[{"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","degree_awarded":"PhD","_id":"20357","year":"2025","date_published":"2025-09-15T00:00:00Z","title":"Effect propagation in biological networks","month":"09","project":[{"name":"Collective behaviour of cells in pancreatic Islets of Langerhans","_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e"}],"author":[{"last_name":"Ruzickova","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia"}],"date_created":"2025-09-15T17:04:48Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-066-4"]},"date_updated":"2026-04-07T12:02:39Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","page":"160","file_date_updated":"2025-11-27T10:00:25Z","keyword":["gene regulation","networks","omnigenic model","pancreas","collective behaviour"],"citation":{"mla":"Ruzickova, Natalia. <i>Effect Propagation in Biological Networks</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20357\">10.15479/AT-ISTA-20357</a>.","ista":"Ruzickova N. 2025. Effect propagation in biological networks. Institute of Science and Technology Austria.","chicago":"Ruzickova, Natalia. “Effect Propagation in Biological Networks.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20357\">https://doi.org/10.15479/AT-ISTA-20357</a>.","ama":"Ruzickova N. Effect propagation in biological networks. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20357\">10.15479/AT-ISTA-20357</a>","apa":"Ruzickova, N. (2025). <i>Effect propagation in biological networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20357\">https://doi.org/10.15479/AT-ISTA-20357</a>","short":"N. Ruzickova, Effect Propagation in Biological Networks, Institute of Science and Technology Austria, 2025.","ieee":"N. Ruzickova, “Effect propagation in biological networks,” Institute of Science and Technology Austria, 2025."},"day":"15","supervisor":[{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"I would also like to acknowledge the Austrian Academy of Sciences for funding through the\r\nDOC Fellowship program (fellowship number 26917), the Grants Office at ISTA for their\r\nassistance with the application, and the Scientific Computing Unit for their support regarding\r\nhigh-performance computation.\r\n","doi":"10.15479/AT-ISTA-20357","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"E-Lib"}],"type":"dissertation","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"file":[{"access_level":"closed","checksum":"991e81bc16a76b4e0c352567728fd2c5","creator":"nruzicko","date_updated":"2025-11-27T10:00:25Z","file_name":"2025_Ruzickova_Natalia_Thesis.pdf","date_created":"2025-09-16T12:56:06Z","relation":"main_file","embargo":"2026-09-14","file_size":43518367,"title":"Effect propagation in biological networks","content_type":"application/pdf","file_id":"20360","embargo_to":"open_access"},{"file_id":"20361","file_size":53464789,"content_type":"application/zip","relation":"source_file","date_created":"2025-09-16T12:59:23Z","date_updated":"2025-09-16T12:59:23Z","file_name":"2025_Ruzickova_Natalia_Thesis_source.zip","checksum":"c4ab257adad116083d8a97fac69b2dde","access_level":"closed","creator":"nruzicko"}],"alternative_title":["ISTA Thesis"],"corr_author":"1","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","related_material":{"record":[{"status":"public","id":"18525","relation":"part_of_dissertation"}]},"has_accepted_license":"1","ddc":["570","530"]},{"oa_version":"Published Version","abstract":[{"text":"Conference travel contributes to the climate footprint of academic research. Here, we provide a quantitative estimate of the carbon emissions associated with conference attendance by analyzing travel data from participants of 10 international conferences in the field of magnetic resonance, namely EUROMAR, ENC and ICMRBS. We find that attending a EUROMAR conference produces, on average, more than 1 t CO2 eq.. For the analyzed conferences outside Europe, the corresponding value is about 2–3 times higher, on average, with intercontinental trips amounting to up to 5 t. We compare these conference-related emissions to other activities associated with research and show that conference travel is a substantial portion of the total climate footprint of a researcher in magnetic resonance. We explore several strategies to reduce these emissions, including the impact of selecting conference