[{"date_updated":"2023-08-04T09:48:56Z","publication":"Frontiers in Neuroscience","article_number":"943355","article_type":"original","oa":1,"keyword":["General Neuroscience"],"year":"2022","publisher":"Frontiers Media","intvolume":" 16","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"AnSa"}],"date_created":"2023-01-16T09:56:43Z","scopus_import":"1","date_published":"2022-09-20T00:00:00Z","external_id":{"isi":["000866287100001"]},"publication_identifier":{"issn":["1662-453X"]},"publication_status":"published","status":"public","acknowledgement":"This work was supported by grants from the Swedish Research Council (grant no. 2015-00143) and the European Research Council (grant no. 340890).","_id":"12251","title":"Influence of denaturants on amyloid β42 aggregation kinetics","author":[{"last_name":"Weiffert","full_name":"Weiffert, Tanja","first_name":"Tanja"},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"last_name":"Curk","full_name":"Curk, Samo","first_name":"Samo"},{"full_name":"Cukalevski, Risto","last_name":"Cukalevski","first_name":"Risto"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"last_name":"Knowles","full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J."},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"}],"doi":"10.3389/fnins.2022.943355","abstract":[{"text":"Amyloid formation is linked to devastating neurodegenerative diseases, motivating detailed studies of the mechanisms of amyloid formation. For Aβ, the peptide associated with Alzheimer’s disease, the mechanism and rate of aggregation have been established for a range of variants and conditions in vitro and in bodily fluids. A key outstanding question is how the relative stabilities of monomers, fibrils and intermediates affect each step in the fibril formation process. By monitoring the kinetics of aggregation of Aβ42, in the presence of urea or guanidinium hydrochloride (GuHCl), we here determine the rates of the underlying microscopic steps and establish the importance of changes in relative stability induced by the presence of denaturant for each individual step. Denaturants shift the equilibrium towards the unfolded state of each species. We find that a non-ionic denaturant, urea, reduces the overall aggregation rate, and that the effect on nucleation is stronger than the effect on elongation. Urea reduces the rate of secondary nucleation by decreasing the coverage of fibril surfaces and the rate of nucleus formation. It also reduces the rate of primary nucleation, increasing its reaction order. The ionic denaturant, GuHCl, accelerates the aggregation at low denaturant concentrations and decelerates the aggregation at high denaturant concentrations. Below approximately 0.25 M GuHCl, the screening of repulsive electrostatic interactions between peptides by the charged denaturant dominates, leading to an increased aggregation rate. At higher GuHCl concentrations, the electrostatic repulsion is completely screened, and the denaturing effect dominates. The results illustrate how the differential effects of denaturants on stability of monomer, oligomer and fibril translate to differential effects on microscopic steps, with the rate of nucleation being most strongly reduced.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2023-01-30T09:15:13Z","file_id":"12442","file_size":19798610,"relation":"main_file","creator":"dernst","file_name":"2022_FrontiersNeuroscience_Weiffert2.pdf","date_updated":"2023-01-30T09:15:13Z","success":1,"checksum":"e67d16113ffb4fb4fa38a183d169f210","content_type":"application/pdf","access_level":"open_access"}],"volume":16,"article_processing_charge":"No","has_accepted_license":"1","ddc":["570"],"file_date_updated":"2023-01-30T09:15:13Z","month":"09","citation":{"mla":"Weiffert, Tanja, et al. “Influence of Denaturants on Amyloid Β42 Aggregation Kinetics.” Frontiers in Neuroscience, vol. 16, 943355, Frontiers Media, 2022, doi:10.3389/fnins.2022.943355.","chicago":"Weiffert, Tanja, Georg Meisl, Samo Curk, Risto Cukalevski, Anđela Šarić, Tuomas P. J. Knowles, and Sara Linse. “Influence of Denaturants on Amyloid Β42 Aggregation Kinetics.” Frontiers in Neuroscience. Frontiers Media, 2022. https://doi.org/10.3389/fnins.2022.943355.","ista":"Weiffert T, Meisl G, Curk S, Cukalevski R, Šarić A, Knowles TPJ, Linse S. 2022. Influence of denaturants on amyloid β42 aggregation kinetics. Frontiers in Neuroscience. 16, 943355.","short":"T. Weiffert, G. Meisl, S. Curk, R. Cukalevski, A. Šarić, T.P.J. Knowles, S. Linse, Frontiers in Neuroscience 16 (2022).","ama":"Weiffert T, Meisl G, Curk S, et al. Influence of denaturants on amyloid β42 aggregation kinetics. Frontiers in Neuroscience. 2022;16. doi:10.3389/fnins.2022.943355","apa":"Weiffert, T., Meisl, G., Curk, S., Cukalevski, R., Šarić, A., Knowles, T. P. J., & Linse, S. (2022). Influence of denaturants on amyloid β42 aggregation kinetics. Frontiers in Neuroscience. Frontiers Media. https://doi.org/10.3389/fnins.2022.943355","ieee":"T. Weiffert et al., “Influence of denaturants on amyloid β42 aggregation kinetics,” Frontiers in Neuroscience, vol. 16. Frontiers Media, 2022."},"day":"20","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/4.0/"},{"has_accepted_license":"1","volume":13,"article_processing_charge":"No","file":[{"date_updated":"2023-01-30T09:22:26Z","success":1,"checksum":"f8f5d8110710033d0532e7e08bf9dad4","content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","file_size":5695892,"file_name":"2022_FrontiersImmunology_Dormeshkin.pdf","date_created":"2023-01-30T09:22:26Z","file_id":"12443"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","citation":{"mla":"Dormeshkin, Dmitri, et al. “Isolation of an Escape-Resistant SARS-CoV-2 Neutralizing Nanobody from a Novel Synthetic Nanobody Library.” Frontiers in Immunology, vol. 13, 965446, Frontiers Media, 2022, doi:10.3389/fimmu.2022.965446.","chicago":"Dormeshkin, Dmitri, Michail Shapira, Simon Dubovik, Anton Kavaleuski, Mikalai Katsin, Alexandr Migas, Alexander Meleshko, and Sergei Semyonov. “Isolation of an Escape-Resistant SARS-CoV-2 Neutralizing Nanobody from a Novel Synthetic Nanobody Library.” Frontiers in Immunology. Frontiers Media, 2022. https://doi.org/10.3389/fimmu.2022.965446.","ieee":"D. Dormeshkin et al., “Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library,” Frontiers in Immunology, vol. 13. Frontiers Media, 2022.","apa":"Dormeshkin, D., Shapira, M., Dubovik, S., Kavaleuski, A., Katsin, M., Migas, A., … Semyonov, S. (2022). Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Frontiers in Immunology. Frontiers Media. https://doi.org/10.3389/fimmu.2022.965446","ista":"Dormeshkin D, Shapira M, Dubovik S, Kavaleuski A, Katsin M, Migas A, Meleshko A, Semyonov S. 2022. Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Frontiers in Immunology. 13, 965446.","ama":"Dormeshkin D, Shapira M, Dubovik S, et al. Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Frontiers in Immunology. 2022;13. doi:10.3389/fimmu.2022.965446","short":"D. Dormeshkin, M. Shapira, S. Dubovik, A. Kavaleuski, M. Katsin, A. Migas, A. Meleshko, S. Semyonov, Frontiers in Immunology 13 (2022)."},"day":"16","ddc":["570"],"file_date_updated":"2023-01-30T09:22:26Z","month":"09","publication_status":"published","acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication.","status":"public","publication_identifier":{"issn":["1664-3224"]},"abstract":[{"text":"The COVID−19 pandemic not only resulted in a global crisis, but also accelerated vaccine development and antibody discovery. Herein we report a synthetic humanized VHH library development pipeline for nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) isolation. Trinucleotide-based randomization of CDRs by Kunkel mutagenesis with the subsequent rolling-cycle amplification resulted in more than 1011 diverse phage display library in a manageable for a single person number of electroporation reactions. We identified a number of nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) by screening a novel synthetic humanized antibody library. In order to explore the most robust and fast method for affinity improvement, we performed affinity maturation by CDR1 and CDR2 shuffling and avidity engineering by multivalent trimeric VHH fusion protein construction. As a result, H7-Fc and G12x3-Fc binders were developed with the affinities in nM and pM range respectively. Importantly, these affinities are weakly influenced by most of SARS-CoV-2 VoC mutations