[{"external_id":{"arxiv":["2206.10032"]},"alternative_title":["PMLR"],"date_published":"2024-05-01T00:00:00Z","arxiv":1,"language":[{"iso":"eng"}],"day":"01","type":"conference","article_processing_charge":"No","page":"3448-3456","corr_author":"1","supplementarymaterial":"no","publication_identifier":{"eissn":["2640-3498"]},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2206.10032"}],"author":[{"orcid":"0009-0007-3977-6462","last_name":"Zakerinia","full_name":"Zakerinia, Hossein","id":"653bd8b6-f394-11eb-9cf6-c0bbf6cd78d4","first_name":"Hossein"},{"last_name":"Talaei","full_name":"Talaei, Shayan","first_name":"Shayan"},{"full_name":"Nadiradze, Giorgi","first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","last_name":"Nadiradze"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X"}],"publication":"Proceedings of the 27th International Conference on Artificial Intelligence and Statistics","oa_version":"Preprint","intvolume":" 238","das_tickbox":"0","oa":1,"date_updated":"2026-10-01T09:34:02Z","date_created":"2024-06-02T22:00:57Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"conference":{"location":"Valencia, Spain","name":"AISTATS: Conference on Artificial Intelligence and Statistics","end_date":"2024-05-04","start_date":"2024-05-02"},"_id":"17093","month":"05","quality_controlled":"1","publisher":"ML Research Press","status":"public","abstract":[{"text":"Federated Learning (FL) enables large-scale distributed training of machine learning models, while still allowing individual nodes to maintain data locally. However, executing FL at scale comes with inherent practical challenges: 1) heterogeneity of the local node data distributions, 2) heterogeneity of node computational speeds (asynchrony), but also 3) constraints in the amount of communication between the clients and the server. In this work, we present the first variant of the classic federated averaging (FedAvg) algorithm which, at the same time, supports data heterogeneity, partial client asynchrony, and communication compression. Our algorithm comes with a novel, rigorous analysis showing that, in spite of these system relaxations, it can provide similar convergence to FedAvg in interesting parameter regimes. Experimental results in the rigorous LEAF benchmark on setups of up to 300 nodes show that our algorithm ensures fast convergence for standard federated tasks, improving upon prior quantized and asynchronous approaches.","lang":"eng"}],"title":"Communication-efficient federated learning with data and client heterogeneity","citation":{"apa":"Zakerinia, H., Talaei, S., Nadiradze, G., & Alistarh, D.-A. (2024). Communication-efficient federated learning with data and client heterogeneity. In Proceedings of the 27th International Conference on Artificial Intelligence and Statistics (Vol. 238, pp. 3448–3456). Valencia, Spain: ML Research Press.","chicago":"Zakerinia, Hossein, Shayan Talaei, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Communication-Efficient Federated Learning with Data and Client Heterogeneity.” In Proceedings of the 27th International Conference on Artificial Intelligence and Statistics, 238:3448–56. ML Research Press, 2024.","ieee":"H. Zakerinia, S. Talaei, G. Nadiradze, and D.-A. Alistarh, “Communication-efficient federated learning with data and client heterogeneity,” in Proceedings of the 27th International Conference on Artificial Intelligence and Statistics, Valencia, Spain, 2024, vol. 238, pp. 3448–3456.","short":"H. Zakerinia, S. Talaei, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 27th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2024, pp. 3448–3456.","ista":"Zakerinia H, Talaei S, Nadiradze G, Alistarh D-A. 2024. Communication-efficient federated learning with data and client heterogeneity. Proceedings of the 27th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 238, 3448–3456.","mla":"Zakerinia, Hossein, et al. “Communication-Efficient Federated Learning with Data and Client Heterogeneity.” Proceedings of the 27th International Conference on Artificial Intelligence and Statistics, vol. 238, ML Research Press, 2024, pp. 3448–56.","ama":"Zakerinia H, Talaei S, Nadiradze G, Alistarh D-A. Communication-efficient federated learning with data and client heterogeneity. In: Proceedings of the 27th International Conference on Artificial Intelligence and Statistics. Vol 238. ML Research Press; 2024:3448-3456."},"publication_status":"published","volume":238,"researchdata_availability":"no","year":"2024"},{"publication":"Proceedings of the 41st International Conference on Machine Learning","oa_version":"Preprint","intvolume":" 235","das_tickbox":"0","related_material":{"link":[{"relation":"software","url":"https://github.com/IST-DASLab/RoSA"}]},"date_updated":"2026-10-01T09:34:36Z","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-09-22T22:01:44Z","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"_id":"18117","conference":{"location":"Vienna, Austria","end_date":"2024-07-27","name":"ICML: International Conference on Machine Learning","start_date":"2024-07-21"},"month":"09","quality_controlled":"1","status":"public","publisher":"ML Research Press","acknowledgement":"The authors would like to thank Eldar Kurtic for experimental support and useful suggestions throughout the project","abstract":[{"text":"We investigate parameter-efficient fine-tuning (PEFT) methods that can provide good accuracy under limited computational and memory budgets in the context of large language models (LLMs). We present a new PEFT method called Robust Adaptation (RoSA) inspired by robust principal component analysis that jointly trains low-rank\r\n and highly-sparse components on top of a set of fixed pretrained weights to efficiently approximate the performance of a full-fine-tuning (FFT) solution. Across a series of challenging generative tasks such as grade-school math and SQL query generation, which require fine-tuning for good performance, we show that RoSA outperforms LoRA, pure sparse fine-tuning, and alternative hybrid methods at the same parameter budget, and can even recover the performance of FFT on some tasks. We provide system support for RoSA to complement the training algorithm, specifically in the form of sparse GPU kernels which enable memory- and computationally-efficient training, and show that it is also compatible with low-precision base weights, resulting in the first joint representation combining quantization, low-rank and sparse approximations. Our code is available at https://github.com/IST-DASLab/RoSA.","lang":"eng"}],"title":"RoSA: Accurate parameter-efficient fine-tuning via robust adaptation","citation":{"ieee":"M. Nikdan, S. Tabesh, E. Crncevic, and D.-A. Alistarh, “RoSA: Accurate parameter-efficient fine-tuning via robust adaptation,” in Proceedings of the 41st International Conference on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 38187–38206.","short":"M. Nikdan, S. Tabesh, E. Crncevic, D.-A. Alistarh, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 38187–38206.","apa":"Nikdan, M., Tabesh, S., Crncevic, E., & Alistarh, D.-A. (2024). RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. In Proceedings of the 41st International Conference on Machine Learning (Vol. 235, pp. 38187–38206). Vienna, Austria: ML Research Press.","chicago":"Nikdan, Mahdi, Soroush Tabesh, Elvir Crncevic, and Dan-Adrian Alistarh. “RoSA: Accurate Parameter-Efficient Fine-Tuning via Robust Adaptation.” In Proceedings of the 41st International Conference on Machine Learning, 235:38187–206. ML Research Press, 2024.","mla":"Nikdan, Mahdi, et al. “RoSA: Accurate Parameter-Efficient Fine-Tuning via Robust Adaptation.” Proceedings of the 41st International Conference on Machine Learning, vol. 235, ML Research Press, 2024, pp. 38187–206.","ama":"Nikdan M, Tabesh S, Crncevic E, Alistarh D-A. RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. In: Proceedings of the 41st International Conference on Machine Learning. Vol 235. ML Research Press; 2024:38187-38206.","ista":"Nikdan M, Tabesh S, Crncevic E, Alistarh D-A. 2024. RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 235, 38187–38206."},"publication_status":"published","researchdata_availability":"yes","volume":235,"year":"2024","date_published":"2024-09-01T00:00:00Z","external_id":{"arxiv":["2401.04679"]},"arxiv":1,"language":[{"iso":"eng"}],"day":"01","type":"conference","article_processing_charge":"No","corr_author":"1","page":"38187-38206","supplementarymaterial":"no","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2401.04679"}],"scopus_import":"1","publication_identifier":{"eissn":["2640-3498"]},"author":[{"last_name":"Nikdan","full_name":"Nikdan, Mahdi","first_name":"Mahdi","id":"66374281-f394-11eb-9cf6-869147deecc0"},{"orcid":"0009-0003-4119-6281","last_name":"Tabesh","id":"06000900-6068-11ef-8d61-c2472ef2e752","first_name":"Soroush","full_name":"Tabesh, Soroush"},{"last_name":"Crncevic","full_name":"Crncevic, Elvir","first_name":"Elvir","id":"41888001-440d-11ef-8299-d0e838b8185e"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh"}]},{"language":[{"iso":"eng"}],"external_id":{"pmid":["38518358"],"arxiv":["2309.00545"],"isi":["001196692400001"]},"pmid":1,"date_published":"2024-04-04T00:00:00Z","arxiv":1,"has_accepted_license":"1","fulldoi":"https://doi.org/10.1088/1361-6633/ad36d2","ddc":["530"],"type":"journal_article","article_processing_charge":"Yes (in subscription journal)","day":"04","scopus_import":"1","publication_identifier":{"issn":["0034-4885"],"eissn":["1361-6633"]},"author":[{"orcid":"0000-0001-7205-2975","last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","full_name":"Brückner, David"},{"full_name":"Broedersz, Chase P.","first_name":"Chase P.","last_name":"Broedersz"}],"article_number":"056601","corr_author":"1","supplementarymaterial":"no","das_tickbox":"1","oa":1,"file":[{"relation":"main_file","checksum":"c5910078230ade20f4dd83592e862a72","file_size":4376898,"content_type":"application/pdf","date_created":"2024-08-20T11:00:03Z","access_level":"open_access","date_updated":"2024-08-20T11:00:03Z","file_id":"17451","success":1,"file_name":"2024_ReportPhysics_Brueckner.pdf","creator":"dernst"}],"date_updated":"2026-10-01T10:09:41Z","isi":1,"publication":"Reports on Progress in Physics","oa_version":"Published Version","intvolume":" 87","file_date_updated":"2024-08-20T11:00:03Z","_id":"15315","month":"04","dataavailabilitystatement":"No new data were created or analysed in this study.","date_created":"2024-04-14T22:01:01Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"review","department":[{"_id":"EdHa"}],"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (German Research Foundation)—Project-ID 201269156—SFB 1032 (Project B12). D B B was supported by an NOMIS Fellowship and an EMBO Fellowship (ALTF 343-2022). We thank Joachim Rädler, Alexandra Fink, Erwin Frey, Pierre Ronceray, Ricard Alert, Edouard Hannezo, Henrik Flyvbjerg, Ulrich Schwarz, Joshua Shaevitz, Greg Stephens, Andrea Cavagna, Grzegorz Gradziuk, Fridtjof Brauns, Nikolas Claussen, Tom Brandstätter, Johannes Flommersfeld, Christoph Schreiber, Nicolas Arlt, Matthew Schmitt, Joris Messelink, Federico Gnesotto, Federica Mura, Bram Hoogland, Manon Wigbers, Isabella Graf, Jessica Lober, and many others for inspiring discussions. We also thank Claudia Flandoli for the artwork in figures 1, 5, 8 and 9.","title":"Learning dynamical models of single and collective cell migration: a review","abstract":[{"lang":"eng","text":"Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical perspective, a broad variety of models for the underlying physical mechanisms that govern cell motility have been developed. A key challenge in the development of such models is how to connect them to experimental observations, which often exhibit complex stochastic behaviours. In this review, we discuss recent advances in data-driven theoretical approaches that directly connect with experimental data to infer dynamical models of stochastic cell migration. Leveraging advances in nanofabrication, image analysis, and tracking technology, experimental studies now provide unprecedented large datasets on cellular dynamics. In parallel, theoretical efforts have been directed towards integrating such datasets into physical models from the single cell to the tissue scale with the aim of conceptualising the emergent behaviour of cells. We first review how this inference problem has been addressed in both freely migrating and confined cells. Next, we discuss why these dynamics typically take the form of underdamped stochastic equations of motion, and how such equations can be inferred from data. We then review applications of data-driven inference and machine learning approaches to heterogeneity in cell behaviour, subcellular degrees of freedom, and to the collective dynamics of multicellular systems. Across these applications, we emphasise how data-driven methods can be integrated with physical active matter models of migrating cells, and help reveal how underlying molecular mechanisms control cell behaviour. Together, these data-driven approaches are a promising avenue for building physical models of cell migration directly from experimental data, and for providing conceptual links between different length-scales of description."}],"quality_controlled":"1","publisher":"IOP Publishing","project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"issue":"5","status":"public","doi":"10.1088/1361-6633/ad36d2","citation":{"ista":"Brückner D, Broedersz CP. 2024. Learning dynamical models of single and collective cell migration: a review. Reports on Progress in Physics. 87(5), 056601.","ama":"Brückner D, Broedersz CP. Learning dynamical models of single and collective cell migration: a review. Reports on Progress in Physics. 2024;87(5). doi:10.1088/1361-6633/ad36d2","mla":"Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single and Collective Cell Migration: A Review.” Reports on Progress in Physics, vol. 87, no. 5, 056601, IOP Publishing, 2024, doi:10.1088/1361-6633/ad36d2.","chicago":"Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single and Collective Cell Migration: A Review.” Reports on Progress in Physics. IOP Publishing, 2024. https://doi.org/10.1088/1361-6633/ad36d2.","apa":"Brückner, D., & Broedersz, C. P. (2024). Learning dynamical models of single and collective cell migration: a review. Reports on Progress in Physics. IOP Publishing. https://doi.org/10.1088/1361-6633/ad36d2","short":"D. Brückner, C.P. Broedersz, Reports on Progress in Physics 87 (2024).","ieee":"D. Brückner and C. P. Broedersz, “Learning dynamical models of single and collective cell migration: a review,” Reports on Progress in Physics, vol. 87, no. 5. IOP Publishing, 2024."