venues more strategically and the possibility of decentralized conferences. Through a detailed comparison of train versus air travel – accounting for both direct and infrastructure-related emissions – we demonstrate that train travel offers considerable carbon savings. These data may provide a basis for strategic choices of future conferences in the field and for individuals deciding on their conference attendance.","lang":"eng"}],"OA_type":"gold","volume":6,"oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-28T13:15:31Z","publication_identifier":{"eissn":["2699-0016"]},"author":[{"first_name":"Lucky","last_name":"Kapoor","id":"84b9700b-15b2-11ec-abd3-831089e67615","orcid":"0000-0001-8319-2148","full_name":"Kapoor, Lucky"},{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","last_name":"Ruzickova","first_name":"Natalia","full_name":"Ruzickova, Natalia"},{"full_name":"Zivadinovic, Predrag","last_name":"Zivadinovic","first_name":"Predrag","id":"68AA0E5A-AFDA-11E9-9994-141DE6697425"},{"full_name":"Leitner, Valentin","first_name":"Valentin","last_name":"Leitner","id":"4c665ce3-0016-11ec-bea0-e44de7a4fa3d"},{"full_name":"Sisak, Maria A","last_name":"Sisak","first_name":"Maria A","id":"44A03D04-AEA4-11E9-B225-EA2DE6697425"},{"last_name":"Mweka","first_name":"Cecelia N","id":"2a69ab4b-896a-11ed-bdf8-cb8641cf2b21","full_name":"Mweka, Cecelia N"},{"id":"c15a5412-de82-11ed-b809-8dc1aa996e40","last_name":"Dobbelaere","first_name":"Jeroen A","full_name":"Dobbelaere, Jeroen A"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda"}],"date_created":"2025-11-23T23:01:39Z","title":"Quantifying the carbon footprint of conference travel: The case of NMR meetings","scopus_import":"1","month":"11","date_published":"2025-11-10T00:00:00Z","year":"2025","_id":"20664","intvolume":"         6","article_type":"original","article_processing_charge":"Yes","language":[{"iso":"eng"}],"DOAJ_listed":"1","PlanS_conform":"1","status":"public","publication":"Magnetic Resonance","ddc":["000"],"OA_place":"publisher","related_material":{"record":[{"relation":"research_data","status":"public","id":"20242"}],"link":[{"relation":"research_data","description":"News on ISTA website","url":"https://ista.ac.at/en/news/carbon-footprint-of-conference-travel/"}]},"has_accepted_license":"1","publisher":"Copernicus Publications","file":[{"file_id":"20672","success":1,"file_size":3081399,"content_type":"application/pdf","relation":"main_file","date_created":"2025-11-24T08:25:19Z","file_name":"2025_MagneticResonance_Kapoor.pdf","date_updated":"2025-11-24T08:25:19Z","checksum":"c63dd47b0e77f9451821436bb77d27c9","access_level":"open_access","creator":"dernst"}],"corr_author":"1","department":[{"_id":"JoFi"},{"_id":"GaTk"},{"_id":"JoCs"},{"_id":"EvBe"},{"_id":"TaHa"},{"_id":"GradSch"},{"_id":"GeKa"},{"_id":"PaSc"}],"quality_controlled":"1","type":"journal_article","publication_status":"published","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"First and foremost, we are grateful to the conference organizers who have provided data, either in the form of tables or by pointing us to abstract books. We thank the reviewers and the handling editor (Gottfried Otting) for the careful reading and suggestions. This project emerged from an interactive course about energy and climate, held at IST Austria by Jeroen Dobbelaere, Georgios Katsaros and Paul Schanda. We are grateful to ISTA's Graduate School for enabling this interdisciplinary course and to all participating students. We thank the following persons for discussions and/or comments about the manuscript: Helene Van Melckebeke, Mei Hong, Jeff Hoch, Gottfried Otting and Matthias Ernst. For the preparation of the manuscript, AI tools have been used, namely for finding relevant literature (ChatGPT) and for correcting the text (Writefull, within Overleaf LaTeX).","doi":"10.5194/mr-6-243-2025","issue":"2","citation":{"mla":"Kapoor, Lucky, et al. “Quantifying the Carbon Footprint of Conference Travel: The Case of NMR Meetings.” <i>Magnetic Resonance</i>, vol. 6, no. 2, Copernicus Publications, 2025, pp. 243–56, doi:<a href=\"https://doi.org/10.5194/mr-6-243-2025\">10.5194/mr-6-243-2025</a>.","ama":"Kapoor L, Ruzickova N, Zivadinovic P, et al. Quantifying the carbon footprint of conference travel: The case of NMR meetings. <i>Magnetic Resonance</i>. 