and they retain moderate binding to BA.4\\5. The plaque reduction neutralization test (PRNT) resulted in IC50 = 100 ng\\ml and 9.6 ng\\ml for H7-Fc and G12x3-Fc antibodies, respectively, for the emerging Omicron BA.1 variant. Therefore, these VHH could expand the present landscape of SARS-CoV-2 neutralization binders with the therapeutic potential for present and future SARS-CoV-2 variants.","lang":"eng"}],"doi":"10.3389/fimmu.2022.965446","title":"Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library","author":[{"last_name":"Dormeshkin","full_name":"Dormeshkin, Dmitri","first_name":"Dmitri"},{"first_name":"Michail","full_name":"Shapira, Michail","last_name":"Shapira"},{"first_name":"Simon","full_name":"Dubovik, Simon","last_name":"Dubovik"},{"full_name":"Kavaleuski, Anton","last_name":"Kavaleuski","id":"4968f7ad-eb97-11eb-a6c2-8ed382e8912c","first_name":"Anton","orcid":"0000-0003-2091-526X"},{"first_name":"Mikalai","full_name":"Katsin, Mikalai","last_name":"Katsin"},{"last_name":"Migas","full_name":"Migas, Alexandr","first_name":"Alexandr"},{"first_name":"Alexander","full_name":"Meleshko, Alexander","last_name":"Meleshko"},{"first_name":"Sergei","last_name":"Semyonov","full_name":"Semyonov, Sergei"}],"_id":"12252","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Frontiers Media","intvolume":" 13","date_published":"2022-09-16T00:00:00Z","external_id":{"isi":["000862479100001"]},"date_created":"2023-01-16T09:56:57Z","scopus_import":"1","department":[{"_id":"LeSa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"965446","article_type":"original","publication":"Frontiers in Immunology","date_updated":"2023-08-04T09:49:24Z","year":"2022","keyword":["Immunology","Immunology and Allergy","COVID-19","SARS-CoV-2","synthetic library","RBD","neutralization nanobody","VHH"],"oa":1},{"article_type":"original","article_number":"eadd2488","date_updated":"2023-08-04T09:49:59Z","publication":"Science Advances","year":"2022","oa":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"intvolume":" 8","publisher":"American Association for the Advancement of Science","scopus_import":"1","date_created":"2023-01-16T09:57:10Z","date_published":"2022-09-14T00:00:00Z","external_id":{"pmid":["36103529"],"isi":["000888875000009"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"EdHa"}],"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"We thank K. Aumayer and the team of the biooptics facility at the Vienna Biocenter, particularly P. Pasierbek and T. Müller, for support with microscopy; K. Panser, C. Pribitzer, and the animal facility personnel for taking care of zebrafish; M. Binner and A. Bandura for help with genotyping; M. Codina Tobias for help with establishing the conditions for the Toddler overexpression compensation experiment; T. Lubiana Alves for sharing the code for scRNA-Seq analyses; the Heisenberg laboratory, particularly D. Pinheiro, for joint laboratory meetings, discussions on the project, and providing the tg(gsc:CAAX-GFP) fish line; the Raz laboratory for providing the Lifeact-GFP plasmid; A. Andersen, A. Schier, C.-P. Heisenberg, and E. Tanaka for comments on the manuscript; and the entire Pauli laboratory, particularly K. Gert and V. Deneke, for valuable discussions and feedback on the manuscript. Funding: Work in A.P.’s laboratory has been supported by the IMP, which receives institutional funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936), as well as the FWF START program (Y 1031-B28 to A.P.), the Human Frontier Science Program (HFSP) Career Development Award (CDA00066/2015 to A.P.) and Young Investigator Grant (RGY0079/2020 to A.P.), the SFB RNA-Deco (project number F 80 to A.P.), a Whitman Center Fellowship from the Marine Biological Laboratory (to A.P.), and EMBO-YIP funds (to A.P.). This work was supported by the European Union (European Research Council Starting Grant 851288 to E.H.). For the purpose of Open Access, the authors have applied a CC BY public copyright license to any Author Accepted Manuscript (AAM) version arising from this submission.","project":[{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"publication_identifier":{"issn":["2375-2548"]},"doi":"10.1126/sciadv.add2488","issue":"37","abstract":[{"lang":"eng","text":"The sculpting of germ layers during gastrulation relies on the coordinated migration of progenitor cells, yet the cues controlling these long-range directed movements remain largely unknown. While directional migration often relies on a chemokine gradient generated from a localized source, we find that zebrafish ventrolateral mesoderm is guided by a self-generated gradient of the initially uniformly expressed and secreted protein Toddler/ELABELA/Apela. We show that the Apelin receptor, which is specifically expressed in mesodermal cells, has a dual role during gastrulation, acting as a scavenger receptor to generate a Toddler gradient, and as a chemokine receptor to sense this guidance cue. Thus, we uncover a single receptor–based self-generated gradient as the enigmatic guidance cue that can robustly steer the directional migration of mesoderm through the complex and continuously changing environment of the gastrulating embryo."}],"_id":"12253","author":[{"first_name":"Jessica","full_name":"Stock, Jessica","last_name":"Stock"},{"full_name":"Kazmar, Tomas","last_name":"Kazmar","first_name":"Tomas"},{"first_name":"Friederike","full_name":"Schlumm, Friederike","last_name":"Schlumm"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"full_name":"Pauli, Andrea","last_name":"Pauli","first_name":"Andrea"}],"title":"A self-generated Toddler gradient guides mesodermal cell migration","article_processing_charge":"No","volume":8,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"12444","date_created":"2023-01-30T09:27:49Z","access_level":"open_access","checksum":"f59cdb824e5d4221045def81f46f6c65","content_type":"application/pdf","success":1,"date_updated":"2023-01-30T09:27:49Z","file_name":"2022_ScienceAdvances_Stock.pdf","file_size":1636732,"creator":"dernst","relation":"main_file"}],"oa_version":"Published Version","ddc":["570"],"file_date_updated":"2023-01-30T09:27:49Z","pmid":1,"month":"09","day":"14","citation":{"chicago":"Stock, Jessica, Tomas Kazmar, Friederike Schlumm, Edouard B Hannezo, and Andrea Pauli. “A Self-Generated Toddler Gradient Guides Mesodermal Cell Migration.” Science Advances. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/sciadv.add2488.","mla":"Stock, Jessica, et al. “A Self-Generated Toddler Gradient Guides Mesodermal Cell Migration.” Science Advances, vol. 8, no. 37, eadd2488, American Association for the Advancement of Science, 2022, doi:10.1126/sciadv.add2488.","ieee":"J. Stock, T. Kazmar, F. Schlumm, E. B. Hannezo, and A. Pauli, “A self-generated Toddler gradient guides mesodermal cell migration,” Science Advances, vol. 8, no. 37. American Association for the Advancement of Science, 2022.","apa":"Stock, J., Kazmar, T., Schlumm, F., Hannezo, E. B., & Pauli, A. (2022). A self-generated Toddler gradient guides mesodermal cell migration. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.add2488","short":"J. Stock, T. Kazmar, F. Schlumm, E.B. Hannezo, A. Pauli, Science Advances 8 (2022).","ista":"Stock J, Kazmar T, Schlumm F, Hannezo EB, Pauli A. 2022. A self-generated Toddler gradient guides mesodermal cell migration. Science Advances. 8(37), eadd2488.","ama":"Stock J, Kazmar T, Schlumm F, Hannezo EB, Pauli A. A self-generated Toddler gradient guides mesodermal cell migration. Science Advances. 2022;8(37). doi:10.1126/sciadv.add2488"}},{"ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"K.C. acknowledges support from ERC Start Grant No. (279307: Graph Games), ERC Consolidator Grant No. (863818: ForM-SMart), and Austrian Science Fund (FWF)\r\nGrants No. P23499-N23 and No. S11407-N23 (RiSE). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 665385.","project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"doi":"10.1103/physreve.106.034321","issue":"3","abstract":[{"lang":"eng","text":"Structural balance theory is an established framework for studying social relationships of friendship and enmity. These relationships are modeled by a signed network whose energy potential measures the level of imbalance, while stochastic dynamics drives the network toward a state of minimum energy that captures social balance. It is known that this energy landscape has local minima that can trap socially aware dynamics, preventing it from reaching balance. Here we first study the robustness and attractor properties of these local minima. We show that a stochastic process can reach them from an abundance of initial states and that some local minima cannot be escaped by mild perturbations of the network. Motivated by these anomalies, we introduce best-edge dynamics (BED), a new plausible stochastic process. We prove that BED always reaches balance and that it does so fast in various interesting settings."