[{"day":"17","year":"2024","publication_status":"published","pmid":1,"status":"public","article_type":"original","publisher":"Springer Nature","date_updated":"2024-10-09T10:08:08Z","extern":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":" 11","has_accepted_license":"1","date_published":"2024-07-17T00:00:00Z","author":[{"first_name":"Aviv A.","last_name":"Rosenberg","full_name":"Rosenberg, Aviv A."},{"full_name":"Marx, Ailie","first_name":"Ailie","last_name":"Marx"},{"id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730","last_name":"Bronstein","first_name":"Alexander"}],"quality_controlled":"1","language":[{"iso":"eng"}],"oa":1,"oa_version":"Published Version","_id":"18203","publication_identifier":{"issn":["2052-4463"]},"doi":"10.1038/s41597-024-03595-4","date_created":"2024-10-08T11:50:30Z","main_file_link":[{"url":"https://doi.org/10.1038/s41597-024-03595-4","open_access":"1"}],"citation":{"ama":"Rosenberg AA, Marx A, Bronstein AM. A dataset of alternately located segments in protein crystal structures. Scientific Data. 2024;11. doi:10.1038/s41597-024-03595-4","chicago":"Rosenberg, Aviv A., Ailie Marx, and Alex M. Bronstein. “A Dataset of Alternately Located Segments in Protein Crystal Structures.” Scientific Data. Springer Nature, 2024. https://doi.org/10.1038/s41597-024-03595-4.","short":"A.A. Rosenberg, A. Marx, A.M. Bronstein, Scientific Data 11 (2024).","mla":"Rosenberg, Aviv A., et al. “A Dataset of Alternately Located Segments in Protein Crystal Structures.” Scientific Data, vol. 11, 783, Springer Nature, 2024, doi:10.1038/s41597-024-03595-4.","ieee":"A. A. Rosenberg, A. Marx, and A. M. Bronstein, “A dataset of alternately located segments in protein crystal structures,” Scientific Data, vol. 11. Springer Nature, 2024.","apa":"Rosenberg, A. A., Marx, A., & Bronstein, A. M. (2024). A dataset of alternately located segments in protein crystal structures. Scientific Data. Springer Nature. https://doi.org/10.1038/s41597-024-03595-4","ista":"Rosenberg AA, Marx A, Bronstein AM. 2024. A dataset of alternately located segments in protein crystal structures. Scientific Data. 11, 783."},"scopus_import":"1","type":"journal_article","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["39019896"]},"article_processing_charge":"No","volume":11,"abstract":[{"lang":"eng","text":"Protein Data Bank (PDB) files list the relative spatial location of atoms in a protein structure as the final output of the process of fitting and refining to experimentally determined electron density measurements. Where experimental evidence exists for multiple conformations, atoms are modelled in alternate locations. Programs reading PDB files commonly ignore these alternate conformations by default leaving users oblivious to the presence of alternate conformations in the structures they analyze. This has led to underappreciation of their prevalence, under characterisation of their features and limited the accessibility to this high-resolution data representing structural ensembles. We have trawled PDB files to extract structural features of residues with alternately located atoms. The output includes the distance between alternate conformations and identifies the location of these segments within the protein chain and in proximity of all other atoms within a defined radius. This dataset should be of use in efforts to predict multiple structures from a single sequence and support studies investigating protein flexibility and the association with protein function."}],"publication":"Scientific Data","article_number":"783","title":"A dataset of alternately located segments in protein crystal structures"},{"oa":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","scopus_import":"1","citation":{"apa":"Elul, Y., Rozenberg, E., Boyarski, A., Yaniv, Y., Schuster, A., & Bronstein, A. M. (2024). Data-driven modeling of interrelated dynamical systems. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-024-01626-5","ista":"Elul Y, Rozenberg E, Boyarski A, Yaniv Y, Schuster A, Bronstein AM. 2024. Data-driven modeling of interrelated dynamical systems. Communications Physics. 7, 141.","chicago":"Elul, Yonatan, Eyal Rozenberg, Amit Boyarski, Yael Yaniv, Assaf Schuster, and Alex M. Bronstein. “Data-Driven Modeling of Interrelated Dynamical Systems.” Communications Physics. Springer Nature, 2024. https://doi.org/10.1038/s42005-024-01626-5.","ama":"Elul Y, Rozenberg E, Boyarski A, Yaniv Y, Schuster A, Bronstein AM. Data-driven modeling of interrelated dynamical systems. Communications Physics. 2024;7. doi:10.1038/s42005-024-01626-5","mla":"Elul, Yonatan, et al. “Data-Driven Modeling of Interrelated Dynamical Systems.” Communications Physics, vol. 7, 141, Springer Nature, 2024, doi:10.1038/s42005-024-01626-5.","ieee":"Y. Elul, E. Rozenberg, A. Boyarski, Y. Yaniv, A. Schuster, and A. M. Bronstein, “Data-driven modeling of interrelated dynamical systems,” Communications Physics, vol. 7. Springer Nature, 2024.","short":"Y. Elul, E. Rozenberg, A. Boyarski, Y. Yaniv, A. Schuster, A.M. Bronstein, Communications Physics 7 (2024)."},"main_file_link":[{"url":"https://doi.org/10.1038/s42005-024-01626-5","open_access":"1"}],"date_created":"2024-10-08T12:45:35Z","doi":"10.1038/s42005-024-01626-5","_id":"18204","publication_identifier":{"issn":["2399-3650"]},"article_processing_charge":"Yes","title":"Data-driven modeling of interrelated dynamical systems","article_number":"141","abstract":[{"lang":"eng","text":"Non-linear dynamical systems describe numerous real-world phenomena, ranging from the weather, to financial markets and disease progression. Individual systems may share substantial common information, for example patients’ anatomy. Lately, deep-learning has emerged as a leading method for data-driven modeling of non-linear dynamical systems. Yet, despite recent breakthroughs, prior works largely ignored the existence of shared information between different systems. However, such cases are quite common, for example, in medicine: we may wish to have a patient-specific model for some disease, but the data collected from a single patient is usually too small to train a deep-learning model. Hence, we must properly utilize data gathered from other patients. Here, we explicitly consider such cases by jointly modeling multiple systems. We show that the current single-system models consistently fail when trying to learn simultaneously from multiple systems. We suggest a framework for jointly approximating the Koopman operators of multiple systems, while intrinsically exploiting common information. We demonstrate how we can adapt to a new system using order-of-magnitude less new data and show the superiority of our model over competing methods, in terms of both forecasting ability and statistical fidelity, across chaotic, cardiac, and climate systems."}],"publication":"Communications Physics","volume":7,"year":"2024","day":"01","date_updated":"2024-10-09T10:12:11Z","article_type":"original","publisher":"Springer Nature","status":"public","publication_status":"published","intvolume":" 7","extern":"1","author":[{"last_name":"Elul","first_name":"Yonatan","full_name":"Elul, Yonatan"},{"full_name":"Rozenberg, Eyal","first_name":"Eyal","last_name":"Rozenberg"},{"full_name":"Boyarski, Amit","last_name":"Boyarski","first_name":"Amit"},{"last_name":"Yaniv","first_name":"Yael","full_name":"Yaniv, Yael"},{"first_name":"Assaf","last_name":"Schuster","full_name":"Schuster, Assaf"},{"last_name":"Bronstein","first_name":"Alexander","orcid":"0000-0001-9699-8730","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","full_name":"Bronstein, Alexander"}],"date_published":"2024-05-01T00:00:00Z"},{"intvolume":" 32","extern":"1","date_published":"2024-03-11T00:00:00Z","author":[{"last_name":"Wengrowicz","first_name":"Omri","full_name":"Wengrowicz, Omri"},{"full_name":"Bronstein, Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","orcid":"0000-0001-9699-8730","first_name":"Alexander","last_name":"Bronstein"},{"last_name":"Cohen","first_name":"Oren","full_name":"Cohen, Oren"}],"year":"2024","day":"11","status":"public","publication_status":"published","pmid":1,"date_updated":"2024-10-09T10:26:44Z","publisher":"Optica Publishing Group","article_type":"original","external_id":{"pmid":["38571128"]},"article_processing_charge":"Yes (in subscription journal)","page":"8791-8803","abstract":[{"lang":"eng","text":"We explore numerically an unsupervised, physics-informed, deep learning-based reconstruction technique for time-resolved imaging by multiplexed ptychography. In our method, the untrained deep learning model replaces the iterative algorithm’s update step, yielding superior reconstructions of multiple dynamic object frames compared to conventional methodologies. More precisely, we demonstrate improvements in image quality and resolution, while reducing sensitivity to the number of recorded frames, the mutual orthogonality of different probe modes, overlap between neighboring probe beams and the cutoff frequency of the ptychographic microscope – properties that are generally of paramount importance for ptychographic reconstruction algorithms."}],"publication":"Optics Express","volume":32,"title":"Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography","issue":"6","quality_controlled":"1","language":[{"iso":"eng"}],"oa":1,"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1364/OE.515445","open_access":"1"}],"doi":"10.1364/oe.515445","date_created":"2024-10-08T12:46:01Z","_id":"18205","publication_identifier":{"issn":["1094-4087"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","type":"journal_article","scopus_import":"1","citation":{"mla":"Wengrowicz, Omri, et al. “Unsupervised Physics-Informed Deep Learning-Based Reconstruction for Time-Resolved Imaging by Multiplexed Ptychography.” Optics Express, vol. 32, no. 6, Optica Publishing Group, 2024, pp. 8791–803, doi:10.1364/oe.515445.","ieee":"O. Wengrowicz, A. M. Bronstein, and O. Cohen, “Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography,” Optics Express, vol. 32, no. 6. Optica Publishing Group, pp. 8791–8803, 2024.","short":"O. Wengrowicz, A.M. Bronstein, O. Cohen, Optics Express 32 (2024) 8791–8803.","chicago":"Wengrowicz, Omri, Alex M. Bronstein, and Oren Cohen. “Unsupervised Physics-Informed Deep Learning-Based Reconstruction for Time-Resolved Imaging by Multiplexed Ptychography.” Optics Express. Optica Publishing Group, 2024. https://doi.org/10.1364/oe.515445.","ama":"Wengrowicz O, Bronstein AM, Cohen O. Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography. Optics Express. 2024;32(6):8791-8803. doi:10.1364/oe.515445","ista":"Wengrowicz O, Bronstein AM, Cohen O. 2024. Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography. Optics Express. 32(6), 8791–8803.","apa":"Wengrowicz, O., Bronstein, A. M., & Cohen, O. (2024). Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography. Optics Express. Optica Publishing Group. https://doi.org/10.1364/oe.515445"}},{"volume":14976,"alternative_title":["LNCS"],"abstract":[{"text":"In the context of in vitro fertilization (IVF), selecting embryos for transfer is critical in determining pregnancy outcomes, with implantation as the essential first milestone for a successful pregnancy. This study introduces the Bonna algorithm, an advanced deep-learning framework engineered to predict embryo implantation probabilities. The algorithm employs a sophisticated integration of machine-learning techniques, utilizing MobileNetV2 for pixel and context embedding, a custom Pix2Pix model for precise segmentation, and a Vision Transformer for additional depth in embedding. MobileNetV2 was chosen for its robust feature extraction capabilities, focusing on textures and edges. The custom Pix2Pix model is adapted for precise segmentation of significant biological features such as the zona pellucida and blastocyst cavity. The Vision Transformer adds a global perspective, capturing complex patterns not apparent in local image segments. Tested on a dataset of images of human blastocysts collected from Ukraine, Israel, and Spain, the Bonna algorithm was rigorously validated through 10-fold cross-validation to ensure its robustness and reliability. It demonstrates superior performance with a mean area under the receiver operating characteristic curve (AUC) of 0.754, significantly outperforming existing models. The study not only advances predictive accuracy in embryo selection but also highlights the algorithm’s clinical applicability due to reliable confidence reporting.","lang":"eng"}],"publication":"First International Conference on Artificial Intelligence in Healthcare","date_published":"2024-08-15T00:00:00Z","title":"Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications","author":[{"last_name":"Rave","first_name":"Gilad","full_name":"Rave, Gilad"},{"full_name":"Fordham, Daniel E.","first_name":"Daniel E.","last_name":"Fordham"},{"orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander","last_name":"Bronstein"},{"last_name":"Silver","first_name":"David H.","full_name":"Silver, David H."}],"intvolume":" 14976","extern":"1","article_processing_charge":"No","page":"160-171","conference":{"location":"Swansea, United Kingdom","name":"AIiH: Artificial Intelligence in Healthcare","end_date":"2024-09-06","start_date":"2024-09-04"},"publication_identifier":{"isbn":["9783031672842"],"eissn":["1611-3349"],"eisbn":["9783031672859"],"issn":["0302-9743"]},"_id":"18206","publication_status":"published","date_created":"2024-10-08T12:46:23Z","doi":"10.1007/978-3-031-67285-9_12","status":"public","type":"conference","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-09T10:33:39Z","publisher":"Springer Nature","citation":{"mla":"Rave, Gilad, et al. “Enhancing Predictive Accuracy in Embryo Implantation: The Bonna Algorithm and Its Clinical Implications.” First International Conference on Artificial Intelligence in Healthcare, vol. 14976, Springer Nature, 2024, pp. 160–71, doi:10.1007/978-3-031-67285-9_12.","ieee":"G. Rave, D. E. Fordham, A. M. Bronstein, and D. H. Silver, “Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications,” in First International Conference on Artificial Intelligence in Healthcare, Swansea, United Kingdom, 2024, vol. 14976, pp. 160–171.","short":"G. Rave, D.E. Fordham, A.M. Bronstein, D.H. Silver, in:, First International Conference on Artificial Intelligence in Healthcare, Springer Nature, 2024, pp. 160–171.","chicago":"Rave, Gilad, Daniel E. Fordham, Alex M. Bronstein, and David H. Silver. “Enhancing Predictive Accuracy in Embryo Implantation: The Bonna Algorithm and Its Clinical Implications.” In First International Conference on Artificial Intelligence in Healthcare, 14976:160–71. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-67285-9_12.","ama":"Rave G, Fordham DE, Bronstein AM, Silver DH. Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. In: First International Conference on Artificial Intelligence in Healthcare. Vol 14976. Springer Nature; 2024:160-171. doi:10.1007/978-3-031-67285-9_12","ista":"Rave G, Fordham DE, Bronstein AM, Silver DH. 2024. Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. First International Conference on Artificial Intelligence in Healthcare. AIiH: Artificial Intelligence in Healthcare, LNCS, vol. 14976, 160–171.","apa":"Rave, G., Fordham, D. E., Bronstein, A. M., & Silver, D. H. (2024). Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. In First International Conference on Artificial Intelligence in Healthcare (Vol. 14976, pp. 160–171). Swansea, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-031-67285-9_12"},"scopus_import":"1","year":"2024","quality_controlled":"1","language":[{"iso":"eng"}],"day":"15","oa_version":"None"},{"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"page":"2433-3282","external_id":{"isi":["001328875900001"]},"article_processing_charge":"No","publication":"Mathematics of Operations Research","abstract":[{"text":"Matrix games are the most basic model in game theory, and yet robustness with respect to small perturbations of the matrix entries is not fully understood. In this paper, we introduce value positivity and uniform value positivity, two properties that refine the notion of optimality in the context of polynomially perturbed matrix games. The first concept captures how the value depends on the perturbation parameter, and the second consists of the existence of a fixed strategy that guarantees the value of the unperturbed matrix game for every sufficiently small positive parameter. We provide polynomial-time algorithms to check whether a polynomially perturbed matrix game satisfies these properties. We further provide the functional form for a parameterized optimal strategy and the value function. Finally, we translate our results to linear programming and stochastic games, where value positivity is related to the existence of robust solutions.","lang":"eng"}],"ec_funded":1,"volume":50,"title":"Value-positivity for matrix games","issue":"4","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"oa_version":"None","date_created":"2024-10-09T07:02:20Z","doi":"10.1287/moor.2022.0332","_id":"18266","publication_identifier":{"eissn":["1526-5471"],"issn":["0364-765X"]},"related_material":{"record":[{"id":"20234","status":"public","relation":"dissertation_contains"}]},"acknowledgement":"This research was supported by Fondation CFM pour la Recherche, the H2020 European Research Council [Grant ERC-CoG-863818 (ForM-SMArt)], the Austrian Science Fund [Grant 10.55776/COE12], ANID Chile [Grant ACT210005], and Agence Nationale de la Recherche [Grant ANR-21-CE40-0020].","scopus_import":"1","citation":{"chicago":"Chatterjee, Krishnendu, Miquel Oliu-Barton, and Raimundo J Saona Urmeneta. “Value-Positivity for Matrix Games.” Mathematics of Operations Research. Institute for Operations Research and the Management Sciences, 2024. https://doi.org/10.1287/moor.2022.0332.","ama":"Chatterjee K, Oliu-Barton M, Saona Urmeneta RJ. Value-positivity for matrix games. Mathematics of Operations Research. 2024;50(4):2433-3282. doi:10.1287/moor.2022.0332","ieee":"K. Chatterjee, M. Oliu-Barton, and R. J. Saona Urmeneta, “Value-positivity for matrix games,” Mathematics of Operations Research, vol. 50, no. 4. Institute for Operations Research and the Management Sciences, pp. 2433–3282, 2024.","mla":"Chatterjee, Krishnendu, et al. “Value-Positivity for Matrix Games.” Mathematics of Operations Research, vol. 50, no. 4, Institute for Operations Research and the Management Sciences, 2024, pp. 2433–3282, doi:10.1287/moor.2022.0332.","short":"K. Chatterjee, M. Oliu-Barton, R.J. Saona Urmeneta, Mathematics of Operations Research 50 (2024) 2433–3282.","apa":"Chatterjee, K., Oliu-Barton, M., & Saona Urmeneta, R. J. (2024). Value-positivity for matrix games. Mathematics of Operations Research. Institute for Operations Research and the Management Sciences. https://doi.org/10.1287/moor.2022.0332","ista":"Chatterjee K, Oliu-Barton M, Saona Urmeneta RJ. 2024. Value-positivity for matrix games. Mathematics of Operations Research. 50(4), 2433–3282."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","type":"journal_article","isi":1,"intvolume":" 50","date_published":"2024-10-01T00:00:00Z","OA_type":"closed access","corr_author":"1","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Oliu-Barton","first_name":"Miquel","full_name":"Oliu-Barton, Miquel"},{"orcid":"0000-0001-5103-038X","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","full_name":"Saona Urmeneta, Raimundo J","last_name":"Saona Urmeneta","first_name":"Raimundo J"}],"day":"01","year":"2024","status":"public","publication_status":"published","article_type":"original","publisher":"Institute for Operations Research and the Management Sciences","date_updated":"2026-04-07T12:31:21Z"},{"day":"26","language":[{"iso":"eng"}],"OA_place":"repository","year":"2024","department":[{"_id":"TiBr"}],"oa_version":"Preprint","oa":1,"doi":"10.48550/arXiv.2405.16648","status":"public","date_created":"2024-10-10T13:15:43Z","_id":"18295","publication_status":"submitted","related_material":{"record":[{"relation":"later_version","status":"public","id":"19013"},{"relation":"dissertation_contains","status":"public","id":"18132"}]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2405.16648","open_access":"1"}],"citation":{"mla":"Glas, Jakob. “Canonical Singularities on Moduli Spaces of Rational Curves via the Circle Method.” ArXiv, doi:10.48550/arXiv.2405.16648.","ieee":"J. Glas, “Canonical singularities on moduli spaces of rational curves via the circle method,” arXiv. .","short":"J. Glas, ArXiv (n.d.).","chicago":"Glas, Jakob. “Canonical Singularities on Moduli Spaces of Rational Curves via the Circle Method.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2405.16648.","ama":"Glas J. Canonical singularities on moduli spaces of rational curves via the circle method. arXiv. doi:10.48550/arXiv.2405.16648","ista":"Glas J. Canonical singularities on moduli spaces of rational curves via the circle method. arXiv, 10.48550/arXiv.2405.16648.","apa":"Glas, J. (n.d.). Canonical singularities on moduli spaces of rational curves via the circle method. arXiv. https://doi.org/10.48550/arXiv.2405.16648"},"month":"05","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-04-07T12:53:53Z","type":"preprint","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"arxiv":1,"project":[{"name":"Rational curves via function field analytic number theory","grant_number":"P36278","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3"}],"article_processing_charge":"No","external_id":{"arxiv":["2405.16648"]},"date_published":"2024-05-26T00:00:00Z","abstract":[{"lang":"eng","text":"By developing a suitable version of the circle method, we show that the space of degree e rational curves on a smooth hypersurface of degree d has only canonical singularities provided its dimension is sufficiently large with respect to e and d."