2025;6(2):243-256. doi:<a href=\"https://doi.org/10.5194/mr-6-243-2025\">10.5194/mr-6-243-2025</a>","apa":"Kapoor, L., Ruzickova, N., Zivadinovic, P., Leitner, V., Sisak, M. A., Mweka, C. N., … Schanda, P. (2025). Quantifying the carbon footprint of conference travel: The case of NMR meetings. <i>Magnetic Resonance</i>. Copernicus Publications. <a href=\"https://doi.org/10.5194/mr-6-243-2025\">https://doi.org/10.5194/mr-6-243-2025</a>","chicago":"Kapoor, Lucky, Natalia Ruzickova, Predrag Zivadinovic, Valentin Leitner, Maria A Sisak, Cecelia N Mweka, Jeroen A Dobbelaere, Georgios Katsaros, and Paul Schanda. “Quantifying the Carbon Footprint of Conference Travel: The Case of NMR Meetings.” <i>Magnetic Resonance</i>. Copernicus Publications, 2025. <a href=\"https://doi.org/10.5194/mr-6-243-2025\">https://doi.org/10.5194/mr-6-243-2025</a>.","ista":"Kapoor L, Ruzickova N, Zivadinovic P, Leitner V, Sisak MA, Mweka CN, Dobbelaere JA, Katsaros G, Schanda P. 2025. Quantifying the carbon footprint of conference travel: The case of NMR meetings. Magnetic Resonance. 6(2), 243–256.","ieee":"L. Kapoor <i>et al.</i>, “Quantifying the carbon footprint of conference travel: The case of NMR meetings,” <i>Magnetic Resonance</i>, vol. 6, no. 2. Copernicus Publications, pp. 243–256, 2025.","short":"L. Kapoor, N. Ruzickova, P. Zivadinovic, V. Leitner, M.A. Sisak, C.N. Mweka, J.A. Dobbelaere, G. Katsaros, P. Schanda, Magnetic Resonance 6 (2025) 243–256."},"day":"10","file_date_updated":"2025-11-24T08:25:19Z","page":"243-256"},{"intvolume":"       121","year":"2024","_id":"18525","date_published":"2024-10-29T00:00:00Z","scopus_import":"1","month":"10","title":"Quantitative omnigenic model discovers interpretable genome-wide associations","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"Yes","article_type":"original","external_id":{"isi":["001349462600001"],"pmid":["39441639"]},"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"OA_type":"hybrid","volume":121,"abstract":[{"text":"As their statistical power grows, genome-wide association studies (GWAS) have identified an increasing number of loci underlying quantitative traits of interest. These loci are scattered throughout the genome and are individually responsible only for small fractions of the total heritable trait variance. The recently proposed omnigenic model provides a conceptual framework to explain these observations by postulating that numerous distant loci contribute to each complex trait via effect propagation through intracellular regulatory networks. We formalize this conceptual framework by proposing the “quantitative omnigenic model” (QOM), a statistical model that combines prior knowledge of the regulatory network topology with genomic data. By applying our model to gene expression traits in yeast, we demonstrate that QOM achieves similar gene expression prediction performance to traditional GWAS with hundreds of times less parameters, while simultaneously extracting candidate causal and quantitative chains of effect propagation through the regulatory network for every individual gene. We estimate the fraction of heritable trait variance in cis- and in trans-, break the latter down by effect propagation order, assess the trans- variance not attributable to transcriptional regulation, and show that QOM correctly accounts for the low-dimensional structure of gene expression covariance. We furthermore demonstrate the relevance of QOM for systems biology, by employing it as a statistical test for the quality of regulatory network reconstructions, and linking it to the propagation of nontranscriptional (including environmental) effects.","lang":"eng"}],"oa_version":"Published Version","project":[{"_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e","name":"Collective behaviour of cells in pancreatic Islets of Langerhans"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018"}],"date_created":"2024-11-10T23:01:59Z","author":[{"first_name":"Natalia","last_name":"Ruzickova","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia"},{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","first_name":"Michal","full_name":"Hledik, Michal"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"date_updated":"2026-04-07T12:02:39Z","day":"29","isi":1,"citation":{"chicago":"Ruzickova, Natalia, Michal Hledik, and Gašper Tkačik. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2402340121\">https://doi.org/10.1073/pnas.2402340121</a>.","ista":"Ruzickova N, Hledik M, Tkačik G. 2024. Quantitative omnigenic model discovers interpretable genome-wide associations. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2402340121.","ama":"Ruzickova N, Hledik M, Tkačik G. Quantitative omnigenic model discovers interpretable genome-wide associations. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(44). doi:<a href=\"https://doi.org/10.1073/pnas.2402340121\">10.1073/pnas.2402340121</a>","apa":"Ruzickova, N., Hledik, M., &#38; Tkačik, G. (2024). Quantitative omnigenic model discovers interpretable genome-wide associations. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2402340121\">https://doi.org/10.1073/pnas.2402340121</a>","mla":"Ruzickova, Natalia, et al. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2402340121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2402340121\">10.1073/pnas.2402340121</a>.","short":"N. Ruzickova, M. Hledik, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ieee":"N. Ruzickova, M. Hledik, and G. Tkačik, “Quantitative omnigenic model discovers interpretable genome-wide associations,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024."},"article_number":"e2402340121","issue":"44","APC_amount":"3062,93 EUR","doi":"10.1073/pnas.2402340121","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"acknowledgement":"N.R.acknowledges the support of the Austrian Academy of Sciences through the Doctoral Fellowship Programme (DOC) of the Austrian Academy of Sciences 26917. M.H. and G.T. were supported in part by the Human Frontiers Science Program Grant RGP0034/2018. We thank Nicholas H. Barton, Fyodor Kondrashov, and Matthew R. Robinson for fruitful discussions.","file_date_updated":"2024-11-11T09:31:00Z","publisher":"National Academy of Sciences","related_material":{"record":[{"id":"20357","status":"public","relation":"dissertation_contains"}]},"OA_place":"publisher","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","ddc":["570"],"publication_status":"published","type":"journal_article","quality_controlled":"1","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"file":[{"file_id":"18536","success":1,"content_type":"application/pdf","file_size":25529709,"date_created":"2024-11-11T09:31:00Z","relation":"main_file","access_level":"open_access","checksum":"d930e2ccf9ec900c7d7509a78cfb3564","creator":"dernst","file_name":"2024_PNAS_Ruzickova.pdf","date_updated":"2024-11-11T09:31:00Z"}],"corr_author":"1"},{"quality_controlled":"1","type":"journal_article","publication_status":"published","file":[{"date_created":"2021-03-22T11:09:34Z","relation":"main_file","checksum":"26d3f2a2c8c8fa8c1002028326b45f64","creator":"dernst","access_level":"open_access","date_updated":"2021-03-22T11:09:34Z","file_name":"2021_NPJQuantumInformation_Pivoluska.pdf","success":1,"file_id":"9274","file_size":1360271,"content_type":"application/pdf"}],"department":[{"_id":"FyKo"}],"has_accepted_license":"1","publisher":"Springer Nature","ddc":["530"],"publication":"npj Quantum Information","file_date_updated":"2021-03-22T11:09:34Z","citation":{"chicago":"Pivoluska, Matej, Martin Plesch, Máté Farkas, Natalia Ruzickova, Clara Flegel, Natalia Herrera Valencia, Will Mccutcheon, Mehul Malik, and Edgar A. Aguilar. “Semi-Device-Independent Random Number Generation with Flexible Assumptions.” <i>Npj Quantum Information</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41534-021-00387-1\">https://doi.org/10.1038/s41534-021-00387-1</a>.","ista":"Pivoluska M, Plesch M, Farkas M, Ruzickova N, Flegel C, Valencia NH, Mccutcheon W, Malik M, Aguilar EA. 2021. Semi-device-independent random number generation with flexible assumptions. npj Quantum Information. 7, 50.","apa":"Pivoluska, M., Plesch, M., Farkas, M., Ruzickova, N., Flegel, C., Valencia, N. H., … Aguilar, E. A. (2021). Semi-device-independent random number generation with flexible assumptions. <i>Npj Quantum Information</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41534-021-00387-1\">https://doi.org/10.1038/s41534-021-00387-1</a>","ama":"Pivoluska M, Plesch M, Farkas M, et al. Semi-device-independent random number generation with flexible assumptions. <i>npj Quantum Information</i>. 