[{"file_date_updated":"2024-10-14T18:11:45Z","date_published":"2022-03-01T00:00:00Z","title":"Dynamics of Hole Singlet-Triplet Qubits with Large 𝑔-Factor Differences","month":"03","article_processing_charge":"No","oa":1,"file":[{"file_size":25566516,"content_type":"application/x-zip-compressed","success":1,"file_name":"SOIPaper.zip","date_updated":"2024-10-09T19:31:35Z","access_level":"open_access","relation":"main_file","date_created":"2024-10-09T19:31:35Z","file_id":"18292","checksum":"3128dffbd09267b93c2d0b1425fd3ba2","creator":"gkatsaro"},{"success":1,"file_name":"Readme.txt","relation":"main_file","date_updated":"2024-10-14T18:11:45Z","access_level":"open_access","date_created":"2024-10-14T18:11:45Z","creator":"gkatsaro","file_id":"18442","checksum":"df077d2f4652afeb3bf100068e88aa48","file_size":6776,"content_type":"text/plain"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"GeKa"}],"citation":{"ista":"Katsaros G, Jirovec D. 2022. Dynamics of Hole Singlet-Triplet Qubits with Large 𝑔-Factor Differences, Institute of Science and Technology Austria, 10.15479/AT:ISTA:18291.","short":"G. Katsaros, D. Jirovec, (2022).","ama":"Katsaros G, Jirovec D. Dynamics of Hole Singlet-Triplet Qubits with Large 𝑔-Factor Differences. 2022. doi:10.15479/AT:ISTA:18291","chicago":"Katsaros, Georgios, and Daniel Jirovec. “Dynamics of Hole Singlet-Triplet Qubits with Large 𝑔-Factor Differences.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:18291.","apa":"Katsaros, G., & Jirovec, D. (2022). Dynamics of Hole Singlet-Triplet Qubits with Large 𝑔-Factor Differences. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:18291","ieee":"G. Katsaros and D. Jirovec, “Dynamics of Hole Singlet-Triplet Qubits with Large 𝑔-Factor Differences.” Institute of Science and Technology Austria, 2022.","mla":"Katsaros, Georgios, and Daniel Jirovec. Dynamics of Hole Singlet-Triplet Qubits with Large 𝑔-Factor Differences. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:18291."},"date_created":"2024-10-09T19:35:03Z","author":[{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7197-4801","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel","last_name":"Jirovec"}],"_id":"18291","year":"2022","oa_version":"None","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","day":"01","type":"research_data","status":"public","corr_author":"1","publisher":"Institute of Science and Technology Austria","date_updated":"2025-04-15T07:15:24Z","doi":"10.15479/AT:ISTA:18291","has_accepted_license":"1","related_material":{"record":[{"id":"10920","status":"public","relation":"research_paper"}]}},{"doi":"10.1016/j.sctalk.2022.100038","acknowledgement":"This talk presents parts of my PhD work, conducted at IUSTI in Marseille under the supervision of YoĂ«l Forterre and Bloen Metzger. It aslo benefited from contributions from Antoine BĂ©rut, and some of the data was acquired by Pauline Dame as part of a summer internship.\r\nThis work was supported by the European Research Council (ERC) under the European Union Horizon 2020 Research and Innovation program (ERC Grant 647384) and by the Labex MEC (ANR-10-LABX-0092) under the 647384) and by the A*MIDEX project (ANR-11-IDEX-0001-02) funded by the French government program Investissements d'Avenir, and by ANR ScienceFriction (No. ANR-18-CE30-0024).","date_updated":"2024-12-11T09:24:57Z","type":"journal_article","publisher":"Elsevier","status":"public","intvolume":" 3","OA_type":"gold","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18606","year":"2022","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2772-5693"]},"quality_controlled":"1","date_created":"2024-12-01T23:01:55Z","oa":1,"article_processing_charge":"No","volume":3,"month":"08","citation":{"short":"C. Clavaud, Science Talks 3 (2022).","ista":"Clavaud C. 2022. Shear thickening in dense suspensions: an experimental study. Science Talks. 3, 100038.","mla":"Clavaud, CĂ©cile. “Shear Thickening in Dense Suspensions: An Experimental Study.” Science Talks, vol. 3, 100038, Elsevier, 2022, doi:10.1016/j.sctalk.2022.100038.","ieee":"C. Clavaud, “Shear thickening in dense suspensions: an experimental study,” Science Talks, vol. 3. Elsevier, 2022.","apa":"Clavaud, C. (2022). Shear thickening in dense suspensions: an experimental study. Science Talks. Elsevier. https://doi.org/10.1016/j.sctalk.2022.100038","ama":"Clavaud C. Shear thickening in dense suspensions: an experimental study. Science Talks. 2022;3. doi:10.1016/j.sctalk.2022.100038","chicago":"Clavaud, CĂ©cile. “Shear Thickening in Dense Suspensions: An Experimental Study.” Science Talks. Elsevier, 2022. https://doi.org/10.1016/j.sctalk.2022.100038."},"file_date_updated":"2024-12-11T09:22:19Z","DOAJ_listed":"1","date_published":"2022-08-01T00:00:00Z","article_number":"100038","has_accepted_license":"1","OA_place":"publisher","corr_author":"1","publication_status":"published","scopus_import":"1","publication":"Science Talks","abstract":[{"text":"Shear thickening is an intriguing rheological behaviour which consists in a brutal increase in the viscosity above a critical shear rate. It is famously encountered in suspensions of corn starch in water. Despite having been discovered in the early 1930's, its underlying mechanisms remained a mystery for a long time. In 2013–14, numerical and theoretical works [[1], [2], [3]] put forward a frictional transition scenario to explain this phenomenon.\r\nIn this talk, I will present experimental work investigating this frictional transition scenario. In order to test the ideas of this model, one has to go further than standard rheological techniques, since they do not provide access to the frictional state of the measured suspension. I will thus focus on the techniques that we developed in order to evidence the frictional transition and link it to the presence of a shear-thickening behaviour.","lang":"eng"}],"ddc":["530"],"day":"01","oa_version":"Published Version","author":[{"orcid":"0000-0002-1843-3803","last_name":"Clavaud","first_name":"CĂ©cile","id":"5f654c5d-04a1-11eb-ab36-ba9ffec58bd8","full_name":"Clavaud, CĂ©cile"}],"file":[{"success":1,"file_name":"2022_ScienceTalks_Clavaud.pdf","file_id":"18607","creator":"dernst","checksum":"379a5f0b2684cd5393a23be374591484","date_created":"2024-12-03T08:41:48Z","date_updated":"2024-12-03T08:41:48Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":1128564},{"file_name":"2024_ScienceTalk_Clavaud_Video.mp4","success":1,"relation":"main_file","access_level":"open_access","date_updated":"2024-12-11T09:22:13Z","date_created":"2024-12-11T09:22:13Z","file_id":"18646","creator":"dernst","checksum":"666c0bd9af8432437554d0c75c540809","file_size":93265727,"content_type":"video/mp4"},{"file_id":"18647","checksum":"8fd0d6224d7a0125fcf7d9ca0d80d700","creator":"dernst","date_created":"2024-12-11T09:22:19Z","access_level":"open_access","relation":"supplementary_material","date_updated":"2024-12-11T09:22:19Z","file_name":"2024_ScienceTalk__Clavaud_QA.mp4","content_type":"video/mp4","file_size":58282147}],"department":[{"_id":"ScWa"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"title":"Shear thickening in dense suspensions: an experimental study"},{"scopus_import":"1","publication_status":"published","has_accepted_license":"1","article_number":"e10490","oa_version":"Published Version","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"}],"ddc":["570"],"day":"01","publication":"Molecular Systems Biology","issue":"9","external_id":{"pmid":["36124745"],"isi":["000856482800001"]},"author":[{"first_name":"Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87","full_name":"Angermayr, Andreas","last_name":"Angermayr","orcid":"0000-0001-8619-2223"},{"last_name":"Pang","first_name":"Tin Yau","full_name":"Pang, Tin Yau"},{"first_name":"Guillaume","full_name":"Chevereau, Guillaume","last_name":"Chevereau"},{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","full_name":"Mitosch, Karin","first_name":"Karin","last_name":"Mitosch"},{"full_name":"Lercher, Martin J","first_name":"Martin J","last_name":"Lercher"},{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias"}],"title":"Growth‐mediated negative feedback shapes