}],"_id":"12257","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Svoboda, Jakub","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","orcid":"0000-0002-1419-3267"},{"orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722"},{"orcid":"0000-0002-1097-9684","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","full_name":"Tkadlec, Josef"}],"title":"Social balance on networks: Local minima and best-edge dynamics","volume":106,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","month":"09","day":"29","citation":{"chicago":"Chatterjee, Krishnendu, Jakub Svoboda, Dorde Zikelic, Andreas Pavlogiannis, and Josef Tkadlec. “Social Balance on Networks: Local Minima and Best-Edge Dynamics.” Physical Review E. American Physical Society, 2022. https://doi.org/10.1103/physreve.106.034321.","mla":"Chatterjee, Krishnendu, et al. “Social Balance on Networks: Local Minima and Best-Edge Dynamics.” Physical Review E, vol. 106, no. 3, 034321, American Physical Society, 2022, doi:10.1103/physreve.106.034321.","ieee":"K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, and J. Tkadlec, “Social balance on networks: Local minima and best-edge dynamics,” Physical Review E, vol. 106, no. 3. American Physical Society, 2022.","apa":"Chatterjee, K., Svoboda, J., Zikelic, D., Pavlogiannis, A., & Tkadlec, J. (2022). Social balance on networks: Local minima and best-edge dynamics. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.106.034321","ista":"Chatterjee K, Svoboda J, Zikelic D, Pavlogiannis A, Tkadlec J. 2022. Social balance on networks: Local minima and best-edge dynamics. Physical Review E. 106(3), 034321.","ama":"Chatterjee K, Svoboda J, Zikelic D, Pavlogiannis A, Tkadlec J. Social balance on networks: Local minima and best-edge dynamics. Physical Review E. 2022;106(3). doi:10.1103/physreve.106.034321","short":"K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, J. Tkadlec, Physical Review E 106 (2022)."},"article_type":"original","article_number":"034321","date_updated":"2025-07-14T09:09:49Z","publication":"Physical Review E","year":"2022","oa":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"intvolume":" 106","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2210.02394"}],"publisher":"American Physical Society","scopus_import":"1","date_created":"2023-01-16T09:57:57Z","external_id":{"arxiv":["2210.02394"],"isi":["000870243100001"]},"date_published":"2022-09-29T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"KrCh"}]},{"year":"2022","keyword":["Applied Mathematics","General Physics and Astronomy","Mathematical Physics","Statistical and Nonlinear Physics"],"oa":1,"article_type":"original","article_number":"093138","publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","date_updated":"2023-08-04T09:51:17Z","external_id":{"arxiv":["2206.01531"],"isi":["000861009600005"]},"date_published":"2022-09-26T00:00:00Z","scopus_import":"1","date_created":"2023-01-16T09:58:16Z","department":[{"_id":"MaSe"},{"_id":"BjHo"},{"_id":"NanoFab"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","intvolume":" 32","publisher":"AIP Publishing","issue":"9","abstract":[{"text":"Theoretical foundations of chaos have been predominantly laid out for finite-dimensional dynamical systems, such as the three-body problem in classical mechanics and the Lorenz model in dissipative systems. In contrast, many real-world chaotic phenomena, e.g., weather, arise in systems with many (formally infinite) degrees of freedom, which limits direct quantitative analysis of such systems using chaos theory. In the present work, we demonstrate that the hydrodynamic pilot-wave systems offer a bridge between low- and high-dimensional chaotic phenomena by allowing for a systematic study of how the former connects to the latter. Specifically, we present experimental results, which show the formation of low-dimensional chaotic attractors upon destabilization of regular dynamics and a final transition to high-dimensional chaos via the merging of distinct chaotic regions through a crisis bifurcation. Moreover, we show that the post-crisis dynamics of the system can be rationalized as consecutive scatterings from the nonattracting chaotic sets with lifetimes following exponential distributions. ","lang":"eng"}],"doi":"10.1063/5.0102904","author":[{"first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","last_name":"Choueiri","full_name":"Choueiri, George H"},{"last_name":"Suri","full_name":"Suri, Balachandra","first_name":"Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof"},{"first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010"}],"title":"Crises and chaotic scattering in hydrodynamic pilot-wave experiments","_id":"12259","publication_status":"published","status":"public","acknowledgement":"This work was partially funded by the Institute of Science and Technology Austria Interdisciplinary Project Committee Grant “Pilot-Wave Hydrodynamics: Chaos and Quantum Analogies.”","publication_identifier":{"eissn":["1089-7682"],"issn":["1054-1500"]},"oa_version":"Published Version","day":"26","citation":{"ista":"Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. 2022. Crises and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary Journal of Nonlinear Science. 32(9), 093138.","short":"G.H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, N.B. Budanur, Chaos: An Interdisciplinary Journal of Nonlinear Science 32 (2022).","ama":"Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. Crises and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary Journal of Nonlinear Science. 2022;32(9). doi:10.1063/5.0102904","apa":"Choueiri, G. H., Suri, B., Merrin, J., Serbyn, M., Hof, B., & Budanur, N. B. (2022). Crises and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing. https://doi.org/10.1063/5.0102904","ieee":"G. H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, and N. B. Budanur, “Crises and chaotic scattering in hydrodynamic pilot-wave experiments,” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 32, no. 9. AIP Publishing, 2022.","chicago":"Choueiri, George H, Balachandra Suri, Jack Merrin, Maksym Serbyn, Björn Hof, and Nazmi B Budanur. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing, 2022. https://doi.org/10.1063/5.0102904.","mla":"Choueiri, George H., et al. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 32, no. 9, 093138, AIP Publishing, 2022, doi:10.1063/5.0102904."},"month":"09","ddc":["530"],"file_date_updated":"2023-01-30T09:41:12Z","has_accepted_license":"1","article_processing_charge":"No","volume":32,"arxiv":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2022_Chaos_Choueiri.pdf","relation":"main_file","file_size":3209644,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"17881eff8b21969359a2dd64620120ba","success":1,"date_updated":"2023-01-30T09:41:12Z","file_id":"12445","date_created":"2023-01-30T09:41:12Z"}]},{"file_date_updated":"2023-01-30T09:49:55Z","ddc":["570"],"month":"09","day":"01","citation":{"mla":"Angermayr, Andreas, et al. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” Molecular Systems Biology, vol. 18, no. 9, e10490, Embo Press, 2022, doi:10.15252/msb.202110490.","chicago":"Angermayr, Andreas, Tin Yau Pang, Guillaume Chevereau, Karin Mitosch, Martin J Lercher, and Mark Tobias Bollenbach. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” Molecular Systems Biology. Embo Press, 2022. https://doi.org/10.15252/msb.202110490.","ieee":"A. Angermayr, T. Y. Pang, G. Chevereau, K. Mitosch, M. J. Lercher, and M. T. Bollenbach, “Growth‐mediated negative feedback shapes quantitative antibiotic response,” Molecular Systems Biology, vol. 18, no. 9. Embo Press, 2022.","apa":"Angermayr, A., Pang, T. Y., Chevereau, G., Mitosch, K., Lercher, M. J., & Bollenbach, M. T. (2022). Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular Systems Biology. Embo Press. https://doi.org/10.15252/msb.202110490","ama":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular Systems Biology. 