[{"file_date_updated":"2023-07-18T08:43:07Z","date_updated":"2026-04-15T06:39:57Z","type":"journal_article","abstract":[{"text":"Currently available quantum processors are dominated by noise, which severely limits their applicability and motivates the search for new physical qubit encodings. In this work, we introduce the inductively shunted transmon, a weakly flux-tunable superconducting qubit that offers charge offset protection for all levels and a 20-fold reduction in flux dispersion compared to the state-of-the-art resulting in a constant coherence over a full flux quantum. The parabolic confinement provided by the inductive shunt as well as the linearity of the geometric superinductor facilitates a high-power readout that resolves quantum jumps with a fidelity and QND-ness of >90% and without the need for a Josephson parametric amplifier. Moreover, the device reveals quantum tunneling physics between the two prepared fluxon ground states with a measured average decay time of up to 3.5 h. In the future, fast time-domain control of the transition matrix elements could offer a new path forward to also achieve full qubit control in the decay-protected fluxon basis.","lang":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication":"Nature Communications","date_created":"2023-07-16T22:01:08Z","has_accepted_license":"1","oa":1,"article_type":"original","title":"Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The authors thank J. Koch for discussions and support with the scQubits python package, I. Rozhansky and A. Poddubny for important insights into photon-assisted tunneling, S. Barzanjeh and G. Arnold for theory, E. Redchenko, S. Pepic, the MIBA workshop and the IST nanofabrication facility for technical contributions, as well as L. Drmic, P. Zielinski and R. Sett for software development. We acknowledge the prompt support of Quantum Machines to implement active state preparation with their OPX+. This work was supported by a NOMIS foundation research grant (J.F.), the Austrian Science Fund (FWF) through BeyondC F7105 (J.F.) and IST Austria.","scopus_import":"1","status":"public","file":[{"file_name":"2023_NatureComm_Hassani.pdf","date_created":"2023-07-18T08:43:07Z","file_id":"13248","file_size":2899592,"creator":"dernst","date_updated":"2023-07-18T08:43:07Z","success":1,"access_level":"open_access","relation":"main_file","checksum":"a85773b5fe23516f60f7d5d31b55c200","content_type":"application/pdf"}],"citation":{"short":"F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, J.M. Fink, Nature Communications 14 (2023).","mla":"Hassani, Farid, et al. “Inductively Shunted Transmons Exhibit Noise Insensitive Plasmon States and a Fluxon Decay Exceeding 3 Hours.” <i>Nature Communications</i>, vol. 14, 3968, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39656-2\">10.1038/s41467-023-39656-2</a>.","chicago":"Hassani, Farid, Matilda Peruzzo, Lucky Kapoor, Andrea Trioni, Martin Zemlicka, and Johannes M Fink. “Inductively Shunted Transmons Exhibit Noise Insensitive Plasmon States and a Fluxon Decay Exceeding 3 Hours.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39656-2\">https://doi.org/10.1038/s41467-023-39656-2</a>.","ista":"Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. 2023. Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. Nature Communications. 14, 3968.","ieee":"F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, and J. M. Fink, “Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Hassani, F., Peruzzo, M., Kapoor, L., Trioni, A., Zemlicka, M., &#38; Fink, J. M. (2023). Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-39656-2\">https://doi.org/10.1038/s41467-023-39656-2</a>","ama":"Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39656-2\">10.1038/s41467-023-39656-2</a>"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa_version":"Published Version","quality_controlled":"1","language":[{"iso":"eng"}],"month":"07","corr_author":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"17133","status":"public"}]},"day":"05","doi":"10.1038/s41467-023-39656-2","publication_status":"published","department":[{"_id":"JoFi"}],"volume":14,"intvolume":"        14","author":[{"first_name":"Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid","last_name":"Hassani"},{"orcid":"0000-0002-3415-4628","first_name":"Matilda","last_name":"Peruzzo","full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kapoor","id":"84b9700b-15b2-11ec-abd3-831089e67615","full_name":"Kapoor, Lucky","first_name":"Lucky","orcid":"0000-0001-8319-2148"},{"id":"42F71B44-F248-11E8-B48F-1D18A9856A87","full_name":"Trioni, Andrea","last_name":"Trioni","first_name":"Andrea"},{"last_name":"Zemlicka","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0005-0878-3032","first_name":"Martin"},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"_id":"13227","external_id":{"isi":["001024729900009"],"pmid":["37407570"]},"article_number":"3968","year":"2023","publisher":"Springer Nature","project":[{"_id":"2622978C-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"ddc":["530"],"article_processing_charge":"No","date_published":"2023-07-05T00:00:00Z","pmid":1},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"relation":"main_file","checksum":"96c759db9cdf94b81e37871a66a6ff48","content_type":"application/pdf","success":1,"access_level":"open_access","file_size":4100596,"creator":"dernst","date_updated":"2023-07-18T07:43:10Z","file_name":"2023_ACM_HenzingerT.pdf","date_created":"2023-07-18T07:43:10Z","file_id":"13245"}],"citation":{"ieee":"T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Runtime monitoring of dynamic fairness properties,” in <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i>, Chicago, IL, United States, 2023, pp. 604–614.","ama":"Henzinger TA, Karimi M, Kueffner K, Mallik K. Runtime monitoring of dynamic fairness properties. In: <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i>. Association for Computing Machinery; 2023:604-614. doi:<a href=\"https://doi.org/10.1145/3593013.3594028\">10.1145/3593013.3594028</a>","apa":"Henzinger, T. A., Karimi, M., Kueffner, K., &#38; Mallik, K. (2023). Runtime monitoring of dynamic fairness properties. In <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i> (pp. 604–614). Chicago, IL, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3593013.3594028\">https://doi.org/10.1145/3593013.3594028</a>","mla":"Henzinger, Thomas A., et al. “Runtime Monitoring of Dynamic Fairness Properties.” <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i>, Association for Computing Machinery, 2023, pp. 604–14, doi:<a href=\"https://doi.org/10.1145/3593013.3594028\">10.1145/3593013.3594028</a>.","short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, Association for Computing Machinery, 2023, pp. 604–614.","chicago":"Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Runtime Monitoring of Dynamic Fairness Properties.” In <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i>, 604–14. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3593013.3594028\">https://doi.org/10.1145/3593013.3594028</a>.","ista":"Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Runtime monitoring of dynamic fairness properties. FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency. FAccT: Conference on Fairness, Accountability and Transparency, 604–614."},"status":"public","acknowledgement":"The authors would like to thank the anonymous reviewers for their valuable comments and helpful suggestions. This work is supported by the European Research Council under Grant No.: ERC-2020-AdG 101020093.","scopus_import":"1","publication_status":"published","department":[{"_id":"ToHe"}],"doi":"10.1145/3593013.3594028","day":"12","ec_funded":1,"month":"06","corr_author":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","arxiv":1,"publication":"FAccT '23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency","date_created":"2023-07-16T22:01:09Z","publication_identifier":{"isbn":["9781450372527"]},"abstract":[{"lang":"eng","text":"A machine-learned system that is fair in static decision-making tasks may have biased societal impacts in the long-run. This may happen when the system interacts with humans and feedback patterns emerge, reinforcing old biases in the system and creating new biases. While existing works try to identify and mitigate long-run biases through smart system design, we introduce techniques for monitoring fairness in real time. Our goal is to build and deploy a monitor that will continuously observe a long sequence of events generated by the system in the wild, and will output, with each event, a verdict on how fair the system is at the current point in time. The advantages of monitoring are two-fold. Firstly, fairness is evaluated at run-time, which is important because unfair behaviors may not be eliminated a priori, at design-time, due to partial knowledge about the system and the environment, as well as uncertainties and dynamic changes in the system and the environment, such as the unpredictability of human behavior. Secondly, monitors are by design oblivious to how the monitored system is constructed, which makes them suitable to be used as trusted third-party fairness watchdogs. They function as computationally lightweight statistical estimators, and their correctness proofs rely on the rigorous analysis of the stochastic process that models the assumptions about the underlying dynamics of the system. We show, both in theory and experiments, how monitors can warn us (1) if a bank’s credit policy over time has created an unfair distribution of credit scores among the population, and (2) if a resource allocator’s allocation policy over time has made unfair allocations. Our experiments demonstrate that the monitors introduce very low overhead. We believe that runtime monitoring is an important and mathematically rigorous new addition to the fairness toolbox."