quantitative antibiotic response","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"ToBo"}],"file":[{"checksum":"8b1d8f5ea20c8408acf466435fb6ae01","file_id":"12446","creator":"dernst","date_created":"2023-01-30T09:49:55Z","access_level":"open_access","relation":"main_file","date_updated":"2023-01-30T09:49:55Z","file_name":"2022_MolecularSystemsBio_Angermayr.pdf","success":1,"content_type":"application/pdf","file_size":1098812}],"intvolume":" 18","date_updated":"2025-06-11T14:10:18Z","type":"journal_article","keyword":["Applied Mathematics","Computational Theory and Mathematics","General Agricultural and Biological Sciences","General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","Information Systems"],"status":"public","publisher":"Embo Press","doi":"10.15252/msb.202110490","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 SkƂodowska-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.","pmid":1,"year":"2022","_id":"12261","acknowledged_ssus":[{"_id":"M-Shop"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"article_type":"original","date_created":"2023-01-16T09:58:34Z","publication_identifier":{"eissn":["1744-4292"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2022-09-01T00:00:00Z","file_date_updated":"2023-01-30T09:49:55Z","citation":{"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","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.","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","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.","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.","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":1,"article_processing_charge":"No","volume":18,"month":"09"},{"article_type":"original","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"942-953","acknowledged_ssus":[{"_id":"EM-Fac"}],"_id":"12262","pmid":1,"year":"2022","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.","doi":"10.1038/s41594-022-00832-5","type":"journal_article","status":"public","publisher":"Springer Nature","keyword":["Molecular Biology","Structural Biology"],"date_updated":"2023-08-04T09:52:20Z","intvolume":" 29","article_processing_charge":"No","month":"09","volume":29,"oa":1,"citation":{"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.","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.","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.","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","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","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."},"file_date_updated":"2023-01-30T10:00:04Z","date_published":"2022-09-12T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"date_created":"2023-01-16T09:59:06Z","publication":"Nature Structural & Molecular Biology","issue":"9","day":"12","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."}],"ddc":["570"],"oa_version":"Published Version","has_accepted_license":"1","publication_status":"published","scopus_import":"1","file":[{"file_name":"2022_NatureStrucMolecBio_Prattes.pdf","success":1,"creator":"dernst","checksum":"2d5c3ec01718fefd7553052b0b8a0793","file_id":"12447","date_updated":"2023-01-30T10:00:04Z","access_level":"open_access","relation":"main_file","date_created":"2023-01-30T10:00:04Z","content_type":"application/pdf","file_size":9935057}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"EM-Fac"}],"title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","author":[{"full_name":"Prattes, Michael","last_name":"Prattes","first_name":"Michael"},{"first_name":"Irina","full_name":"Grishkovskaya, Irina","last_name":"Grishkovskaya"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin"},{"first_name":"Christina","full_name":"Hetzmannseder, Christina","last_name":"Hetzmannseder"},{"last_name":"Zisser","full_name":"Zisser, Gertrude","first_name":"Gertrude"},{"full_name":"Sailer, Carolin","last_name":"Sailer","first_name":"Carolin"},{"first_name":"Vasileios","full_name":"Kargas, Vasileios","last_name":"Kargas"},{"last_name":"Loibl","full_name":"Loibl, Mathias","first_name":"Mathias"},{"last_name":"Gerhalter","full_name":"Gerhalter, Magdalena","first_name":"Magdalena"},{"last_name":"Kofler","full_name":"Kofler, Lisa","first_name":"Lisa"},{"last_name":"Warren","full_name":"Warren, Alan J.","first_name":"Alan J."},{"first_name":"Florian","full_name":"Stengel, Florian","last_name":"Stengel"},{"last_name":"Haselbach","full_name":"Haselbach, David","first_name":"David"},{"first_name":"Helmut","last_name":"Bergler","full_name":"Bergler, Helmut"}],"external_id":{"isi":["000852942100004"],"pmid":["36097293"]}},{"doi":"10.1111/jeb.14005","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)","intvolume":" 35","date_updated":"2025-04-15T08:20:40Z","type":"journal_article","keyword":["Ecology","Evolution","Behavior and Systematics"],"status":"public","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"article_type":"review","year":"2022","pmid":1,"_id":"12264","page":"1143-1164","quality_controlled":"1","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"language":[{"iso":"eng"}],"date_created":"2023-01-16T09:59:24Z","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.","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","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","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.","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.","ista":"Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. What is reproductive isolation? Journal of Evolutionary Biology. 35(9), 1143–1164.","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1143–1164."},"oa":1,"month":"09","article_processing_charge":"Yes (via OA deal)","volume":35,"date_published":"2022-09-01T00:00:00Z","file_date_updated":"2023-01-30T10:05:31Z","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"other","id":"12265"}]},"scopus_import":"1","corr_author":"1","publication_status":"published","ddc":["570"],"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"}],"day":"01","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation","grant_number":"P32166"}],"publication":"Journal of Evolutionary Biology","issue":"9","oa_version":"Published Version","author":[{"last_name":"Westram","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"orcid":"0000-0001-6395-386X","full_name":"Surendranadh, Parvathy","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["36063156"],"isi":["000849851100002"]},"department":[{"_id":"NiBa"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"content_type":"application/pdf","file_size":3146793,"file_id":"12448","creator":"dernst","checksum":"f08de57112330a7ee88d2e1b20576a1e","date_updated":"2023-01-30T10:05:31Z","access_level":"open_access","relation":"main_file","date_created":"2023-01-30T10:05:31Z","file_name":"2022_JourEvoBiology_Westram.pdf","success":1}],"title":"What is reproductive isolation?"},{"oa_version":"Published Version","project":[{"grant_number":"P32166","name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"day":"01","ddc":["570"],"publication":"Journal of Evolutionary Biology","issue":"9","scopus_import":"1","corr_author":"1","publication_status":"published","related_material":{"record":[{"relation":"other","status":"public","id":"12264"}]},"has_accepted_license":"1","title":"Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"NiBa"}],"file":[{"success":1,"file_name":"2022_JourEvoBiology_Westram_Response.pdf","file_id":"12449","checksum":"27268009e5eec030bc10667a4ac5ed4c","creator":"dernst","date_created":"2023-01-30T10:14:09Z","date_updated":"2023-01-30T10:14:09Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":349603}],"external_id":{"isi":["000849851100009"]},"author":[{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"},{"full_name":"Surendranadh, Parvathy","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","orcid":"0000-0001-6395-386X"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"year":"2022","page":"1200-1205","_id":"12265","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"letter_note","isi":1,"intvolume":" 35","status":"public","keyword":["Ecology","Evolution","Behavior and Systematics"],"type":"journal_article","publisher":"Wiley","date_updated":"2025-04-15T08:20:40Z","doi":"10.1111/jeb.14082","acknowledgement":"We are very grateful to the authors of the commentaries for the interesting discussion and to Luke Holman for handling this set of manuscripts. