[{"author":[{"last_name":"Westram","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy","orcid":"0000-0001-6395-386X","last_name":"Surendranadh","full_name":"Surendranadh, Parvathy"},{"last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"title":"Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"date_updated":"2025-04-15T08:20:40Z","related_material":{"record":[{"relation":"other","id":"12264","status":"public"}]},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"article_processing_charge":"Yes (via OA deal)","year":"2022","citation":{"ama":"Westram AM, Stankowski S, Surendranadh P, Barton NH. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 2022;35(9):1200-1205. doi:10.1111/jeb.14082","ieee":"A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?,’” Journal of Evolutionary Biology, vol. 35, no. 9. Wiley, pp. 1200–1205, 2022.","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1200–1205.","chicago":"Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14082.","ista":"Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 35(9), 1200–1205.","mla":"Westram, Anja M., et al. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1200–05, doi:10.1111/jeb.14082.","apa":"Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022). Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14082"},"license":"https://creativecommons.org/licenses/by/4.0/","department":[{"_id":"NiBa"}],"date_published":"2022-09-01T00:00:00Z","file_date_updated":"2023-01-30T10:14:09Z","article_type":"letter_note","issue":"9","scopus_import":"1","quality_controlled":"1","intvolume":" 35","date_created":"2023-01-16T09:59:37Z","doi":"10.1111/jeb.14082","acknowledgement":"We are very grateful to the authors of the commentaries for the interesting discussion and to Luke Holman for handling this set of manuscripts. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166).","page":"1200-1205","ddc":["570"],"oa":1,"status":"public","volume":35,"corr_author":"1","file":[{"file_name":"2022_JourEvoBiology_Westram_Response.pdf","date_created":"2023-01-30T10:14:09Z","checksum":"27268009e5eec030bc10667a4ac5ed4c","file_size":349603,"file_id":"12449","success":1,"date_updated":"2023-01-30T10:14:09Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access"}],"month":"09","keyword":["Ecology","Evolution","Behavior and Systematics"],"publication_status":"published","type":"journal_article","publication":"Journal of Evolutionary Biology","day":"01","_id":"12265","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"Snapdragon Speciation"}],"external_id":{"isi":["000849851100009"]},"publisher":"Wiley"},{"isi":1,"date_updated":"2023-08-04T09:54:16Z","author":[{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","orcid":"0000-0003-1843-3173","last_name":"Basilico","full_name":"Basilico, Bernadette"},{"last_name":"Palamà","full_name":"Palamà, Ilaria Elena","first_name":"Ilaria Elena"},{"first_name":"Stefania","full_name":"D’Amone, Stefania","last_name":"D’Amone"},{"last_name":"Lauro","full_name":"Lauro, Clotilde","first_name":"Clotilde"},{"first_name":"Maria","last_name":"Rosito","full_name":"Rosito, Maria"},{"first_name":"Maddalena","last_name":"Grieco","full_name":"Grieco, Maddalena"},{"last_name":"Ratano","full_name":"Ratano, Patrizia","first_name":"Patrizia"},{"last_name":"Cordella","full_name":"Cordella, Federica","first_name":"Federica"},{"first_name":"Caterina","full_name":"Sanchini, Caterina","last_name":"Sanchini"},{"full_name":"Di Angelantonio, Silvia","last_name":"Di Angelantonio","first_name":"Silvia"},{"first_name":"Davide","full_name":"Ragozzino, Davide","last_name":"Ragozzino"},{"last_name":"Cascione","full_name":"Cascione, Mariafrancesca","first_name":"Mariafrancesca"},{"first_name":"Giuseppe","last_name":"Gigli","full_name":"Gigli, Giuseppe"},{"first_name":"Barbara","last_name":"Cortese","full_name":"Cortese, Barbara"}],"title":"Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma cells","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","citation":{"ieee":"B. Basilico et al., “Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma cells,” Frontiers in Oncology, vol. 12. Frontiers Media, 2022.","ama":"Basilico B, Palamà IE, D’Amone S, et al. Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma cells. Frontiers in Oncology. 2022;12. doi:10.3389/fonc.2022.983507","mla":"Basilico, Bernadette, et al. “Substrate Stiffness Effect on Molecular Crosstalk of Epithelial-Mesenchymal Transition Mediators of Human Glioblastoma Cells.” Frontiers in Oncology, vol. 12, 983507, Frontiers Media, 2022, doi:10.3389/fonc.2022.983507.","ista":"Basilico B, Palamà IE, D’Amone S, Lauro C, Rosito M, Grieco M, Ratano P, Cordella F, Sanchini C, Di Angelantonio S, Ragozzino D, Cascione M, Gigli G, Cortese B. 2022. Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma cells. Frontiers in Oncology. 12, 983507.","short":"B. Basilico, I.E. Palamà, S. D’Amone, C. Lauro, M. Rosito, M. Grieco, P. Ratano, F. Cordella, C. Sanchini, S. Di Angelantonio, D. Ragozzino, M. Cascione, G. Gigli, B. Cortese, Frontiers in Oncology 12 (2022).","chicago":"Basilico, Bernadette, Ilaria Elena Palamà, Stefania D’Amone, Clotilde Lauro, Maria Rosito, Maddalena Grieco, Patrizia Ratano, et al. “Substrate Stiffness Effect on Molecular Crosstalk of Epithelial-Mesenchymal Transition Mediators of Human Glioblastoma Cells.” Frontiers in Oncology. Frontiers Media, 2022. https://doi.org/10.3389/fonc.2022.983507.","apa":"Basilico, B., Palamà, I. E., D’Amone, S., Lauro, C., Rosito, M., Grieco, M., … Cortese, B. (2022). Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma cells. Frontiers in Oncology. Frontiers Media. https://doi.org/10.3389/fonc.2022.983507"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2234-943X"]},"article_processing_charge":"No","date_published":"2022-08-25T00:00:00Z","abstract":[{"text":"The complexity of the microenvironment effects on cell response, show accumulating evidence that glioblastoma (GBM) migration and invasiveness are influenced by the mechanical rigidity of their surroundings. The epithelial–mesenchymal transition (EMT) is a well-recognized driving force of the invasive behavior of cancer. However, the primary mechanisms of EMT initiation and progression remain unclear. We have previously showed that certain substrate stiffness can selectively stimulate human GBM U251-MG and GL15 glioblastoma cell lines motility. The present study unifies several known EMT mediators to uncover the reason of the regulation and response to these stiffnesses. Our results revealed that changing the rigidity of the mechanical environment tuned the response of both cell lines through change in morphological features, epithelial-mesenchymal markers (E-, N-Cadherin), EGFR and ROS expressions in an interrelated manner. Specifically, a stiffer microenvironment induced a mesenchymal cell shape, a more fragmented morphology, higher intracellular cytosolic ROS expression and lower mitochondrial ROS. Finally, we observed that cells more motile showed a more depolarized mitochondrial membrane potential. Unravelling the process that regulates GBM cells’ infiltrative behavior could provide new opportunities for identification of new targets and less invasive approaches for treatment.","lang":"eng"}],"department":[{"_id":"GaNo"}],"intvolume":" 12","date_created":"2023-01-16T10:00:28Z","doi":"10.3389/fonc.2022.983507","file_date_updated":"2023-01-30T10:25:21Z","article_type":"original","scopus_import":"1","quality_controlled":"1","status":"public","ddc":["570"],"oa":1,"acknowledgement":"The research leading to these results has received funding from AIRC under IG 2021 - ID. 26328 project – P.I. Cortese Barbara and AIRC under MFAG 2015 - ID. 16803 project – “P.I. Cortese Barbara”. The authors are also grateful to the ”Tecnopolo per la medicina di precisione” (TecnoMed Puglia) - Regione Puglia: DGR n.2117 del 21/11/2018, CUP: B84I18000540002 and “Tecnopolo di Nanotecnologia e Fotonica per la medicina di precisione” (TECNOMED) - FISR/MIUR-CNR: delibera CIPE n.3449 del 7-08-2017, CUP: B83B17000010001.\r\nWe thank Dr. Francesca Pagani for useful technical support. We thank also Irene Iacuitto, Giovanna Loffredo and Manuela Marchetti for practical administrative support.","keyword":["Cancer Research","Oncology"],"publication_status":"published","type":"journal_article","volume":12,"file":[{"creator":"dernst","date_updated":"2023-01-30T10:25:21Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"2022_FrontiersOntology_Basilico.pdf","date_created":"2023-01-30T10:25:21Z","file_size":13588502,"checksum":"efc7edf9f626af31853790c5b598a68c","success":1,"file_id":"12450"}],"month":"08","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pmid":1,"day":"25","publication":"Frontiers in Oncology","article_number":"983507","_id":"12268","external_id":{"pmid":["36091138"],"isi":["000856524900001"]},"publisher":"Frontiers Media","has_accepted_license":"1"},{"doi":"10.1103/physrevb.106.054314","date_created":"2023-01-16T10:00:39Z","intvolume":" 106","quality_controlled":"1","scopus_import":"1","article_type":"original","issue":"5","abstract":[{"lang":"eng","text":"We study the thermalization of a small XX chain coupled to long, gapped XXZ leads at either side by observing the relaxation dynamics of the whole system. Using extensive tensor network simulations, we show that such systems, although not integrable, appear to show either extremely slow thermalization or even lack thereof since the two cannot be distinguished within the accuracy of our numerics. We show that the persistent oscillations observed in the spin current in the middle of the XX chain are related to eigenstates of the entire system located within the gap of the boundary chains. We find from exact diagonalization that some of these states remain strictly localized within the XX chain and do not hybridize with the rest of the system. The frequencies of the persistent oscillations determined by numerical simulations of dynamics match the energy differences between these states exactly. This has important implications for open systems, where the strongly interacting leads are often assumed to thermalize the central system. Our results suggest that, if we employ gapped systems for the leads, this assumption does not hold."}],"arxiv":1,"date_published":"2022-08-31T00:00:00Z","department":[{"_id":"MaSe"}],"citation":{"short":"M. Ljubotina, D. Roy, T. Prosen, Physical Review B 106 (2022).","ista":"Ljubotina M, Roy D, Prosen T. 2022. Absence of thermalization of free systems coupled to gapped interacting reservoirs. Physical Review B. 106(5), 054314.","chicago":"Ljubotina, Marko, Dibyendu Roy, and Tomaž Prosen. “Absence of Thermalization of Free Systems Coupled to Gapped Interacting Reservoirs.” Physical Review B. American Physical Society, 2022. https://doi.org/10.1103/physrevb.106.054314.","mla":"Ljubotina, Marko, et al. “Absence of Thermalization of Free Systems Coupled to Gapped Interacting Reservoirs.” Physical Review B, vol. 106, no. 5, 054314, American Physical Society, 2022, doi:10.1103/physrevb.106.054314.","apa":"Ljubotina, M., Roy, D., & Prosen, T. (2022). Absence of thermalization of free systems coupled to gapped interacting reservoirs. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.106.054314","ama":"Ljubotina M, Roy D, Prosen T. Absence of thermalization of free systems coupled to gapped interacting reservoirs. Physical Review B. 2022;106(5). doi:10.1103/physrevb.106.054314","ieee":"M. Ljubotina, D. Roy, and T. Prosen, “Absence of thermalization of free systems coupled to gapped interacting reservoirs,” Physical Review B, vol. 106, no. 5. American Physical Society, 2022."},"year":"2022","article_processing_charge":"No","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"language":[{"iso":"eng"}],"isi":1,"date_updated":"2025-04-14T07:52:06Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","orcid":"0000-0003-0038-7068","first_name":"Marko","last_name":"Ljubotina","full_name":"Ljubotina, Marko"},{"first_name":"Dibyendu","full_name":"Roy, Dibyendu","last_name":"Roy"},{"full_name":"Prosen, Tomaž","last_name":"Prosen","first_name":"Tomaž"}],"title":"Absence of thermalization of free systems coupled to gapped interacting reservoirs","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2106.08373"}],"publisher":"American Physical Society","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"external_id":{"arxiv":["2106.08373"],"isi":["000861332900005"]},"oa_version":"Preprint","ec_funded":1,"_id":"12269","article_number":"054314","publication":"Physical Review B","day":"31","publication_status":"published","type":"journal_article","month":"08","volume":106,"status":"public","oa":1,"acknowledgement":"M.L. and T.P. acknowledge support from the European Research Council (ERC) through the advanced grant 694544 – OMNES and the grant P1-0402 of Slovenian Research Agency (ARRS). M.L. acknowledges support from the European Research Council (ERC) through the starting grant 850899 – NEQuM. D.R. acknowledges support from the Ministry of Electronics & Information Technology (MeitY), India under the grant for “Centre for Excellence in Quantum\r\nTechnologies” with Ref. No. 4(7)/2020-ITEA. "},{"department":[{"_id":"MaMo"}],"arxiv":1,"date_published":"2022-08-01T00:00:00Z","abstract":[{"text":"We study communication in the presence of a jamming adversary where quadratic power constraints are imposed on the transmitter and the jammer. The jamming signal is allowed to be a function of the codebook, and a noncausal but noisy observation of the transmitted codeword. For a certain range of the noise-to-signal ratios (NSRs) of the transmitter and the jammer, we are able to characterize the capacity of this channel under deterministic encoding or stochastic encoding, i.e., with no common randomness between the encoder/decoder pair. For the remaining NSR regimes, we determine the capacity under the assumption of a small amount of common randomness (at most 2log(n) bits in one sub-regime, and at most Ω(n) bits in the other sub-regime) available to the encoder-decoder pair. Our proof techniques involve a novel myopic list-decoding result for achievability, and a Plotkin-type push attack for the converse in a subregion of the NSRs, both of which may be of independent interest. We also give bounds on the strong secrecy capacity of this channel assuming that the jammer is simultaneously eavesdropping.","lang":"eng"}],"article_type":"original","issue":"8","scopus_import":"1","quality_controlled":"1","date_created":"2023-01-16T10:01:19Z","intvolume":" 68","doi":"10.1109/tit.2022.3167554","author":[{"first_name":"Yihan","orcid":"0000-0002-6465-6258","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","full_name":"Zhang, Yihan","last_name":"Zhang"},{"first_name":"Shashank","full_name":"Vatedka, Shashank","last_name":"Vatedka"},{"first_name":"Sidharth","last_name":"Jaggi","full_name":"Jaggi, Sidharth"},{"last_name":"Sarwate","full_name":"Sarwate, Anand D.","first_name":"Anand D."}],"title":"Quadratically constrained myopic adversarial channels","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"date_updated":"2024-10-09T21:03:54Z","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2022","citation":{"apa":"Zhang, Y., Vatedka, S., Jaggi, S., & Sarwate, A. D. (2022). Quadratically constrained myopic adversarial channels. IEEE Transactions on Information Theory. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/tit.2022.3167554","mla":"Zhang, Yihan, et al. “Quadratically Constrained Myopic Adversarial Channels.” IEEE Transactions on Information Theory, vol. 68, no. 8, Institute of Electrical and Electronics Engineers, 2022, pp. 4901–48, doi:10.1109/tit.2022.3167554.","short":"Y. Zhang, S. Vatedka, S. Jaggi, A.D. Sarwate, IEEE Transactions on Information Theory 68 (2022) 4901–4948.","chicago":"Zhang, Yihan, Shashank Vatedka, Sidharth Jaggi, and Anand D. Sarwate. “Quadratically Constrained Myopic Adversarial Channels.” IEEE Transactions on Information Theory. Institute of Electrical and Electronics Engineers, 2022. https://doi.org/10.1109/tit.2022.3167554.","ista":"Zhang Y, Vatedka S, Jaggi S, Sarwate AD. 2022. Quadratically constrained myopic adversarial channels. IEEE Transactions on Information Theory. 68(8), 4901–4948.","ieee":"Y. Zhang, S. Vatedka, S. Jaggi, and A. D. Sarwate, “Quadratically constrained myopic adversarial channels,” IEEE Transactions on Information Theory, vol. 68, no. 8. Institute of Electrical and Electronics Engineers, pp. 4901–4948, 2022.","ama":"Zhang Y, Vatedka S, Jaggi S, Sarwate AD. Quadratically constrained myopic adversarial channels. IEEE Transactions on Information Theory. 2022;68(8):4901-4948. doi:10.1109/tit.2022.3167554"},"publication":"IEEE Transactions on Information Theory","day":"01","_id":"12273","oa_version":"Preprint","publisher":"Institute of Electrical and Electronics Engineers","external_id":{"isi":["000838527100004"],"arxiv":["1801.05951"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1801.05951"}],"page":"4901-4948","status":"public","oa":1,"volume":68,"month":"08","corr_author":"1","type":"journal_article","publication_status":"published"},{"date_updated":"2025-04-14T07:52:27Z","isi":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/JaccovanRheenenLab/Retrograde_movement_Azkanaz_Nature_2022"}]},"author":[{"first_name":"Maria","full_name":"Azkanaz, Maria","last_name":"Azkanaz"},{"first_name":"Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra"},{"first_name":"Saskia I. J.","last_name":"Ellenbroek","full_name":"Ellenbroek, Saskia I. J."},{"last_name":"Bruens","full_name":"Bruens, Lotte","first_name":"Lotte"},{"full_name":"Webb, Anna T.","last_name":"Webb","first_name":"Anna T."},{"first_name":"Dimitrios","full_name":"Laskaris, Dimitrios","last_name":"Laskaris"},{"first_name":"Koen C.","last_name":"Oost","full_name":"Oost, Koen C."},{"first_name":"Simona J. A.","full_name":"Lafirenze, Simona J. A.","last_name":"Lafirenze"},{"first_name":"Karl","last_name":"Annusver","full_name":"Annusver, Karl"},{"full_name":"Messal, Hendrik A.","last_name":"Messal","first_name":"Hendrik A."},{"first_name":"Sharif","full_name":"Iqbal, Sharif","last_name":"Iqbal"},{"first_name":"Dustin J.","last_name":"Flanagan","full_name":"Flanagan, Dustin J."},{"first_name":"David J.","last_name":"Huels","full_name":"Huels, David J."},{"first_name":"Felipe","full_name":"Rojas-Rodríguez, Felipe","last_name":"Rojas-Rodríguez"},{"first_name":"Miguel","last_name":"Vizoso","full_name":"Vizoso, Miguel"},{"first_name":"Maria","last_name":"Kasper","full_name":"Kasper, Maria"},{"last_name":"Sansom","full_name":"Sansom, Owen J.","first_name":"Owen J."},{"last_name":"Snippert","full_name":"Snippert, Hugo J.","first_name":"Hugo J."},{"full_name":"Liberali, Prisca","last_name":"Liberali","first_name":"Prisca"},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."},{"first_name":"Pekka","full_name":"Katajisto, Pekka","last_name":"Katajisto"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"first_name":"Jacco","last_name":"van Rheenen","full_name":"van Rheenen, Jacco"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Retrograde movements determine effective stem cell numbers in the intestine","year":"2022","citation":{"mla":"Azkanaz, Maria, et al. “Retrograde Movements Determine Effective Stem Cell Numbers in the Intestine.” Nature, vol. 607, no. 7919, Springer Nature, 2022, pp. 548–54, doi:10.1038/s41586-022-04962-0.","chicago":"Azkanaz, Maria, Bernat Corominas-Murtra, Saskia I. J. Ellenbroek, Lotte Bruens, Anna T. Webb, Dimitrios Laskaris, Koen C. Oost, et al. “Retrograde Movements Determine Effective Stem Cell Numbers in the Intestine.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-04962-0.","short":"M. Azkanaz, B. Corominas-Murtra, S.I.J. Ellenbroek, L. Bruens, A.T. Webb, D. Laskaris, K.C. Oost, S.J.A. Lafirenze, K. Annusver, H.A. Messal, S. Iqbal, D.J. Flanagan, D.J. Huels, F. Rojas-Rodríguez, M. Vizoso, M. Kasper, O.J. Sansom, H.J. Snippert, P. Liberali, B.D. Simons, P. Katajisto, E.B. Hannezo, J. van Rheenen, Nature 607 (2022) 548–554.","ista":"Azkanaz M, Corominas-Murtra B, Ellenbroek SIJ, Bruens L, Webb AT, Laskaris D, Oost KC, Lafirenze SJA, Annusver K, Messal HA, Iqbal S, Flanagan DJ, Huels DJ, Rojas-Rodríguez F, Vizoso M, Kasper M, Sansom OJ, Snippert HJ, Liberali P, Simons BD, Katajisto P, Hannezo EB, van Rheenen J. 2022. Retrograde movements determine effective stem cell numbers in the intestine. Nature. 607(7919), 548–554.","apa":"Azkanaz, M., Corominas-Murtra, B., Ellenbroek, S. I. J., Bruens, L., Webb, A. T., Laskaris, D., … van Rheenen, J. (2022). Retrograde movements determine effective stem cell numbers in the intestine. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-04962-0","ieee":"M. Azkanaz et al., “Retrograde movements determine effective stem cell numbers in the intestine,” Nature, vol. 607, no. 7919. Springer Nature, pp. 548–554, 2022.","ama":"Azkanaz M, Corominas-Murtra B, Ellenbroek SIJ, et al. Retrograde movements determine effective stem cell numbers in the intestine. Nature. 2022;607(7919):548-554. doi:10.1038/s41586-022-04962-0"},"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","date_published":"2022-07-13T00:00:00Z","abstract":[{"lang":"eng","text":"The morphology and functionality of the epithelial lining differ along the intestinal tract, but tissue renewal at all sites is driven by stem cells at the base of crypts1,2,3. Whether stem cell numbers and behaviour vary at different sites is unknown. Here we show using intravital microscopy that, despite similarities in the number and distribution of proliferative cells with an Lgr5 signature in mice, small intestinal crypts contain twice as many effective stem cells as large intestinal crypts. We find that, although passively displaced by a conveyor-belt-like upward movement, small intestinal cells positioned away from the crypt base can function as long-term effective stem cells owing to Wnt-dependent retrograde cellular movement. By contrast, the near absence of retrograde movement in the large intestine restricts cell repositioning, leading to a reduction in effective stem cell number. Moreover, after suppression of the retrograde movement in the small intestine, the number of effective stem cells is reduced, and the rate of monoclonal conversion of crypts is accelerated. Together, these results show that the number of effective stem cells is determined by active retrograde movement, revealing a new channel of stem cell regulation that can be experimentally and pharmacologically manipulated."