[{"pmid":1,"date_created":"2023-08-06T22:01:10Z","corr_author":"1","_id":"13965","ddc":["570"],"article_type":"original","author":[{"id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","first_name":"Elizabeth","full_name":"Hollwey, Elizabeth","last_name":"Hollwey"},{"last_name":"Briffa","first_name":"Amy","full_name":"Briffa, Amy"},{"full_name":"Howard, Martin","first_name":"Martin","last_name":"Howard"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman"}],"doi":"10.1016/j.gde.2023.102087","quality_controlled":"1","department":[{"_id":"DaZi"}],"scopus_import":"1","month":"08","publication":"Current Opinion in Genetics & Development","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa_version":"Published Version","volume":81,"date_updated":"2026-08-12T09:55:32Z","oa":1,"has_accepted_license":"1","type":"journal_article","issue":"8","abstract":[{"lang":"eng","text":"Many modes and mechanisms of epigenetic inheritance have been elucidated in eukaryotes. Most of them are relatively short-term, generally not exceeding one or a few organismal generations. However, emerging evidence indicates that one mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much longer timescales, which are mostly or completely inaccessible in the laboratory. Here we discuss the evidence for, and mechanisms and implications of, such long-term epigenetic inheritance. We argue that compelling evidence supports the long-term epigenetic inheritance of gene body methylation, at least in the model angiosperm Arabidopsis thaliana, and that variation in such methylation can therefore serve as an epigenetic basis for phenotypic variation in natural populations."}],"license":"https://creativecommons.org/licenses/by/4.0/","isi":1,"date_published":"2023-08-01T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0959-437X"],"eissn":["1879-0380"]},"external_id":{"isi":["001047020200001"],"pmid":["37441873"]},"article_number":"102087","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"01","file":[{"file_id":"13980","file_size":2568632,"date_updated":"2023-08-07T08:32:26Z","checksum":"a294cd9506b80ed6ef218ef44ed32765","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_name":"2023_CurrentOpinionGenetics_Hollwey.pdf","success":1,"access_level":"open_access","date_created":"2023-08-07T08:32:26Z"}],"title":"Concepts, mechanisms and implications of long-term epigenetic inheritance","file_date_updated":"2023-08-07T08:32:26Z","publisher":"Elsevier","article_processing_charge":"Yes (via OA deal)","intvolume":" 81","citation":{"chicago":"Hollwey, Elizabeth, Amy Briffa, Martin Howard, and Daniel Zilberman. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” Current Opinion in Genetics & Development. Elsevier, 2023. https://doi.org/10.1016/j.gde.2023.102087.","ista":"Hollwey E, Briffa A, Howard M, Zilberman D. 2023. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics & Development. 81(8), 102087.","ama":"Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics & Development. 2023;81(8). doi:10.1016/j.gde.2023.102087","mla":"Hollwey, Elizabeth, et al. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” Current Opinion in Genetics & Development, vol. 81, no. 8, 102087, Elsevier, 2023, doi:10.1016/j.gde.2023.102087.","apa":"Hollwey, E., Briffa, A., Howard, M., & Zilberman, D. (2023). Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2023.102087","ieee":"E. Hollwey, A. Briffa, M. Howard, and D. Zilberman, “Concepts, mechanisms and implications of long-term epigenetic inheritance,” Current Opinion in Genetics & Development, vol. 81, no. 8. Elsevier, 2023.","short":"E. Hollwey, A. Briffa, M. Howard, D. Zilberman, Current Opinion in Genetics & Development 81 (2023)."},"year":"2023"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"date_published":"2023-10-01T00:00:00Z","abstract":[{"lang":"eng","text":"Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging with single-molecule fluorescence correlation spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin, propagates by diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate that extracellular diffusion of the protein from the source is crucial for it to achieve its morphogenic potential."}],"isi":1,"keyword":["Developmental Biology","Molecular Biology"],"citation":{"apa":"Harish, R. K., Gupta, M., Zöller, D., Hartmann, H., Gheisari, A., Machate, A., … Brand, M. (2023). Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.201559","mla":"Harish, Rohit K., et al. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” Development, vol. 150, no. 19, dev201559, Company of Biologists, 2023, doi:10.1242/dev.201559.","ama":"Harish RK, Gupta M, Zöller D, et al. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. 2023;150(19). doi:10.1242/dev.201559","ista":"Harish RK, Gupta M, Zöller D, Hartmann H, Gheisari A, Machate A, Hans S, Brand M. 2023. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. 150(19), dev201559.","chicago":"Harish, Rohit K, Mansi Gupta, Daniela Zöller, Hella Hartmann, Ali Gheisari, Anja Machate, Stefan Hans, and Michael Brand. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” Development. Company of Biologists, 2023. https://doi.org/10.1242/dev.201559.","short":"R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S. Hans, M. Brand, Development 150 (2023).","ieee":"R. K. Harish et al., “Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation,” Development, vol. 150, no. 19. Company of Biologists, 2023."},"year":"2023","publisher":"Company of Biologists","file_date_updated":"2024-01-10T12:41:13Z","article_processing_charge":"Yes (via OA deal)","intvolume":" 150","title":"Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation","file":[{"creator":"dernst","file_id":"14790","date_updated":"2024-01-10T12:41:13Z","checksum":"2d6f52dc33260a9b2352b8f28374ba5f","file_size":12836306,"file_name":"2023_Development_Harish.pdf","content_type":"application/pdf","relation":"main_file","success":1,"access_level":"open_access","date_created":"2024-01-10T12:41:13Z"}],"article_number":"dev201559","external_id":{"pmid":["37665167"],"isi":["001097449100002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"01","doi":"10.1242/dev.201559","quality_controlled":"1","department":[{"_id":"AnKi"}],"_id":"14774","ddc":["570"],"article_type":"original","author":[{"full_name":"Harish, Rohit K","first_name":"Rohit K","id":"1bae78aa-ee0e-11ec-9b76-bc42990f409d","last_name":"Harish"},{"full_name":"Gupta, Mansi","first_name":"Mansi","last_name":"Gupta"},{"full_name":"Zöller, Daniela","first_name":"Daniela","last_name":"Zöller"},{"full_name":"Hartmann, Hella","first_name":"Hella","last_name":"Hartmann"},{"last_name":"Gheisari","full_name":"Gheisari, Ali","first_name":"Ali"},{"last_name":"Machate","full_name":"Machate, Anja","first_name":"Anja"},{"last_name":"Hans","first_name":"Stefan","full_name":"Hans, Stefan"},{"last_name":"Brand","full_name":"Brand, Michael","first_name":"Michael"}],"date_created":"2024-01-10T09:18:54Z","publication_status":"published","acknowledgement":"We thank members of the Brand lab, as well as Justina Stark (Ivo Sbalzarini group, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany) for project-related discussions; Darren Gilmour (University of Zurich), Karuna Sampath (University of Warwick) and Gokul Kesavan (Vowels Lifesciences Private Limited, Bangalore) for comments on the manuscript; personnel of the CMCB technology platform, TU Dresden for imaging and image analysis-related support; and Maurizio Abbate (Technical support, Arivis) for help with image analysis. We are also grateful to Stapornwongkul and Briscoe for commenting on a preprint version of our work (Stapornwongkul and Briscoe, 2022).\r\nThis work was supported by the Deutsche Forschungsgemeinschaft (BR 1746/6-2, BR 1746/11-1 and BR 1746/3 to M.B.), by a Cluster of Excellence ‘Physics of Life’ seed grant and by institutional funds from Technische Universitat Dresden (to M.B.). Open Access funding provided by Technische Universitat Dresden. Deposited in PMC for immediate release.","pmid":1,"oa":1,"type":"journal_article","has_accepted_license":"1","issue":"19","volume":150,"date_updated":"2026-08-12T09:59:59Z","publication":"Development","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","status":"public","month":"10"},{"edition":"2","abstract":[{"lang":"eng","text":"Water Use Efficiency (WUE) expresses the trade-off between carbon assimilation (or subsequent carbon storage) and water release, two concurrent gas fluxes essential for plant functioning. Here, we review metrics that have been introduced to quantify WUE across spatial and temporal scales and corresponding observational methods. The physiological and environmental dependencies of WUE for crops and unmanaged ecosystems are discussed with a quantitative examination of observed and simulated WUE values. A constrained range of WUE across ecosystems and climates is highlighted. However, WUE increased considerably in the past century in response to growing atmospheric CO2 concentration and it will likely continue along the same trajectory in the near future."}],"page":"527-542","date_published":"2023-08-14T00:00:00Z","publication_identifier":{"isbn":["9780323951333"]},"das_tickbox":"1","extern":"1","language":[{"iso":"eng"}],"day":"14","OA_type":"closed access","title":"Water use efficiency: A review of spatial and temporal variability","editor":[{"full_name":"Goss, Michael J.","first_name":"Michael J.","last_name":"Goss"},{"last_name":"Oliver","first_name":"Margaret","full_name":"Oliver, Margaret"}],"intvolume":" 5","publisher":"Elsevier","article_processing_charge":"No","year":"2023","citation":{"short":"S. Fatichi, A. Paschalis, S. Bonetti, G. Manoli, C. Pappas, in:, M.J. Goss, M. Oliver (Eds.), Encyclopedia of Soils in the Environment, 2nd ed., Elsevier, 2023, pp. 527–542.","ieee":"S. Fatichi, A. Paschalis, S. Bonetti, G. Manoli, and C. Pappas, “Water use efficiency: A review of spatial and temporal variability,” in Encyclopedia of Soils in the Environment, 2nd ed., vol. 5, M. J. Goss and M. Oliver, Eds. Elsevier, 2023, pp. 527–542.","ama":"Fatichi S, Paschalis A, Bonetti S, Manoli G, Pappas C. Water use efficiency: A review of spatial and temporal variability. In: Goss MJ, Oliver M, eds. Encyclopedia of Soils in the Environment. Vol 5. 