[{"publication_identifier":{"eissn":["1335-8871"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.2478/msr-2023-0023","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"file_date_updated":"2023-10-31T12:07:23Z","volume":23,"date_updated":"2023-10-31T12:12:47Z","date_created":"2023-10-22T22:01:15Z","author":[{"full_name":"Jakubík, Jozef","last_name":"Jakubík","first_name":"Jozef"},{"id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong","last_name":"Bui Thi Mai","full_name":"Bui Thi Mai, Phuong"},{"first_name":"Martina","last_name":"Chvosteková","full_name":"Chvosteková, Martina"},{"last_name":"Krakovská","first_name":"Anna","full_name":"Krakovská, Anna"}],"department":[{"_id":"ChLa"}],"publisher":"Sciendo","publication_status":"published","acknowledgement":"The work was supported by the Scientific Grant Agency of the Ministry of Education of the Slovak Republic and the Slovak Academy of Sciences, projects APVV-21-0216, VEGA2-0096-21 and VEGA 2-0023-22.","year":"2023","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","scopus_import":"1","date_published":"2023-08-01T00:00:00Z","page":"175-183","article_type":"original","citation":{"chicago":"Jakubík, Jozef, Mary Phuong, Martina Chvosteková, and Anna Krakovská. “Against the Flow of Time with Multi-Output Models.” Measurement Science Review. Sciendo, 2023. https://doi.org/10.2478/msr-2023-0023.","mla":"Jakubík, Jozef, et al. “Against the Flow of Time with Multi-Output Models.” Measurement Science Review, vol. 23, no. 4, Sciendo, 2023, pp. 175–83, doi:10.2478/msr-2023-0023.","short":"J. Jakubík, M. Phuong, M. Chvosteková, A. Krakovská, Measurement Science Review 23 (2023) 175–183.","ista":"Jakubík J, Phuong M, Chvosteková M, Krakovská A. 2023. Against the flow of time with multi-output models. Measurement Science Review. 23(4), 175–183.","apa":"Jakubík, J., Phuong, M., Chvosteková, M., & Krakovská, A. (2023). Against the flow of time with multi-output models. Measurement Science Review. Sciendo. https://doi.org/10.2478/msr-2023-0023","ieee":"J. Jakubík, M. Phuong, M. Chvosteková, and A. Krakovská, “Against the flow of time with multi-output models,” Measurement Science Review, vol. 23, no. 4. Sciendo, pp. 175–183, 2023.","ama":"Jakubík J, Phuong M, Chvosteková M, Krakovská A. Against the flow of time with multi-output models. Measurement Science Review. 2023;23(4):175-183. doi:10.2478/msr-2023-0023"},"publication":"Measurement Science Review","issue":"4","abstract":[{"text":"Recent work has paid close attention to the first principle of Granger causality, according to which cause precedes effect. In this context, the question may arise whether the detected direction of causality also reverses after the time reversal of unidirectionally coupled data. Recently, it has been shown that for unidirectionally causally connected autoregressive (AR) processes X → Y, after time reversal of data, the opposite causal direction Y → X is indeed detected, although typically as part of the bidirectional X↔ Y link. As we argue here, the answer is different when the measured data are not from AR processes but from linked deterministic systems. When the goal is the usual forward data analysis, cross-mapping-like approaches correctly detect X → Y, while Granger causality-like approaches, which should not be used for deterministic time series, detect causal independence X → Y. The results of backward causal analysis depend on the predictability of the reversed data. Unlike AR processes, observables from deterministic dynamical systems, even complex nonlinear ones, can be predicted well forward, while backward predictions can be difficult (notably when the time reversal of a function leads to one-to-many relations). To address this problem, we propose an approach based on models that provide multiple candidate predictions for the target, combined with a loss function that consideres only the best candidate. The resulting good forward and backward predictability supports the view that unidirectionally causally linked deterministic dynamical systems X → Y can be expected to detect the same link both before and after time reversal.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2023-10-31T12:07:23Z","date_updated":"2023-10-31T12:07:23Z","checksum":"b069cc10fa6a7c96b2bc9f728165f9e6","success":1,"relation":"main_file","file_id":"14476","content_type":"application/pdf","file_size":2639783,"creator":"dernst","file_name":"2023_MeasurementScienceRev_Jakubik.pdf","access_level":"open_access"}],"intvolume":" 23","title":"Against the flow of time with multi-output models","ddc":["510"],"status":"public","_id":"14446","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14443","intvolume":" 80","status":"public","title":"Addressing global environmental challenges to mental health using population neuroscience: A review","issue":"10","abstract":[{"lang":"eng","text":"Importance Climate change, pollution, urbanization, socioeconomic inequality, and psychosocial effects of the COVID-19 pandemic have caused massive changes in environmental conditions that affect brain health during the life span, both on a population level as well as on the level of the individual. How these environmental factors influence the brain, behavior, and mental illness is not well known.\r\nObservations A research strategy enabling population neuroscience to contribute to identify brain mechanisms underlying environment-related mental illness by leveraging innovative enrichment tools for data federation, geospatial observation, climate and pollution measures, digital health, and novel data integration techniques is described. This strategy can inform innovative treatments that target causal cognitive and molecular mechanisms of mental illness related to the environment. An example is presented of the environMENTAL Project that is leveraging federated cohort data of over 1.5 million European citizens and patients enriched with deep phenotyping data from large-scale behavioral neuroimaging cohorts to identify brain mechanisms related to environmental adversity underlying symptoms of depression, anxiety, stress, and substance misuse.\r\nConclusions and Relevance This research will lead to the development of objective biomarkers and evidence-based interventions that will significantly improve outcomes of environment-related mental illness."}],"type":"journal_article","date_published":"2023-10-01T00:00:00Z","citation":{"ista":"Schumann G, Andreassen OA, Banaschewski T, Calhoun VD, Clinton N, Desrivieres S, Brandlistuen RE, Feng J, Hese S, Hitchen E, Hoffmann P, Jia T, Jirsa V, Marquand AF, Nees F, Nöthen MM, Novarino G, Polemiti E, Ralser M, Rapp M, Schepanski K, Schikowski T, Slater M, Sommer P, Stahl BC, Thompson PM, Twardziok S, Van Der Meer D, Walter H, Westlye L. 2023. Addressing global environmental challenges to mental health using population neuroscience: A review. JAMA Psychiatry. 80(10), 1066–1074.","apa":"Schumann, G., Andreassen, O. A., Banaschewski, T., Calhoun, V. D., Clinton, N., Desrivieres, S., … Westlye, L. (2023). Addressing global environmental challenges to mental health using population neuroscience: A review. JAMA Psychiatry. American Medical Association. https://doi.org/10.1001/jamapsychiatry.2023.2996","ieee":"G. Schumann et al., “Addressing global environmental challenges to mental health using population neuroscience: A review,” JAMA Psychiatry, vol. 80, no. 10. American Medical Association, pp. 1066–1074, 2023.","ama":"Schumann G, Andreassen OA, Banaschewski T, et al. Addressing global environmental challenges to mental health using population neuroscience: A review. JAMA Psychiatry. 2023;80(10):1066-1074. doi:10.1001/jamapsychiatry.2023.2996","chicago":"Schumann, Gunter, Ole A. Andreassen, Tobias Banaschewski, Vince D. Calhoun, Nicholas Clinton, Sylvane Desrivieres, Ragnhild Eek Brandlistuen, et al. “Addressing Global Environmental Challenges to Mental Health Using Population Neuroscience: A Review.” JAMA Psychiatry. American Medical Association, 2023. https://doi.org/10.1001/jamapsychiatry.2023.2996.","mla":"Schumann, Gunter, et al. “Addressing Global Environmental Challenges to Mental Health Using Population Neuroscience: A Review.” JAMA Psychiatry, vol. 80, no. 10, American Medical Association, 2023, pp. 1066–74, doi:10.1001/jamapsychiatry.2023.2996.","short":"G. Schumann, O.A. Andreassen, T. Banaschewski, V.D. Calhoun, N. Clinton, S. Desrivieres, R.E. Brandlistuen, J. Feng, S. Hese, E. Hitchen, P. Hoffmann, T. Jia, V. Jirsa, A.F. Marquand, F. Nees, M.M. Nöthen, G. Novarino, E. Polemiti, M. Ralser, M. Rapp, K. Schepanski, T. Schikowski, M. Slater, P. Sommer, B.C. Stahl, P.M. Thompson, S. Twardziok, D. Van Der Meer, H. Walter, L. Westlye, JAMA Psychiatry 80 (2023) 1066–1074."},"publication":"JAMA Psychiatry","page":"1066-1074","article_type":"review","article_processing_charge":"No","day":"01","scopus_import":"1","author":[{"full_name":"Schumann, Gunter","first_name":"Gunter","last_name":"Schumann"},{"full_name":"Andreassen, Ole A.","first_name":"Ole A.","last_name":"Andreassen"},{"full_name":"Banaschewski, Tobias","first_name":"Tobias","last_name":"Banaschewski"},{"last_name":"Calhoun","first_name":"Vince D.","full_name":"Calhoun, Vince D."},{"first_name":"Nicholas","last_name":"Clinton","full_name":"Clinton, Nicholas"},{"first_name":"Sylvane","last_name":"Desrivieres","full_name":"Desrivieres, Sylvane"},{"last_name":"Brandlistuen","first_name":"Ragnhild Eek","full_name":"Brandlistuen, Ragnhild Eek"},{"full_name":"Feng, Jianfeng","first_name":"Jianfeng","last_name":"Feng"},{"full_name":"Hese, Soeren","first_name":"Soeren","last_name":"Hese"},{"first_name":"Esther","last_name":"Hitchen","full_name":"Hitchen, Esther"},{"last_name":"Hoffmann","first_name":"Per","full_name":"Hoffmann, Per"},{"first_name":"Tianye","last_name":"Jia","full_name":"Jia, Tianye"},{"full_name":"Jirsa, Viktor","last_name":"Jirsa","first_name":"Viktor"},{"full_name":"Marquand, Andre F.","first_name":"Andre F.","last_name":"Marquand"},{"last_name":"Nees","first_name":"Frauke","full_name":"Nees, Frauke"},{"full_name":"Nöthen, Markus M.","first_name":"Markus M.","last_name":"Nöthen"},{"last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"},{"first_name":"Elli","last_name":"Polemiti","full_name":"Polemiti, Elli"},{"full_name":"Ralser, Markus","first_name":"Markus","last_name":"Ralser"},{"first_name":"Michael","last_name":"Rapp","full_name":"Rapp, Michael"},{"first_name":"Kerstin","last_name":"Schepanski","full_name":"Schepanski, Kerstin"},{"full_name":"Schikowski, Tamara","last_name":"Schikowski","first_name":"Tamara"},{"full_name":"Slater, Mel","first_name":"Mel","last_name":"Slater"},{"full_name":"Sommer, Peter","last_name":"Sommer","first_name":"Peter"},{"first_name":"Bernd Carsten","last_name":"Stahl","full_name":"Stahl, Bernd Carsten"},{"full_name":"Thompson, Paul M.","last_name":"Thompson","first_name":"Paul M."},{"full_name":"Twardziok, Sven","first_name":"Sven","last_name":"Twardziok"},{"full_name":"Van Der Meer, Dennis","first_name":"Dennis","last_name":"Van Der Meer"},{"first_name":"Henrik","last_name":"Walter","full_name":"Walter, Henrik"},{"full_name":"Westlye, Lars","last_name":"Westlye","first_name":"Lars"}],"volume":80,"date_updated":"2023-10-31T12:17:20Z","date_created":"2023-10-22T22:01:14Z","pmid":1,"year":"2023","publisher":"American Medical Association","department":[{"_id":"GaNo"}],"publication_status":"published","doi":"10.1001/jamapsychiatry.2023.2996","language":[{"iso":"eng"}],"external_id":{"pmid":["37610741"]},"quality_controlled":"1","publication_identifier":{"eissn":["2168-6238"]},"month":"10"},{"publication":"Communications in Mathematical Physics","citation":{"ama":"Brooks M, Seiringer R. The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy. Communications in Mathematical Physics. 2023;404:287-337. doi:10.1007/s00220-023-04841-3","ista":"Brooks M, Seiringer R. 2023. The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy. Communications in Mathematical Physics. 404, 287–337.","apa":"Brooks, M., & Seiringer, R. (2023). The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-023-04841-3","ieee":"M. Brooks and R. Seiringer, “The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy,” Communications in Mathematical Physics, vol. 404. Springer Nature, pp. 287–337, 2023.","mla":"Brooks, Morris, and Robert Seiringer. “The Fröhlich Polaron at Strong Coupling: Part I - The Quantum Correction to the Classical Energy.” Communications in Mathematical Physics, vol. 404, Springer Nature, 2023, pp. 287–337, doi:10.1007/s00220-023-04841-3.","short":"M. Brooks, R. Seiringer, Communications in Mathematical Physics 404 (2023) 287–337.","chicago":"Brooks, Morris, and Robert Seiringer. “The Fröhlich Polaron at Strong Coupling: Part I - The Quantum Correction to the Classical Energy.” Communications in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s00220-023-04841-3."},"article_type":"original","page":"287-337","date_published":"2023-11-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14441","title":"The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy","ddc":["510"],"status":"public","intvolume":" 404","oa_version":"Published Version","file":[{"checksum":"1ae49b39247cb6b40ff75997381581b8","success":1,"date_updated":"2023-10-31T12:21:39Z","date_created":"2023-10-31T12:21:39Z","relation":"main_file","file_id":"14477","content_type":"application/pdf","file_size":832375,"creator":"dernst","access_level":"open_access","file_name":"2023_CommMathPhysics_Brooks.pdf"}],"type":"journal_article","abstract":[{"text":"We study the Fröhlich polaron model in R3, and establish the subleading term in the strong coupling asymptotics of its ground state energy, corresponding to the quantum corrections to the classical energy determined by the Pekar approximation.","lang":"eng"}],"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"},"oa":1,"external_id":{"arxiv":["2207.03156"]},"quality_controlled":"1","project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"doi":"10.1007/s00220-023-04841-3","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"year":"2023","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Open access funding provided by Institute of Science and Technology (IST Austria).","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"RoSe"}],"author":[{"full_name":"Brooks, Morris","first_name":"Morris","last_name":"Brooks","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","orcid":"0000-0002-6249-0928"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"date_updated":"2023-10-31T12:22:51Z","date_created":"2023-10-22T22:01:13Z","volume":404,"file_date_updated":"2023-10-31T12:21:39Z","ec_funded":1},{"date_published":"2023-08-22T00:00:00Z","page":"11980-11989","citation":{"chicago":"Kolmogorov, Vladimir. “Solving Relaxations of MAP-MRF Problems: Combinatorial in-Face Frank-Wolfe Directions.” In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2023:11980–89. IEEE, 2023. https://doi.org/10.1109/CVPR52729.2023.01153.","short":"V. Kolmogorov, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2023, pp. 11980–11989.","mla":"Kolmogorov, Vladimir. “Solving Relaxations of MAP-MRF Problems: Combinatorial in-Face Frank-Wolfe Directions.” Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, vol. 2023, IEEE, 2023, pp. 11980–89, doi:10.1109/CVPR52729.2023.01153.","ieee":"V. Kolmogorov, “Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions,” in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Vancouver, Canada, 2023, vol. 2023, pp. 11980–11989.","apa":"Kolmogorov, V. (2023). Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions. In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (Vol. 2023, pp. 11980–11989). Vancouver, Canada: IEEE. https://doi.org/10.1109/CVPR52729.2023.01153","ista":"Kolmogorov V. 2023. Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition vol. 2023, 11980–11989.","ama":"Kolmogorov V. Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions. In: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Vol 2023. IEEE; 2023:11980-11989. doi:10.1109/CVPR52729.2023.01153"},"publication":"Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition","article_processing_charge":"No","day":"22","scopus_import":"1","oa_version":"Preprint","intvolume":" 2023","title":"Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions","status":"public","_id":"14448","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We consider the problem of solving LP relaxations of MAP-MRF inference problems, and in particular the method proposed recently in [16], [35]. As a key computational subroutine, it uses a variant of the Frank-Wolfe (FW) method to minimize a smooth convex function over a combinatorial polytope. We propose an efficient implementation of this subroutine based on in-face Frank-Wolfe directions, introduced in [4] in a different context. More generally, we define an abstract data structure for a combinatorial subproblem that enables in-face FW directions, and describe its specialization for tree-structured MAP-MRF inference subproblems. Experimental results indicate that the resulting method is the current state-of-art LP solver for some classes of problems. Our code is available at pub.ist.ac.at/~vnk/papers/IN-FACE-FW.html."}],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1109/CVPR52729.2023.01153","conference":{"location":"Vancouver, Canada","start_date":"2023-06-17","end_date":"2023-06-24","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"quality_controlled":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2010.09567","open_access":"1"}],"external_id":{"arxiv":["2010.09567"]},"oa":1,"publication_identifier":{"isbn":["9798350301298"],"issn":["1063-6919"]},"month":"08","volume":2023,"date_updated":"2023-10-31T12:01:24Z","date_created":"2023-10-22T22:01:16Z","author":[{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"VlKo"}],"publisher":"IEEE","publication_status":"published","year":"2023"},{"day":"28","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2023-03-28T00:00:00Z","publication":"Cell Reports","citation":{"ista":"Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng X, Howard M, Zilberman D. 2023. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 42(3), 112132.","ieee":"D. B. Lyons et al., “Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons,” Cell Reports, vol. 42, no. 3. Elsevier, 2023.","apa":"Lyons, D. B., Briffa, A., He, S., Choi, J., Hollwey, E., Colicchio, J., … Zilberman, D. (2023). Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.112132","ama":"Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 2023;42(3). doi:10.1016/j.celrep.2023.112132","chicago":"Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey, Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.112132.","mla":"Lyons, David B., et al. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” Cell Reports, vol. 42, no. 3, 112132, Elsevier, 2023, doi:10.1016/j.celrep.2023.112132.","short":"D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson, X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023)."},"article_type":"original","abstract":[{"lang":"eng","text":"Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation."}],"issue":"3","type":"journal_article","file":[{"file_name":"2023_CellReports_Lyons.pdf","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","file_size":8401261,"file_id":"12941","relation":"main_file","date_created":"2023-05-11T10:41:42Z","date_updated":"2023-05-11T10:41:42Z","success":1,"checksum":"6cbc44fdb18bf18834c9e2a5b9c67123"}],"oa_version":"Published Version","_id":"12672","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons","status":"public","ddc":["580"],"intvolume":" 42","month":"03","publication_identifier":{"eissn":["2211-1247"]},"doi":"10.1016/j.celrep.2023.112132","language":[{"iso":"eng"}],"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"},"external_id":{"isi":["000944921600001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"725746","_id":"62935a00-2b32-11ec-9570-eff30fa39068","name":"Quantitative analysis of DNA methylation maintenance with chromatin","call_identifier":"H2020"}],"file_date_updated":"2023-05-11T10:41:42Z","ec_funded":1,"article_number":"112132","author":[{"full_name":"Lyons, David B.","first_name":"David B.","last_name":"Lyons"},{"full_name":"Briffa, Amy","first_name":"Amy","last_name":"Briffa"},{"first_name":"Shengbo","last_name":"He","full_name":"He, Shengbo"},{"full_name":"Choi, Jaemyung","first_name":"Jaemyung","last_name":"Choi"},{"full_name":"Hollwey, Elizabeth","last_name":"Hollwey","first_name":"Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd"},{"full_name":"Colicchio, Jack","last_name":"Colicchio","first_name":"Jack"},{"last_name":"Anderson","first_name":"Ian","full_name":"Anderson, Ian"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi"},{"full_name":"Howard, Martin","last_name":"Howard","first_name":"Martin"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel"}],"date_created":"2023-02-23T09:17:44Z","date_updated":"2023-11-02T12:23:45Z","volume":42,"acknowledgement":"The authors would like to thank Jasper Rine for advice and mentorship to D.B.L., Lesley Philips, Timothy Wells, Sophie Able, and Christina Wistrom for support with plant growth, and Bhagyshree Jamge and Frédéric Berger for help with analysis of ddm1 × WT RNA-sequencing data. This work was supported by BBSRC Institute Strategic Program GEN (BB/P013511/1) to X.F., M.H., and D.Z., a European Research Council grant MaintainMeth (725746) to D.Z., and a postdoctoral fellowship from the Helen Hay Whitney Foundation to D.B.L.","year":"2023","publication_status":"published","publisher":"Elsevier","department":[{"_id":"DaZi"},{"_id":"XiFe"}]},{"date_published":"2023-06-13T00:00:00Z","publication":"Forum of Mathematics","citation":{"mla":"Mitrouskas, David Johannes, et al. “Optimal Parabolic Upper Bound for the Energy-Momentum Relation of a Strongly Coupled Polaron.” Forum of Mathematics, vol. 11, Cambridge University Press, 2023, pp. 1–52, doi:10.1017/fms.2023.45.","short":"D.J. Mitrouskas, K. Mysliwy, R. Seiringer, Forum of Mathematics 11 (2023) 1–52.","chicago":"Mitrouskas, David Johannes, Krzysztof Mysliwy, and Robert Seiringer. “Optimal Parabolic Upper Bound for the Energy-Momentum Relation of a Strongly Coupled Polaron.” Forum of Mathematics. Cambridge University Press, 2023. https://doi.org/10.1017/fms.2023.45.","ama":"Mitrouskas DJ, Mysliwy K, Seiringer R. Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron. Forum of Mathematics. 2023;11:1-52. doi:10.1017/fms.2023.45","ista":"Mitrouskas DJ, Mysliwy K, Seiringer R. 2023. Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron. Forum of Mathematics. 11, 1–52.","ieee":"D. J. Mitrouskas, K. Mysliwy, and R. Seiringer, “Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron,” Forum of Mathematics, vol. 11. Cambridge University Press, pp. 1–52, 2023.","apa":"Mitrouskas, D. J., Mysliwy, K., & Seiringer, R. (2023). Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron. Forum of Mathematics. Cambridge University Press. https://doi.org/10.1017/fms.2023.45"},"article_type":"original","page":"1-52","day":"13","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","file":[{"relation":"main_file","file_id":"13186","date_created":"2023-07-03T10:36:25Z","date_updated":"2023-07-03T10:36:25Z","checksum":"f672eb7dd015c472c9a04f1b9bf9df7d","success":1,"file_name":"2023_ForumofMathematics.Sigma_Mitrouskas.pdf","access_level":"open_access","file_size":943192,"content_type":"application/pdf","creator":"alisjak"}],"oa_version":"Published Version","_id":"13178","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron","status":"public","ddc":["500"],"intvolume":" 11","abstract":[{"text":"We consider the large polaron described by the Fröhlich Hamiltonian and study its energy-momentum relation defined as the lowest possible energy as a function of the total momentum. Using a suitable family of trial states, we derive an optimal parabolic upper bound for the energy-momentum relation in the limit of strong coupling. The upper bound consists of a momentum independent term that agrees with the predicted two-term expansion for the ground state energy of the strongly coupled polaron at rest and a term that is quadratic in the momentum with coefficient given by the inverse of twice the classical effective mass introduced by Landau and Pekar.","lang":"eng"}],"type":"journal_article","doi":"10.1017/fms.2023.45","language":[{"iso":"eng"}],"oa":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"},"external_id":{"arxiv":["2203.02454"],"isi":["001005008800001"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"month":"06","publication_identifier":{"eissn":["2050-5094"]},"author":[{"last_name":"Mitrouskas","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","full_name":"Mitrouskas, David Johannes"},{"full_name":"Mysliwy, Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","last_name":"Mysliwy","first_name":"Krzysztof"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-07-02T22:00:43Z","date_updated":"2023-11-02T12:30:50Z","volume":11,"year":"2023","acknowledgement":"This research was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement No. 694227 (R.S.) and the Maria Skłodowska-Curie grant agreement No. 665386 (K.M.).","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Cambridge University Press","file_date_updated":"2023-07-03T10:36:25Z","ec_funded":1},{"abstract":[{"text":"Intercellular signaling molecules, known as morphogens, act at a long range in developing tissues to provide spatial information and control properties such as cell fate and tissue growth. The production, transport, and removal of morphogens shape their concentration profiles in time and space. Downstream signaling cascades and gene regulatory networks within cells then convert the spatiotemporal morphogen profiles into distinct cellular responses. Current challenges are to understand the diverse molecular and cellular mechanisms underlying morphogen gradient formation, as well as the logic of downstream regulatory circuits involved in morphogen interpretation. This knowledge, combining experimental and theoretical results, is essential to understand emerging properties of morphogen-controlled systems, such as robustness and scaling.","lang":"eng"}],"type":"journal_article","file":[{"creator":"dernst","file_size":434819,"content_type":"application/pdf","file_name":"2023_AnnualReviews_Kicheva.pdf","access_level":"open_access","date_created":"2023-11-06T09:47:50Z","date_updated":"2023-11-06T09:47:50Z","success":1,"checksum":"461726014cf5907010afbd418d3c13ec","file_id":"14491","relation":"main_file"}],"oa_version":"Published Version","_id":"14484","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 39","status":"public","title":"Control of tissue development by morphogens","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"16","scopus_import":"1","date_published":"2023-10-16T00:00:00Z","citation":{"chicago":"Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.” Annual Review of Cell and Developmental Biology. Annual Reviews, 2023. https://doi.org/10.1146/annurev-cellbio-020823-011522.","mla":"Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.” Annual Review of Cell and Developmental Biology, vol. 39, Annual Reviews, 2023, pp. 91–121, doi:10.1146/annurev-cellbio-020823-011522.","short":"A. Kicheva, J. Briscoe, Annual Review of Cell and Developmental Biology 39 (2023) 91–121.","ista":"Kicheva A, Briscoe J. 2023. Control of tissue development by morphogens. Annual Review of Cell and Developmental Biology. 39, 91–121.","ieee":"A. Kicheva and J. Briscoe, “Control of tissue development by morphogens,” Annual Review of Cell and Developmental Biology, vol. 39. Annual Reviews, pp. 91–121, 2023.","apa":"Kicheva, A., & Briscoe, J. (2023). Control of tissue development by morphogens. Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev-cellbio-020823-011522","ama":"Kicheva A, Briscoe J. Control of tissue development by morphogens. Annual Review of Cell and Developmental Biology. 