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166).","date_published":"2022-09-01T00:00:00Z","file_date_updated":"2023-01-30T10:14:09Z","citation":{"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.","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.","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.","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","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"},"month":"09","volume":35,"article_processing_charge":"Yes (via OA deal)","oa":1,"date_created":"2023-01-16T09:59:37Z","quality_controlled":"1","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"language":[{"iso":"eng"}]},{"oa_version":"Published Version","day":"25","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"}],"ddc":["570"],"publication":"Frontiers in Oncology","scopus_import":"1","publication_status":"published","has_accepted_license":"1","article_number":"983507","title":"Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma cells","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"GaNo"}],"file":[{"checksum":"efc7edf9f626af31853790c5b598a68c","creator":"dernst","file_id":"12450","relation":"main_file","access_level":"open_access","date_updated":"2023-01-30T10:25:21Z","date_created":"2023-01-30T10:25:21Z","success":1,"file_name":"2022_FrontiersOntology_Basilico.pdf","content_type":"application/pdf","file_size":13588502}],"external_id":{"isi":["000856524900001"],"pmid":["36091138"]},"author":[{"orcid":"0000-0003-1843-3173","last_name":"Basilico","first_name":"Bernadette","full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425"},{"last_name":"PalamĂ ","full_name":"PalamĂ , Ilaria Elena","first_name":"Ilaria Elena"},{"last_name":"D’Amone","first_name":"Stefania","full_name":"D’Amone, Stefania"},{"full_name":"Lauro, Clotilde","last_name":"Lauro","first_name":"Clotilde"},{"full_name":"Rosito, Maria","last_name":"Rosito","first_name":"Maria"},{"last_name":"Grieco","full_name":"Grieco, Maddalena","first_name":"Maddalena"},{"first_name":"Patrizia","last_name":"Ratano","full_name":"Ratano, Patrizia"},{"full_name":"Cordella, Federica","first_name":"Federica","last_name":"Cordella"},{"first_name":"Caterina","full_name":"Sanchini, Caterina","last_name":"Sanchini"},{"full_name":"Di Angelantonio, Silvia","last_name":"Di Angelantonio","first_name":"Silvia"},{"first_name":"Davide","full_name":"Ragozzino, Davide","last_name":"Ragozzino"},{"full_name":"Cascione, Mariafrancesca","last_name":"Cascione","first_name":"Mariafrancesca"},{"last_name":"Gigli","first_name":"Giuseppe","full_name":"Gigli, Giuseppe"},{"first_name":"Barbara","last_name":"Cortese","full_name":"Cortese, Barbara"}],"year":"2022","pmid":1,"_id":"12268","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","isi":1,"intvolume":" 12","status":"public","publisher":"Frontiers Media","type":"journal_article","keyword":["Cancer Research","Oncology"],"date_updated":"2023-08-04T09:54:16Z","doi":"10.3389/fonc.2022.983507","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.","date_published":"2022-08-25T00:00:00Z","file_date_updated":"2023-01-30T10:25:21Z","citation":{"short":"B. Basilico, I.E. PalamĂ , 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).","ista":"Basilico B, PalamĂ  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.","ama":"Basilico B, PalamĂ  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","chicago":"Basilico, Bernadette, Ilaria Elena PalamĂ , 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.","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.","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.","apa":"Basilico, B., PalamĂ , 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"},"month":"08","article_processing_charge":"No","volume":12,"oa":1,"date_created":"2023-01-16T10:00:28Z","publication_identifier":{"issn":["2234-943X"]},"quality_controlled":"1","language":[{"iso":"eng"}]},{"author":[{"orcid":"0000-0003-0038-7068","full_name":"Ljubotina, Marko","first_name":"Marko","last_name":"Ljubotina","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E"},{"last_name":"Roy","full_name":"Roy, Dibyendu","first_name":"Dibyendu"},{"full_name":"Prosen, TomaĆŸ","last_name":"Prosen","first_name":"TomaĆŸ"}],"external_id":{"arxiv":["2106.08373"],"isi":["000861332900005"]},"department":[{"_id":"MaSe"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.08373","open_access":"1"}],"title":"Absence of thermalization of free systems coupled to gapped interacting reservoirs","article_number":"054314","scopus_import":"1","publication_status":"published","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."}],"day":"31","project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"issue":"5","publication":"Physical Review B","oa_version":"Preprint","ec_funded":1,"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"quality_controlled":"1","language":[{"iso":"eng"}],"arxiv":1,"date_created":"2023-01-16T10:00:39Z","citation":{"short":"M. Ljubotina, D. Roy, T. Prosen, Physical Review B 106 (2022).","ista":"Ljubotina M, Roy D, Prosen T. 2022. Absence of thermalization of free systems coupled to gapped interacting reservoirs. Physical Review B. 106(5), 054314.","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","chicago":"Ljubotina, Marko, Dibyendu Roy, and TomaĆŸ 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"},"oa":1,"article_processing_charge":"No","month":"08","volume":106,"date_published":"2022-08-31T00:00:00Z","doi":"10.1103/physrevb.106.054314","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. ","intvolume":" 106","date_updated":"2025-04-14T07:52:06Z","status":"public","type":"journal_article","publisher":"American Physical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"article_type":"original","year":"2022","_id":"12269"},{"corr_author":"1","publication_status":"published","scopus_import":"1","publication":"IEEE Transactions on Information Theory","issue":"8","abstract":[{"text":"We study communication in the presence of a jamming adversary where quadratic power constraints are imposed on the transmitter and the jammer. The jamming signal is allowed to be a function of the codebook, and a noncausal but noisy observation of the transmitted codeword. For a certain range of the noise-to-signal ratios (NSRs) of the transmitter and the jammer, we are able to characterize the capacity of this channel under deterministic encoding or stochastic encoding, i.e., with no common randomness between the encoder/decoder pair. For the remaining NSR regimes, we determine the capacity under the assumption of a small amount of common randomness (at most 2log(n) bits in one sub-regime, and at most Ω(n) bits in the other sub-regime) available to the encoder-decoder pair. Our proof techniques involve a novel myopic list-decoding result for achievability, and a Plotkin-type push attack for the converse in a subregion of the NSRs, both of which may be of independent interest. We also give bounds on the strong secrecy capacity of this channel assuming that the jammer is simultaneously eavesdropping.","lang":"eng"}],"day":"01","oa_version":"Preprint","author":[{"last_name":"Zhang","full_name":"Zhang, Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","first_name":"Yihan","orcid":"0000-0002-6465-6258"},{"first_name":"Shashank","last_name":"Vatedka","full_name":"Vatedka, Shashank"},{"first_name":"Sidharth","full_name":"Jaggi, Sidharth","last_name":"Jaggi"},{"full_name":"Sarwate, Anand D.","last_name":"Sarwate","first_name":"Anand D."