2nd ed. Elsevier; 2023:527-542. doi:10.1016/b978-0-12-822974-3.00166-x","ista":"Fatichi S, Paschalis A, Bonetti S, Manoli G, Pappas C. 2023.Water use efficiency: A review of spatial and temporal variability. In: Encyclopedia of Soils in the Environment. vol. 5, 527–542.","chicago":"Fatichi, Simone, Athanasios Paschalis, Sara Bonetti, Gabriele Manoli, and Christoforos Pappas. “Water Use Efficiency: A Review of Spatial and Temporal Variability.” In Encyclopedia of Soils in the Environment, edited by Michael J. Goss and Margaret Oliver, 2nd ed., 5:527–42. Elsevier, 2023. https://doi.org/10.1016/b978-0-12-822974-3.00166-x.","apa":"Fatichi, S., Paschalis, A., Bonetti, S., Manoli, G., & Pappas, C. (2023). Water use efficiency: A review of spatial and temporal variability. In M. J. Goss & M. Oliver (Eds.), Encyclopedia of Soils in the Environment (2nd ed., Vol. 5, pp. 527–542). Elsevier. https://doi.org/10.1016/b978-0-12-822974-3.00166-x","mla":"Fatichi, Simone, et al. “Water Use Efficiency: A Review of Spatial and Temporal Variability.” Encyclopedia of Soils in the Environment, edited by Michael J. Goss and Margaret Oliver, 2nd ed., vol. 5, Elsevier, 2023, pp. 527–42, doi:10.1016/b978-0-12-822974-3.00166-x."},"publication_status":"published","date_created":"2026-07-27T12:30:24Z","author":[{"last_name":"Fatichi","first_name":"Simone","full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6"},{"last_name":"Paschalis","first_name":"Athanasios","full_name":"Paschalis, Athanasios"},{"full_name":"Bonetti, Sara","first_name":"Sara","last_name":"Bonetti"},{"full_name":"Manoli, Gabriele","first_name":"Gabriele","last_name":"Manoli"},{"last_name":"Pappas","full_name":"Pappas, Christoforos","first_name":"Christoforos"}],"_id":"22530","OA_place":"publisher","scopus_import":"1","quality_controlled":"1","doi":"10.1016/b978-0-12-822974-3.00166-x","month":"08","oa_version":"None","status":"public","publication":"Encyclopedia of Soils in the Environment","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-08-12T11:52:58Z","volume":5,"type":"book_chapter"},{"date_created":"2023-12-10T23:00:58Z","publication_status":"published","acknowledgement":"K.C. acknowledges support from the ERC CoG 863818(ForM-SMArt). J.T. is supported by Center for Foundations ofModern Computer Science (Charles Univ. project UNCE/SCI/004).","pmid":1,"quality_controlled":"1","doi":"10.1098/rsif.2023.0355","department":[{"_id":"KrCh"}],"scopus_import":"1","_id":"14657","ddc":["000","570"],"article_type":"original","author":[{"last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kaveh","first_name":"Kamran","full_name":"Kaveh, Kamran"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Nowak","full_name":"Nowak, Martin A.","first_name":"Martin A."}],"publication":"Journal of the Royal Society Interface","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","status":"public","month":"11","oa":1,"ec_funded":1,"has_accepted_license":"1","type":"journal_article","issue":"208","volume":20,"date_updated":"2026-08-12T14:05:25Z","abstract":[{"text":"Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring on a different graph than the resident wild-type. We find that more densely connected dispersal graphs tend to increase the invader’s fixation probability, but the exact relationship between structure and fixation probability is subtle. We present three main results. First, we prove that if both invader and resident are on complete dispersal graphs, then removing a single edge in the invader’s dispersal graph reduces its fixation probability. Second, we show that for certain island models higher invader’s connectivity increases its fixation probability, but the magnitude of the effect depends on the exact layout of the connections. Third, we show that for lattices the effect of different connectivity is comparable to that of different fitness: for large population size, the invader’s fixation probability is either constant or exponentially small, depending on whether it is more or less connected than the resident.","lang":"eng"}],"isi":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1742-5662"]},"date_published":"2023-11-29T00:00:00Z","title":"Evolutionary dynamics of mutants that modify population structure","file":[{"success":1,"access_level":"open_access","date_created":"2023-12-11T11:10:32Z","file_id":"14673","date_updated":"2023-12-11T11:10:32Z","checksum":"2eefab13127c7786dbd33303c482a004","file_size":1720243,"creator":"dernst","relation":"main_file","file_name":"2023_RoyalInterface_Tkadlec.pdf","content_type":"application/pdf"}],"article_number":"20230355","external_id":{"pmid":["38016637"],"isi":["001124419300002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"29","citation":{"short":"J. Tkadlec, K. Kaveh, K. Chatterjee, M.A. Nowak, Journal of the Royal Society Interface 20 (2023).","ieee":"J. Tkadlec, K. Kaveh, K. Chatterjee, and M. A. Nowak, “Evolutionary dynamics of mutants that modify population structure,” Journal of the Royal Society Interface, vol. 20, no. 208. Royal Society, 2023.","apa":"Tkadlec, J., Kaveh, K., Chatterjee, K., & Nowak, M. A. (2023). Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society Interface. Royal Society. https://doi.org/10.1098/rsif.2023.0355","mla":"Tkadlec, Josef, et al. “Evolutionary Dynamics of Mutants That Modify Population Structure.” Journal of the Royal Society Interface, vol. 20, no. 208, 20230355, Royal Society, 2023, doi:10.1098/rsif.2023.0355.","ama":"Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society Interface. 2023;20(208). doi:10.1098/rsif.2023.0355","ista":"Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. 2023. Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society Interface. 20(208), 20230355.","chicago":"Tkadlec, Josef, Kamran Kaveh, Krishnendu Chatterjee, and Martin A. Nowak. “Evolutionary Dynamics of Mutants That Modify Population Structure.” Journal of the Royal Society Interface. Royal Society, 2023. https://doi.org/10.1098/rsif.2023.0355."},"year":"2023","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"file_date_updated":"2023-12-11T11:10:32Z","publisher":"Royal Society","article_processing_charge":"Yes (in subscription journal)","intvolume":" 20"},{"publication_identifier":{"isbn":["9781713899921"],"eissn":["1049-5258"]},"language":[{"iso":"eng"}],"das_tickbox":"0","page":"3325-3337","date_published":"2023-10-27T00:00:00Z","abstract":[{"lang":"eng","text":"This paper provides statistical sample complexity bounds for score-matching and\r\nits applications in causal discovery. We demonstrate that accurate estimation of the\r\nscore function is achievable by training a standard deep ReLU neural network using\r\nstochastic gradient descent. We establish bounds on the error rate of recovering\r\ncausal relationships using the score-matching-based causal discovery method of\r\nRolland et al. [2022], assuming a sufficiently good estimation of the score function.\r\nFinally, we analyze the upper bound of score-matching estimation within the scorebased generative modeling, which has been applied for causal discovery but is also\r\nof independent interest within the domain of generative models.y"}],"year":"2023","citation":{"mla":"Zhu, Zhenyu, et al. “Sample Complexity Bounds for Score-Matching: Causal Discovery and Generative Modeling.” 37th Conference on Neural Information Processing Systems, vol. 36, Neural Information Processing Systems Foundation, 2023, pp. 3325–37, doi:10.52202/075280-0147.","apa":"Zhu, Z., Locatello, F., & Cevher, V. (2023). Sample complexity bounds for score-matching: Causal discovery and generative modeling. In 37th Conference on Neural Information Processing Systems (Vol. 36, pp. 3325–3337). New Orleans, LO, United States: Neural Information Processing Systems Foundation. https://doi.org/10.52202/075280-0147","chicago":"Zhu, Zhenyu, Francesco Locatello, and Volkan Cevher. “Sample Complexity Bounds for Score-Matching: Causal Discovery and Generative Modeling.” In 37th Conference on Neural Information Processing Systems, 36:3325–37. Neural Information Processing Systems Foundation, 2023. https://doi.org/10.52202/075280-0147.","ama":"Zhu Z, Locatello F, Cevher V. Sample complexity bounds for score-matching: Causal discovery and generative modeling. In: 37th Conference on Neural Information Processing Systems. Vol 36. Neural Information Processing Systems Foundation; 2023:3325-3337. doi:10.52202/075280-0147","ista":"Zhu Z, Locatello F, Cevher V. 2023. Sample complexity bounds for score-matching: Causal discovery and generative modeling. 37th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 36, 3325–3337.","short":"Z. Zhu, F. Locatello, V. Cevher, in:, 37th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2023, pp. 3325–3337.","ieee":"Z. Zhu, F. Locatello, and V. Cevher, “Sample complexity bounds for score-matching: Causal discovery and generative modeling,” in 37th Conference on Neural Information Processing Systems, New Orleans, LO, United States, 2023, vol. 36, pp. 3325–3337."