2023;39:91-121. doi:10.1146/annurev-cellbio-020823-011522"},"publication":"Annual Review of Cell and Developmental Biology","page":"91-121","article_type":"review","ec_funded":1,"file_date_updated":"2023-11-06T09:47:50Z","author":[{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","first_name":"Anna","last_name":"Kicheva","full_name":"Kicheva, Anna"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"}],"volume":39,"date_created":"2023-11-05T23:00:53Z","date_updated":"2023-11-06T09:56:24Z","pmid":1,"acknowledgement":"We are grateful to Zena Hadjivasiliou for comments on this article. A.K. is supported by grants from the European Research Council under the European Union (EU) Horizon 2020 research and innovation program (680037) and Horizon Europe (101044579), and the Austrian Science Fund (F78) (Stem Cell Modulation). J.B. is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051), and by a grant from the European Research Council under the EU Horizon 2020 research and innovation program (742138).","year":"2023","department":[{"_id":"AnKi"}],"publisher":"Annual Reviews","publication_status":"published","publication_identifier":{"issn":["1081-0706"],"eissn":["1530-8995"]},"month":"10","doi":"10.1146/annurev-cellbio-020823-011522","language":[{"iso":"eng"}],"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"},"external_id":{"pmid":["37418774"]},"oa":1,"project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020"},{"name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579"},{"name":"Morphogen control of growth and pattern in the spinal cord","grant_number":"F07802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1"},{"author":[{"first_name":"Pramod","last_name":"Rao","full_name":"Rao, Pramod"},{"full_name":"Mallikarjun, B. R.","first_name":"B. R.","last_name":"Mallikarjun"},{"full_name":"Fox, Gereon","last_name":"Fox","first_name":"Gereon"},{"full_name":"Weyrich, Tim","first_name":"Tim","last_name":"Weyrich"},{"full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"first_name":"Hanspeter","last_name":"Pfister","full_name":"Pfister, Hanspeter"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"first_name":"Fangneng","last_name":"Zhan","full_name":"Zhan, Fangneng"},{"last_name":"Tewari","first_name":"Ayush","full_name":"Tewari, Ayush"},{"last_name":"Theobalt","first_name":"Christian","full_name":"Theobalt, Christian"},{"first_name":"Mohamed","last_name":"Elgharib","full_name":"Elgharib, Mohamed"}],"date_created":"2023-11-05T23:00:54Z","date_updated":"2023-11-06T08:52:30Z","oa_version":"Published Version","year":"2023","_id":"14488","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Open Access funding enabled and organized by Projekt DEAL.","publication_status":"epub_ahead","status":"public","title":"A deeper analysis of volumetric relightiable faces","publisher":"Springer Nature","department":[{"_id":"BeBi"}],"abstract":[{"text":"Portrait viewpoint and illumination editing is an important problem with several applications in VR/AR, movies, and photography. Comprehensive knowledge of geometry and illumination is critical for obtaining photorealistic results. Current methods are unable to explicitly model in 3D while handling both viewpoint and illumination editing from a single image. In this paper, we propose VoRF, a novel approach that can take even a single portrait image as input and relight human heads under novel illuminations that can be viewed from arbitrary viewpoints. VoRF represents a human head as a continuous volumetric field and learns a prior model of human heads using a coordinate-based MLP with individual latent spaces for identity and illumination. The prior model is learned in an auto-decoder manner over a diverse class of head shapes and appearances, allowing VoRF to generalize to novel test identities from a single input image. Additionally, VoRF has a reflectance MLP that uses the intermediate features of the prior model for rendering One-Light-at-A-Time (OLAT) images under novel views. We synthesize novel illuminations by combining these OLAT images with target environment maps. Qualitative and quantitative evaluations demonstrate the effectiveness of VoRF for relighting and novel view synthesis, even when applied to unseen subjects under uncontrolled illumination. This work is an extension of Rao et al. (VoRF: Volumetric Relightable Faces 2022). We provide extensive evaluation and ablative studies of our model and also provide an application, where any face can be relighted using textual input.","lang":"eng"}],"type":"journal_article","date_published":"2023-10-31T00:00:00Z","doi":"10.1007/s11263-023-01899-3","language":[{"iso":"eng"}],"publication":"International Journal of Computer Vision","main_file_link":[{"url":"https://doi.org/10.1007/s11263-023-01899-3","open_access":"1"}],"oa":1,"citation":{"ama":"Rao P, Mallikarjun BR, Fox G, et al. A deeper analysis of volumetric relightiable faces. International Journal of Computer Vision. 2023. doi:10.1007/s11263-023-01899-3","apa":"Rao, P., Mallikarjun, B. R., Fox, G., Weyrich, T., Bickel, B., Pfister, H., … Elgharib, M. (2023). A deeper analysis of volumetric relightiable faces. International Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-023-01899-3","ieee":"P. Rao et al., “A deeper analysis of volumetric relightiable faces,” International Journal of Computer Vision. Springer Nature, 2023.","ista":"Rao P, Mallikarjun BR, Fox G, Weyrich T, Bickel B, Pfister H, Matusik W, Zhan F, Tewari A, Theobalt C, Elgharib M. 2023. A deeper analysis of volumetric relightiable faces. International Journal of Computer Vision.","short":"P. Rao, B.R. Mallikarjun, G. Fox, T. Weyrich, B. Bickel, H. Pfister, W. Matusik, F. Zhan, A. Tewari, C. Theobalt, M. Elgharib, International Journal of Computer Vision (2023).","mla":"Rao, Pramod, et al. “A Deeper Analysis of Volumetric Relightiable Faces.” International Journal of Computer Vision, Springer Nature, 2023, doi:10.1007/s11263-023-01899-3.","chicago":"Rao, Pramod, B. R. Mallikarjun, Gereon Fox, Tim Weyrich, Bernd Bickel, Hanspeter Pfister, Wojciech Matusik, et al. “A Deeper Analysis of Volumetric Relightiable Faces.” International Journal of Computer Vision. Springer Nature, 2023. https://doi.org/10.1007/s11263-023-01899-3."},"article_type":"original","quality_controlled":"1","day":"31","month":"10","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["0920-5691"],"eissn":["1573-1405"]},"scopus_import":"1"},{"acknowledgement":"This project has received funding from the JSPS-SNSF (Japan Society for the Promotion of Science and Swiss National Science Foundation) Bilateral Programmes project (HOPE, High-ele-vation precipitation in High Mountain Asia; Grant 183633), and the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (RAVEN, Rapid mass losses of debris-covered glaciers in High Mountain Asia; Grant 772751). We want to thank in particular T. Gurung, S. Joshi, J. Shea, W. Immerzeel, and others involved, as well as ICIMOD, for their efforts over the past years in observing the meteorology of the Langtang catchment, collecting and organizing the data and making them publicly available. We also thank the National Geographic Society (Grant NGS-61784R-19) and the Mount Everest Foundation (reference 19-24) for providing fieldwork funding for C. L. Fyffe. We thank T. Kramer for help with the WSL Hyperion cluster. We are grate-ful for comments by three anonymous reviewers and the Associate Editor, who greatly helped to improve the manuscript further. Open access funding provided by ETH-Bereich Forschungsanstalten.","year":"2023","publication_status":"published","publisher":"Wiley","department":[{"_id":"FrPe"}],"author":[{"full_name":"Buri, Pascal","first_name":"Pascal","last_name":"Buri"},{"last_name":"Fatichi","first_name":"Simone","full_name":"Fatichi, Simone"},{"last_name":"Shaw","first_name":"Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","full_name":"Shaw, Thomas"},{"last_name":"Miles","first_name":"Evan S.","full_name":"Miles, Evan S."},{"full_name":"Mccarthy, Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f","last_name":"Mccarthy","first_name":"Michael"},{"full_name":"Fyffe, Catriona Louise","id":"001b0422-8d15-11ed-bc51-cab6c037a228","first_name":"Catriona Louise","last_name":"Fyffe"},{"first_name":"Stefan","last_name":"Fugger","full_name":"Fugger, Stefan"},{"first_name":"Shaoting","last_name":"Ren","full_name":"Ren, Shaoting"},{"first_name":"Marin","last_name":"Kneib","full_name":"Kneib, Marin"},{"full_name":"Jouberton, Achille","last_name":"Jouberton","first_name":"Achille"},{"full_name":"Steiner, Jakob","first_name":"Jakob","last_name":"Steiner"},{"first_name":"Koji","last_name":"Fujita","full_name":"Fujita, Koji"},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","first_name":"Francesca","orcid":"0000-0002-5554-8087","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"}],"related_material":{"record":[{"id":"14494","relation":"research_data","status":"public"}]},"date_created":"2023-11-05T23:00:53Z","date_updated":"2023-11-07T08:12:34Z","volume":59,"article_number":"e2022WR033841","file_date_updated":"2023-11-07T08:10:44Z","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","doi":"10.1029/2022WR033841","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["1944-7973"],"issn":["0043-1397"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14487","status":"public","title":"Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment","ddc":["550"],"intvolume":" 59","file":[{"checksum":"7ba9c87228dc09029b16bc800a0ef1a1","success":1,"date_updated":"2023-11-07T08:10:44Z","date_created":"2023-11-07T08:10:44Z","relation":"main_file","file_id":"14495","file_size":5554901,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_WaterResourcesResearch_Buri.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"High Mountain Asia (HMA) is among the most vulnerable water towers globally and yet future projections of water availability in and from its high-mountain catchments remain uncertain, as their hydrologic response to ongoing environmental changes is complex. Mechanistic modeling approaches incorporating cryospheric, hydrological, and vegetation processes in high spatial, temporal, and physical detail have never been applied for high-elevation catchments of HMA. We use a land surface model at high spatial and temporal resolution (100 m and hourly) to simulate the coupled dynamics of energy, water, and vegetation for the 350 km2 Langtang catchment (Nepal). We compare our model outputs for one hydrological year against a large set of observations to gain insight into the partitioning of the water balance at the subseasonal scale and across elevation bands. During the simulated hydrological year, we find that evapotranspiration is a key component of the total water balance, as it causes about the equivalent of 20% of all the available precipitation or 154% of the water production from glacier melt in the basin to return directly to the atmosphere. The depletion of the cryospheric water budget is dominated by snow melt, but at high elevations is primarily dictated by snow and ice sublimation. Snow sublimation is the dominant vapor flux (49%) at the catchment scale, accounting for the equivalent of 11% of snowfall, 17% of snowmelt, and 75% of ice melt, respectively. We conclude that simulations should consider sublimation and other evaporative fluxes explicitly, as otherwise water balance estimates can be ill-quantified.","lang":"eng"}],"issue":"10","publication":"Water Resources Research","citation":{"short":"P. Buri, S. Fatichi, T. Shaw, E.S. Miles, M. McCarthy, C.L. Fyffe, S. Fugger, S. Ren, M. Kneib, A. Jouberton, J. Steiner, K. Fujita, F. Pellicciotti, Water Resources Research 59 (2023).","mla":"Buri, Pascal, et al. “Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High-Elevation Catchment.” Water Resources Research, vol. 59, no. 10, e2022WR033841, Wiley, 2023, doi:10.1029/2022WR033841.","chicago":"Buri, Pascal, Simone Fatichi, Thomas Shaw, Evan S. Miles, Michael McCarthy, Catriona Louise Fyffe, Stefan Fugger, et al. “Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High-Elevation Catchment.” Water Resources Research. Wiley, 2023. https://doi.org/10.1029/2022WR033841.","ama":"Buri P, Fatichi S, Shaw T, et al. Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment. Water Resources Research. 2023;59(10). doi:10.1029/2022WR033841","ieee":"P. Buri et al., “Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment,” Water Resources Research, vol. 59, no. 10. Wiley, 2023.","apa":"Buri, P., Fatichi, S., Shaw, T., Miles, E. S., McCarthy, M., Fyffe, C. L., … Pellicciotti, F. (2023). Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment. Water Resources Research. Wiley. https://doi.org/10.1029/2022WR033841","ista":"Buri P, Fatichi S, Shaw T, Miles ES, McCarthy M, Fyffe CL, Fugger S, Ren S, Kneib M, Jouberton A, Steiner J, Fujita K, Pellicciotti F. 2023. Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment. Water Resources Research. 59(10), e2022WR033841."},"article_type":"original","date_published":"2023-10-25T00:00:00Z","scopus_import":"1","day":"25","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)"},{"article_number":"35","file_date_updated":"2023-11-06T11:45:21Z","year":"2023","publication_status":"published","department":[{"_id":"GradSch"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"first_name":"Vitaly","last_name":"Aksenov","full_name":"Aksenov, Vitaly"},{"full_name":"Anoprenko, Michael","last_name":"Anoprenko","first_name":"Michael"},{"full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","last_name":"Fedorov","first_name":"Alexander"},{"first_name":"Michael","last_name":"Spear","full_name":"Spear, Michael"}],"date_updated":"2023-11-07T07:48:01Z","date_created":"2023-11-05T23:00:53Z","volume":281,"month":"10","publication_identifier":{"isbn":["9783959773010"],"issn":["1868-8969"]},"oa":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"},"quality_controlled":"1","conference":{"location":"L'Aquila, Italy","start_date":"2023-10-09","end_date":"2023-10-13","name":"DISC: Symposium on Distributed Computing"},"doi":"10.4230/LIPIcs.DISC.2023.35","language":[{"iso":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"Batching is a technique that stores multiple keys/values in each node of a data structure. In sequential search data structures, batching reduces latency by reducing the number of cache misses and shortening the chain of pointers to dereference. Applying batching to concurrent data structures is challenging, because it is difficult to maintain the search property and keep contention low in the presence of batching.\r\nIn this paper, we present a general methodology for leveraging batching in concurrent search data structures, called BatchBoost. BatchBoost builds a search data structure from distinct \"data\" and \"index\" layers. The data layer’s purpose is to store a batch of key/value pairs in each of its nodes. The index layer uses an unmodified concurrent search data structure to route operations to a position in the data layer that is \"close\" to where the corresponding key should exist. The requirements on the index and data layers are low: with minimal effort, we were able to compose three highly scalable concurrent search data structures based on three original data structures as the index layers with a batched version of the Lazy List as the data layer. The resulting BatchBoost data structures provide significant performance improvements over their original counterparts.","lang":"eng"}],"_id":"14485","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Brief announcement: BatchBoost: Universal batching for concurrent data structures","ddc":["000"],"intvolume":" 281","file":[{"success":1,"checksum":"d9f8d2915cccdf2df5905b7cd1b4a560","date_updated":"2023-11-06T11:45:21Z","date_created":"2023-11-06T11:45:21Z","file_id":"14492","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":646665,"access_level":"open_access","file_name":"2023_LIPIcs_Aksenov.pdf"}],"oa_version":"Published Version","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes","publication":"37th International Symposium on Distributed Computing","citation":{"apa":"Aksenov, V., Anoprenko, M., Fedorov, A., & Spear, M. (2023). Brief announcement: BatchBoost: Universal batching for concurrent data structures. In 37th International Symposium on Distributed Computing (Vol. 281). L’Aquila, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2023.35","ieee":"V. Aksenov, M. Anoprenko, A. Fedorov, and M. Spear, “Brief announcement: BatchBoost: Universal batching for concurrent data structures,” in 37th International Symposium on Distributed Computing, L’Aquila, Italy, 2023, vol. 281.","ista":"Aksenov V, Anoprenko M, Fedorov A, Spear M. 2023. Brief announcement: BatchBoost: Universal batching for concurrent data structures. 