas, and Adam Polak. “Connectivity Oracles for Predictable Vertex Failures.” In <i>32nd Annual European Symposium on Algorithms</i>, Vol. 308. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2024.72\">https://doi.org/10.4230/LIPIcs.ESA.2024.72</a>.","ista":"Hu B, Kosinas E, Polak A. 2024. Connectivity oracles for predictable vertex failures. 32nd Annual European Symposium on Algorithms. ESA: European Symposium on Algorithms, LIPIcs, vol. 308, 72.","ama":"Hu B, Kosinas E, Polak A. Connectivity oracles for predictable vertex failures. In: <i>32nd Annual European Symposium on Algorithms</i>. Vol 308. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2024.72\">10.4230/LIPIcs.ESA.2024.72</a>","apa":"Hu, B., Kosinas, E., &#38; Polak, A. (2024). Connectivity oracles for predictable vertex failures. In <i>32nd Annual European Symposium on Algorithms</i> (Vol. 308). London, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2024.72\">https://doi.org/10.4230/LIPIcs.ESA.2024.72</a>","short":"B. Hu, E. Kosinas, A. Polak, in:, 32nd Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ieee":"B. Hu, E. Kosinas, and A. Polak, “Connectivity oracles for predictable vertex failures,” in <i>32nd Annual European Symposium on Algorithms</i>, London, United Kingdom, 2024, vol. 308.","mla":"Hu, Bingbing, et al. “Connectivity Oracles for Predictable Vertex Failures.” <i>32nd Annual European Symposium on Algorithms</i>, vol. 308, 72, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2024.72\">10.4230/LIPIcs.ESA.2024.72</a>."},"language":[{"iso":"eng"}],"_id":"18309","abstract":[{"text":"The problem of designing connectivity oracles supporting vertex failures is one of the basic data structures problems for undirected graphs. It is already well understood: previous works [Duan-Pettie STOC'10; Long-Saranurak FOCS'22] achieve query time linear in the number of failed vertices, and it is conditionally optimal as long as we require preprocessing time polynomial in the size of the graph and update time polynomial in the number of failed vertices. We revisit this problem in the paradigm of algorithms with predictions: we ask if the query time can be improved if the set of failed vertices can be predicted beforehand up to a small number of errors. More specifically, we design a data structure that, given a graph G = (V,E) and a set of vertices predicted to fail D̂ ⊆ V of size d = |D̂|, preprocesses it in time Õ(d|E|) and then can receive an update given as the symmetric difference between the predicted and the actual set of failed vertices D̂△D = (D̂ ⧵ D) ∪ (D ⧵ D̂) of size η = |D̂△D|, process it in time Õ(η⁴), and after that answer connectivity queries in G ⧵ D in time O(η). Viewed from another perspective, our data structure provides an improvement over the state of the art for the fully dynamic subgraph connectivity problem in the sensitivity setting [Henzinger-Neumann ESA'16]. We argue that the preprocessing time and query time of our data structure are conditionally optimal under standard fine-grained complexity assumptions.","lang":"eng"}],"external_id":{"arxiv":["2312.08489"],"isi":["001545622400072"]},"type":"conference","quality_controlled":"1","scopus_import":"1","status":"public","date_updated":"2025-12-02T13:49:52Z","publication":"32nd Annual European Symposium on Algorithms","isi":1,"file_date_updated":"2024-10-21T10:03:48Z"},{"publication_status":"published","publication_identifier":{"issn":["0261-1929"],"eissn":["2632-3559"]},"OA_type":"closed access","oa_version":"None","title":"Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE)","date_created":"2024-10-13T22:01:51Z","doi":"10.1177/02611929241286024","department":[{"_id":"PreCl"}],"month":"11","article_type":"original","author":[{"last_name":"Kitsara","full_name":"Kitsara, Maria","first_name":"Maria"},{"last_name":"Smajlhodžić-Deljo","full_name":"Smajlhodžić-Deljo, Merima","first_name":"Merima"},{"last_name":"Gurbeta Pokvic","full_name":"Gurbeta