},"intvolume":" 36","article_processing_charge":"No","file_date_updated":"2026-08-13T07:02:51Z","publisher":"Neural Information Processing Systems Foundation","supplementarymaterial":"yes","title":"Sample complexity bounds for score-matching: Causal discovery and generative modeling","OA_type":"gold","file":[{"relation":"main_file","content_type":"application/pdf","file_name":"2023_Neurips_Zhu.pdf","checksum":"6f10adadefceb3bb50ad0b2637493381","date_updated":"2026-08-13T07:02:51Z","file_size":305362,"file_id":"22700","creator":"dernst","date_created":"2026-08-13T07:02:51Z","access_level":"open_access","success":1}],"day":"27","external_id":{"arxiv":["2310.18123"]},"scopus_import":"1","OA_place":"publisher","arxiv":1,"department":[{"_id":"FrLo"}],"quality_controlled":"1","doi":"10.52202/075280-0147","author":[{"last_name":"Zhu","first_name":"Zhenyu","full_name":"Zhu, Zhenyu"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello"},{"last_name":"Cevher","first_name":"Volkan","full_name":"Cevher, Volkan"}],"ddc":["000"],"corr_author":"1","_id":"14953","date_created":"2024-02-07T15:11:11Z","conference":{"end_date":"2023-12-16","name":"NeurIPS: Neural Information Processing Systems","start_date":"2023-12-12","location":"New Orleans, LO, United States"},"acknowledgement":"We are thankful to the reviewers for providing constructive feedback and Kun Zhang and Dominik\r\nJanzing for helpful discussion on the special case of deterministic children. This work was supported\r\nby Hasler Foundation Program: Hasler Responsible AI (project number 21043). This work was\r\nsupported by the Swiss National Science Foundation (SNSF) under grant number 200021_205011.\r\nFrancesco Locatello did not contribute to this work at Amazon. ","publication_status":"published","alternative_title":["Advances in Neural Information Processing Systems"],"type":"conference","has_accepted_license":"1","oa":1,"date_updated":"2026-08-13T07:09:06Z","volume":36,"status":"public","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","researchdata_availability":"no","publication":"37th Conference on Neural Information Processing Systems","month":"10"},{"date_published":"2023-12-20T00:00:00Z","das_tickbox":"0","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1049-5258"]},"abstract":[{"text":"When domain knowledge is limited and experimentation is restricted by ethical,\r\nfinancial, or time constraints, practitioners turn to observational causal discovery\r\nmethods to recover the causal structure, exploiting the statistical properties of their\r\ndata. Because causal discovery without further assumptions is an ill-posed problem,\r\neach algorithm comes with its own set of usually untestable assumptions, some\r\nof which are hard to meet in real datasets. Motivated by these considerations, this\r\npaper extensively benchmarks the empirical performance of recent causal discovery\r\nmethods on observational iid data generated under different background conditions,\r\nallowing for violations of the critical assumptions required by each selected approach. Our experimental findings show that score matching-based methods demonstrate surprising performance in the false positive and false negative rate of the\r\ninferred graph in these challenging scenarios, and we provide theoretical insights\r\ninto their performance. This work is also the first effort to benchmark the stability of\r\ncausal discovery algorithms with respect to the values of their hyperparameters. Finally, we hope this paper will set a new standard for the evaluation of causal discovery methods and can serve as an accessible entry point for practitioners interested\r\nin the field, highlighting the empirical implications of different algorithm choices.","lang":"eng"}],"file_date_updated":"2026-08-13T07:49:38Z","supplementarymaterial":"yes","publisher":"Neural Information Processing Systems Foundation","article_processing_charge":"No","intvolume":" 36","citation":{"ama":"Montagna F, Mastakouri AA, Eulig E, et al. Assumption violations in causal discovery and the robustness of score matching. In: 37th Conference on Neural Information Processing Systems. Vol 36. Neural Information Processing Systems Foundation; 2023. doi:10.52202/075280-2050","ista":"Montagna F, Mastakouri AA, Eulig E, Noceti N, Rosasco L, Janzing D, Aragam B, Locatello F. 2023. Assumption violations in causal discovery and the robustness of score matching. 37th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 36.","chicago":"Montagna, Francesco, Atalanti A. Mastakouri, Elias Eulig, Nicoletta Noceti, Lorenzo Rosasco, Dominik Janzing, Bryon Aragam, and Francesco Locatello. “Assumption Violations in Causal Discovery and the Robustness of Score Matching.” In 37th Conference on Neural Information Processing Systems, Vol. 36. Neural Information Processing Systems Foundation, 2023. https://doi.org/10.52202/075280-2050.","apa":"Montagna, F., Mastakouri, A. A., Eulig, E., Noceti, N., Rosasco, L., Janzing, D., … Locatello, F. (2023). Assumption violations in causal discovery and the robustness of score matching. In 37th Conference on Neural Information Processing Systems (Vol. 36). New Orleans, LO, United States: Neural Information Processing Systems Foundation. https://doi.org/10.52202/075280-2050","mla":"Montagna, Francesco, et al. “Assumption Violations in Causal Discovery and the Robustness of Score Matching.” 37th Conference on Neural Information Processing Systems, vol. 36, Neural Information Processing Systems Foundation, 2023, doi:10.52202/075280-2050.","ieee":"F. Montagna et al., “Assumption violations in causal discovery and the robustness of score matching,” in 37th Conference on Neural Information Processing Systems, New Orleans, LO, United States, 2023, vol. 36.","short":"F. Montagna, A.A. Mastakouri, E. Eulig, N. Noceti, L. Rosasco, D. Janzing, B. Aragam, F. Locatello, in:, 37th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2023."},"year":"2023","external_id":{"arxiv":["2310.13387"]},"day":"20","OA_type":"gold","title":"Assumption violations in causal discovery and the robustness of score matching","file":[{"success":1,"access_level":"open_access","date_created":"2026-08-13T07:49:38Z","file_id":"22701","file_size":7640984,"checksum":"71d38402b4edef4c084b39f3e2f04526","date_updated":"2026-08-13T07:49:38Z","creator":"dernst","relation":"main_file","file_name":"2023_Neurips_Montagna.pdf","content_type":"application/pdf"}],"_id":"14954","ddc":["000"],"author":[{"full_name":"Montagna, Francesco","first_name":"Francesco","last_name":"Montagna"},{"last_name":"Mastakouri","full_name":"Mastakouri, Atalanti A.","first_name":"Atalanti A."},{"last_name":"Eulig","first_name":"Elias","full_name":"Eulig, Elias"},{"full_name":"Noceti, Nicoletta","first_name":"Nicoletta","last_name":"Noceti"},{"last_name":"Rosasco","first_name":"Lorenzo","full_name":"Rosasco, Lorenzo"},{"first_name":"Dominik","full_name":"Janzing, Dominik","last_name":"Janzing"},{"first_name":"Bryon","full_name":"Aragam, Bryon","last_name":"Aragam"},{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"}],"doi":"10.52202/075280-2050","quality_controlled":"1","arxiv":1,"OA_place":"publisher","department":[{"_id":"FrLo"}],"alternative_title":["Advances in Neural Information Processing Systems"],"acknowledgement":"We thank Kun Zhang and Carl-Johann Simon-Gabriel for the insightful discussions. This work\r\nhas been supported by AFOSR, grant n. FA8655-20-1-7035. FM is supported by Programma\r\nOperativo Nazionale ricerca e innovazione 2014-2020. FM partially contributed to this work during an internship at Amazon Web Services with FL. FL partially contributed while at AWS.","publication_status":"published","conference":{"location":"New Orleans, LO, United States","start_date":"2023-12-12","end_date":"2023-12-16","name":"NeurIPS: Neural Information Processing Systems"},"date_created":"2024-02-07T15:11:56Z","volume":36,"date_updated":"2026-08-13T07:51:13Z","oa":1,"has_accepted_license":"1","type":"conference","month":"12","publication":"37th Conference on Neural Information Processing Systems","researchdata_availability":"no","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa_version":"Published Version"},{"issue":"10","oa":1,"type":"journal_article","date_updated":"2025-04-14T09:10:17Z","volume":82,"oa_version":"Published Version","status":"public","publication":"Current Opinion in Structural Biology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","department":[{"_id":"PaSc"}],"scopus_import":"1","quality_controlled":"1","doi":"10.1016/j.sbi.2023.102660","author":[{"last_name":"Napoli","orcid":"0000-0002-9043-136X","first_name":"Federico","full_name":"Napoli, Federico","id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b"},{"full_name":"Becker, Lea Marie","orcid":"0000-0002-6401-5151","first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","last_name":"Becker"},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","first_name":"Paul","orcid":"0000-0002-9350-7606"}],"corr_author":"1","_id":"14036","article_type":"original","ddc":["570"],"date_created":"2023-08-13T22:01:11Z","pmid":1,"acknowledgement":"We thank Petra Rovó for critical reading of this manuscript. We acknowledge the Austrian Science Foundation FWF (project AlloSpace, number I5812–B) and funding by the Institute of Science and Technology Austria.","publication_status":"published","year":"2023","citation":{"short":"F. Napoli, L.M. Becker, P. Schanda, Current Opinion in Structural Biology 82 (2023).","ieee":"F. Napoli, L. M. Becker, and P. Schanda, “Protein dynamics detected by magic-angle spinning relaxation dispersion NMR,” Current Opinion in Structural Biology, vol. 82, no. 10. Elsevier, 2023.","mla":"Napoli, Federico, et al. “Protein Dynamics Detected by Magic-Angle Spinning Relaxation Dispersion NMR.” Current Opinion in Structural Biology, vol. 82, no. 10, 102660, Elsevier, 2023, doi:10.1016/j.sbi.2023.102660.","apa":"Napoli, F., Becker, L. M., & Schanda, P. (2023). Protein dynamics detected by magic-angle spinning relaxation dispersion NMR. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2023.102660","chicago":"Napoli, Federico, Lea Marie Becker, and Paul Schanda. “Protein Dynamics Detected by Magic-Angle Spinning Relaxation Dispersion NMR.” Current Opinion in Structural Biology. Elsevier, 2023. https://doi.org/10.1016/j.sbi.2023.102660.","ama":"Napoli F, Becker LM, Schanda P. Protein dynamics detected by magic-angle spinning relaxation dispersion NMR. Current Opinion in Structural Biology. 2023;82(10). doi:10.1016/j.sbi.2023.102660","ista":"Napoli F, Becker LM, Schanda P. 2023. Protein dynamics detected by magic-angle spinning relaxation dispersion NMR. Current Opinion in Structural Biology. 82(10), 102660."},"intvolume":" 82","file_date_updated":"2024-01-30T12:36:39Z","project":[{"grant_number":"I05812","name":"AlloSpace. The emergence and mechanisms of allostery","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf"}],"publisher":"Elsevier","article_processing_charge":"Yes (via OA deal)","title":"Protein dynamics detected by magic-angle spinning relaxation dispersion NMR","file":[{"file_size":1231998,"date_updated":"2024-01-30T12:36:39Z","checksum":"c850f7ac8a4234319755b672c1df69ae","file_id":"14907","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_name":"2023_CurrentOpinionStrucBio_Napoli.pdf","success":1,"date_created":"2024-01-30T12:36:39Z","access_level":"open_access"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"01","article_number":"102660","external_id":{"isi":["001053616200001"],"pmid":["37536064"]},"publication_identifier":{"eissn":["1879-033X"],"issn":["0959-440X"]},"language":[{"iso":"eng"}],"date_published":"2023-10-01T00:00:00Z","isi":1,"abstract":[{"text":"Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing itself as a powerful method for the characterization of protein dynamics at the atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling, and pulse sequence design has paved the way for quantitative analyses of even rare structural fluctuations. In addition to isotropic chemical-shift fluctuations exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has a wider arsenal of observables, allowing to see motions even if the exchanging states do not differ in their chemical shifts. We demonstrate the potential of the technique for probing motions in challenging large enzymes, membrane proteins, and protein assemblies.","lang":"eng"}]},{"date_published":"2023-08-01T00:00:00Z","publication_identifier":{"eissn":["1422-6952"],"issn":["1422-6928"]},"language":[{"iso":"eng"}],"isi":1,"abstract":[{"lang":"eng","text":"Long-time and large-data existence of weak solutions for initial- and boundary-value problems concerning three-dimensional flows of incompressible fluids is nowadays available not only for Navier–Stokes fluids but also for various fluid models where the relation between the Cauchy stress tensor and the symmetric part of the velocity gradient is nonlinear. The majority of such studies however concerns models where such a dependence is explicit (the stress is a function of the velocity gradient), which makes the class of studied models unduly restrictive. The same concerns boundary conditions, or more precisely the slipping mechanisms on the boundary, where the no-slip is still the most preferred condition considered in the literature. Our main objective is to develop a robust mathematical theory for unsteady internal flows of implicitly constituted incompressible fluids with implicit relations between the tangential projections of the velocity and the normal traction on the boundary. The theory covers numerous rheological models used in chemistry, biorheology, polymer and food industry as well as in geomechanics. It also includes, as special cases, nonlinear slip as well as stick–slip boundary conditions. Unlike earlier studies, the conditions characterizing admissible classes of constitutive equations are expressed by means of tools of elementary calculus. In addition, a fully constructive proof (approximation scheme) is incorporated. Finally, we focus on the question of uniqueness of such weak solutions."}],"intvolume":" 25","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2023-08-14T07:24:17Z","publisher":"Springer Nature","year":"2023","citation":{"apa":"Bulíček, M., Málek, J., & Maringová, E. (2023). On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. Springer Nature. https://doi.org/10.1007/s00021-023-00803-w","mla":"Bulíček, Miroslav, et al. “On Unsteady Internal Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.” Journal of Mathematical Fluid Mechanics, vol. 25, no. 3, 72, Springer Nature, 2023, doi:10.1007/s00021-023-00803-w.","ama":"Bulíček M, Málek J, Maringová E. On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. 2023;25(3). doi:10.1007/s00021-023-00803-w","ista":"Bulíček M, Málek J, Maringová E. 2023. On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. 25(3), 72.","chicago":"Bulíček, Miroslav, Josef Málek, and Erika Maringová. “On Unsteady Internal Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.” Journal of Mathematical Fluid Mechanics. Springer Nature, 2023. https://doi.org/10.1007/s00021-023-00803-w.","ieee":"M. Bulíček, J. Málek, and E. Maringová, “On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary,” Journal of Mathematical Fluid Mechanics, vol. 25, no. 3. Springer Nature, 2023.","short":"M. Bulíček, J. Málek, E. Maringová, Journal of Mathematical Fluid Mechanics 25 (2023)."},"day":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"article_number":"72","external_id":{"isi":["001040354900001"],"arxiv":["2301.12834"]},"file":[{"date_updated":"2023-08-14T07:24:17Z","checksum":"c549cd8f0dd02ed60477a05ca045f481","file_size":845748,"file_id":"14046","creator":"dernst","relation":"main_file","file_name":"2023_JourMathFluidMech_Bulicek.pdf","content_type":"application/pdf","success":1,"date_created":"2023-08-14T07:24:17Z","access_level":"open_access"}],"title":"On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary","author":[{"first_name":"Miroslav","full_name":"Bulíček, Miroslav","last_name":"Bulíček"},{"last_name":"Málek","first_name":"Josef","full_name":"Málek, Josef"},{"full_name":"Maringová, Erika","first_name":"Erika","id":"dbabca31-66eb-11eb-963a-fb9c22c880b4","last_name":"Maringová"}],"article_type":"original","ddc":["510"],"_id":"14042","scopus_import":"1","arxiv":1,"department":[{"_id":"JuFi"}],"quality_controlled":"1","doi":"10.1007/s00021-023-00803-w","acknowledgement":"M. Bulíček and J. Málek acknowledge the support of the project No. 20-11027X financed by the Czech Science foundation (GAČR). M. Bulíček and J. Málek are members of the Nečas Center for Mathematical Modelling.\r\nOpen access publishing supported by the National Technical Library in Prague.","publication_status":"published","date_created":"2023-08-13T22:01:13Z","date_updated":"2026-08-18T07:47:38Z","volume":25,"issue":"3","type":"journal_article","has_accepted_license":"1","oa":1,"month":"08","status":"public","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Mathematical Fluid Mechanics"},{"status":"public","oa_version":"Preprint","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"21st International Conference on Theory of Cryptography","month":"11","type":"conference","oa":1,"date_updated":"2026-08-21T10:53:16Z","volume":14371,"date_created":"2023-12-17T23:00:53Z","conference":{"location":"Taipei, Taiwan","start_date":"2023-11-29","name":"TCC: Theory of Cryptography","end_date":"2023-12-02"},"publication_status":"published","alternative_title":["LNCS"],"scopus_import":"1","department":[{"_id":"KrPi"}],"doi":"10.1007/978-3-031-48621-0_10","quality_controlled":"1","author":[{"last_name":"Auerbach","first_name":"Benedikt","orcid":"0000-0002-7553-6606","full_name":"Auerbach, Benedikt","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425"},{"last_name":"Cueto Noval","full_name":"Cueto Noval, Miguel","orcid":"0000-0002-2505-4246","first_name":"Miguel","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc"},{"id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8630-415X","first_name":"Guillermo","full_name":"Pascual Perez, Guillermo","last_name":"Pascual Perez"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"22664","status":"public","relation":"dissertation_contains"}]},"_id":"14691","corr_author":"1","title":"On the cost of post-compromise security in concurrent Continuous Group-Key Agreement","day":"27","external_id":{"isi":["001160724400010"]},"year":"2023","citation":{"ista":"Auerbach B, Cueto Noval M, Pascual Perez G, Pietrzak KZ. 2023. On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. 21st International Conference on Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 14371, 271–300.","ama":"Auerbach B, Cueto Noval M, Pascual Perez G, Pietrzak KZ. On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. In: 21st International Conference on Theory of Cryptography. Vol 14371. Springer Nature; 2023:271-300. doi:10.1007/978-3-031-48621-0_10","chicago":"Auerbach, Benedikt, Miguel Cueto Noval, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “On the Cost of Post-Compromise Security in Concurrent Continuous Group-Key Agreement.” In 21st International Conference on Theory of Cryptography, 14371:271–300. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48621-0_10.","apa":"Auerbach, B., Cueto Noval, M., Pascual Perez, G., & Pietrzak, K. Z. (2023). On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. In 21st International Conference on Theory of Cryptography (Vol. 14371, pp. 271–300). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-031-48621-0_10","mla":"Auerbach, Benedikt, et al. “On the Cost of Post-Compromise Security in Concurrent Continuous Group-Key Agreement.” 21st International Conference on Theory of Cryptography, vol. 14371, Springer Nature, 2023, pp. 271–300, doi:10.1007/978-3-031-48621-0_10.","ieee":"B. Auerbach, M. Cueto Noval, G. Pascual Perez, and K. Z. Pietrzak, “On the cost of post-compromise security in concurrent Continuous Group-Key Agreement,” in 21st International Conference on Theory of Cryptography, Taipei, Taiwan, 2023, vol. 14371, pp. 271–300.","short":"B. Auerbach, M. Cueto Noval, G. Pascual Perez, K.Z. Pietrzak, in:, 21st International Conference on Theory of Cryptography, Springer Nature, 2023, pp. 271–300."},"intvolume":" 14371","main_file_link":[{"url":"https://eprint.iacr.org/2023/1123","open_access":"1"}],"article_processing_charge":"No","publisher":"Springer Nature","isi":1,"abstract":[{"lang":"eng","text":"Continuous Group-Key Agreement (CGKA) allows a group of users to maintain a shared key. It is the fundamental cryptographic primitive underlying group messaging schemes and related protocols, most notably TreeKEM, the underlying key agreement protocol of the Messaging Layer Security (MLS) protocol, a standard for group messaging by the IETF. CKGA works in an asynchronous setting where parties only occasionally must come online, and their messages are relayed by an untrusted server. The most expensive operation provided by CKGA is that which allows for a user to refresh their key material in order to achieve forward secrecy (old messages are secure when a user is compromised) and post-compromise security (users can heal from compromise). One caveat of early CGKA protocols is that these update operations had to be performed sequentially, with any user wanting to update their key material having had to receive and process all previous updates. Late versions of TreeKEM do allow for concurrent updates at the cost of a communication overhead per update message that is linear in the number of updating parties. This was shown to be indeed necessary when achieving PCS in just two rounds of communication by [Bienstock et al. TCC’20].\r\nThe recently proposed protocol CoCoA [Alwen et al. Eurocrypt’22], however, shows that this overhead can be reduced if PCS requirements are relaxed, and only a logarithmic number of rounds is required. The natural question, thus, is whether CoCoA is optimal in this setting.\r\nIn this work we answer this question, providing a lower bound on the cost (concretely, the amount of data to be uploaded to the server) for CGKA protocols that heal in an arbitrary k number of rounds, that shows that CoCoA is very close to optimal. Additionally, we extend CoCoA to heal in an arbitrary number of rounds, and propose a modification of it, with a reduced communication cost for certain k.\r\nWe prove our bound in a combinatorial setting where the state of the protocol progresses in rounds, and the state of the protocol in each round is captured by a set system, each set specifying a set of users who share a secret key. We show this combinatorial model is equivalent to a symbolic model capturing building blocks including PRFs and public-key encryption, related to the one used by Bienstock et al.\r\nOur lower bound is of order k•n1+1/(k-1)/log(k), where 2≤k≤log(n) is the number of updates per user the protocol requires to heal. This generalizes the n2 bound for k=2 from Bienstock et al.. This bound almost matches the k⋅n1+2/(k-1) or k2⋅n1+1/(k-1) efficiency we get for the variants of the CoCoA protocol also introduced in this paper."}],"publication_identifier":{"issn":["0302-9743"],"isbn":["9783031486203"],"eissn":["1611-3349"]},"language":[{"iso":"eng"}],"page":"271-300","date_published":"2023-11-27T00:00:00Z"},{"month":"02","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","oa_version":"Published Version","date_updated":"2026-04-07T13:49:23Z","type":"dissertation","has_accepted_license":"1","oa":1,"publication_status":"published","alternative_title":["ISTA Thesis"],"date_created":"2023-02-02T14:50:20Z","ddc":["570"],"corr_author":"1","_id":"12491","author":[{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","orcid":"0000-0002-9561-1239","full_name":"Zens, Bettina","last_name":"Zens"}],"supervisor":[{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8586"}]},"doi":"10.15479/at:ista:12491","degree_awarded":"PhD","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"day":"02","file":[{"date_created":"2023-02-07T13:07:38Z","access_level":"open_access","relation":"main_file","embargo":"2024-02-07","file_name":"PhDThesis_BettinaZens_2023_final.pdf","content_type":"application/pdf","checksum":"069d87f025e0799bf9e3c375664264f2","file_size":23082464,"date_updated":"2024-02-08T23:30:04Z","file_id":"12527","creator":"bzens"},{"access_level":"closed","date_created":"2023-02-07T13:09:05Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhDThesis_BettinaZens_2023_final.docx","relation":"source_file","creator":"bzens","embargo_to":"open_access","file_id":"12528","file_size":106169509,"checksum":"8c66ed203495d6e078ed1002a866520c","date_updated":"2024-02-08T23:30:04Z"}],"title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","article_processing_charge":"No","project":[{"name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions","_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÃ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-02-08T23:30:04Z","citation":{"apa":"Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491","mla":"Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491.","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023."},"year":"2023","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions."}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"date_published":"2023-02-02T00:00:00Z","page":"187","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-027-5"]}},{"abstract":[{"text":"Social insects fight disease using their individual immune systems and the cooperative\r\nsanitary behaviors of colony members. These social defenses are well explored against\r\nexternally-infecting pathogens, but little is known about defense strategies against\r\ninternally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades\r\nit has become evident that also many ant species harbor viruses. We present one of the first\r\nstudies addressing transmission dynamics and collective disease defenses against viruses in\r\nants on a mechanistic level. I successfully established an experimental ant host – viral\r\npathogen system as a model for the defense strategies used by social insects against internal\r\npathogen infections, as outlined in the third chapter. In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’\r\nhemolymph because it allowed us to use a defined exposure dose. Here we show that this is a\r\ngood model system, as the virus is replicating and thus infecting the host. The ants mount a\r\nclear individual immune response against the viral infection, which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this immune response is consistent with the timeline\r\nof viral replication that starts already within two days post injection. The disease manifests in\r\ndecreased survival over a course of two to three weeks.\r\nRegarding group living, we find that infected ants show a strong individual immune response,\r\nbut that their course of disease is little affected by nestmate presence, as described in chapter\r\nfour. Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed that 94 % of the nestmates contract active virus within four days of social contact to\r\nan infected individual. Virus is transmitted in low doses, thus not causing disease\r\ntransmission within the colony. While virus can be transmitted during short direct contacts,\r\nwe also assume transmission from deceased ants and show that the nestmates’ immune\r\nsystem gets activated after contracting a low viral dose. We find considerable potential for\r\nindirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one\r\nweek and is also picked up by other ants. Apart from that, we want to underline the potential\r\nof ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize the nest space.\r\nOn the other hand, local application of ant poison by oral poison uptake, which is part of the\r\nants prophylactic behavioral repertoire, probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize that oral poison uptake might be the reason why we did\r\nnot find viable virus in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data on potential social immunization. However,\r\nour experiments do not confirm an actual survival benefit for the nestmates upon pathogen\r\nchallenge under the given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility for nestmate immunization, but rather emphasize that considering different\r\nexperimental timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,\r\nmight play a role in preventing viral disease transmission. Compared to colony defense\r\nagainst external pathogens, internal pathogen infections require a stronger component of\r\nindividual physiological immunity than behavioral social immunity, yet could still lead to\r\ncollective protection.