}],"external_id":{"isi":["000838527100004"],"arxiv":["1801.05951"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1801.05951"}],"department":[{"_id":"MaMo"}],"title":"Quadratically constrained myopic adversarial channels","doi":"10.1109/tit.2022.3167554","date_updated":"2024-10-09T21:03:54Z","publisher":"Institute of Electrical and Electronics Engineers","status":"public","type":"journal_article","intvolume":" 68","isi":1,"article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12273","page":"4901-4948","year":"2022","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"arxiv":1,"date_created":"2023-01-16T10:01:19Z","oa":1,"month":"08","volume":68,"article_processing_charge":"No","citation":{"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","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.","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.","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","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."},"date_published":"2022-08-01T00:00:00Z"},{"main_file_link":[{"open_access":"1","url":"https://helda.helsinki.fi/items/94433455-4854-45c0-9de8-7326caea8780"}],"department":[{"_id":"EdHa"}],"title":"Retrograde movements determine effective stem cell numbers in the intestine","author":[{"last_name":"Azkanaz","full_name":"Azkanaz, Maria","first_name":"Maria"},{"last_name":"Corominas-Murtra","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643"},{"last_name":"Ellenbroek","first_name":"Saskia I. J.","full_name":"Ellenbroek, Saskia I. J."},{"full_name":"Bruens, Lotte","first_name":"Lotte","last_name":"Bruens"},{"full_name":"Webb, Anna T.","first_name":"Anna T.","last_name":"Webb"},{"full_name":"Laskaris, Dimitrios","first_name":"Dimitrios","last_name":"Laskaris"},{"full_name":"Oost, Koen C.","first_name":"Koen C.","last_name":"Oost"},{"full_name":"Lafirenze, Simona J. A.","first_name":"Simona J. A.","last_name":"Lafirenze"},{"first_name":"Karl","last_name":"Annusver","full_name":"Annusver, Karl"},{"last_name":"Messal","first_name":"Hendrik A.","full_name":"Messal, Hendrik A."},{"last_name":"Iqbal","full_name":"Iqbal, Sharif","first_name":"Sharif"},{"first_name":"Dustin J.","full_name":"Flanagan, Dustin J.","last_name":"Flanagan"},{"full_name":"Huels, David J.","last_name":"Huels","first_name":"David J."},{"full_name":"Rojas-RodrĂ­guez, Felipe","first_name":"Felipe","last_name":"Rojas-RodrĂ­guez"},{"full_name":"Vizoso, Miguel","first_name":"Miguel","last_name":"Vizoso"},{"last_name":"Kasper","first_name":"Maria","full_name":"Kasper, Maria"},{"full_name":"Sansom, Owen J.","last_name":"Sansom","first_name":"Owen J."},{"first_name":"Hugo J.","full_name":"Snippert, Hugo J.","last_name":"Snippert"},{"last_name":"Liberali","first_name":"Prisca","full_name":"Liberali, Prisca"},{"first_name":"Benjamin D.","full_name":"Simons, Benjamin D.","last_name":"Simons"},{"last_name":"Katajisto","full_name":"Katajisto, Pekka","first_name":"Pekka"},{"first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"full_name":"van Rheenen, Jacco","first_name":"Jacco","last_name":"van Rheenen"}],"external_id":{"isi":["000824430000004"],"pmid":["35831497"]},"publication":"Nature","issue":"7919","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288"}],"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"}],"day":"13","ec_funded":1,"oa_version":"Submitted Version","related_material":{"link":[{"relation":"software","url":"https://github.com/JaccovanRheenenLab/Retrograde_movement_Azkanaz_Nature_2022"}]},"publication_status":"published","corr_author":"1","scopus_import":"1","volume":607,"article_processing_charge":"No","month":"07","oa":1,"citation":{"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-RodrĂ­guez, M. Vizoso, M. Kasper, O.J. Sansom, H.J. Snippert, P. Liberali, B.D. Simons, P. Katajisto, E.B. Hannezo, J. van Rheenen, Nature 607 (2022) 548–554.","ista":"Azkanaz M, Corominas-Murtra B, Ellenbroek SIJ, Bruens L, Webb AT, Laskaris D, Oost KC, Lafirenze SJA, Annusver K, Messal HA, Iqbal S, Flanagan DJ, Huels DJ, Rojas-RodrĂ­guez 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.","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.","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","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.","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"},"date_published":"2022-07-13T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"quality_controlled":"1","date_created":"2023-01-16T10:01:29Z","article_type":"original","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"548-554","_id":"12274","year":"2022","pmid":1,"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).","doi":"10.1038/s41586-022-04962-0","type":"journal_article","status":"public","publisher":"Springer Nature","keyword":["Multidisciplinary"],"date_updated":"2025-04-14T07:52:27Z","intvolume":" 607"},{"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."}],"day":"05","publication":"EMBO Reports","issue":"7","oa_version":"Published Version","has_accepted_license":"1","article_number":"e54163","scopus_import":"1","publication_status":"published","department":[{"_id":"MaDe"}],"main_file_link":[{"url":"https://doi.org/10.15252/embr.202154163","open_access":"1"}],"title":"Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning","author":[{"full_name":"Rahman, Maisha","first_name":"Maisha","last_name":"Rahman"},{"full_name":"Ramirez, Nelson","last_name":"Ramirez","first_name":"Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425"},{"last_name":"Diaz‐Balzac","full_name":"Diaz‐Balzac, Carlos A","first_name":"Carlos A"},{"full_name":"BĂŒlow, Hannes E","first_name":"Hannes E","last_name":"BĂŒlow"}],"external_id":{"isi":["000797302700001"],"pmid":["35586945"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","isi":1,"pmid":1,"year":"2022","_id":"12275","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","doi":"10.15252/embr.202154163","intvolume":" 23","status":"public","publisher":"Embo Press","type":"journal_article","keyword":["Genetics","Molecular Biology","Biochemistry"],"date_updated":"2023-10-03T11:25:54Z","citation":{"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.","ieee":"M. Rahman, N. Ramirez, C. A. Diaz‐Balzac, and H. E. BĂŒlow, “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., & BĂŒlow, 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","ama":"Rahman M, Ramirez N, Diaz‐Balzac CA, BĂŒlow HE. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. EMBO Reports. 2022;23(7). doi:10.15252/embr.202154163","chicago":"Rahman, Maisha, Nelson Ramirez, Carlos A Diaz‐Balzac, and Hannes E BĂŒlow. “Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory Dendrite Patterning.” EMBO Reports. Embo Press, 2022. https://doi.org/10.15252/embr.202154163.","short":"M. Rahman, N. Ramirez, C.A. Diaz‐Balzac, H.E. BĂŒlow, EMBO Reports 23 (2022).","ista":"Rahman M, Ramirez N, Diaz‐Balzac CA, BĂŒlow HE. 2022. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. EMBO Reports. 23(7), e54163."},"month":"07","article_processing_charge":"No","volume":23,"oa":1,"date_published":"2022-07-05T00:00:00Z","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2023-01-16T10:01:44Z"},{"_id":"12276","year":"2022","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-14T07:52:07Z","status":"public","keyword":["General Medicine"],"type":"journal_article","publisher":"American Physical Society","intvolume":" 3","doi":"10.1103/prxquantum.3.030343","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].","file_date_updated":"2023-01-30T11:02:50Z","date_published":"2022-09-23T00:00:00Z","oa":1,"month":"09","volume":3,"article_processing_charge":"No","citation":{"apa":"Ljubotina, M., Roos, B., Abanin, D. A., & Serbyn, M. (2022). Optimal steering of matrix product states and quantum many-body scars. PRX Quantum. American Physical Society. https://doi.org/10.1103/prxquantum.3.030343","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.","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.","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.","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)."