},"publication_status":"published","tmp":{"image":"/images/cc_by.png","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"researchdata_availability":"not applicable","volume":87,"year":"2024"},{"quality_controlled":"1","publisher":"National Academy of Sciences","status":"public","issue":"13","acknowledgement":"We thank the Metabolomics Facility at Vienna BioCenter Core Facilities, which is a member of the Vienna BioCenter and funded by the City of Vienna through the Vienna Business Agency (shared research facility), for the LC–MS/MS analysis; and the BioImaging Facility at IST Austria for technical support and assistance. The authors want to thank N. Kastner for help with the live cell imaging and A. Korošec for help with flow cytometry. This work was supported by the Austrian Science Fund (FWF), grant P 36621- B (to M.R.), grant P 36667 (to W.S.), and core funding from IST Austria (to D.S.).","title":"Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transport","abstract":[{"lang":"eng","text":"Orphan solute carrier (SLC) represents a group of membrane transporters whose exact functions and substrate specificities are not known. Elucidating the function and regulation of orphan SLC transporters is not only crucial for advancing our knowledge of cellular and molecular biology but can potentially lead to the development of new therapeutic strategies. Here, we provide evidence for the biological function of a ubiquitous orphan lysosomal SLC, the Major Facilitator Superfamily Domain-containing Protein 1 (MFSD1), which has remained phylogenetically unassigned. Targeted metabolomics revealed that dipeptides containing either lysine or arginine residues accumulate in lysosomes of cells lacking MFSD1. Whole-cell patch-clamp electrophysiological recordings of HEK293-cells expressing MFSD1 on the cell surface displayed transport affinities for positively charged dipeptides in the lower mM range, while dipeptides that carry a negative net charge were not transported. This was also true for single amino acids and tripeptides, which MFSD1 failed to transport. Our results identify MFSD1 as a highly selective lysosomal lysine/arginine/histidine-containing dipeptide exporter, which functions as a uniporter."}],"publication_status":"published","citation":{"short":"D. Boytsov, G.M. Madej, G. Horn, N. Blaha, T. Köcher, H.H. Sitte, D.E. Siekhaus, C. Ziegler, W. Sandtner, M. Roblek, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ieee":"D. Boytsov et al., “Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transport,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 13. National Academy of Sciences, 2024.","chicago":"Boytsov, Danila, Gregor M. Madej, Georg Horn, Nadine Blaha, Thomas Köcher, Harald H. Sitte, Daria E Siekhaus, Christine Ziegler, Walter Sandtner, and Marko Roblek. “Orphan Lysosomal Solute Carrier MFSD1 Facilitates Highly Selective Dipeptide Transport.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2319686121.","apa":"Boytsov, D., Madej, G. M., Horn, G., Blaha, N., Köcher, T., Sitte, H. H., … Roblek, M. (2024). Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transport. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2319686121","ama":"Boytsov D, Madej GM, Horn G, et al. Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transport. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(13). doi:10.1073/pnas.2319686121","mla":"Boytsov, Danila, et al. “Orphan Lysosomal Solute Carrier MFSD1 Facilitates Highly Selective Dipeptide Transport.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 13, e2319686121, National Academy of Sciences, 2024, doi:10.1073/pnas.2319686121.","ista":"Boytsov D, Madej GM, Horn G, Blaha N, Köcher T, Sitte HH, Siekhaus DE, Ziegler C, Sandtner W, Roblek M. 2024. Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transport. Proceedings of the National Academy of Sciences of the United States of America. 121(13), e2319686121."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"researchdata_availability":"yes (supplementary data)","year":"2024","volume":121,"doi":"10.1073/pnas.2319686121","publication":"Proceedings of the National Academy of Sciences of the United States of America","oa_version":"Published Version","intvolume":" 121","file_date_updated":"2024-04-02T08:54:28Z","das_tickbox":"1","oa":1,"isi":1,"file":[{"file_name":"2024_PNAS_Boytsov.pdf","creator":"dernst","success":1,"file_id":"15256","date_updated":"2024-04-02T08:54:28Z","access_level":"open_access","date_created":"2024-04-02T08:54:28Z","content_type":"application/pdf","file_size":2483787,"checksum":"06f9e60b1146a685d58bf33999422fa8","relation":"main_file"}],"date_updated":"2026-10-01T09:36:29Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-03-31T22:01:12Z","article_type":"original","department":[{"_id":"DaSi"}],"_id":"15250","month":"03","dataavailabilitystatement":"All study data are included in the article and/or SI Appendix.","day":"26","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","acknowledged_ssus":[{"_id":"Bio"}],"article_number":"e2319686121","corr_author":"1","supplementarymaterial":"yes","scopus_import":"1","publication_identifier":{"eissn":["1091-6490"]},"author":[{"first_name":"Danila","full_name":"Boytsov, Danila","last_name":"Boytsov"},{"full_name":"Madej, Gregor M.","first_name":"Gregor M.","last_name":"Madej"},{"last_name":"Horn","full_name":"Horn, Georg","first_name":"Georg"},{"last_name":"Blaha","full_name":"Blaha, Nadine","first_name":"Nadine"},{"first_name":"Thomas","full_name":"Köcher, Thomas","last_name":"Köcher"},{"full_name":"Sitte, Harald H.","first_name":"Harald H.","last_name":"Sitte"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus"},{"full_name":"Ziegler, Christine","first_name":"Christine","last_name":"Ziegler"},{"full_name":"Sandtner, Walter","first_name":"Walter","last_name":"Sandtner"},{"id":"3047D808-F248-11E8-B48F-1D18A9856A87","first_name":"Marko","full_name":"Roblek, Marko","last_name":"Roblek","orcid":"0000-0001-9588-1389"}],"pmid":1,"date_published":"2024-03-26T00:00:00Z","external_id":{"pmid":["38507452"],"isi":["001206419000003"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","fulldoi":"https://doi.org/10.1073/pnas.2319686121","ddc":["570"]},{"has_accepted_license":"1","ddc":["540"],"fulldoi":"https://doi.org/10.1063/5.0188215","language":[{"iso":"eng"}],"pmid":1,"date_published":"2024-02-14T00:00:00Z","external_id":{"isi":["001161104900003"],"arxiv":["2311.11784"],"pmid":["38349632"]},"arxiv":1,"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"scopus_import":"1","author":[{"full_name":"Robin, Paul","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","first_name":"Paul","last_name":"Robin","orcid":"0000-0002-5728-9189"}],"corr_author":"1","article_number":"064503","supplementarymaterial":"no","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","day":"14","_id":"15024","ec_funded":1,"dataavailabilitystatement":"Data sharing is not applicable to this article as no new data were created. Data supporting the findings of this study are accessible in the literature, as indicated throughout the article.","month":"02","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-02-25T23:00:55Z","department":[{"_id":"EdHa"}],"article_type":"original","das_tickbox":"1","file":[{"file_name":"2024_JourChemicalPhysics_Robin.pdf","creator":"dernst","date_updated":"2024-02-27T08:12:52Z","file_id":"15034","success":1,"content_type":"application/pdf","date_created":"2024-02-27T08:12:52Z","access_level":"open_access","relation":"main_file","file_size":5452738,"checksum":"0a5e0ae70849bce674466fc054390ec0"}],"isi":1,"date_updated":"2026-10-01T10:08:50Z","oa":1,"oa_version":"Published Version","publication":"Journal of Chemical Physics","file_date_updated":"2024-02-27T08:12:52Z","intvolume":" 160","doi":"10.1063/5.0188215","publication_status":"published","citation":{"ieee":"P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,” Journal of Chemical Physics, vol. 160, no. 6. AIP Publishing, 2024.","short":"P. Robin, Journal of Chemical Physics 160 (2024).","apa":"Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0188215","chicago":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0188215.","mla":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics, vol. 160, no. 6, 064503, AIP Publishing, 2024, doi:10.1063/5.0188215.","ama":"Robin P. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 2024;160(6). doi:10.1063/5.0188215","ista":"Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 160(6), 064503."},"year":"2024","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"researchdata_availability":"not applicable","volume":160,"acknowledgement":"The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu Lizée for fruitful discussions. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","title":"Correlation-induced viscous dissipation in concentrated electrolytes","abstract":[{"text":"Electrostatic correlations between ions dissolved in water are known to impact their transport properties in numerous ways, from conductivity to ion selectivity. The effects of these correlations on the solvent itself remain, however, much less clear. In particular, the addition of salt has been consistently reported to affect the solution’s viscosity, but most modeling attempts fail to reproduce experimental data even at moderate salt concentrations. Here, we use an approach based on stochastic density functional theory, which accurately captures charge fluctuations and correlations. We derive a simple analytical expression for the viscosity correction in concentrated electrolytes, by directly linking it to the liquid’s structure factor. Our prediction compares quantitatively to experimental data at all temperatures and all salt concentrations up to the saturation limit. This universal link between the microscopic structure and viscosity allows us to shed light on the nanoscale dynamics of water and ions under highly concentrated and correlated conditions.","lang":"eng"}],"quality_controlled":"1","issue":"6","status":"public","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"publisher":"AIP Publishing"},{"day":"01","article_processing_charge":"Yes (in subscription journal)","type":"journal_article","supplementarymaterial":"no","corr_author":"1","article_number":"024404","author":[{"first_name":"Fabrizio","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","full_name":"Olmeda, Fabrizio","last_name":"Olmeda"},{"first_name":"Steffen","full_name":"Rulands, Steffen","last_name":"Rulands"}],"scopus_import":"1","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"pmid":1,"date_published":"2024-08-01T00:00:00Z","external_id":{"pmid":["39294986"],"isi":["001299670100004"]},"language":[{"iso":"eng"}],"ddc":["530"],"fulldoi":"https://doi.org/10.1103/PhysRevE.110.024404","has_accepted_license":"1","issue":"2","status":"public","project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020"}],"publisher":"American Physical Society","quality_controlled":"1","title":"Field theory of enzyme-substrate systems with restricted long-range interactions","abstract":[{"lang":"eng","text":"Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here we study a general model of enzyme-substrate kinetics with restricted long-range interactions described by an exponent −𝛾. We employ a coherent-state path integral and renormalization group approach to calculate the first moment and two-point correlation function of the enzyme-binding profile. We show that starting from an empty substrate the average occupancy follows a power law with an exponent 1/(1−𝛾) over time. The correlation function decays algebraically with two distinct spatial regimes characterized by exponents −𝛾 on short distances and −(2/3)(2−𝛾) on long distances. The crossover between both regimes scales inversely with the average substrate occupancy. Our work allows associating experimental measurements of bound enzyme locations with their binding kinetics and the spatial conformation of the substrate."}],"acknowledgement":"We thank F. Piazza, M. Henkel, and F. Jülicher for helpful feedback and the entire Rulands group for fruitful discussions. We thank W. Reik, S. Clark, T. Lohoff, and I. Kafetzopoulos for fruitful discussions about the biological aspects of this work. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant No. 950349). This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 101034413.","volume":110,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"researchdata_availability":"no","year":"2024","citation":{"ieee":"F. Olmeda and S. Rulands, “Field theory of enzyme-substrate systems with restricted long-range interactions,” Physical Review E, vol. 110, no. 2. American Physical Society, 2024.","short":"F. Olmeda, S. Rulands, Physical Review E 110 (2024).","apa":"Olmeda, F., & Rulands, S. (2024). Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.110.024404","chicago":"Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E. American Physical Society, 2024. https://doi.org/10.1103/PhysRevE.110.024404.","mla":"Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E, vol. 110, no. 2, 024404, American Physical Society, 2024, doi:10.1103/PhysRevE.110.024404.","ama":"Olmeda F, Rulands S. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 2024;110(2). doi:10.1103/PhysRevE.110.024404","ista":"Olmeda F, Rulands S. 2024. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 110(2), 024404."