}],"type":"conference","date_updated":"2026-01-21T07:23:43Z","file_date_updated":"2023-07-18T07:43:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Runtime monitoring of dynamic fairness properties","has_accepted_license":"1","oa":1,"conference":{"location":"Chicago, IL, United States","end_date":"2023-06-15","name":"FAccT: Conference on Fairness, Accountability and Transparency","start_date":"2023-06-12"},"ddc":["000"],"project":[{"grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"publisher":"Association for Computing Machinery","year":"2023","date_published":"2023-06-12T00:00:00Z","page":"604-614","article_processing_charge":"Yes (via OA deal)","_id":"13228","external_id":{"isi":["001062819300057"],"arxiv":["2305.04699"]},"isi":1,"author":[{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"6e5417ba-5355-11ee-ae5a-94c2e510b26b","full_name":"Karimi, Mahyar","last_name":"Karimi","first_name":"Mahyar","orcid":"0009-0005-0820-1696"},{"last_name":"Kueffner","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","full_name":"Kueffner, Konstantin","first_name":"Konstantin","orcid":"0000-0001-8974-2542"},{"id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","full_name":"Mallik, Kaushik","last_name":"Mallik","first_name":"Kaushik","orcid":"0000-0001-9864-7475"}]},{"year":"2023","ddc":["570"],"project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"publisher":"Public Library of Science","page":"e3002146","article_processing_charge":"No","pmid":1,"date_published":"2023-06-08T00:00:00Z","volume":21,"intvolume":"        21","author":[{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan","last_name":"Shamipour","first_name":"Shayan"},{"full_name":"Hofmann, Laura","id":"b88d43f2-dc74-11ea-a0a7-e41b7912e031","last_name":"Hofmann","first_name":"Laura"},{"last_name":"Steccari","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","full_name":"Steccari, Irene","first_name":"Irene"},{"first_name":"Roland","last_name":"Kardos","full_name":"Kardos, Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"isi":1,"external_id":{"pmid":["37289834"],"isi":["001003199100005"]},"_id":"13229","issue":"6","acknowledgement":"This work was supported by funding from the European Union (European Research Council Advanced grant 742573) to C.-P.H. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"date_updated":"2023-07-18T07:59:58Z","file_size":4431723,"creator":"dernst","file_id":"13246","date_created":"2023-07-18T07:59:58Z","file_name":"2023_PloSBiology_Shamipour.pdf","content_type":"application/pdf","relation":"main_file","checksum":"8e88cb0e5a6433a2f1939a9030bed384","success":1,"access_level":"open_access"}],"citation":{"ama":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. <i>PLoS Biology</i>. 2023;21(6):e3002146. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002146\">10.1371/journal.pbio.3002146</a>","apa":"Shamipour, S., Hofmann, L., Steccari, I., Kardos, R., &#38; Heisenberg, C.-P. J. (2023). Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3002146\">https://doi.org/10.1371/journal.pbio.3002146</a>","ieee":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, and C.-P. J. Heisenberg, “Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes,” <i>PLoS Biology</i>, vol. 21, no. 6. Public Library of Science, p. e3002146, 2023.","ista":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. 2023. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 21(6), e3002146.","chicago":"Shamipour, Shayan, Laura Hofmann, Irene Steccari, Roland Kardos, and Carl-Philipp J Heisenberg. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” <i>PLoS Biology</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pbio.3002146\">https://doi.org/10.1371/journal.pbio.3002146</a>.","mla":"Shamipour, Shayan, et al. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” <i>PLoS Biology</i>, vol. 21, no. 6, Public Library of Science, 2023, p. e3002146, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002146\">10.1371/journal.pbio.3002146</a>.","short":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, C.-P.J. Heisenberg, PLoS Biology 21 (2023) e3002146."},"status":"public","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","department":[{"_id":"CaHe"}],"publication_status":"published","ec_funded":1,"doi":"10.1371/journal.pbio.3002146","day":"08","month":"06","corr_author":"1","type":"journal_article","date_updated":"2025-04-14T07:46:59Z","file_date_updated":"2023-07-18T07:59:58Z","date_created":"2023-07-16T22:01:09Z","publication":"PLoS Biology","publication_identifier":{"eissn":["1545-7885"]},"abstract":[{"text":"Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation.","lang":"eng"}],"oa":1,"has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes","article_type":"original"},{"pmid":1,"date_published":"2023-06-08T00:00:00Z","article_processing_charge":"No","publisher":"Public Library of Science","ddc":["570"],"year":"2023","article_number":"e1011104","external_id":{"isi":["001003410200003"],"pmid":["37289753"]},"_id":"13230","issue":"6","isi":1,"author":[{"full_name":"Charlton, Julie A.","last_name":"Charlton","first_name":"Julie A."},{"last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F"},{"first_name":"Yoon H.","full_name":"Bai, Yoon H.","last_name":"Bai"},{"first_name":"Ann M.","full_name":"Hermundstad, Ann M.","last_name":"Hermundstad"},{"first_name":"Robbe L.T.","last_name":"Goris","full_name":"Goris, Robbe L.T."}],"intvolume":"        19","volume":19,"month":"06","publication_status":"published","department":[{"_id":"MaJö"}],"day":"08","doi":"10.1371/journal.pcbi.1011104","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ama":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. Environmental dynamics shape perceptual decision bias. <i>PLoS Computational Biology</i>. 2023;19(6). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">10.1371/journal.pcbi.1011104</a>","apa":"Charlton, J. A., Mlynarski, W. F., Bai, Y. H., Hermundstad, A. M., &#38; Goris, R. L. T. (2023). Environmental dynamics shape perceptual decision bias. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">https://doi.org/10.1371/journal.pcbi.1011104</a>","ieee":"J. A. Charlton, W. F. Mlynarski, Y. H. Bai, A. M. Hermundstad, and R. L. T. Goris, “Environmental dynamics shape perceptual decision bias,” <i>PLoS Computational Biology</i>, vol. 19, no. 6. Public Library of Science, 2023.","ista":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. 2023. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 19(6), e1011104.","mla":"Charlton, Julie A., et al. “Environmental Dynamics Shape Perceptual Decision Bias.” <i>PLoS Computational Biology</i>, vol. 19, no. 6, e1011104, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">10.1371/journal.pcbi.1011104</a>.","short":"J.A. Charlton, W.F. Mlynarski, Y.H. Bai, A.M. Hermundstad, R.L.T. Goris, PLoS Computational Biology 19 (2023).","chicago":"Charlton, Julie A., Wiktor F Mlynarski, Yoon H. Bai, Ann M. Hermundstad, and Robbe L.T. Goris. “Environmental Dynamics Shape Perceptual Decision Bias.” <i>PLoS Computational Biology</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">https://doi.org/10.1371/journal.pcbi.1011104</a>."},"file":[{"content_type":"application/pdf","checksum":"800761fa2c647fabd6ad034589bc526e","relation":"main_file","access_level":"open_access","success":1,"date_updated":"2023-07-18T08:07:59Z","creator":"dernst","file_size":2281868,"date_created":"2023-07-18T08:07:59Z","file_id":"13247","file_name":"2023_PloSCompBio_Charlton.pdf"}],"acknowledgement":"The authors thank Corey Ziemba and Zoe Boundy-Singer for valuable discussion and feedback.","scopus_import":"1","article_type":"original","title":"Environmental dynamics shape perceptual decision bias","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","oa":1,"abstract":[{"text":"To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals.","lang":"eng"}],"publication":"PLoS Computational Biology","date_created":"2023-07-16T22:01:09Z","publication_identifier":{"eissn":["1553-7358"]},"file_date_updated":"2023-07-18T08:07:59Z","type":"journal_article","date_updated":"2023-08-02T06:33:50Z"},{"acknowledgement":"We want to thank P. Sperling, B. Witte, M. French, G. Röpke, H. J. Lee and A. Cangi for many helpful discussions. M. S. and R. R. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) within the Research Unit FOR 2440. All simulations and analyses were performed at the North-German Supercomputing Alliance (HLRN) and the ITMZ of the University of Rostock. M. B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Sklodowska-Curie actions (xICE grant 894725) and the\r\nNOMIS foundation. The work of T. D. was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344.","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.01545","open_access":"1"}],"status":"public","citation":{"mla":"Schörner, Maximilian, et al. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” <i>Physical Review E</i>, vol. 107, no. 6, 065207, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">10.1103/PhysRevE.107.065207</a>.","chicago":"Schörner, Maximilian, Mandy Bethkenhagen, Tilo Döppner, Dominik Kraus, Luke B. Fletcher, Siegfried H. Glenzer, and Ronald Redmer. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">https://doi.org/10.1103/PhysRevE.107.065207</a>.","short":"M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer, R. Redmer, Physical Review E 107 (2023).","ista":"Schörner M, Bethkenhagen M, Döppner T, Kraus D, Fletcher LB, Glenzer SH, Redmer R. 2023. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 107(6), 065207.","ieee":"M. Schörner <i>et al.