37th International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 281, 35.","ama":"Aksenov V, Anoprenko M, Fedorov A, Spear M. Brief announcement: BatchBoost: Universal batching for concurrent data structures. In: 37th International Symposium on Distributed Computing. Vol 281. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.DISC.2023.35","chicago":"Aksenov, Vitaly, Michael Anoprenko, Alexander Fedorov, and Michael Spear. “Brief Announcement: BatchBoost: Universal Batching for Concurrent Data Structures.” In 37th International Symposium on Distributed Computing, Vol. 281. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.DISC.2023.35.","short":"V. Aksenov, M. Anoprenko, A. Fedorov, M. Spear, in:, 37th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","mla":"Aksenov, Vitaly, et al. “Brief Announcement: BatchBoost: Universal Batching for Concurrent Data Structures.” 37th International Symposium on Distributed Computing, vol. 281, 35, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.DISC.2023.35."},"date_published":"2023-10-01T00:00:00Z"},{"external_id":{"arxiv":["2301.09875"]},"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"},"oa":1,"quality_controlled":"1","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"doi":"10.1103/PhysRevResearch.5.043016","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["2643-1564"]},"acknowledgement":"We thank Zh. Alpichshev, A. Volosniev, and A. V. Zampetaki for fruitful discussions and comments. This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","year":"2023","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"author":[{"id":"d7b23d3a-9e21-11ec-b482-f76739596b95","last_name":"Koutentakis","first_name":"Georgios","full_name":"Koutentakis, Georgios"},{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan","full_name":"Ghazaryan, Areg"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-11-07T07:53:39Z","date_created":"2023-11-05T23:00:53Z","volume":5,"article_number":"043016","file_date_updated":"2023-11-07T07:52:46Z","ec_funded":1,"publication":"Physical Review Research","citation":{"chicago":"Koutentakis, Georgios, Areg Ghazaryan, and Mikhail Lemeshko. “Rotor Lattice Model of Ferroelectric Large Polarons.” Physical Review Research. American Physical Society, 2023. https://doi.org/10.1103/PhysRevResearch.5.043016.","mla":"Koutentakis, Georgios, et al. “Rotor Lattice Model of Ferroelectric Large Polarons.” Physical Review Research, vol. 5, no. 4, 043016, American Physical Society, 2023, doi:10.1103/PhysRevResearch.5.043016.","short":"G. Koutentakis, A. Ghazaryan, M. Lemeshko, Physical Review Research 5 (2023).","ista":"Koutentakis G, Ghazaryan A, Lemeshko M. 2023. Rotor lattice model of ferroelectric large polarons. Physical Review Research. 5(4), 043016.","ieee":"G. Koutentakis, A. Ghazaryan, and M. Lemeshko, “Rotor lattice model of ferroelectric large polarons,” Physical Review Research, vol. 5, no. 4. American Physical Society, 2023.","apa":"Koutentakis, G., Ghazaryan, A., & Lemeshko, M. (2023). Rotor lattice model of ferroelectric large polarons. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.5.043016","ama":"Koutentakis G, Ghazaryan A, Lemeshko M. Rotor lattice model of ferroelectric large polarons. Physical Review Research. 2023;5(4). doi:10.1103/PhysRevResearch.5.043016"},"article_type":"original","date_published":"2023-10-05T00:00:00Z","scopus_import":"1","day":"05","has_accepted_license":"1","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14486","title":"Rotor lattice model of ferroelectric large polarons","status":"public","ddc":["530"],"intvolume":" 5","oa_version":"Published Version","file":[{"file_size":1127522,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_PhysReviewResearch_Koutentakis.pdf","checksum":"cb8de8fed6e09df1a18bd5a5aec5c55c","success":1,"date_created":"2023-11-07T07:52:46Z","date_updated":"2023-11-07T07:52:46Z","relation":"main_file","file_id":"14493"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We present a minimal model of ferroelectric large polarons, which are suggested as one of the mechanisms responsible for the unique charge transport properties of hybrid perovskites. We demonstrate that short-ranged charge–rotor interactions lead to long-range ferroelectric ordering of rotors, which strongly affects the carrier mobility. In the nonperturbative regime, where our theory cannot be reduced to any of the earlier models, we reveal that the polaron is characterized by large coherence length and a roughly tenfold increase of the effective mass as compared to the bare mass. These results are in good agreement with other theoretical predictions for ferroelectric polarons. Our model establishes a general phenomenological framework for ferroelectric polarons providing the starting point for future studies of their role in the transport properties of hybrid organic-inorganic perovskites."}],"issue":"4"},{"author":[{"full_name":"Fiedler, Lukas","first_name":"Lukas","last_name":"Fiedler","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"volume":75,"date_created":"2023-09-10T22:01:11Z","date_updated":"2023-11-07T08:17:13Z","pmid":1,"year":"2023","acknowledgement":"The opening quote is not intended to reflect any political views of the authors. The authors by no means endorse the rhetoric of Donald Rumsfeld or the 2003 invasion of Iraq by the United States. Nevertheless, Rumsfeld's quote led to both public and academic debates on the concept of known and unknown unknowns, which can be applied to the recent unexpected developments in the auxin signaling field. We thank Linlin Qi and Huihuang Chen for their suggestions on figure presentation and inspiring discussions of TIR1/AFB signaling. Finally, we thank Aroosa Hussain for discussion of Greek mythology.","department":[{"_id":"JiFr"}],"publisher":"Elsevier","publication_status":"published","file_date_updated":"2023-11-02T17:03:20Z","article_number":"102443","doi":"10.1016/j.pbi.2023.102443","language":[{"iso":"eng"}],"external_id":{"pmid":["37666097"]},"oa":1,"quality_controlled":"1","publication_identifier":{"issn":["1369-5266"]},"month":"10","file":[{"file_id":"14482","relation":"main_file","success":1,"checksum":"1c476c3414d2dfb0c85db0cb6cfd8a28","date_updated":"2023-11-02T17:03:20Z","date_created":"2023-11-02T17:03:20Z","access_level":"open_access","file_name":"Fiedler CurrOpinOlantBiol 2023_revised.pdf","creator":"amally","file_size":737872,"content_type":"application/pdf"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14313","intvolume":" 75","ddc":["580"],"title":"Rapid auxin signaling: Unknowns old and new","status":"public","issue":"10","abstract":[{"lang":"eng","text":"To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling."}],"type":"journal_article","date_published":"2023-10-01T00:00:00Z","citation":{"mla":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” Current Opinion in Plant Biology, vol. 75, no. 10, 102443, Elsevier, 2023, doi:10.1016/j.pbi.2023.102443.","short":"L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023).","chicago":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” Current Opinion in Plant Biology. Elsevier, 2023. https://doi.org/10.1016/j.pbi.2023.102443.","ama":"Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 2023;75(10). doi:10.1016/j.pbi.2023.102443","ista":"Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 75(10), 102443.","ieee":"L. Fiedler and J. Friml, “Rapid auxin signaling: Unknowns old and new,” Current Opinion in Plant Biology, vol. 75, no. 10. Elsevier, 2023.","apa":"Fiedler, L., & Friml, J. (2023). Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2023.102443"},"publication":"Current Opinion in Plant Biology","article_type":"review","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1"},{"article_processing_charge":"No","has_accepted_license":"1","day":"03","month":"10","doi":"10.5281/ZENODO.8402426","date_published":"2023-10-03T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ama":"Buri P, Fatichi S, Shaw T, et al. Model output data to “Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment.” 2023. doi:10.5281/ZENODO.8402426","ista":"Buri P, Fatichi S, Shaw T, Miles E, McCarthy M, Fyffe CL, Fugger S, Ren S, Kneib M, Jouberton A, Steiner J, Fujita K, Pellicciotti F. 2023. Model output data to ‘Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment’, Zenodo, 10.5281/ZENODO.8402426.","apa":"Buri, P., Fatichi, S., Shaw, T., Miles, E., McCarthy, M., Fyffe, C. L., … Pellicciotti, F. (2023). Model output data to “Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment.” Zenodo. https://doi.org/10.5281/ZENODO.8402426","ieee":"P. Buri et al., “Model output data to ‘Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment.’” Zenodo, 2023.","mla":"Buri, Pascal, et al. Model Output Data to “Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High Elevation Catchment.” Zenodo, 2023, doi:10.5281/ZENODO.8402426.","short":"P. Buri, S. Fatichi, T. Shaw, E. Miles, M. McCarthy, C.L. Fyffe, S. Fugger, S. Ren, M. Kneib, A. Jouberton, J. Steiner, K. Fujita, F. Pellicciotti, (2023).","chicago":"Buri, Pascal, Simone Fatichi, Thomas Shaw, Evan Miles, Michael McCarthy, Catriona Louise Fyffe, Stefan Fugger, et al. “Model Output Data to ‘Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High Elevation Catchment.’” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8402426."},"main_file_link":[{"url":"https://10.5281/ZENODO.8402426","open_access":"1"}],"oa":1,"abstract":[{"text":"We provide i) gridded initial conditions (.tif), ii) modeled gridded monthly outputs (.tif), and iii) modeled hourly outputs at the station locations (.txt) for the hydrological year 2019. Information about the variables and units can be found in the figures (.png) associated to each dataset. Details about the datasets can be found in the original publication by Buri and others (2023).\r\n\r\nBuri, P., Fatichi, S., Shaw, T. E., Miles, E. S., McCarthy, M. J., Fyffe, C. L., ... & Pellicciotti, F. (2023). Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High‐Elevation Catchment. Water Resources Research, 59(10), e2022WR033841. DOI: 10.1029/2022WR033841","lang":"eng"}],"type":"research_data_reference","related_material":{"record":[{"id":"14487","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Buri, Pascal","last_name":"Buri","first_name":"Pascal"},{"first_name":"Simone","last_name":"Fatichi","full_name":"Fatichi, Simone"},{"full_name":"Shaw, Thomas","first_name":"Thomas","last_name":"Shaw","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e"},{"full_name":"Miles, Evan ","last_name":"Miles","first_name":"Evan "},{"id":"22a2674a-61ce-11ee-94b5-d18813baf16f","first_name":"Michael","last_name":"McCarthy","full_name":"McCarthy, Michael"},{"last_name":"Fyffe","first_name":"Catriona Louise","id":"001b0422-8d15-11ed-bc51-cab6c037a228","full_name":"Fyffe, Catriona Louise"},{"first_name":"Stefan","last_name":"Fugger","full_name":"Fugger, Stefan"},{"last_name":"Ren","first_name":"Shaoting","full_name":"Ren, Shaoting"},{"full_name":"Kneib, Marin","first_name":"Marin","last_name":"Kneib"},{"first_name":"Achille","last_name":"Jouberton","full_name":"Jouberton, Achille"},{"first_name":"Jakob","last_name":"Steiner","full_name":"Steiner, Jakob"},{"full_name":"Fujita, Koji","last_name":"Fujita","first_name":"Koji"},{"last_name":"Pellicciotti","first_name":"Francesca","orcid":"0000-0002-5554-8087","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"}],"oa_version":"Published Version","date_updated":"2023-11-07T08:12:35Z","date_created":"2023-11-07T08:01:39Z","year":"2023","_id":"14494","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"FrPe"}],"publisher":"Zenodo","status":"public","ddc":["550"],"title":"Model output data to \"Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment\""},{"_id":"14499","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture","ddc":["510"],"intvolume":" 11","file":[{"success":1,"checksum":"54b824098d59073cc87a308d458b0a3e","date_updated":"2023-11-07T09:16:23Z","date_created":"2023-11-07T09:16:23Z","file_id":"14500","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1218719,"access_level":"open_access","file_name":"2023_ForumMathematics_Kwan.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"An n-vertex graph is called C-Ramsey if it has no clique or independent set of size Clog2n (i.e., if it has near-optimal Ramsey behavior). In this paper, we study edge statistics in Ramsey graphs, in particular obtaining very precise control of the distribution of the number of edges in a random vertex subset of a C-Ramsey graph. This brings together two ongoing lines of research: the study of ‘random-like’ properties of Ramsey graphs and the study of small-ball probability for low-degree polynomials of independent random variables.\r\n\r\nThe proof proceeds via an ‘additive structure’ dichotomy on the degree sequence and involves a wide range of different tools from Fourier analysis, random matrix theory, the theory of Boolean functions, probabilistic combinatorics and low-rank approximation. In particular, a key ingredient is a new sharpened version of the quadratic Carbery–Wright theorem on small-ball probability for polynomials of Gaussians, which we believe is of independent interest. One of the consequences of our result is the resolution of an old conjecture of Erdős and McKay, for which Erdős reiterated in several of his open problem collections and for which he offered one of his notorious monetary prizes.","lang":"eng"}],"publication":"Forum of Mathematics, Pi","citation":{"chicago":"Kwan, Matthew Alan, Ashwin Sah, Lisa Sauermann, and Mehtaab Sawhney. “Anticoncentration in Ramsey Graphs and a Proof of the Erdős–McKay Conjecture.” Forum of Mathematics, Pi. Cambridge University Press, 2023. https://doi.org/10.1017/fmp.2023.17.","mla":"Kwan, Matthew Alan, et al. “Anticoncentration in Ramsey Graphs and a Proof of the Erdős–McKay Conjecture.” Forum of Mathematics, Pi, vol. 11, e21, Cambridge University Press, 2023, doi:10.1017/fmp.2023.17.","short":"M.A. Kwan, A. Sah, L. Sauermann, M. Sawhney, Forum of Mathematics, Pi 11 (2023).","ista":"Kwan MA, Sah A, Sauermann L, Sawhney M. 2023. Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture. Forum of Mathematics, Pi. 11, e21.","apa":"Kwan, M. A., Sah, A., Sauermann, L., & Sawhney, M. (2023). Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture. Forum of Mathematics, Pi. Cambridge University Press. https://doi.org/10.1017/fmp.2023.17","ieee":"M. A. Kwan, A. Sah, L. Sauermann, and M. Sawhney, “Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture,” Forum of Mathematics, Pi, vol. 11. Cambridge University Press, 2023.","ama":"Kwan MA, Sah A, Sauermann L, Sawhney M. Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture. Forum of Mathematics, Pi. 2023;11. doi:10.1017/fmp.2023.17"},"article_type":"original","date_published":"2023-08-24T00:00:00Z","scopus_import":"1","keyword":["Discrete Mathematics and Combinatorics","Geometry and Topology","Mathematical Physics","Statistics and Probability","Algebra and Number Theory","Analysis"],"day":"24","article_processing_charge":"Yes","has_accepted_license":"1","acknowledgement":"Kwan was supported for part of this work by ERC Starting Grant ‘RANDSTRUCT’ No. 101076777. Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE-2141064. Sah was supported by the PD Soros Fellowship. Sauermann was supported by NSF Award DMS-2100157, and for part of this work by a Sloan Research Fellowship.","year":"2023","publication_status":"published","department":[{"_id":"MaKw"}],"publisher":"Cambridge University Press","author":[{"full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan","first_name":"Matthew Alan"},{"first_name":"Ashwin","last_name":"Sah","full_name":"Sah, Ashwin"},{"full_name":"Sauermann, Lisa","first_name":"Lisa","last_name":"Sauermann"},{"first_name":"Mehtaab","last_name":"Sawhney","full_name":"Sawhney, Mehtaab"}],"date_created":"2023-11-07T09:02:48Z","date_updated":"2023-11-07T09:18:57Z","volume":11,"article_number":"e21","file_date_updated":"2023-11-07T09:16:23Z","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"},"oa":1,"external_id":{"arxiv":["2208.02874"]},"quality_controlled":"1","project":[{"grant_number":"101076777","_id":"bd95085b-d553-11ed-ba76-e55d3349be45","name":"Randomness and structure in combinatorics"}],"doi":"10.1017/fmp.2023.17","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["2050-5086"]}},{"publication":"Science","citation":{"mla":"Praetorius, Florian M., et al. “Design of Stimulus-Responsive Two-State Hinge Proteins.” Science, vol. 381, no. 6659, American Association for the Advancement of Science, 2023, pp. 754–60, doi:10.1126/science.adg7731.","short":"F.M. Praetorius, P.J.Y. Leung, M.H. Tessmer, A. Broerman, C. Demakis, A.F. Dishman, A. Pillai, A. Idris, D. Juergens, J. Dauparas, X. Li, P.M. Levine, M. Lamb, R.K. Ballard, S.R. Gerben, H. Nguyen, A. Kang, B. Sankaran, A.K. Bera, B.F. Volkman, J. Nivala, S. Stoll, D. Baker, Science 381 (2023) 754–760.","chicago":"Praetorius, Florian M, Philip J. Y. Leung, Maxx H. Tessmer, Adam Broerman, Cullen Demakis, Acacia F. Dishman, Arvind Pillai, et al. “Design of Stimulus-Responsive Two-State Hinge Proteins.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adg7731.","ama":"Praetorius FM, Leung PJY, Tessmer MH, et al. Design of stimulus-responsive two-state hinge proteins. Science. 2023;381(6659):754-760. doi:10.1126/science.adg7731","ista":"Praetorius FM, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben SR, Nguyen H, Kang A, Sankaran B, Bera AK, Volkman BF, Nivala J, Stoll S, Baker D. 2023. Design of stimulus-responsive two-state hinge proteins. Science. 381(6659), 754–760.","ieee":"F. M. Praetorius et al., “Design of stimulus-responsive two-state hinge proteins,” Science, vol. 381, no. 6659. American Association for the Advancement of Science, pp. 754–760, 2023.","apa":"Praetorius, F. M., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis, C., Dishman, A. F., … Baker, D. (2023). Design of stimulus-responsive two-state hinge proteins. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adg7731"},"article_type":"original","page":"754-760","date_published":"2023-08-17T00:00:00Z","scopus_import":"1","day":"17","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14281","status":"public","title":"Design of stimulus-responsive two-state hinge proteins","intvolume":" 381","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing proteins with two distinct but fully structured conformations is a challenge for protein design as it requires sculpting an energy landscape with two distinct minima. Here we describe the design of “hinge” proteins that populate one designed state in the absence of ligand and a second designed state in the presence of ligand. X-ray crystallography, electron microscopy, double electron-electron resonance spectroscopy, and binding measurements demonstrate that despite the significant structural differences the two states are designed with atomic level accuracy and that the conformational and binding equilibria are closely coupled."}],"issue":"6659","external_id":{"pmid":["37590357"]},"quality_controlled":"1","doi":"10.1126/science.adg7731","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"year":"2023","pmid":1,"publication_status":"published","publisher":"American Association for the Advancement of Science","author":[{"last_name":"Praetorius","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M"},{"first_name":"Philip J. Y.","last_name":"Leung","full_name":"Leung, Philip J. Y."},{"last_name":"Tessmer","first_name":"Maxx H.","full_name":"Tessmer, Maxx H."},{"full_name":"Broerman, Adam","first_name":"Adam","last_name":"Broerman"},{"full_name":"Demakis, Cullen","last_name":"Demakis","first_name":"Cullen"},{"last_name":"Dishman","first_name":"Acacia F.","full_name":"Dishman, Acacia F."},{"first_name":"Arvind","last_name":"Pillai","full_name":"Pillai, Arvind"},{"full_name":"Idris, Abbas","last_name":"Idris","first_name":"Abbas"},{"last_name":"Juergens","first_name":"David","full_name":"Juergens, David"},{"last_name":"Dauparas","first_name":"Justas","full_name":"Dauparas, Justas"},{"first_name":"Xinting","last_name":"Li","full_name":"Li, Xinting"},{"full_name":"Levine, Paul M.","last_name":"Levine","first_name":"Paul M."},{"first_name":"Mila","last_name":"Lamb","full_name":"Lamb, Mila"},{"full_name":"Ballard, Ryanne K.","first_name":"Ryanne K.","last_name":"Ballard"},{"full_name":"Gerben, Stacey R.","first_name":"Stacey R.","last_name":"Gerben"},{"full_name":"Nguyen, Hannah","first_name":"Hannah","last_name":"Nguyen"},{"full_name":"Kang, Alex","first_name":"Alex","last_name":"Kang"},{"first_name":"Banumathi","last_name":"Sankaran","full_name":"Sankaran, Banumathi"},{"full_name":"Bera, Asim K.","first_name":"Asim K.","last_name":"Bera"},{"first_name":"Brian F.","last_name":"Volkman","full_name":"Volkman, Brian F."},{"full_name":"Nivala, Jeff","first_name":"Jeff","last_name":"Nivala"},{"full_name":"Stoll, Stefan","last_name":"Stoll","first_name":"Stefan"},{"full_name":"Baker, David","last_name":"Baker","first_name":"David"}],"date_created":"2023-09-06T12:04:23Z","date_updated":"2023-11-07T12:42:09Z","volume":381,"extern":"1"},{"publication":"bioRxiv","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.03.14.532666"}],"citation":{"mla":"Edman, Natasha I., et al. “Modulation of FGF Pathway Signaling and Vascular Differentiation Using Designed Oligomeric Assemblies.” BioRxiv, doi:10.1101/2023.03.14.532666.","short":"N.I. Edman, R.L. Redler, A. Phal, T. Schlichthaerle, S.R. Srivatsan, A. Etemadi, S. An, A. Favor, D. Ehnes, Z. Li, F.M. Praetorius, M. Gordon, W. Yang, B. Coventry, D.R. Hicks, L. Cao, N. Bethel, P. Heine, A.N. Murray, S. Gerben, L. Carter, M. Miranda, B. Negahdari, S. Lee, C. Trapnell, L. Stewart, D.C. Ekiert, J. Schlessinger, J. Shendure, G. Bhabha, H. Ruohola-Baker, D. Baker, BioRxiv (n.d.).","chicago":"Edman, Natasha I, Rachel L Redler, Ashish Phal, Thomas Schlichthaerle, Sanjay R Srivatsan, Ali Etemadi, Seong An, et al. “Modulation of FGF Pathway Signaling and Vascular Differentiation Using Designed Oligomeric Assemblies.” BioRxiv, n.d. https://doi.org/10.1101/2023.03.14.532666.","ama":"Edman NI, Redler RL, Phal A, et al. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. bioRxiv. doi:10.1101/2023.03.14.532666","ista":"Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An S, Favor A, Ehnes D, Li Z, Praetorius FM, Gordon M, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray AN, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. bioRxiv, 10.1101/2023.03.14.532666.","apa":"Edman, N. I., Redler, R. L., Phal, A., Schlichthaerle, T., Srivatsan, S. R., Etemadi, A., … Baker, D. (n.d.). Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. bioRxiv. https://doi.org/10.1101/2023.03.14.532666","ieee":"N. I. Edman et al., “Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies,” bioRxiv. ."},"language":[{"iso":"eng"}],"date_published":"2023-03-15T00:00:00Z","doi":"10.1101/2023.03.14.532666","day":"15","month":"03","article_processing_charge":"No","status":"public","title":"Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies","publication_status":"submitted","year":"2023","_id":"14294","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-11-07T12:21:58Z","date_created":"2023-09-06T12:31:49Z","oa_version":"Preprint","author":[{"first_name":"Natasha I","last_name":"Edman","full_name":"Edman, Natasha I"},{"full_name":"Redler, Rachel L","last_name":"Redler","first_name":"Rachel L"},{"first_name":"Ashish","last_name":"Phal","full_name":"Phal, Ashish"},{"full_name":"Schlichthaerle, Thomas","last_name":"Schlichthaerle","first_name":"Thomas"},{"full_name":"Srivatsan, Sanjay R","first_name":"Sanjay R","last_name":"Srivatsan"},{"first_name":"Ali","last_name":"Etemadi","full_name":"Etemadi, Ali"},{"full_name":"An, Seong","last_name":"An","first_name":"Seong"},{"full_name":"Favor, Andrew","last_name":"Favor","first_name":"Andrew"},{"first_name":"Devon","last_name":"Ehnes","full_name":"Ehnes, Devon"},{"first_name":"Zhe","last_name":"Li","full_name":"Li, Zhe"},{"last_name":"Praetorius","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M"},{"first_name":"Max","last_name":"Gordon","full_name":"Gordon, Max"},{"full_name":"Yang, Wei","last_name":"Yang","first_name":"Wei"},{"full_name":"Coventry, Brian","first_name":"Brian","last_name":"Coventry"},{"last_name":"Hicks","first_name":"Derrick R","full_name":"Hicks, Derrick R"},{"full_name":"Cao, Longxing","last_name":"Cao","first_name":"Longxing"},{"full_name":"Bethel, Neville","last_name":"Bethel","first_name":"Neville"},{"full_name":"Heine, Piper","last_name":"Heine","first_name":"Piper"},{"last_name":"Murray","first_name":"Analisa N","full_name":"Murray, Analisa N"},{"full_name":"Gerben, Stacey","last_name":"Gerben","first_name":"Stacey"},{"full_name":"Carter, Lauren","last_name":"Carter","first_name":"Lauren"},{"last_name":"Miranda","first_name":"Marcos","full_name":"Miranda, Marcos"},{"last_name":"Negahdari","first_name":"Babak","full_name":"Negahdari, Babak"},{"last_name":"Lee","first_name":"Sangwon","full_name":"Lee, Sangwon"},{"last_name":"Trapnell","first_name":"Cole","full_name":"Trapnell, Cole"},{"first_name":"Lance","last_name":"Stewart","full_name":"Stewart, Lance"},{"full_name":"Ekiert, Damian C","first_name":"Damian C","last_name":"Ekiert"},{"first_name":"Joseph","last_name":"Schlessinger","full_name":"Schlessinger, Joseph"},{"full_name":"Shendure, Jay","last_name":"Shendure","first_name":"Jay"},{"full_name":"Bhabha, Gira","last_name":"Bhabha","first_name":"Gira"},{"last_name":"Ruohola-Baker","first_name":"Hannele","full_name":"Ruohola-Baker, Hannele"},{"last_name":"Baker","first_name":"David","full_name":"Baker, David"}],"type":"preprint","extern":"1","abstract":[{"text":"Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affects signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo designed fibroblast growth-factor receptor (FGFR) binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation. The high specificity of the designed agonists reveal distinct roles for two FGFR splice variants in driving endothelial and mesenchymal cell fates during early vascular development. The ability to incorporate receptor binding domains and repeat extensions in a modular fashion makes our designed scaffolds broadly useful for probing and manipulating cellular signaling pathways.","lang":"eng"}]},{"doi":"10.1016/j.physrep.2023.10.004","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2202.11071"}],"external_id":{"arxiv":["2202.11071"]},"oa":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","publication_identifier":{"issn":["0370-1573"]},"month":"11","author":[{"full_name":"Mistakidis, S. I.","last_name":"Mistakidis","first_name":"S. I."},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"},{"full_name":"Barfknecht, R. E.","first_name":"R. E.","last_name":"Barfknecht"},{"full_name":"Fogarty, T.","last_name":"Fogarty","first_name":"T."},{"last_name":"Busch","first_name":"Th","full_name":"Busch, Th"},{"last_name":"Foerster","first_name":"A.","full_name":"Foerster, A."},{"first_name":"P.","last_name":"Schmelcher","full_name":"Schmelcher, P."},{"full_name":"Zinner, N. T.","last_name":"Zinner","first_name":"N. T."}],"volume":1042,"date_updated":"2023-11-13T08:01:57Z","date_created":"2023-11-12T23:00:54Z","acknowledgement":"This review could not have been written without the many fruitful discussions and great collaborations with colleagues throughout the years, there are too many to mention. Here we acknowledge conversations regarding the context of the review with Joachim Brand, Fabian Brauneis, Adolfo del Campo, Alberto Cappellaro, Panagiotis Giannakeas, Tommaso Macrí, Oleksandr Marchukov, Lukas Rammelmüller and Manuel Valiente. S. I. M. acknowledges support from the NSF through a grant for ITAMP at Harvard University. T.F. acknowledges support from JSPS KAKENHI Grant Number JP23K03290 and T.F. and Th.B. acknowledge support from the Okinawa Institute for Science and Technology Graduate University, and JST Grant Number JPMJPF2221. A.F. and R. E. B. acknowledge support from CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) - Edital Universal 406563/2021-7. A. G. V. acknowledges support by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. P. S. is supported by the Cluster of Excellence ‘Advanced Imaging of Matter’ of the Deutsche Forschungsgemeinschaft (DFG) - EXC2056 - project ID 390715994. N. T. Z. is partially supported by the Independent Research Fund Denmark .","year":"2023","department":[{"_id":"MiLe"}],"publisher":"Elsevier","publication_status":"published","ec_funded":1,"date_published":"2023-11-29T00:00:00Z","citation":{"chicago":"Mistakidis, S. I., Artem Volosniev, R. E. Barfknecht, T. Fogarty, Th Busch, A. Foerster, P. Schmelcher, and N. T. Zinner. “Few-Body Bose Gases in Low Dimensions - A Laboratory for Quantum Dynamics.” Physics Reports. Elsevier, 2023. https://doi.org/10.1016/j.physrep.2023.10.004.","short":"S.I. Mistakidis, A. Volosniev, R.E. Barfknecht, T. Fogarty, T. Busch, A. Foerster, P. Schmelcher, N.T. Zinner, Physics Reports 1042 (2023) 1–108.","mla":"Mistakidis, S. I., et al. “Few-Body Bose Gases in Low Dimensions - A Laboratory for Quantum Dynamics.” Physics Reports, vol. 1042, Elsevier, 2023, pp. 1–108, doi:10.1016/j.physrep.2023.10.004.","apa":"Mistakidis, S. I., Volosniev, A., Barfknecht, R. E., Fogarty, T., Busch, T., Foerster, A., … Zinner, N. T. (2023). Few-body Bose gases in low dimensions - A laboratory for quantum dynamics. Physics Reports. Elsevier. https://doi.org/10.1016/j.physrep.2023.10.004","ieee":"S. I. Mistakidis et al., “Few-body Bose gases in low dimensions - A laboratory for quantum dynamics,” Physics Reports, vol. 1042. Elsevier, pp. 1–108, 2023.","ista":"Mistakidis SI, Volosniev A, Barfknecht RE, Fogarty T, Busch T, Foerster A, Schmelcher P, Zinner NT. 2023. Few-body Bose gases in low dimensions - A laboratory for quantum dynamics. Physics Reports. 