}],"publication":"arXiv","corr_author":"1","author":[{"last_name":"Glas","first_name":"Jakob","id":"d6423cba-dc74-11ea-a0a7-ee61689ff5fb","full_name":"Glas, Jakob"}],"title":"Canonical singularities on moduli spaces of rational curves via the circle method"},{"title":"Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons","file_date_updated":"2024-10-11T10:04:23Z","abstract":[{"text":"It is widely believed that information storage in neuronal circuits involves nanoscopic structural changes at synapses, resulting in the formation of synaptic engrams. However, direct evidence for this hypothesis is lacking. To test this conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic recordings, and structural analysis by electron microscopy (EM) and freeze-fracture replica labeling (FRL) at the murine hippocampal mossy fiber synapse, a key synapse in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic transmission revealed that forskolin-induced chemical potentiation increased the readily releasable vesicle pool size and vesicular release probability by 146% and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL demonstrated an increase in the number of vesicles close to the plasma membrane and the number of clusters of the priming protein Munc13-1, indicating an increase in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels, suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our results indicate that presynaptic plasticity is associated with structural reorganization of active zones. We propose that changes in potential nanoscopic organization at synaptic vesicle release sites may be correlates of learning and memory at a plastic central synapse.","lang":"eng"}],"ec_funded":1,"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"}],"article_processing_charge":"No","citation":{"ama":"Kim O. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. 2024. doi:10.15479/AT:ISTA:18296","chicago":"Kim, Olena. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:18296.","short":"O. Kim, (2024).","mla":"Kim, Olena. Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons. Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:18296.","ieee":"O. Kim, “Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons.” Institute of Science and Technology Austria, 2024.","apa":"Kim, O. (2024). Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:18296","ista":"Kim O. 2024. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons, Institute of Science and Technology Austria, 10.15479/AT:ISTA:18296."},"month":"10","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","type":"research_data","doi":"10.15479/AT:ISTA:18296","date_created":"2024-10-11T10:12:17Z","_id":"18296","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"18603"}]},"department":[{"_id":"PeJo"},{"_id":"RySh"},{"_id":"EM-Fac"}],"oa":1,"oa_version":"Submitted Version","author":[{"first_name":"Olena","last_name":"Kim","orcid":"0000-0003-2344-1039","full_name":"Kim, Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"date_published":"2024-10-11T00:00:00Z","corr_author":"1","keyword":["Hippocampal mossy fiber synapses","short-term potentiation","long-term potentiation","presynaptic plasticity","electron microscopy","freeze-fracture replica labeling","paired recordings","forskolin","cyclic adenosine monophosphate (cAMP)","protein kinase A (PKA)","neuromodulation","synaptic vesicle pools","presynaptic Ca2+ channels","Munc13","docking","priming","active zone"],"contributor":[{"first_name":"Olena","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"},{"contributor_type":"researcher","id":"3337E116-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0408-6094","last_name":"Okamoto","first_name":"Yuji"},{"contributor_type":"researcher","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter"},{"first_name":"Nils ","last_name":"Brose","contributor_type":"researcher"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Shigemoto","first_name":"Ryuichi"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"}],"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publisher":"Institute of Science and Technology Austria","date_updated":"2026-04-16T12:20:33Z","status":"public","file":[{"creator":"okim","date_updated":"2024-10-11T10:04:19Z","content_type":"application/zip","file_size":164382,"relation":"main_file","checksum":"0a977e7df54c418251b10dfd3f8a015c","date_created":"2024-10-11T10:04:19Z","access_level":"open_access","success":1,"file_name":"Kim_et_al_2024_PlosBio_Source_data.zip","file_id":"18297"},{"file_id":"18298","file_name":"info.txt","success":1,"access_level":"open_access","relation":"main_file","checksum":"5b9343d6b2035ac3185e390fad4d3830","date_created":"2024-10-11T10:04:23Z","content_type":"text/plain","date_updated":"2024-10-11T10:04:23Z","file_size":654,"creator":"okim"}],"day":"11","year":"2024"},{"doi":"10.15479/at:ista:18301","date_created":"2024-10-11T19:52:20Z","_id":"18301","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"17219"}]},"publication_identifier":{"issn":["2791-4585"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"10","type":"dissertation","degree_awarded":"MS","citation":{"ista":"Etemadi A. 2024. Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. Institute of Science and Technology Austria.","apa":"Etemadi, A. (2024). Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18301","short":"A. Etemadi, Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking, Institute of Science and Technology Austria, 2024.","mla":"Etemadi, Arian. Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18301.","ieee":"A. Etemadi, “Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking,” Institute of Science and Technology Austria, 2024.","ama":"Etemadi A. Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. 2024. doi:10.15479/at:ista:18301","chicago":"Etemadi, Arian. “Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18301."},"OA_place":"publisher","language":[{"iso":"eng"}],"oa_version":"Published Version","oa":1,"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"abstract":[{"lang":"eng","text":"Physics simulation in computer graphics can bring triangle meshes into topologically invalid states. The method in this thesis contributed to Heiss-Synak* and Kalinov* et al. [2024] who devised a non-manifold hybrid surface tracker—a surface tracker that repairs explicit non-manifold triangle meshes with the help of the implicit domain. Specifically, this thesis provides an algorithm for filling the holes that are left after removing problematic parts of the mesh."}],"alternative_title":["ISTA Master's Thesis"],"file_date_updated":"2024-10-24T14:34:54Z","title":"Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking","page":"39","article_processing_charge":"No","supervisor":[{"first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"status":"public","publication_status":"published","date_updated":"2026-04-07T13:02:36Z","publisher":"Institute of Science and Technology Austria","year":"2024","day":"15","file":[{"file_name":"thesis-arian-etemadi.pdf","file_id":"18469","success":1,"relation":"main_file","checksum":"80fb7923e229ad9d39253d7c8a8083d0","date_created":"2024-10-24T14:34:42Z","access_level":"open_access","creator":"aetemadi","file_size":8914218,"date_updated":"2024-10-24T14:34:42Z","content_type":"application/pdf"},{"file_id":"18470","file_name":"thesis-arian-etemadi-latex-source.zip","access_level":"closed","relation":"source_file","date_created":"2024-10-24T14:34:54Z","checksum":"1c02586ed7d441d5ec441867650568d1","content_type":"application/x-zip-compressed","date_updated":"2024-10-24T14:34:54Z","file_size":9802650,"creator":"aetemadi"}],"corr_author":"1","date_published":"2024-10-15T00:00:00Z","ddc":["000"],"author":[{"full_name":"Etemadihaghighi, Arian","id":"36cea3aa-f38e-11ec-8ae0-c65ae6f6098f","first_name":"Arian","last_name":"Etemadihaghighi"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"keyword":["surface tracking","non-manifold","hole-filling","topology change","multi-material","solid-modeling"],"has_accepted_license":"1"},{"citation":{"ista":"Kratsios P, Zampieri N, Carrillo R, Mizumoto K, Sweeney LB, Philippidou P. 2024. Molecular and cellular mechanisms of motor circuit development. The Journal of Neuroscience. 44(40), e1238242024.","apa":"Kratsios, P., Zampieri, N., Carrillo, R., Mizumoto, K., Sweeney, L. B., & Philippidou, P. (2024). Molecular and cellular mechanisms of motor circuit development. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1238-24.2024","mla":"Kratsios, Paschalis, et al. “Molecular and Cellular Mechanisms of Motor Circuit Development.” The Journal of Neuroscience, vol. 44, no. 40, e1238242024, Society for Neuroscience, 2024, doi:10.1523/JNEUROSCI.1238-24.2024.","ieee":"P. Kratsios, N. Zampieri, R. Carrillo, K. Mizumoto, L. B. Sweeney, and P. Philippidou, “Molecular and cellular mechanisms of motor circuit development,” The Journal of Neuroscience, vol. 44, no. 40. Society for Neuroscience, 2024.","short":"P. Kratsios, N. Zampieri, R. Carrillo, K. Mizumoto, L.B. Sweeney, P. Philippidou, The Journal of Neuroscience 44 (2024).","chicago":"Kratsios, Paschalis, Niccolò Zampieri, Robert Carrillo, Kota Mizumoto, Lora B. Sweeney, and Polyxeni Philippidou. “Molecular and Cellular Mechanisms of Motor Circuit Development.” The Journal of Neuroscience. Society for Neuroscience, 2024. https://doi.org/10.1523/JNEUROSCI.1238-24.2024.","ama":"Kratsios P, Zampieri N, Carrillo R, Mizumoto K, Sweeney LB, Philippidou P. Molecular and cellular mechanisms of motor circuit development. The Journal of Neuroscience. 2024;44(40). doi:10.1523/JNEUROSCI.1238-24.2024"},"scopus_import":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","publication_identifier":{"eissn":["1529-2401"]},"_id":"18305","doi":"10.1523/JNEUROSCI.1238-24.2024","date_created":"2024-10-13T22:01:49Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1523/JNEUROSCI.1238-24.2024"}],"acknowledgement":"Work in the authors’ labs is funded by the Helmholtz Association (N.Z.), National Institute of Neurological Disorders and Stroke (NINDS) R01NS116365 (P.K.), NINDS R01NS123439 and National Science Foundation IOS-2048080 (R.C.), NINDS R01NS114510 (P.P.), Natural Sciences and Engineering Research Council of Canada RGPIN-2021-03154 (K.M.) and Horizon Europe European Research Council Starting Grant Number 101041551 (L.B.S.). P.P. is the Weidenthal Family Designated Professor in Career Development.","department":[{"_id":"LoSw"}],"oa_version":"Published Version","oa":1,"language":[{"iso":"eng"}],"quality_controlled":"1","issue":"40","OA_place":"publisher","article_number":"e1238242024","title":"Molecular and cellular mechanisms of motor circuit development","volume":44,"abstract":[{"lang":"eng","text":"Motor circuits represent the main output of the central nervous system and produce dynamic behaviors ranging from relatively simple rhythmic activities like swimming in fish and breathing in mammals to highly sophisticated dexterous movements in humans. Despite decades of research, the development and function of motor circuits remain poorly understood. Breakthroughs in the field recently provided new tools and tractable model systems that set the stage to discover the molecular mechanisms and circuit logic underlying motor control. Here, we describe recent advances from both vertebrate (mouse, frog) and invertebrate (nematode, fruit fly) systems on cellular and molecular mechanisms that enable motor circuits to develop and function and highlight conserved and divergent mechanisms necessary for motor circuit development."