},"arxiv":1,"date_created":"2023-01-16T10:01:56Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2691-3399"]},"quality_controlled":"1","ec_funded":1,"oa_version":"Published Version","publication":"PRX Quantum","issue":"3","abstract":[{"text":"Ongoing development of quantum simulators allows for a progressively finer degree of control of quantum many-body systems. This motivates the development of efficient approaches to facilitate the control of such systems and enable the preparation of nontrivial quantum states. Here we formulate an approach to control quantum systems based on matrix product states (MPSs). We compare counterdiabatic and leakage minimization approaches to the so-called local steering problem that consists in finding the best value of the control parameters for generating a unitary evolution of the specific MPS in a given direction. In order to benchmark the different approaches, we apply them to the generalization of the PXP model known to exhibit coherent quantum dynamics due to quantum many-body scars. We find that the leakage-based approach generally outperforms the counterdiabatic framework and use it to construct a Floquet model with quantum scars. We perform the first steps towards global trajectory optimization and demonstrate entanglement steering capabilities in the generalized PXP model. Finally, we apply our leakage minimization approach to construct quantum scars in the periodically driven nonintegrable Ising model.","lang":"eng"}],"day":"23","ddc":["530"],"project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"publication_status":"published","corr_author":"1","scopus_import":"1","article_number":"030343","has_accepted_license":"1","title":"Optimal steering of matrix product states and quantum many-body scars","file":[{"content_type":"application/pdf","file_size":7661905,"success":1,"file_name":"2022_PRXQuantum_Ljubotina.pdf","creator":"dernst","checksum":"ef8f0a1b5a019b3958009162de0fa4c3","file_id":"12457","date_created":"2023-01-30T11:02:50Z","date_updated":"2023-01-30T11:02:50Z","access_level":"open_access","relation":"main_file"}],"department":[{"_id":"MaSe"},{"_id":"RoSe"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2204.02899"]},"author":[{"orcid":"0000-0003-0038-7068","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina","first_name":"Marko","full_name":"Ljubotina, Marko"},{"orcid":"0000-0002-9071-5880","full_name":"Roos, Barbara","first_name":"Barbara","last_name":"Roos","id":"5DA90512-D80F-11E9-8994-2E2EE6697425"},{"last_name":"Abanin","first_name":"Dmitry A.","full_name":"Abanin, Dmitry A."},{"orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"}]},{"doi":"10.1103/physrevx.12.031041","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.","type":"journal_article","publisher":"American Physical Society","status":"public","keyword":["General Physics and Astronomy"],"date_updated":"2023-08-04T10:25:49Z","intvolume":" 12","article_type":"original","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12277","year":"2022","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2160-3308"]},"quality_controlled":"1","date_created":"2023-01-16T10:02:06Z","arxiv":1,"volume":12,"article_processing_charge":"No","month":"09","oa":1,"citation":{"short":"D. BrĂŒckner, M. Schmitt, A. Fink, G. Ladurner, J. Flommersfeld, N. Arlt, E.B. Hannezo, J.O. RĂ€dler, C.P. Broedersz, Physical Review X 12 (2022).","ista":"BrĂŒckner D, Schmitt M, Fink A, Ladurner G, Flommersfeld J, Arlt N, Hannezo EB, RĂ€dler JO, Broedersz CP. 2022. Geometry adaptation of protrusion and polarity dynamics in confined cell migration. Physical Review X. 12(3), 031041.","ama":"BrĂŒckner 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","chicago":"BrĂŒckner, David, Matthew Schmitt, Alexandra Fink, Georg Ladurner, Johannes Flommersfeld, Nicolas Arlt, Edouard B Hannezo, Joachim O. RĂ€dler, 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.","mla":"BrĂŒckner, 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.","ieee":"D. BrĂŒckner et al., “Geometry adaptation of protrusion and polarity dynamics in confined cell migration,” Physical Review X, vol. 12, no. 3. American Physical Society, 2022.","apa":"BrĂŒckner, 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"},"file_date_updated":"2023-01-30T11:07:27Z","date_published":"2022-09-20T00:00:00Z","article_number":"031041","has_accepted_license":"1","publication_status":"published","scopus_import":"1","publication":"Physical Review X","issue":"3","ddc":["530","570"],"abstract":[{"text":"Cell migration in confining physiological environments relies on the concerted dynamics of several cellular components, including protrusions, adhesions with the environment, and the cell nucleus. However, it remains poorly understood how the dynamic interplay of these components and the cell polarity determine the emergent migration behavior at the cellular scale. Here, we combine data-driven inference with a mechanistic bottom-up approach to develop a model for protrusion and polarity dynamics in confined cell migration, revealing how the cellular dynamics adapt to confining geometries. Specifically, we use experimental data of joint protrusion-nucleus migration trajectories of cells on confining micropatterns to systematically determine a mechanistic model linking the stochastic dynamics of cell polarity, protrusions, and nucleus. This model indicates that the cellular dynamics adapt to confining constrictions through a switch in the polarity dynamics from a negative to a positive self-reinforcing feedback loop. Our model further reveals how this feedback loop leads to stereotypical cycles of protrusion-nucleus dynamics that drive the migration of the cell through constrictions. These cycles are disrupted upon perturbation of cytoskeletal components, indicating that the positive feedback is controlled by cellular migration mechanisms. Our data-driven theoretical approach therefore identifies polarity feedback adaptation as a key mechanism in confined cell migration.","lang":"eng"}],"day":"20","oa_version":"Published Version","author":[{"orcid":"0000-0001-7205-2975","last_name":"BrĂŒckner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","full_name":"BrĂŒckner, David"},{"full_name":"Schmitt, Matthew","first_name":"Matthew","last_name":"Schmitt"},{"full_name":"Fink, Alexandra","first_name":"Alexandra","last_name":"Fink"},{"last_name":"Ladurner","full_name":"Ladurner, Georg","first_name":"Georg"},{"last_name":"Flommersfeld","first_name":"Johannes","full_name":"Flommersfeld, Johannes"},{"first_name":"Nicolas","full_name":"Arlt, Nicolas","last_name":"Arlt"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"full_name":"RĂ€dler, Joachim O.","first_name":"Joachim O.","last_name":"RĂ€dler"},{"last_name":"Broedersz","full_name":"Broedersz, Chase P.","first_name":"Chase P."}],"external_id":{"arxiv":["2106.01014"],"isi":["000861534700001"]},"file":[{"date_created":"2023-01-30T11:07:27Z","access_level":"open_access","date_updated":"2023-01-30T11:07:27Z","relation":"main_file","checksum":"40a8fbc3663bf07b37cb80020974d40d","file_id":"12458","creator":"dernst","file_name":"2022_PhysicalReviewX_Brueckner.pdf","success":1,"file_size":4686804,"content_type":"application/pdf"}],"department":[{"_id":"EdHa"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"title":"Geometry adaptation of protrusion and polarity dynamics in confined cell migration"},{"year":"2022","pmid":1,"_id":"12278","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","isi":1,"intvolume":" 12","type":"journal_article","publisher":"MDPI","keyword":["General Materials Science","General Chemical Engineering"],"status":"public","date_updated":"2025-06-11T13:45:36Z","doi":"10.3390/nano12142492","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).","date_published":"2022-07-20T00:00:00Z","file_date_updated":"2023-01-30T11:16:54Z","citation":{"ista":"Shuvaev A, Dziom V, Gospodarič J, Novik EG, Dobretsova AA, Mikhailov NN, Kvon ZD, Pimenov A. 2022. Band structure near the Dirac Point in HgTe quantum wells with critical thickness. Nanomaterials. 12(14), 2492.","short":"A. Shuvaev, V. Dziom, J. Gospodarič, E.G. Novik, A.A. Dobretsova, N.N. Mikhailov, Z.D. Kvon, A. Pimenov, Nanomaterials 12 (2022).","apa":"Shuvaev, A., Dziom, V., Gospodarič, J., Novik, E. G., Dobretsova, A. A., Mikhailov, N. N., 