1042, 1–108.","ama":"Mistakidis SI, Volosniev A, Barfknecht RE, et al. Few-body Bose gases in low dimensions - A laboratory for quantum dynamics. Physics Reports. 2023;1042:1-108. doi:10.1016/j.physrep.2023.10.004"},"publication":"Physics Reports","page":"1-108","article_type":"original","article_processing_charge":"No","day":"29","scopus_import":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14513","intvolume":" 1042","title":"Few-body Bose gases in low dimensions - A laboratory for quantum dynamics","status":"public","abstract":[{"lang":"eng","text":"Cold atomic gases have become a paradigmatic system for exploring fundamental physics, which at the same time allows for applications in quantum technologies. The accelerating developments in the field have led to a highly advanced set of engineering techniques that, for example, can tune interactions, shape the external geometry, select among a large set of atomic species with different properties, or control the number of atoms. In particular, it is possible to operate in lower dimensions and drive atomic systems into the strongly correlated regime. In this review, we discuss recent advances in few-body cold atom systems confined in low dimensions from a theoretical viewpoint. We mainly focus on bosonic systems in one dimension and provide an introduction to the static properties before we review the state-of-the-art research into quantum dynamical processes stimulated by the presence of correlations. Besides discussing the fundamental physical phenomena arising in these systems, we also provide an overview of the calculational and numerical tools and methods that are commonly used, thus delivering a balanced and comprehensive overview of the field. We conclude by giving an outlook on possible future directions that are interesting to explore in these correlated systems."}],"type":"journal_article"},{"file_date_updated":"2023-04-26T12:30:06Z","abstract":[{"lang":"eng","text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage. We first analyse the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. 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","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"publisher":"Institute of Science and Technology Austria","ddc":["000"],"status":"public","title":"Research data for: A stochastic cellular automaton model of culture formation","article_processing_charge":"No","has_accepted_license":"1","day":"26","month":"04","doi":"10.15479/AT:ISTA:12869","date_published":"2023-04-26T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"ieee":"F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular automaton model of culture formation.” Institute of Science and Technology Austria, 2023.","apa":"Klausen, F. R., & Lauritsen, A. B. (2023). Research data for: A stochastic cellular automaton model of culture formation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12869","ista":"Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular automaton model of culture formation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12869.","ama":"Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton model of culture formation. 2023. doi:10.15479/AT:ISTA:12869","chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12869.","short":"F.R. Klausen, A.B. Lauritsen, (2023).","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. Research Data for: A Stochastic Cellular Automaton Model of Culture Formation. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12869."}},{"doi":"10.1103/PhysRevE.108.054307","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2305.02153","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2305.02153"]},"quality_controlled":"1","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"month":"11","related_material":{"link":[{"url":"https://github.com/FrederikRavnKlausen/model-for-culture-formation","relation":"software"}],"record":[{"relation":"research_data","status":"public","id":"12869"}]},"author":[{"full_name":"Klausen, Frederik Ravn","first_name":"Frederik Ravn","last_name":"Klausen"},{"first_name":"Asbjørn Bækgaard","last_name":"Lauritsen","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard"}],"volume":108,"date_created":"2023-05-04T08:35:01Z","date_updated":"2023-11-13T07:47:30Z","year":"2023","acknowledgement":"Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.","publisher":"American Physical Society","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"publication_status":"published","article_number":"054307","date_published":"2023-11-08T00:00:00Z","citation":{"chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.108.054307.","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” Physical Review E, vol. 108, no. 5, 054307, American Physical Society, 2023, doi:10.1103/PhysRevE.108.054307.","short":"F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023).","ista":"Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307.","apa":"Klausen, F. R., & Lauritsen, A. B. (2023). Stochastic cellular automaton model of culture formation. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.108.054307","ieee":"F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of culture formation,” Physical Review E, vol. 108, no. 5. American Physical Society, 2023.","ama":"Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation. Physical Review E. 2023;108(5). doi:10.1103/PhysRevE.108.054307"},"publication":"Physical Review E","article_type":"original","article_processing_charge":"No","day":"08","scopus_import":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12890","intvolume":" 108","status":"public","title":"Stochastic cellular automaton model of culture formation","issue":"5","abstract":[{"lang":"eng","text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders."}],"type":"journal_article"},{"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"We revisit decentralized random beacons with a focus on practical distributed applications. Decentralized random beacons (Beaver and So, Eurocrypt'93) provide the functionality for n parties to generate an unpredictable sequence of bits in a way that cannot be biased, which is useful for any decentralized protocol requiring trusted randomness. Existing beacon constructions are highly inefficient in practical settings where protocol parties need to rejoin after crashes or disconnections, and more significantly where smart contracts may rely on arbitrary index points in high-volume streams. For this, we introduce a new notion of history-generating decentralized random beacons (HGDRBs). Roughly, the history-generation property of HGDRBs allows for previous beacon outputs to be efficiently generated knowing only the current value and the public key. At application layers, history-generation supports registering a sparser set of on-chain values if desired, so that apps like lotteries can utilize on-chain values without incurring high-frequency costs, enjoying all the benefits of DRBs implemented off-chain or with decoupled, special-purpose chains. Unlike rollups, HG is tailored specifically to recovering and verifying pseudorandom bit sequences and thus enjoys unique optimizations investigated in this work. We introduce STROBE: an efficient HGDRB construction which generalizes the original squaring-based RSA approach of Beaver and So. STROBE enjoys several useful properties that make it suited for practical applications that use beacons: 1) history-generating: it can regenerate and verify high-throughput beacon streams, supporting sparse (thus cost-effective) ledger entries; 2) concisely self-verifying: NIZK-free, with state and validation employing a single ring element; 3) eco-friendly: stake-based rather than work based; 4) unbounded: refresh-free, addressing limitations of Beaver and So; 5) delay-free: results are immediately available. 6) storage-efficient: the last beacon suffices to derive all past outputs, thus O(1) storage requirements for nodes serving the whole history.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14516","title":"STROBE: Streaming Threshold Random Beacons","status":"public","ddc":["000"],"intvolume":" 282","file":[{"date_updated":"2023-11-13T08:44:34Z","date_created":"2023-11-13T08:44:34Z","success":1,"checksum":"c1f98831cb5149d6c030c41999e6e960","file_id":"14521","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":793495,"file_name":"2023_LIPIcs_Beaver.pdf","access_level":"open_access"}],"oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","publication":"5th Conference on Advances in Financial Technologies","citation":{"ieee":"D. Beaver et al., “STROBE: Streaming Threshold Random Beacons,” in 5th Conference on Advances in Financial Technologies, Princeton, NJ, United States, 2023, vol. 282.","apa":"Beaver, D., Kelkar, M., Lewi, K., Nikolaenko, V., Sonnino, A., Chalkias, K., … Roy, A. (2023). STROBE: Streaming Threshold Random Beacons. In 5th Conference on Advances in Financial Technologies (Vol. 282). Princeton, NJ, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.AFT.2023.7","ista":"Beaver D, Kelkar M, Lewi K, Nikolaenko V, Sonnino A, Chalkias K, Kokoris Kogias E, Naurois LD, Roy A. 2023. STROBE: Streaming Threshold Random Beacons. 5th Conference on Advances in Financial Technologies. AFT: Conference on Advances in Financial Technologies, LIPIcs, vol. 282, 7.","ama":"Beaver D, Kelkar M, Lewi K, et al. STROBE: Streaming Threshold Random Beacons. In: 5th Conference on Advances in Financial Technologies. Vol 282. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.AFT.2023.7","chicago":"Beaver, Donald, Mahimna Kelkar, Kevin Lewi, Valeria Nikolaenko, Alberto Sonnino, Konstantinos Chalkias, Eleftherios Kokoris Kogias, Ladi De Naurois, and Arnab Roy. “STROBE: Streaming Threshold Random Beacons.” In 5th Conference on Advances in Financial Technologies, Vol. 282. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.AFT.2023.7.","short":"D. Beaver, M. Kelkar, K. Lewi, V. Nikolaenko, A. Sonnino, K. Chalkias, E. Kokoris Kogias, L.D. Naurois, A. Roy, in:, 5th Conference on Advances in Financial Technologies, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","mla":"Beaver, Donald, et al. “STROBE: Streaming Threshold Random Beacons.” 5th Conference on Advances in Financial Technologies, vol. 282, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.AFT.2023.7."},"date_published":"2023-10-01T00:00:00Z","article_number":"7","file_date_updated":"2023-11-13T08:44:34Z","acknowledgement":"Work done when all the authors were at Novi Research, Meta.","year":"2023","publication_status":"published","department":[{"_id":"ElKo"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"full_name":"Beaver, Donald","first_name":"Donald","last_name":"Beaver"},{"last_name":"Kelkar","first_name":"Mahimna","full_name":"Kelkar, Mahimna"},{"full_name":"Lewi, Kevin","first_name":"Kevin","last_name":"Lewi"},{"full_name":"Nikolaenko, Valeria","last_name":"Nikolaenko","first_name":"Valeria"},{"first_name":"Alberto","last_name":"Sonnino","full_name":"Sonnino, Alberto"},{"last_name":"Chalkias","first_name":"Konstantinos","full_name":"Chalkias, Konstantinos"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"first_name":"Ladi De","last_name":"Naurois","full_name":"Naurois, Ladi De"},{"last_name":"Roy","first_name":"Arnab","full_name":"Roy, Arnab"}],"date_created":"2023-11-12T23:00:55Z","date_updated":"2023-11-13T08:52:01Z","volume":282,"month":"10","publication_identifier":{"isbn":["9783959773034"],"issn":["1868-8969"]},"oa":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"},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1643"}],"quality_controlled":"1","conference":{"start_date":"2023-10-23","location":"Princeton, NJ, United States","end_date":"2023-10-25","name":"AFT: Conference on Advances in Financial Technologies"},"doi":"10.4230/LIPIcs.AFT.2023.7","language":[{"iso":"eng"}]},{"publication_identifier":{"eissn":["2331-7019"]},"month":"10","doi":"10.1103/PhysRevApplied.20.044054","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2206.14104"}],"external_id":{"arxiv":["2206.14104"]},"project":[{"grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Integrating superconducting quantum circuits"},{"grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"},{"_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"},{"_id":"bdb7cfc1-d553-11ed-ba76-d2eaab167738","grant_number":"101080139","name":"Open Superconducting Quantum Computers (OpenSuperQPlus)"}],"quality_controlled":"1","ec_funded":1,"article_number":"044054","related_material":{"record":[{"id":"14520","relation":"research_data","status":"public"}]},"author":[{"full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Zemlicka"},{"first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena"},{"first_name":"Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda"},{"full_name":"Hassani, Farid","first_name":"Farid","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773"},{"full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","last_name":"Trioni","first_name":"Andrea"},{"full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","first_name":"Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"volume":20,"date_updated":"2023-11-13T09:22:47Z","date_created":"2023-11-12T23:00:55Z","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105), the European Research Council under Grant Agreement No. 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. M.Z. was the recipient of a SAIA scholarship, E.R. of\r\na DOC fellowship of the Austrian Academy of Sciences, and M.P. of a Pöttinger scholarship at IST Austria. S.B. acknowledges support from Marie Skłodowska Curie Program No. 707438 (MSC-IF SUPEREOM). J.M.F. acknowledges support from the Horizon Europe Program HORIZON-CL4-2022-QUANTUM-01-SGA via Project No. 101113946 OpenSuperQPlus100 and the ISTA Nanofabrication Facility.","year":"2023","publisher":"American Physical Society","department":[{"_id":"JoFi"}],"publication_status":"published","article_processing_charge":"No","day":"20","scopus_import":"1","date_published":"2023-10-20T00:00:00Z","citation":{"ama":"Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. 