}],"publication":"The Journal of Neuroscience","project":[{"grant_number":"101041551","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","name":"Development and Evolution of Tetrapod Motor Circuits"}],"article_processing_charge":"No","external_id":{"pmid":["39358025"],"isi":["001335212200016"]},"OA_embargo":"6 months","publisher":"Society for Neuroscience","article_type":"original","date_updated":"2026-01-05T14:01:26Z","publication_status":"published","pmid":1,"status":"public","day":"02","year":"2024","author":[{"last_name":"Kratsios","first_name":"Paschalis","full_name":"Kratsios, Paschalis"},{"last_name":"Zampieri","first_name":"Niccolò","full_name":"Zampieri, Niccolò"},{"first_name":"Robert","last_name":"Carrillo","full_name":"Carrillo, Robert"},{"full_name":"Mizumoto, Kota","last_name":"Mizumoto","first_name":"Kota"},{"orcid":"0000-0001-9242-5601","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","full_name":"Sweeney, Lora Beatrice Jaeger","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger"},{"last_name":"Philippidou","first_name":"Polyxeni","full_name":"Philippidou, Polyxeni"}],"date_published":"2024-10-02T00:00:00Z","ddc":["570"],"OA_type":"hybrid","has_accepted_license":"1","isi":1,"intvolume":" 44"},{"publication_status":"published","status":"public","date_updated":"2025-09-08T14:18:18Z","article_type":"original","publisher":"IOP Publishing","year":"2024","day":"01","file":[{"file_name":"2024_AstrophysicalJourn_Oza.pdf","file_id":"18456","success":1,"date_created":"2024-10-21T11:05:11Z","checksum":"23eea2a6a0519694a84998957ad7b7fb","relation":"main_file","access_level":"open_access","creator":"dernst","file_size":1249747,"date_updated":"2024-10-21T11:05:11Z","content_type":"application/pdf"}],"OA_type":"gold","ddc":["520"],"date_published":"2024-10-01T00:00:00Z","author":[{"full_name":"Oza, Apurva V.","first_name":"Apurva V.","last_name":"Oza"},{"full_name":"Seidel, Julia V.","first_name":"Julia V.","last_name":"Seidel"},{"full_name":"Hoeijmakers, H. Jens","last_name":"Hoeijmakers","first_name":"H. Jens"},{"last_name":"Unni","first_name":"Athira","full_name":"Unni, Athira"},{"last_name":"Kesseli","first_name":"Aurora Y.","full_name":"Kesseli, Aurora Y."},{"last_name":"Schmidt","first_name":"Carl A.","full_name":"Schmidt, Carl A."},{"first_name":"Thirupathi","last_name":"Sivarani","full_name":"Sivarani, Thirupathi"},{"first_name":"Aaron","last_name":"Bello-Arufe","full_name":"Bello-Arufe, Aaron"},{"first_name":"Andrea","last_name":"Gebek","full_name":"Gebek, Andrea"},{"full_name":"Meyer Zu Westram, Moritz","last_name":"Meyer Zu Westram","first_name":"Moritz"},{"last_name":"Sousa","first_name":"Sérgio G.","full_name":"Sousa, Sérgio G."},{"first_name":"Rosaly M.C.","last_name":"Lopes","full_name":"Lopes, Rosaly M.C."},{"last_name":"Hu","first_name":"Renyu","full_name":"Hu, Renyu"},{"last_name":"De Kleer","first_name":"Katherine","full_name":"De Kleer, Katherine"},{"full_name":"Fisher, Chloe","first_name":"Chloe","last_name":"Fisher"},{"first_name":"Sébastien","last_name":"Charnoz","full_name":"Charnoz, Sébastien"},{"first_name":"Ashley D.","last_name":"Baker","full_name":"Baker, Ashley D."},{"full_name":"Halverson, Samuel P.","first_name":"Samuel P.","last_name":"Halverson"},{"first_name":"Nick M.","last_name":"Schneider","full_name":"Schneider, Nick M."},{"full_name":"Psaridi, Angelica","first_name":"Angelica","last_name":"Psaridi"},{"last_name":"Wyttenbach","first_name":"Aurélien","full_name":"Wyttenbach, Aurélien"},{"last_name":"Torres Rodriguez","first_name":"Santiago","id":"a8df4360-4328-11ee-8f1a-e502d0c83fc2","full_name":"Torres Rodriguez, Santiago","orcid":"0000-0002-3150-8988"},{"full_name":"Bhatnagar, Ishita","first_name":"Ishita","last_name":"Bhatnagar"},{"full_name":"Johnson, Robert E.","first_name":"Robert E.","last_name":"Johnson"}],"intvolume":" 973","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"has_accepted_license":"1","acknowledgement":"The research described in this Letter was carried out in part at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics Space Administration, © 2024. California Institute of Technology. Government sponsorship acknowledged. A.V.O. and J.V.S. thank M. Lendl for constraints and discussions on the mass of WASP-49 A b. S.G.S acknowledges the support from FCT through Investigador FCT contract nr. CEECIND/00826/2018 and POPH/FSE (EC).","_id":"18306","publication_identifier":{"issn":["2041-8205"],"eissn":["2041-8213"]},"date_created":"2024-10-13T22:01:49Z","doi":"10.3847/2041-8213/ad6b29","type":"journal_article","month":"10","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"apa":"Oza, A. V., Seidel, J. V., Hoeijmakers, H. J., Unni, A., Kesseli, A. Y., Schmidt, C. A., … Johnson, R. E. (2024). Redshifted sodium transient near exoplanet transit. Astrophysical Journal Letters. IOP Publishing. https://doi.org/10.3847/2041-8213/ad6b29","ista":"Oza AV, Seidel JV, Hoeijmakers HJ, Unni A, Kesseli AY, Schmidt CA, Sivarani T, Bello-Arufe A, Gebek A, Meyer Zu Westram M, Sousa SG, Lopes RMC, Hu R, De Kleer K, Fisher C, Charnoz S, Baker AD, Halverson SP, Schneider NM, Psaridi A, Wyttenbach A, Torres Rodriguez S, Bhatnagar I, Johnson RE. 2024. Redshifted sodium transient near exoplanet transit. Astrophysical Journal Letters. 973(2), L53.","ama":"Oza AV, Seidel JV, Hoeijmakers HJ, et al. Redshifted sodium transient near exoplanet transit. Astrophysical Journal Letters. 2024;973(2). doi:10.3847/2041-8213/ad6b29","chicago":"Oza, Apurva V., Julia V. Seidel, H. Jens Hoeijmakers, Athira Unni, Aurora Y. Kesseli, Carl A. Schmidt, Thirupathi Sivarani, et al. “Redshifted Sodium Transient near Exoplanet Transit.” Astrophysical Journal Letters. IOP Publishing, 2024. https://doi.org/10.3847/2041-8213/ad6b29.","short":"A.V. Oza, J.V. Seidel, H.J. Hoeijmakers, A. Unni, A.Y. Kesseli, C.A. Schmidt, T. Sivarani, A. Bello-Arufe, A. Gebek, M. Meyer Zu Westram, S.G. Sousa, R.M.C. Lopes, R. Hu, K. De Kleer, C. Fisher, S. Charnoz, A.D. Baker, S.P. Halverson, N.M. Schneider, A. Psaridi, A. Wyttenbach, S. Torres Rodriguez, I. Bhatnagar, R.E. Johnson, Astrophysical Journal Letters 973 (2024).","ieee":"A. V. Oza et al., “Redshifted sodium transient near exoplanet transit,” Astrophysical Journal Letters, vol. 973, no. 2. IOP Publishing, 2024.","mla":"Oza, Apurva V., et al. “Redshifted Sodium Transient near Exoplanet Transit.” Astrophysical Journal Letters, vol. 973, no. 2, L53, IOP Publishing, 2024, doi:10.3847/2041-8213/ad6b29."},"scopus_import":"1","OA_place":"publisher","quality_controlled":"1","language":[{"iso":"eng"}],"issue":"2","oa":1,"oa_version":"Published Version","department":[{"_id":"LiBu"}],"DOAJ_listed":"1","volume":973,"publication":"Astrophysical Journal Letters","abstract":[{"text":"Neutral sodium (Na i) is an alkali metal with a favorable absorption cross section such that tenuous gases are easily illuminated at select transiting exoplanet systems. We examine both the time-averaged and time-series alkali spectral flux individually, over 4 nights at a hot Saturn system on a ∼2.8 day orbit about a Sun-like star WASP-49 A. Very Large Telescope/ESPRESSO observations are analyzed, providing new constraints. We recover the previously confirmed residual sodium flux uniquely when averaged, whereas night-to-night Na i varies by more than an order of magnitude. On HARPS/3.6 m Epoch II, we report a Doppler redshift at vΓ,NaD = + 9.7 ± 1.6 km s−1 with respect to the planet's rest frame. Upon examining the lightcurves, we confirm night-to-night variability, on the order of ∼1%–4% in NaD, rarely coinciding with exoplanet transit, not readily explained by stellar activity, starspots, tellurics, or the interstellar medium. Coincident with the ∼+10 km s−1 Doppler redshift, we detect a transient sodium absorption event dFNaD/F⋆ = 3.6% ± 1% at a relative difference of ΔFNaD(t) ∼ 4.4% ± 1%, lasting ΔtNaD ≳ 40 minutes. Since exoplanetary alkali signatures are blueshifted due to the natural vector of radiation pressure, estimated here at roughly ∼−5.7 km s−1, the radial velocity is rather at +15.4 km s−1, far larger than any known exoplanet system. Given that the redshift magnitude vΓ is in between the Roche limit and dynamically stable satellite orbits, the transient sodium may be a putative indication of a natural satellite orbiting WASP-49 A b.","lang":"eng"}],"file_date_updated":"2024-10-21T11:05:11Z","title":"Redshifted sodium transient near exoplanet transit","article_number":"L53","arxiv":1,"external_id":{"isi":["001322169500001"],"arxiv":["2409.19844"]},"article_processing_charge":"Yes"},{"intvolume":" 78","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"isi":1,"has_accepted_license":"1","OA_type":"hybrid","corr_author":"1","date_published":"2024-10-01T00:00:00Z","ddc":["570"],"author":[{"first_name":"Simon","last_name":"Rella","full_name":"Rella, Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425"},{"full_name":"Kulikova, Yuliya A.","first_name":"Yuliya A.","last_name":"Kulikova"},{"id":"87DF77F0-1D9A-11EA-B6AE-CE443DDC885E","full_name":"Minnegalieva, Aygul","last_name":"Minnegalieva","first_name":"Aygul"},{"first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"year":"2024","day":"01","file":[{"file_name":"2024_Evolution_Rella.pdf","file_id":"18453","success":1,"relation":"main_file","date_created":"2024-10-21T09:34:50Z","checksum":"5c6e8475bb88b07d424a5130d5e91e74","access_level":"open_access","creator":"dernst","file_size":29360811,"content_type":"application/pdf","date_updated":"2024-10-21T09:34:50Z"}],"status":"public","publication_status":"published","pmid":1,"date_updated":"2026-04-07T12:34:57Z","publisher":"Oxford University Press","article_type":"original","article_processing_charge":"Yes (via OA deal)","page":"1722-1738","external_id":{"pmid":["38990788"],"isi":["001286581900001"]},"publication":"Evolution: International journal of organic evolution","abstract":[{"text":"Vaccination is the most effective tool to control infectious diseases. However, the evolution of vaccine resistance, exemplified by vaccine resistance in SARS-CoV-2, remains a concern. Here, we model complex vaccination strategies against a pathogen with multiple epitopes—molecules targeted by the vaccine. We found that a vaccine targeting one epitope was ineffective