}],"department":[{"_id":"EdHa"}],"date_created":"2023-01-16T10:01:29Z","intvolume":" 607","doi":"10.1038/s41586-022-04962-0","issue":"7919","article_type":"original","scopus_import":"1","quality_controlled":"1","oa":1,"status":"public","acknowledgement":"We thank the members of the van Rheenen laboratory for reading the manuscript, and the members of the bioimaging, FACS and animal facility of the NKI for experimental support. We acknowledge the staff at the MedH Flow Cytometry core facility, Karolinska Institutet, and LCI facility/Nikon Center of Excellence, Karolinska Institutet. This work was financially supported by the Netherlands Organization of Scientific Research NWO (Veni grant 863.15.011 to S.I.J.E. and Vici grant 09150182110004 to J.v.R.) and the CancerGenomics.nl (Netherlands Organisation for Scientific Research) program (to J.v.R.) the Doctor Josef Steiner Foundation (to J.v.R). B.D.S. acknowledges funding from the Royal Society E.P. Abraham Research Professorship (RP\\R1\\180165) and the Wellcome Trust (098357/Z/12/Z and 219478/Z/19/Z). B.C.-M. acknowledges the support of the field of excellence ‘Complexity of life in basic research and innovation’ of the University of Graz. O.J.S. and their laboratory acknowledge CRUK core funding to the CRUK Beatson Institute (A17196 and A31287) and CRUK core funding to the Sansom laboratory (A21139). P.K. and their laboratory are supported by grants from the Swedish Research Council (2018-03078), Cancerfonden (190634), Academy of Finland Centre of Excellence (266869, 304591 and 320185) and the Jane and Aatos Erkko Foundation. P.L. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 758617). E.H. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 851288).","page":"548-554","keyword":["Multidisciplinary"],"publication_status":"published","type":"journal_article","volume":607,"month":"07","corr_author":"1","oa_version":"Submitted Version","pmid":1,"day":"13","publication":"Nature","ec_funded":1,"_id":"12274","publisher":"Springer Nature","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"}],"external_id":{"pmid":["35831497"],"isi":["000824430000004"]},"main_file_link":[{"open_access":"1","url":"https://helda.helsinki.fi/items/94433455-4854-45c0-9de8-7326caea8780"}]},{"doi":"10.15252/embr.202154163","date_created":"2023-01-16T10:01:44Z","intvolume":" 23","quality_controlled":"1","scopus_import":"1","article_type":"original","issue":"7","abstract":[{"text":"N-glycans are molecularly diverse sugars borne by over 70% of proteins transiting the secretory pathway and have been implicated in protein folding, stability, and localization. Mutations in genes important for N-glycosylation result in congenital disorders of glycosylation that are often associated with intellectual disability. Here, we show that structurally distinct N-glycans regulate an extracellular protein complex involved in the patterning of somatosensory dendrites in Caenorhabditis elegans. Specifically, aman-2/Golgi alpha-mannosidase II, a conserved key enzyme in the biosynthesis of specific N-glycans, regulates the activity of the Menorin adhesion complex without obviously affecting the protein stability and localization of its components. AMAN-2 functions cell-autonomously to allow for decoration of the neuronal transmembrane receptor DMA-1/LRR-TM with the correct set of high-mannose/hybrid/paucimannose N-glycans. Moreover, distinct types of N-glycans on specific N-glycosylation sites regulate DMA-1/LRR-TM receptor function, which, together with three other extracellular proteins, forms the Menorin adhesion complex. In summary, specific N-glycan structures regulate dendrite patterning by coordinating the activity of an extracellular adhesion complex, suggesting that the molecular diversity of N-glycans can contribute to developmental specificity in the nervous system.","lang":"eng"}],"date_published":"2022-07-05T00:00:00Z","department":[{"_id":"MaDe"}],"citation":{"apa":"Rahman, M., Ramirez, N., Diaz‐Balzac, C. A., & Bülow, H. E. (2022). Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. EMBO Reports. Embo Press. https://doi.org/10.15252/embr.202154163","chicago":"Rahman, Maisha, Nelson Ramirez, Carlos A Diaz‐Balzac, and Hannes E Bülow. “Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory Dendrite Patterning.” EMBO Reports. Embo Press, 2022. https://doi.org/10.15252/embr.202154163.","short":"M. Rahman, N. Ramirez, C.A. Diaz‐Balzac, H.E. Bülow, EMBO Reports 23 (2022).","ista":"Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. 2022. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. EMBO Reports. 23(7), e54163.","mla":"Rahman, Maisha, et al. “Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory Dendrite Patterning.” EMBO Reports, vol. 23, no. 7, e54163, Embo Press, 2022, doi:10.15252/embr.202154163.","ama":"Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. EMBO Reports. 2022;23(7). doi:10.15252/embr.202154163","ieee":"M. Rahman, N. Ramirez, C. A. Diaz‐Balzac, and H. E. Bülow, “Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning,” EMBO Reports, vol. 23, no. 7. Embo Press, 2022."},"year":"2022","article_processing_charge":"No","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"language":[{"iso":"eng"}],"isi":1,"date_updated":"2023-10-03T11:25:54Z","title":"Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Rahman","full_name":"Rahman, Maisha","first_name":"Maisha"},{"full_name":"Ramirez, Nelson","last_name":"Ramirez","first_name":"Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425"},{"first_name":"Carlos A","full_name":"Diaz‐Balzac, Carlos A","last_name":"Diaz‐Balzac"},{"first_name":"Hannes E","last_name":"Bülow","full_name":"Bülow, Hannes E"}],"main_file_link":[{"url":"https://doi.org/10.15252/embr.202154163","open_access":"1"}],"publisher":"Embo Press","external_id":{"isi":["000797302700001"],"pmid":["35586945"]},"has_accepted_license":"1","pmid":1,"oa_version":"Published Version","_id":"12275","publication":"EMBO Reports","day":"05","article_number":"e54163","publication_status":"published","type":"journal_article","keyword":["Genetics","Molecular Biology","Biochemistry"],"month":"07","volume":23,"status":"public","oa":1,"acknowledgement":"We thank Scott Garforth, Sarah Garrett, Peri Kurshan, Yehuda Salzberg, PamelaStanley, Robert Townley, and members of the B€ulow laboratory for commentson the manuscript or helpful discussions during the course of this work. Wethank David Miller, Shohei Mitani, Kang Shen, and Iain Wilson for reagents,and Yuji Kohara for theyk11g705cDNA clone. We are grateful to MeeraTrivedi for sharing thedzIs117strain prior to publication. Some strains wereprovided by the Caenorhabditis Genome Center (funded by the NIH Office ofResearch Infrastructure Programs P40OD010440). This work was supportedby grants from the National Institute of Health (NIH): R01NS096672andR21NS111145to HEB; F31NS100370to MR; T32GM007288and F31HD066967to CADB; P30HD071593to Albert Einstein College of Medicine. We acknowl-edge support to MR by the Department of Neuroscience. NJRS was the recipi-ent of a Colciencias-Fulbright Fellowship and HEB of an Irma T. Hirschl/Monique Weill-Caulier research fellowship"},{"title":"Optimal steering of matrix product states and quantum many-body scars","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Marko","orcid":"0000-0003-0038-7068","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","full_name":"Ljubotina, Marko","last_name":"Ljubotina"},{"full_name":"Roos, Barbara","last_name":"Roos","orcid":"0000-0002-9071-5880","first_name":"Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425"},{"full_name":"Abanin, Dmitry A.","last_name":"Abanin","first_name":"Dmitry A."},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827"}],"date_updated":"2025-04-14T07:52:07Z","article_processing_charge":"No","publication_identifier":{"eissn":["2691-3399"]},"language":[{"iso":"eng"}],"citation":{"apa":"Ljubotina, M., Roos, B., Abanin, D. A., & Serbyn, M. (2022). Optimal steering of matrix product states and quantum many-body scars. PRX Quantum. American Physical Society. https://doi.org/10.1103/prxquantum.3.030343","ista":"Ljubotina M, Roos B, Abanin DA, Serbyn M. 2022. Optimal steering of matrix product states and quantum many-body scars. PRX Quantum. 3(3), 030343.","chicago":"Ljubotina, Marko, Barbara Roos, Dmitry A. Abanin, and Maksym Serbyn. “Optimal Steering of Matrix Product States and Quantum Many-Body Scars.” PRX Quantum. American Physical Society, 2022. https://doi.org/10.1103/prxquantum.3.030343.","short":"M. Ljubotina, B. Roos, D.A. Abanin, M. Serbyn, PRX Quantum 3 (2022).","mla":"Ljubotina, Marko, et al. “Optimal Steering of Matrix Product States and Quantum Many-Body Scars.” PRX Quantum, vol. 3, no. 3, 030343, American Physical Society, 2022, doi:10.1103/prxquantum.3.030343.","ama":"Ljubotina M, Roos B, Abanin DA, Serbyn M. Optimal steering of matrix product states and quantum many-body scars. PRX Quantum. 2022;3(3). doi:10.1103/prxquantum.3.030343","ieee":"M. Ljubotina, B. Roos, D. A. Abanin, and M. Serbyn, “Optimal steering of matrix product states and quantum many-body scars,” PRX Quantum, vol. 3, no. 3. American Physical Society, 2022."