 Pimenov, A. (2022). Band structure near the Dirac Point in HgTe quantum wells with critical thickness. Nanomaterials. MDPI. https://doi.org/10.3390/nano12142492","ieee":"A. Shuvaev et al., “Band structure near the Dirac Point in HgTe quantum wells with critical thickness,” Nanomaterials, vol. 12, no. 14. MDPI, 2022.","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.","ama":"Shuvaev A, Dziom V, Gospodarič J, et al. Band structure near the Dirac Point in HgTe quantum wells with critical thickness. Nanomaterials. 2022;12(14). doi:10.3390/nano12142492","chicago":"Shuvaev, Alexey, Vlad Dziom, Jan Gospodarič, Elena G. Novik, Alena A. Dobretsova, Nikolay N. Mikhailov, Ze Don Kvon, and Andrei Pimenov. “Band Structure near the Dirac Point in HgTe Quantum Wells with Critical Thickness.” Nanomaterials. MDPI, 2022. https://doi.org/10.3390/nano12142492."},"volume":12,"month":"07","article_processing_charge":"Yes","oa":1,"date_created":"2023-01-16T10:02:31Z","quality_controlled":"1","publication_identifier":{"issn":["2079-4991"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","ddc":["530"],"abstract":[{"lang":"eng","text":"Mercury telluride (HgTe) thin films with a critical thickness of 6.5 nm are predicted to possess a gapless Dirac-like band structure. We report a comprehensive study on gated and optically doped samples by magnetooptical spectroscopy in the THz range. The quasi-classical analysis of the cyclotron resonance allowed the mapping of the band dispersion of Dirac charge carriers in a broad range of electron and hole doping. A smooth transition through the charge neutrality point between Dirac holes and electrons was observed. An additional peak coming from a second type of holes with an almost density-independent mass of around 0.04m0 was detected in the hole-doping range and attributed to an asymmetric spin splitting of the Dirac cone. Spectroscopic evidence for disorder-induced band energy fluctuations could not be detected in present cyclotron resonance experiments."}],"day":"20","publication":"Nanomaterials","issue":"14","scopus_import":"1","publication_status":"published","has_accepted_license":"1","article_number":"2492","title":"Band structure near the Dirac Point in HgTe quantum wells with critical thickness","department":[{"_id":"ZhAl"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"checksum":"efad6742f89f39a18bec63116dd689a0","file_id":"12459","creator":"dernst","relation":"main_file","date_updated":"2023-01-30T11:16:54Z","access_level":"open_access","date_created":"2023-01-30T11:16:54Z","success":1,"file_name":"2022_Nanomaterials_Shuvaev.pdf","content_type":"application/pdf","file_size":464840}],"external_id":{"isi":["000834401600001"],"pmid":["35889716"]},"author":[{"first_name":"Alexey","full_name":"Shuvaev, Alexey","last_name":"Shuvaev"},{"full_name":"Dziom, Uladzislau","last_name":"Dziom","id":"6A9A37C2-8C5C-11E9-AE53-F2FDE5697425","first_name":"Uladzislau","orcid":"0000-0002-1648-0999"},{"last_name":"Gospodarič","full_name":"Gospodarič, Jan","first_name":"Jan"},{"first_name":"Elena G.","last_name":"Novik","full_name":"Novik, Elena G."},{"last_name":"Dobretsova","full_name":"Dobretsova, Alena A.","first_name":"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"},{"last_name":"Pimenov","full_name":"Pimenov, Andrei","first_name":"Andrei"}]},{"title":"Relaminarization of elastic turbulence","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2205.12871"}],"department":[{"_id":"BjHo"}],"external_id":{"arxiv":["2205.12871"],"isi":["000836397000001"]},"author":[{"full_name":"Kumar, M. Vijay","last_name":"Kumar","first_name":"M. Vijay"},{"id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul","last_name":"Varshney","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999"},{"full_name":"Li, Dongyang","first_name":"Dongyang","last_name":"Li"},{"first_name":"Victor","full_name":"Steinberg, Victor","last_name":"Steinberg"}],"oa_version":"Preprint","publication":"Physical Review Fluids","issue":"8","abstract":[{"lang":"eng","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."}],"day":"03","corr_author":"1","publication_status":"published","scopus_import":"1","article_number":"L081301","date_published":"2022-08-03T00:00:00Z","volume":7,"article_processing_charge":"No","month":"08","oa":1,"citation":{"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","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.","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.","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.","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","ista":"Kumar MV, Varshney A, Li D, Steinberg V. 2022. Relaminarization of elastic turbulence. Physical Review Fluids. 7(8), L081301.","short":"M.V. Kumar, A. Varshney, D. Li, V. Steinberg, Physical Review Fluids 7 (2022)."},"date_created":"2023-01-16T10:02:40Z","arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["2469-990X"]},"_id":"12279","year":"2022","article_type":"original","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["Fluid Flow and Transfer Processes","Modeling and Simulation","Computational Mechanics"],"status":"public","type":"journal_article","publisher":"American Physical Society","date_updated":"2024-10-09T21:03:55Z","intvolume":" 7","doi":"10.1103/physrevfluids.7.l081301","acknowledgement":"We thank G. Falkovich for discussion and Guy Han for technical support. We are grateful to N. Jha for his help in ”PIV 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). "},{"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.","doi":"10.1371/journal.pcbi.1010149","intvolume":" 18","date_updated":"2025-04-14T07:52:47Z","type":"journal_article","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"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"article_type":"original","year":"2022","pmid":1,"_id":"12280","quality_controlled":"1","publication_identifier":{"eissn":["1553-7358"]},"language":[{"iso":"eng"}],"date_created":"2023-01-16T10:02:51Z","citation":{"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.","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.","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.","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.","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"},"oa":1,"article_processing_charge":"No","volume":18,"month":"06","date_published":"2022-06-14T00:00:00Z","file_date_updated":"2023-01-30T11:28:13Z","has_accepted_license":"1","article_number":"e1010149","scopus_import":"1","publication_status":"published","corr_author":"1","abstract":[{"text":"In repeated interactions, players can use strategies that respond to the outcome of previous rounds. Much of the existing literature on direct reciprocity assumes that all competing individuals use the same strategy space. Here, we study both learning and evolutionary dynamics of players that differ in the strategy space they explore. We focus on the infinitely repeated donation game and compare three natural strategy spaces: memory-1 strategies, which consider the last moves of both players, reactive strategies, which respond to the last move of the co-player, and unconditional strategies. These three strategy spaces differ in the memory capacity that is needed. We compute the long term average payoff that is achieved in a pairwise learning process. We find that smaller strategy spaces can dominate larger ones. For weak selection, unconditional players dominate both reactive and memory-1 players. For intermediate selection, reactive players dominate memory-1 players. Only for strong selection and low cost-to-benefit ratio, memory-1 players dominate the others. We observe that the supergame between strategy spaces can be a social dilemma: maximum payoff is achieved if both players explore a larger strategy space, but smaller strategy spaces dominate.","lang":"eng"}],"ddc":["000","570"],"day":"14","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"publication":"PLOS Computational Biology","issue":"6","oa_version":"Published