2022;18(9). doi:10.15252/msb.202110490","ista":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. 2022. Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular Systems Biology. 18(9), e10490.","short":"A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach, Molecular Systems Biology 18 (2022)."},"oa_version":"Published Version","file":[{"file_name":"2022_MolecularSystemsBio_Angermayr.pdf","creator":"dernst","file_size":1098812,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"8b1d8f5ea20c8408acf466435fb6ae01","success":1,"date_updated":"2023-01-30T09:49:55Z","file_id":"12446","date_created":"2023-01-30T09:49:55Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":18,"article_processing_charge":"No","has_accepted_license":"1","_id":"12261","author":[{"full_name":"Angermayr, Andreas","last_name":"Angermayr","id":"4677C796-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0001-8619-2223"},{"last_name":"Pang","full_name":"Pang, Tin Yau","first_name":"Tin Yau"},{"full_name":"Chevereau, Guillaume","last_name":"Chevereau","first_name":"Guillaume"},{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin","full_name":"Mitosch, Karin","last_name":"Mitosch"},{"last_name":"Lercher","full_name":"Lercher, Martin J","first_name":"Martin J"},{"orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias"}],"title":"Growth‐mediated negative feedback shapes quantitative antibiotic response","doi":"10.15252/msb.202110490","issue":"9","abstract":[{"text":"Dose–response relationships are a general concept for quantitatively describing biological systems across multiple scales, from the molecular to the whole-cell level. A clinically relevant example is the bacterial growth response to antibiotics, which is routinely characterized by dose–response curves. The shape of the dose–response curve varies drastically between antibiotics and plays a key role in treatment, drug interactions, and resistance evolution. However, the mechanisms shaping the dose–response curve remain largely unclear. Here, we show in Escherichia coli that the distinctively shallow dose–response curve of the antibiotic trimethoprim is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim but follows a universal trend line that depends primarily on the growth rate, irrespective of its cause. Rewiring the feedback loop alters the dose–response curve in a predictable manner, which we corroborate using a mathematical model of cellular resource allocation and growth. Our results indicate that growth-mediated feedback loops may shape drug responses more generally and could be exploited to design evolutionary traps that enable selection against drug resistance.","lang":"eng"}],"publication_identifier":{"eissn":["1744-4292"]},"acknowledgement":"This work was in part supported by Human Frontier Science Program GrantRGP0042/2013, Marie Curie Career Integration Grant303507, AustrianScience Fund (FWF) Grant P27201-B22, and German Research Foundation(DFG) Collaborative Research Center (SFB)1310to TB. SAA was supportedby the European Union’s Horizon2020Research and Innovation Programunder the Marie Skłodowska-Curie Grant agreement No707352. We wouldlike to thank the Bollenbach group for regular fruitful discussions. We areparticularly thankful for the technical assistance of Booshini Fernando andfor discussions of the theoretical aspects with Gerrit Ansmann. We areindebted to Bor Kavˇciˇc for invaluable advice, help with setting up theluciferase-based growth monitoring system, and for sharing plasmids. Weacknowledge the IST Austria Miba Machine Shop for their support inbuilding a housing for the stacker of the plate reader, which enabled thehigh-throughput luciferase-based experiments. We are grateful to RosalindAllen, Bor Kavˇciˇc and Dor Russ for feedback on the manuscript. Open Accessfunding enabled and organized by Projekt DEAL.","publication_status":"published","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ToBo"}],"scopus_import":"1","acknowledged_ssus":[{"_id":"M-Shop"}],"date_created":"2023-01-16T09:58:34Z","external_id":{"isi":["000856482800001"]},"date_published":"2022-09-01T00:00:00Z","intvolume":" 18","publisher":"Embo Press","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"oa":1,"keyword":["Applied Mathematics","Computational Theory and Mathematics","General Agricultural and Biological Sciences","General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","Information Systems"],"year":"2022","date_updated":"2023-08-04T09:51:49Z","publication":"Molecular Systems Biology","article_type":"original","article_number":"e10490"},{"date_published":"2022-09-12T00:00:00Z","external_id":{"pmid":["36097293"],"isi":["000852942100004"]},"date_created":"2023-01-16T09:59:06Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"scopus_import":"1","department":[{"_id":"EM-Fac"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Springer Nature","intvolume":" 29","year":"2022","keyword":["Molecular Biology","Structural Biology"],"oa":1,"page":"942-953","article_type":"original","publication":"Nature Structural & Molecular Biology","date_updated":"2023-08-04T09:52:20Z","oa_version":"Published Version","citation":{"apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Hetzmannseder, C., Zisser, G., Sailer, C., … Bergler, H. (2022). Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-022-00832-5","ieee":"M. Prattes et al., “Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1,” Nature Structural & Molecular Biology, vol. 29, no. 9. Springer Nature, pp. 942–953, 2022.","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. 2022;29(9):942-953. doi:10.1038/s41594-022-00832-5","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, C. Hetzmannseder, G. Zisser, C. Sailer, V. Kargas, M. Loibl, M. Gerhalter, L. Kofler, A.J. Warren, F. Stengel, D. Haselbach, H. Bergler, Nature Structural & Molecular Biology 29 (2022) 942–953.","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Hetzmannseder C, Zisser G, Sailer C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D, Bergler H. 2022. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. 29(9), 942–953.","mla":"Prattes, Michael, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” Nature Structural & Molecular Biology, vol. 29, no. 9, Springer Nature, 2022, pp. 942–53, doi:10.1038/s41594-022-00832-5.","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Christina Hetzmannseder, Gertrude Zisser, Carolin Sailer, Vasileios Kargas, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” Nature Structural & Molecular Biology. Springer Nature, 2022. https://doi.org/10.1038/s41594-022-00832-5."},"day":"12","month":"09","file_date_updated":"2023-01-30T10:00:04Z","pmid":1,"ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","volume":29,"file":[{"file_size":9935057,"creator":"dernst","relation":"main_file","file_name":"2022_NatureStrucMolecBio_Prattes.pdf","date_updated":"2023-01-30T10:00:04Z","success":1,"checksum":"2d5c3ec01718fefd7553052b0b8a0793","content_type":"application/pdf","access_level":"open_access","date_created":"2023-01-30T10:00:04Z","file_id":"12447"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","text":"The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases."}],"issue":"9","doi":"10.1038/s41594-022-00832-5","title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","author":[{"first_name":"Michael","last_name":"Prattes","full_name":"Prattes, Michael"},{"last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina","first_name":"Irina"},{"last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hetzmannseder","full_name":"Hetzmannseder, Christina","first_name":"Christina"},{"first_name":"Gertrude","last_name":"Zisser","full_name":"Zisser, Gertrude"},{"full_name":"Sailer, Carolin","last_name":"Sailer","first_name":"Carolin"},{"first_name":"Vasileios","full_name":"Kargas, Vasileios","last_name":"Kargas"},{"first_name":"Mathias","full_name":"Loibl, Mathias","last_name":"Loibl"},{"first_name":"Magdalena","last_name":"Gerhalter","full_name":"Gerhalter, Magdalena"},{"first_name":"Lisa","full_name":"Kofler, Lisa","last_name":"Kofler"},{"first_name":"Alan J.","last_name":"Warren","full_name":"Warren, Alan J."