},"year":"2022","department":[{"_id":"MaSe"},{"_id":"RoSe"}],"abstract":[{"text":"Ongoing development of quantum simulators allows for a progressively finer degree of control of quantum many-body systems. This motivates the development of efficient approaches to facilitate the control of such systems and enable the preparation of nontrivial quantum states. Here we formulate an approach to control quantum systems based on matrix product states (MPSs). We compare counterdiabatic and leakage minimization approaches to the so-called local steering problem that consists in finding the best value of the control parameters for generating a unitary evolution of the specific MPS in a given direction. In order to benchmark the different approaches, we apply them to the generalization of the PXP model known to exhibit coherent quantum dynamics due to quantum many-body scars. We find that the leakage-based approach generally outperforms the counterdiabatic framework and use it to construct a Floquet model with quantum scars. We perform the first steps towards global trajectory optimization and demonstrate entanglement steering capabilities in the generalized PXP model. Finally, we apply our leakage minimization approach to construct quantum scars in the periodically driven nonintegrable Ising model.","lang":"eng"}],"arxiv":1,"date_published":"2022-09-23T00:00:00Z","quality_controlled":"1","scopus_import":"1","article_type":"original","issue":"3","file_date_updated":"2023-01-30T11:02:50Z","doi":"10.1103/prxquantum.3.030343","date_created":"2023-01-16T10:01:56Z","intvolume":" 3","acknowledgement":"We thank A. A. Michailidis for insightful discussions. M.L. and M.S. acknowledge support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 850899). D.A. is supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 864597) and by the Swiss National Science Foundation. The infinite TEBD simulations were performed using the ITensor library [67].","oa":1,"status":"public","ddc":["530"],"month":"09","file":[{"success":1,"file_id":"12457","file_name":"2022_PRXQuantum_Ljubotina.pdf","date_created":"2023-01-30T11:02:50Z","file_size":7661905,"checksum":"ef8f0a1b5a019b3958009162de0fa4c3","access_level":"open_access","relation":"main_file","creator":"dernst","date_updated":"2023-01-30T11:02:50Z","content_type":"application/pdf"}],"corr_author":"1","volume":3,"publication_status":"published","type":"journal_article","keyword":["General Medicine"],"_id":"12276","ec_funded":1,"publication":"PRX Quantum","article_number":"030343","day":"23","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","has_accepted_license":"1","publisher":"American Physical Society","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"external_id":{"arxiv":["2204.02899"]}},{"date_published":"2022-09-20T00:00:00Z","arxiv":1,"abstract":[{"text":"Cell migration in confining physiological environments relies on the concerted dynamics of several cellular components, including protrusions, adhesions with the environment, and the cell nucleus. However, it remains poorly understood how the dynamic interplay of these components and the cell polarity determine the emergent migration behavior at the cellular scale. Here, we combine data-driven inference with a mechanistic bottom-up approach to develop a model for protrusion and polarity dynamics in confined cell migration, revealing how the cellular dynamics adapt to confining geometries. Specifically, we use experimental data of joint protrusion-nucleus migration trajectories of cells on confining micropatterns to systematically determine a mechanistic model linking the stochastic dynamics of cell polarity, protrusions, and nucleus. This model indicates that the cellular dynamics adapt to confining constrictions through a switch in the polarity dynamics from a negative to a positive self-reinforcing feedback loop. Our model further reveals how this feedback loop leads to stereotypical cycles of protrusion-nucleus dynamics that drive the migration of the cell through constrictions. These cycles are disrupted upon perturbation of cytoskeletal components, indicating that the positive feedback is controlled by cellular migration mechanisms. Our data-driven theoretical approach therefore identifies polarity feedback adaptation as a key mechanism in confined cell migration.","lang":"eng"}],"department":[{"_id":"EdHa"}],"intvolume":" 12","date_created":"2023-01-16T10:02:06Z","doi":"10.1103/physrevx.12.031041","file_date_updated":"2023-01-30T11:07:27Z","article_type":"original","issue":"3","quality_controlled":"1","scopus_import":"1","date_updated":"2023-08-04T10:25:49Z","isi":1,"author":[{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","first_name":"David","last_name":"Brückner","full_name":"Brückner, David"},{"first_name":"Matthew","last_name":"Schmitt","full_name":"Schmitt, Matthew"},{"full_name":"Fink, Alexandra","last_name":"Fink","first_name":"Alexandra"},{"full_name":"Ladurner, Georg","last_name":"Ladurner","first_name":"Georg"},{"first_name":"Johannes","full_name":"Flommersfeld, Johannes","last_name":"Flommersfeld"},{"first_name":"Nicolas","last_name":"Arlt","full_name":"Arlt, Nicolas"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rädler, Joachim O.","last_name":"Rädler","first_name":"Joachim O."},{"first_name":"Chase P.","full_name":"Broedersz, Chase P.","last_name":"Broedersz"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Geometry adaptation of protrusion and polarity dynamics in confined cell migration","year":"2022","citation":{"apa":"Brückner, D., Schmitt, M., Fink, A., Ladurner, G., Flommersfeld, J., Arlt, N., … Broedersz, C. P. (2022). Geometry adaptation of protrusion and polarity dynamics in confined cell migration. Physical Review X. American Physical Society. https://doi.org/10.1103/physrevx.12.031041","mla":"Brückner, David, et al. “Geometry Adaptation of Protrusion and Polarity Dynamics in Confined Cell Migration.” Physical Review X, vol. 12, no. 3, 031041, American Physical Society, 2022, doi:10.1103/physrevx.12.031041.","short":"D. Brückner, M. Schmitt, A. Fink, G. Ladurner, J. Flommersfeld, N. Arlt, E.B. Hannezo, J.O. Rädler, C.P. Broedersz, Physical Review X 12 (2022).","ista":"Brückner D, Schmitt M, Fink A, Ladurner G, Flommersfeld J, Arlt N, Hannezo EB, Rädler JO, Broedersz CP. 2022. Geometry adaptation of protrusion and polarity dynamics in confined cell migration. Physical Review X. 12(3), 031041.","chicago":"Brückner, David, Matthew Schmitt, Alexandra Fink, Georg Ladurner, Johannes Flommersfeld, Nicolas Arlt, Edouard B Hannezo, Joachim O. Rädler, and Chase P. Broedersz. “Geometry Adaptation of Protrusion and Polarity Dynamics in Confined Cell Migration.” Physical Review X. American Physical Society, 2022. https://doi.org/10.1103/physrevx.12.031041.","ieee":"D. Brückner et al., “Geometry adaptation of protrusion and polarity dynamics in confined cell migration,” Physical Review X, vol. 12, no. 3. American Physical Society, 2022.","ama":"Brückner D, Schmitt M, Fink A, et al. Geometry adaptation of protrusion and polarity dynamics in confined cell migration. Physical Review X. 2022;12(3). doi:10.1103/physrevx.12.031041"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2160-3308"]},"article_processing_charge":"No","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"day":"20","article_number":"031041","publication":"Physical Review X","_id":"12277","external_id":{"isi":["000861534700001"],"arxiv":["2106.01014"]},"publisher":"American Physical Society","has_accepted_license":"1","status":"public","oa":1,"ddc":["530","570"],"acknowledgement":"We thank Grzegorz Gradziuk, StevenRiedijk, Janni Harju, and M. R. Schnucki for helpful discussions, and Andriy Goychuk for advice on the image segmentation. This project\r\nwas funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Project No. 201269156—SFB 1032 (Projects B01 and B12). D. B. B. is supported by the NOMIS Foundation and in part by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM), as well as by the Joachim Herz Stiftung.","keyword":["General Physics and Astronomy"],"publication_status":"published","type":"journal_article","volume":12,"month":"09","file":[{"success":1,"file_id":"12458","file_name":"2022_PhysicalReviewX_Brueckner.pdf","file_size":4686804,"checksum":"40a8fbc3663bf07b37cb80020974d40d","date_created":"2023-01-30T11:07:27Z","access_level":"open_access","relation":"main_file","creator":"dernst","date_updated":"2023-01-30T11:07:27Z","content_type":"application/pdf"}]},{"scopus_import":"1","quality_controlled":"1","issue":"14","article_type":"original","file_date_updated":"2023-01-30T11:16:54Z","doi":"10.3390/nano12142492","date_created":"2023-01-16T10:02:31Z","intvolume":" 12","department":[{"_id":"ZhAl"}],"abstract":[{"lang":"eng","text":"Mercury telluride (HgTe) thin films with a critical thickness of 6.5 nm are predicted to possess a gapless Dirac-like band structure. We report a comprehensive study on gated and optically doped samples by magnetooptical spectroscopy in the THz range. The quasi-classical analysis of the cyclotron resonance allowed the mapping of the band dispersion of Dirac charge carriers in a broad range of electron and hole doping. A smooth transition through the charge neutrality point between Dirac holes and electrons was observed. An additional peak coming from a second type of holes with an almost density-independent mass of around 0.04m0 was detected in the hole-doping range and attributed to an asymmetric spin splitting of the Dirac cone. Spectroscopic evidence for disorder-induced band energy fluctuations could not be detected in present cyclotron resonance experiments."}],"date_published":"2022-07-20T00:00:00Z","article_processing_charge":"Yes","publication_identifier":{"issn":["2079-4991"]},"language":[{"iso":"eng"}],"citation":{"mla":"Shuvaev, Alexey, et al. “Band Structure near the Dirac Point in HgTe Quantum Wells with Critical Thickness.” Nanomaterials, vol. 12, no. 14, 2492, MDPI, 2022, doi:10.3390/nano12142492.","short":"A. Shuvaev, V. Dziom, J. Gospodarič, E.G. Novik, A.A. Dobretsova, N.N. Mikhailov, Z.D. Kvon, A. Pimenov, Nanomaterials 12 (2022).","chicago":"Shuvaev, Alexey, Vlad Dziom, Jan Gospodarič, Elena G. Novik, Alena A. Dobretsova, Nikolay N. Mikhailov, Ze Don Kvon, and Andrei Pimenov. “Band Structure near the Dirac Point in HgTe Quantum Wells with Critical Thickness.” Nanomaterials. MDPI, 2022. https://doi.org/10.3390/nano12142492.","ista":"Shuvaev A, Dziom V, Gospodarič J, Novik EG, Dobretsova AA, Mikhailov NN, Kvon ZD, Pimenov A. 2022. Band structure near the Dirac Point in HgTe quantum wells with critical thickness. Nanomaterials. 12(14), 2492.","apa":"Shuvaev, A., Dziom, V., Gospodarič, J., Novik, E. G., Dobretsova, A. A., Mikhailov, N. N., … Pimenov, A. (2022). Band structure near the Dirac Point in HgTe quantum wells with critical thickness. Nanomaterials. MDPI. https://doi.org/10.3390/nano12142492","ieee":"A. Shuvaev et al., “Band structure near the Dirac Point in HgTe quantum wells with critical thickness,” Nanomaterials, vol. 12, no. 14. MDPI, 2022.","ama":"Shuvaev A, Dziom V, Gospodarič J, et al. Band structure near the Dirac Point in HgTe quantum wells with critical thickness. Nanomaterials. 2022;12(14). doi:10.3390/nano12142492"},"year":"2022","title":"Band structure near the Dirac Point in HgTe quantum wells with critical thickness","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Shuvaev, Alexey","last_name":"Shuvaev","first_name":"Alexey"},{"id":"6A9A37C2-8C5C-11E9-AE53-F2FDE5697425","first_name":"Uladzislau","orcid":"0000-0002-1648-0999","last_name":"Dziom","full_name":"Dziom, Uladzislau"},{"first_name":"Jan","full_name":"Gospodarič, Jan","last_name":"Gospodarič"},{"full_name":"Novik, Elena G.","last_name":"Novik","first_name":"Elena G."},{"first_name":"Alena A.","last_name":"Dobretsova","full_name":"Dobretsova, Alena A."},{"first_name":"Nikolay N.","full_name":"Mikhailov, Nikolay N.","last_name":"Mikhailov"},{"first_name":"Ze Don","full_name":"Kvon, Ze Don","last_name":"Kvon"},{"first_name":"Andrei","last_name":"Pimenov","full_name":"Pimenov, Andrei"}],"isi":1,"date_updated":"2025-06-11T13:45:36Z","has_accepted_license":"1","publisher":"MDPI","external_id":{"pmid":["35889716"],"isi":["000834401600001"]},"_id":"12278","publication":"Nanomaterials","day":"20","article_number":"2492","pmid":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","month":"07","file":[{"access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_updated":"2023-01-30T11:16:54Z","success":1,"file_id":"12459","file_size":464840,"checksum":"efad6742f89f39a18bec63116dd689a0","date_created":"2023-01-30T11:16:54Z","file_name":"2022_Nanomaterials_Shuvaev.pdf"}],"volume":12,"type":"journal_article","publication_status":"published","keyword":["General Materials Science","General Chemical Engineering"],"acknowledgement":"This work was supported by the Austrian Science Funds (W1243, I 3456-N27, I 5539-N).