</i>, “X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula,” <i>Physical Review E</i>, vol. 107, no. 6. American Physical Society, 2023.","apa":"Schörner, M., Bethkenhagen, M., Döppner, T., Kraus, D., Fletcher, L. B., Glenzer, S. H., &#38; Redmer, R. (2023). X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">https://doi.org/10.1103/PhysRevE.107.065207</a>","ama":"Schörner M, Bethkenhagen M, Döppner T, et al. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. <i>Physical Review E</i>. 2023;107(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">10.1103/PhysRevE.107.065207</a>"},"arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Preprint","month":"06","day":"14","doi":"10.1103/PhysRevE.107.065207","department":[{"_id":"BiCh"}],"publication_status":"published","date_updated":"2025-03-06T14:02:33Z","type":"journal_article","abstract":[{"text":"We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles.","lang":"eng"}],"publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"publication":"Physical Review E","date_created":"2023-07-16T22:01:10Z","oa":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula","article_number":"065207","year":"2023","publisher":"American Physical Society","article_processing_charge":"No","date_published":"2023-06-14T00:00:00Z","pmid":1,"volume":107,"intvolume":"       107","isi":1,"author":[{"first_name":"Maximilian","full_name":"Schörner, Maximilian","last_name":"Schörner"},{"last_name":"Bethkenhagen","full_name":"Bethkenhagen, Mandy","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","orcid":"0000-0002-1838-2129","first_name":"Mandy"},{"last_name":"Döppner","full_name":"Döppner, Tilo","first_name":"Tilo"},{"last_name":"Kraus","full_name":"Kraus, Dominik","first_name":"Dominik"},{"first_name":"Luke B.","full_name":"Fletcher, Luke B.","last_name":"Fletcher"},{"first_name":"Siegfried H.","last_name":"Glenzer","full_name":"Glenzer, Siegfried H."},{"first_name":"Ronald","last_name":"Redmer","full_name":"Redmer, Ronald"}],"issue":"6","_id":"13231","external_id":{"isi":["001020265000002"],"arxiv":["2301.01545"],"pmid":["37464593"]}},{"article_number":"1014","year":"2023","ddc":["570"],"publisher":"MDPI","article_processing_charge":"No","date_published":"2023-06-01T00:00:00Z","pmid":1,"volume":11,"intvolume":"        11","author":[{"full_name":"Dormeshkin, Dmitri","last_name":"Dormeshkin","first_name":"Dmitri"},{"first_name":"Mikalai","last_name":"Katsin","full_name":"Katsin, Mikalai"},{"last_name":"Stegantseva","full_name":"Stegantseva, Maria","first_name":"Maria"},{"first_name":"Sergey","full_name":"Golenchenko, Sergey","last_name":"Golenchenko"},{"full_name":"Shapira, Michail","last_name":"Shapira","first_name":"Michail"},{"first_name":"Simon","last_name":"Dubovik","full_name":"Dubovik, Simon"},{"full_name":"Lutskovich, Dzmitry","last_name":"Lutskovich","first_name":"Dzmitry"},{"last_name":"Kavaleuski","full_name":"Kavaleuski, Anton","id":"62304f89-eb97-11eb-a6c2-8903dd183976","orcid":"0000-0003-2091-526X","first_name":"Anton"},{"full_name":"Meleshko, Alexander","last_name":"Meleshko","first_name":"Alexander"}],"isi":1,"_id":"13232","issue":"6","external_id":{"pmid":["37376403"],"isi":["001017740000001"]},"acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication. The authors express their gratitude to the Institute of Physiology of the National Academy of Sciences of Belarus for providing assistance in keeping laboratory animals.","scopus_import":"1","citation":{"mla":"Dormeshkin, Dmitri, et al. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” <i>Vaccines</i>, vol. 11, no. 6, 1014, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/vaccines11061014\">10.3390/vaccines11061014</a>.","chicago":"Dormeshkin, Dmitri, Mikalai Katsin, Maria Stegantseva, Sergey Golenchenko, Michail Shapira, Simon Dubovik, Dzmitry Lutskovich, Anton Kavaleuski, and Alexander Meleshko. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” <i>Vaccines</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/vaccines11061014\">https://doi.org/10.3390/vaccines11061014</a>.","short":"D. Dormeshkin, M. Katsin, M. Stegantseva, S. Golenchenko, M. Shapira, S. Dubovik, D. Lutskovich, A. Kavaleuski, A. Meleshko, Vaccines 11 (2023).","ista":"Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S, Lutskovich D, Kavaleuski A, Meleshko A. 2023. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 11(6), 1014.","ieee":"D. Dormeshkin <i>et al.</i>, “Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein,” <i>Vaccines</i>, vol. 11, no. 6. MDPI, 2023.","apa":"Dormeshkin, D., Katsin, M., Stegantseva, M., Golenchenko, S., Shapira, M., Dubovik, S., … Meleshko, A. (2023). Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. <i>Vaccines</i>. MDPI. <a href=\"https://doi.org/10.3390/vaccines11061014\">https://doi.org/10.3390/vaccines11061014</a>","ama":"Dormeshkin D, Katsin M, Stegantseva M, et al. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. <i>Vaccines</i>. 2023;11(6). doi:<a href=\"https://doi.org/10.3390/vaccines11061014\">10.3390/vaccines11061014</a>"},"file":[{"access_level":"open_access","success":1,"checksum":"8f484c0f30f8699c589b1c29a0fd7d7f","relation":"main_file","content_type":"application/pdf","file_name":"2023_Vaccines_Dormeshkin.pdf","file_id":"13244","date_created":"2023-07-18T07:25:43Z","creator":"dernst","file_size":2339746,"date_updated":"2023-07-18T07:25:43Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","doi":"10.3390/vaccines11061014","day":"01","department":[{"_id":"LeSa"}],"publication_status":"published","month":"06","date_updated":"2025-04-23T13:01:23Z","type":"journal_article","file_date_updated":"2023-07-18T07:25:43Z","publication_identifier":{"eissn":["2076-393X"]},"publication":"Vaccines","date_created":"2023-07-16T22:01:10Z","abstract":[{"lang":"eng","text":"The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study."}],"has_accepted_license":"1","oa":1,"title":"Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original"},{"article_type":"letter_note","title":"Finite-range bias in fitting three-body loss to the zero-range model","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"abstract":[{"lang":"eng","text":"We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters."}],"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"date_created":"2023-07-16T22:01:10Z","publication":"Physical Review A","date_updated":"2025-04-14T07:48:53Z","type":"journal_article","corr_author":"1","month":"06","doi":"10.1103/PhysRevA.107.L061304","ec_funded":1,"day":"20","department":[{"_id":"MiLe"},{"_id":"OnHo"}],"publication_status":"published","arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Preprint","status":"public","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2302.01022","open_access":"1"}],"citation":{"apa":"Agafonova, S., Lemeshko, M., &#38; Volosniev, A. (2023). Finite-range bias in fitting three-body loss to the zero-range model. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">https://doi.org/10.1103/PhysRevA.107.L061304</a>","ama":"Agafonova S, Lemeshko M, Volosniev A. Finite-range bias in fitting three-body loss to the zero-range model. <i>Physical Review A</i>. 2023;107(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">10.1103/PhysRevA.107.L061304</a>","ieee":"S. Agafonova, M. Lemeshko, and A. Volosniev, “Finite-range bias in fitting three-body loss to the zero-range model,” <i>Physical Review A</i>, vol. 107, no. 6. American Physical Society, 2023.","ista":"Agafonova S, Lemeshko M, Volosniev A. 2023. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 107(6), L061304.","mla":"Agafonova, Sofya, et al. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” <i>Physical Review A</i>, vol. 107, no. 6, L061304, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">10.1103/PhysRevA.107.L061304</a>.","short":"S. Agafonova, M. Lemeshko, A. Volosniev, Physical Review A 107 (2023).","chicago":"Agafonova, Sofya, Mikhail Lemeshko, and Artem Volosniev. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">https://doi.org/10.1103/PhysRevA.107.L061304</a>."},"acknowledgement":"We thank Jan Arlt, Hans-Werner Hammer, and Karsten Riisager for useful discussions. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","scopus_import":"1","issue":"6","_id":"13233","external_id":{"arxiv":["2302.01022"],"isi":["001019748000005"]},"isi":1,"author":[{"first_name":"Sofya","orcid":"0000-0003-0582-2946","last_name":"Agafonova","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","full_name":"Agafonova, Sofya"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"},{"last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","first_name":"Artem","orcid":"0000-0003-0393-5525"}],"intvolume":"       107","volume":107,"date_published":"2023-06-20T00:00:00Z","article_processing_charge":"No","publisher":"American Physical Society","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"}],"article_number":"L061304","year":"2023"},{"isi":1,"author":[{"orcid":"0000-0001-8974-2542","first_name":"Konstantin","last_name":"Kueffner","full_name":"Kueffner, Konstantin","id":"8121a2d0-dc85-11ea-9058-af578f3b4515"},{"first_name":"Anna","last_name":"Lukina","full_name":"Lukina, Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425"},{"first_name":"Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","full_name":"Schilling, Christian","last_name":"Schilling"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"_id":"13234","external_id":{"isi":["001020160000001"],"arxiv":["2009.06429"]},"volume":25,"intvolume":"        25","article_processing_charge":"Yes (in subscription journal)","page":"575-592","date_published":"2023-08-01T00:00:00Z","year":"2023","publisher":"Springer Nature","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"ddc":["000"],"has_accepted_license":"1","oa":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Into