Pokvic, Lejla","first_name":"Lejla"},{"first_name":"Bettina","last_name":"Bert","full_name":"Bert, Bettina"},{"first_name":"Nataliia","full_name":"Bubalo, Nataliia","last_name":"Bubalo"},{"full_name":"Erden, Sevilay","last_name":"Erden","first_name":"Sevilay"},{"full_name":"Franco, Nuno Henrique","last_name":"Franco","first_name":"Nuno Henrique"},{"first_name":"Giuseppe","last_name":"Chirico","full_name":"Chirico, Giuseppe"},{"last_name":"Gómez Raja","full_name":"Gómez Raja, Jonathan","first_name":"Jonathan"},{"first_name":"Fernando","last_name":"Gonzalez-Uarquin","full_name":"Gonzalez-Uarquin, Fernando"},{"full_name":"Lang, Annemarie","last_name":"Lang","first_name":"Annemarie"},{"first_name":"Nicole","full_name":"Linklater, Nicole","last_name":"Linklater"},{"first_name":"Sandra","full_name":"Mojsova, Sandra","last_name":"Mojsova"},{"last_name":"Olsson","full_name":"Olsson, I. Anna S.","first_name":"I. Anna S."},{"first_name":"Ioanna","last_name":"Sandvig","full_name":"Sandvig, Ioanna"},{"first_name":"Alexandra","last_name":"Schaffert","full_name":"Schaffert, Alexandra"},{"full_name":"Schmit, Marthe","last_name":"Schmit","first_name":"Marthe"},{"full_name":"Schober, Sophie","last_name":"Schober","first_name":"Sophie","id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8"},{"first_name":"Bogdan","full_name":"Sevastre, Bogdan","last_name":"Sevastre"},{"first_name":"Doris","full_name":"Wilflingseder, Doris","last_name":"Wilflingseder"},{"last_name":"Ahluwalia","full_name":"Ahluwalia, Arti","first_name":"Arti"},{"full_name":"Neuhaus, Winfried","last_name":"Neuhaus","first_name":"Winfried"}],"volume":52,"publisher":"SAGE Publications","article_processing_charge":"No","pmid":1,"quality_controlled":"1","type":"journal_article","external_id":{"isi":["001348633700007"],"pmid":["39333027"]},"language":[{"iso":"eng"}],"_id":"18310","day":"01","citation":{"ieee":"M. Kitsara <i>et al.</i>, “Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE),” <i>Alternatives to Laboratory Animals</i>, vol. 52, no. 6. SAGE Publications, pp. 326–333, 2024.","short":"M. Kitsara, M. Smajlhodžić-Deljo, L. Gurbeta Pokvic, B. Bert, N. Bubalo, S. Erden, N.H. Franco, G. Chirico, J. Gómez Raja, F. Gonzalez-Uarquin, A. Lang, N. Linklater, S. Mojsova, I.A.S. Olsson, I. Sandvig, A. Schaffert, M. Schmit, S. Schober, B. Sevastre, D. Wilflingseder, A. Ahluwalia, W. Neuhaus, Alternatives to Laboratory Animals 52 (2024) 326–333.","mla":"Kitsara, Maria, et al. “Introducing the COST Action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE).” <i>Alternatives to Laboratory Animals</i>, vol. 52, no. 6, SAGE Publications, 2024, pp. 326–33, doi:<a href=\"https://doi.org/10.1177/02611929241286024\">10.1177/02611929241286024</a>.","apa":"Kitsara, M., Smajlhodžić-Deljo, M., Gurbeta Pokvic, L., Bert, B., Bubalo, N., Erden, S., … Neuhaus, W. (2024). Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE). <i>Alternatives to Laboratory Animals</i>. SAGE Publications. <a href=\"https://doi.org/10.1177/02611929241286024\">https://doi.org/10.1177/02611929241286024</a>","ista":"Kitsara M, Smajlhodžić-Deljo M, Gurbeta Pokvic L, Bert B, Bubalo N, Erden S, Franco NH, Chirico G, Gómez Raja J, Gonzalez-Uarquin F, Lang A, Linklater N, Mojsova S, Olsson IAS, Sandvig I, Schaffert A, Schmit M, Schober S, Sevastre B, Wilflingseder D, Ahluwalia A, Neuhaus W. 2024. Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE). Alternatives to Laboratory Animals. 52(6), 326–333.","ama":"Kitsara M, Smajlhodžić-Deljo M, Gurbeta Pokvic L, et al. Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE). <i>Alternatives to Laboratory Animals</i>. 