\r\nOpen Access Funding by the Austrian Science Fund (FWF).","status":"public","oa":1,"ddc":["530"]},{"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2205.12871","open_access":"1"}],"external_id":{"isi":["000836397000001"],"arxiv":["2205.12871"]},"publisher":"American Physical Society","oa_version":"Preprint","_id":"12279","article_number":"L081301","day":"03","publication":"Physical Review Fluids","publication_status":"published","type":"journal_article","keyword":["Fluid Flow and Transfer Processes","Modeling and Simulation","Computational Mechanics"],"corr_author":"1","month":"08","volume":7,"oa":1,"status":"public","acknowledgement":"We thank G. Falkovich for discussion and Guy Han for technical support. We are grateful to N. Jha for his help in µPIV measurements. This work is partially supported by the grants from\r\nIsrael Science Foundation (ISF; grant #882/15 and grant #784/19) and Binational USA-Israel Foundation (BSF;grant #2016145). ","doi":"10.1103/physrevfluids.7.l081301","intvolume":" 7","date_created":"2023-01-16T10:02:40Z","quality_controlled":"1","scopus_import":"1","article_type":"original","issue":"8","abstract":[{"text":"We report frictional drag reduction and a complete flow relaminarization of elastic turbulence (ET) at vanishing inertia in a viscoelastic channel flow past an obstacle. We show that the intensity of the observed elastic waves and wall-normal vorticity correlate well with the measured drag above the onset of ET. Moreover, we find that the elastic wave frequency grows with the Weissenberg number, and at sufficiently high frequency it causes a decay of the elastic waves, resulting in ET attenuation and drag reduction. Thus, this allows us to substantiate a physical mechanism, involving the interaction of elastic waves with wall-normal vorticity fluctuations, leading to the drag reduction and relaminarization phenomena at low Reynolds number.","lang":"eng"}],"date_published":"2022-08-03T00:00:00Z","arxiv":1,"department":[{"_id":"BjHo"}],"citation":{"ama":"Kumar MV, Varshney A, Li D, Steinberg V. Relaminarization of elastic turbulence. Physical Review Fluids. 2022;7(8). doi:10.1103/physrevfluids.7.l081301","ieee":"M. V. Kumar, A. Varshney, D. Li, and V. Steinberg, “Relaminarization of elastic turbulence,” Physical Review Fluids, vol. 7, no. 8. American Physical Society, 2022.","apa":"Kumar, M. V., Varshney, A., Li, D., & Steinberg, V. (2022). Relaminarization of elastic turbulence. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/physrevfluids.7.l081301","chicago":"Kumar, M. Vijay, Atul Varshney, Dongyang Li, and Victor Steinberg. “Relaminarization of Elastic Turbulence.” Physical Review Fluids. American Physical Society, 2022. https://doi.org/10.1103/physrevfluids.7.l081301.","short":"M.V. Kumar, A. Varshney, D. Li, V. Steinberg, Physical Review Fluids 7 (2022).","ista":"Kumar MV, Varshney A, Li D, Steinberg V. 2022. Relaminarization of elastic turbulence. Physical Review Fluids. 7(8), L081301.","mla":"Kumar, M. Vijay, et al. “Relaminarization of Elastic Turbulence.” Physical Review Fluids, vol. 7, no. 8, L081301, American Physical Society, 2022, doi:10.1103/physrevfluids.7.l081301."},"year":"2022","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-990X"]},"date_updated":"2024-10-09T21:03:55Z","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"M. Vijay","full_name":"Kumar, M. Vijay","last_name":"Kumar"},{"id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999","first_name":"Atul","last_name":"Varshney","full_name":"Varshney, Atul"},{"first_name":"Dongyang","last_name":"Li","full_name":"Li, Dongyang"},{"full_name":"Steinberg, Victor","last_name":"Steinberg","first_name":"Victor"}],"title":"Relaminarization of elastic turbulence"},{"acknowledgement":"This work was supported by the European Research Council (https://erc.europa.eu/)\r\nCoG 863818 (ForM-SMArt) (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","status":"public","oa":1,"ddc":["000","570"],"volume":18,"corr_author":"1","file":[{"file_name":"2022_PlosCompBio_Schmid.pdf","checksum":"31b6b311b6731f1658277a9dfff6632c","date_created":"2023-01-30T11:28:13Z","file_size":3143222,"success":1,"file_id":"12460","creator":"dernst","date_updated":"2023-01-30T11:28:13Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"month":"06","keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"publication_status":"published","type":"journal_article","publication":"PLOS Computational Biology","day":"14","article_number":"e1010149","_id":"12280","ec_funded":1,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pmid":1,"has_accepted_license":"1","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"}],"external_id":{"pmid":["35700167"],"isi":["000843626800031"]},"publisher":"Public Library of Science","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Laura","orcid":"0000-0002-6978-7329","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","full_name":"Schmid, Laura","last_name":"Schmid"},{"first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","last_name":"Hilbe"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"title":"Direct reciprocity between individuals that use different strategy spaces","isi":1,"date_updated":"2025-04-14T07:52:47Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1553-7358"]},"article_processing_charge":"No","year":"2022","citation":{"apa":"Schmid, L., Hilbe, C., Chatterjee, K., & Nowak, M. (2022). Direct reciprocity between individuals that use different strategy spaces. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010149","mla":"Schmid, Laura, et al. “Direct Reciprocity between Individuals That Use Different Strategy Spaces.” PLOS Computational Biology, vol. 18, no. 6, e1010149, Public Library of Science, 2022, doi:10.1371/journal.pcbi.1010149.","short":"L. Schmid, C. Hilbe, K. Chatterjee, M. Nowak, PLOS Computational Biology 18 (2022).","chicago":"Schmid, Laura, Christian Hilbe, Krishnendu Chatterjee, and Martin Nowak. “Direct Reciprocity between Individuals That Use Different Strategy Spaces.” PLOS Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1010149.","ista":"Schmid L, Hilbe C, Chatterjee K, Nowak M. 2022. Direct reciprocity between individuals that use different strategy spaces. PLOS Computational Biology. 18(6), e1010149.","ieee":"L. Schmid, C. Hilbe, K. Chatterjee, and M. Nowak, “Direct reciprocity between individuals that use different strategy spaces,” PLOS Computational Biology, vol. 18, no. 6. Public Library of Science, 2022.","ama":"Schmid L, Hilbe C, Chatterjee K, Nowak M. Direct reciprocity between individuals that use different strategy spaces. PLOS Computational Biology. 2022;18(6). doi:10.1371/journal.pcbi.1010149"},"department":[{"_id":"KrCh"}],"date_published":"2022-06-14T00:00:00Z","abstract":[{"text":"In repeated interactions, players can use strategies that respond to the outcome of previous rounds. Much of the existing literature on direct reciprocity assumes that all competing individuals use the same strategy space. Here, we study both learning and evolutionary dynamics of players that differ in the strategy space they explore. We focus on the infinitely repeated donation game and compare three natural strategy spaces: memory-1 strategies, which consider the last moves of both players, reactive strategies, which respond to the last move of the co-player, and unconditional strategies. These three strategy spaces differ in the memory capacity that is needed. We compute the long term average payoff that is achieved in a pairwise learning process. We find that smaller strategy spaces can dominate larger ones. For weak selection, unconditional players dominate both reactive and memory-1 players. For intermediate selection, reactive players dominate memory-1 players. Only for strong selection and low cost-to-benefit ratio, memory-1 players dominate the others. We observe that the supergame between strategy spaces can be a social dilemma: maximum payoff is achieved if both players explore a larger strategy space, but smaller strategy spaces dominate.","lang":"eng"}],"file_date_updated":"2023-01-30T11:28:13Z","article_type":"original","issue":"6","quality_controlled":"1","scopus_import":"1","intvolume":" 18","date_created":"2023-01-16T10:02:51Z","doi":"10.1371/journal.pcbi.1010149"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1350-7265"]},"article_processing_charge":"No","year":"2022","citation":{"apa":"Franceschini, C., Gonçalves, P., & Sau, F. (2022). Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics. Bernoulli. Bernoulli Society for Mathematical Statistics and Probability. https://doi.org/10.3150/21-bej1390","ista":"Franceschini C, Gonçalves P, Sau F. 2022. Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics. Bernoulli. 28(2), 1340–1381.","short":"C. Franceschini, P. Gonçalves, F. Sau, Bernoulli 28 (2022) 1340–1381.","chicago":"Franceschini, Chiara, Patrícia Gonçalves, and Federico Sau. “Symmetric Inclusion Process with Slow Boundary: Hydrodynamics and Hydrostatics.” Bernoulli. Bernoulli Society for Mathematical Statistics and Probability, 2022. https://doi.org/10.3150/21-bej1390.","mla":"Franceschini, Chiara, et al. “Symmetric Inclusion Process with Slow Boundary: Hydrodynamics and Hydrostatics.” Bernoulli, vol. 28, no. 2, Bernoulli Society for Mathematical Statistics and Probability, 2022, pp. 1340–81, doi:10.3150/21-bej1390.","ama":"Franceschini C, Gonçalves P, Sau F. Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics. Bernoulli. 2022;28(2):1340-1381. doi:10.3150/21-bej1390","ieee":"C. Franceschini, P. Gonçalves, and F. Sau, “Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics,” Bernoulli, vol. 28, no. 2. Bernoulli Society for Mathematical Statistics and Probability, pp. 1340–1381, 2022."},"title":"Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Franceschini, Chiara","last_name":"Franceschini","first_name":"Chiara"},{"full_name":"Gonçalves, Patrícia","last_name":"Gonçalves","first_name":"Patrícia"},{"last_name":"Sau","full_name":"Sau, Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425","first_name":"Federico"}],"date_updated":"2025-04-14T07:44:00Z","isi":1,"article_type":"original","issue":"2","scopus_import":"1","quality_controlled":"1","intvolume":" 28","date_created":"2023-01-16T10:03:04Z","doi":"10.3150/21-bej1390","department":[{"_id":"JaMa"}],"date_published":"2022-05-01T00:00:00Z","arxiv":1,"abstract":[{"lang":"eng","text":"We study the hydrodynamic and hydrostatic limits of the one-dimensional open symmetric inclusion process with slow boundary. Depending on the value of the parameter tuning the interaction rate of the bulk of the system with the boundary, we obtain a linear heat equation with either Dirichlet, Robin or Neumann boundary conditions as hydrodynamic equation. In our approach, we combine duality and first-second class particle techniques to reduce the scaling limit of the inclusion process to the limiting behavior of a single, non-interacting, particle."