},"publication_status":"published","doi":"10.1103/PhysRevE.110.024404","file_date_updated":"2024-09-11T05:59:36Z","intvolume":" 110","publication":"Physical Review E","oa_version":"Published Version","date_updated":"2026-10-01T10:06:45Z","isi":1,"file":[{"relation":"main_file","file_size":445696,"checksum":"67fc2cc8eee3155e5c3b7380307d8284","content_type":"application/pdf","date_created":"2024-09-11T05:59:36Z","access_level":"open_access","file_id":"18053","date_updated":"2024-09-11T05:59:36Z","success":1,"creator":"dernst","file_name":"2024_PhysReviewE_Olmeda.pdf"}],"oa":1,"das_tickbox":"0","department":[{"_id":"EdHa"}],"article_type":"original","date_created":"2024-09-08T22:01:12Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"08","_id":"17892","ec_funded":1},{"das_tickbox":"1","related_material":{"record":[{"status":"public","id":"23022","relation":"research_data"}]},"isi":1,"date_updated":"2026-10-01T09:44:06Z","file":[{"success":1,"date_updated":"2024-06-03T11:18:51Z","file_id":"17109","file_name":"2024_SciPostPhys_Kraemer.pdf","creator":"dernst","relation":"main_file","file_size":4973291,"checksum":"6fdeecd21c166db8dedb927ecc2e6025","date_created":"2024-06-03T11:18:51Z","content_type":"application/pdf","access_level":"open_access"}],"oa":1,"oa_version":"Published Version","publication":"SciPost Physics","file_date_updated":"2024-06-03T11:18:51Z","intvolume":" 16","_id":"17104","dataavailabilitystatement":"Source code, simulation data, and analysis scripts will be made publicly available on zenodo.org (10.5281/zenodo.8410957) after acceptance of the manuscript.","month":"04","date_created":"2024-06-03T08:58:44Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"EdHa"}],"article_type":"original","acknowledgement":"JE and JK gratefully acknowledge financial support from the Initiative and Networking Fund (IVF) via the grant number ERC-RA-004. Simulations were performed with computing resources granted by RWTH Aachen University under project ‘rwth0475’.","title":"Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells","abstract":[{"text":"The homeostasis of epithelial tissue relies on a balance between the self-renewal of stem cell populations, cellular differentiation, and loss. Although this balance needs to be tightly regulated to avoid pathologies, such as tumor growth, the regulatory mechanisms, both cell-intrinsic and collective, which ensure tissue steady-state are still poorly understood. Here, we develop a computational model that incorporates basic assumptions of stem cell renewal into distinct populations and mechanical interactions between cells. We find that the model generates unexpected dynamic features: stem cells repel each other in the bulk tissue and are thus found rather isolated, as in a number of in vivo contexts. By mapping the system onto a gas of passive Brownian particles with effective repulsive interactions, that arise from the generated flows of differentiated cells, we show that we can quantitatively describe such stem cell distribution in tissues. The interaction potential between a pair of stem cells decays exponentially with a characteristic length that spans several cell sizes, corresponding to the volume of cells generated per stem cell division. Our findings may help understanding the dynamics of normal and cancerous epithelial tissues.","lang":"eng"}],"quality_controlled":"1","issue":"4","status":"public","publisher":"SciPost Foundation","doi":"10.21468/scipostphys.16.4.097","citation":{"ista":"Krämer JC, Hannezo EB, Gompper G, Elgeti J. 2024. Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. SciPost Physics. 16(4), 097.","ama":"Krämer JC, Hannezo EB, Gompper G, Elgeti J. Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. SciPost Physics. 2024;16(4). doi:10.21468/scipostphys.16.4.097","mla":"Krämer, Johannes C., et al. “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” SciPost Physics, vol. 16, no. 4, 097, SciPost Foundation, 2024, doi:10.21468/scipostphys.16.4.097.","chicago":"Krämer, Johannes C., Edouard B Hannezo, Gerhard Gompper, and Jens Elgeti. “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” SciPost Physics. SciPost Foundation, 2024. https://doi.org/10.21468/scipostphys.16.4.097.","apa":"Krämer, J. C., Hannezo, E. B., Gompper, G., & Elgeti, J. (2024). Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.16.4.097","short":"J.C. Krämer, E.B. Hannezo, G. Gompper, J. Elgeti, SciPost Physics 16 (2024).","ieee":"J. C. Krämer, E. B. Hannezo, G. Gompper, and J. Elgeti, “Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells,” SciPost Physics, vol. 16, no. 4. SciPost Foundation, 2024."},"publication_status":"published","researchdata_availability":"yes","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2024","volume":16,"language":[{"iso":"eng"}],"date_published":"2024-04-08T00:00:00Z","external_id":{"isi":["001202370200001"],"arxiv":["2310.04272"]},"arxiv":1,"has_accepted_license":"1","ddc":["530"],"fulldoi":"https://doi.org/10.21468/scipostphys.16.4.097","type":"journal_article","article_processing_charge":"No","day":"08","publication_identifier":{"issn":["2542-4653"]},"scopus_import":"1","author":[{"first_name":"Johannes C.","full_name":"Krämer, Johannes C.","last_name":"Krämer"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"full_name":"Gompper, Gerhard","first_name":"Gerhard","last_name":"Gompper"},{"last_name":"Elgeti","first_name":"Jens","full_name":"Elgeti, Jens"}],"article_number":"097","supplementarymaterial":"yes"},{"date_published":"2024-05-01T00:00:00Z","external_id":{"isi":["001162208200002"]},"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1038/s41567-024-02401-7","day":"01","type":"journal_article","article_processing_charge":"No","page":"684-685","corr_author":"1","supplementarymaterial":"no","scopus_import":"1","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"author":[{"full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","orcid":"0000-0002-7438-1139"}],"publication":"Nature Physics","oa_version":"None","intvolume":" 20","das_tickbox":"0","date_updated":"2026-10-01T09:37:00Z","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2025-01-27T14:29:20Z","department":[{"_id":"DeBa"}],"article_type":"letter_note","_id":"18919","month":"05","quality_controlled":"1","issue":"5","status":"public","publisher":"Springer Nature","title":"Through the slopes of a light-induced phase transition","abstract":[{"text":"The integration of theory and experiment makes possible tracking the slow evolution of a photodoped Mott insulator to a distinct non-equilibrium metallic phase under the influence of electron-lattice coupling.","lang":"eng"}],"citation":{"chicago":"Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase Transition.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-024-02401-7.","apa":"Baykusheva, D. R. (2024). Through the slopes of a light-induced phase transition. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02401-7","short":"D.R. Baykusheva, Nature Physics 20 (2024) 684–685.","ieee":"D. R. Baykusheva, “Through the slopes of a light-induced phase transition,” Nature Physics, vol. 20, no. 5. Springer Nature, pp. 684–685, 2024.","ista":"Baykusheva DR. 2024. Through the slopes of a light-induced phase transition. Nature Physics. 20(5), 684–685.","ama":"Baykusheva DR. Through the slopes of a light-induced phase transition. Nature Physics. 2024;20(5):684-685. doi:10.1038/s41567-024-02401-7","mla":"Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase Transition.” Nature Physics, vol. 20, no. 5, Springer Nature, 2024, pp. 684–85, doi:10.1038/s41567-024-02401-7."},"publication_status":"published","researchdata_availability":"no","year":"2024","volume":20,"doi":"10.1038/s41567-024-02401-7","OA_type":"closed access"},{"date_published":"2024-03-25T00:00:00Z","oa_version":"None","oa":1,"date_updated":"2026-10-01T09:44:07Z","related_material":{"record":[{"status":"public","id":"17104","relation":"used_in_publication"}]},"department":[{"_id":"EdHa"}],"date_created":"2026-10-01T09:44:01Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"03","fulldoi":"https://doi.org/10.5281/zenodo.8410956","ddc":["530"],"_id":"23022","day":"25","publisher":"Zenodo","status":"public","article_processing_charge":"No","title":"Data for Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating Daughter Cells","abstract":[{"lang":"eng","text":"Contains animations, data, and source code used for the paper \"Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating Daughter Cells\" by the same authors. \r\n\r\n\r\nThis repository contains all the data and analysis scripts to support the manuscript\r\nThe file structure is as follows:\r\n- \"analysis\" contains all the analysis scripts\r\n- \"gfx\" and \"animations\" the figures and supporting animations\r\n- \"1-SCpair\", \"2-SCtissue\", \"3-BDsimulation\", \"4-tissue-stochdiv\", \"6-inertia-effects\" all the source code and data for the respective models."}],"type":"research_data_reference","year":"2024","citation":{"mla":"Elgeti, Jens, and Johannes Krämer. Data for Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells. Zenodo, 2024, doi:10.5281/zenodo.8410956.","ama":"Elgeti J, Krämer J. Data for Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating Daughter Cells. 2024. doi:10.5281/zenodo.8410956","ista":"Elgeti J, Krämer J. 2024. Data for Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating Daughter Cells, Zenodo, 10.5281/zenodo.8410956.","ieee":"J. Elgeti and J. Krämer, “Data for Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating Daughter Cells.” Zenodo, 2024.","short":"J. Elgeti, J. Krämer, (2024).","apa":"Elgeti, J., & Krämer, J. (2024). Data for Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating Daughter Cells. Zenodo. https://doi.org/10.5281/zenodo.8410956","chicago":"Elgeti, Jens, and Johannes Krämer. “Data for Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” Zenodo, 2024. https://doi.org/10.5281/zenodo.8410956."},"OA_place":"repository","OA_type":"green","author":[{"full_name":"Elgeti, Jens","first_name":"Jens","last_name":"Elgeti"},{"last_name":"Krämer","full_name":"Krämer, Johannes","first_name":"Johannes"}],"doi":"10.5281/zenodo.8410956","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8410956","open_access":"1"}]},{"language":[{"iso":"eng"}],"external_id":{"isi":["001244835000006"],"pmid":["38819997"]},"pmid":1,"date_published":"2024-06-04T00:00:00Z","has_accepted_license":"1","ddc":["570"],"fulldoi":"https://doi.org/10.1073/pnas.2322326121","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","day":"04","scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"author":[{"orcid":"0000-0001-7205-2975","last_name":"Brückner","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"}],"corr_author":"1","article_number":"e2322326121","supplementarymaterial":"yes","related_material":{"link":[{"url":"https://github.com/dbrueckner/SelforgInformation","relation":"software"},{"description":"News on the ISTA website","url":"https://ista.ac.at/en/news/the-embryo-assembles-itself/","relation":"press_release"}]},"das_tickbox":"1","isi":1,"file":[{"relation":"main_file","checksum":"59797a75db7beb3721ed7a4d14c241f9","file_size":12329234,"content_type":"application/pdf","date_created":"2024-06-10T10:27:37Z","access_level":"open_access","date_updated":"2024-06-10T10:27:37Z","file_id":"17130","success":1,"creator":"dernst","file_name":"2024_PNAS_Brueckner.pdf"}],"date_updated":"2026-10-01T11:03:59Z","oa":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","oa_version":"Published Version","file_date_updated":"2024-06-10T10:27:37Z","intvolume":" 121","_id":"17123","dataavailabilitystatement":"There were no data generated as part of this study. Code to perform simulations, evaluate entropy and information quantities, and optimize parameters is available at https://github.com/dbrueckner/SelforgInformation (90).","month":"06","date_created":"2024-06-09T22:01:02Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"APC_amount":"2570,79 EUR","article_type":"original","acknowledgement":"We thank Wiktor Młynarski, Juraj Majek, Michal Hledík, Fridtjof Brauns, Nikolas Claussen, Benjamin Zoller, Erwin Frey, Thomas Gregor, and Edouard Hannezo for inspiring discussions. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 343-2022). This research was performed in part at the Aspen Center for Physics, which is supported by NSF Grant No. PHY-1607611, and Kavli Institute for Theoretical Physics (KITP) Santa Barbara, supported by NSF Grant No. PHY-1748958 and the Gordon and Betty Moore Foundation Grant No. 2919.02.","abstract":[{"text":"A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and even harnessing intrinsic and extrinsic fluctuations. While the relevant molecular processes are increasingly well understood, we lack a principled framework to quantify the performance of such stochastic self-organizing systems. To that end, we introduce an information-theoretic measure for self-organized fate specification during embryonic development. We show that the proposed measure assesses the total information content of fate patterns and decomposes it into interpretable contributions corresponding to the positional and correlational information. By optimizing the proposed measure, our framework provides a normative theory for developmental circuits, which we demonstrate on lateral inhibition, cell type proportioning, and reaction–diffusion models of self-organization. This paves a way toward a classification of developmental systems based on a common information-theoretic language, thereby organizing the zoo of implicated chemical and mechanical signaling processes.","lang":"eng"}],"title":"Information content and optimization of self-organized developmental systems","quality_controlled":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","status":"public","issue":"23","publisher":"National Academy of Sciences","project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022"}],"doi":"10.1073/pnas.2322326121","OA_type":"hybrid","publication_status":"published","citation":{"mla":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 23, e2322326121, National Academy of Sciences, 2024, doi:10.1073/pnas.2322326121.","ama":"Brückner D, Tkačik G. Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(23). doi:10.1073/pnas.2322326121","ista":"Brückner D, Tkačik G. 2024. Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America. 121(23), e2322326121.","ieee":"D. Brückner and G. Tkačik, “Information content and optimization of self-organized developmental systems,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 23. National Academy of Sciences, 2024.","short":"D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","apa":"Brückner, D., & Tkačik, G. (2024). Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2322326121","chicago":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2322326121."},"OA_place":"publisher","year":"2024","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","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)"},"researchdata_availability":"not applicable","volume":121},{"day":"29","acknowledged_ssus":[{"_id":"EM-Fac"}],"article_processing_charge":"Yes","type":"journal_article","supplementarymaterial":"yes","article_number":"7511","author":[{"full_name":"Kofler, Lisa","first_name":"Lisa","last_name":"Kofler"},{"full_name":"Grundmann, Lorenz","first_name":"Lorenz","last_name":"Grundmann"},{"last_name":"Gerhalter","first_name":"Magdalena","full_name":"Gerhalter, Magdalena"},{"last_name":"Prattes","full_name":"Prattes, Michael","first_name":"Michael"},{"first_name":"Juliane","full_name":"Merl-Pham, Juliane","last_name":"Merl-Pham"},{"full_name":"Zisser, Gertrude","first_name":"Gertrude","last_name":"Zisser"},{"full_name":"Grishkovskaya, Irina","first_name":"Irina","last_name":"Grishkovskaya"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau","orcid":"0000-0003-3904-947X"},{"last_name":"Vareka","first_name":"Martin","full_name":"Vareka, Martin"},{"first_name":"Rolf","full_name":"Breinbauer, Rolf","last_name":"Breinbauer"},{"full_name":"Hauck, Stefanie M.","first_name":"Stefanie M.","last_name":"Hauck"},{"full_name":"Haselbach, David","first_name":"David","last_name":"Haselbach"},{"first_name":"Helmut","full_name":"Bergler, Helmut","last_name":"Bergler"}],"scopus_import":"1","publication_identifier":{"eissn":["2041-1723"]},"external_id":{"pmid":["39209816"],"isi":["001457895200001"]},"date_published":"2024-08-29T00:00:00Z","pmid":1,"language":[{"iso":"eng"}],"ddc":["570"],"fulldoi":"https://doi.org/10.1038/s41467-024-51754-3","has_accepted_license":"1","status":"public","publisher":"Springer Nature","quality_controlled":"1","title":"The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation","abstract":[{"text":"The formation of new ribosomes is tightly coordinated with cell growth and proliferation. In eukaryotes, the correct assembly of all ribosomal proteins and RNAs follows an intricate scheme of maturation and rearrangement steps across three cellular compartments: the nucleolus, nucleoplasm, and cytoplasm. We demonstrate that usnic acid, a lichen secondary metabolite, inhibits the maturation of the large ribosomal subunit in yeast. We combine biochemical characterization of pre-ribosomal particles with a quantitative single-particle cryo-EM approach to monitor changes in nucleolar particle populations upon drug treatment. Usnic acid rapidly blocks the transition from nucleolar state B to C of Nsa1-associated pre-ribosomes, depleting key maturation factors such as Dbp10 and hindering pre-rRNA processing. This primary nucleolar block rapidly rebounds on earlier stages of the pathway which highlights the regulatory linkages between different steps. In summary, we provide an in-depth characterization of the effect of usnic acid on ribosome biogenesis, which may have implications for its reported anti-cancer activities.","lang":"eng"}],"acknowledgement":"We thank Michael A. McAlear, Micheline Fromont-Racin, Philipp Milkereit, Arlen W. Johnson, Sabine Rospert, Ed Hurt, C. Yam, Günter Daum, Wolfgang Zachariae, Katrin Karbstein, Juan P. G. Ballesta, Mercedes Dosil, Miguel Remacha und Jesus de la Cruz for sharing strains or providing antibodies. We thank the members of the Bergler lab and the Haselbach lab for their helpful discussion. We thank Ellen Zhong for helpful discussions about the quantitative cryoDRGN analysis. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility. This research was funded in whole, or in part, by the Austrian Science Foundation grants [https://doi.org/10.55776/P32977], [https://doi.org/10.55776/P29451] and [https://doi.org/10.55776/P32536] (to H.B.). Research at the IMP is generously supported by Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2024","volume":15,"researchdata_availability":"yes","publication_status":"published","OA_place":"publisher","citation":{"ama":"Kofler L, Grundmann L, Gerhalter M, et al. The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. 2024;15. doi:10.1038/s41467-024-51754-3","mla":"Kofler, Lisa, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” Nature Communications, vol. 15, 7511, Springer Nature, 2024, doi:10.1038/s41467-024-51754-3.","ista":"Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau V-V, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. 2024. The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. 15, 7511.","short":"L. Kofler, L. Grundmann, M. Gerhalter, M. Prattes, J. Merl-Pham, G. Zisser, I. Grishkovskaya, V.-V. Hodirnau, M. Vareka, R. Breinbauer, S.M. Hauck, D. Haselbach, H. Bergler, Nature Communications 15 (2024).","ieee":"L. Kofler et al., “The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation,” Nature Communications, vol. 15. Springer Nature, 2024.","chicago":"Kofler, Lisa, Lorenz Grundmann, Magdalena Gerhalter, Michael Prattes, Juliane Merl-Pham, Gertrude Zisser, Irina Grishkovskaya, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-51754-3.","apa":"Kofler, L., Grundmann, L., Gerhalter, M., Prattes, M., Merl-Pham, J., Zisser, G., … Bergler, H. (2024). The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-51754-3"},"OA_type":"gold","doi":"10.1038/s41467-024-51754-3","file_date_updated":"2024-09-09T08:56:12Z","intvolume":" 15","oa_version":"Published Version","publication":"Nature Communications","date_updated":"2026-10-01T11:05:46Z","file":[{"success":1,"file_id":"17946","date_updated":"2024-09-09T08:56:12Z","file_name":"2024_NatureComm_Kofler.pdf","creator":"dernst","file_size":3735024,"checksum":"7c044538a47182c826d1b526c52958a2","relation":"main_file","access_level":"open_access","date_created":"2024-09-09T08:56:12Z","content_type":"application/pdf"}],"isi":1,"oa":1,"das_tickbox":"1","department":[{"_id":"EM-Fac"}],"article_type":"original","date_created":"2024-09-08T22:01:10Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","dataavailabilitystatement":"Strains generated in this study are available from the corresponding authors upon request. For cryo-EM model building, published pre-60S models PDB-6EM3, PDB-6EM4, PDB-6C0F, PDB-6EM1 and PDB-8V87 were used. Motion-corrected micrographs with annotated particle locations were deposited in EMPIAR with the accession number EMPIAR-12237. The cryo-EM maps of clusters 1 to 4 with the combined datasets were deposited in the EMDB with the accession numbers EMD-51122, EMD-51126, EMD-51128, and EMD-51129. The reconstructions for the treated dataset were deposited with the accession numbers EMD-51175, EMD-51176, EMD-51177, and EMD-51178, while the untreated reconstructions of reported clusters can be found via EMD-51164, EMD-51165, EMD-51166, EMD-51167. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE101 partner repository with the dataset identifier PXD046691. Source data are provided with this paper.","month":"08","_id":"17885","DOAJ_listed":"1"},{"oa":1,"date_updated":"2026-10-01T10:54:33Z","related_material":{"record":[{"id":"18446","status":"public","relation":"used_in_publication"}]},"date_published":"2024-07-25T00:00:00Z","oa_version":"None","month":"07","fulldoi":"https://doi.org/10.5281/zenodo.12819780","_id":"23023","department":[{"_id":"EdHa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2026-10-01T10:54:27Z","abstract":[{"lang":"eng","text":"In this repository, you will find the R-scripts used to generate the figures, along with the data necessary to make the plots. You will also find the Python-scripts used to compute the pair-wise distance between embryos, to estimate the surface, the volume, the α-parameter, to identify the closest rigid packing and to generate the morphomap. Additionally, you have access to the base model used with Plantseg to predict and label the cells at the 8-cell stage. Note that a more accurate and more specific model was generated for each embryo based on the curation of at least 5 timepoints.\r\n\r\nFigures\r\nThe plots in Figure 1-7 and Figure S1-S7 can be generated with the respective files. The code is written in R and requires RStudio to work out-of-the-box. The R scripts are located in figures/. Figures and supplemental figures are generated with the same file (e.g., Figure 1.R generates all the computed panels of Figure 1 and Figure S1). Data required to generate the plots are located in figures/data/. Note that the code to work with the morphomap and the tracking data is located in local packages figures/fabreges.morphomap and figures/fabreges.tracking. An additional package figures/fabreges.generic contains utility functions.\r\n\r\nPython packages\r\nFor the needs of this study, we developed a series of package for Python located in python-packages/. The packages can be directly imported within your scripts. Along with the packages, you will find 6 scripts used to compute, extract or estimate the data from the source. The folder is organised as follow:\r\n\r\npackage interfaces is located in python-packages/interfaces/ and can be tested by running the scripts to extract the angles an estimate the surface of contact (compute-angles.py and estimate-contacts.py respectively) in folder python-packages,\r\npackage morphomap is located in python-packages/morphomap/ and can be tested by running the script to compute the geometrical distances between embryos, project the data in 2D and compute the volume of the cells (compute-distances.py, process-distances.py and compute-volumes.py respectively) in folder python-packages,\r\npackage splinefit is included in morphomap in python-packages/morphomap/splinefit/, but can function independently,\r\npackage rbb is located in python-packages/rbb/ and can be tested by running the script to identify the closest rigid packing of an embryo at the 8-cell stage (identify-packing.py) in folder python-packages.\r\nWe provide example of segmented data in python-packages/samples/.\r\n\r\nCNN\r\nWe provide a convolutional neural network (CNN) used in our study, located in cnn. Please note that we optimised the CNN further for each dataset by doing manual curation of at least 5 time points and by retraining the network with those ground truth. The CNN were trained using pytorch-3dunet. The CNN can be used with Plantseg. Currently (plantseg v.1.6.0 and pytorch-3dunet v.1.6.0), the output model from pytorch-3dunet must currently be modified to work with plantseg:\r\n\r\n# python\r\nimport torch\r\nfor model in ('best_checkpoint.pytorch', 'last_checkpoint.pytorch'):\r\n state = torch.load(model, map_location='cpu')\r\n state = state['model_state_dict']\r\n torch.save(state, model)\r\n\r\nRequierements\r\nFigures\r\nThe figures were generated with R (v. 4.4.0) and RStudio (v. 2024.04.1+748). The following packages must be installed prior to execution:\r\n\r\nalphashape3d (v. 1.3.2)\r\ndevtools (v. 2.4.5)\r\nggplot2 (v. 3.5.1)\r\nggrepel (v. 0.9.5)\r\nrstudioapi (v. 0.16.0)\r\nTo install all these packages, run the following command in the RStudio console:\r\n\r\n# R\r\ninstall.packages(c(\"alphashape3d@1.3.2\", \"devtools@2.4.5\", \"ggplot2@3.5.1\", \"ggrepel@0.9.5\", \"rstudioapi@0.16\"))\r\n\r\nMore recent version of R, RStudio and the packages may also work (not tested).\r\n\r\nPython packages\r\nPython 3.12.3 was used to analyse the data. The scripts may work with more recent version of Python and with Python 3.8 or earlier (not tested). To run the code, you must first install the following packages:\r\n\r\nnumpy (v. 1.26.4)\r\nimageio (v. 2.34.1)\r\nscipy (v. 1.13.1)\r\nscikit-image (v. 0.23.2)\r\nscikit-learn (v. 1.5.0)\r\nAlternatively, you can create a conda environment:\r\n\r\n# Shell script\r\nconda create -y --name fabreges2024 python=3.12.3\r\nconda activate fabreges2024\r\npython -m pip install numpy==1.26.4 imageio==2.34.1 scipy==1.13.1 scikit-image==0.23.2 scikit-learn==1.5.0\r\n\r\nMore recent version of the dependencies may work (not tested).\r\n\r\nUsage\r\nFigures\r\nOpen one of the figure script in RStudio and run the entire code. You may have to create a folder output in figures/ if it does not exist.\r\n\r\nThe code has local dependencies that will be installed on your computer when encountering them for the first time. They start with fabreges.* and are necessary to generate the figures.\r\n\r\nPython packages (example)\r\nCompute angles\r\n# Shell script\r\n# Compute a summary (mean, median, s.d.) of the angles in embryo C1 at time 40\r\npython compute-angles.py -s -r 15 -R 20 samples/C1_t040.tif.gz output/C1_t040_angles.csv\r\n# Compute a detailed list of angle values\r\npython compute-angles.py -r 15 -R 20 samples/C1_t041.tif.gz output/C1_t041_angles.csv\r\n\r\nCompute distances\r\n# Shell script\r\n# Compute the distance between two embryos\r\npython compute-distances.py -c 5 -s 5 samples/C1_t040.tif.gz samples/C1_t041.tif.gz output/distances.csv\r\n# Append another distance measurement\r\npython compute-distances.py -a -c 5 -s 5 samples/C1_t040.tif.gz samples/C1_t042.tif.gz output/distances.csv\r\n\r\nCompute volumes\r\n# Shell script\r\n# Compute the volume in isotropic data\r\npython compute-volumes.py -r 0.416 0.416 0.416 samples/C1_t040.tif.gz output/volumes.csv\r\n\r\nEstimate contacts\r\n# Shell script\r\n# Estimate the contacts and the free surface area\r\npython estimate-contacts.py -r 0.416 0.416 0.416 samples/C1_t040.tif.gz output/contacts.csv\r\n\r\nIdentify the closest rigid packing\r\n# Shell script\r\n# Assuming the file `output/contacts.csv` exists and contains the output\r\n# from command `estimate-contacts.py`.