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"date_published":"2023-08-08T00:00:00Z","page":"89","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-034-3"]},"day":"08","title":"Individual and social immunity against viral infections in ants","file":[{"title":"Combined Version of original Thesis and Addendum","date_created":"2024-03-01T08:56:06Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"Print_Version_Franschitz_Anna_Thesis.pdf","date_updated":"2024-10-29T23:31:04Z","checksum":"55c876b73d49db15228a7f571592ec77","file_size":10416761,"file_id":"15044","embargo_to":"open_access","creator":"cchlebak"},{"relation":"main_file","file_name":"Thesis_AnnaFranschitz_202308.pdf","content_type":"application/pdf","embargo":"2024-08-08","date_updated":"2024-08-09T22:30:03Z","checksum":"27220243d5d51c3b0d7d61c0879d7a0c","file_size":10797612,"file_id":"13986","creator":"afransch","date_created":"2023-08-08T18:01:28Z","access_level":"open_access"},{"file_size":2619085,"date_updated":"2024-08-09T22:30:03Z","checksum":"40abf7ccca14a3893f72dc7fb88585d6","embargo_to":"open_access","file_id":"13987","creator":"afransch","relation":"source_file","file_name":"Thesis_AnnaFranschitz_202308.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2023-08-08T18:02:25Z","access_level":"closed"},{"access_level":"open_access","title":"Addendum","date_created":"2024-03-01T08:37:15Z","description":"Minor modifications and clarifications - Feb 2024","relation":"main_file","embargo":"2024-08-08","file_name":"Addendum_AnnaFranschitz202402.pdf","content_type":"application/pdf","file_id":"15042","checksum":"8b991ecc2d59d045cc3cf0d676785ec7","file_size":85956,"date_updated":"2024-10-29T23:31:04Z","creator":"cchlebak"},{"file_name":"Addendum_AnnaFranschitz202402.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","creator":"cchlebak","file_size":11818,"date_updated":"2024-08-09T22:30:03Z","checksum":"66745aa01f960f17472c024875c049ed","embargo_to":"open_access","file_id":"15043","title":"Addendum - source file","date_created":"2024-03-01T08:39:20Z","access_level":"closed"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-10-29T23:31:04Z","citation":{"mla":"Franschitz, Anna. Individual and Social Immunity against Viral Infections in Ants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13984.","apa":"Franschitz, A. (2023). Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13984","chicago":"Franschitz, Anna. “Individual and Social Immunity against Viral Infections in Ants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13984.","ista":"Franschitz A. 2023. Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria.","ama":"Franschitz A. Individual and social immunity against viral infections in ants. 2023. doi:10.15479/at:ista:13984","short":"A. Franschitz, Individual and Social Immunity against Viral Infections in Ants, Institute of Science and Technology Austria, 2023.","ieee":"A. Franschitz, “Individual and social immunity against viral infections in ants,” Institute of Science and Technology Austria, 2023."},"year":"2023","publication_status":"published","alternative_title":["ISTA Thesis"],"date_created":"2023-08-08T15:33:29Z","ddc":["570","577"],"corr_author":"1","_id":"13984","supervisor":[{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"author":[{"id":"480826C8-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Franschitz, Anna","last_name":"Franschitz"}],"doi":"10.15479/at:ista:13984","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"degree_awarded":"PhD","month":"08","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","status":"public","date_updated":"2026-04-07T13:51:29Z","type":"dissertation","has_accepted_license":"1","oa":1},{"article_processing_charge":"No","project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-12-08T23:30:04Z","citation":{"ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","apa":"Hafner, C. (2023). Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12897","mla":"Hafner, Christian. Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12897.","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12897."},"year":"2023","day":"05","title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","file":[{"date_created":"2023-05-11T10:43:20Z","access_level":"open_access","relation":"main_file","file_name":"thesis-hafner-2023may11-a2b.pdf","embargo":"2023-12-07","content_type":"application/pdf","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","file_size":50714445,"date_updated":"2023-12-08T23:30:04Z","file_id":"12942","creator":"chafner"},{"creator":"chafner","file_id":"12943","embargo_to":"open_access","date_updated":"2023-12-08T23:30:04Z","file_size":265319,"checksum":"a6b51334be2b81672357b1549afab40c","file_name":"thesis-release-form.pdf","content_type":"application/pdf","relation":"source_file","access_level":"closed","date_created":"2023-05-11T10:43:44Z"}],"date_published":"2023-05-05T00:00:00Z","page":"180","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-031-2"],"issn":["2663-337X"]},"abstract":[{"text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"date_updated":"2025-04-15T07:16:15Z","ec_funded":1,"type":"dissertation","has_accepted_license":"1","oa":1,"month":"05","user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","status":"public","oa_version":"Published Version","ddc":["516","004","518","531"],"_id":"12897","corr_author":"1","author":[{"last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hafner, Christian"}],"supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9817"},{"id":"13188","relation":"dissertation_contains","status":"public"},{"id":"7117","status":"public","relation":"part_of_dissertation"}]},"doi":"10.15479/at:ista:12897","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"degree_awarded":"PhD","publication_status":"published","alternative_title":["ISTA Thesis"],"date_created":"2023-05-05T10:40:14Z"},{"isi":1,"acknowledged_ssus":[{"_id":"M-Shop"}],"abstract":[{"lang":"eng","text":"The Kirchhoff rod model describes the bending and twisting of slender elastic rods in three dimensions, and has been widely studied to enable the prediction of how a rod will deform, given its geometry and boundary conditions. In this work, we study a number of inverse problems with the goal of computing the geometry of a straight rod that will automatically deform to match a curved target shape after attaching its endpoints to a support structure. Our solution lets us finely control the static equilibrium state of a rod by varying the cross-sectional profiles along its length.\r\nWe also show that the set of physically realizable equilibrium states admits a concise geometric description in terms of linear line complexes, which leads to very efficient computational design algorithms. Implemented in an interactive software tool, they allow us to convert three-dimensional hand-drawn spline curves to elastic rods, and give feedback about the feasibility and practicality of a design in real time. We demonstrate the efficacy of our method by designing and manufacturing several physical prototypes with applications to interior design and soft robotics."}],"keyword":["Computer Graphics","Computational Design","Computational Geometry","Shape Modeling"],"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"language":[{"iso":"eng"}],"date_published":"2023-09-20T00:00:00Z","title":"The design space of Kirchhoff rods","file":[{"content_type":"application/pdf","file_name":"kirchhoff-rods.pdf","relation":"main_file","creator":"chafner","date_updated":"2023-07-04T08:11:28Z","file_size":19635168,"checksum":"4954c1cfa487725bc156dcfec872478a","file_id":"13194","date_created":"2023-07-04T08:11:28Z","access_level":"open_access","success":1},{"creator":"chafner","checksum":"79c9975fbc82ff71f1767331d2204cca","file_size":420909,"date_updated":"2023-07-04T07:46:28Z","file_id":"13190","file_name":"supp-main.pdf","content_type":"application/pdf","relation":"supplementary_material","date_created":"2023-07-04T07:46:28Z","title":"Supplemental Material with Proofs","access_level":"open_access"},{"access_level":"open_access","date_created":"2023-07-04T07:46:30Z","title":"Cheat Sheet for Notation","file_id":"13191","file_size":430086,"checksum":"4ab647e4f03c711e1e6a5fc1eb8684db","date_updated":"2023-07-04T07:46:30Z","creator":"chafner","relation":"supplementary_material","content_type":"application/pdf","file_name":"supp-cheat.pdf"},{"title":"Supplemental Video","date_created":"2023-07-04T07:46:39Z","access_level":"open_access","creator":"chafner","checksum":"c0fd9a57d012046de90c185ffa904b76","date_updated":"2023-07-04T07:46:39Z","file_size":268088064,"file_id":"13192","content_type":"video/mp4","file_name":"kirchhoff-video-final.mp4","relation":"supplementary_material"},{"creator":"chafner","file_id":"13193","file_size":25790,"checksum":"71b00712b489ada2cd9815910ee180a9","date_updated":"2023-07-04T07:47:10Z","content_type":"application/x-zip-compressed","file_name":"matlab-submission.zip","relation":"supplementary_material","access_level":"open_access","date_created":"2023-07-04T07:47:10Z","title":"Matlab Source Code with Example"}],"day":"20","article_number":"171","external_id":{"isi":["001086833300010"]},"year":"2023","citation":{"ieee":"C. Hafner and B. Bickel, “The design space of Kirchhoff rods,” ACM Transactions on Graphics, vol. 42, no. 5. Association for Computing Machinery, 2023.","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 42 (2023).","apa":"Hafner, C., & Bickel, B. (2023). The design space of Kirchhoff rods. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3606033","mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Kirchhoff Rods.” ACM Transactions on Graphics, vol. 42, no. 5, 171, Association for Computing Machinery, 2023, doi:10.1145/3606033.","ista":"Hafner C, Bickel B. 2023. The design space of Kirchhoff rods. ACM Transactions on Graphics. 42(5), 171.","ama":"Hafner C, Bickel B. The design space of Kirchhoff rods. ACM Transactions on Graphics. 2023;42(5). doi:10.1145/3606033","chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Kirchhoff Rods.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3606033."