in preventing vaccine escape. Vaccine resistance in highly infectious pathogens was prevented by the full-epitope vaccine, that is, one targeting all available epitopes, but only when the rate of pathogen evolution was low. Strikingly, a bet-hedging strategy of random administration of vaccines targeting different epitopes was the most effective in preventing vaccine resistance in pathogens with the low rate of infection and high rate of evolution. Thus, complex vaccination strategies, when biologically feasible, may be preferable to the currently used single-vaccine approaches for long-term control of disease outbreaks, especially when applied to livestock with near 100% vaccination rates.","lang":"eng"}],"volume":78,"file_date_updated":"2024-10-21T09:34:50Z","title":"Complex vaccination strategies prevent the emergence of vaccine resistance","OA_place":"publisher","issue":"10","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","oa":1,"department":[{"_id":"GaTk"}],"acknowledgement":"We thank Raimundo Julian Saona Urmeneta, Maike Morrison, Sergey Kryazhimskiy, Hiroki Ishikawa, Simone Pigolotti, and Shingo Miyauchi for fruitful discussions. We also thank the participants of the FRISBI seminar at ISTA for useful comments.","date_created":"2024-10-13T22:01:50Z","doi":"10.1093/evolut/qpae106","_id":"18307","related_material":{"link":[{"relation":"software","url":"https://github.com/Simon-Re/complex-vaccination"}],"record":[{"status":"public","relation":"research_data","id":"14862"},{"id":"20811","status":"public","relation":"dissertation_contains"}]},"publication_identifier":{"eissn":["1558-5646"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"10","type":"journal_article","scopus_import":"1","citation":{"ista":"Rella S, Kulikova YA, Minnegalieva A, Kondrashov F. 2024. Complex vaccination strategies prevent the emergence of vaccine resistance. Evolution: International journal of organic evolution. 78(10), 1722–1738.","apa":"Rella, S., Kulikova, Y. A., Minnegalieva, A., & Kondrashov, F. (2024). Complex vaccination strategies prevent the emergence of vaccine resistance. Evolution: International Journal of Organic Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpae106","mla":"Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” Evolution: International Journal of Organic Evolution, vol. 78, no. 10, Oxford University Press, 2024, pp. 1722–38, doi:10.1093/evolut/qpae106.","ieee":"S. Rella, Y. A. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” Evolution: International journal of organic evolution, vol. 78, no. 10. Oxford University Press, pp. 1722–1738, 2024.","short":"S. Rella, Y.A. Kulikova, A. Minnegalieva, F. Kondrashov, Evolution: International Journal of Organic Evolution 78 (2024) 1722–1738.","chicago":"Rella, Simon, Yuliya A. Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” Evolution: International Journal of Organic Evolution. Oxford University Press, 2024. https://doi.org/10.1093/evolut/qpae106.","ama":"Rella S, Kulikova YA, Minnegalieva A, Kondrashov F. Complex vaccination strategies prevent the emergence of vaccine resistance. Evolution: International journal of organic evolution. 2024;78(10):1722-1738. doi:10.1093/evolut/qpae106"}},{"date_updated":"2025-12-02T13:49:11Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","status":"public","publication_status":"published","file":[{"file_size":873561,"content_type":"application/pdf","date_updated":"2024-10-21T09:41:48Z","creator":"dernst","access_level":"open_access","date_created":"2024-10-21T09:41:48Z","relation":"main_file","checksum":"8e8c0b13049f11bb0133dfac22e32718","success":1,"file_id":"18454","file_name":"2024_LIPICs_DuprelaTour.pdf"}],"year":"2024","day":"23","author":[{"full_name":"La Tour, Max Dupré","last_name":"La Tour","first_name":"Max Dupré"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H"},{"id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","full_name":"Saulpic, David","last_name":"Saulpic","first_name":"David"}],"corr_author":"1","OA_type":"gold","date_published":"2024-09-23T00:00:00Z","ddc":["000"],"has_accepted_license":"1","intvolume":" 308","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","scopus_import":"1","citation":{"short":"M.D. La Tour, M. Henzinger, D. Saulpic, in:, 32nd Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ieee":"M. D. La Tour, M. Henzinger, and D. Saulpic, “Fully dynamic k-means coreset in near-optimal update time,” in 32nd Annual European Symposium on Algorithms, London, United Kingdom, 2024, vol. 308.","mla":"La Tour, Max Dupré, et al. “Fully Dynamic K-Means Coreset in near-Optimal Update Time.” 32nd Annual European Symposium on Algorithms, vol. 308, 100, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.ESA.2024.100.","ama":"La Tour MD, Henzinger M, Saulpic D. Fully dynamic k-means coreset in near-optimal update time. In: 32nd Annual European Symposium on Algorithms. Vol 308. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.ESA.2024.100","chicago":"La Tour, Max Dupré, Monika Henzinger, and David Saulpic. “Fully Dynamic K-Means Coreset in near-Optimal Update Time.” In 32nd Annual European Symposium on Algorithms, Vol. 308. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.ESA.2024.100.","ista":"La Tour MD, Henzinger M, Saulpic D. 2024. Fully dynamic k-means coreset in near-optimal update time. 32nd Annual European Symposium on Algorithms. ESA: European Symposium on Algorithms, LIPIcs, vol. 308, 100.","apa":"La Tour, M. D., Henzinger, M., & Saulpic, D. (2024). Fully dynamic k-means coreset in near-optimal update time. In 32nd Annual European Symposium on Algorithms (Vol. 308). London, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ESA.2024.100"},"acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct Grant agreement No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/Z422, grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nDavid Saulpic: Work partially done while at ISTA. Received funding from the European Union’s\r\nHorizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 101034413. This work was partially funded by the grant ANR-19-CE48-0016 from the French National Research Agency (ANR).","date_created":"2024-10-13T22:01:50Z","doi":"10.4230/LIPIcs.ESA.2024.100","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773386"]},"_id":"18308","oa":1,"oa_version":"Published Version","department":[{"_id":"MoHe"}],"OA_place":"publisher","language":[{"iso":"eng"}],"quality_controlled":"1","article_number":"100","title":"Fully dynamic k-means coreset in near-optimal update time","abstract":[{"text":"We study in this paper the problem of maintaining a solution to k-median and k-means clustering in a fully dynamic setting. To do so, we present an algorithm to efficiently maintain a coreset, a compressed version of the dataset, that allows easy computation of a clustering solution at query time. Our coreset algorithm has near-optimal update time of Õ(k) in general metric spaces, which reduces to Õ(d) in the Euclidean space ℝ^d. The query time is O(k²) in general metrics, and O(kd) in ℝ^d. To maintain a constant-factor approximation for k-median and k-means clustering in Euclidean space, this directly leads to an algorithm with update time Õ(d), and query time Õ(kd + k²). To maintain a O(polylog k)-approximation, the query time is reduced to Õ(kd).","lang":"eng"}],"publication":"32nd Annual European Symposium on Algorithms","volume":308,"ec_funded":1,"alternative_title":["LIPIcs"],"file_date_updated":"2024-10-21T09:41:48Z","article_processing_charge":"Yes","conference":{"end_date":"2024-09-04","start_date":"2024-09-02","location":"London, United Kingdom","name":"ESA: European Symposium on Algorithms"},"external_id":{"isi":["001545622400100"],"arxiv":["2406.19926"]},"project":[{"name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"name":"Efficient algorithms","grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer"},{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"arxiv":1},{"conference":{"name":"ESA: European Symposium on Algorithms","location":"London, United Kingdom","start_date":"2024-09-02","end_date":"2024-09-04"},"external_id":{"arxiv":["2312.08489"],"isi":["001545622400072"]},"article_processing_charge":"Yes","arxiv":1,"article_number":"72","title":"Connectivity oracles for predictable vertex failures","abstract":[{"lang":"eng","text":"The problem of designing connectivity oracles supporting vertex failures is one of the basic data structures problems for undirected graphs. It is already well understood: previous works [Duan-Pettie STOC'10; Long-Saranurak FOCS'22] achieve query time linear in the number of failed vertices, and it is conditionally optimal as long as we require preprocessing time polynomial in the size of the graph and update time polynomial in the number of failed vertices. We revisit this problem in the paradigm of algorithms with predictions: we ask if the query time can be improved if the set of failed vertices can be predicted beforehand up to a small number of errors. More specifically, we design a data structure that, given a graph G = (V,E) and a set of vertices predicted to fail D̂ ⊆ V of size d = |D̂|, preprocesses it in time Õ(d|E|) and then can receive an update given as the symmetric difference between the predicted and the actual set of failed vertices D̂△D = (D̂ ⧵ D) ∪ (D ⧵ D̂) of size η = |D̂△D|, process it in time Õ(η⁴), and after that answer connectivity queries in G ⧵ D in time O(η). Viewed from another perspective, our data structure provides an improvement over the state of the art for the fully dynamic subgraph connectivity problem in the sensitivity setting [Henzinger-Neumann ESA'16]. We argue that the preprocessing time and query time of our data structure are conditionally optimal under standard fine-grained complexity assumptions."}],"publication":"32nd Annual European Symposium on Algorithms","volume":308,"alternative_title":["LIPIcs"],"file_date_updated":"2024-10-21T10:03:48Z","oa_version":"Published Version","oa":1,"department":[{"_id":"MoHe"}],"OA_place":"publisher","language":[{"iso":"eng"}],"quality_controlled":"1","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","scopus_import":"1","citation":{"ista":"Hu B, Kosinas E, Polak A. 2024. Connectivity oracles for predictable vertex failures. 32nd Annual European Symposium on Algorithms. ESA: European Symposium on Algorithms, LIPIcs, vol. 308, 72.","apa":"Hu, B., Kosinas, E., & Polak, A. (2024). Connectivity oracles for predictable vertex failures. In 32nd Annual European Symposium on Algorithms (Vol. 308). London, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ESA.2024.72","short":"B. Hu, E. Kosinas, A. Polak, in:, 32nd Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Hu, Bingbing, et al. “Connectivity Oracles for Predictable Vertex Failures.” 