the unknown: Active monitoring of neural networks (extended version)","file_date_updated":"2024-01-30T12:06:07Z","date_updated":"2025-04-15T06:55:00Z","type":"journal_article","abstract":[{"text":"Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. We consider the problem of monitoring the classification decisions of neural networks in the presence of novel classes. For this purpose, we generalize our recently proposed abstraction-based monitor from binary output to real-valued quantitative output. This quantitative output enables new applications, two of which we investigate in the paper. As our first application, we introduce an algorithmic framework for active monitoring of a neural network, which allows us to learn new classes dynamically and yet maintain high monitoring performance. As our second application, we present an offline procedure to retrain the neural network to improve the monitor’s detection performance without deteriorating the network’s classification accuracy. Our experimental evaluation demonstrates both the benefits of our active monitoring framework in dynamic scenarios and the effectiveness of the retraining procedure.","lang":"eng"}],"publication_identifier":{"issn":["1433-2779"],"eissn":["1433-2787"]},"date_created":"2023-07-16T22:01:11Z","publication":"International Journal on Software Tools for Technology Transfer","arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","corr_author":"1","month":"08","related_material":{"record":[{"relation":"shorter_version","id":"10206","status":"public"}]},"ec_funded":1,"day":"01","doi":"10.1007/s10009-023-00711-4","department":[{"_id":"ToHe"}],"publication_status":"published","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, by DIREC - Digital Research Centre Denmark, and by the Villum Investigator Grant S4OS.","scopus_import":"1","status":"public","file":[{"date_created":"2024-01-30T12:06:07Z","file_id":"14903","file_name":"2023_JourSoftwareTools_Kueffner.pdf","date_updated":"2024-01-30T12:06:07Z","creator":"dernst","file_size":13387667,"access_level":"open_access","success":1,"content_type":"application/pdf","checksum":"3c4b347f39412a76872f9a6f30101f94","relation":"main_file"}],"citation":{"chicago":"Kueffner, Konstantin, Anna Lukina, Christian Schilling, and Thomas A Henzinger. “Into the Unknown: Active Monitoring of Neural Networks (Extended Version).” <i>International Journal on Software Tools for Technology Transfer</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s10009-023-00711-4\">https://doi.org/10.1007/s10009-023-00711-4</a>.","mla":"Kueffner, Konstantin, et al. “Into the Unknown: Active Monitoring of Neural Networks (Extended Version).” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 25, Springer Nature, 2023, pp. 575–92, doi:<a href=\"https://doi.org/10.1007/s10009-023-00711-4\">10.1007/s10009-023-00711-4</a>.","short":"K. Kueffner, A. Lukina, C. Schilling, T.A. Henzinger, International Journal on Software Tools for Technology Transfer 25 (2023) 575–592.","ista":"Kueffner K, Lukina A, Schilling C, Henzinger TA. 2023. Into the unknown: Active monitoring of neural networks (extended version). International Journal on Software Tools for Technology Transfer. 25, 575–592.","ieee":"K. Kueffner, A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: Active monitoring of neural networks (extended version),” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 25. Springer Nature, pp. 575–592, 2023.","apa":"Kueffner, K., Lukina, A., Schilling, C., &#38; Henzinger, T. A. (2023). Into the unknown: Active monitoring of neural networks (extended version). <i>International Journal on Software Tools for Technology Transfer</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10009-023-00711-4\">https://doi.org/10.1007/s10009-023-00711-4</a>","ama":"Kueffner K, Lukina A, Schilling C, Henzinger TA. Into the unknown: Active monitoring of neural networks (extended version). <i>International Journal on Software Tools for Technology Transfer</i>. 2023;25:575-592. doi:<a href=\"https://doi.org/10.1007/s10009-023-00711-4\">10.1007/s10009-023-00711-4</a>"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"}},{"author":[{"first_name":"Da Wei","full_name":"Zheng, Da Wei","last_name":"Zheng"},{"orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"isi":1,"_id":"13236","external_id":{"isi":["001281059600032"],"arxiv":["2301.09217"]},"alternative_title":["LNCS"],"volume":13904,"intvolume":"     13904","page":"453-465","article_processing_charge":"No","date_published":"2023-05-22T00:00:00Z","year":"2023","publisher":"Springer Nature","project":[{"name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775"}],"oa":1,"conference":{"end_date":"2023-06-23","location":"Madison, WI, United States","start_date":"2023-06-21","name":"IPCO: Integer Programming and Combinatorial Optimization"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Multiplicative auction algorithm for approximate maximum weight bipartite matching","date_updated":"2025-09-09T12:39:59Z","type":"conference","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031327254"],"issn":["0302-9743"]},"publication":"International Conference on Integer Programming and Combinatorial Optimization","date_created":"2023-07-16T22:01:11Z","abstract":[{"lang":"eng","text":"We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1−ε)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time O(mε−1log(ε−1)), matching the running time of the linear-time approximation algorithm of Duan and Pettie [JACM ’14]. Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1−ε)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is O(mε−1log(ε−1)), where m is the sum of the number of initially existing and inserted edges."}],"language":[{"iso":"eng"}],"oa_version":"Preprint","quality_controlled":"1","arxiv":1,"doi":"10.1007/978-3-031-32726-1_32","day":"22","ec_funded":1,"publication_status":"published","department":[{"_id":"MoHe"}],"month":"05","related_material":{"record":[{"status":"public","relation":"later_version","id":"15121"}]},"acknowledgement":"The first author thanks to Chandra Chekuri for useful discussions about this paper. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","scopus_import":"1","citation":{"chicago":"Zheng, Da Wei, and Monika Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” In <i>International Conference on Integer Programming and Combinatorial Optimization</i>, 13904:453–65. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-32726-1_32\">https://doi.org/10.1007/978-3-031-32726-1_32</a>.","mla":"Zheng, Da Wei, and Monika Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” <i>International Conference on Integer Programming and Combinatorial Optimization</i>, vol. 13904, Springer Nature, 2023, pp. 453–65, doi:<a href=\"https://doi.org/10.1007/978-3-031-32726-1_32\">10.1007/978-3-031-32726-1_32</a>.","short":"D.W. Zheng, M. Henzinger, in:, International Conference on Integer Programming and Combinatorial Optimization, Springer Nature, 2023, pp. 453–465.","ista":"Zheng DW, Henzinger M. 2023. Multiplicative auction algorithm for approximate maximum weight bipartite matching. International Conference on Integer Programming and Combinatorial Optimization. IPCO: Integer Programming and Combinatorial Optimization, LNCS, vol. 13904, 453–465.","ieee":"D. W. Zheng and M. Henzinger, “Multiplicative auction algorithm for approximate maximum weight bipartite matching,” in <i>International Conference on Integer Programming and Combinatorial Optimization</i>, Madison, WI, United States, 2023, vol. 13904, pp. 453–465.","apa":"Zheng, D. W., &#38; Henzinger, M. (2023). Multiplicative auction algorithm for approximate maximum weight bipartite matching. In <i>International Conference on Integer Programming and Combinatorial Optimization</i> (Vol. 13904, pp. 453–465). Madison, WI, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-32726-1_32\">https://doi.org/10.1007/978-3-031-32726-1_32</a>","ama":"Zheng DW, Henzinger M. Multiplicative auction algorithm for approximate maximum weight bipartite matching. In: <i>International Conference on Integer Programming and Combinatorial Optimization</i>. Vol 13904. Springer Nature; 2023:453-465. doi:<a href=\"https://doi.org/10.1007/978-3-031-32726-1_32\">10.1007/978-3-031-32726-1_32</a>"},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.09217","open_access":"1"}],"status":"public"},{"file_date_updated":"2023-07-19T06:55:39Z","type":"journal_article","date_updated":"2025-04-23T13:01:50Z","abstract":[{"lang":"eng","text":"A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy."}],"date_created":"2023-07-18T11:13:17Z","publication":"The Journal of Physical Chemistry Letters","publication_identifier":{"eissn":["1948-7185"]},"keyword":["General Materials Science","Physical and Theoretical Chemistry"],"oa":1,"has_accepted_license":"1","article_type":"original","title":"Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","acknowledgement":"We thank Bingqing Cheng and Hong-Zhou Ye for valuable discussions; Y.W.’s work at IST Austria was supported through ISTernship summer internship program funded by OeADGmbH; D.L. and Z.A. acknowledge support by IST Austria (ISTA); M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).\r\nA.A.Z. and O.M.B. acknowledge support by KAUST.","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"checksum":"c0c040063f06a51b9c463adc504f1a23","relation":"main_file","content_type":"application/pdf","access_level":"open_access","success":1,"creator":"dernst","file_size":2121252,"date_updated":"2023-07-19T06:55:39Z","file_name":"2023_JourPhysChemistry_Wei.pdf","date_created":"2023-07-19T06:55:39Z","file_id":"13253"}],"citation":{"apa":"Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., Lemeshko, M., &#38; Alpichshev, Z. (2023). Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">https://doi.org/10.1021/acs.jpclett.3c01158</a>","ama":"Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. <i>The Journal of Physical Chemistry Letters</i>. 2023;14(27):6309-6314. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">10.1021/acs.jpclett.3c01158</a>","ieee":"Y. Wei <i>et al.</i>, “Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites,” <i>The Journal of Physical Chemistry Letters</i>, vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023.","ista":"Wei Y, Volosniev A, Lorenc D, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 14(27), 6309–6314.","mla":"Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” <i>The Journal of Physical Chemistry Letters</i>, vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">10.1021/acs.jpclett.3c01158</a>.","short":"Y. Wei, A. Volosniev, D. Lorenc, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, The Journal of Physical Chemistry Letters 14 (2023) 6309–6314.","chicago":"Wei, Yujing, Artem Volosniev, Dusan Lorenc, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">https://doi.org/10.1021/acs.jpclett.3c01158</a>."},"arxiv":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","corr_author":"1","month":"07","department":[{"_id":"MiLe"},{"_id":"ZhAl"}],"publication_status":"published","doi":"10.1021/acs.jpclett.3c01158","day":"05","ec_funded":1,"volume":14,"intvolume":"        14","isi":1,"author":[{"last_name":"Wei","full_name":"Wei, Yujing","id":"0c5ff007-2600-11ee-b896-98bd8d663294","orcid":"0000-0001-8913-9719","first_name":"Yujing"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","orcid":"0000-0003-0393-5525","first_name":"Artem"},{"full_name":"Lorenc, Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","last_name":"Lorenc","first_name":"Dusan"},{"full_name":"Zhumekenov, Ayan A.","last_name":"Zhumekenov","first_name":"Ayan A."},{"full_name":"Bakr, Osman M.","last_name":"Bakr","first_name":"Osman M."},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"first_name":"Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev"}],"_id":"13251","external_id":{"arxiv":["2304.14198"],"isi":["001022811500001"],"pmid":["37405449"]},"issue":"27","year":"2023","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"publisher":"American Chemical Society","ddc":["530"],"article_processing_charge":"Yes (via OA deal)","page":"6309-6314","date_published":"2023-07-05T00:00:00Z","pmid":1},{"date_published":"2023-07-08T00:00:00Z","article_processing_charge":"Yes","publisher":"Springer Nature","ddc":["550"],"article_number":"82","year":"2023","_id":"13256","external_id":{"isi":["001024920300002"]},"author":[{"last_name":"Goswami","full_name":"Goswami, Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","first_name":"Bidyut B"},{"full_name":"An, Soon Il","last_name":"An","first_name":"Soon Il"}],"isi":1,"intvolume":"         6","volume":6,"month":"07","doi":"10.1038/s41612-023-00411-5","day":"08","publication_status":"published","department":[{"_id":"CaMu"}],"quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","status":"public","file":[{"success":1,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"e9967d436a83b8ffcc6f58782e1f7500","file_id":"13326","date_created":"2023-07-31T08:00:01Z","file_name":"2023_npjclimate_Goswami.pdf","date_updated":"2023-07-31T08:00:01Z","file_size":1750712,"creator":"dernst"}],"citation":{"ieee":"B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection in a warming climate,” <i>npj Climate and Atmospheric Science</i>, vol. 6. Springer Nature, 2023.","apa":"GOSWAMI, B. B., &#38; An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection in a warming climate. <i>Npj Climate and Atmospheric Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41612-023-00411-5\">https://doi.org/10.1038/s41612-023-00411-5</a>","ama":"GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming climate. <i>npj Climate and Atmospheric Science</i>. 2023;6. doi:<a href=\"https://doi.org/10.1038/s41612-023-00411-5\">10.1038/s41612-023-00411-5</a>","mla":"GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” <i>Npj Climate and Atmospheric Science</i>, vol. 6, 82, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41612-023-00411-5\">10.1038/s41612-023-00411-5</a>.","chicago":"GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” <i>Npj Climate and Atmospheric Science</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41612-023-00411-5\">https://doi.org/10.1038/s41612-023-00411-5</a>.","short":"B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023).","ista":"GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 6, 82."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"scopus_import":"1","acknowledgement":"This work was supported by National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of the Korea Meteorological Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET), respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science and Technology, Pohang, South Korea for the model simulations.","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"An assessment of the ENSO-monsoon teleconnection in a warming climate","oa":1,"has_accepted_license":"1","abstract":[{"text":"The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate.","lang":"eng"}],"publication_identifier":{"eissn":["2397-3722"]},"date_created":"2023-07-23T22:01:10Z","publication":"npj Climate and Atmospheric Science","file_date_updated":"2023-07-31T08:00:01Z","date_updated":"2023-08-02T06:38:07Z","type":"journal_article"},{"author":[{"full_name":"Shekhter, A.","last_name":"Shekhter","first_name":"A."},{"first_name":"R. D.","full_name":"Mcdonald, R. D.","last_name":"Mcdonald"},{"first_name":"B. J.","full_name":"Ramshaw, B. J.","last_name":"Ramshaw"},{"last_name":"Modic","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","full_name":"Modic, Kimberly A","first_name":"Kimberly A","orcid":"0000-0001-9760-3147"}],"isi":1,"external_id":{"arxiv":["2208.10038"],"isi":["001062708600002"]},"_id":"13257","issue":"3","volume":108,"intvolume":"       108","article_processing_charge":"No","date_published":"2023-07-15T00:00:00Z","year":"2023","article_number":"035111","publisher":"American Physical Society","oa":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Magnetotropic susceptibility","type":"journal_article","date_updated":"2023-12-13T11:58:57Z","abstract":[{"lang":"eng","text":"The magnetotropic susceptibility is the thermodynamic coefficient associated with the rotational anisotropy of the free energy in an external magnetic field and is closely related to the magnetic susceptibility. It emerges naturally in frequency-shift measurements of oscillating mechanical cantilevers, which are becoming an increasingly important tool in the quantitative study of the thermodynamics of modern condensed-matter systems. Here we discuss the basic properties of the magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift measurements, as well as to the interpretation of those experiments in terms of the intrinsic properties of the system under study."}],"date_created":"2023-07-23T22:01:10Z","publication":"Physical Review B","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Preprint","month":"07","publication_status":"published","department":[{"_id":"KiMo"}],"day":"15","doi":"10.1103/PhysRevB.108.035111","acknowledgement":"We thank Aharon Kapitulnik, Philip Moll, and Andreas Rydh for illuminating discussions. The work at the Los Alamos National Laboratory is supported by National Science Foundation Cooperative Agreements No. DMR-1157490 and No. DMR-1644779, the state of Florida, and the U.S. Department of Energy. A.S. acknowledges support from the DOE/BES Science of 100T grant. B.J.R. acknowledges funding from the National Science Foundation under Grant No.\r\nDMR-1752784.","scopus_import":"1","status":"public","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2208.10038","open_access":"1"}],"citation":{"ista":"Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. 2023. Magnetotropic susceptibility. Physical Review B. 108(3), 035111.","mla":"Shekhter, A., et al. “Magnetotropic Susceptibility.” <i>Physical Review B</i>, vol. 108, no. 3, 035111, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">10.1103/PhysRevB.108.035111</a>.","short":"A. Shekhter, R.D. Mcdonald, B.J. Ramshaw, K.A. Modic, Physical Review B 108 (2023).","chicago":"Shekhter, A., R. D. Mcdonald, B. J. Ramshaw, and Kimberly A Modic. “Magnetotropic Susceptibility.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">https://doi.org/10.1103/PhysRevB.108.035111</a>.","ama":"Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. Magnetotropic susceptibility. <i>Physical Review B</i>. 2023;108(3). doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">10.1103/PhysRevB.108.035111</a>","apa":"Shekhter, A., Mcdonald, R. D., Ramshaw, B. J., &#38; Modic, K. A. (2023). Magnetotropic susceptibility. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">https://doi.org/10.1103/PhysRevB.108.035111</a>","ieee":"A. Shekhter, R. D. Mcdonald, B. J. Ramshaw, and K. A. Modic, “Magnetotropic susceptibility,” <i>Physical Review B</i>, vol. 108, no. 3. American Physical Society, 2023."