},"intvolume":" 42","article_processing_charge":"No","project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"publisher":"Association for Computing Machinery","file_date_updated":"2023-07-04T08:11:28Z","date_created":"2023-07-04T07:41:30Z","acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Julian Fischer for his help in proving Proposition 1. 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. 715767).","publication_status":"published","scopus_import":"1","department":[{"_id":"BeBi"}],"quality_controlled":"1","doi":"10.1145/3606033","author":[{"last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hafner, Christian"},{"first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12897"}]},"article_type":"original","ddc":["516"],"_id":"13188","corr_author":"1","oa_version":"Submitted Version","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"ACM Transactions on Graphics","month":"09","issue":"5","has_accepted_license":"1","ec_funded":1,"type":"journal_article","oa":1,"volume":42,"date_updated":"2026-08-23T22:30:04Z"},{"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","abstract":[{"text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability.","lang":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-032-9"]},"language":[{"iso":"eng"}],"page":"146","date_published":"2023-05-17T00:00:00Z","file":[{"date_created":"2023-05-17T13:39:54Z","access_level":"open_access","creator":"dboocock","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","file_size":40414730,"date_updated":"2024-05-18T22:30:03Z","file_id":"12988","embargo":"2024-05-17","file_name":"thesis_boocock.pdf","content_type":"application/pdf","relation":"main_file"},{"access_level":"closed","date_created":"2023-05-17T13:39:53Z","creator":"dboocock","embargo_to":"open_access","file_id":"12989","date_updated":"2024-05-18T22:30:03Z","file_size":34338567,"checksum":"581a2313ffeb40fe77e8a122a25a7795","file_name":"thesis_boocock.zip","content_type":"application/zip","relation":"source_file"}],"title":"Mechanochemical pattern formation across biological scales","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"day":"17","year":"2023","citation":{"short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023.","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","mla":"Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964.","apa":"Boocock, D. R. (2023). Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964.","ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:10.15479/at:ista:12964"},"file_date_updated":"2024-05-18T22:30:03Z","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","date_created":"2023-05-15T14:52:36Z","alternative_title":["ISTA Thesis"],"publication_status":"published","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:12964","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8602"}]},"supervisor":[{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"author":[{"full_name":"Boocock, Daniel R","first_name":"Daniel R","orcid":"0000-0002-1585-2631","id":"453AF628-F248-11E8-B48F-1D18A9856A87","last_name":"Boocock"}],"_id":"12964","corr_author":"1","ddc":["530"],"status":"public","oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"05","oa":1,"type":"dissertation","ec_funded":1,"has_accepted_license":"1","date_updated":"2026-04-07T13:52:57Z"},{"citation":{"short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","mla":"Alcarva, Catarina. Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12809.","apa":"Alcarva, C. (2023). Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12809","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12809.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:10.15479/at:ista:12809","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria."},"year":"2023","article_processing_charge":"No","file_date_updated":"2024-04-08T22:30:03Z","publisher":"Institute of Science and Technology Austria","project":[{"_id":"267DFB90-B435-11E9-9278-68D0E5697425","name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?"}],"title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","file":[{"relation":"main_file","embargo":"2024-04-07","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","content_type":"application/pdf","date_updated":"2024-04-08T22:30:03Z","file_size":9881969,"checksum":"35b5997d2b0acb461f9d33d073da0df5","file_id":"12814","creator":"cchlebak","date_created":"2023-04-07T06:16:06Z","access_level":"open_access"},{"date_created":"2023-04-07T06:17:11Z","access_level":"closed","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","content_type":"application/pdf","relation":"source_file","creator":"cchlebak","checksum":"81198f63c294890f6d58e8b29782efdc","date_updated":"2024-04-08T22:30:03Z","file_size":44201583,"embargo_to":"open_access","file_id":"12815"},{"file_name":"Thesis_CatarinaAlcarva_final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","creator":"cchlebak","file_id":"12816","embargo_to":"open_access","file_size":84731244,"checksum":"0317bf7f457bb585f99d453ffa69eb53","date_updated":"2024-04-08T22:30:03Z","access_level":"closed","date_created":"2023-04-07T06:18:05Z"}],"day":"06","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"date_published":"2023-04-06T00:00:00Z","page":"115","abstract":[{"lang":"eng","text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. "}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"has_accepted_license":"1","type":"dissertation","oa":1,"date_updated":"2026-04-07T13:53:28Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","status":"public","month":"04","doi":"10.15479/at:ista:12809","department":[{"_id":"GradSch"},{"_id":"RySh"}],"OA_place":"publisher","degree_awarded":"PhD","ddc":["570"],"_id":"12809","corr_author":"1","author":[{"last_name":"Alcarva","id":"3A96634C-F248-11E8-B48F-1D18A9856A87","full_name":"Alcarva, Catarina","first_name":"Catarina"}],"supervisor":[{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"}],"date_created":"2023-04-06T07:54:09Z","publication_status":"published","alternative_title":["ISTA Thesis"]},{"alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2023-09-06T10:58:25Z","_id":"14280","corr_author":"1","ddc":["572"],"related_material":{"record":[{"id":"10934","relation":"research_data","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"11373"},{"id":"7387","relation":"part_of_dissertation","status":"public"}]},"supervisor":[{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler"}],"doi":"10.15479/at:ista:14280","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"degree_awarded":"PhD","month":"09","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","status":"public","date_updated":"2026-04-07T14:06:05Z","oa":1,"type":"dissertation","has_accepted_license":"1","ec_funded":1,"keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"abstract":[{"lang":"eng","text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_published":"2023-09-25T00:00:00Z","page":"156","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-033-6"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"25","title":"Spatiotemporal signaling during assembly of the bacterial divisome","file":[{"file_size":114932847,"checksum":"87eef11fbc5c7df0826f12a3a629b444","date_updated":"2024-10-05T22:30:03Z","embargo_to":"open_access","file_id":"14390","creator":"pradler","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhD Thesis_Philipp Radler_20231004.docx","date_created":"2023-10-04T10:11:53Z","access_level":"closed"},{"access_level":"open_access","date_created":"2023-10-04T10:11:21Z","file_id":"14391","checksum":"3253e099b7126469d941fd9419d68b4f","date_updated":"2024-10-05T22:30:03Z","file_size":37838778,"creator":"pradler","relation":"main_file","embargo":"2024-10-04","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","content_type":"application/pdf"}],"file_date_updated":"2024-10-05T22:30:03Z","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","grant_number":"679239"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"In vitro reconstitution of bacterial cell division","grant_number":"P34607"},{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall"},{"name":"Reconstitution of bacterial cell wall synthesis","grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","citation":{"ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","mla":"Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280.","apa":"Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:10.15479/at:ista:14280","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria."},"year":"2023"},{"ec_funded":1,"has_accepted_license":"1","type":"dissertation","oa":1,"date_updated":"2026-04-07T14:10:40Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","oa_version":"Published Version","month":"03","doi":"10.15479/at:ista:12781","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"degree_awarded":"PhD","ddc":["570","572"],"_id":"12781","corr_author":"1","supervisor":[{"last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A"}],"author":[{"last_name":"Kravchuk","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","first_name":"Vladyslav","orcid":"0000-0001-9523-9089","full_name":"Kravchuk, Vladyslav"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12138"}]},"date_created":"2023-03-31T12:24:42Z","publication_status":"published","alternative_title":["ISTA Thesis"],"citation":{"apa":"Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781","mla":"Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781.","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023."