2021;7. doi:<a href=\"https://doi.org/10.1038/s41534-021-00387-1\">10.1038/s41534-021-00387-1</a>","mla":"Pivoluska, Matej, et al. “Semi-Device-Independent Random Number Generation with Flexible Assumptions.” <i>Npj Quantum Information</i>, vol. 7, 50, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41534-021-00387-1\">10.1038/s41534-021-00387-1</a>.","short":"M. Pivoluska, M. Plesch, M. Farkas, N. Ruzickova, C. Flegel, N.H. Valencia, W. Mccutcheon, M. Malik, E.A. Aguilar, Npj Quantum Information 7 (2021).","ieee":"M. Pivoluska <i>et al.</i>, “Semi-device-independent random number generation with flexible assumptions,” <i>npj Quantum Information</i>, vol. 7. Springer Nature, 2021."},"isi":1,"day":"15","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We would like to thank Robert Fickler for discussions about the experimental realization and Marek Sýs for running the NIST randomness test on the data we acquired in the experiment. We would like to thank Ugo Zanforlin, Gerald Buller, Daniel White, and Cristian Bonato for their help with the experiment. M. Pivoluska, M. Plesch, and M.M. acknowledge Czech-Austrian project MultiQUEST (I3053-N27 and GF17-33780L). M. Pivoluska and M. Plesch additionally acknowledge the support of VEGA project 2/0136/19. M.F. acknowledges support from the Polish NCN grant Sonata UMO-2014/14/E/ST2/00020, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program ERC AdG CERQUTE (grant agreement No 834266), the State Research Agency (AEI) TRANQI (PID2019-106888GB-I00/10.13039/501100011033), the Government of Spain (FIS2020-TRANQI; Severo Ochoa CEX2019-000910-S), Fundació Cellex, Fundació Mir-Puig, and Generalitat de Catalunya (CERCA, AGAUR). M.M., W.M., N.H.V., and C.F. acknowledge support from the QuantERA ERA-NET Co-fund (FWF Project I3773-N36) and the UK Engineering and Physical Sciences Research Council (EPSRC) (EP/P024114/1).","doi":"10.1038/s41534-021-00387-1","article_number":"50","author":[{"full_name":"Pivoluska, Matej","first_name":"Matej","last_name":"Pivoluska"},{"first_name":"Martin","last_name":"Plesch","full_name":"Plesch, Martin"},{"full_name":"Farkas, Máté","first_name":"Máté","last_name":"Farkas"},{"full_name":"Ruzickova, Natalia","last_name":"Ruzickova","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425"},{"last_name":"Flegel","first_name":"Clara","full_name":"Flegel, Clara"},{"full_name":"Valencia, Natalia Herrera","last_name":"Valencia","first_name":"Natalia Herrera"},{"last_name":"Mccutcheon","first_name":"Will","full_name":"Mccutcheon, Will"},{"first_name":"Mehul","last_name":"Malik","full_name":"Malik, Mehul"},{"last_name":"Aguilar","first_name":"Edgar A.","full_name":"Aguilar, Edgar A."}],"date_created":"2021-03-21T23:01:19Z","date_updated":"2023-08-07T14:17:26Z","publication_identifier":{"eissn":["2056-6387"]},"volume":7,"oa":1,"external_id":{"isi":["000629173100001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","abstract":[{"text":"Our ability to trust that a random number is truly random is essential for fields as diverse as cryptography and fundamental tests of quantum mechanics. Existing solutions both come with drawbacks—device-independent quantum random number generators (QRNGs) are highly impractical and standard semi-device-independent QRNGs are limited to a specific physical implementation and level of trust. Here we propose a framework for semi-device-independent randomness certification, using a source of trusted vacuum in the form of a signal shutter. It employs a flexible set of assumptions and levels of trust, allowing it to be applied in a wide range of physical scenarios involving both quantum and classical entropy sources. We experimentally demonstrate our protocol with a photonic setup and generate secure random bits under three different assumptions with varying degrees of security and resulting data rates.","lang":"eng"}],"status":"public","article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2021","_id":"9255","intvolume":"         7","title":"Semi-device-independent random number generation with flexible assumptions","scopus_import":"1","month":"03","date_published":"2021-03-15T00:00:00Z"},{"external_id":{"isi":["000573519500002"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":17,"abstract":[{"lang":"eng","text":"Collective cell migration offers a rich field of study