}},{"pmid":1,"date_published":"2023-07-12T00:00:00Z","article_processing_charge":"Yes","publisher":"Springer Nature","project":[{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"ddc":["000"],"article_number":"4153","year":"2023","_id":"13258","external_id":{"isi":["001029450400031"],"pmid":["37438341"]},"author":[{"first_name":"Maria","full_name":"Kleshnina, Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","last_name":"Kleshnina"},{"orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Simsa, Stepan","id":"409d615c-2f95-11ee-b934-90a352102c1e","last_name":"Simsa","orcid":"0000-0001-6687-1210","first_name":"Stepan"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"isi":1,"intvolume":"        14","volume":14,"corr_author":"1","month":"07","related_material":{"record":[{"status":"public","id":"13336","relation":"research_data"}]},"ec_funded":1,"doi":"10.1038/s41467-023-39625-9","day":"12","department":[{"_id":"KrCh"}],"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"status":"public","citation":{"apa":"Kleshnina, M., Hilbe, C., Simsa, S., Chatterjee, K., &#38; Nowak, M. A. (2023). The effect of environmental information on evolution of cooperation in stochastic games. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-39625-9\">https://doi.org/10.1038/s41467-023-39625-9</a>","ama":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. The effect of environmental information on evolution of cooperation in stochastic games. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39625-9\">10.1038/s41467-023-39625-9</a>","ieee":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, and M. A. Nowak, “The effect of environmental information on evolution of cooperation in stochastic games,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. 2023. The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. 14, 4153.","mla":"Kleshnina, Maria, et al. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” <i>Nature Communications</i>, vol. 14, 4153, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39625-9\">10.1038/s41467-023-39625-9</a>.","short":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, M.A. Nowak, Nature Communications 14 (2023).","chicago":"Kleshnina, Maria, Christian Hilbe, Stepan Simsa, Krishnendu Chatterjee, and Martin A. Nowak. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39625-9\">https://doi.org/10.1038/s41467-023-39625-9</a>."},"file":[{"access_level":"open_access","success":1,"content_type":"application/pdf","checksum":"5aceefdfe76686267b93ae4fe81899f1","relation":"main_file","date_created":"2023-07-31T11:32:36Z","file_id":"13337","file_name":"2023_NatureComm_Kleshnina.pdf","date_updated":"2023-07-31T11:32:36Z","creator":"dernst","file_size":1601682}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir programme, ANR-17-EURE-0010) (to M.K.).","scopus_import":"1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The effect of environmental information on evolution of cooperation in stochastic games","oa":1,"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation."}],"publication_identifier":{"eissn":["2041-1723"]},"date_created":"2023-07-23T22:01:11Z","publication":"Nature Communications","file_date_updated":"2023-07-31T11:32:36Z","date_updated":"2025-04-14T07:43:55Z","type":"journal_article"},{"article_type":"original","title":"WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"has_accepted_license":"1","abstract":[{"text":"Plants can regenerate their bodies via de novo establishment of shoot apical meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells is eventually specified into SAMs but the molecular mechanisms underlying fate specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark of SAM fate acquisition. Here, we show that a WUS paralog, WUSCHEL-RELATED HOMEOBOX 13 (WOX13), negatively regulates SAM formation from callus in Arabidopsis thaliana. WOX13 promotes non-meristematic cell fate via transcriptional repression of WUS and other SAM regulators and activation of cell wall modifiers. Our Quartz-Seq2–based single cell transcriptome revealed that WOX13 plays key roles in determining cellular identity of callus cell population. We propose that reciprocal inhibition between WUS and WOX13 mediates critical cell fate determination in pluripotent cell population, which has a major impact on regeneration efficiency.","lang":"eng"}],"publication":"Science Advances","date_created":"2023-07-23T22:01:11Z","publication_identifier":{"eissn":["2375-2548"]},"file_date_updated":"2023-08-01T06:40:35Z","type":"journal_article","date_updated":"2023-12-13T11:59:29Z","month":"07","publication_status":"published","doi":"10.1126/sciadv.adg6983","day":"07","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"file_name":"2023_ScienceAdvance_Ogura.pdf","file_id":"13338","date_created":"2023-08-01T06:40:35Z","file_size":1759993,"creator":"dernst","date_updated":"2023-08-01T06:40:35Z","success":1,"access_level":"open_access","relation":"main_file","checksum":"f59217e1083767777318b5d0cc5e141d","content_type":"application/pdf"}],"citation":{"ista":"Ogura N, Sasagawa Y, Ito T, Tameshige T, Kawai S, Sano M, Doll Y, Iwase A, Kawamura A, Suzuki T, Nikaido I, Sugimoto K, Ikeuchi M. 2023. WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. Science Advances. 9(27), eadg6983.","chicago":"Ogura, Nao, Yohei Sasagawa, Tasuku Ito, Toshiaki Tameshige, Satomi Kawai, Masaki Sano, Yuki Doll, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo Shoot Regeneration via Cell Fate Control of Pluripotent Callus.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.adg6983\">https://doi.org/10.1126/sciadv.adg6983</a>.","short":"N. Ogura, Y. Sasagawa, T. Ito, T. Tameshige, S. Kawai, M. Sano, Y. Doll, A. Iwase, A. Kawamura, T. Suzuki, I. Nikaido, K. Sugimoto, M. Ikeuchi, Science Advances 9 (2023) eadg6983.","mla":"Ogura, Nao, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo Shoot Regeneration via Cell Fate Control of Pluripotent Callus.” <i>Science Advances</i>, vol. 9, no. 27, American Association for the Advancement of Science, 2023, p. eadg6983, doi:<a href=\"https://doi.org/10.1126/sciadv.adg6983\">10.1126/sciadv.adg6983</a>.","ama":"Ogura N, Sasagawa Y, Ito T, et al. WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. <i>Science Advances</i>. 2023;9(27):eadg6983. doi:<a href=\"https://doi.org/10.1126/sciadv.adg6983\">10.1126/sciadv.adg6983</a>","apa":"Ogura, N., Sasagawa, Y., Ito, T., Tameshige, T., Kawai, S., Sano, M., … Ikeuchi, M. (2023). WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adg6983\">https://doi.org/10.1126/sciadv.adg6983</a>","ieee":"N. Ogura <i>et al.</i>, “WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus,” <i>Science Advances</i>, vol. 9, no. 27. American Association for the Advancement of Science, p. eadg6983, 2023."},"scopus_import":"1","acknowledgement":"Wethank Y.Iwayama, K.Ohtawa, K.Fukumoto,andN. Mataga (RIKENRRD) for technical assistance in Quartz-Seq2analyses; M. Mouri(RIKENCSRS)for technical support with plasmid construction and transactivation assay; Y. Ikeda (NAIST) for technical support with tissue culture; and A. Furuta for technical support in bulk RNA-seq analysis. We also thank the Single-cell Omics Laboratory for technical consultation in scRNA-seq analyses, the members of the Laboratory for Bioinformatics Research at the RIKEN Center for Biosystems Dynamics Research, and A. Matsushima and T. Ichikawa for IT infrastructure management. This work was supported by JSPS KAKENHI(17K15146,19H05670,20K06712,20H04894,20H05431,and 22H04713 to M.I. and 20H03284 and 20H05911 to K.S.), by the JST FOREST Program (JPMJFR214H to M.I.), by The Naito Foundation to M.I.; by Takeda Science Foundation to M.I,and by the Shiseido Female Researcher Science Grant to M.I. This work was partially supported by RIKENE pigenome Control Program, Medical Research Center Initiative for High Depth Omics, and JST CREST(JPMJCR16G3and JPMJCR1926)to I.N.","external_id":{"pmid":["37418524"],"isi":["001030983100012"]},"_id":"13259","issue":"27","isi":1,"author":[{"last_name":"Ogura","full_name":"Ogura, Nao","first_name":"Nao"},{"first_name":"Yohei","last_name":"Sasagawa","full_name":"Sasagawa, Yohei"},{"last_name":"Ito","id":"d5a17a4a-e534-11eb-93ec-91fa2aa9bd57","full_name":"Ito, Tasuku","first_name":"Tasuku","orcid":"0000-0002-2482-9089"},{"last_name":"Tameshige","full_name":"Tameshige, Toshiaki","first_name":"Toshiaki"},{"first_name":"Satomi","last_name":"Kawai","full_name":"Kawai, Satomi"},{"full_name":"Sano, Masaki","last_name":"Sano","first_name":"Masaki"},{"first_name":"Yuki","full_name":"Doll, Yuki","last_name":"Doll"},{"full_name":"Iwase, Akira","last_name":"Iwase","first_name":"Akira"},{"first_name":"Ayako","last_name":"Kawamura","full_name":"Kawamura, Ayako"},{"first_name":"Takamasa","full_name":"Suzuki, Takamasa","last_name":"Suzuki"},{"last_name":"Nikaido","full_name":"Nikaido, Itoshi","first_name":"Itoshi"},{"first_name":"Keiko","full_name":"Sugimoto, Keiko","last_name":"Sugimoto"},{"first_name":"Momoko","full_name":"Ikeuchi, Momoko","last_name":"Ikeuchi"}],"intvolume":"         9","volume":9,"pmid":1,"date_published":"2023-07-07T00:00:00Z","article_processing_charge":"Yes","page":"eadg6983","publisher":"American Association for the Advancement of Science","ddc":["580"],"year":"2023"},{"day":"01","doi":"10.1093/gbe/evad113","department":[{"_id":"BeVi"}],"publication_status":"published","month":"07","corr_author":"1","related_material":{"link":[{"url":"https://github.com/carolbarata/dpseudo-n-beyond","relation":"software"}]},"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"ieee":"C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C. Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura,” <i>Genome biology and evolution</i>, vol. 15, no. 7. Oxford University Press, 2023.","ama":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. <i>Genome biology and evolution</i>. 2023;15(7). doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">10.1093/gbe/evad113</a>","apa":"de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., &#38; Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>","chicago":"Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>.","short":"C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (2023).","mla":"de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology and Evolution</i>, vol. 15, no. 7, evad113, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">10.1093/gbe/evad113</a>.","ista":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113."