},"year":"2023","article_processing_charge":"No","file_date_updated":"2024-04-22T22:30:06Z","project":[{"name":"Structural characterization of E. coli complex I: an important mechanistic model","grant_number":"25541","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E"},{"name":"Structure and mechanism of respiratory chain molecular machines","grant_number":"101020697","call_identifier":"H2020","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3"}],"publisher":"Institute of Science and Technology Austria","file":[{"date_created":"2023-04-19T14:33:41Z","access_level":"open_access","creator":"vkravchu","checksum":"5ebb6345cb4119f93460c81310265a6d","date_updated":"2024-04-22T22:30:06Z","file_size":6071553,"file_id":"12852","content_type":"application/pdf","embargo":"2024-04-20","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","relation":"main_file"},{"creator":"vkravchu","file_id":"12853","date_updated":"2024-04-22T22:30:06Z","checksum":"c12055c48411d030d2afa51de2166221","file_size":19468766,"embargo":"2024-04-20","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","relation":"source_file","access_level":"open_access","date_created":"2023-04-19T14:33:52Z"}],"title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","day":"23","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-029-9"]},"date_published":"2023-03-23T00:00:00Z","page":"127","abstract":[{"lang":"eng","text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n"}],"acknowledged_ssus":[{"_id":"EM-Fac"}]},{"publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"page":"190","date_published":"2023-05-05T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context.","lang":"eng"}],"year":"2023","citation":{"apa":"Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12891","mla":"Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12891.","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:10.15479/at:ista:12891","chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12891.","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023."},"publisher":"Institute of Science and Technology Austria","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239"}],"file_date_updated":"2024-05-06T22:30:03Z","article_processing_charge":"No","file":[{"file_id":"12907","file_size":31434230,"checksum":"59b0303dc483f40a96a610a90aab7ee9","date_updated":"2024-05-06T22:30:03Z","creator":"aschauer","relation":"main_file","content_type":"application/pdf","embargo":"2024-05-05","file_name":"Thesis_Schauer_final.pdf","access_level":"open_access","date_created":"2023-05-05T13:01:14Z"},{"embargo_to":"open_access","file_id":"12908","file_size":43809109,"checksum":"25f54e12479b6adaabd129a20568e6c1","date_updated":"2024-05-06T22:30:03Z","creator":"aschauer","relation":"source_file","file_name":"Thesis_Schauer_final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_created":"2023-05-05T13:04:15Z"}],"title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","day":"05","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:12891","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7888"},{"status":"public","relation":"part_of_dissertation","id":"8966"}]},"author":[{"full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer"}],"supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"corr_author":"1","_id":"12891","ddc":["570"],"date_created":"2023-05-05T08:48:20Z","alternative_title":["ISTA Thesis"],"publication_status":"published","oa":1,"type":"dissertation","ec_funded":1,"has_accepted_license":"1","date_updated":"2025-06-12T06:56:58Z","oa_version":"Published Version","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05"},{"isi":1,"abstract":[{"lang":"eng","text":"As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3− availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to NO3− limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3− availability."}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_published":"2023-06-12T00:00:00Z","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"day":"12","tmp":{"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)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_number":"e2221313120","external_id":{"pmid":["37307446"],"isi":["001030689600003"]},"title":"The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation","file":[{"access_level":"open_access","date_created":"2023-07-10T08:48:40Z","embargo":"2023-12-12","content_type":"application/pdf","file_name":"2023_PNAS_Wang.pdf","relation":"main_file","creator":"alisjak","file_id":"13204","file_size":5244581,"date_updated":"2023-12-13T23:30:03Z","checksum":"d800e06252eaefba28531fa9440f23f0"}],"intvolume":" 120","article_processing_charge":"No","publisher":"National Academy of Sciences","file_date_updated":"2023-12-13T23:30:03Z","year":"2023","citation":{"mla":"Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 25, e2221313120, National Academy of Sciences, 2023, doi:10.1073/pnas.2221313120.","apa":"Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023). The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2221313120","chicago":"Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo, Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2221313120.","ista":"Wang Y, Yuan Z, Wang J, Xiao H, Wan L, Li L, Guo Y, Gong Z, Friml J, Zhang J. 2023. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 120(25), e2221313120.","ama":"Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(25). doi:10.1073/pnas.2221313120","ieee":"Y. Wang et al., “The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 25. National Academy of Sciences, 2023.","short":"Y. Wang, Z. Yuan, J. Wang, H. Xiao, L. Wan, L. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Proceedings of the National Academy of Sciences of the United States of America 120 (2023)."},"pmid":1,"publication_status":"published","acknowledgement":"We are grateful to Caifu Jiang for providing ethyl metha-nesulfonate- mutagenized population, Yi Wang for providing Xenopus oocytes, Jun Fan and Zhaosheng Kong for providing tobacco BY- 2 cells, and Claus Schwechheimer, Alain Gojon, and Shutang Tan for helpful discussions. This work was supported by the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), Hainan Provincial Natural Science Foundation of China (323CXTD379), Chinese Universities Scientific Fund (2023TC019), Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, and China Postdoctoral Science Foundation (BH2020259460).","date_created":"2023-07-09T22:01:12Z","author":[{"last_name":"Wang","full_name":"Wang, Yalu","first_name":"Yalu"},{"first_name":"Zhi","full_name":"Yuan, Zhi","last_name":"Yuan"},{"last_name":"Wang","full_name":"Wang, Jinyi","first_name":"Jinyi"},{"last_name":"Xiao","first_name":"Huixin","full_name":"Xiao, Huixin"},{"last_name":"Wan","first_name":"Lu","full_name":"Wan, Lu"},{"orcid":"0000-0002-5607-272X","first_name":"Lanxin","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li"},{"full_name":"Guo, Yan","first_name":"Yan","last_name":"Guo"},{"full_name":"Gong, Zhizhong","first_name":"Zhizhong","last_name":"Gong"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"first_name":"Jing","full_name":"Zhang, Jing","last_name":"Zhang"}],"article_type":"original","ddc":["570"],"_id":"13201","scopus_import":"1","department":[{"_id":"JiFr"}],"doi":"10.1073/pnas.2221313120","quality_controlled":"1","month":"06","oa_version":"Published Version","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_updated":"2023-12-13T23:30:04Z","volume":120,"issue":"25","type":"journal_article","has_accepted_license":"1","oa":1},{"date_updated":"2026-04-07T14:06:26Z","oa":1,"type":"dissertation","has_accepted_license":"1","month":"02","status":"public","oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"full_name":"Kirillova, Kseniia","first_name":"Kseniia","id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","last_name":"Kirillova"}],"supervisor":[{"last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","full_name":"Jösch, Maximilian A"}],"_id":"12531","corr_author":"1","ddc":["570"],"degree_awarded":"MS","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"doi":"10.15479/at:ista:12531","alternative_title":["ISTA Master's Thesis"],"publication_status":"published","date_created":"2023-02-09T07:45:05Z","file_date_updated":"2024-02-09T23:30:03Z","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","year":"2023","citation":{"ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023.","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12531.","ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria.","ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:10.15479/at:ista:12531","mla":"Kirillova, Kseniia. Panoramic Functional Gradients across the Mouse Retina. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12531.","apa":"Kirillova, K. (2023). Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12531"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"day":"08","file":[{"embargo":"2024-02-08","content_type":"application/pdf","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf","relation":"main_file","creator":"cchlebak","date_updated":"2024-02-09T23:30:03Z","file_size":8369317,"checksum":"57d8da3a6c749eb1556b7435fe266a5f","file_id":"12532","date_created":"2023-02-09T08:03:32Z","access_level":"open_access"},{"access_level":"closed","date_created":"2023-02-10T09:32:06Z","file_id":"12535","embargo_to":"open_access","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","date_updated":"2024-02-09T23:30:03Z","file_size":11204408,"creator":"cchlebak","relation":"source_file","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip","content_type":"application/x-zip-compressed"}],"title":"Panoramic functional gradients across the mouse retina","page":"46","date_published":"2023-02-08T00:00:00Z","publication_identifier":{"issn":["2791-4585"]},"language":[{"iso":"eng"}],"abstract":[{"text":"All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics.","lang":"eng"}]}]