for non-equilibrium physics and cellular biology, revealing phenomena such as glassy dynamics, pattern formation and active turbulence. However, how mechanical and chemical signalling are integrated at the cellular level to give rise to such collective behaviours remains unclear. We address this by focusing on the highly conserved phenomenon of spatiotemporal waves of density and extracellular signal-regulated kinase (ERK) activation, which appear both in vitro and in vivo during collective cell migration and wound healing. First, we propose a biophysical theory, backed by mechanical and optogenetic perturbation experiments, showing that patterns can be quantitatively explained by a mechanochemical coupling between active cellular tensions and the mechanosensitive ERK pathway. Next, we demonstrate how this biophysical mechanism can robustly induce long-ranged order and migration in a desired orientation, and we determine the theoretically optimal wavelength and period for inducing maximal migration towards free edges, which fits well with experimentally observed dynamics. We thereby provide a bridge between the biophysical origin of spatiotemporal instabilities and the design principles of robust and efficient long-ranged migration."}],"oa_version":"Preprint","project":[{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-10-04T22:01:37Z","author":[{"id":"453AF628-F248-11E8-B48F-1D18A9856A87","last_name":"Boocock","first_name":"Daniel R","full_name":"Boocock, Daniel R","orcid":"0000-0002-1585-2631"},{"full_name":"Hino, Naoya","last_name":"Hino","first_name":"Naoya"},{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","last_name":"Ruzickova","first_name":"Natalia","full_name":"Ruzickova, Natalia"},{"first_name":"Tsuyoshi","last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"}],"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"date_updated":"2026-05-05T22:30:17Z","intvolume":"        17","_id":"8602","year":"2021","date_published":"2021-02-01T00:00:00Z","month":"02","scopus_import":"1","title":"Theory of mechanochemical patterning and optimal migration in cell monolayers","status":"public","ec_funded":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","publisher":"Springer Nature","related_material":{"link":[{"url":"https://ist.ac.at/en/news/wound-healing-waves/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"relation":"dissertation_contains","id":"12964","status":"public"}]},"publication":"Nature Physics","publication_status":"published","type":"journal_article","quality_controlled":"1","department":[{"_id":"EdHa"}],"corr_author":"1","isi":1,"day":"01","main_file_link":[{"url":"https://doi.org/10.1101/2020.05.15.096479","open_access":"1"}],"citation":{"short":"D.R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, E.B. Hannezo, Nature Physics 17 (2021) 267–274.","ieee":"D. R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, and E. B. Hannezo, “Theory of mechanochemical patterning and optimal migration in cell monolayers,” <i>Nature Physics</i>, vol. 17. Springer Nature, pp. 267–274, 2021.","chicago":"Boocock, Daniel R, Naoya Hino, Natalia Ruzickova, Tsuyoshi Hirashima, and Edouard B Hannezo. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” <i>Nature Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41567-020-01037-7\">https://doi.org/10.1038/s41567-020-01037-7</a>.","ista":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. 2021. Theory of mechanochemical patterning and optimal migration in cell monolayers. Nature Physics. 17, 267–274.","apa":"Boocock, D. R., Hino, N., Ruzickova, N., Hirashima, T., &#38; Hannezo, E. B. (2021). Theory of mechanochemical patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-020-01037-7\">https://doi.org/10.1038/s41567-020-01037-7</a>","ama":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. Theory of mechanochemical patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. 2021;17:267-274. doi:<a href=\"https://doi.org/10.1038/s41567-020-01037-7\">10.1038/s41567-020-01037-7</a>","mla":"Boocock, Daniel R., et al. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” <i>Nature Physics</i>, vol. 17, Springer Nature, 2021, pp. 267–74, doi:<a href=\"https://doi.org/10.1038/s41567-020-01037-7\">10.1038/s41567-020-01037-7</a>."