},"file":[{"content_type":"application/pdf","checksum":"70de3c4878de6efe00dc56de2df8812f","relation":"main_file","access_level":"open_access","success":1,"date_updated":"2023-08-01T06:58:34Z","creator":"dernst","file_size":2382587,"file_id":"13339","date_created":"2023-08-01T06:58:34Z","file_name":"2023_GBE_Barata.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","acknowledgement":"This work was supported by the Vienna Science and Technology Fund (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about the project as well as providing us with the resequencing data they had produced as a result of previous work on this experiment. We are especially grateful to Tanya Sneddon for her help with the DNA extraction process and shipping.","scopus_import":"1","title":"Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","oa":1,"has_accepted_license":"1","publication_identifier":{"eissn":["1759-6653"]},"date_created":"2023-07-23T22:01:11Z","publication":"Genome biology and evolution","abstract":[{"lang":"eng","text":"Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines."}],"date_updated":"2025-05-14T11:08:37Z","type":"journal_article","file_date_updated":"2023-08-01T06:58:34Z","pmid":1,"date_published":"2023-07-01T00:00:00Z","article_processing_charge":"Yes","ddc":["570"],"publisher":"Oxford University Press","article_number":"evad113","year":"2023","issue":"7","_id":"13260","external_id":{"pmid":["37341535"],"isi":["001023444700003"]},"isi":1,"author":[{"full_name":"De Castro Barbosa Rodrigues Barata, Carolina","id":"20565186-803f-11ed-ab7e-96a4ff7694ef","last_name":"De Castro Barbosa Rodrigues Barata","orcid":"0000-0003-1945-2245","first_name":"Carolina"},{"full_name":"Snook, Rhonda R.","last_name":"Snook","first_name":"Rhonda R."},{"first_name":"Michael G.","last_name":"Ritchie","full_name":"Ritchie, Michael G."},{"last_name":"Kosiol","full_name":"Kosiol, Carolin","first_name":"Carolin"}],"intvolume":"        15","volume":15},{"citation":{"ama":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. 2023;380(6652):1357-1362. doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>","apa":"Brückner, D., Chen, H., Barinov, L., Zoller, B., &#38; Gregor, T. (2023). Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>","ieee":"D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,” <i>Science</i>, vol. 380, no. 6652. American Association for the Advancement of Science, pp. 1357–1362, 2023.","ista":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 380(6652), 1357–1362.","chicago":"Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>.","short":"D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023) 1357–1362.","mla":"Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>, vol. 380, no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62, doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>."},"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.adf5568"}],"scopus_import":"1","acknowledgement":"This work was supported in part by the U.S. National Science Foundation, the Center for the Physics of Biological Function (grant PHY-1734030), and the National Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B. was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship (ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.","doi":"10.1126/science.adf5568","day":"29","department":[{"_id":"EdHa"}],"publication_status":"published","month":"06","oa_version":"Preprint","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"]},"publication":"Science","date_created":"2023-07-23T22:01:12Z","abstract":[{"lang":"eng","text":"Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression."}],"date_updated":"2025-04-14T08:55:54Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome","article_type":"original","oa":1,"publisher":"American Association for the Advancement of Science","project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022"}],"year":"2023","date_published":"2023-06-29T00:00:00Z","page":"1357-1362","article_processing_charge":"No","intvolume":"       380","volume":380,"issue":"6652","_id":"13261","external_id":{"isi":["001106405600028"]},"isi":1,"author":[{"first_name":"David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David","last_name":"Brückner"},{"last_name":"Chen","full_name":"Chen, Hongtao","first_name":"Hongtao"},{"full_name":"Barinov, Lev","last_name":"Barinov","first_name":"Lev"},{"last_name":"Zoller","full_name":"Zoller, Benjamin","first_name":"Benjamin"},{"last_name":"Gregor","full_name":"Gregor, Thomas","first_name":"Thomas"}]},{"date_published":"2023-06-17T00:00:00Z","page":"261-271","article_processing_charge":"Yes (via OA deal)","ddc":["000"],"publisher":"Association for Computing Machinery","year":"2023","_id":"13262","external_id":{"arxiv":["2304.09331"],"isi":["001108889000024"]},"author":[{"full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","last_name":"Fedorov","first_name":"Alexander"},{"id":"ed9595ea-2f8f-11ee-ba95-d2b546540783","full_name":"Hashemi, Diba","last_name":"Hashemi","first_name":"Diba"},{"last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","full_name":"Nadiradze, Giorgi","first_name":"Giorgi","orcid":"0000-0001-5634-0731"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian"}],"isi":1,"department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publication_status":"published","doi":"10.1145/3558481.3591082","day":"17","month":"06","corr_author":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"content_type":"application/pdf","relation":"main_file","checksum":"72e312aabf0c5248c99b5cd3a88e4c88","success":1,"access_level":"open_access","date_updated":"2023-07-31T10:53:08Z","file_size":2087937,"creator":"dernst","date_created":"2023-07-31T10:53:08Z","file_id":"13334","file_name":"2023_SPAA_Fedorov.pdf"}],"citation":{"apa":"Fedorov, A., Hashemi, D., Nadiradze, G., &#38; Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3558481.3591082\">https://doi.org/10.1145/3558481.3591082</a>","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2023:261-271. doi:<a href=\"https://doi.org/10.1145/3558481.3591082\">10.1145/3558481.3591082</a>","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Orlando, FL, United States, 2023, pp. 261–271.","ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271.","short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271.","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Association for Computing Machinery, 2023, pp. 261–71, doi:<a href=\"https://doi.org/10.1145/3558481.3591082\">10.1145/3558481.3591082</a>.","chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, 261–71. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3558481.3591082\">https://doi.org/10.1145/3558481.3591082</a>."},"status":"public","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Provably-efficient and internally-deterministic parallel Union-Find","oa":1,"has_accepted_license":"1","conference":{"location":"Orlando, FL, United States","end_date":"2023-06-19","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2023-06-17"},"date_created":"2023-07-23T22:01:12Z","publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","publication_identifier":{"isbn":["9781450395458"]},"abstract":[{"text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited.","lang":"eng"}],"type":"conference","date_updated":"2025-09-09T12:43:18Z","file_date_updated":"2023-07-31T10:53:08Z"},{"year":"2023","project":[{"grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"publisher":"Oxford University Press","ddc":["000"],"article_processing_charge":"Yes","page":"i513-i522","date_published":"2023-06-30T00:00:00Z","pmid":1,"volume":39,"intvolume":"        39","isi":1,"author":[{"full_name":"Trinh, Van Giang","last_name":"Trinh","first_name":"Van Giang"},{"first_name":"Belaid","full_name":"Benhamou, Belaid","last_name":"Benhamou"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724"},{"orcid":"0000-0003-1993-0331","first_name":"Samuel","full_name":"Pastva, Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","last_name":"Pastva"}],"_id":"13263","issue":"Supplement_1","external_id":{"pmid":["37387165"],"isi":["001027457000060"]},"acknowledgement":"This work was supported by L’Institut Carnot STAR, Marseille, France, and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. [101034413].","scopus_import":"1","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ama":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. Trap spaces of multi-valued networks: Definition, computation, and applications. <i>Bioinformatics</i>. 2023;39(Supplement_1):i513-i522. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad262\">10.1093/bioinformatics/btad262</a>","apa":"Trinh, V. G., Benhamou, B., Henzinger, T. A., &#38; Pastva, S. (2023). Trap spaces of multi-valued networks: Definition, computation, and applications. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btad262\">https://doi.org/10.1093/bioinformatics/btad262</a>","ieee":"V. G. Trinh, B. Benhamou, T. A. Henzinger, and S. Pastva, “Trap spaces of multi-valued networks: Definition, computation, and applications,” <i>Bioinformatics</i>, vol. 39, no. Supplement_1. Oxford University Press, pp. i513–i522, 2023.","ista":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. 2023. Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. 39(Supplement_1), i513–i522.","mla":"Trinh, Van Giang, et al. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” <i>Bioinformatics</i>, vol. 39, no. Supplement_1, Oxford University Press, 2023, pp. i513–22, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad262\">10.1093/bioinformatics/btad262</a>.","chicago":"Trinh, Van Giang, Belaid Benhamou, Thomas A Henzinger, and Samuel Pastva. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” <i>Bioinformatics</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/bioinformatics/btad262\">https://doi.org/10.1093/bioinformatics/btad262</a>.","short":"V.G. Trinh, B. Benhamou, T.A. Henzinger, S. Pastva, Bioinformatics 39 (2023) i513–i522."},"file":[{"access_level":"open_access","success":1,"checksum":"ba3abe1171df1958413b7c7f957f5486","relation":"main_file","content_type":"application/pdf","file_name":"2023_Bioinformatics_Trinh.pdf","file_id":"13335","date_created":"2023-07-31T11:09:05Z","creator":"dernst","file_size":641736,"date_updated":"2023-07-31T11:09:05Z"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/giang-trinh/trap-mvn"}]},"month":"06","corr_author":"1","publication_status":"published","department":[{"_id":"ToHe"}],"day":"30","ec_funded":1,"doi":"10.1093/bioinformatics/btad262","file_date_updated":"2023-07-31T11:09:05Z","type":"journal_article","date_updated":"2025-05-14T11:07:28Z","abstract":[{"text":"Motivation: Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date.\r\n\r\nResults: In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models.","lang":"eng"}],"date_created":"2023-07-23T22:01:12Z","publication":"Bioinformatics","publication_identifier":{"issn":["1367-4803"],"eissn":["1367-4811"]},"has_accepted_license":"1","oa":1,"article_type":"original","title":"Trap spaces of multi-valued networks: Definition, computation, and applications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"AnHi"},{"_id":"OnHo"}],"publication_status":"published","doi":"10.1103/PhysRevApplied.19.064032","day":"09","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14547"}]},"month":"06","corr_author":"1","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Preprint","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"arxiv":1,"citation":{"ista":"Phan DT, Falthansl-Scheinecker P, Mishra U, Strickland WM, Langone D, Shabani J, Higginbotham AP. 2023. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 19(6), 064032.","short":"D.T. Phan, P. Falthansl-Scheinecker, U. Mishra, W.M. Strickland, D. Langone, J. Shabani, A.P. Higginbotham, Physical Review Applied 19 (2023).","mla":"Phan, Duc T., et al. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” <i>Physical Review Applied</i>, vol. 19, no. 6, 064032, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">10.1103/PhysRevApplied.19.064032</a>.","chicago":"Phan, Duc T, Paul Falthansl-Scheinecker, Umang Mishra, W. M. Strickland, D. Langone, J. Shabani, and Andrew P Higginbotham. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” <i>Physical Review Applied</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">https://doi.org/10.1103/PhysRevApplied.19.064032</a>.","ama":"Phan DT, Falthansl-Scheinecker P, Mishra U, et al. Gate-tunable superconductor-semiconductor parametric amplifier. <i>Physical Review Applied</i>. 2023;19(6). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">10.1103/PhysRevApplied.19.064032</a>","apa":"Phan, D. T., Falthansl-Scheinecker, P., Mishra, U., Strickland, W. M., Langone, D., Shabani, J., &#38; Higginbotham, A. P. (2023). Gate-tunable superconductor-semiconductor parametric amplifier. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">https://doi.org/10.1103/PhysRevApplied.19.064032</a>","ieee":"D. T. Phan <i>et al.</i>, “Gate-tunable superconductor-semiconductor parametric amplifier,” <i>Physical Review Applied</i>, vol. 19, no. 6. American Physical Society, 2023."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2206.05746"}],"status":"public","scopus_import":"1","acknowledgement":"We thank Shyam Shankar for helpful feedback on the manuscript. We gratefully acknowledge the support of the ISTA nanofabrication facility, the Miba Machine Shop, and the eMachine Shop. The NYU team acknowledges support from Army Research Office Grant No. W911NF2110303.","title":"Gate-tunable superconductor-semiconductor parametric amplifier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","oa":1,"publication":"Physical Review Applied","date_created":"2023-07-23T22:01:12Z","publication_identifier":{"eissn":["2331-7019"]},"abstract":[{"lang":"eng","text":"We build a parametric amplifier with a Josephson field-effect transistor (JoFET) as the active element. The resonant frequency of the device is field-effect tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated at a fixed resonance frequency.\r\n\r\n"}],"type":"journal_article","date_updated":"2026-04-07T13:25:51Z","date_published":"2023-06-09T00:00:00Z","article_processing_charge":"No","publisher":"American Physical Society","year":"2023","article_number":"064032","_id":"13264","external_id":{"arxiv":["2206.05746"],"isi":["001012022600004"]},"issue":"6","author":[{"id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan, Duc T","last_name":"Phan","first_name":"Duc T"},{"first_name":"Paul","last_name":"Falthansl-Scheinecker","full_name":"Falthansl-Scheinecker, Paul","id":"85b43b21-15b2-11ec-abd3-e2c252cc2285"},{"first_name":"Umang","full_name":"Mishra, Umang","id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","last_name":"Mishra"},{"first_name":"W. M.","full_name":"Strickland, W. M.","last_name":"Strickland"},{"first_name":"D.","last_name":"Langone","full_name":"Langone, D."},{"last_name":"Shabani","full_name":"Shabani, J.","first_name":"J."},{"orcid":"0000-0003-2607-2363","first_name":"Andrew P","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"intvolume":"        19","volume":19},{"oa":1,"article_type":"original","title":"As-Continuous-As-Possible extrusion-based fabrication of surface models","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-12-13T11:34:59Z","type":"journal_article","abstract":[{"lang":"eng","text":"In this study, we propose a computational framework for optimizing the continuity of the toolpath in fabricating surface models on an extrusion-based 3D printer. Toolpath continuity is a critical issue that influences both the quality and the efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy surfaces, where this phenomenon worsens for materials with large viscosity, like clay. The effects of continuity on the surface models are even more severe in terms of the quality of the surface and the stability of the model. We introduce a criterion called the one–path patch (OPP) to represent a patch on the surface of the shell that can be traversed along one path by considering the constraints on fabrication. We study the properties of the OPPs and their merging operations to propose a bottom-up OPP merging procedure to decompose the given shell surface into a minimal number of OPPs, and to generate the “as-continuous-as-possible” (ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer printing scheme that reduces staircase defects and improves the continuity of the toolpath by connecting multiple segments. We evaluated the ACAP algorithm on ceramic and thermoplastic materials, and the results showed that it improves the fabrication of surface models in terms of both efficiency and surface quality."}],"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"publication":"ACM Transactions on Graphics","date_created":"2023-07-23T22:01:13Z","arxiv":1,"oa_version":"Preprint","language":[{"iso":"eng"}],"quality_controlled":"1","month":"03","doi":"10.1145/3575859","day":"17","department":[{"_id":"BeBi"}],"publication_status":"published","scopus_import":"1","acknowledgement":"This work was supported in part by grants from the NSFC (61972232), Science and Technology Program of Shenzhen, China (CJGJZD20200617102202007). ","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2201.02374"}],"status":"public","citation":{"ama":"Zhong F, Xu Y, Zhao H, Lu L. As-Continuous-As-Possible extrusion-based fabrication of surface models. <i>ACM Transactions on Graphics</i>. 2023;42(3). doi:<a href=\"https://doi.org/10.1145/3575859\">10.1145/3575859</a>","apa":"Zhong, F., Xu, Y., Zhao, H., &#38; Lu, L. (2023). As-Continuous-As-Possible extrusion-based fabrication of surface models. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3575859\">https://doi.org/10.1145/3575859</a>","ieee":"F. Zhong, Y. Xu, H. Zhao, and L. Lu, “As-Continuous-As-Possible extrusion-based fabrication of surface models,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 3. Association for Computing Machinery, 2023.","ista":"Zhong F, Xu Y, Zhao H, Lu L. 2023. As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. 42(3), 26.","chicago":"Zhong, Fanchao, Yonglai Xu, Haisen Zhao, and Lin Lu. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3575859\">https://doi.org/10.1145/3575859</a>.","short":"F. Zhong, Y. Xu, H. Zhao, L. Lu, ACM Transactions on Graphics 42 (2023).","mla":"Zhong, Fanchao, et al. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 3, 26, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3575859\">10.1145/3575859</a>."},"isi":1,"author":[{"full_name":"Zhong, Fanchao","last_name":"Zhong","first_name":"Fanchao"},{"last_name":"Xu","full_name":"Xu, Yonglai","first_name":"Yonglai"},{"first_name":"Haisen","orcid":"0000-0002-6389-1045","id":"fb7f793a-80d1-11eb-8869-d56e5b2a8ff4","full_name":"Zhao, Haisen","last_name":"Zhao"},{"first_name":"Lin","last_name":"Lu","full_name":"Lu, Lin"}],"issue":"3","_id":"13265","external_id":{"arxiv":["2201.02374"],"isi":["001018739600002"]},"volume":42,"intvolume":"        42","article_processing_charge":"No","date_published":"2023-03-17T00:00:00Z","article_number":"26","year":"2023","publisher":"Association for Computing Machinery"}]