Version","ec_funded":1,"author":[{"orcid":"0000-0002-6978-7329","last_name":"Schmid","full_name":"Schmid, Laura","first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5116-955X","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hilbe, Christian"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"external_id":{"pmid":["35700167"],"isi":["000843626800031"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"KrCh"}],"file":[{"file_size":3143222,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2023-01-30T11:28:13Z","date_created":"2023-01-30T11:28:13Z","creator":"dernst","file_id":"12460","checksum":"31b6b311b6731f1658277a9dfff6632c","success":1,"file_name":"2022_PlosCompBio_Schmid.pdf"}],"title":"Direct reciprocity between individuals that use different strategy spaces"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2007.11998"}],"department":[{"_id":"JaMa"}],"title":"Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics","author":[{"last_name":"Franceschini","full_name":"Franceschini, Chiara","first_name":"Chiara"},{"full_name":"Gonçalves, PatrĂ­cia","first_name":"PatrĂ­cia","last_name":"Gonçalves"},{"last_name":"Sau","full_name":"Sau, Federico","first_name":"Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425"}],"external_id":{"isi":["000766619100025"],"arxiv":["2007.11998"]},"issue":"2","publication":"Bernoulli","abstract":[{"text":"We study the hydrodynamic and hydrostatic limits of the one-dimensional open symmetric inclusion process with slow boundary. Depending on the value of the parameter tuning the interaction rate of the bulk of the system with the boundary, we obtain a linear heat equation with either Dirichlet, Robin or Neumann boundary conditions as hydrodynamic equation. In our approach, we combine duality and first-second class particle techniques to reduce the scaling limit of the inclusion process to the limiting behavior of a single, non-interacting, particle.","lang":"eng"}],"day":"01","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"oa_version":"Preprint","publication_status":"published","scopus_import":"1","oa":1,"article_processing_charge":"No","month":"05","volume":28,"citation":{"ieee":"C. Franceschini, P. Gonçalves, and F. Sau, “Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics,” Bernoulli, vol. 28, no. 2. Bernoulli Society for Mathematical Statistics and Probability, pp. 1340–1381, 2022.","mla":"Franceschini, Chiara, et al. “Symmetric Inclusion Process with Slow Boundary: Hydrodynamics and Hydrostatics.” Bernoulli, vol. 28, no. 2, Bernoulli Society for Mathematical Statistics and Probability, 2022, pp. 1340–81, doi:10.3150/21-bej1390.","apa":"Franceschini, C., Gonçalves, P., & Sau, F. (2022). Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics. Bernoulli. Bernoulli Society for Mathematical Statistics and Probability. https://doi.org/10.3150/21-bej1390","ama":"Franceschini C, Gonçalves P, Sau F. Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics. Bernoulli. 2022;28(2):1340-1381. doi:10.3150/21-bej1390","chicago":"Franceschini, Chiara, PatrĂ­cia Gonçalves, and Federico Sau. “Symmetric Inclusion Process with Slow Boundary: Hydrodynamics and Hydrostatics.” Bernoulli. Bernoulli Society for Mathematical Statistics and Probability, 2022. https://doi.org/10.3150/21-bej1390.","short":"C. Franceschini, P. Gonçalves, F. Sau, Bernoulli 28 (2022) 1340–1381.","ista":"Franceschini C, Gonçalves P, Sau F. 2022. Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics. Bernoulli. 28(2), 1340–1381."},"date_published":"2022-05-01T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1350-7265"]},"quality_controlled":"1","arxiv":1,"date_created":"2023-01-16T10:03:04Z","isi":1,"article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12281","page":"1340-1381","year":"2022","doi":"10.3150/21-bej1390","acknowledgement":"C.F. and P.G. thank FCT/Portugal for support through the project UID/MAT/04459/2013.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovative programme (grant agreement No. 715734). F.S. was founded by the European Union’s Horizon 2020 research and innovation programme under the Marie-SkƂodowska-Curie grant agreement No. 754411.\r\nF.S. wishes to thank Joe P. Chen for some fruitful discussions at an early stage of this work. F.S. thanks CAMGSD, IST, Lisbon, where part of this work has been done, and the European research and innovative programme No. 715734 for the kind hospitality.","date_updated":"2025-04-14T07:44:00Z","keyword":["Statistics and Probability"],"type":"journal_article","status":"public","publisher":"Bernoulli Society for Mathematical Statistics and Probability","intvolume":" 28"},{"citation":{"mla":"Amberg, Nicole, et al. “Operation STEM Fatale – How an Equity, Diversity and Inclusion Initiative Has Brought Us to Reflect on the Current Challenges in Cell Biology and Science as a Whole.” Journal of Cell Science, vol. 135, no. 8, 260017, The Company of Biologists, 2022, doi:10.1242/jcs.260017.","ieee":"N. Amberg, M. A. Stouffer, and I. Vercellino, “Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole,” Journal of Cell Science, vol. 135, no. 8. The Company of Biologists, 2022.","apa":"Amberg, N., Stouffer, M. A., & Vercellino, I. (2022). Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.260017","chicago":"Amberg, Nicole, Melissa A Stouffer, and Irene Vercellino. “Operation STEM Fatale – How an Equity, Diversity and Inclusion Initiative Has Brought Us to Reflect on the Current Challenges in Cell Biology and Science as a Whole.” Journal of Cell Science. The Company of Biologists, 2022. https://doi.org/10.1242/jcs.260017.","ama":"Amberg N, Stouffer MA, Vercellino I. Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. Journal of Cell Science. 2022;135(8). doi:10.1242/jcs.260017","short":"N. Amberg, M.A. Stouffer, I. Vercellino, Journal of Cell Science 135 (2022).","ista":"Amberg N, Stouffer MA, Vercellino I. 2022. Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. Journal of Cell Science. 135(8), 260017."},"month":"04","volume":135,"article_processing_charge":"No","date_published":"2022-04-19T00:00:00Z","quality_controlled":"1","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"language":[{"iso":"eng"}],"date_created":"2023-01-16T10:03:14Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"article_type":"letter_note","pmid":1,"year":"2022","_id":"12282","acknowledgement":"The authors want to thank Professors Carrie Bernecky, Tom Henzinger, Martin Loose and Gaia Novarino for accepting to be interviewed, thus giving significant contribution to the discussion that lead to this article.","doi":"10.1242/jcs.260017","intvolume":" 135","date_updated":"2024-10-09T21:03:55Z","type":"journal_article","status":"public","publisher":"The Company of Biologists","department":[{"_id":"SiHi"},{"_id":"LeSa"}],"title":"Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole","author":[{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg","orcid":"0000-0002-3183-8207"},{"full_name":"Stouffer, Melissa A","id":"4C9372C4-F248-11E8-B48F-1D18A9856A87","last_name":"Stouffer","first_name":"Melissa A"},{"orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","last_name":"Vercellino","first_name":"Irene"}],"external_id":{"isi":["000798123600015"],"pmid":["35438168"]},"abstract":[{"text":"From a simple thought to a multicellular movement","lang":"eng"}],"day":"19","publication":"Journal of Cell Science","issue":"8","oa_version":"None","article_number":"260017","scopus_import":"1","corr_author":"1","publication_status":"published"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Neurons extend axons to form the complex circuitry of the mature brain. This depends on the coordinated response and continuous remodelling of the microtubule and F-actin networks in the axonal growth cone. Growth cone architecture remains poorly understood at nanoscales. We therefore investigated mouse hippocampal neuron growth cones using cryo-electron tomography to directly visualise their three-dimensional subcellular architecture with molecular detail. Our data showed that the hexagonal arrays of actin bundles that form filopodia penetrate and terminate deep within the growth cone interior. We directly observed the modulation of these and other growth cone actin bundles by alteration of individual F-actin helical structures. Microtubules with blunt, slightly flared or gently curved ends predominated in the growth cone, frequently contained lumenal particles and exhibited lattice defects. Investigation of the effect of absence of doublecortin, a neurodevelopmental cytoskeleton regulator, on growth cone cytoskeleton showed no major anomalies in overall growth cone organisation or in F-actin subpopulations. However, our data suggested that microtubules sustained more structural defects, highlighting the importance of microtubule integrity during growth cone migration."