}],"volume":28,"month":"05","keyword":["Statistics and Probability"],"type":"journal_article","publication_status":"published","acknowledgement":"C.F. and P.G. thank FCT/Portugal for support through the project UID/MAT/04459/2013.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovative programme (grant agreement No. 715734). F.S. was founded by the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411.\r\nF.S. wishes to thank Joe P. Chen for some fruitful discussions at an early stage of this work. F.S. thanks CAMGSD, IST, Lisbon, where part of this work has been done, and the European research and innovative programme No. 715734 for the kind hospitality.","page":"1340-1381","oa":1,"status":"public","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"external_id":{"arxiv":["2007.11998"],"isi":["000766619100025"]},"publisher":"Bernoulli Society for Mathematical Statistics and Probability","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2007.11998"}],"publication":"Bernoulli","day":"01","ec_funded":1,"_id":"12281","oa_version":"Preprint"},{"department":[{"_id":"SiHi"},{"_id":"LeSa"}],"abstract":[{"lang":"eng","text":"From a simple thought to a multicellular movement"}],"date_published":"2022-04-19T00:00:00Z","quality_controlled":"1","scopus_import":"1","article_type":"letter_note","issue":"8","doi":"10.1242/jcs.260017","date_created":"2023-01-16T10:03:14Z","intvolume":" 135","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","last_name":"Amberg"},{"full_name":"Stouffer, Melissa A","last_name":"Stouffer","first_name":"Melissa A","id":"4C9372C4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vercellino, Irene","last_name":"Vercellino","orcid":"0000-0001-5618-3449","first_name":"Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87"}],"title":"Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole","date_updated":"2024-10-09T21:03:55Z","isi":1,"article_processing_charge":"No","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"language":[{"iso":"eng"}],"citation":{"apa":"Amberg, N., Stouffer, M. A., & Vercellino, I. (2022). Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.260017","mla":"Amberg, Nicole, et al. “Operation STEM Fatale – How an Equity, Diversity and Inclusion Initiative Has Brought Us to Reflect on the Current Challenges in Cell Biology and Science as a Whole.” Journal of Cell Science, vol. 135, no. 8, 260017, The Company of Biologists, 2022, doi:10.1242/jcs.260017.","ista":"Amberg N, Stouffer MA, Vercellino I. 2022. Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. Journal of Cell Science. 135(8), 260017.","chicago":"Amberg, Nicole, Melissa A Stouffer, and Irene Vercellino. “Operation STEM Fatale – How an Equity, Diversity and Inclusion Initiative Has Brought Us to Reflect on the Current Challenges in Cell Biology and Science as a Whole.” Journal of Cell Science. The Company of Biologists, 2022. https://doi.org/10.1242/jcs.260017.","short":"N. Amberg, M.A. Stouffer, I. Vercellino, Journal of Cell Science 135 (2022).","ieee":"N. Amberg, M. A. Stouffer, and I. Vercellino, “Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole,” Journal of Cell Science, vol. 135, no. 8. The Company of Biologists, 2022.","ama":"Amberg N, Stouffer MA, Vercellino I. Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. Journal of Cell Science. 2022;135(8). doi:10.1242/jcs.260017"},"year":"2022","_id":"12282","publication":"Journal of Cell Science","day":"19","article_number":"260017","pmid":1,"oa_version":"None","publisher":"The Company of Biologists","external_id":{"pmid":["35438168"],"isi":["000798123600015"]},"acknowledgement":"The authors want to thank Professors Carrie Bernecky, Tom Henzinger, Martin Loose and Gaia Novarino for accepting to be interviewed, thus giving significant contribution to the discussion that lead to this article.","status":"public","month":"04","corr_author":"1","volume":135,"publication_status":"published","type":"journal_article"},{"publisher":"The Company of Biologists","external_id":{"isi":["000783840400010"],"pmid":["35383828"]},"has_accepted_license":"1","pmid":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","_id":"12283","article_number":"259234","publication":"Journal of Cell Science","day":"01","publication_status":"published","type":"journal_article","keyword":["Cell Biology"],"month":"04","file":[{"file_id":"12461","success":1,"file_name":"2022_JourCellBiology_Atherton.pdf","file_size":13868733,"date_created":"2023-01-30T11:41:01Z","checksum":"4346ed32cb7c89a8ca051c7da68a9a1c","relation":"main_file","access_level":"open_access","date_updated":"2023-01-30T11:41:01Z","content_type":"application/pdf","creator":"dernst"}],"volume":135,"ddc":["570"],"oa":1,"status":"public","acknowledgement":"J.A. was supported by a grant from the Medical Research Council (MRC), UK (MR/R000352/1) to C.A.M. Cryo-EM data were collected on equipment funded by the Wellcome Trust, UK (079605/Z/06/Z) and the Biotechnology and Biological Sciences Research Council (BBSRC) UK (BB/L014211/1). F.F.’s salary and institute were supported by Inserm (Institut National de la Santé et de la Recherche Médicale), CNRS (Centre National de la Recherche Scientifique) and Sorbonne Université. F.F.’s group was particularly supported by Agence Nationale de la\r\nRecherche (ANR-16-CE16-0011-03) and Seventh Framework Programme (EUHEALTH-\r\n2013, DESIRE, N° 60253; also funding M.S.’s salary) and the European Cooperation in Science and Technology (COST Action CA16118). Open Access funding provided by Birkbeck College: Birkbeck University of London. Deposited in PMC for immediate release.","doi":"10.1242/jcs.259234","date_created":"2023-01-16T10:03:24Z","intvolume":" 135","quality_controlled":"1","scopus_import":"1","issue":"7","article_type":"original","file_date_updated":"2023-01-30T11:41:01Z","abstract":[{"text":"Neurons extend axons to form the complex circuitry of the mature brain. This depends on the coordinated response and continuous remodelling of the microtubule and F-actin networks in the axonal growth cone. Growth cone architecture remains poorly understood at nanoscales. We therefore investigated mouse hippocampal neuron growth cones using cryo-electron tomography to directly visualise their three-dimensional subcellular architecture with molecular detail. Our data showed that the hexagonal arrays of actin bundles that form filopodia penetrate and terminate deep within the growth cone interior. We directly observed the modulation of these and other growth cone actin bundles by alteration of individual F-actin helical structures. Microtubules with blunt, slightly flared or gently curved ends predominated in the growth cone, frequently contained lumenal particles and exhibited lattice defects. Investigation of the effect of absence of doublecortin, a neurodevelopmental cytoskeleton regulator, on growth cone cytoskeleton showed no major anomalies in overall growth cone organisation or in F-actin subpopulations. However, our data suggested that microtubules sustained more structural defects, highlighting the importance of microtubule integrity during growth cone migration.","lang":"eng"}],"date_published":"2022-04-01T00:00:00Z","department":[{"_id":"SiHi"}],"citation":{"apa":"Atherton, J., Stouffer, M. A., Francis, F., & Moores, C. A. (2022). Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.259234","mla":"Atherton, Joseph, et al. “Visualising the Cytoskeletal Machinery in Neuronal Growth Cones Using Cryo-Electron Tomography.” Journal of Cell Science, vol. 135, no. 7, 259234, The Company of Biologists, 2022, doi:10.1242/jcs.259234.","chicago":"Atherton, Joseph, Melissa A Stouffer, Fiona Francis, and Carolyn A. Moores. “Visualising the Cytoskeletal Machinery in Neuronal Growth Cones Using Cryo-Electron Tomography.” Journal of Cell Science. The Company of Biologists, 2022. https://doi.org/10.1242/jcs.259234.","short":"J. Atherton, M.A. Stouffer, F. Francis, C.A. Moores, Journal of Cell Science 135 (2022).","ista":"Atherton J, Stouffer MA, Francis F, Moores CA. 2022. Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. Journal of Cell Science. 135(7), 259234.","ieee":"J. Atherton, M. A. Stouffer, F. Francis, and C. A. Moores, “Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography,” Journal of Cell Science, vol. 135, no. 7. The Company of Biologists, 2022.","ama":"Atherton J, Stouffer MA, Francis F, Moores CA. Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. Journal of Cell Science. 2022;135(7). doi:10.1242/jcs.259234"},"year":"2022","article_processing_charge":"No","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"language":[{"iso":"eng"}],"isi":1,"date_updated":"2023-08-04T10:28:34Z","title":"Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Atherton, Joseph","last_name":"Atherton","first_name":"Joseph"},{"full_name":"Stouffer, Melissa A","last_name":"Stouffer","first_name":"Melissa A","id":"4C9372C4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Francis, Fiona","last_name":"Francis","first_name":"Fiona"},{"last_name":"Moores","full_name":"Moores, Carolyn A.","first_name":"Carolyn A."}]},{"publication_identifier":{"eissn":["1077-8926"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2022","citation":{"ama":"Cooley O, Kang M, Zalla J. Loose cores and cycles in random hypergraphs. The Electronic Journal of Combinatorics. 2022;29(4). doi:10.37236/10794","ieee":"O. Cooley, M. Kang, and J. Zalla, “Loose cores and cycles in random hypergraphs,” The Electronic Journal of Combinatorics, vol. 29, no. 4. The Electronic Journal of Combinatorics, 2022.","ista":"Cooley O, Kang M, Zalla J. 2022. Loose cores and cycles in random hypergraphs. The Electronic Journal of Combinatorics. 29(4), P4.13.","short":"O. Cooley, M. Kang, J. Zalla, The Electronic Journal of Combinatorics 29 (2022).","chicago":"Cooley, Oliver, Mihyun Kang, and Julian Zalla. “Loose Cores and Cycles in Random Hypergraphs.” The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics, 2022. https://doi.org/10.37236/10794.","mla":"Cooley, Oliver, et al. “Loose Cores and Cycles in Random Hypergraphs.” The Electronic Journal of Combinatorics, vol. 29, no. 4, P4.13, The Electronic Journal of Combinatorics, 2022, doi:10.37236/10794.","apa":"Cooley, O., Kang, M., & Zalla, J. (2022). Loose cores and cycles in random hypergraphs. The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics. https://doi.org/10.37236/10794"},"author":[{"first_name":"Oliver","id":"43f4ddd0-a46b-11ec-8df6-ef3703bd721d","full_name":"Cooley, Oliver","last_name":"Cooley"},{"first_name":"Mihyun","last_name":"Kang","full_name":"Kang, Mihyun"},{"last_name":"Zalla","full_name":"Zalla, Julian","first_name":"Julian"}],"title":"Loose cores and cycles in random hypergraphs","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T10:29:18Z","isi":1,"issue":"4","article_type":"original","file_date_updated":"2023-01-30T11:45:13Z","quality_controlled":"1","scopus_import":"1","date_created":"2023-01-16T10:03:57Z","intvolume":" 29","doi":"10.37236/10794","department":[{"_id":"MaKw"}],"date_published":"2022-10-21T00:00:00Z","abstract":[{"lang":"eng","text":"Inspired by the study of loose cycles in hypergraphs, we define the loose core in hypergraphs as a structurewhich mirrors the close relationship between cycles and $2$-cores in graphs. We prove that in the $r$-uniform binomial random hypergraph $H^r(n,p)$, the order of the loose core undergoes a phase transition at a certain critical threshold and determine this order, as well as the number of edges, asymptotically in the subcritical and supercritical regimes.