\r\n# Identify the closest rigid packings\r\npython identify-packing.py output/contacts.csv output/backbones.csv\r\n\r\nGenerate the seeds for Surface Evolver\r\n# Shell script\r\n# Assuming the file `output/contacts.csv` exists and contains the output\r\n# from command `estimate-contacts.py`, and the file `output/volumes.csv`\r\n# exists and contains the output from command `compute-volumes.py`\r\n# Generate the seeds for Surface Evolver using automatic thresholding\r\n# Automatic threshold will determine the highest cell-cell contact threshold\r\n# that preserves rigidity of the embryo (or 0 if not rigid)\r\npython generate-seed.py output/contacts.csv output/volumes.csv output/seed.fe\r\n# Generate the seeds for Surface Evolver with custom threshold\r\npython generate-seed.py --threshold 0.1 output/contacts.csv output/volumes.csv output/seed.fe\r\n\r\nProject in 2D and generate a distance matrix\r\n# Shell script\r\n# Assuming the folder `foo` only contains one or more CSV\r\n# from command `compute-distances.py`.\r\n\r\n# Compute the tSNE 2D projection\r\npython process-distances.py -D2 -t output/tsne_2d.csv foo/\r\n\r\n# Compute the tSNE 3D projection\r\npython process-distances.py -D3 -t output/tsne_2d.csv foo/\r\n\r\n# Generate the distance matrix\r\npython process-distances.py -m output/dismat.csv foo/"}],"article_processing_charge":"No","title":"Data and software from: Temporal variability and cell mechanics control robustness in mammalian embryogenesis","contributor":[{"last_name":"Fabrèges","first_name":"Dimitri","contributor_type":"contact_person"}],"type":"research_data_reference","publisher":"Institute of Science and Technology Austria","day":"25","status":"public","OA_type":"green","author":[{"first_name":"Bernat","full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra"},{"full_name":" Moghe, Prachiti","first_name":"Prachiti","last_name":" Moghe"},{"first_name":"Alison","full_name":"Kickuth, Alison","last_name":"Kickuth"},{"last_name":"Ichikawa","first_name":"Takafumi","full_name":"Ichikawa, Takafumi"},{"last_name":"Iwatani","full_name":"Iwatani, Chizuru","first_name":"Chizuru"},{"last_name":"Tsukiyama","first_name":"Tomoyuki","full_name":"Tsukiyama, Tomoyuki"},{"last_name":"Daniel","full_name":"Daniel, Nathalie","first_name":"Nathalie"},{"last_name":"Gering","full_name":"Gering, Julie","first_name":"Julie"},{"full_name":"Stokkermans, Anniek","first_name":"Anniek","last_name":"Stokkermans"},{"last_name":"Wolny","full_name":"Wolny, Adrian","first_name":"Adrian"},{"last_name":"Kreshuk","full_name":"Kreshuk, Anna","first_name":"Anna"},{"first_name":"Véronique","full_name":"Duranthon, Véronique","last_name":"Duranthon"},{"last_name":"Uhlmann","first_name":"Virginie","full_name":"Uhlmann, Virginie"},{"first_name":"Edouard","full_name":"Hannezo, Edouard","last_name":"Hannezo"},{"last_name":"Hiiragi","first_name":"Takashi","full_name":"Hiiragi, Takashi"}],"doi":"10.5281/zenodo.12819780","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.12819780","open_access":"1"}],"year":"2024","citation":{"mla":"Corominas-Murtra, Bernat, et al. Data and Software from: Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis. Institute of Science and Technology Austria, 2024, doi:10.5281/zenodo.12819780.","ama":"Corominas-Murtra B, Moghe P, Kickuth A, et al. Data and software from: Temporal variability and cell mechanics control robustness in mammalian embryogenesis. 2024. doi:10.5281/zenodo.12819780","ista":"Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C, Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon V, Uhlmann V, Hannezo E, Hiiragi T. 2024. Data and software from: Temporal variability and cell mechanics control robustness in mammalian embryogenesis, Institute of Science and Technology Austria, 10.5281/zenodo.12819780.","ieee":"B. Corominas-Murtra et al., “Data and software from: Temporal variability and cell mechanics control robustness in mammalian embryogenesis.” Institute of Science and Technology Austria, 2024.","short":"B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani, T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon, V. Uhlmann, E. Hannezo, T. Hiiragi, (2024).","apa":"Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani, C., Tsukiyama, T., … Hiiragi, T. (2024). Data and software from: Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Institute of Science and Technology Austria. https://doi.org/10.5281/zenodo.12819780","chicago":"Corominas-Murtra, Bernat, Prachiti Moghe, Alison Kickuth, Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, Nathalie Daniel, et al. “Data and Software from: Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Institute of Science and Technology Austria, 2024. https://doi.org/10.5281/zenodo.12819780."},"OA_place":"repository"},{"OA_type":"hybrid","doi":"10.1145/3634737.3656997","year":"2024","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"researchdata_availability":"no","OA_place":"publisher","publication_status":"published","citation":{"ista":"Giuliari G, Sonnino A, Frei M, Streun F, Kokoris Kogias E, Perrig A. 2024. An empirical study of consensus protocols’ DoS resilience. Proceedings of the 19th ACM Asia Conference on Computer and Communications Security. ASIACCS: Asia Conference on Computer and Communications Security, 1345–1360.","mla":"Giuliari, Giacomo, et al. “An Empirical Study of Consensus Protocols’ DoS Resilience.” Proceedings of the 19th ACM Asia Conference on Computer and Communications Security, ACM, 2024, pp. 1345–60, doi:10.1145/3634737.3656997.","ama":"Giuliari G, Sonnino A, Frei M, Streun F, Kokoris Kogias E, Perrig A. An empirical study of consensus protocols’ DoS resilience. In: Proceedings of the 19th ACM Asia Conference on Computer and Communications Security. ACM; 2024:1345-1360. doi:10.1145/3634737.3656997","apa":"Giuliari, G., Sonnino, A., Frei, M., Streun, F., Kokoris Kogias, E., & Perrig, A. (2024). An empirical study of consensus protocols’ DoS resilience. In Proceedings of the 19th ACM Asia Conference on Computer and Communications Security (pp. 1345–1360). Singapore, Singapore: ACM. https://doi.org/10.1145/3634737.3656997","chicago":"Giuliari, Giacomo, Alberto Sonnino, Marc Frei, Fabio Streun, Eleftherios Kokoris Kogias, and Adrian Perrig. “An Empirical Study of Consensus Protocols’ DoS Resilience.” In Proceedings of the 19th ACM Asia Conference on Computer and Communications Security, 1345–60. ACM, 2024. https://doi.org/10.1145/3634737.3656997.","ieee":"G. Giuliari, A. Sonnino, M. Frei, F. Streun, E. Kokoris Kogias, and A. Perrig, “An empirical study of consensus protocols’ DoS resilience,” in Proceedings of the 19th ACM Asia Conference on Computer and Communications Security, Singapore, Singapore, 2024, pp. 1345–1360.","short":"G. Giuliari, A. Sonnino, M. Frei, F. Streun, E. Kokoris Kogias, A. Perrig, in:, Proceedings of the 19th ACM Asia Conference on Computer and Communications Security, ACM, 2024, pp. 1345–1360."},"title":"An empirical study of consensus protocols’ DoS resilience","abstract":[{"lang":"eng","text":"With the proliferation of blockchain technology in high-value sectors, consensus protocols are becoming critical infrastructures. The rapid innovation cycle in Byzantine fault tolerant (BFT) consensus protocols has culminated in HotStuff, which provides linear message complexity in the partially synchronous setting. To achieve this, HotStuff leverages a leader that collects, aggregates, and broadcasts the messages of other validators. This paper analyzes the security implications of such approaches in practice, from the perspective of liveness and availability.\r\nBy implementing attacks in a globally-distributed testbed, we show that state-of-the-art leader-based protocols are vulnerable to denial-of-service (DoS) attacks on the leader. Our attacks, demonstrated on committees of up to 64 validators, manage to disrupt liveness within seconds, using only a few tens of Mbps of attack bandwidth per validator. Crucially, the cost and effectiveness of the attacks are independent of the committee size. Based on the outcome of these experiments, we then propose and test effective mitigations. Our findings show that advancements in both protocol design and network-layer defenses can greatly improve the practical resilience of BFT consensus protocols."}],"acknowledgement":"This work was mostly realized while Alberto Sonnino and Lefteris Kokoris-Kogias were employed at Meta. We gratefully acknowledge support for this project from ETH Zurich and Mysten Labs.","publisher":"ACM","status":"public","quality_controlled":"1","month":"07","conference":{"start_date":"2024-07-01","end_date":"2024-07-05","name":"ASIACCS: Asia Conference on Computer and Communications Security","location":"Singapore, Singapore"},"_id":"18913","department":[{"_id":"ElKo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2025-01-27T13:57:00Z","oa":1,"file":[{"success":1,"date_updated":"2025-01-27T14:04:12Z","file_id":"18914","creator":"dernst","file_name":"2024_ACMAsiaCCS_Giuliari.pdf","relation":"main_file","checksum":"1e743ddf49d35390eb56e11eb0759150","file_size":951940,"date_created":"2025-01-27T14:04:12Z","content_type":"application/pdf","access_level":"open_access"}],"isi":1,"date_updated":"2026-10-01T11:04:34Z","das_tickbox":"0","file_date_updated":"2025-01-27T14:04:12Z","oa_version":"Published Version","publication":"Proceedings of the 19th ACM Asia Conference on Computer and Communications Security","author":[{"last_name":"Giuliari","full_name":"Giuliari, Giacomo","first_name":"Giacomo"},{"full_name":"Sonnino, Alberto","first_name":"Alberto","last_name":"Sonnino"},{"last_name":"Frei","full_name":"Frei, Marc","first_name":"Marc"},{"first_name":"Fabio","full_name":"Streun, Fabio","last_name":"Streun"},{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","orcid":"0000-0002-8827-3382","last_name":"Kokoris Kogias"},{"full_name":"Perrig, Adrian","first_name":"Adrian","last_name":"Perrig"}],"publication_identifier":{"isbn":["9798400704826"]},"scopus_import":"1","supplementarymaterial":"no","page":"1345-1360","article_processing_charge":"Yes (in subscription journal)","type":"conference","day":"01","fulldoi":"https://doi.org/10.1145/3634737.3656997","ddc":["000"],"has_accepted_license":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001283918100095"]},"date_published":"2024-07-01T00:00:00Z"},{"day":"09","type":"conference","article_processing_charge":"No","page":"2606-2620","supplementarymaterial":"no","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.18042"}],"publication_identifier":{"isbn":["9798400706363"]},"author":[{"last_name":"Blackshear","first_name":"Sam","full_name":"Blackshear, Sam"},{"last_name":"Chursin","first_name":"Andrey","full_name":"Chursin, Andrey"},{"full_name":"Danezis, George","first_name":"George","last_name":"Danezis"},{"first_name":"Anastasios","full_name":"Kichidis, Anastasios","last_name":"Kichidis"},{"first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","orcid":"0000-0002-8827-3382","last_name":"Kokoris Kogias"},{"first_name":"Xun","full_name":"Li, Xun","last_name":"Li"},{"last_name":"Logan","full_name":"Logan, Mark","first_name":"Mark"},{"first_name":"Ashok","full_name":"Menon, Ashok","last_name":"Menon"},{"full_name":"Nowacki, Todd","first_name":"Todd","last_name":"Nowacki"},{"last_name":"Sonnino","full_name":"Sonnino, Alberto","first_name":"Alberto"},{"first_name":"Brandon","full_name":"Williams, Brandon","last_name":"Williams"},{"last_name":"Zhang","full_name":"Zhang, Lu","first_name":"Lu"}],"date_published":"2024-12-09T00:00:00Z","external_id":{"arxiv":["2310.18042"],"isi":["001436367300178"]},"arxiv":1,"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1145/3658644.3670286","quality_controlled":"1","status":"public","publisher":"ACM","acknowledgement":"This work is funded by MystenLabs. We thank the Mysten Labs Engineering teams for valuable feedback broadly, and specifically Dmitry Perelman and Todd Fiala for managing the implementation effort. A number of folks contributed to specific aspects of the implementation of Sui Lutris (amongst many other contributions to the overall blockchain): Francois Garillot, Laura Makdah, Mingwei Tian, Andrew Schran, Sadhan Sood and William Smith implemented and optimized aspects of both Sui Lutris and Narwhal / Bullshark consensus; Alonso de Gortari oversaw the cryptoeconomics of the blockchain, and Emma Zhong, Ade Adepoju, Tim Zakia and Dario Russi designed and implemented staking and gas mechanisms. Adam Welc designed several Move tools and provided great feedback on the manuscript. We also extend our thanks to Patrick Kuo, Ge Gao, Chris Li, and Arun Koshy for their work on the Sui Lutris SDK, clients, and RPC layer; Kostas Chalkias, Jonas Lindstrøm, and Joy Wang built cryptographic components.","title":"Sui Lutris: A blockchain combining broadcast and consensus","abstract":[{"text":"Sui Lutris is the first smart-contract platform to sustainably achieve sub-second finality. It achieves this significant decrease by employing consensusless agreement not only for simple payments but for a large variety of transactions. Unlike prior work, Sui Lutris neither compromises expressiveness nor throughput and can run perpetually without restarts. Sui Lutris achieves this by safely integrating consensuless agreement with a high-throughput consensus protocol that is invoked out of the critical finality path but ensures that when a transaction is at risk of inconsistent concurrent accesses, its settlement is delayed until the total ordering is resolved. Building such a hybrid architecture is especially delicate during reconfiguration events, where the system needs to preserve the safety of the consensusless path without compromising the long-term liveness of potentially misconfigured clients. We thus develop a novel reconfiguration protocol, the first to provably show the safe and efficient reconfiguration of a consensusless blockchain. Sui Lutris is currently running in production and underpins the Sui smart-contract platform. Combined with the use of Objects instead of accounts it enables the safe execution of smart contracts that expose objects as a first-class resource. In our experiments Sui Lutris achieves latency lower than 0.5 seconds for throughput up to 5,000 certificates per second (150k ops/s with transaction blocks), compared to the state-of-the-art real-world consensus latencies of 3 seconds. Furthermore, it gracefully handles validators crash-recovery and does not suffer visible performance degradation during reconfiguration.","lang":"eng"}],"publication_status":"published","citation":{"ista":"Blackshear S, Chursin A, Danezis G, Kichidis A, Kokoris Kogias E, Li X, Logan M, Menon A, Nowacki T, Sonnino A, Williams B, Zhang L. 2024. Sui Lutris: A blockchain combining broadcast and consensus. Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security. CCS: Conference on Computer and Communications Security, 2606–2620.","mla":"Blackshear, Sam, et al. “Sui Lutris: A Blockchain Combining Broadcast and Consensus.” Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security, ACM, 2024, pp. 2606–20, doi:10.1145/3658644.3670286.","ama":"Blackshear S, Chursin A, Danezis G, et al. Sui Lutris: A blockchain combining broadcast and consensus. In: Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security. ACM; 2024:2606-2620. doi:10.1145/3658644.3670286","apa":"Blackshear, S., Chursin, A., Danezis, G., Kichidis, A., Kokoris Kogias, E., Li, X., … Zhang, L. (2024). Sui Lutris: A blockchain combining broadcast and consensus. In Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security (pp. 2606–2620). Salt Lake City, UT, United States: ACM. https://doi.org/10.1145/3658644.3670286","chicago":"Blackshear, Sam, Andrey Chursin, George Danezis, Anastasios Kichidis, Eleftherios Kokoris Kogias, Xun Li, Mark Logan, et al. “Sui Lutris: A Blockchain Combining Broadcast and Consensus.” In Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security, 2606–20. ACM, 2024. https://doi.org/10.1145/3658644.3670286.","ieee":"S. Blackshear et al., “Sui Lutris: A blockchain combining broadcast and consensus,” in Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security, Salt Lake City, UT, United States, 2024, pp. 2606–2620.","short":"S. Blackshear, A. Chursin, G. Danezis, A. Kichidis, E. Kokoris Kogias, X. Li, M. Logan, A. Menon, T. Nowacki, A. Sonnino, B. Williams, L. Zhang, in:, Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security, ACM, 2024, pp. 2606–2620."},"OA_place":"repository","year":"2024","researchdata_availability":"no","doi":"10.1145/3658644.3670286","OA_type":"hybrid","oa_version":"Preprint","publication":"Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security","das_tickbox":"0","isi":1,"date_updated":"2026-10-01T11:04:52Z","oa":1,"date_created":"2025-01-29T12:42:21Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"ElKo"}],"_id":"18957","conference":{"start_date":"2024-10-14","location":"Salt Lake City, UT, United States","end_date":"2024-10-18","name":"CCS: Conference on Computer and Communications Security"},"month":"12"},{"acknowledgement":"M.L., E.V. and S.G. acknowledge funding from the European Regional Development Fund (ERDF) Prostem Research Project (No. 1510614, Wallonia DG06), the Epiforce Project of the National Fund for Scientific Research, Belgium (FRS-FNRS; Project No. T.0092.21), the Cellsqueezer Project of FRS-FNRS (Project No. J.0061.23), the Optopattern Project of FRS-FNRS (Project no. U.NO26.22) and the Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen, ERDF). A.R. and M.L. are financially supported by FRS-FNRS as a research fellow (Aspirant FNRS) and Postdoctoral Researcher (Chargée de Recherches FNRS), respectively. E.V. and Y.K. are financially supported by FRS-FNRS through grants from the Fund for Research Training in Industry and Agriculture (FRIA). This project was supported by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 851288 to E.H.) and Marie Skłodowska-Curie Actions (Grant Agreement No. 797621 to M.G.-G.). D.B.B. was supported by the NOMIS foundation as a NOMIS fellow and by the European Molecular Biology Organization (Postdoctoral Fellowship ALTF 343-2022) and performed this work in part at the Aspen Center for Physics, which is supported by the National Science Foundation (Grant No. PHY-1607611). X.T. and M.G.-G. acknowledge support from the Government of Catalonia (Grant No. AGAUR SGR-2017-01602 and a CERCA Programme), the Spanish Ministry for Science and Innovation and ERDF (Grant No. PGC2018-099645-B-I00), the European Research Council (Grant No. Adv-883739), Fundació la Marató de TV3 (201903-30-31-32), the European Commission (Grant No. H2020-FETPROACT-01-2016-731957), La Caixa Foundation and the Biomedical Research Center Consortium in Red (Grant No. CB15/00153) at the Carlos III Health Institute, Ministry of Science and Innovation. IBEC is recipient of a Severo Ochoa Award of Excellence from the Spanish Ministry of Economy, Trade and Business.","title":"Geometry-driven migration efficiency of autonomous epithelial cell clusters","abstract":[{"text":"The directed migration of epithelial cell collectives through coordinated movements plays a crucial role in various physiological processes and is increasingly understood at the level of large confluent monolayers. However, numerous processes rely on the migration of small groups of polarized epithelial clusters in complex environments, and their responses to external geometries remain poorly understood. To address this, we cultivate primary epithelial keratocyte tissues on adhesive microstripes to create autonomous epithelial clusters with well-defined geometries. We show that their migration efficiency is strongly influenced by the contact geometry and the orientation of cell–cell contacts with respect to the direction of migration. A combination of velocity and polarity alignment with contact regulation of locomotion in an active matter model captures quantitatively the experimental data. Furthermore, we predict that this combination of rules enables efficient navigation in complex geometries, which we confirm experimentally. Altogether, our findings provide a conceptual framework for extracting the interaction rules of active systems from their interaction with physical boundaries, as well as design principles for collective navigation in complex microenvironments.","lang":"eng"}],"quality_controlled":"1","publisher":"Springer Nature","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis"},{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022"}],"status":"public","doi":"10.1038/s41567-024-02532-x","OA_type":"green","publication_status":"published","OA_place":"repository","citation":{"chicago":"Vercruysse, Eléonore, David Brückner, Manuel Gómez-González, Alexandre Remson, Marine Luciano, Yohalie Kalukula, Leone Rossetti, Xavier Trepat, Edouard B Hannezo, and Sylvain Gabriele. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-024-02532-x.","apa":"Vercruysse, E., Brückner, D., Gómez-González, M., Remson, A., Luciano, M., Kalukula, Y., … Gabriele, S. (2024). Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02532-x","short":"E. Vercruysse, D. Brückner, M. Gómez-González, A. Remson, M. Luciano, Y. Kalukula, L. Rossetti, X. Trepat, E.B. Hannezo, S. Gabriele, Nature Physics 20 (2024) 1492–1500.","ieee":"E. Vercruysse et al., “Geometry-driven migration efficiency of autonomous epithelial cell clusters,” Nature Physics, vol. 20. Springer Nature, pp. 1492–1500, 2024.","ista":"Vercruysse E, Brückner D, Gómez-González M, Remson A, Luciano M, Kalukula Y, Rossetti L, Trepat X, Hannezo EB, Gabriele S. 2024. Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. 20, 1492–1500.","ama":"Vercruysse E, Brückner D, Gómez-González M, et al. Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. 2024;20:1492-1500. doi:10.1038/s41567-024-02532-x","mla":"Vercruysse, Eléonore, et al. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” Nature Physics, vol. 20, Springer Nature, 2024, pp. 1492–500, doi:10.1038/s41567-024-02532-x."},"volume":20,"year":"2024","researchdata_availability":"yes","das_tickbox":"1","related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/a-railroad-of-cells/"}]},"oa":1,"isi":1,"date_updated":"2026-10-01T11:02:43Z","publication":"Nature Physics","oa_version":"Preprint","intvolume":" 20","ec_funded":1,"_id":"17269","month":"09","dataavailabilitystatement":"All data are available from the corresponding authors upon request. Source data are provided with this paper.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-07-16T12:32:17Z","article_type":"original","department":[{"_id":"EdHa"}],"type":"journal_article","article_processing_charge":"No","day":"01","scopus_import":"1","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"main_file_link":[{"url":"https://doi.org/10.1101/2022.07.17.500364","open_access":"1"}],"author":[{"last_name":"Vercruysse","first_name":"Eléonore","full_name":"Vercruysse, Eléonore"},{"full_name":"Brückner, David","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","orcid":"0000-0001-7205-2975"},{"last_name":"Gómez-González","first_name":"Manuel","full_name":"Gómez-González, Manuel"},{"last_name":"Remson","full_name":"Remson, Alexandre","first_name":"Alexandre"},{"last_name":"Luciano","full_name":"Luciano, Marine","first_name":"Marine"},{"first_name":"Yohalie","full_name":"Kalukula, Yohalie","last_name":"Kalukula"},{"last_name":"Rossetti","full_name":"Rossetti, Leone","first_name":"Leone"},{"last_name":"Trepat","first_name":"Xavier","full_name":"Trepat, Xavier"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"first_name":"Sylvain","full_name":"Gabriele, Sylvain","last_name":"Gabriele"}],"page":"1492-1500","corr_author":"1","supplementarymaterial":"yes","language":[{"iso":"eng"}],"date_published":"2024-09-01T00:00:00Z","external_id":{"isi":["001250246200004"]},"fulldoi":"https://doi.org/10.1038/s41567-024-02532-x"},{"oa":1,"isi":1,"date_updated":"2026-10-01T10:54:32Z","das_tickbox":"1","related_material":{"record":[{"id":"23023","status":"public","relation":"research_data"}]},"intvolume":" 386","oa_version":"Submitted Version","publication":"Science","month":"10","dataavailabilitystatement":"All original code and data reported in this paper is publicly available as of the date of publication on Zenodo (124).\r\n124\r\nD. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani, T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon, V. Uhlmann, E. Hannezo, T. Hiiragi, Temporal variability and cell mechanics control robustness in mammalian embryogenesis, version 1.0, Zenodo (2024); https://doi.org/10.5281/ZENODO.12819781.","_id":"18446","article_type":"original","department":[{"_id":"EdHa"}],"date_created":"2024-10-20T22:02:06Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these morphomaps revealed that although blastomere divisions desynchronized passively, 8-cell embryos converged toward robust three-dimensional shapes. Using topological analysis and genetic perturbations, we found that embryos progressively changed their cellular connectivity to a preferred topology, which could be predicted by a physical model in which actomyosin contractility and noise facilitate topological transitions, lowering surface energy. This mechanism favored regular embryo packing and promoted a higher number of inner cells in the 16-cell embryo. Synchronized division reduced embryo packing and generated substantially more misallocated cells and fewer inner-cell–mass cells. These findings suggest that stochasticity in division timing contributes to robust patterning."}],"title":"Temporal variability and cell mechanics control robustness in mammalian embryogenesis","acknowledgement":"We are grateful to the members of the Hiiragi laboratory for discussions and comments on the manuscript: R. Bloehs, S. Friese, S. Hozeifi, L. Pérez, and W. Schwarzer for their technical support; V. Janssen for establishing the PAB protocol; members of the Tsukiyama group for the animal care with monkeys, in particular H. Tsuchiya and M. Nakaya; Unité Commune d’Expérimentation Animale (UCEA, Jouy-en-Josas, France) for the animal care with rabbits; the EMBL electronic and mechanical workshops and the EMBL animal facility for their support; We thank Luxendo for the close collaboration in developing the light-sheet microscopy for mammalian embryos.\r\nFunding: This work was funded by the following: EMBL Interdisciplinary Postdoc Program (EIPOD) under Marie Sklodowska Curie Actions COFUND III RTD (to D.F.); JSPS Overseas Research Fellowship (to T.I.); Field of excellence “Complexity of life in basic research and innovation” of the University of Graz (to B.C.M.); European Research Council, ERC Advanced Grant “SelforganisingEmbryo”, grant agreement 742732; ERC Advanced Grant “COORDINATION” grant agreement 101055287 (to T.H.); Stichting LSH-TKI, grant LSHM21020 (to T.H.) JSPS KAKENHI grants JP21H05038 and JP22H05166 (to T.H.)","publisher":"AAAS","issue":"6718","status":"public","quality_controlled":"1","OA_type":"green","doi":"10.1126/science.adh1145","volume":386,"year":"2024","researchdata_availability":"yes","citation":{"apa":"Fabrèges, D., Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani, C., … Hiiragi, T. (2024). Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. AAAS. https://doi.org/10.1126/science.adh1145","chicago":"Fabrèges, Dimitri, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth, Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Science. AAAS, 2024. https://doi.org/10.1126/science.adh1145.","ieee":"D. Fabrèges et al., “Temporal variability and cell mechanics control robustness in mammalian embryogenesis,” Science, vol. 386, no. 6718. AAAS, 2024.","short":"D. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani, T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon, V. Uhlman, E.B. Hannezo, T. Hiiragi, Science 386 (2024).","ista":"Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C, Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon V, Uhlman V, Hannezo EB, Hiiragi T. 2024. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. 386(6718), eadh1145.","mla":"Fabrèges, Dimitri, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Science, vol. 386, no. 6718, eadh1145, AAAS, 2024, doi:10.1126/science.adh1145.","ama":"Fabrèges D, Corominas-Murtra B, Moghe P, et al. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. 