},{"full_name":"Stengel, Florian","last_name":"Stengel","first_name":"Florian"},{"last_name":"Haselbach","full_name":"Haselbach, David","first_name":"David"},{"full_name":"Bergler, Helmut","last_name":"Bergler","first_name":"Helmut"}],"_id":"12262","status":"public","acknowledgement":"We thank M. Fromont-Racine, A. Johnson, J. Woolford, S. Rospert, J. P. G. Ballesta and\r\nE. Hurt for supplying antibodies. The work was supported by Boehringer Ingelheim (to\r\nD. H.), the Austrian Science Foundation FWF (grants 32536 and 32977 to H. B.), the\r\nUK Medical Research Council (MR/T012412/1 to A. J. W.) and the German Research\r\nFoundation (Emmy Noether Programme STE 2517/1-1 and STE 2517/5-1 to F.S.). We\r\nthank Norberto Escudero-Urquijo, Pablo Castro-Hartmann and K. Dent, Cambridge\r\nInstitute for Medical Research, for their help in cryo-EM during early phases of this\r\nproject. This research was supported by the Scientific Service Units of IST Austria through\r\nresources provided by the Electron Microscopy Facility. We thank S. Keller, Institute of\r\nMolecular Biosciences (Biophysics), University Graz for support with the quantification of\r\nthe SPR particle release assay. We thank I. Schaffner, University of Natural Resources and\r\nLife Sciences, Vienna for her help in early stages of the SPR experiments.","publication_status":"published","publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]}},{"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","volume":35,"file":[{"file_name":"2022_JourEvoBiology_Westram.pdf","creator":"dernst","file_size":3146793,"relation":"main_file","access_level":"open_access","checksum":"f08de57112330a7ee88d2e1b20576a1e","content_type":"application/pdf","success":1,"date_updated":"2023-01-30T10:05:31Z","file_id":"12448","date_created":"2023-01-30T10:05:31Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","day":"01","citation":{"chicago":"Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “What Is Reproductive Isolation?” Journal of Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14005.","mla":"Westram, Anja M., et al. “What Is Reproductive Isolation?” Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1143–64, doi:10.1111/jeb.14005.","ieee":"A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “What is reproductive isolation?,” Journal of Evolutionary Biology, vol. 35, no. 9. Wiley, pp. 1143–1164, 2022.","apa":"Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022). What is reproductive isolation? Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14005","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1143–1164.","ama":"Westram AM, Stankowski S, Surendranadh P, Barton NH. What is reproductive isolation? Journal of Evolutionary Biology. 2022;35(9):1143-1164. doi:10.1111/jeb.14005","ista":"Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. What is reproductive isolation? Journal of Evolutionary Biology. 35(9), 1143–1164."},"pmid":1,"month":"09","file_date_updated":"2023-01-30T10:05:31Z","ddc":["570"],"publication_status":"published","acknowledgement":"We are grateful to the participants of the ESEB satellite symposium ‘Understanding reproductive isolation: bridging conceptual barriers in speciation research’ in 2021 for the interesting discussions that helped us clarify the thoughts presented in this article. We thank Roger Butlin, Michael Turelli and two anonymous reviewers for their thoughtful comments on this manuscript. We are also very grateful to Roger Butlin and the Barton Group for the continued conversa-tions about RI. In addition, we thank all participants of the speciation survey. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166)","status":"public","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"issue":"9","abstract":[{"text":"Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since the modern synthesis and is the basis by which biological species are defined. Despite this, the term is used in seemingly different ways, and attempts to quantify RI have used very different approaches. After showing that the field lacks a clear definition of the term, we attempt to clarify key issues, including what RI is, how it can be quantified in principle, and how it can be measured in practice. Following other definitions with a genetic focus, we propose that RI is a quantitative measure of the effect that genetic differences between populations have on gene flow. Specifically, RI compares the flow of neutral alleles in the presence of these genetic differences to the flow without any such differences. RI is thus greater than zero when genetic differences between populations reduce the flow of neutral alleles between populations. We show how RI can be quantified in a range of scenarios. A key conclusion is that RI depends strongly on circumstances—including the spatial, temporal and genomic context—making it difficult to compare across systems. After reviewing methods for estimating RI from data, we conclude that it is difficult to measure in practice. We discuss our findings in light of the goals of speciation research and encourage the use of methods for estimating RI that integrate organismal and genetic approaches.","lang":"eng"}],"doi":"10.1111/jeb.14005","author":[{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M","last_name":"Westram"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"last_name":"Surendranadh","full_name":"Surendranadh, Parvathy","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"title":"What is reproductive isolation?","_id":"12264","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"intvolume":" 35","publisher":"Wiley","external_id":{"pmid":["36063156"],"isi":["000849851100002"]},"date_published":"2022-09-01T00:00:00Z","scopus_import":"1","date_created":"2023-01-16T09:59:24Z","department":[{"_id":"NiBa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"id":"12265","relation":"other","status":"public"}]},"article_type":"review","page":"1143-1164","publication":"Journal of Evolutionary Biology","date_updated":"2023-08-04T09:53:40Z","year":"2022","keyword":["Ecology","Evolution","Behavior and Systematics"],"oa":1},{"project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"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).","publication_status":"published","status":"public","_id":"12265","author":[{"orcid":"0000-0003-1050-4969","last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"full_name":"Surendranadh, Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"}],"title":"Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’","doi":"10.1111/jeb.14082","issue":"9","file":[{"file_id":"12449","date_created":"2023-01-30T10:14:09Z","file_name":"2022_JourEvoBiology_Westram_Response.pdf","file_size":349603,"creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"27268009e5eec030bc10667a4ac5ed4c","content_type":"application/pdf","success":1,"date_updated":"2023-01-30T10:14:09Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","volume":35,"has_accepted_license":"1","file_date_updated":"2023-01-30T10:14:09Z","ddc":["570"],"month":"09","day":"01","citation":{"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.","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.","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","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1200–1205.","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.","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","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."