\r\nOur main tool is an algorithm called CoreConstruct, which enables us to analyse a peeling process for the loose core. By analysing this algorithm we determine the asymptotic degree distribution of vertices in the loose core and in particular how many vertices and edges the loose core contains. As a corollary we obtain an improved upper bound on the length of the longest loose cycle in $H^r(n,p)$."}],"volume":29,"file":[{"file_size":626953,"date_created":"2023-01-30T11:45:13Z","checksum":"00122b2459f09b5ae43073bfba565e94","file_name":"2022_ElecJournCombinatorics_Cooley_Kang_Zalla.pdf","success":1,"file_id":"12462","creator":"dernst","content_type":"application/pdf","date_updated":"2023-01-30T11:45:13Z","access_level":"open_access","relation":"main_file"}],"month":"10","keyword":["Computational Theory and Mathematics","Geometry and Topology","Theoretical Computer Science","Applied Mathematics","Discrete Mathematics and Combinatorics"],"publication_status":"published","type":"journal_article","acknowledgement":"Supported by Austrian Science Fund (FWF): I3747, W1230.","oa":1,"ddc":["510"],"status":"public","has_accepted_license":"1","publisher":"The Electronic Journal of Combinatorics","external_id":{"isi":["000876763300001"]},"day":"21","publication":"The Electronic Journal of Combinatorics","article_number":"P4.13","_id":"12286","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa_version":"Published Version"},{"file":[{"access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_updated":"2023-01-30T11:50:53Z","success":1,"file_id":"12463","date_created":"2023-01-30T11:50:53Z","checksum":"5a2a65e3e7225090c3d8199f3bbd7b7b","file_size":8506811,"file_name":"2022_eLife_Sumser.pdf"}],"month":"09","corr_author":"1","volume":11,"publication_status":"published","type":"journal_article","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"acknowledgement":"We thank F Marr for technical assistance, A Murray for RVdG-CVS-N2c viruses and Neuro2A packaging cell-lines and J Watson for reading the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Imaging and Optics Facility (IOF) and the Preclinical Facility (PCF). This project was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC advanced grant No 692692, PJ, ERC starting grant No 756502, MJ), the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, PJ), the Human Frontier Science Program (LT000256/2018-L, AS) and EMBO (ALTF 1098-2017, AS).","status":"public","ddc":["570"],"oa":1,"has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publisher":"eLife Sciences Publications","project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692"},{"name":"Circuits of Visual Attention","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"756502"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1098-2017","name":"Connecting sensory with motor processing in the superior colliculus"}],"external_id":{"pmid":["36040301"],"isi":["000892204300001"]},"ec_funded":1,"_id":"12288","day":"15","article_number":"79848","publication":"eLife","pmid":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","article_processing_charge":"No","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"citation":{"mla":"Sumser, Anton L., et al. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” ELife, vol. 11, 79848, eLife Sciences Publications, 2022, doi:10.7554/elife.79848.","ista":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. 2022. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. eLife. 11, 79848.","short":"A.L. Sumser, M.A. Jösch, P.M. Jonas, Y. Ben Simon, ELife 11 (2022).","chicago":"Sumser, Anton L, Maximilian A Jösch, Peter M Jonas, and Yoav Ben Simon. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/elife.79848.","apa":"Sumser, A. L., Jösch, M. A., Jonas, P. M., & Ben Simon, Y. (2022). Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.79848","ieee":"A. L. Sumser, M. A. Jösch, P. M. Jonas, and Y. Ben Simon, “Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling,” eLife, vol. 11. eLife Sciences Publications, 2022.","ama":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. eLife. 2022;11. doi:10.7554/elife.79848"},"year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling","author":[{"last_name":"Sumser","full_name":"Sumser, Anton L","id":"3320A096-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4792-1881","first_name":"Anton L"},{"last_name":"Jösch","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","orcid":"0000-0002-3937-1330"},{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","full_name":"Ben Simon, Yoav","last_name":"Ben Simon"}],"isi":1,"date_updated":"2025-04-15T08:29:05Z","scopus_import":"1","quality_controlled":"1","article_type":"original","file_date_updated":"2023-01-30T11:50:53Z","doi":"10.7554/elife.79848","date_created":"2023-01-16T10:04:15Z","intvolume":" 11","department":[{"_id":"MaJö"},{"_id":"PeJo"}],"abstract":[{"lang":"eng","text":"To understand the function of neuronal circuits, it is crucial to disentangle the connectivity patterns within the network. However, most tools currently used to explore connectivity have low throughput, low selectivity, or limited accessibility. Here, we report the development of an improved packaging system for the production of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers orders of magnitude higher with no background contamination, at a fraction of the production time, while preserving the efficiency of transsynaptic labeling. Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal populations, tailored for diverse experimental requirements. We demonstrate the power and flexibility of the new system by uncovering hidden local and distal inhibitory connections in the mouse hippocampal formation and by imaging the functional properties of a cortical microcircuit across weeks. Our novel production pipeline provides a convenient approach to generate new rabies vectors, while our toolkit flexibly and efficiently expands the current capacity to label, manipulate and image the neuronal activity of interconnected neuronal circuits in vitro and in vivo."}],"date_published":"2022-09-15T00:00:00Z"},{"has_accepted_license":"1","external_id":{"isi":["000910863700003"]},"project":[{"grant_number":"101020331","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"publisher":"Institute of Mathematical Statistics","day":"12","publication":"Electronic Journal of Probability","_id":"12290","ec_funded":1,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":27,"corr_author":"1","month":"09","file":[{"file_id":"12464","success":1,"file_name":"2022_ElecJournProbability_Cipolloni.pdf","date_created":"2023-01-30T11:59:21Z","file_size":502149,"checksum":"bb647b48fbdb59361210e425c220cdcb","relation":"main_file","access_level":"open_access","date_updated":"2023-01-30T11:59:21Z","content_type":"application/pdf","creator":"dernst"}],"keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"type":"journal_article","publication_status":"published","acknowledgement":"L. Erdős was supported by ERC Advanced Grant “RMTBeyond” No. 101020331. D. Schröder was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation.","page":"1-38","ddc":["510"],"status":"public","oa":1,"file_date_updated":"2023-01-30T11:59:21Z","article_type":"original","scopus_import":"1","quality_controlled":"1","intvolume":" 27","date_created":"2023-01-16T10:04:38Z","doi":"10.1214/22-ejp838","department":[{"_id":"LaEr"}],"date_published":"2022-09-12T00:00:00Z","abstract":[{"text":"We prove local laws, i.e. optimal concentration estimates for arbitrary products of resolvents of a Wigner random matrix with deterministic matrices in between. We find that the size of such products heavily depends on whether some of the deterministic matrices are traceless. Our estimates correctly account for this dependence and they hold optimally down to the smallest possible spectral scale.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1083-6489"]},"article_processing_charge":"No","year":"2022","citation":{"short":"G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 27 (2022) 1–38.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Optimal multi-resolvent local laws for Wigner matrices. Electronic Journal of Probability. 27, 1–38.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Optimal Multi-Resolvent Local Laws for Wigner Matrices.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2022. https://doi.org/10.1214/22-ejp838.","mla":"Cipolloni, Giorgio, et al. “Optimal Multi-Resolvent Local Laws for Wigner Matrices.” Electronic Journal of Probability, vol. 27, Institute of Mathematical Statistics, 2022, pp. 1–38, doi:10.1214/22-ejp838.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2022). Optimal multi-resolvent local laws for Wigner matrices. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/22-ejp838","ama":"Cipolloni G, Erdös L, Schröder DJ. Optimal multi-resolvent local laws for Wigner matrices. Electronic Journal of Probability. 2022;27:1-38. doi:10.1214/22-ejp838","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Optimal multi-resolvent local laws for Wigner matrices,” Electronic Journal of Probability, vol. 27. Institute of Mathematical Statistics, pp. 1–38, 2022."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Optimal multi-resolvent local laws for Wigner matrices","author":[{"full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","orcid":"0000-0002-4901-7992","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"Erdös, László"},{"last_name":"Schröder","full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","first_name":"Dominik J"}],"isi":1,"date_updated":"2025-04-14T07:57:19Z"},{"type":"book_chapter","publication_status":"published","volume":676,"month":"10","status":"public","page":"49-69","publisher":"Elsevier","external_id":{"pmid":["36280361"]},"oa_version":"None","pmid":1,"day":"21","publication":"Biochemical Pathways and Environmental Responses in Plants: Part A","_id":"12294","year":"2022","citation":{"apa":"Kumar, R., Reichelt, M., & Bisht, N. C. (2022). An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis. In J. Jez (Ed.), Biochemical Pathways and Environmental Responses in Plants: Part A (Vol. 676, pp. 49–69). Elsevier. https://doi.org/10.1016/bs.mie.2022.07.019","chicago":"Kumar, Roshan, Michael Reichelt, and Naveen C. Bisht. “An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis.” In Biochemical Pathways and Environmental Responses in Plants: Part A, edited by Joseph Jez, 676:49–69. Elsevier, 2022. https://doi.org/10.1016/bs.mie.2022.07.019.","short":"R. Kumar, M. Reichelt, N.C. Bisht, in:, J. Jez (Ed.), Biochemical Pathways and Environmental Responses in Plants: Part A, Elsevier, 2022, pp. 49–69.","ista":"Kumar R, Reichelt M, Bisht NC. 2022.An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis. In: Biochemical Pathways and Environmental Responses in Plants: Part A. Methods in Enzymology, vol. 676, 49–69.","mla":"Kumar, Roshan, et al. “An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis.” Biochemical Pathways and Environmental Responses in Plants: Part A, edited by Joseph Jez, vol. 676, Elsevier, 2022, pp. 49–69, doi:10.1016/bs.mie.2022.07.019.","ama":"Kumar R, Reichelt M, Bisht NC. An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis. In: Jez J, ed. Biochemical Pathways and Environmental Responses in Plants: Part A. Vol 676. Elsevier; 2022:49-69. doi:10.1016/bs.mie.2022.07.019","ieee":"R. Kumar, M. Reichelt, and N. C. Bisht, “An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis,” in Biochemical Pathways and Environmental Responses in Plants: Part A, vol. 676, J. Jez, Ed. Elsevier, 2022, pp. 49–69."