},"doi":"10.1038/s41567-020-01037-7","acknowledgement":"We would like to thank G. Tkacik and all of the members of the Hannezo and Hirashima groups for useful discussions, X. Trepat for help on traction force microscopy and M. Matsuda for use of the lab facility. E.H. acknowledges grants from the Austrian Science Fund (FWF) (P 31639) and the European Research Council (851288). T.H. acknowledges a grant from JST, PRESTO (JPMJPR1949). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 665385 (to D.B.), from JSPS KAKENHI grant no. 17J02107 (to N.H.) and from the SPIRITS 2018 of Kyoto University (to E.H. and T.H.).","page":"267-274"},{"scopus_import":"1","month":"02","title":"The IYPT and the 'Ring Oiler' problem","date_published":"2020-02-24T00:00:00Z","_id":"7622","year":"2020","intvolume":"        41","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","arxiv":1,"abstract":[{"lang":"eng","text":"The International Young Physicists' Tournament (IYPT) continued in 2018 in Beijing, China and 2019 in Warsaw, Poland with its 31st and 32nd editions. The IYPT is a modern scientific competition for teams of high school students, also known as the Physics World Cup. It involves long-term theoretical and experimental work focused on solving 17 publicly announced open-ended problems in teams of five. On top of that, teams have to present their solutions in front of other teams and a scientific jury, and get opposed and reviewed by their peers. Here we present a brief information about the competition with a specific focus on one of the IYPT 2018 tasks, the 'Ring Oiler'. This seemingly simple mechanical problem appeared to be of such a complexity that even the dozens of participating teams and jurying scientists were not able to solve all of its subtleties."}],"oa":1,"volume":41,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","external_id":{"arxiv":["1910.03290"],"isi":["000537425400001"]},"date_updated":"2026-04-02T14:22:29Z","publication_identifier":{"eissn":["1361-6404"],"issn":["0143-0807"]},"date_created":"2020-03-31T11:25:04Z","author":[{"last_name":"Plesch","first_name":"Martin","full_name":"Plesch, Martin"},{"last_name":"Plesník","first_name":"Samuel","full_name":"Plesník, Samuel"},{"first_name":"Natalia","last_name":"Ruzickova","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia"}],"doi":"10.1088/1361-6404/ab6414","issue":"3","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"034001","isi":1,"day":"24","citation":{"mla":"Plesch, Martin, et al. “The IYPT and the ‘Ring Oiler’ Problem.” <i>European Journal of Physics</i>, vol. 41, no. 3, 034001, IOP Publishing, 2020, doi:<a href=\"https://doi.org/10.1088/1361-6404/ab6414\">10.1088/1361-6404/ab6414</a>.","apa":"Plesch, M., Plesník, S., &#38; Ruzickova, N. (2020). The IYPT and the “Ring Oiler” problem. <i>European Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6404/ab6414\">https://doi.org/10.1088/1361-6404/ab6414</a>","ama":"Plesch M, Plesník S, Ruzickova N. The IYPT and the “Ring Oiler” problem. <i>European Journal of Physics</i>. 2020;41(3). doi:<a href=\"https://doi.org/10.1088/1361-6404/ab6414\">10.1088/1361-6404/ab6414</a>","ista":"Plesch M, Plesník S, Ruzickova N. 2020. The IYPT and the ‘Ring Oiler’ problem. European Journal of Physics. 41(3), 034001.","chicago":"Plesch, Martin, Samuel Plesník, and Natalia Ruzickova. “The IYPT and the ‘Ring Oiler’ Problem.” <i>European Journal of Physics</i>. IOP Publishing, 2020. <a href=\"https://doi.org/10.1088/1361-6404/ab6414\">https://doi.org/10.1088/1361-6404/ab6414</a>.","ieee":"M. Plesch, S. Plesník, and N. Ruzickova, “The IYPT and the ‘Ring Oiler’ problem,” <i>European Journal of Physics</i>, vol. 41, no. 3. IOP Publishing, 2020.","short":"M. Plesch, S. Plesník, N. Ruzickova, European Journal of Physics 41 (2020)."},"file_date_updated":"2020-07-14T12:48:01Z","publication":"European Journal of Physics","ddc":["530"],"has_accepted_license":"1","publisher":"IOP Publishing","file":[{"file_name":"2020_EuropJourPhysics_Plesch.pdf","date_updated":"2020-07-14T12:48:01Z","access_level":"open_access","creator":"dernst","checksum":"47dda164e33b6c0c6c3ed14aad298376","relation":"main_file","date_created":"2020-04-06T08:53:53Z","file_size":1533672,"content_type":"application/pdf","file_id":"7641"}],"department":[{"_id":"FyKo"}],"quality_controlled":"1","publication_status":"published","type":"journal_article"}]