},"oa_version":"Published Version","date_updated":"2023-08-04T09:53:41Z","publication":"Journal of Evolutionary Biology","article_type":"letter_note","page":"1200-1205","related_material":{"record":[{"id":"12264","relation":"other","status":"public"}]},"oa":1,"keyword":["Ecology","Evolution","Behavior and Systematics"],"year":"2022","intvolume":" 35","publisher":"Wiley","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"NiBa"}],"scopus_import":"1","date_created":"2023-01-16T09:59:37Z","external_id":{"isi":["000849851100009"]},"date_published":"2022-09-01T00:00:00Z"},{"oa":1,"keyword":["Cancer Research","Oncology"],"year":"2022","date_updated":"2023-08-04T09:54:16Z","publication":"Frontiers in Oncology","article_number":"983507","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"GaNo"}],"date_created":"2023-01-16T10:00:28Z","scopus_import":"1","external_id":{"pmid":["36091138"],"isi":["000856524900001"]},"date_published":"2022-08-25T00:00:00Z","publisher":"Frontiers Media","intvolume":" 12","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"_id":"12268","title":"Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma cells","author":[{"last_name":"Basilico","full_name":"Basilico, Bernadette","first_name":"Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173"},{"full_name":"Palamà, Ilaria Elena","last_name":"Palamà","first_name":"Ilaria Elena"},{"last_name":"D’Amone","full_name":"D’Amone, Stefania","first_name":"Stefania"},{"first_name":"Clotilde","full_name":"Lauro, Clotilde","last_name":"Lauro"},{"last_name":"Rosito","full_name":"Rosito, Maria","first_name":"Maria"},{"first_name":"Maddalena","full_name":"Grieco, Maddalena","last_name":"Grieco"},{"full_name":"Ratano, Patrizia","last_name":"Ratano","first_name":"Patrizia"},{"first_name":"Federica","full_name":"Cordella, Federica","last_name":"Cordella"},{"full_name":"Sanchini, Caterina","last_name":"Sanchini","first_name":"Caterina"},{"last_name":"Di Angelantonio","full_name":"Di Angelantonio, Silvia","first_name":"Silvia"},{"full_name":"Ragozzino, Davide","last_name":"Ragozzino","first_name":"Davide"},{"full_name":"Cascione, Mariafrancesca","last_name":"Cascione","first_name":"Mariafrancesca"},{"last_name":"Gigli","full_name":"Gigli, Giuseppe","first_name":"Giuseppe"},{"full_name":"Cortese, Barbara","last_name":"Cortese","first_name":"Barbara"}],"doi":"10.3389/fonc.2022.983507","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"}],"publication_identifier":{"issn":["2234-943X"]},"status":"public","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.","publication_status":"published","ddc":["570"],"pmid":1,"month":"08","file_date_updated":"2023-01-30T10:25:21Z","citation":{"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.","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.","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).","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","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","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."},"day":"25","oa_version":"Published Version","file":[{"file_id":"12450","date_created":"2023-01-30T10:25:21Z","file_name":"2022_FrontiersOntology_Basilico.pdf","file_size":13588502,"relation":"main_file","creator":"dernst","access_level":"open_access","checksum":"efc7edf9f626af31853790c5b598a68c","content_type":"application/pdf","success":1,"date_updated":"2023-01-30T10:25:21Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":12,"article_processing_charge":"No","has_accepted_license":"1"},{"publisher":"American Physical Society","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.08373","open_access":"1"}],"intvolume":" 106","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaSe"}],"date_created":"2023-01-16T10:00:39Z","scopus_import":"1","date_published":"2022-08-31T00:00:00Z","external_id":{"isi":["000861332900005"],"arxiv":["2106.08373"]},"date_updated":"2023-08-04T10:07:33Z","publication":"Physical Review B","article_number":"054314","article_type":"original","oa":1,"year":"2022","arxiv":1,"article_processing_charge":"No","volume":106,"month":"08","citation":{"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.","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.","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","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.","short":"M. Ljubotina, D. Roy, T. Prosen, Physical Review B 106 (2022)."},"day":"31","oa_version":"Preprint","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"ec_funded":1,"publication_status":"published","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. ","status":"public","_id":"12269","title":"Absence of thermalization of free systems coupled to gapped interacting reservoirs","author":[{"first_name":"Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina","full_name":"Ljubotina, Marko"},{"full_name":"Roy, Dibyendu","last_name":"Roy","first_name":"Dibyendu"},{"first_name":"Tomaž","last_name":"Prosen","full_name":"Prosen, Tomaž"}],"doi":"10.1103/physrevb.106.054314","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."}],"issue":"5"},{"scopus_import":"1","date_created":"2023-01-16T10:01:08Z","date_published":"2022-07-20T00:00:00Z","external_id":{"pmid":["35856919"],"isi":["000874717200001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MiSi"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"intvolume":" 221","publisher":"Rockefeller University Press","keyword":["Cell Biology"],"year":"2022","oa":1,"article_type":"original","article_number":"e202206127","related_material":{"record":[{"id":"14697","status":"public","relation":"dissertation_contains"}]},"date_updated":"2023-12-21T14:30:01Z","publication":"Journal of Cell Biology","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2023-01-30T10:39:34Z","pmid":1,"month":"07","ddc":["570"],"day":"20","citation":{"mla":"Stopp, Julian A., and Michael K. Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” Journal of Cell Biology, vol. 221, no. 8, e202206127, Rockefeller University Press, 2022, doi:10.1083/jcb.202206127.","chicago":"Stopp, Julian A, and Michael K Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” Journal of Cell Biology. Rockefeller University Press, 2022. https://doi.org/10.1083/jcb.202206127.","ieee":"J. A. Stopp and M. K. Sixt, “Plan your trip before you leave: The neutrophils’ search-and-run journey,” Journal of Cell Biology, vol. 221, no. 8. Rockefeller University Press, 2022.","apa":"Stopp, J. A., & Sixt, M. K. (2022). Plan your trip before you leave: The neutrophils’ search-and-run journey. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202206127","short":"J.A. Stopp, M.K. Sixt, Journal of Cell Biology 221 (2022).","ama":"Stopp JA, Sixt MK. Plan your trip before you leave: The neutrophils’ search-and-run journey. Journal of Cell Biology. 2022;221(8). doi:10.1083/jcb.202206127","ista":"Stopp JA, Sixt MK. 2022. Plan your trip before you leave: The neutrophils’ search-and-run journey. Journal of Cell Biology. 221(8), e202206127."},"article_processing_charge":"No","volume":221,"has_accepted_license":"1","file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"6b1620743669679b48b9389bb40f5a11","success":1,"date_updated":"2023-01-30T10:39:34Z","file_name":"2022_JourCellBiology_Stopp.pdf","relation":"main_file","creator":"dernst","file_size":969969,"file_id":"12451","date_created":"2023-01-30T10:39:34Z"}],"tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"doi":"10.1083/jcb.202206127","issue":"8","abstract":[{"lang":"eng","text":"Reading, interpreting and crawling along gradients of chemotactic cues is one of the most complex questions in cell biology. In this issue, Georgantzoglou et al. (2022. J. Cell. Biol.https://doi.org/10.1083/jcb.202103207) use in vivo models to map the temporal sequence of how neutrophils respond to an acutely arising gradient of chemoattractant."}],"_id":"12272","author":[{"last_name":"Stopp","full_name":"Stopp, Julian A","first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"}],"title":"Plan your trip before you leave: The neutrophils’ search-and-run journey","status":"public","publication_status":"published","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]}},{"oa_version":"Preprint","month":"08","day":"01","citation":{"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.","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.","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","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.","short":"Y. Zhang, S. Vatedka, S. Jaggi, A.D. Sarwate, IEEE Transactions on Information Theory 68 (2022) 4901–4948.","ista":"Zhang Y, Vatedka S, Jaggi S, Sarwate AD. 2022. Quadratically constrained myopic adversarial channels. IEEE Transactions on Information Theory. 68(8), 4901–4948.","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"},"article_processing_charge":"No","volume":68,"arxiv":1,"doi":"10.1109/tit.2022.3167554","issue":"8","abstract":[{"lang":"eng","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."}],"_id":"12273","author":[{"first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","last_name":"Zhang","full_name":"Zhang, Yihan"},{"last_name":"Vatedka","full_name":"Vatedka, Shashank","first_name":"Shashank"},{"last_name":"Jaggi","full_name":"Jaggi, Sidharth","first_name":"Sidharth"},{"last_name":"Sarwate","full_name":"Sarwate, Anand D.","first_name":"Anand D."