2023;20(4). doi:10.1103/PhysRevApplied.20.044054","ista":"Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink JM. 2023. Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. 20(4), 044054.","ieee":"M. Zemlicka et al., “Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses,” Physical Review Applied, vol. 20, no. 4. American Physical Society, 2023.","apa":"Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., & Fink, J. M. (2023). Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.20.044054","mla":"Zemlicka, Martin, et al. “Compact Vacuum-Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Physical Review Applied, vol. 20, no. 4, 044054, American Physical Society, 2023, doi:10.1103/PhysRevApplied.20.044054.","short":"M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, Physical Review Applied 20 (2023).","chicago":"Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum-Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Physical Review Applied. American Physical Society, 2023. https://doi.org/10.1103/PhysRevApplied.20.044054."},"publication":"Physical Review Applied","article_type":"original","issue":"4","abstract":[{"lang":"eng","text":"State-of-the-art transmon qubits rely on large capacitors, which systematically improve their coherence due to reduced surface-loss participation. However, this approach increases both the footprint and the parasitic cross-coupling and is ultimately limited by radiation losses—a potential roadblock for scaling up quantum processors to millions of qubits. In this work we present transmon qubits with sizes as low as 36 × 39 µm2 with 100-nm-wide vacuum-gap capacitors that are micromachined from commercial silicon-on-insulator wafers and shadow evaporated with aluminum. We achieve a vacuum participation ratio up to 99.6% in an in-plane design that is compatible with standard coplanar circuits. Qubit relaxationtime measurements for small gaps with high zero-point electric field variance of up to 22 V/m reveal a double exponential decay indicating comparably strong qubit interaction with long-lived two-level systems. The exceptionally high selectivity of up to 20 dB to the superconductor-vacuum interface allows us to precisely back out the sub-single-photon dielectric loss tangent of aluminum oxide previously exposed to ambient conditions. In terms of future scaling potential, we achieve a ratio of qubit quality factor to a footprint area equal to 20 µm−2, which is comparable with the highest T1 devices relying on larger geometries, a value that could improve substantially for lower surface-loss superconductors. "}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14517","intvolume":" 20","status":"public","title":"Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses"},{"year":"2023","acknowledgement":"We thank Bela Mulder, Tom Shimizu, Fotios Avgidis, Peter Bolhuis, and Daan Frenkel for useful discussions and a careful reading of the manuscript, and we thank Age Tjalma for support with obtaining the Gaussian approximation of the chemotaxis system. This work is part of the Dutch Research Council (NWO) and was performed at the research institute AMOLF. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 885065) and was\r\nfinancially supported by NWO through the “Building a Synthetic Cell (BaSyC)” Gravitation Grant (024.003.019).","publisher":"American Physical Society","department":[{"_id":"GaTk"}],"publication_status":"published","author":[{"last_name":"Reinhardt","first_name":"Manuel","full_name":"Reinhardt, Manuel"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"first_name":"Pieter Rein","last_name":"Ten Wolde","full_name":"Ten Wolde, Pieter Rein"}],"volume":13,"date_updated":"2023-11-13T09:03:30Z","date_created":"2023-11-12T23:00:55Z","article_number":"041017","file_date_updated":"2023-11-13T09:00:19Z","oa":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"},"external_id":{"arxiv":["2203.03461"]},"quality_controlled":"1","doi":"10.1103/PhysRevX.13.041017","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2160-3308"]},"month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14515","intvolume":" 13","title":"Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories","ddc":["530"],"status":"public","oa_version":"Published Version","file":[{"file_name":"2023_PhysReviewX_Reinhardt.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1595223,"file_id":"14522","relation":"main_file","date_created":"2023-11-13T09:00:19Z","date_updated":"2023-11-13T09:00:19Z","success":1,"checksum":"32574aeebcca7347a4152c611b66b3d5"}],"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Most natural and engineered information-processing systems transmit information via signals that vary in time. Computing the information transmission rate or the information encoded in the temporal characteristics of these signals requires the mutual information between the input and output signals as a function of time, i.e., between the input and output trajectories. Yet, this is notoriously difficult because of the high-dimensional nature of the trajectory space, and all existing techniques require approximations. We present an exact Monte Carlo technique called path weight sampling (PWS) that, for the first time, makes it possible to compute the mutual information between input and output trajectories for any stochastic system that is described by a master equation. The principal idea is to use the master equation to evaluate the exact conditional probability of an individual output trajectory for a given input trajectory and average this via Monte Carlo sampling in trajectory space to obtain the mutual information. We present three variants of PWS, which all generate the trajectories using the standard stochastic simulation algorithm. While direct PWS is a brute-force method, Rosenbluth-Rosenbluth PWS exploits the analogy between signal trajectory sampling and polymer sampling, and thermodynamic integration PWS is based on a reversible work calculation in trajectory space. PWS also makes it possible to compute the mutual information between input and output trajectories for systems with hidden internal states as well as systems with feedback from output to input. Applying PWS to the bacterial chemotaxis system, consisting of 182 coupled chemical reactions, demonstrates not only that the scheme is highly efficient but also that the number of receptor clusters is much smaller than hitherto believed, while their size is much larger."}],"citation":{"chicago":"Reinhardt, Manuel, Gašper Tkačik, and Pieter Rein Ten Wolde. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.041017.","mla":"Reinhardt, Manuel, et al. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” Physical Review X, vol. 13, no. 4, 041017, American Physical Society, 2023, doi:10.1103/PhysRevX.13.041017.","short":"M. Reinhardt, G. Tkačik, P.R. Ten Wolde, Physical Review X 13 (2023).","ista":"Reinhardt M, Tkačik G, Ten Wolde PR. 2023. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. 13(4), 041017.","ieee":"M. Reinhardt, G. Tkačik, and P. R. Ten Wolde, “Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories,” Physical Review X, vol. 13, no. 4. American Physical Society, 2023.","apa":"Reinhardt, M., Tkačik, G., & Ten Wolde, P. R. (2023). Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.13.041017","ama":"Reinhardt M, Tkačik G, Ten Wolde PR. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. 2023;13(4). doi:10.1103/PhysRevX.13.041017"},"publication":"Physical Review X","article_type":"original","date_published":"2023-10-26T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"26"},{"doi":"10.1103/PhysRevLett.131.168201","language":[{"iso":"eng"}],"oa":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"},"quality_controlled":"1","month":"10","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"author":[{"first_name":"Jack","last_name":"Binysh","full_name":"Binysh, Jack"},{"first_name":"Indrajit","last_name":"Chakraborty","full_name":"Chakraborty, Indrajit"},{"last_name":"Chubynsky","first_name":"Mykyta V.","full_name":"Chubynsky, Mykyta V."},{"id":"b6798902-eea0-11ea-9cbc-a8e14286c631","first_name":"Vicente L","last_name":"Diaz Melian","full_name":"Diaz Melian, Vicente L"},{"last_name":"Waitukaitis","first_name":"Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","full_name":"Waitukaitis, Scott R"},{"last_name":"Sprittles","first_name":"James E.","full_name":"Sprittles, James E."},{"last_name":"Souslov","first_name":"Anton","full_name":"Souslov, Anton"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"14523"}]},"date_updated":"2023-11-13T09:21:30Z","date_created":"2023-11-12T23:00:55Z","volume":131,"year":"2023","acknowledgement":"We are grateful to Dominic Vella, Jens Eggers, John Kolinski, Joshua Dijksman, and Daniel Bonn for insightful discussions. J. B. and A. S. acknowledge the support of the Engineering and Physical Sciences Research Council (EPSRC) through New Investigator Award No. EP/\r\nT000961/1. A. S. acknowledges the support of Royal Society under Grant No. RGS/R2/202135. J. E. S. acknowledges EPSRC Grants No. EP/N016602/1, EP/S022848/1, EP/S029966/1, and EP/P031684/1.","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"ScWa"}],"file_date_updated":"2023-11-13T09:12:58Z","article_number":"168201","date_published":"2023-10-20T00:00:00Z","publication":"Physical Review Letters","citation":{"ista":"Binysh J, Chakraborty I, Chubynsky MV, Diaz Melian VL, Waitukaitis SR, Sprittles JE, Souslov A. 2023. Modeling Leidenfrost levitation of soft elastic solids. Physical Review Letters. 131(16), 168201.","apa":"Binysh, J., Chakraborty, I., Chubynsky, M. V., Diaz Melian, V. L., Waitukaitis, S. R., Sprittles, J. E., & Souslov, A. (2023). Modeling Leidenfrost levitation of soft elastic solids. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.131.168201","ieee":"J. Binysh et al., “Modeling Leidenfrost levitation of soft elastic solids,” Physical Review Letters, vol. 131, no. 16. American Physical Society, 2023.","ama":"Binysh J, Chakraborty I, Chubynsky MV, et al. Modeling Leidenfrost levitation of soft elastic solids. Physical Review Letters. 2023;131(16). doi:10.1103/PhysRevLett.131.168201","chicago":"Binysh, Jack, Indrajit Chakraborty, Mykyta V. Chubynsky, Vicente L Diaz Melian, Scott R Waitukaitis, James E. Sprittles, and Anton Souslov. “Modeling Leidenfrost Levitation of Soft Elastic Solids.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.168201.","mla":"Binysh, Jack, et al. “Modeling Leidenfrost Levitation of Soft Elastic Solids.” Physical Review Letters, vol. 131, no. 16, 168201, American Physical Society, 2023, doi:10.1103/PhysRevLett.131.168201.","short":"J. Binysh, I. Chakraborty, M.V. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis, J.E. Sprittles, A. Souslov, Physical Review Letters 131 (2023)."},"article_type":"original","day":"20","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","file":[{"file_id":"14524","relation":"main_file","success":1,"checksum":"1a419e25b762aadffbcc8eb2e609bd97","date_created":"2023-11-13T09:12:58Z","date_updated":"2023-11-13T09:12:58Z","access_level":"open_access","file_name":"2023_PhysRevLetters_Binysh.pdf","creator":"dernst","content_type":"application/pdf","file_size":724098}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14514","status":"public","title":"Modeling Leidenfrost levitation of soft elastic solids","ddc":["530"],"intvolume":" 131","abstract":[{"text":"The elastic Leidenfrost effect occurs when a vaporizable soft solid is lowered onto a hot surface. Evaporative flow couples to elastic deformation, giving spontaneous bouncing or steady-state floating. The effect embodies an unexplored interplay between thermodynamics, elasticity, and lubrication: despite being observed, its basic theoretical description remains a challenge. Here, we provide a theory of elastic Leidenfrost floating. As weight increases, a rigid solid sits closer to the hot surface. By contrast, we discover an elasticity-dominated regime where the heavier the solid, the higher it floats. This geometry-governed behavior is reminiscent of the dynamics of large liquid Leidenfrost drops. We show that this elastic regime is characterized by Hertzian behavior of the solid’s underbelly and derive how the float height scales with materials parameters. Introducing a dimensionless elastic Leidenfrost number, we capture the crossover between rigid and Hertzian behavior. Our results provide theoretical underpinning for recent experiments, and point to the design of novel soft machines.","lang":"eng"}],"issue":"16","type":"journal_article"},{"doi":"10.5281/ZENODO.8329143","date_published":"2023-09-08T00:00:00Z","oa":1,"citation":{"ieee":"J. Binysh et al., “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1.” Zenodo, 2023.","apa":"Binysh, J., Chakraborty, I., Chubynsky, M., Diaz Melian, V. L., Waitukaitis, S. R., Sprittles, J., & Souslov, A. (2023). SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1. Zenodo. https://doi.org/10.5281/ZENODO.8329143","ista":"Binysh J, Chakraborty I, Chubynsky M, Diaz Melian VL, Waitukaitis SR, Sprittles J, Souslov A. 2023. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1, Zenodo, 10.5281/ZENODO.8329143.","ama":"Binysh J, Chakraborty I, Chubynsky M, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1. 2023. doi:10.5281/ZENODO.8329143","chicago":"Binysh, Jack, Indrajit Chakraborty, Mykyta Chubynsky, Vicente L Diaz Melian, Scott R Waitukaitis, James Sprittles, and Anton Souslov. “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: V1.0.1.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8329143.","short":"J. Binysh, I. Chakraborty, M. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis, J. Sprittles, A. Souslov, (2023).","mla":"Binysh, Jack, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: V1.0.1. Zenodo, 2023, doi:10.5281/ZENODO.8329143."