2024;386(6718). doi:10.1126/science.adh1145"},"publication_status":"published","OA_place":"repository","language":[{"iso":"eng"}],"pmid":1,"date_published":"2024-10-11T00:00:00Z","external_id":{"pmid":["39388574"],"isi":["001422132300018"]},"fulldoi":"https://doi.org/10.1126/science.adh1145","article_processing_charge":"No","type":"journal_article","day":"11","author":[{"last_name":"Fabrèges","first_name":"Dimitri","full_name":"Fabrèges, Dimitri"},{"orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Moghe","first_name":"Prachiti","full_name":"Moghe, Prachiti"},{"full_name":"Kickuth, Alison","first_name":"Alison","last_name":"Kickuth"},{"full_name":"Ichikawa, Takafumi","first_name":"Takafumi","last_name":"Ichikawa"},{"last_name":"Iwatani","first_name":"Chizuru","full_name":"Iwatani, Chizuru"},{"full_name":"Tsukiyama, Tomoyuki","first_name":"Tomoyuki","last_name":"Tsukiyama"},{"first_name":"Nathalie","full_name":"Daniel, Nathalie","last_name":"Daniel"},{"last_name":"Gering","full_name":"Gering, Julie","first_name":"Julie"},{"first_name":"Anniek","full_name":"Stokkermans, Anniek","last_name":"Stokkermans"},{"first_name":"Adrian","full_name":"Wolny, Adrian","last_name":"Wolny"},{"full_name":"Kreshuk, Anna","first_name":"Anna","last_name":"Kreshuk"},{"last_name":"Duranthon","first_name":"Véronique","full_name":"Duranthon, Véronique"},{"first_name":"Virginie","full_name":"Uhlman, Virginie","last_name":"Uhlman"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"first_name":"Takashi","full_name":"Hiiragi, Takashi","last_name":"Hiiragi"}],"scopus_import":"1","publication_identifier":{"eissn":["1095-9203"]},"main_file_link":[{"url":"https://hal.inrae.fr/hal-04447081v1/file/2023.01.24.525420.full.pdf","open_access":"1"}],"supplementarymaterial":"yes","article_number":"eadh1145","corr_author":"1"},{"department":[{"_id":"ElKo"}],"date_created":"2024-09-15T22:01:41Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"07","_id":"18071","conference":{"name":"ICDCS: International Conference on Distributed Computing Systems","end_date":"2024-07-26","location":"Jersey City, NJ, United States","start_date":"2024-07-23"},"publication":"Proceedings - International Conference on Distributed Computing Systems","oa_version":"Preprint","isi":1,"date_updated":"2026-10-01T11:04:17Z","oa":1,"das_tickbox":"0","year":"2024","researchdata_availability":"no","citation":{"ista":"Tsimos G, Kichidis A, Sonnino A, Kokoris Kogias E. 2024. HammerHead: Leader reputation for dynamic scheduling. Proceedings - International Conference on Distributed Computing Systems. ICDCS: International Conference on Distributed Computing Systems, 1377–1387.","mla":"Tsimos, Giorgos, et al. “HammerHead: Leader Reputation for Dynamic Scheduling.” Proceedings - International Conference on Distributed Computing Systems, IEEE, 2024, pp. 1377–87, doi:10.1109/ICDCS60910.2024.00129.","ama":"Tsimos G, Kichidis A, Sonnino A, Kokoris Kogias E. HammerHead: Leader reputation for dynamic scheduling. In: Proceedings - International Conference on Distributed Computing Systems. IEEE; 2024:1377-1387. doi:10.1109/ICDCS60910.2024.00129","apa":"Tsimos, G., Kichidis, A., Sonnino, A., & Kokoris Kogias, E. (2024). HammerHead: Leader reputation for dynamic scheduling. In Proceedings - International Conference on Distributed Computing Systems (pp. 1377–1387). Jersey City, NJ, United States: IEEE. https://doi.org/10.1109/ICDCS60910.2024.00129","chicago":"Tsimos, Giorgos, Anastasios Kichidis, Alberto Sonnino, and Eleftherios Kokoris Kogias. “HammerHead: Leader Reputation for Dynamic Scheduling.” In Proceedings - International Conference on Distributed Computing Systems, 1377–87. IEEE, 2024. https://doi.org/10.1109/ICDCS60910.2024.00129.","ieee":"G. Tsimos, A. Kichidis, A. Sonnino, and E. Kokoris Kogias, “HammerHead: Leader reputation for dynamic scheduling,” in Proceedings - International Conference on Distributed Computing Systems, Jersey City, NJ, United States, 2024, pp. 1377–1387.","short":"G. Tsimos, A. Kichidis, A. Sonnino, E. Kokoris Kogias, in:, Proceedings - International Conference on Distributed Computing Systems, IEEE, 2024, pp. 1377–1387."},"publication_status":"published","doi":"10.1109/ICDCS60910.2024.00129","status":"public","publisher":"IEEE","quality_controlled":"1","abstract":[{"text":"Recent advancements on DAG-based consensus protocols allow for blockchains with improved metrics and properties, such as throughput and censorship-resistance. Variants of the Bullshark [18] consensus protocol are adopted for practical use by the Sui blockchain, for improved latency. However, the protocol is leader-based, and is strongly affected by crashed leaders that can lead to various performance issues, for example, decreased transaction throughput. In this paper, we propose HammerHead, a DAG-based consensus protocol, that is inspired by Carousel [8] and provides Leader-Utilization. Our proposal differs from Carousel, which is built for a chained consensus protocol; in HammerHead chain quality is inherited by the DAG. HammerHead needs to preserve safety and liveness, despite validators committing leader vertices asynchronously. The key idea is to update leader schedules dynamically, based on the validators' scores during the previous schedule. We implement HammerHead and show a minor improvement in performance for cases without faults. The major improvements in comparison to Bullshark appear in faulty settings. Specifically, we show a drastic, 2x-latency improvement and up to 40% increased throughput when crash faults occur (100 validators, 33 faults).","lang":"eng"}],"title":"HammerHead: Leader reputation for dynamic scheduling","acknowledgement":"This work is supported by Mysten Labs. We thank the Mysten Labs Engineering teams for valuable feedback broadly, and specifically to Laura Makdah for helping implementing the early reputation score system for validators and Dmitry Perelman for managing the overall implementation effort.","fulldoi":"https://doi.org/10.1109/ICDCS60910.2024.00129","arxiv":1,"external_id":{"arxiv":["2309.12713"],"isi":["001304430200120"]},"date_published":"2024-07-26T00:00:00Z","language":[{"iso":"eng"}],"supplementarymaterial":"no","page":"1377-1387","author":[{"first_name":"Giorgos","full_name":"Tsimos, Giorgos","last_name":"Tsimos"},{"last_name":"Kichidis","full_name":"Kichidis, Anastasios","first_name":"Anastasios"},{"full_name":"Sonnino, Alberto","first_name":"Alberto","last_name":"Sonnino"},{"first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","orcid":"0000-0002-8827-3382"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2309.12713"}],"publication_identifier":{"issn":["1063-6927"],"isbn":["9798350386059"],"eissn":["2575-8411"]},"scopus_import":"1","day":"26","article_processing_charge":"No","type":"conference"},{"year":"2024","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":631,"researchdata_availability":"upon request","publication_status":"published","citation":{"short":"F.R. Gärtner, H. Ishikawa-Ankerhold, S. Stutte, W. Fu, J. Weitz, A. Dueck, B. Nelakuditi, V. Fumagalli, D. Van Den Heuvel, L. Belz, G. Sobirova, Z. Zhang, A. Titova, A.M. Navarro, K. Pekayvaz, M. Lorenz, L. Von Baumgarten, J. Kranich, T. Straub, B. Popper, V. Zheden, W. Kaufmann, C. Guo, G. Piontek, S. Von Stillfried, P. Boor, M. Colonna, S. Clauß, C. Schulz, T. Brocker, B. Walzog, C. Scheiermann, W.C. Aird, C. Nerlov, K. Stark, T. Petzold, S. Engelhardt, M.K. Sixt, R. Hauschild, M. Rudelius, R.A.J. Oostendorp, M. Iannacone, M. Heinig, S. Massberg, Nature 631 (2024) 645–653.","ieee":"F. R. Gärtner et al., “Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis,” Nature, vol. 631. Springer Nature, pp. 645–653, 2024.","chicago":"Gärtner, Florian R, Hellen Ishikawa-Ankerhold, Susanne Stutte, Wenwen Fu, Jutta Weitz, Anne Dueck, Bhavishya Nelakuditi, et al. “Plasmacytoid Dendritic Cells Control Homeostasis of Megakaryopoiesis.” Nature. Springer Nature, 2024. https://doi.org/10.1038/s41586-024-07671-y.","apa":"Gärtner, F. R., Ishikawa-Ankerhold, H., Stutte, S., Fu, W., Weitz, J., Dueck, A., … Massberg, S. (2024). Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. Nature. Springer Nature. https://doi.org/10.1038/s41586-024-07671-y","ama":"Gärtner FR, Ishikawa-Ankerhold H, Stutte S, et al. Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. Nature. 2024;631:645-653. doi:10.1038/s41586-024-07671-y","mla":"Gärtner, Florian R., et al. “Plasmacytoid Dendritic Cells Control Homeostasis of Megakaryopoiesis.” Nature, vol. 631, Springer Nature, 2024, pp. 645–53, doi:10.1038/s41586-024-07671-y.","ista":"Gärtner FR, Ishikawa-Ankerhold H, Stutte S, Fu W, Weitz J, Dueck A, Nelakuditi B, Fumagalli V, Van Den Heuvel D, Belz L, Sobirova G, Zhang Z, Titova A, Navarro AM, Pekayvaz K, Lorenz M, Von Baumgarten L, Kranich J, Straub T, Popper B, Zheden V, Kaufmann W, Guo C, Piontek G, Von Stillfried S, Boor P, Colonna M, Clauß S, Schulz C, Brocker T, Walzog B, Scheiermann C, Aird WC, Nerlov C, Stark K, Petzold T, Engelhardt S, Sixt MK, Hauschild R, Rudelius M, Oostendorp RAJ, Iannacone M, Heinig M, Massberg S. 2024. Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. Nature. 631, 645–653."},"doi":"10.1038/s41586-024-07671-y","publisher":"Springer Nature","project":[{"call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"}],"status":"public","quality_controlled":"1","abstract":[{"lang":"eng","text":"Platelet homeostasis is essential for vascular integrity and immune defence1,2. Although the process of platelet formation by fragmenting megakaryocytes (MKs; thrombopoiesis) has been extensively studied, the cellular and molecular mechanisms required to constantly replenish the pool of MKs by their progenitor cells (megakaryopoiesis) remains unclear3,4. Here we use intravital imaging to track the cellular dynamics of megakaryopoiesis over days. We identify plasmacytoid dendritic cells (pDCs) as homeostatic sensors that monitor the bone marrow for apoptotic MKs and deliver IFNα to the MK niche triggering local on-demand proliferation and maturation of MK progenitors. This pDC-dependent feedback loop is crucial for MK and platelet homeostasis at steady state and under stress. pDCs are best known for their ability to function as vigilant detectors of viral infection5. We show that virus-induced activation of pDCs interferes with their function as homeostatic sensors of megakaryopoiesis. Consequently, activation of pDCs by SARS-CoV-2 leads to excessive megakaryopoiesis. Together, we identify a pDC-dependent homeostatic circuit that involves innate immune sensing and demand-adapted release of inflammatory mediators to maintain homeostasis of the megakaryocytic lineage."}],"title":"Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis","acknowledgement":"We thank S. Helmer, N. Blount, E. Raatz and Z. Sisic for technical assistance. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) SFB 1123 (S.M. project B06); SFB 914 (S.M. projects B02 and Z01, H.I.-A. project Z01, S.S. project A06, K.S. project B02, C. Schulz project A10, B.W. project A02, C. Scheiermann project B09); SFB 1054 (T.B. project B03); FOR2033 (F.G., R.A.J.O., S.M.); Individual research grant project ID: 514478744 (F.G.); Heisenberg Programme project ID: 514477451 (F.G.); the DZHK (German Center for Cardiovascular Research) (MHA 1.4VD (S.M.), Postdoc Start-up Grant, 81×3600213 (F.G.)); and LMUexcellence NFF (F.G.). W.F. received funding from China Scholarship Council (CSC, no. 201306270012). P.B. is supported by the German Research Foundation (DFG, project IDs 322900939, 432698239 and 445703531), European Research Council (ERC Consolidator grant no. 101001791) and the Federal Ministry of Education and Research (BMBF, STOP-FSGS-01GM2202C and NATON within the framework of the Network of University Medicine, no. 01KX2121). S.v.S. is supported by the START-Program of the Faculty of Medicine of the RWTH Aachen University (AZ 125/17). A.D. and S.E. are supported by the German Research Foundation (SFB TRR 267); S.E. by the BMBF in the framework of the Cluster4future program (CNATM—Cluster for Nucleic Acid Therapeutics Munich). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 833440 to S.M.). F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687. The project is funded by the European Union (ERC, MEKanics, 101078110). Views and opinions expressed are those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.","article_type":"original","department":[{"_id":"EM-Fac"},{"_id":"MiSi"},{"_id":"Bio"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-07-21T22:01:02Z","month":"07","dataavailabilitystatement":"Imaging and flow cytometry raw data are available on request. scRNA-seq data are accessible at the GEO (GSE261996). Bulk RNA-seq data are accessible at the GEO (GSE185488). Source data are provided with this paper.","ec_funded":1,"_id":"17284","intvolume":" 631","file_date_updated":"2024-07-22T06:16:11Z","oa_version":"Published Version","publication":"Nature","oa":1,"file":[{"creator":"dernst","file_name":"2024_Nature_Gaertner.pdf","file_id":"17286","date_updated":"2024-07-22T06:16:11Z","success":1,"access_level":"open_access","content_type":"application/pdf","date_created":"2024-07-22T06:16:11Z","file_size":15704819,"checksum":"aa004afc72d2489f0fb0fcbc9919fbbd","relation":"main_file"}],"isi":1,"date_updated":"2026-10-01T11:17:11Z","related_material":{"link":[{"relation":"software","url":"https://github.com/heiniglab/gaertner_megakaryocytes"}]},"das_tickbox":"1","supplementarymaterial":"yes","page":"645-653","corr_author":"1","author":[{"last_name":"Gärtner","orcid":"0000-0001-6120-3723","first_name":"Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R"},{"last_name":"Ishikawa-Ankerhold","first_name":"Hellen","full_name":"Ishikawa-Ankerhold, Hellen"},{"first_name":"Susanne","full_name":"Stutte, Susanne","last_name":"Stutte"},{"last_name":"Fu","full_name":"Fu, Wenwen","first_name":"Wenwen"},{"last_name":"Weitz","full_name":"Weitz, Jutta","first_name":"Jutta"},{"last_name":"Dueck","full_name":"Dueck, Anne","first_name":"Anne"},{"full_name":"Nelakuditi, Bhavishya","first_name":"Bhavishya","last_name":"Nelakuditi"},{"last_name":"Fumagalli","first_name":"Valeria","full_name":"Fumagalli, Valeria"},{"last_name":"Van Den Heuvel","full_name":"Van Den Heuvel, Dominic","first_name":"Dominic"},{"last_name":"Belz","first_name":"Larissa","full_name":"Belz, Larissa"},{"last_name":"Sobirova","first_name":"Gulnoza","full_name":"Sobirova, Gulnoza"},{"full_name":"Zhang, Zhe","first_name":"Zhe","last_name":"Zhang"},{"last_name":"Titova","full_name":"Titova, Anna","first_name":"Anna"},{"first_name":"Alejandro Martinez","full_name":"Navarro, Alejandro Martinez","last_name":"Navarro"},{"last_name":"Pekayvaz","full_name":"Pekayvaz, Kami","first_name":"Kami"},{"full_name":"Lorenz, Michael","first_name":"Michael","last_name":"Lorenz"},{"full_name":"Von Baumgarten, Louisa","first_name":"Louisa","last_name":"Von Baumgarten"},{"last_name":"Kranich","first_name":"Jan","full_name":"Kranich, Jan"},{"full_name":"Straub, Tobias","first_name":"Tobias","last_name":"Straub"},{"full_name":"Popper, Bastian","first_name":"Bastian","last_name":"Popper"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","last_name":"Zheden"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315"},{"full_name":"Guo, Chenglong","first_name":"Chenglong","last_name":"Guo"},{"full_name":"Piontek, Guido","first_name":"Guido","last_name":"Piontek"},{"last_name":"Von Stillfried","full_name":"Von Stillfried, Saskia","first_name":"Saskia"},{"last_name":"Boor","first_name":"Peter","full_name":"Boor, Peter"},{"full_name":"Colonna, Marco","first_name":"Marco","last_name":"Colonna"},{"last_name":"Clauß","first_name":"Sebastian","full_name":"Clauß, Sebastian"},{"last_name":"Schulz","full_name":"Schulz, Christian","first_name":"Christian"},{"last_name":"Brocker","first_name":"Thomas","full_name":"Brocker, Thomas"},{"full_name":"Walzog, Barbara","first_name":"Barbara","last_name":"Walzog"},{"full_name":"Scheiermann, Christoph","first_name":"Christoph","last_name":"Scheiermann"},{"last_name":"Aird","full_name":"Aird, William C.","first_name":"William C."