}],"title":"Quadratically constrained myopic adversarial channels","status":"public","publication_status":"published","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"scopus_import":"1","date_created":"2023-01-16T10:01:19Z","date_published":"2022-08-01T00:00:00Z","external_id":{"isi":["000838527100004"],"arxiv":["1801.05951"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaMo"}],"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"intvolume":" 68","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1801.05951"}],"publisher":"Institute of Electrical and Electronics Engineers","year":"2022","oa":1,"article_type":"original","page":"4901-4948","date_updated":"2023-08-04T10:08:49Z","publication":"IEEE Transactions on Information Theory"},{"publication":"Nature","date_updated":"2023-10-03T11:16:30Z","related_material":{"link":[{"url":"https://github.com/JaccovanRheenenLab/Retrograde_movement_Azkanaz_Nature_2022","relation":"software"}]},"page":"548-554","article_type":"original","oa":1,"year":"2022","keyword":["Multidisciplinary"],"publisher":"Springer Nature","intvolume":" 607","main_file_link":[{"url":"https://helda.helsinki.fi/items/94433455-4854-45c0-9de8-7326caea8780","open_access":"1"}],"isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"EdHa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-07-13T00:00:00Z","external_id":{"isi":["000824430000004"],"pmid":["35831497"]},"date_created":"2023-01-16T10:01:29Z","scopus_import":"1","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis"}],"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).","status":"public","publication_status":"published","ec_funded":1,"title":"Retrograde movements determine effective stem cell numbers in the intestine","author":[{"first_name":"Maria","last_name":"Azkanaz","full_name":"Azkanaz, Maria"},{"orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat"},{"last_name":"Ellenbroek","full_name":"Ellenbroek, Saskia I. J.","first_name":"Saskia I. J."},{"full_name":"Bruens, Lotte","last_name":"Bruens","first_name":"Lotte"},{"last_name":"Webb","full_name":"Webb, Anna T.","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","full_name":"Annusver, Karl","last_name":"Annusver"},{"full_name":"Messal, Hendrik A.","last_name":"Messal","first_name":"Hendrik A."},{"first_name":"Sharif","full_name":"Iqbal, Sharif","last_name":"Iqbal"},{"last_name":"Flanagan","full_name":"Flanagan, Dustin J.","first_name":"Dustin J."},{"first_name":"David J.","full_name":"Huels, David J.","last_name":"Huels"},{"first_name":"Felipe","full_name":"Rojas-Rodríguez, Felipe","last_name":"Rojas-Rodríguez"},{"last_name":"Vizoso","full_name":"Vizoso, Miguel","first_name":"Miguel"},{"full_name":"Kasper, Maria","last_name":"Kasper","first_name":"Maria"},{"first_name":"Owen J.","full_name":"Sansom, Owen J.","last_name":"Sansom"},{"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","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jacco","full_name":"van Rheenen, Jacco","last_name":"van Rheenen"}],"_id":"12274","abstract":[{"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.","lang":"eng"}],"issue":"7919","doi":"10.1038/s41586-022-04962-0","article_processing_charge":"No","volume":607,"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.","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.","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","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.","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.","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"},"day":"13","month":"07","pmid":1,"oa_version":"Submitted Version"},{"department":[{"_id":"MaDe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["35586945"],"isi":["000797302700001"]},"date_published":"2022-07-05T00:00:00Z","date_created":"2023-01-16T10:01:44Z","scopus_import":"1","publisher":"Embo Press","intvolume":" 23","main_file_link":[{"open_access":"1","url":"https://doi.org/10.15252/embr.202154163"}],"isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","oa":1,"year":"2022","keyword":["Genetics","Molecular Biology","Biochemistry"],"publication":"EMBO Reports","date_updated":"2023-10-03T11:25:54Z","article_number":"e54163","article_type":"original","citation":{"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.","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","short":"M. Rahman, N. Ramirez, C.A. Diaz‐Balzac, H.E. Bülow, EMBO Reports 23 (2022).","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.","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","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.","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."},"day":"05","pmid":1,"month":"07","oa_version":"Published Version","has_accepted_license":"1","volume":23,"article_processing_charge":"No","title":"Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning","author":[{"first_name":"Maisha","full_name":"Rahman, Maisha","last_name":"Rahman"},{"last_name":"Ramirez","full_name":"Ramirez, Nelson","first_name":"Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425"},{"full_name":"Diaz‐Balzac, Carlos A","last_name":"Diaz‐Balzac","first_name":"Carlos A"},{"first_name":"Hannes E","last_name":"Bülow","full_name":"Bülow, Hannes E"}],"_id":"12275","abstract":[{"lang":"eng","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."}],"issue":"7","doi":"10.15252/embr.202154163","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"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","publication_status":"published","status":"public"},{"publisher":"American Physical Society","intvolume":" 3","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"MaSe"},{"_id":"RoSe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2204.02899"]},"date_published":"2022-09-23T00:00:00Z","date_created":"2023-01-16T10:01:56Z","scopus_import":"1","publication":"PRX Quantum","date_updated":"2023-01-30T11:05:23Z","article_number":"030343","article_type":"original","oa":1,"year":"2022","keyword":["General Medicine"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"file":[{"file_name":"2022_PRXQuantum_Ljubotina.pdf","relation":"main_file","file_size":7661905,"creator":"dernst","success":1,"date_updated":"2023-01-30T11:02:50Z","access_level":"open_access","content_type":"application/pdf","checksum":"ef8f0a1b5a019b3958009162de0fa4c3","file_id":"12457","date_created":"2023-01-30T11:02:50Z"}],"has_accepted_license":"1","volume":3,"article_processing_charge":"No","citation":{"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.","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.","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","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.","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","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.","short":"M. Ljubotina, B. Roos, D.A. Abanin, M. Serbyn, PRX Quantum 3 (2022)."},"day":"23","month":"09","file_date_updated":"2023-01-30T11:02:50Z","ddc":["530"],"oa_version":"Published Version","publication_identifier":{"eissn":["2691-3399"]},"project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"status":"public","publication_status":"published","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].","ec_funded":1,"title":"Optimal steering of matrix product states and quantum many-body scars","author":[{"id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","first_name":"Marko","full_name":"Ljubotina, Marko","last_name":"Ljubotina"},{"full_name":"Roos, Barbara","last_name":"Roos","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","first_name":"Barbara","orcid":"0000-0002-9071-5880"},{"full_name":"Abanin, Dmitry A.","last_name":"Abanin","first_name":"Dmitry A."},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"_id":"12276","abstract":[{"lang":"eng","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."}],"issue":"3","doi":"10.1103/prxquantum.3.030343"},{"author":[{"orcid":"0000-0001-7205-2975","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","full_name":"Brückner, David"},{"first_name":"Matthew","full_name":"Schmitt, Matthew","last_name":"Schmitt"},{"first_name":"Alexandra","last_name":"Fink","full_name":"Fink, Alexandra"},{"full_name":"Ladurner, Georg","last_name":"Ladurner","first_name":"Georg"},{"last_name":"Flommersfeld","full_name":"Flommersfeld, Johannes","first_name":"Johannes"},{"last_name":"Arlt","full_name":"Arlt, Nicolas","first_name":"Nicolas"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"first_name":"Joachim O.","last_name":"Rädler","full_name":"Rädler, Joachim O."},{"full_name":"Broedersz, Chase P.","last_name":"Broedersz","first_name":"Chase P."}],"title":"Geometry adaptation of protrusion and polarity dynamics in confined cell migration","_id":"12277","issue":"3","abstract":[{"lang":"eng","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."