2024;52(6):326-333. doi:<a href=\"https://doi.org/10.1177/02611929241286024\">10.1177/02611929241286024</a>","chicago":"Kitsara, Maria, Merima Smajlhodžić-Deljo, Lejla Gurbeta Pokvic, Bettina Bert, Nataliia Bubalo, Sevilay Erden, Nuno Henrique Franco, et al. “Introducing the COST Action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE).” <i>Alternatives to Laboratory Animals</i>. SAGE Publications, 2024. <a href=\"https://doi.org/10.1177/02611929241286024\">https://doi.org/10.1177/02611929241286024</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","intvolume":"        52","date_published":"2024-11-01T00:00:00Z","isi":1,"publication":"Alternatives to Laboratory Animals","date_updated":"2025-09-08T09:56:39Z","status":"public","page":"326-333","scopus_import":"1","issue":"6"},{"doi":"10.1038/s41422-024-01035-x","author":[{"last_name":"Hörmayer","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"volume":34,"month":"11","department":[{"_id":"JiFr"}],"article_type":"original","article_processing_charge":"No","corr_author":"1","publisher":"Springer Nature","pmid":1,"publication_status":"published","publication_identifier":{"issn":["1001-0602"],"eissn":["1748-7838"]},"date_created":"2024-10-13T22:01:51Z","title":"Feeling the danger: Local wound signaling in plants","OA_type":"closed access","oa_version":"None","publication":"Cell Research","date_updated":"2025-09-08T09:57:18Z","isi":1,"status":"public","page":"761-762","scopus_import":"1","external_id":{"pmid":["39354142"],"isi":["001326684200001"]},"language":[{"iso":"eng"}],"_id":"18311","abstract":[{"lang":"eng","text":"Local wound signaling in plants informs the surrounding tissues about an injury and initiates the regeneration process. In a recent paper published in Cell, Yang and colleagues show the involvement of a single Pep family member from tomato in wound signaling and how exogenous application of this regeneration factor enhances transformation efficiency in crops."}],"quality_controlled":"1","type":"journal_article","citation":{"mla":"Hörmayer, Lukas, and Jiří Friml. “Feeling the Danger: Local Wound Signaling in Plants.” <i>Cell Research</i>, vol. 34, Springer Nature, 2024, pp. 761–62, doi:<a href=\"https://doi.org/10.1038/s41422-024-01035-x\">10.1038/s41422-024-01035-x</a>.","ieee":"L. Hörmayer and J. Friml, “Feeling the danger: Local wound signaling in plants,” <i>Cell Research</i>, vol. 34. Springer Nature, pp. 761–762, 2024.","short":"L. Hörmayer, J. Friml, Cell Research 34 (2024) 761–762.","apa":"Hörmayer, L., &#38; Friml, J. (2024). Feeling the danger: Local wound signaling in plants. <i>Cell Research</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41422-024-01035-x\">https://doi.org/10.1038/s41422-024-01035-x</a>","ama":"Hörmayer L, Friml J. Feeling the danger: Local wound signaling in plants. <i>Cell Research</i>. 2024;34:761-762. doi:<a href=\"https://doi.org/10.1038/s41422-024-01035-x\">10.1038/s41422-024-01035-x</a>","ista":"Hörmayer L, Friml J. 2024. Feeling the danger: Local wound signaling in plants. Cell Research. 34, 761–762.","chicago":"Hörmayer, Lukas, and Jiří Friml. “Feeling the Danger: Local Wound Signaling in Plants.” <i>Cell Research</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41422-024-01035-x\">https://doi.org/10.1038/s41422-024-01035-x</a>."},"day":"01","intvolume":"        34","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","date_published":"2024-11-01T00:00:00Z"},{"citation":{"apa":"Zupančič, M., Keimpema, E., Tretiakov, E. O., Eder, S. J., Lev, I., Englmaier, L., … Harkany, T. (2024). Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-52762-z\">https://doi.org/10.1038/s41467-024-52762-z</a>","ieee":"M. Zupančič <i>et al.</i>, “Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","short":"M. Zupančič, E. Keimpema, E.O. Tretiakov, S.J. Eder, I. Lev, L. Englmaier, P. Bhandari, S.A. Fietz, W. Härtig, E. Renaux, A. Villunger, T. Hökfelt, M. Zimmer, F. Clotman, T. Harkany, Nature Communications 15 (2024).","mla":"Zupančič, Maja, et al. “Concerted Transcriptional Regulation of the Morphogenesis of Hypothalamic Neurons by ONECUT3.” <i>Nature Communications</i>, vol. 15, 8631, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-52762-z\">10.1038/s41467-024-52762-z</a>.","chicago":"Zupančič, Maja, Erik Keimpema, Evgenii O. Tretiakov, Stephanie J. Eder, Itamar Lev, Lukas Englmaier, Pradeep Bhandari, et al. “Concerted Transcriptional Regulation of the Morphogenesis of Hypothalamic Neurons by ONECUT3.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-52762-z\">https://doi.org/10.1038/s41467-024-52762-z</a>.","ista":"Zupančič M, Keimpema E, Tretiakov EO, Eder SJ, Lev I, Englmaier L, Bhandari P, Fietz SA, Härtig W, Renaux E, Villunger A, Hökfelt T, Zimmer M, Clotman F, Harkany T. 2024. Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. Nature Communications. 15, 8631.","ama":"Zupančič M, Keimpema E, Tretiakov EO, et al. Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-52762-z\">10.1038/s41467-024-52762-z</a>"},"day":"05","has_accepted_license":"1","external_id":{"pmid":["39366958"],"isi":["001409493300014"]},"abstract":[{"text":"Acquisition of specialized cellular features is controlled by the ordered expression of transcription factors (TFs) along differentiation trajectories. Here, we find a member of the Onecut TF family, ONECUT3, expressed in postmitotic neurons that leave their Ascl1+/Onecut1/2+ proliferative domain in the vertebrate hypothalamus to instruct neuronal differentiation. We combined single-cell RNA-seq and gain-of-function experiments for gene network reconstruction to show that ONECUT3 affects the polarization and morphogenesis of both hypothalamic GABA-derived dopamine and thyrotropin-releasing hormone (TRH)+ glutamate neurons through neuron navigator-2 (NAV2). In vivo, siRNA-mediated knockdown of ONECUT3 in neonatal mice reduced NAV2 mRNA, as well as neurite complexity in Onecut3-containing neurons, while genetic deletion of Onecut3/ceh-48 in C. elegans impaired neurocircuit wiring, and sensory discrimination-based behaviors. Thus, ONECUT3, conserved across neuronal subtypes and many species, underpins the polarization and morphological plasticity of phenotypically distinct neurons that descend from a common pool of Ascl1+ progenitors in the hypothalamus.","lang":"eng"}],"_id":"18445","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","OA_place":"publisher","date_published":"2024-10-05T00:00:00Z","intvolume":"        15","article_number":"8631","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","publication":"Nature Communications","date_updated":"2025-09-08T14:25:06Z","isi":1,"file_date_updated":"2024-10-21T12:15:38Z","DOAJ_listed":"1","scopus_import":"1","PlanS_conform":"1","status":"public","file":[{"file_name":"2024_NatureComm_Zupancic.pdf","checksum":"03d6dd1b84efa24e9e9ede748d08764d","file_id":"18460","date_updated":"2024-10-21T12:15:38Z","relation":"main_file","creator":"dernst","access_level":"open_access","file_size":7215329,"date_created":"2024-10-21T12:15:38Z","success":1,"content_type":"application/pdf"}],"publication_status":"published","title":"Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3","date_created":"2024-10-20T22:02:05Z","OA_type":"gold","oa_version":"Published Version","publication_identifier":{"eissn":["2041-1723"]},"volume":15,"author":[{"first_name":"Maja","last_name":"Zupančič","full_name":"Zupančič, Maja"},{"last_name":"Keimpema","full_name":"Keimpema, Erik","first_name":"Erik"},{"first_name":"Evgenii O.","full_name":"Tretiakov, Evgenii O.","last_name":"Tretiakov"},{"first_name":"Stephanie J.","last_name":"Eder","full_name":"Eder, Stephanie J."},{"first_name":"Itamar","last_name":"Lev","full_name":"Lev, Itamar"},{"full_name":"Englmaier, Lukas","last_name":"Englmaier","first_name":"Lukas"},{"full_name":"Bhandari, Pradeep","last_name":"Bhandari","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0863-4481"},{"last_name":"Fietz","full_name":"Fietz, Simone A.","first_name":"Simone A."},{"full_name":"Härtig, Wolfgang","last_name":"Härtig","first_name":"Wolfgang"},{"first_name":"Estelle","last_name":"Renaux","full_name":"Renaux, Estelle"},{"full_name":"Villunger, Andreas","last_name":"Villunger","first_name":"Andreas"},{"full_name":"Hökfelt, Tomas","last_name":"Hökfelt","first_name":"Tomas"},{"first_name":"Manuel","last_name":"Zimmer","full_name":"Zimmer, Manuel"},{"first_name":"Frédéric","last_name":"Clotman","full_name":"Clotman, Frédéric"},{"first_name":"Tibor","full_name":"Harkany, Tibor","last_name":"Harkany"}],"month":"10","department":[{"_id":"RySh"}],"article_type":"original","doi":"10.1038/s41467-024-52762-z","oa":1,"acknowledgement":"The authors thank Z. Máté, G. Szabó, and F. Erdélyi for the custom generation of transgenic mouse