32nd Annual European Symposium on Algorithms, vol. 308, 72, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.ESA.2024.72.","ieee":"B. Hu, E. Kosinas, and A. Polak, “Connectivity oracles for predictable vertex failures,” in 32nd Annual European Symposium on Algorithms, London, United Kingdom, 2024, vol. 308.","ama":"Hu B, Kosinas E, Polak A. Connectivity oracles for predictable vertex failures. 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Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.ESA.2024.72."},"acknowledgement":"Part of this work was done when Evangelos Kosinas was at University of Ioannina and Adam Polak was at Max Planck Institute of Informatics.\r\n","doi":"10.4230/LIPIcs.ESA.2024.72","date_created":"2024-10-13T22:01:50Z","_id":"18309","publication_identifier":{"isbn":["9783959773386"],"issn":["1868-8969"]},"has_accepted_license":"1","intvolume":" 308","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"author":[{"full_name":"Hu, Bingbing","last_name":"Hu","first_name":"Bingbing"},{"id":"4c7f9625-dbbc-11ee-9d86-bdcc2db5a949","full_name":"Kosinas, Evangelos","last_name":"Kosinas","first_name":"Evangelos"},{"full_name":"Polak, Adam","last_name":"Polak","first_name":"Adam"}],"corr_author":"1","OA_type":"gold","date_published":"2024-09-01T00:00:00Z","ddc":["000"],"file":[{"file_id":"18455","file_name":"2024_LIPICs_Hu.pdf","success":1,"access_level":"open_access","date_created":"2024-10-21T10:03:48Z","checksum":"ab1f2f9161549a8763eda15db40e022c","relation":"main_file","content_type":"application/pdf","date_updated":"2024-10-21T10:03:48Z","file_size":853914,"creator":"dernst"}],"year":"2024","day":"01","date_updated":"2025-12-02T13:49:52Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","status":"public","publication_status":"published"},{"author":[{"first_name":"Maria","last_name":"Kitsara","full_name":"Kitsara, Maria"},{"last_name":"Smajlhodžić-Deljo","first_name":"Merima","full_name":"Smajlhodžić-Deljo, Merima"},{"last_name":"Gurbeta Pokvic","first_name":"Lejla","full_name":"Gurbeta Pokvic, Lejla"},{"full_name":"Bert, Bettina","first_name":"Bettina","last_name":"Bert"},{"last_name":"Bubalo","first_name":"Nataliia","full_name":"Bubalo, Nataliia"},{"full_name":"Erden, Sevilay","last_name":"Erden","first_name":"Sevilay"},{"first_name":"Nuno Henrique","last_name":"Franco","full_name":"Franco, Nuno Henrique"},{"first_name":"Giuseppe","last_name":"Chirico","full_name":"Chirico, Giuseppe"},{"first_name":"Jonathan","last_name":"Gómez Raja","full_name":"Gómez Raja, Jonathan"},{"full_name":"Gonzalez-Uarquin, Fernando","first_name":"Fernando","last_name":"Gonzalez-Uarquin"},{"full_name":"Lang, Annemarie","first_name":"Annemarie","last_name":"Lang"},{"full_name":"Linklater, Nicole","first_name":"Nicole","last_name":"Linklater"},{"full_name":"Mojsova, Sandra","first_name":"Sandra","last_name":"Mojsova"},{"last_name":"Olsson","first_name":"I. Anna S.","full_name":"Olsson, I. Anna S."},{"first_name":"Ioanna","last_name":"Sandvig","full_name":"Sandvig, Ioanna"},{"full_name":"Schaffert, Alexandra","first_name":"Alexandra","last_name":"Schaffert"},{"full_name":"Schmit, Marthe","last_name":"Schmit","first_name":"Marthe"},{"full_name":"Schober, Sophie","id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","first_name":"Sophie","last_name":"Schober"},{"first_name":"Bogdan","last_name":"Sevastre","full_name":"Sevastre, Bogdan"},{"full_name":"Wilflingseder, Doris","last_name":"Wilflingseder","first_name":"Doris"},{"full_name":"Ahluwalia, Arti","first_name":"Arti","last_name":"Ahluwalia"},{"first_name":"Winfried","last_name":"Neuhaus","full_name":"Neuhaus, Winfried"}],"date_published":"2024-11-01T00:00:00Z","OA_type":"closed access","isi":1,"intvolume":" 52","article_type":"original","publisher":"SAGE Publications","date_updated":"2025-09-08T09:56:39Z","pmid":1,"publication_status":"published","status":"public","day":"01","year":"2024","title":"Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE)","volume":52,"publication":"Alternatives to Laboratory Animals","page":"326-333","article_processing_charge":"No","external_id":{"isi":["001348633700007"],"pmid":["39333027"]},"citation":{"ista":"Kitsara M, Smajlhodžić-Deljo M, Gurbeta Pokvic L, Bert B, Bubalo N, Erden S, Franco NH, Chirico G, Gómez Raja J, Gonzalez-Uarquin F, Lang A, Linklater N, Mojsova S, Olsson IAS, Sandvig I, Schaffert A, Schmit M, Schober S, Sevastre B, Wilflingseder D, Ahluwalia A, Neuhaus W. 2024. Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE). Alternatives to Laboratory Animals. 52(6), 326–333.","apa":"Kitsara, M., Smajlhodžić-Deljo, M., Gurbeta Pokvic, L., Bert, B., Bubalo, N., Erden, S., … Neuhaus, W. (2024). Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE). Alternatives to Laboratory Animals. SAGE Publications. https://doi.org/10.1177/02611929241286024","mla":"Kitsara, Maria, et al. “Introducing the COST Action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE).” Alternatives to Laboratory Animals, vol. 52, no. 6, SAGE Publications, 2024, pp. 326–33, doi:10.1177/02611929241286024.","ieee":"M. Kitsara et al., “Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE),” Alternatives to Laboratory Animals, vol. 52, no. 6. SAGE Publications, pp. 326–333, 2024.","short":"M. Kitsara, M. Smajlhodžić-Deljo, L. Gurbeta Pokvic, B. Bert, N. Bubalo, S. Erden, N.H. Franco, G. Chirico, J. Gómez Raja, F. Gonzalez-Uarquin, A. Lang, N. Linklater, S. Mojsova, I.A.S. Olsson, I. Sandvig, A. Schaffert, M. Schmit, S. Schober, B. Sevastre, D. Wilflingseder, A. Ahluwalia, W. Neuhaus, Alternatives to Laboratory Animals 52 (2024) 326–333.","chicago":"Kitsara, Maria, Merima Smajlhodžić-Deljo, Lejla Gurbeta Pokvic, Bettina Bert, Nataliia Bubalo, Sevilay Erden, Nuno Henrique Franco, et al. “Introducing the COST Action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE).” Alternatives to Laboratory Animals. SAGE Publications, 2024. https://doi.org/10.1177/02611929241286024.","ama":"Kitsara M, Smajlhodžić-Deljo M, Gurbeta Pokvic L, et al. Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE). 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In a recent paper published in Cell, Yang and colleagues show the involvement of a single Pep family member from tomato in wound signaling and how exogenous application of this regeneration factor enhances transformation efficiency in crops.","lang":"eng"}],"publication":"Cell Research","title":"Feeling the danger: Local wound signaling in plants","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"None","department":[{"_id":"JiFr"}],"_id":"18311","publication_identifier":{"issn":["1001-0602"],"eissn":["1748-7838"]},"doi":"10.1038/s41422-024-01035-x","date_created":"2024-10-13T22:01:51Z","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"11","citation":{"apa":"Hörmayer, L., & Friml, J. (2024). Feeling the danger: Local wound signaling in plants. Cell Research. Springer Nature. https://doi.org/10.1038/s41422-024-01035-x","ista":"Hörmayer L, Friml J. 2024. Feeling the danger: Local wound signaling in plants. Cell Research. 34, 761–762.","chicago":"Hörmayer, Lukas, and Jiří Friml. “Feeling the Danger: Local Wound Signaling in Plants.” Cell Research. Springer Nature, 2024. https://doi.org/10.1038/s41422-024-01035-x.","ama":"Hörmayer L, Friml J. Feeling the danger: Local wound signaling in plants. Cell Research. 2024;34:761-762. doi:10.1038/s41422-024-01035-x","ieee":"L. Hörmayer and J. Friml, “Feeling the danger: Local wound signaling in plants,” Cell Research, vol. 34. Springer Nature, pp. 761–762, 2024.","mla":"Hörmayer, Lukas, and Jiří Friml. “Feeling the Danger: Local Wound Signaling in Plants.” Cell Research, vol. 34, Springer Nature, 2024, pp. 761–62, doi:10.1038/s41422-024-01035-x.","short":"L. Hörmayer, J. Friml, Cell Research 34 (2024) 761–762."},"scopus_import":"1","intvolume":" 34","isi":1,"corr_author":"1","OA_type":"closed access","date_published":"2024-11-01T00:00:00Z","author":[{"last_name":"Hörmayer","first_name":"Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"year":"2024","day":"01","publication_status":"published","pmid":1,"status":"public","date_updated":"2025-09-08T09:57:18Z","article_type":"original","publisher":"Springer Nature"},{"corr_author":"1","OA_type":"free access","date_published":"2024-10-24T00:00:00Z","ddc":["516"],"author":[{"id":"44A03D04-AEA4-11E9-B225-EA2DE6697425","full_name":"Sisak, Maria A","last_name":"Sisak","first_name":"Maria A"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"keyword":["hyperkaehler geometry","branes","mirror symmetry","T-duality"],"has_accepted_license":"1","status":"public","publication_status":"published","date_updated":"2026-04-07T12:42:44Z","publisher":"Institute of Science and Technology Austria","year":"2024","day":"24","file":[{"relation":"main_file","checksum":"8c4893e726aaa4b3efb82758da9b6851","date_created":"2024-10-23T14:42:45Z","access_level":"open_access","creator":"msisak","date_updated":"2024-10-23T14:42:45Z","content_type":"application/pdf","file_size":1672547,"file_name":"MASisak_dissertation.pdf","file_id":"18467","success":1},{"file_id":"18468","file_name":"MASisak_source.zip","file_size":617913,"content_type":"application/x-zip-compressed","date_updated":"2024-10-24T08:09:13Z","creator":"msisak","access_level":"closed","date_created":"2024-10-23T14:43:56Z","checksum":"1831b072e861a1e5481024ca9d02b036","relation":"source_file"}],"abstract":[{"text":"In [KW06] Kapustin and Witten conjectured that there is a mirror symmetry relation between\r\nthe hyperkähler structures on certain Higgs bundle moduli spaces. As a consequence, they\r\nconjecture an equivalence between categories of BBB and BAA-branes. At the classical\r\nlevel, this mirror symmetry is given by T-duality between semi-flat hyperkähler structures on\r\nalgebraic integrable systems.\r\nIn this thesis, we investigate the T-duality relation between hyperkähler structures and the\r\ncorresponding branes on affine torus bundles. We use the techniques of generalized geometry\r\nto show that semi-flat hyperkähler structures are T-dual on algebraic integrable systems.\r\nWe also describe T-duality for generalized branes. Motivated by Fourier-Mukai transform\r\nwe upgrade the T-duality between generalized branes to T-duality of submanifolds endowed\r\nwith U(1)-bundles and connections. This T-duality in the appropriate context specializes to\r\nT-duality between BBB and BAA-branes.\r\n","lang":"eng"}],"alternative_title":["ISTA Thesis"],"file_date_updated":"2024-10-24T08:09:13Z","title":"T-dual branes on hyperkähler manifolds","page":"178","article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-9582-2634","full_name":"Hausel, Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamás","last_name":"Hausel"}],"project":[{"grant_number":"26069","_id":"6286e8c4-2b32-11ec-9570-f5297902f67f","name":"Branes on hyperkähler manifolds"}],"date_created":"2024-10-19T12:00:37Z","doi":"10.15479/at:ista:18443","publication_identifier":{"issn":["2663-337X"]},"_id":"18443","month":"10","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"dissertation","degree_awarded":"PhD","citation":{"ista":"Sisak MA. 2024. T-dual branes on hyperkähler manifolds. Institute of Science and Technology Austria.","apa":"Sisak, M. A. (2024). T-dual branes on hyperkähler manifolds. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18443","short":"M.A. Sisak, T-Dual Branes on Hyperkähler Manifolds, Institute of Science and Technology Austria, 2024.","ieee":"M. A. Sisak, “T-dual branes on hyperkähler manifolds,” Institute of Science and Technology Austria, 2024.","mla":"Sisak, Maria A. T-Dual Branes on Hyperkähler Manifolds. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18443.","ama":"Sisak MA. T-dual branes on hyperkähler manifolds. 2024. doi:10.15479/at:ista:18443","chicago":"Sisak, Maria A. “T-Dual Branes on Hyperkähler Manifolds.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18443."},"OA_place":"publisher","language":[{"iso":"eng"}],"oa":1,"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"TaHa"}]},{"author":[{"last_name":"Dymond","first_name":"Michael","full_name":"Dymond, Michael"},{"last_name":"Kaluza","first_name":"Vojtech","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","full_name":"Kaluza, Vojtech","orcid":"0000-0002-2512-8698"}],"ddc":["510"],"date_published":"2024-02-01T00:00:00Z","corr_author":"1","OA_type":"hybrid","has_accepted_license":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":" 218","publisher":"Springer Nature","article_type":"original","date_updated":"2025-04-23T07:37:26Z","pmid":1,"publication_status":"published","status":"public","file":[{"file_id":"17257","file_name":"2024_GeometriaeDedicata_Dymond.pdf","success":1,"access_level":"open_access","checksum":"9418534ac2f3d6f1f091a8b8ccaed01e","relation":"main_file","date_created":"2024-07-16T10:14:13Z","date_updated":"2024-07-16T10:14:13Z","content_type":"application/pdf","file_size":540981,"creator":"dernst"}],"day":"01","year":"2024","title":"Divergence of separated nets with respect to displacement equivalence","article_number":"15","file_date_updated":"2024-07-16T10:14:13Z","volume":218,"publication":"Geometriae Dedicata","abstract":[{"lang":"eng","text":"We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence."}],"external_id":{"isi":["001105681500001"],"pmid":["38021107"],"arxiv":["2102.13046"]},"article_processing_charge":"Yes (via OA deal)","arxiv":1,"citation":{"apa":"Dymond, M., & Kaluza, V. (2024). Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. Springer Nature. https://doi.org/10.1007/s10711-023-00862-3","ista":"Dymond M, Kaluza V. 2024. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 218, 15.","chicago":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata. Springer Nature, 2024. https://doi.org/10.1007/s10711-023-00862-3.","ama":"Dymond M, Kaluza V. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 2024;218. doi:10.1007/s10711-023-00862-3","mla":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata, vol. 218, 15, Springer Nature, 2024, doi:10.1007/s10711-023-00862-3.","ieee":"M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement equivalence,” Geometriae Dedicata, vol. 218. Springer Nature, 2024.","short":"M. Dymond, V. Kaluza, Geometriae Dedicata 218 (2024)."},"scopus_import":"1","type":"journal_article","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0046-5755"],"eissn":["1572-9168"]},"_id":"9651","date_created":"2021-07-14T07:01:27Z","doi":"10.1007/s10711-023-00862-3","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was started while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35. It was continued when the first named author was employed at University of Leipzig and the second named author was employed at Institute of Science and Technology of Austria, where he was supported by an IST Fellowship.","department":[{"_id":"UlWa"}],"oa":1,"oa_version":"Published Version","quality_controlled":"1","language":[{"iso":"eng"}],"OA_place":"publisher"},{"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L"}],"page":"89","article_processing_charge":"No","title":"Adaptive hierarchical representations in the hippocampus","file_date_updated":"2025-01-19T23:30:04Z","ec_funded":1,"alternative_title":["ISTA Thesis"],"abstract":[{"text":"The hippocampus is central to memory formation, storage and retrieval over many\r\ntimescales. Neurons in this brain area are highly selective to spatial position as well as to many\r\nother variables of the environment. It is believed that the selectivity patterns of hippocampal\r\nneurons reflect the structure of tasks an animal performs. However, especially at timescales\r\nlonger than a few minutes or hours it is not fully known how these representations evolve, nor\r\nhow they map to behaviour in the process. In this thesis, I monitored the evolution of\r\nhippocampal representations in a novel spatial-associative memory task for rats. Reward\r\nlocations were associated with global sensory cues (i.e. context); animals had to remember the\r\nassociations and dig for food in those locations only. I used in vivo electrophysiology to record\r\nthe activity of the hippocampus dorsal CA1 neurons during the learning period of a few days.\r\nI report here a novel and simple method to classify behaviour performance to account\r\nfor individual variability in learning speed and spurious performance unrelated to true task rule\r\nlearning. Using this classification I was then able to investigate neural responses on different\r\nstages of learning matched across animals. On the first day of learning, I observed a fast\r\nformation of single-cell selectivity to task variables which remained stable over days. I also\r\nobserved that reward tuning was not a single process but dependent on task-related cognitive\r\nload. At the population level, a linear decoding approach revealed a hierarchy in the\r\nrepresentation of task variables that changed with learning. In the high-dimensional space of\r\npopulation activity, the representation of contexts was specific to each position in the maze, and\r\ncould thus be better decoded if the position was known. The decoding of position did not improve\r\nwith knowledge of other variables. As learning progressed, the hippocampal code underwent a\r\nreorganisation of high-variance directions in population activity, identified by principal\r\ncomponent analysis. I found that dominant dimensions started carrying increasing amounts of\r\ninformation about task context specifically at those positions where it mattered for task\r\nperformance. When I contrasted this with variables less relevant to task performance (e.g.\r\nmovement direction), I did not observe differences in decoding quality over positions nor a\r\nreduction of dimensionality with learning.\r\nOverall, the largest changes in CA1 neural response with task learning happened in a\r\nmatter of a few trials; over days, changes undetectable in single-cell statistics were responsible\r\nfor re-structuring the hierarchy of neural representations at the population level; these changes\r\nwere task-specific and reflected different stages of learning. This indicates that complex task\r\nlearning may involve different magnitudes of response modulation in CA1, which happen at\r\nspecific time scales linked to behaviour.","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JoCs"}],"oa_version":"Published Version","oa":1,"language":[{"iso":"eng"}],"OA_place":"publisher","citation":{"ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria.","apa":"Chiossi, H. S. C. (2024). Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14821","short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024.","mla":"Chiossi, Heloisa S. C. Adaptive Hierarchical Representations in the Hippocampus. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14821.","ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024.","ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:10.15479/at:ista:14821","chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14821."},"degree_awarded":"PhD","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"01","_id":"14821","publication_identifier":{"issn":["2663-337X"]},"date_created":"2024-01-16T14:25:21Z","doi":"10.15479/at:ista:14821","has_accepted_license":"1","author":[{"first_name":"Heloisa","last_name":"Chiossi","orcid":"0009-0004-2973-278X","full_name":"Chiossi, Heloisa","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"date_published":"2024-01-19T00:00:00Z","corr_author":"1","file":[{"date_created":"2024-01-19T11:04:05Z","relation":"source_file","checksum":"d3fa3de1abd5af5204c13e9d55375615","access_level":"closed","creator":"hchiossi","file_size":8656268,"embargo_to":"open_access","date_updated":"2025-01-19T23:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhD_Thesis_190124.docx","file_id":"14838"},{"creator":"hchiossi","content_type":"application/pdf","date_updated":"2025-01-19T23:30:04Z","file_size":6567275,"checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd","relation":"main_file","date_created":"2024-01-19T11:03:59Z","access_level":"open_access","embargo":"2025-01-19","file_name":"PhD_Thesis_190124.pdf","file_id":"14839"}],"day":"19","year":"2024","publisher":"Institute of Science and Technology Austria","date_updated":"2026-04-07T13:21:56Z","publication_status":"published","status":"public"},{"author":[{"orcid":"0000-0002-8489-9281","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kelemen, Réka K","last_name":"Kelemen","first_name":"Réka K"}],"ddc":["576"],"date_published":"2024-06-20T00:00:00Z","corr_author":"1","has_accepted_license":"1","keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"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)"},"publisher":"Institute of Science and Technology Austria","date_updated":"2026-04-07T13:21:37Z","publication_status":"published","status":"public","file":[{"file_name":"thesis.zip","file_id":"17121","creator":"rkelemen","content_type":"application/zip","date_updated":"2025-01-10T23:30:10Z","file_size":180557931,"embargo_to":"open_access","relation":"source_file","date_created":"2024-06-07T16:09:17Z","checksum":"fab59146e3b3dc2e5d214576984a2a63","access_level":"closed"},{"embargo":"2025-01-10","file_name":"thesis_to_archive.pdf","file_id":"17213","creator":"rkelemen","content_type":"application/pdf","date_updated":"2025-01-10T23:30:10Z","file_size":19405484,"checksum":"91cc4c25a792239e8a7688e8aec7c62a","relation":"main_file","date_created":"2024-07-10T08:00:20Z","access_level":"open_access"}],"day":"20","year":"2024","title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","file_date_updated":"2025-01-10T23:30:10Z","ec_funded":1,"alternative_title":["ISTA Thesis"],"abstract":[{"text":"Genomes are shaped by natural selection at the level of the organism, as genomic variants that\r\nhave a beneficial effect on the viability or fecundity of their carriers are on average expected\r\nto be passed on to more offspring than less beneficial alleles. However, selection also favors\r\ngenomic variants that drive their own transmission to the next generation above the mendelian\r\nexpectation of 50 percent in heterozygotes, even if these self-promoting variants are less\r\nbeneficial to the organism than other variants at the same locus. Such variants, called meiotic\r\ndrivers, are found in diverse taxa, and often impose fitness costs on their host organisms. As\r\nmeiotic drivers often require multiple genes and sequences for transmission ratio distortion,\r\nthey are often found in regions of low recombination, such as inversions, which prevent their\r\nrecombination with the non-driving homologous regions. Reduced recombination rates are\r\nexpected to lead to the accumulation of deleterious mutations, which may affect hundreds\r\nof genes trapped in the inversions of meiotic drivers. Although the observed fitness costs of\r\nself-promoting haplotypes are thought to possibly reflect sequence degeneration, no study has\r\nsystematically investigated the level of degeneration on a meiotic driver. Further, the low\r\nrates of recombination between driving and non-driving haplotypes have limited the power of\r\ntraditional genetic studies in uncovering the gene content of meiotic drivers, and made the\r\nthe identification of the genes causing transmission ratio distortion difficult.