}],"day":"01","ddc":["570"],"publication":"Journal of Cell Science","issue":"7","scopus_import":"1","publication_status":"published","has_accepted_license":"1","article_number":"259234","title":"Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"SiHi"}],"file":[{"content_type":"application/pdf","file_size":13868733,"file_name":"2022_JourCellBiology_Atherton.pdf","success":1,"file_id":"12461","checksum":"4346ed32cb7c89a8ca051c7da68a9a1c","creator":"dernst","date_updated":"2023-01-30T11:41:01Z","access_level":"open_access","relation":"main_file","date_created":"2023-01-30T11:41:01Z"}],"external_id":{"pmid":["35383828"],"isi":["000783840400010"]},"author":[{"last_name":"Atherton","first_name":"Joseph","full_name":"Atherton, Joseph"},{"id":"4C9372C4-F248-11E8-B48F-1D18A9856A87","full_name":"Stouffer, Melissa A","first_name":"Melissa A","last_name":"Stouffer"},{"last_name":"Francis","full_name":"Francis, Fiona","first_name":"Fiona"},{"full_name":"Moores, Carolyn A.","last_name":"Moores","first_name":"Carolyn A."}],"pmid":1,"year":"2022","_id":"12283","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","isi":1,"intvolume":" 135","status":"public","publisher":"The Company of Biologists","type":"journal_article","keyword":["Cell Biology"],"date_updated":"2023-08-04T10:28:34Z","doi":"10.1242/jcs.259234","acknowledgement":"J.A. was supported by a grant from the Medical Research Council (MRC), UK (MR/R000352/1) to C.A.M. Cryo-EM data were collected on equipment funded by the Wellcome Trust, UK (079605/Z/06/Z) and the Biotechnology and Biological Sciences Research Council (BBSRC) UK (BB/L014211/1). F.F.’s salary and institute were supported by Inserm (Institut National de la Santé et de la Recherche Médicale), CNRS (Centre National de la Recherche Scientifique) and Sorbonne Université. F.F.’s group was particularly supported by Agence Nationale de la\r\nRecherche (ANR-16-CE16-0011-03) and Seventh Framework Programme (EUHEALTH-\r\n2013, DESIRE, N° 60253; also funding M.S.’s salary) and the European Cooperation in Science and Technology (COST Action CA16118). Open Access funding provided by Birkbeck College: Birkbeck University of London. Deposited in PMC for immediate release.","date_published":"2022-04-01T00:00:00Z","file_date_updated":"2023-01-30T11:41:01Z","citation":{"ista":"Atherton J, Stouffer MA, Francis F, Moores CA. 2022. Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. Journal of Cell Science. 135(7), 259234.","short":"J. Atherton, M.A. Stouffer, F. Francis, C.A. Moores, Journal of Cell Science 135 (2022).","ama":"Atherton J, Stouffer MA, Francis F, Moores CA. Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. Journal of Cell Science. 2022;135(7). doi:10.1242/jcs.259234","chicago":"Atherton, Joseph, Melissa A Stouffer, Fiona Francis, and Carolyn A. Moores. “Visualising the Cytoskeletal Machinery in Neuronal Growth Cones Using Cryo-Electron Tomography.” Journal of Cell Science. The Company of Biologists, 2022. https://doi.org/10.1242/jcs.259234.","apa":"Atherton, J., Stouffer, M. A., Francis, F., & Moores, C. A. (2022). Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.259234","mla":"Atherton, Joseph, et al. “Visualising the Cytoskeletal Machinery in Neuronal Growth Cones Using Cryo-Electron Tomography.” Journal of Cell Science, vol. 135, no. 7, 259234, The Company of Biologists, 2022, doi:10.1242/jcs.259234.","ieee":"J. Atherton, M. A. Stouffer, F. Francis, and C. A. Moores, “Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography,” Journal of Cell Science, vol. 135, no. 7. The Company of Biologists, 2022."},"month":"04","article_processing_charge":"No","volume":135,"oa":1,"date_created":"2023-01-16T10:03:24Z","quality_controlled":"1","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"language":[{"iso":"eng"}]},{"file":[{"content_type":"application/pdf","file_size":626953,"creator":"dernst","checksum":"00122b2459f09b5ae43073bfba565e94","file_id":"12462","date_created":"2023-01-30T11:45:13Z","date_updated":"2023-01-30T11:45:13Z","relation":"main_file","access_level":"open_access","file_name":"2022_ElecJournCombinatorics_Cooley_Kang_Zalla.pdf","success":1}],"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"department":[{"_id":"MaKw"}],"title":"Loose cores and cycles in random hypergraphs","license":"https://creativecommons.org/licenses/by-nd/4.0/","author":[{"last_name":"Cooley","id":"43f4ddd0-a46b-11ec-8df6-ef3703bd721d","full_name":"Cooley, Oliver","first_name":"Oliver"},{"first_name":"Mihyun","last_name":"Kang","full_name":"Kang, Mihyun"},{"first_name":"Julian","full_name":"Zalla, Julian","last_name":"Zalla"}],"external_id":{"isi":["000876763300001"]},"issue":"4","publication":"The Electronic Journal of Combinatorics","abstract":[{"lang":"eng","text":"Inspired by the study of loose cycles in hypergraphs, we define the loose core in hypergraphs as a structurewhich mirrors the close relationship between cycles and $2$-cores in graphs. We prove that in the $r$-uniform binomial random hypergraph $H^r(n,p)$, the order of the loose core undergoes a phase transition at a certain critical threshold and determine this order, as well as the number of edges, asymptotically in the subcritical and supercritical regimes. \r\nOur main tool is an algorithm called CoreConstruct, which enables us to analyse a peeling process for the loose core. By analysing this algorithm we determine the asymptotic degree distribution of vertices in the loose core and in particular how many vertices and edges the loose core contains. As a corollary we obtain an improved upper bound on the length of the longest loose cycle in $H^r(n,p)$."}],"day":"21","ddc":["510"],"oa_version":"Published Version","article_number":"P4.13","has_accepted_license":"1","publication_status":"published","scopus_import":"1","article_processing_charge":"No","month":"10","volume":29,"oa":1,"citation":{"ista":"Cooley O, Kang M, Zalla J. 2022. Loose cores and cycles in random hypergraphs. The Electronic Journal of Combinatorics. 29(4), P4.13.","short":"O. Cooley, M. Kang, J. Zalla, The Electronic Journal of Combinatorics 29 (2022).","apa":"Cooley, O., Kang, M., & Zalla, J. (2022). Loose cores and cycles in random hypergraphs. The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics. https://doi.org/10.37236/10794","ieee":"O. Cooley, M. Kang, and J. Zalla, “Loose cores and cycles in random hypergraphs,” The Electronic Journal of Combinatorics, vol. 29, no. 4. The Electronic Journal of Combinatorics, 2022.","mla":"Cooley, Oliver, et al. “Loose Cores and Cycles in Random Hypergraphs.” The Electronic Journal of Combinatorics, vol. 29, no. 4, P4.13, The Electronic Journal of Combinatorics, 2022, doi:10.37236/10794.","chicago":"Cooley, Oliver, Mihyun Kang, and Julian Zalla. “Loose Cores and Cycles in Random Hypergraphs.” The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics, 2022. https://doi.org/10.37236/10794.","ama":"Cooley O, Kang M, Zalla J. Loose cores and cycles in random hypergraphs. The Electronic Journal of Combinatorics. 2022;29(4). doi:10.37236/10794"},"file_date_updated":"2023-01-30T11:45:13Z","date_published":"2022-10-21T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1077-8926"]},"date_created":"2023-01-16T10:03:57Z","article_type":"original","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12286","year":"2022","acknowledgement":"Supported by Austrian Science Fund (FWF): I3747, W1230.","doi":"10.37236/10794","status":"public","keyword":["Computational Theory and Mathematics","Geometry and Topology","Theoretical Computer Science","Applied Mathematics","Discrete Mathematics and Combinatorics"],"publisher":"The Electronic Journal of Combinatorics","type":"journal_article","date_updated":"2023-08-04T10:29:18Z","intvolume":" 29"}]