},"publication_identifier":{"issn":["0076-6879"],"isbn":["9780323955614"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","date_updated":"2025-07-03T14:02:58Z","editor":[{"full_name":"Jez, Joseph","last_name":"Jez","first_name":"Joseph"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis","author":[{"id":"50e95140-3016-11ec-9e1a-881b648a1367","first_name":"Roshan","orcid":"0000-0002-0346-9125","last_name":"Kumar","full_name":"Kumar, Roshan"},{"first_name":"Michael","last_name":"Reichelt","full_name":"Reichelt, Michael"},{"first_name":"Naveen C.","full_name":"Bisht, Naveen C.","last_name":"Bisht"}],"date_created":"2023-01-16T10:05:13Z","intvolume":" 676","doi":"10.1016/bs.mie.2022.07.019","quality_controlled":"1","scopus_import":"1","date_published":"2022-10-21T00:00:00Z","abstract":[{"lang":"eng","text":"Brassicaceae are blessed with specialized metabolites called glucosinolates (GSLs), which along with their degradation products, are beneficial in agriculture and human health. To date, more than 130 GSL structures have been identified, mostly derived from the amino acid methionine. The biosynthesis of methionine-derived aliphatic GSLs starts with a side-chain elongation step involving a recursive three-step cyclic process that incorporates a new methylene group into the 2-oxo acid to form a series of elongated 2-oxo acids. Methylthioalkylmalate synthase (MAMS) catalyzes the first committed step in the side-chain elongation of methionine-derived GSLs. The substrate specificity of MAMS with different 2-oxo acids determines whether reaction products of a given cycle enter for an additional round of chain elongation or enter into core GSLs structure formation. Multiple MAMS encoding genes are present in the Brassicaceae species and are known to play a central role in shaping the diverse profile of aliphatic GSLs. We recently established a highly sensitive LC-MS/MS-based methodology that quantifies the MAMS activity by estimating the amount of the next intermediate of the pathway, the 2-malate derivatives. Overall, this chapter describes the protocol for the expression, purification, and steady-state kinetic analysis of the recombinant MAMS protein."}],"alternative_title":["Methods in Enzymology"]},{"title":"Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback","author":[{"last_name":"Gelashvili","full_name":"Gelashvili, Rati","first_name":"Rati"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"first_name":"Alberto","last_name":"Sonnino","full_name":"Sonnino, Alberto"},{"full_name":"Spiegelman, Alexander","last_name":"Spiegelman","first_name":"Alexander"},{"first_name":"Zhuolun","full_name":"Xiang, Zhuolun","last_name":"Xiang"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-10T09:52:23Z","isi":1,"article_processing_charge":"No","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783031182839"],"eissn":["1611-3349"],"isbn":["9783031182822"]},"language":[{"iso":"eng"}],"citation":{"apa":"Gelashvili, R., Kokoris Kogias, E., Sonnino, A., Spiegelman, A., & Xiang, Z. (2022). Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback. In Financial Cryptography and Data Security (Vol. 13411, pp. 296–315). Radisson Grenada Beach Resort, Grenada: Springer Nature. https://doi.org/10.1007/978-3-031-18283-9_14","mla":"Gelashvili, Rati, et al. “Jolteon and Ditto: Network-Adaptive Efficient Consensus with Asynchronous Fallback.” Financial Cryptography and Data Security, vol. 13411, Springer Nature, 2022, pp. 296–315, doi:10.1007/978-3-031-18283-9_14.","short":"R. Gelashvili, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, Z. Xiang, in:, Financial Cryptography and Data Security, Springer Nature, 2022, pp. 296–315.","ista":"Gelashvili R, Kokoris Kogias E, Sonnino A, Spiegelman A, Xiang Z. 2022. Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback. Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 13411, 296–315.","chicago":"Gelashvili, Rati, Eleftherios Kokoris Kogias, Alberto Sonnino, Alexander Spiegelman, and Zhuolun Xiang. “Jolteon and Ditto: Network-Adaptive Efficient Consensus with Asynchronous Fallback.” In Financial Cryptography and Data Security, 13411:296–315. Springer Nature, 2022. https://doi.org/10.1007/978-3-031-18283-9_14.","ieee":"R. Gelashvili, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, and Z. Xiang, “Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback,” in Financial Cryptography and Data Security, Radisson Grenada Beach Resort, Grenada, 2022, vol. 13411, pp. 296–315.","ama":"Gelashvili R, Kokoris Kogias E, Sonnino A, Spiegelman A, Xiang Z. Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback. In: Financial Cryptography and Data Security. Vol 13411. Springer Nature; 2022:296-315. doi:10.1007/978-3-031-18283-9_14"},"year":"2022","conference":{"end_date":"2022-05-06","location":"Radisson Grenada Beach Resort, Grenada","name":"FC: Financial Cryptography","start_date":"2022-05-02"},"department":[{"_id":"ElKo"}],"alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Existing committee-based Byzantine state machine replication (SMR) protocols, typically deployed in production blockchains, face a clear trade-off: (1) they either achieve linear communication cost in the steady state, but sacrifice liveness during periods of asynchrony, or (2) they are robust (progress with probability one) but pay quadratic communication cost. We believe this trade-off is unwarranted since existing linear protocols still have asymptotic quadratic cost in the worst case. We design Ditto, a Byzantine SMR protocol that enjoys the best of both worlds: optimal communication on and off the steady state (linear and quadratic, respectively) and progress guarantee under asynchrony and DDoS attacks. We achieve this by replacing the view-synchronization of partially synchronous protocols with an asynchronous fallback mechanism at no extra asymptotic cost. Specifically, we start from HotStuff, a state-of-the-art linear protocol, and gradually build Ditto. As a separate contribution and an intermediate step, we design a 2-chain version of HotStuff, Jolteon, which leverages a quadratic view-change mechanism to reduce the latency of the standard 3-chain HotStuff. We implement and experimentally evaluate all our systems to prove that breaking the robustness-efficiency trade-off is in the realm of practicality."}],"arxiv":1,"date_published":"2022-10-22T00:00:00Z","quality_controlled":"1","scopus_import":"1","doi":"10.1007/978-3-031-18283-9_14","date_created":"2023-01-16T10:05:51Z","intvolume":" 13411","page":"296-315","acknowledgement":"We thank our shepherd Aniket Kate and the anonymous reviewers at FC 2022 for their helpful feedback. This work is supported by the Novi team at Facebook. We also thank the Novi Research and Engineering teams for valuable feedback, and in particular Mathieu Baudet, Andrey Chursin, George Danezis, Zekun Li, and Dahlia Malkhi for discussions that shaped this work.","status":"public","oa":1,"month":"10","volume":13411,"type":"conference","publication_status":"published","_id":"12298","publication":"Financial Cryptography and Data Security","day":"22","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2106.10362"}],"publisher":"Springer Nature","external_id":{"isi":["001423640200014"],"arxiv":["2106.10362"]}},{"department":[{"_id":"ElKo"}],"day":"27","publication":"2022 IEEE Symposium on Security and Privacy","conference":{"start_date":"2022-05-23","location":"San Francisco, CA, United States","name":"SP: Symposium on Security and Privacy","end_date":"2022-05-26"},"_id":"12300","oa_version":"Preprint","date_published":"2022-07-27T00:00:00Z","abstract":[{"text":"Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted third party and is a building block to decentralized protocols such as randomness beacons, threshold signatures, and general multiparty computation. Until recently, DKG protocols have assumed the synchronous model and thus are vulnerable when their underlying network assumptions do not hold. The recent advancements in asynchronous DKG protocols are insufficient as they either have poor efficiency or limited functionality, resulting in a lack of concrete implementations. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol. In a network of n nodes, our ADKG protocol can tolerate up to t2022 IEEE Symposium on Security and Privacy, San Francisco, CA, United States, 2022, pp. 2518–2534.","ama":"Das S, Yurek T, Xiang Z, Miller A, Kokoris Kogias E, Ren L. Practical asynchronous distributed key generation. In: 2022 IEEE Symposium on Security and Privacy. Institute of Electrical and Electronics Engineers; 2022:2518-2534. doi:10.1109/sp46214.2022.9833584","apa":"Das, S., Yurek, T., Xiang, Z., Miller, A., Kokoris Kogias, E., & Ren, L. (2022). Practical asynchronous distributed key generation. In 2022 IEEE Symposium on Security and Privacy (pp. 2518–2534). San Francisco, CA, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/sp46214.2022.9833584","mla":"Das, Sourav, et al. “Practical Asynchronous Distributed Key Generation.” 2022 IEEE Symposium on Security and Privacy, Institute of Electrical and Electronics Engineers, 2022, pp. 2518–34, doi:10.1109/sp46214.2022.9833584.","ista":"Das S, Yurek T, Xiang Z, Miller A, Kokoris Kogias E, Ren L. 2022. Practical asynchronous distributed key generation. 2022 IEEE Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 2518–2534.","chicago":"Das, Sourav, Thomas Yurek, Zhuolun Xiang, Andrew Miller, Eleftherios Kokoris Kogias, and Ling Ren. “Practical Asynchronous Distributed Key Generation.” In 2022 IEEE Symposium on Security and Privacy, 2518–34. Institute of Electrical and Electronics Engineers, 2022. https://doi.org/10.1109/sp46214.2022.9833584.","short":"S. Das, T. Yurek, Z. Xiang, A. Miller, E. Kokoris Kogias, L. Ren, in:, 2022 IEEE Symposium on Security and Privacy, Institute of Electrical and Electronics Engineers, 2022, pp. 2518–2534."}}]