\r\nAfter an introduction to meiotic drivers in Chapter 1, this thesis presents three studies that\r\nmake use of next generation sequencing data to characterize the sequence and expression\r\nevolution of genes on the t-haplotype, a large and ancient meiotic driver in house mice that is\r\ntransmitted to up to 100% of the offspring in males heterozygous for it. Chapter 2 presents\r\na comprehensive assessment of the t-haplotype’s sequence evolution, which shows signs of\r\nsequence degeneration counteracted by occasional recombination with the non-driving homolog\r\nover large parts of the meiotic driver, proposing an explanation for its long-term survival.\r\nChapter 3 investigates the sequence and expression evolution of genes on the t-haplotype,\r\nand finds widespread expression and copy number changes and signs of less efficient purifying\r\nselection compared to the genes on the non-driving homolog. Further, this chapter finds\r\ncandidates for involvment in drive: two positively selected genes on the t-haplotype, and\r\nthe discovery of a t-specific gene duplicate, which was gained from another chromosome,\r\nand which acquired novel sequence and testis-specific expression on the t-haplotype. Finally,\r\nChapter 4 provides unprecedented insights into the gene expression landscape in testes of\r\nt-carrier mice, using single nucleus sequencing. Cell-resolved RNA-sequencing allows the\r\ncomparison of expression in spermatids carrying or not carrying the t-haplotype as well as the\r\ntiming of t-haplotype-induced expression changes along spermatogenesis. This study shows\r\nthe timing of previously found drive-associated genes, and uncovers novel candidate genes and\r\nbiological processes that may underlie the complex biology of transmission ratio distortion of\r\nthe t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses them in\r\nthe context of the current state of meiotic drive research.","lang":"eng"}],"project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"},{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"}],"supervisor":[{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"}],"article_processing_charge":"No","page":"105","citation":{"ama":"Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:10.15479/at:ista:17119","chicago":"Kelemen, Réka K. “Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17119.","short":"R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria, 2024.","ieee":"R. K. Kelemen, “Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria, 2024.","mla":"Kelemen, Réka K. Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17119.","apa":"Kelemen, R. K. (2024). Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17119","ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria."},"degree_awarded":"PhD","type":"dissertation","month":"06","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"17119","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-039-8"]},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"542"},{"id":"10767","relation":"part_of_dissertation","status":"public"}]},"date_created":"2024-06-07T16:14:13Z","doi":"10.15479/at:ista:17119","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"oa_version":"Published Version","oa":1,"language":[{"iso":"eng"}],"OA_place":"publisher"},{"supervisor":[{"last_name":"Bernecky","first_name":"Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A"}],"page":"124","article_processing_charge":"No","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"title":"Biochemical and structural insights into ADAR1 RNA editing","alternative_title":["ISTA Thesis"],"abstract":[{"text":"ADAR1 is broadly expressed across various tissues and is vital in regulating pathways\r\nassociated with innate immune responses. ADAR1 marks double-stranded RNA as \"self\"\r\nthrough its A-to-I editing activity, effectively repressing autoimmunity and maintaining\r\nimmune tolerance. This editing process has been detected at millions of sites across the\r\nhuman genome. However, the mechanism underlying ADAR1's substrate selectivity\r\nproperties remains largely unclear, with much of the current knowledge derived from\r\ncomparisons to its more extensively studied homolog, ADAR2. By studying ADAR1 in complex\r\nwith its RNA substrates and applying a combination of biochemical techniques and structural\r\nstudies using CryoEM, we aim to gain a more comprehensive understanding of the substrate\r\nselectivity characteristics of ADAR1.\r\nIn this thesis, the purification protocol for ADAR1 was successfully optimized, resulting in the\r\nfirst report in the literature to achieve high protein purity and activity. This advancement\r\nenabled the investigation of complex formation between ADAR1 and various RNA substrates,\r\nleading to the identification of optimal conditions for preparing the cryoEM sample. However,\r\ndespite comprehensive optimization of the cryo-EM conditions, the resulting data lacked the\r\ndesired quality, highlighting the need for similar rigorous optimization of the RNA substrates\r\nto facilitate structural studies of the ADAR1-RNA complex. The study was complemented by\r\nAlphaFold predictions, which provided some insights into this mechanism.\r\nMoreover, during this project I established a collaboration with a research group focused on\r\nstudying ADAR homologs. Notably ADAR homologs were identified in bivalve species, and it\r\nwas further demonstrated that ADAR and its A-to-I editing activity are upregulated in Pacific\r\noysters during infections with Ostreid herpesvirus-1—a highly infectious virus that leads to\r\nsignificant losses in oyster populations globally. I successfully purified oyster ADAR and\r\nprepared in vitro edited RNA for nanopore sequencing—a direct sequencing technology\r\ncapable of detecting modified nucleotides without the need for reverse transcription. The\r\ncollaborators initiated optimization of this nanopore-based approach. However, current\r\ntechnological limitations still constrain the reliable detection of modified nucleotides.\r\nThe project also examined the impact of RNA editing on RNA binding and filament formation\r\nby MDA5, a key cytosolic dsRNA sensor that triggers an interferon response. A primary target\r\nof ADAR1's editing activity is RNA derived from repetitive elements present in the genome,\r\nparticularly Alu elements forming double-stranded RNA. When unedited, these RNA\r\nsequences are recognized by MDA5. However, the mechanisms by which MDA5 interacts with\r\nAlu RNAs, as well as the role of A-to-I editing in influencing this binding, are still not well\r\nunderstood.\r\nThe interaction between MDA5 and Alu elements, was successfully established. This was\r\nachieved through the testing of different RNA variants and the evaluation of filament\r\nformation using binding techniques and electron microscopy imaging. This groundwork has\r\nset the conditions for further evaluation using CryoEM. Furthermore, the effects of A-to-I\r\nediting on the binding properties of MDA5 with Alu RNA were investigated. Given the recent\r\nresearch that has provided new insights into MDA5's interaction with dsRNA, it is essential to\r\nrevise the experimental setup to integrate these findings before moving forward with the\r\nCryoEM sample analysis.","lang":"eng"}],"file_date_updated":"2025-10-29T23:30:02Z","oa_version":"Published Version","oa":1,"department":[{"_id":"GradSch"},{"_id":"CaBe"}],"OA_place":"publisher","language":[{"iso":"eng"}],"type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"10","citation":{"chicago":"Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA Editing.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18477.","ama":"Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024. doi:10.15479/at:ista:18477","mla":"Kaczmarek, Beata M. Biochemical and Structural Insights into ADAR1 RNA Editing. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18477.","ieee":"B. M. Kaczmarek, “Biochemical and structural insights into ADAR1 RNA editing,” Institute of Science and Technology Austria, 2024.","short":"B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024.","apa":"Kaczmarek, B. M. (2024). Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18477","ista":"Kaczmarek BM. 2024. Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria."},"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-045-9"]},"_id":"18477","doi":"10.15479/at:ista:18477","date_created":"2024-10-27T07:35:13Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"author":[{"full_name":"Kaczmarek, Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","first_name":"Beata M","last_name":"Kaczmarek"}],"corr_author":"1","date_published":"2024-10-29T00:00:00Z","ddc":["572"],"file":[{"file_id":"18485","file_name":"20241029_PhD_thesis_BKaczmarek.docx","access_level":"closed","checksum":"2053294ea4d770c495e4cc501e2a218b","relation":"source_file","date_created":"2024-10-29T11:56:36Z","embargo_to":"open_access","file_size":23136626,"date_updated":"2025-10-29T23:30:02Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"bkaczmar"},{"embargo":"2025-10-29","file_id":"18486","file_name":"20241029_PhD_thesis_BKaczmarek.pdf","date_updated":"2025-10-29T23:30:02Z","content_type":"application/pdf","file_size":11707360,"creator":"bkaczmar","access_level":"open_access","relation":"main_file","date_created":"2024-10-29T11:56:44Z","checksum":"8ce857a4cd44b776791eaf180ac9dbb3"}],"year":"2024","day":"29","date_updated":"2026-04-07T13:23:59Z","publisher":"Institute of Science and Technology Austria","publication_status":"published","status":"public"}]