lines, C. Fekete for Trh transgenic tissues (all from the Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary), A. Goudmaeker for IVF recovery of a frozen mouse line (SSS animal facility, Université catholique de Louvain), and Y. Yanagawa (Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Japan) for providing GAD67gfp/+ mice. We also thank S. Cloer, D. Preininger, and A. Weissenbacher (Tiergarten Schönbrunn, Vienna, Austria) for providing naked mole rats, Seba’s fruit bats, and Indian flying foxes, as well as F. Aujard (CNRS, UMR 7179 ‘Adaptive mechanisms and evolution’, France) for Microcebus tissues. I. Milenkovic and G.G. Kovács (Clinical Institute of Neurology, Medical University of Vienna, Vienna, Austria) are acknowledged for providing post-mortem human brain samples. We are indebted to S. Rehman (Medical University of Vienna), M. Kalusa (University of Leipzig, Leipzig, Germany), and W. Reimann (Paul Flechsig Institute for Brain Research, Leipzig, Germany) for their technical assistance. C. elegans strains were provided by the National Bioresource Project for the nematode, Japan, and the CGC, with the latter being funded by the NIH Office of Research Infrastructure Programs (P40 OD010440). This work was supported by the Austrian Science Fund (FWF, P 34121-B; to E.K.), the Swedish Research Council (2023-03058, T.Ha; 2020-01688, T.Hö.), the Swedish Brain Foundation (Hjärnfonden, FO2022-0300, to T.Ha.), the Novo Nordisk Foundation (NNF23OC0084476, to T.Ha.), the European Research Council (FOODFORLIFE, ERC-2020-AdG-101021016; to T.Ha.), the Université Catholique de Louvain (‘Fonds spéciaux de recherche’-FSR, to F.C.), and Fonds de la Recherche Scientifique F.R.S.-FNRS (‘Project de recherche (PDR)’ #T.0039.21, to F.C.). S.J.E. is supported by the Simons Foundation #543069. I.L. is supported by a post-doctoral fellowship from the Human Frontiers Science Program (LT000335/2020-L). E.R. holds a PhD grant from the FRIA (F.R.S.-FNRS, Belgium). F.C. is a Research Director of the F.R.S.-FNRS (Belgium).\r\nOpen access funding provided by Karolinska Institute.","pmid":1,"article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"Springer Nature"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","article_number":"eadh1145","intvolume":"       386","main_file_link":[{"open_access":"1","url":"https://hal.inrae.fr/hal-04447081v1/file/2023.01.24.525420.full.pdf"}],"OA_place":"repository","date_published":"2024-10-11T00:00:00Z","quality_controlled":"1","type":"journal_article","external_id":{"isi":["001422132300018"],"pmid":["39388574"]},"language":[{"iso":"eng"}],"_id":"18446","abstract":[{"text":"How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these morphomaps revealed that although blastomere divisions desynchronized passively, 8-cell embryos converged toward robust three-dimensional shapes. Using topological analysis and genetic perturbations, we found that embryos progressively changed their cellular connectivity to a preferred topology, which could be predicted by a physical model in which actomyosin contractility and noise facilitate topological transitions, lowering surface energy. This mechanism favored regular embryo packing and promoted a higher number of inner cells in the 16-cell embryo. Synchronized division reduced embryo packing and generated substantially more misallocated cells and fewer inner-cell–mass cells. These findings suggest that stochasticity in division timing contributes to robust patterning.","lang":"eng"}],"citation":{"apa":"Fabrèges, D., Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani, C., … Hiiragi, T. (2024). Temporal variability and cell mechanics control robustness in mammalian embryogenesis. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adh1145\">https://doi.org/10.1126/science.adh1145</a>","short":"D. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani, T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon, V. Uhlman, E.B. Hannezo, T. Hiiragi, Science 386 (2024).","ieee":"D. Fabrèges <i>et al.