}],"doi":"10.1103/physrevx.12.031041","publication_identifier":{"issn":["2160-3308"]},"status":"public","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.","publication_status":"published","day":"20","citation":{"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.","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.","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","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.","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).","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","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."},"month":"09","file_date_updated":"2023-01-30T11:07:27Z","ddc":["530","570"],"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"file":[{"date_created":"2023-01-30T11:07:27Z","file_id":"12458","date_updated":"2023-01-30T11:07:27Z","success":1,"checksum":"40a8fbc3663bf07b37cb80020974d40d","content_type":"application/pdf","access_level":"open_access","file_size":4686804,"creator":"dernst","relation":"main_file","file_name":"2022_PhysicalReviewX_Brueckner.pdf"}],"has_accepted_license":"1","article_processing_charge":"No","volume":12,"oa":1,"year":"2022","keyword":["General Physics and Astronomy"],"publication":"Physical Review X","date_updated":"2023-08-04T10:25:49Z","article_type":"original","article_number":"031041","department":[{"_id":"EdHa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-09-20T00:00:00Z","external_id":{"arxiv":["2106.01014"],"isi":["000861534700001"]},"scopus_import":"1","date_created":"2023-01-16T10:02:06Z","intvolume":" 12","publisher":"American Physical Society","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article"},{"article_number":"2492","article_type":"original","date_updated":"2023-10-17T11:41:28Z","publication":"Nanomaterials","keyword":["General Materials Science","General Chemical Engineering"],"year":"2022","oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"publisher":"MDPI","intvolume":" 12","date_created":"2023-01-16T10:02:31Z","scopus_import":"1","external_id":{"isi":["000834401600001"]},"date_published":"2022-07-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ZhAl"}],"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).","publication_status":"published","status":"public","publication_identifier":{"issn":["2079-4991"]},"doi":"10.3390/nano12142492","abstract":[{"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.","lang":"eng"}],"issue":"14","_id":"12278","title":"Band structure near the Dirac Point in HgTe quantum wells with critical thickness","author":[{"full_name":"Shuvaev, Alexey","last_name":"Shuvaev","first_name":"Alexey"},{"last_name":"Dziom","full_name":"Dziom, Uladzislau","first_name":"Uladzislau","id":"6A9A37C2-8C5C-11E9-AE53-F2FDE5697425","orcid":"0000-0002-1648-0999"},{"first_name":"Jan","full_name":"Gospodarič, Jan","last_name":"Gospodarič"},{"first_name":"Elena G.","last_name":"Novik","full_name":"Novik, Elena G."},{"first_name":"Alena A.","last_name":"Dobretsova","full_name":"Dobretsova, Alena A."},{"last_name":"Mikhailov","full_name":"Mikhailov, Nikolay N.","first_name":"Nikolay N."},{"first_name":"Ze Don","last_name":"Kvon","full_name":"Kvon, Ze Don"},{"first_name":"Andrei","last_name":"Pimenov","full_name":"Pimenov, Andrei"}],"volume":12,"article_processing_charge":"Yes","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2023-01-30T11:16:54Z","file_id":"12459","relation":"main_file","file_size":464840,"creator":"dernst","file_name":"2022_Nanomaterials_Shuvaev.pdf","date_updated":"2023-01-30T11:16:54Z","success":1,"content_type":"application/pdf","checksum":"efad6742f89f39a18bec63116dd689a0","access_level":"open_access"}],"oa_version":"Published Version","file_date_updated":"2023-01-30T11:16:54Z","month":"07","ddc":["530"],"citation":{"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.","apa":"Shuvaev, A., Dziom, U., 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","ama":"Shuvaev A, Dziom U, 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","ista":"Shuvaev A, Dziom U, 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.","short":"A. Shuvaev, U. Dziom, J. Gospodarič, E.G. Novik, A.A. Dobretsova, N.N. Mikhailov, Z.D. Kvon, A. Pimenov, Nanomaterials 12 (2022).","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.","chicago":"Shuvaev, Alexey, Uladzislau 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."},"day":"20"},{"external_id":{"arxiv":["2205.12871"],"isi":["000836397000001"]},"date_published":"2022-08-03T00:00:00Z","scopus_import":"1","date_created":"2023-01-16T10:02:40Z","department":[{"_id":"BjHo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":" 7","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2205.12871","open_access":"1"}],"publisher":"American Physical Society","year":"2022","keyword":["Fluid Flow and Transfer Processes","Modeling and Simulation","Computational Mechanics"],"oa":1,"article_type":"original","article_number":"L081301","publication":"Physical Review Fluids","date_updated":"2023-08-04T10:26:40Z","oa_version":"Preprint","day":"03","citation":{"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.","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.","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","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.","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"},"month":"08","volume":7,"article_processing_charge":"No","arxiv":1,"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"}],"doi":"10.1103/physrevfluids.7.l081301","author":[{"full_name":"Kumar, M. Vijay","last_name":"Kumar","first_name":"M. Vijay"},{"orcid":"0000-0002-3072-5999","first_name":"Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","last_name":"Varshney","full_name":"Varshney, Atul"},{"first_name":"Dongyang","full_name":"Li, Dongyang","last_name":"Li"},{"first_name":"Victor","full_name":"Steinberg, Victor","last_name":"Steinberg"}],"title":"Relaminarization of elastic turbulence","_id":"12279","publication_status":"published","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). ","status":"public","publication_identifier":{"issn":["2469-990X"]}},{"oa_version":"Published Version","file_date_updated":"2023-01-30T11:28:13Z","ddc":["000","570"],"pmid":1,"month":"06","day":"14","citation":{"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.","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.","short":"L. Schmid, C. Hilbe, K. Chatterjee, M. Nowak, PLOS Computational Biology 18 (2022).","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.","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","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.","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"},"volume":18,"article_processing_charge":"No","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"success":1,"date_updated":"2023-01-30T11:28:13Z","access_level":"open_access","content_type":"application/pdf","checksum":"31b6b311b6731f1658277a9dfff6632c","file_name":"2022_PlosCompBio_Schmid.pdf","relation":"main_file","creator":"dernst","file_size":3143222,"file_id":"12460","date_created":"2023-01-30T11:28:13Z"}],"doi":"10.1371/journal.pcbi.1010149","issue":"6","abstract":[{"lang":"eng","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."}],"_id":"12280","author":[{"orcid":"0000-0002-6978-7329","first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","full_name":"Schmid, Laura"},{"orcid":"0000-0001-5116-955X","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","full_name":"Hilbe, Christian"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"title":"Direct reciprocity between individuals that use different strategy spaces","ec_funded":1,"status":"public","publication_status":"published","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.","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"publication_identifier":{"eissn":["1553-7358"]},"scopus_import":"1","date_created":"2023-01-16T10:02:51Z","date_published":"2022-06-14T00:00:00Z","external_id":{"isi":["000843626800031"],"pmid":["35700167"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"KrCh"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"intvolume":" 18","publisher":"Public Library of Science","keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"year":"2022","oa":1,"article_type":"original","article_number":"e1010149","date_updated":"2025-07-14T09:09:49Z","publication":"PLOS Computational Biology"}]