},{"full_name":"Nerlov, Claus","first_name":"Claus","last_name":"Nerlov"},{"full_name":"Stark, Konstantin","first_name":"Konstantin","last_name":"Stark"},{"last_name":"Petzold","first_name":"Tobias","full_name":"Petzold, Tobias"},{"first_name":"Stefan","full_name":"Engelhardt, Stefan","last_name":"Engelhardt"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"first_name":"Martina","full_name":"Rudelius, Martina","last_name":"Rudelius"},{"full_name":"Oostendorp, Robert A.J.","first_name":"Robert A.J.","last_name":"Oostendorp"},{"full_name":"Iannacone, Matteo","first_name":"Matteo","last_name":"Iannacone"},{"full_name":"Heinig, Matthias","first_name":"Matthias","last_name":"Heinig"},{"full_name":"Massberg, Steffen","first_name":"Steffen","last_name":"Massberg"}],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"scopus_import":"1","day":"18","article_processing_charge":"Yes (in subscription journal)","type":"journal_article","fulldoi":"https://doi.org/10.1038/s41586-024-07671-y","ddc":["570"],"has_accepted_license":"1","date_published":"2024-07-18T00:00:00Z","pmid":1,"external_id":{"isi":["001281636500020"],"pmid":["38987596"]},"language":[{"iso":"eng"}]},{"article_number":"eadk1954 ","supplementarymaterial":"yes","publication_identifier":{"eissn":["2375-2548"]},"scopus_import":"1","author":[{"full_name":"Homola, Miroslav","first_name":"Miroslav","last_name":"Homola"},{"last_name":"Büttner","first_name":"Renate Carina","id":"3b7984c9-17ff-11ed-b6fe-f943c4a5b626","full_name":"Büttner, Renate Carina"},{"full_name":"Füzik, Tibor","first_name":"Tibor","last_name":"Füzik"},{"full_name":"Křepelka, Pavel","first_name":"Pavel","last_name":"Křepelka"},{"full_name":"Holbová, Radka","first_name":"Radka","last_name":"Holbová"},{"first_name":"Jiří","full_name":"Nováček, Jiří","last_name":"Nováček"},{"first_name":"Marten L.","full_name":"Chaillet, Marten L.","last_name":"Chaillet"},{"first_name":"Jakub","full_name":"Žák, Jakub","last_name":"Žák"},{"last_name":"Grybchuk","first_name":"Danyil","full_name":"Grybchuk, Danyil"},{"last_name":"Förster","full_name":"Förster, Friedrich","first_name":"Friedrich"},{"last_name":"Wilson","full_name":"Wilson, William H.","first_name":"William H."},{"last_name":"Schroeder","full_name":"Schroeder, Declan C.","first_name":"Declan C."},{"last_name":"Plevka","first_name":"Pavel","full_name":"Plevka, Pavel"}],"day":"01","type":"journal_article","article_processing_charge":"Yes","has_accepted_license":"1","ddc":["570"],"fulldoi":"https://doi.org/10.1126/sciadv.adk1954","external_id":{"pmid":["38598627"]},"date_published":"2024-04-01T00:00:00Z","pmid":1,"language":[{"iso":"eng"}],"publication_status":"published","OA_place":"publisher","citation":{"apa":"Homola, M., Büttner, R. C., Füzik, T., Křepelka, P., Holbová, R., Nováček, J., … Plevka, P. (2024). Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adk1954","chicago":"Homola, Miroslav, Renate Carina Büttner, Tibor Füzik, Pavel Křepelka, Radka Holbová, Jiří Nováček, Marten L. Chaillet, et al. “Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1954.","ieee":"M. Homola et al., “Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi,” Science Advances, vol. 10, no. 15. American Association for the Advancement of Science, 2024.","short":"M. Homola, R.C. Büttner, T. Füzik, P. Křepelka, R. Holbová, J. Nováček, M.L. Chaillet, J. Žák, D. Grybchuk, F. Förster, W.H. Wilson, D.C. Schroeder, P. Plevka, Science Advances 10 (2024).","ista":"Homola M, Büttner RC, Füzik T, Křepelka P, Holbová R, Nováček J, Chaillet ML, Žák J, Grybchuk D, Förster F, Wilson WH, Schroeder DC, Plevka P. 2024. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Science Advances. 10(15), eadk1954.","mla":"Homola, Miroslav, et al. “Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” Science Advances, vol. 10, no. 15, eadk1954, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adk1954.","ama":"Homola M, Büttner RC, Füzik T, et al. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Science Advances. 2024;10(15). doi:10.1126/sciadv.adk1954"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"researchdata_availability":"yes","year":"2024","volume":10,"doi":"10.1126/sciadv.adk1954","OA_type":"gold","quality_controlled":"1","issue":"15","status":"public","publisher":"American Association for the Advancement of Science","acknowledgement":"We acknowledge (i) the Cryo-Electron Microscopy and Tomography Core Facility and Proteomics Core Facility of the Central European Institute of Technology (CEITEC), Masaryk University, supported by the Ministry of Education, Youth, and Sports of the Czech Republic (grant LM2018127); (ii) the Cellular Imaging Core Facility supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR); and (iii) Plant Sciences Core Facility for support with obtaining scientific data presented here. We acknowledge support from the project National Institute of Virology and Bacteriology (Program EXCELES, ID project no. LX22NPO5103), funded by the European Union - Next Generation EU. This work received funding from the Czech Science Foundation grant GX 19-259882X to P.P., from European Regional Development Fund-Project “MSCAfellow2@MUNI” (no. CZ.02.2.69/0.0/0.0/18_070/0009846) to C.R.B., and from Brno PhD talent scholarship funded by Brno city municipality to M.H.","abstract":[{"text":"The globally distributed marine alga Emiliania huxleyi has cooling effect on the Earth’s climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse the virus’ inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum–derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which enables the continuous release of virions by exocytosis.","lang":"eng"}],"title":"Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi","date_created":"2025-01-27T14:32:34Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"EM-Fac"}],"article_type":"original","_id":"18920","DOAJ_listed":"1","dataavailabilitystatement":"Cryo-EM maps and structure coordinates were deposited to the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB), respectively, with the following accession numbers: (i) EhV-201 virion vertex reconstructed using a single-particle approach and a mask with the diameter of 50 nm (EMD-17650); (ii) EhV-201 virion vertex reconstructed using sub-tomogram averaging and a mask with the diameter of 50 nm (EMD-17649); (iii) EhV-201 virion vertex reconstructed using sub-tomogram averaging and a mask with the diameter of 50 nm and a mask covering only the capsid layer (EMD-19036) and the fitted structure of AlphaFold2 predicted EhV-201 major capsid protein and penton protein (PDB 8RBT); (iv) EhV-201 virion vertex reconstructed by sub-tomogram averaging and a mask with the diameter of 120 nm (EMD-17651); and (v) composite map of the EhV201 virion (EMD-19035) and corresponding structure of icosahedral asymmetric unit (PDB 8RBS). All custom scripts used during tomographic reconstruction have been made available at https://github.com/fuzikt/tomostarpy. Additional files have been made available at https://doi.org/10.5061/dryad.p5hqbzkw0: (i) cryo-ET tilt series of lamellas of control and EhV-201 infected E. huxleyi cells; (ii) segmentations of cryo-tomograms of infected and control cells; (iii) block face imaging data series of high-pressure frozen and resin-embedded E. huxleyi infected by EhV-201; (iv) scripts used during tomographic reconstruction; (v) fluorescence microscopy images of E. huxleyi infected by EhV-201; and (vi) mass spectrometry report of EhV-201 virion protein composition. Cryo-ET tilt series used for EhV-201 virion structure determination were deposited to EMPIAR and linked to the file EMD-17649. All other data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.","month":"04","oa_version":"Published Version","publication":"Science Advances","file_date_updated":"2025-01-27T14:40:08Z","intvolume":" 10","das_tickbox":"1","related_material":{"link":[{"url":" https://github.com/fuzikt/tomostarpy.","relation":"software"}],"record":[{"relation":"research_data","id":"23025","status":"public"}]},"file":[{"creator":"dernst","file_name":"2024_ScienceAdv_Homola.pdf","date_updated":"2025-01-27T14:40:08Z","file_id":"18921","success":1,"content_type":"application/pdf","date_created":"2025-01-27T14:40:08Z","access_level":"open_access","relation":"main_file","file_size":40623405,"checksum":"291dd7ceccbe6bfd8e0a9157584f88e9"}],"date_updated":"2026-10-01T11:15:30Z","oa":1},{"supplementarymaterial":"no","corr_author":"1","page":"123-137","author":[{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Kleindienst"},{"first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso","last_name":"Costanzo","orcid":"0000-0001-9732-3815"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"}],"scopus_import":"1","publication_identifier":{"eisbn":["9781071640197"],"eissn":["1940-6045"],"isbn":["9781071640180"],"issn":["0893-2336"]},"day":"27","place":"New York","article_processing_charge":"No","acknowledged_ssus":[{"_id":"EM-Fac"}],"type":"book_chapter","fulldoi":"https://doi.org/10.1007/978-1-0716-4019-7_8","date_published":"2024-08-27T00:00:00Z","alternative_title":["Neuromethods"],"language":[{"iso":"eng"}],"year":"2024","researchdata_availability":"no","publication_status":"published","citation":{"short":"D. Kleindienst, T. Costanzo, R. Shigemoto, in:, J.H.R. Lübke, A. Rollenhagen (Eds.), New Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed., Springer Nature, New York, 2024, pp. 123–137.","ieee":"D. Kleindienst, T. Costanzo, and R. Shigemoto, “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning,” in New Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed., J. H. R. Lübke and A. Rollenhagen, Eds. New York: Springer Nature, 2024, pp. 123–137.","chicago":"Kleindienst, David, Tommaso Costanzo, and Ryuichi Shigemoto. “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning.” In New Aspects in Analyzing the Synaptic Organization of the Brain, edited by Joachim H.R. Lübke and Astrid Rollenhagen, 1st ed., 123–37. New York: Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-4019-7_8.","apa":"Kleindienst, D., Costanzo, T., & Shigemoto, R. (2024). Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In J. H. R. Lübke & A. Rollenhagen (Eds.), New Aspects in Analyzing the Synaptic Organization of the Brain (1st ed., pp. 123–137). New York: Springer Nature. https://doi.org/10.1007/978-1-0716-4019-7_8","ama":"Kleindienst D, Costanzo T, Shigemoto R. Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: Lübke JHR, Rollenhagen A, eds. New Aspects in Analyzing the Synaptic Organization of the Brain. 1st ed. New York: Springer Nature; 2024:123-137. doi:10.1007/978-1-0716-4019-7_8","mla":"Kleindienst, David, et al. “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning.” New Aspects in Analyzing the Synaptic Organization of the Brain, edited by Joachim H.R. Lübke and Astrid Rollenhagen, 1st ed., Springer Nature, 2024, pp. 123–37, doi:10.1007/978-1-0716-4019-7_8.","ista":"Kleindienst D, Costanzo T, Shigemoto R. 2024.Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: New Aspects in Analyzing the Synaptic Organization of the Brain. Neuromethods, , 123–137."},"doi":"10.1007/978-1-0716-4019-7_8","publisher":"Springer Nature","project":[{"grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"}],"status":"public","quality_controlled":"1","title":"Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning","abstract":[{"lang":"eng","text":"Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is an electron microscope (EM) sample preparation technique which allows for high-resolution visualization of membrane proteins with high sensitivity. However, image acquisition of specific replica profiles such as synapses in a large field of EM view needs a valid experience and a long time for manual searching. Here, we describe how to utilize deep learning for automatizing image acquisition of specific profiles of interest in replica samples. This protocol facilitates the labor-intensive collection of EM images, in particular for rare profiles. We provide instructions for using SerialEM image acquisition software in conjunction with object detection by our newly developed deep learning software DarEM, to automatically acquire tilt series of all synapses in a selected region. We then show how to perform a mostly automated analysis of gold particle labeling in the acquired images by utilizing Darea software."}],"edition":"1","acknowledgement":"This research was supported by the European Research Council Advanced Grant 694539 to RS and by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility.","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-09-10T12:32:38Z","month":"08","editor":[{"full_name":"Lübke, Joachim H.R. ","first_name":"Joachim H.R. ","last_name":"Lübke"},{"last_name":"Rollenhagen","first_name":"Astrid","full_name":"Rollenhagen, Astrid"}],"_id":"18052","ec_funded":1,"publication":"New Aspects in Analyzing the Synaptic Organization of the Brain","oa_version":"None","date_updated":"2026-10-01T11:17:28Z","das_tickbox":"0"}]