</i>, “Temporal variability and cell mechanics control robustness in mammalian embryogenesis,” <i>Science</i>, vol. 386, no. 6718. AAAS, 2024.","mla":"Fabrèges, Dimitri, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” <i>Science</i>, vol. 386, no. 6718, eadh1145, AAAS, 2024, doi:<a href=\"https://doi.org/10.1126/science.adh1145\">10.1126/science.adh1145</a>.","chicago":"Fabrèges, Dimitri, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth, Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” <i>Science</i>. AAAS, 2024. <a href=\"https://doi.org/10.1126/science.adh1145\">https://doi.org/10.1126/science.adh1145</a>.","ista":"Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C, Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon V, Uhlman V, Hannezo EB, Hiiragi T. 2024. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. 386(6718), eadh1145.","ama":"Fabrèges D, Corominas-Murtra B, Moghe P, et al. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. <i>Science</i>. 2024;386(6718). doi:<a href=\"https://doi.org/10.1126/science.adh1145\">10.1126/science.adh1145</a>"},"day":"11","status":"public","scopus_import":"1","issue":"6718","isi":1,"date_updated":"2025-09-08T14:22:13Z","publication":"Science","publication_identifier":{"eissn":["1095-9203"]},"OA_type":"green","oa_version":"Submitted Version","date_created":"2024-10-20T22:02:06Z","title":"Temporal variability and cell mechanics control robustness in mammalian embryogenesis","publication_status":"published","publisher":"AAAS","article_processing_charge":"No","corr_author":"1","pmid":1,"doi":"10.1126/science.adh1145","oa":1,"acknowledgement":"We are grateful to the members of the Hiiragi laboratory for discussions and comments on the manuscript: R. Bloehs, S. Friese, S. Hozeifi, L. Pérez, and W. Schwarzer for their technical support; V. Janssen for establishing the PAB protocol; members of the Tsukiyama group for the animal care with monkeys, in particular H. Tsuchiya and M. Nakaya; Unité Commune d’Expérimentation Animale (UCEA, Jouy-en-Josas, France) for the animal care with rabbits; the EMBL electronic and mechanical workshops and the EMBL animal facility for their support; We thank Luxendo for the close collaboration in developing the light-sheet microscopy for mammalian embryos.\r\nFunding: This work was funded by the following: EMBL Interdisciplinary Postdoc Program (EIPOD) under Marie Sklodowska Curie Actions COFUND III RTD (to D.F.); JSPS Overseas Research Fellowship (to T.I.); Field of excellence “Complexity of life in basic research and innovation” of the University of Graz (to B.C.M.); European Research Council, ERC Advanced Grant “SelforganisingEmbryo”, grant agreement 742732; ERC Advanced Grant “COORDINATION” grant agreement 101055287 (to T.H.); Stichting LSH-TKI, grant LSHM21020 (to T.H.) JSPS KAKENHI grants JP21H05038 and JP22H05166 (to T.H.)","month":"10","department":[{"_id":"EdHa"}],"article_type":"original","author":[{"last_name":"Fabrèges","full_name":"Fabrèges, Dimitri","first_name":"Dimitri"},{"last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643"},{"full_name":"Moghe, Prachiti","last_name":"Moghe","first_name":"Prachiti"},{"full_name":"Kickuth, Alison","last_name":"Kickuth","first_name":"Alison"},{"last_name":"Ichikawa","full_name":"Ichikawa, Takafumi","first_name":"Takafumi"},{"full_name":"Iwatani, Chizuru","last_name":"Iwatani","first_name":"Chizuru"},{"last_name":"Tsukiyama","full_name":"Tsukiyama, Tomoyuki","first_name":"Tomoyuki"},{"first_name":"Nathalie","full_name":"Daniel, Nathalie","last_name":"Daniel"},{"first_name":"Julie","last_name":"Gering","full_name":"Gering, Julie"},{"full_name":"Stokkermans, Anniek","last_name":"Stokkermans","first_name":"Anniek"},{"first_name":"Adrian","full_name":"Wolny, Adrian","last_name":"Wolny"},{"first_name":"Anna","last_name":"Kreshuk","full_name":"Kreshuk, Anna"},{"last_name":"Duranthon","full_name":"Duranthon, Véronique","first_name":"Véronique"},{"first_name":"Virginie","full_name":"Uhlman, Virginie","last_name":"Uhlman"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Takashi","last_name":"Hiiragi","full_name":"Hiiragi, Takashi"}],"volume":386}]