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.8329143"}],"article_processing_charge":"No","day":"08","month":"09","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14514"}]},"author":[{"last_name":"Binysh","first_name":"Jack","full_name":"Binysh, Jack"},{"last_name":"Chakraborty","first_name":"Indrajit","full_name":"Chakraborty, Indrajit"},{"first_name":"Mykyta","last_name":"Chubynsky","full_name":"Chubynsky, Mykyta"},{"full_name":"Diaz Melian, Vicente L","first_name":"Vicente L","last_name":"Diaz Melian","id":"b6798902-eea0-11ea-9cbc-a8e14286c631"},{"full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R"},{"full_name":"Sprittles, James","last_name":"Sprittles","first_name":"James"},{"full_name":"Souslov, Anton","first_name":"Anton","last_name":"Souslov"}],"oa_version":"Published Version","date_updated":"2023-11-13T09:21:31Z","date_created":"2023-11-13T09:12:11Z","_id":"14523","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","department":[{"_id":"ScWa"}],"publisher":"Zenodo","status":"public","ddc":["530"],"title":"SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1","abstract":[{"text":"see Readme file","lang":"eng"}],"type":"research_data_reference"},{"date_updated":"2023-11-13T10:18:45Z","date_created":"2023-11-12T23:00:56Z","volume":372,"author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy"},{"orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","first_name":"Tobias","full_name":"Meggendorfer, Tobias"},{"first_name":"Suman","last_name":"Sadhukhan","full_name":"Sadhukhan, Suman"},{"last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"},{"full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","first_name":"Dorde","last_name":"Zikelic"}],"publication_status":"published","publisher":"IOS Press","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"acknowledgement":"This research was supported in part by ISF grant no. 1679/21, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie Grant Agreement No. 665385.","year":"2023","file_date_updated":"2023-11-13T10:16:10Z","ec_funded":1,"language":[{"iso":"eng"}],"conference":{"location":"Krakow, Poland","start_date":"2023-09-30","end_date":"2023-10-04","name":"ECAI: European Conference on Artificial Intelligence"},"doi":"10.3233/FAIA230264","quality_controlled":"1","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"arxiv":["2307.15218"]},"month":"09","publication_identifier":{"issn":["0922-6389"],"isbn":["9781643684369"]},"file":[{"success":1,"checksum":"1390ca38480fa4cf286b0f1a42e8c12f","date_updated":"2023-11-13T10:16:10Z","date_created":"2023-11-13T10:16:10Z","file_id":"14529","relation":"main_file","creator":"dernst","file_size":501011,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_FAIA_Avni.pdf"}],"oa_version":"Published Version","ddc":["000"],"title":"Reachability poorman discrete-bidding games","status":"public","intvolume":" 372","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14518","abstract":[{"lang":"eng","text":"We consider bidding games, a class of two-player zero-sum graph games. The game proceeds as follows. Both players have bounded budgets. A token is placed on a vertex of a graph, in each turn the players simultaneously submit bids, and the higher bidder moves the token, where we break bidding ties in favor of Player 1. Player 1 wins the game iff the token visits a designated target vertex. We consider, for the first time, poorman discrete-bidding in which the granularity of the bids is restricted and the higher bid is paid to the bank. Previous work either did not impose granularity restrictions or considered Richman bidding (bids are paid to the opponent). While the latter mechanisms are technically more accessible, the former is more appealing from a practical standpoint. Our study focuses on threshold budgets, which is the necessary and sufficient initial budget required for Player 1 to ensure winning against a given Player 2 budget. We first show existence of thresholds. In DAGs, we show that threshold budgets can be approximated with error bounds by thresholds under continuous-bidding and that they exhibit a periodic behavior. We identify closed-form solutions in special cases. We implement and experiment with an algorithm to find threshold budgets."}],"type":"conference","date_published":"2023-09-28T00:00:00Z","page":"141-148","publication":"Frontiers in Artificial Intelligence and Applications","citation":{"apa":"Avni, G., Meggendorfer, T., Sadhukhan, S., Tkadlec, J., & Zikelic, D. (2023). Reachability poorman discrete-bidding games. In Frontiers in Artificial Intelligence and Applications (Vol. 372, pp. 141–148). Krakow, Poland: IOS Press. https://doi.org/10.3233/FAIA230264","ieee":"G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, and D. Zikelic, “Reachability poorman discrete-bidding games,” in Frontiers in Artificial Intelligence and Applications, Krakow, Poland, 2023, vol. 372, pp. 141–148.","ista":"Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. 2023. Reachability poorman discrete-bidding games. Frontiers in Artificial Intelligence and Applications. ECAI: European Conference on Artificial Intelligence vol. 372, 141–148.","ama":"Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. Reachability poorman discrete-bidding games. In: Frontiers in Artificial Intelligence and Applications. Vol 372. IOS Press; 2023:141-148. doi:10.3233/FAIA230264","chicago":"Avni, Guy, Tobias Meggendorfer, Suman Sadhukhan, Josef Tkadlec, and Dorde Zikelic. “Reachability Poorman Discrete-Bidding Games.” In Frontiers in Artificial Intelligence and Applications, 372:141–48. IOS Press, 2023. https://doi.org/10.3233/FAIA230264.","short":"G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, D. Zikelic, in:, Frontiers in Artificial Intelligence and Applications, IOS Press, 2023, pp. 141–148.","mla":"Avni, Guy, et al. “Reachability Poorman Discrete-Bidding Games.” Frontiers in Artificial Intelligence and Applications, vol. 372, IOS Press, 2023, pp. 141–48, doi:10.3233/FAIA230264."},"day":"28","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"doi":"10.1038/s41586-023-05991-z","acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"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"},"external_id":{"isi":["000991386800011"]},"oa":1,"isi":1,"quality_controlled":"1","month":"06","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"author":[{"first_name":"Morris","last_name":"Degen","full_name":"Degen, Morris"},{"full_name":"Santos, José Carlos","first_name":"José Carlos","last_name":"Santos"},{"full_name":"Pluhackova, Kristyna","first_name":"Kristyna","last_name":"Pluhackova"},{"last_name":"Cebrero","first_name":"Gonzalo","full_name":"Cebrero, Gonzalo"},{"full_name":"Ramos, Saray","first_name":"Saray","last_name":"Ramos"},{"first_name":"Gytis","last_name":"Jankevicius","full_name":"Jankevicius, Gytis"},{"last_name":"Hartenian","first_name":"Ella","full_name":"Hartenian, Ella"},{"full_name":"Guillerm, Undina","id":"bb74f472-ae54-11eb-9835-bc9c22fb1183","first_name":"Undina","last_name":"Guillerm"},{"last_name":"Mari","first_name":"Stefania A.","full_name":"Mari, Stefania A."},{"full_name":"Kohl, Bastian","last_name":"Kohl","first_name":"Bastian"},{"full_name":"Müller, Daniel J.","last_name":"Müller","first_name":"Daniel J."},{"last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"},{"full_name":"Maier, Timm","first_name":"Timm","last_name":"Maier"},{"first_name":"Camilo","last_name":"Perez","full_name":"Perez, Camilo"},{"first_name":"Christian","last_name":"Sieben","full_name":"Sieben, Christian"},{"last_name":"Broz","first_name":"Petr","full_name":"Broz, Petr"},{"full_name":"Hiller, Sebastian","first_name":"Sebastian","last_name":"Hiller"}],"date_created":"2023-05-28T22:01:04Z","date_updated":"2023-11-14T11:49:21Z","volume":618,"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2075–390740016 and the Stuttgart Center for Simulation Science (SC SimTech) to K.P., by ERC-CoG 770988 (InflamCellDeath) and SNF Project funding (310030B_198005, 310030B_192523) to P.B., by the Swiss Nanoscience Institute and the Swiss National Science Foundation via the NCCR AntiResist (180541) to S.H. and the NCCR Molecular Systems Engineering (51NF40-205608) to D.J.M., by the Helmholtz Young Investigator Program of the Helmholtz Association to C.S., by the SNF Professorship funding (PP00P3_198903) to C.P., EMBO postdoctoral fellowship ALTF 27-2022 to E.H. and by the Scientific Service Units of IST Austria through resources provided by the NMR and Life Science Facilities to P.S. Molecular dynamics simulations were performed on the HoreKa supercomputer funded by the Ministry of Science, Research and the Arts Baden-Württemberg and by the Federal Ministry of Education and Research. The authors thank the BioEM Lab of the Biozentrum, University of Basel for support; V. Mack, K. Shkarina and J. Fricke for technical support; D. Ricklin and S. Vogt for peptide synthesis; P. Pelczar for support with animals; S.-J. Marrink and P. Telles de Souza for supply with Martini3 parameters and scripts; and P. Radler und M. Loose for help with QCM. Fig. 4g and Extended Data Fig. 1a were in part created with BioRender.com.\r\nOpen access funding provided by University of Basel.","year":"2023","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"PaSc"}],"file_date_updated":"2023-11-14T11:48:18Z","date_published":"2023-06-29T00:00:00Z","publication":"Nature","citation":{"ama":"Degen M, Santos JC, Pluhackova K, et al. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. 2023;618:1065-1071. doi:10.1038/s41586-023-05991-z","apa":"Degen, M., Santos, J. C., Pluhackova, K., Cebrero, G., Ramos, S., Jankevicius, G., … Hiller, S. (2023). Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-05991-z","ieee":"M. Degen et al., “Structural basis of NINJ1-mediated plasma membrane rupture in cell death,” Nature, vol. 618. Springer Nature, pp. 1065–1071, 2023.","ista":"Degen M, Santos JC, Pluhackova K, Cebrero G, Ramos S, Jankevicius G, Hartenian E, Guillerm U, Mari SA, Kohl B, Müller DJ, Schanda P, Maier T, Perez C, Sieben C, Broz P, Hiller S. 2023. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. 618, 1065–1071.","short":"M. Degen, J.C. Santos, K. Pluhackova, G. Cebrero, S. Ramos, G. Jankevicius, E. Hartenian, U. Guillerm, S.A. Mari, B. Kohl, D.J. Müller, P. Schanda, T. Maier, C. Perez, C. Sieben, P. Broz, S. Hiller, Nature 618 (2023) 1065–1071.","mla":"Degen, Morris, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” Nature, vol. 618, Springer Nature, 2023, pp. 1065–71, doi:10.1038/s41586-023-05991-z.","chicago":"Degen, Morris, José Carlos Santos, Kristyna Pluhackova, Gonzalo Cebrero, Saray Ramos, Gytis Jankevicius, Ella Hartenian, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-05991-z."},"article_type":"original","page":"1065-1071","day":"29","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":12292188,"access_level":"open_access","file_name":"2023_Nature_Degen.pdf","success":1,"checksum":"0fab69252453bff1de7f0e2eceb76d34","date_created":"2023-11-14T11:48:18Z","date_updated":"2023-11-14T11:48:18Z","file_id":"14533","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13096","title":"Structural basis of NINJ1-mediated plasma membrane rupture in cell death","ddc":["570"],"status":"public","intvolume":" 618","abstract":[{"lang":"eng","text":"Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death."}],"type":"journal_article"},{"article_number":"e202300128","file_date_updated":"2023-11-14T11:27:16Z","department":[{"_id":"StFr"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"The authors (N.L.F and R.B.J) would like to acknowledge the funding contributions of Shell and the EPRSC via I–Case studentships (grants no. EP/V519662/1 and EP/R511870/1 respectively). T.I would like to thank the ERC advanced Investigator Grant for CPG (EC H2020 835073). Thank you to Zhen Wang from the University of Cambridge for measuring GPC, the Yusuf Hamied Department of Chemistry's mass spectrometry service for MS measurements and analysis and Dr Andrew Bond from the University of Cambridge for XRD measurement and analysis.","volume":16,"date_created":"2023-05-21T22:01:05Z","date_updated":"2023-11-14T11:28:23Z","author":[{"full_name":"Farag, Nadia L.","last_name":"Farag","first_name":"Nadia L."},{"last_name":"Jethwa","first_name":"Rajesh B","orcid":"0000-0002-0404-4356","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","full_name":"Jethwa, Rajesh B"},{"last_name":"Beardmore","first_name":"Alice E.","full_name":"Beardmore, Alice E."},{"full_name":"Insinna, Teresa","last_name":"Insinna","first_name":"Teresa"},{"full_name":"O'Keefe, Christopher A.","first_name":"Christopher A.","last_name":"O'Keefe"},{"first_name":"Peter A.A.","last_name":"Klusener","full_name":"Klusener, Peter A.A."},{"last_name":"Grey","first_name":"Clare P.","full_name":"Grey, Clare P."},{"full_name":"Wright, Dominic S.","last_name":"Wright","first_name":"Dominic S."}],"publication_identifier":{"eissn":["1864-564X"],"issn":["1864-5631"]},"month":"07","quality_controlled":"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"},"external_id":{"isi":["000985051300001"],"pmid":["36970847"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/cssc.202300128","type":"journal_article","issue":"13","abstract":[{"lang":"eng","text":"A series of triarylamines was synthesised and screened for their suitability as catholytes in redox flow batteries using cyclic voltammetry (CV). Tris(4-aminophenyl)amine was found to be the strongest candidate. Solubility and initial electrochemical performance were promising; however, polymerisation was observed during electrochemical cycling leading to rapid capacity fade prescribed to a loss of accessible active material and the limitation of ion transport processes within the cell. A mixed electrolyte system of H3PO4 and HCl was found to inhibit polymerisation producing oligomers that consumed less active material reducing rates of degradation in the redox flow battery. Under these conditions Coulombic efficiency improved by over 4 %, the maximum number of cycles more than quadrupled and an additional theoretical capacity of 20 % was accessed. This paper is, to our knowledge, the first example of triarylamines as catholytes in all-aqueous redox flow batteries and emphasises the impact supporting electrolytes can have on electrochemical performance."}],"intvolume":" 16","status":"public","ddc":["540"],"title":"Triarylamines as catholytes in aqueous organic redox flow batteries","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13041","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1168683,"file_name":"2023_ChemSusChem_Farag.pdf","access_level":"open_access","date_updated":"2023-11-14T11:27:16Z","date_created":"2023-11-14T11:27:16Z","success":1,"checksum":"efa0713289995af83a2147b3e8e1d6a6","file_id":"14532","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"06","article_type":"original","citation":{"ieee":"N. L. Farag et al., “Triarylamines as catholytes in aqueous organic redox flow batteries,” ChemSusChem, vol. 16, no. 13. Wiley, 2023.","apa":"Farag, N. L., Jethwa, R. B., Beardmore, A. E., Insinna, T., O’Keefe, C. A., Klusener, P. A. A., … Wright, D. S. (2023). Triarylamines as catholytes in aqueous organic redox flow batteries. ChemSusChem. Wiley. https://doi.org/10.1002/cssc.202300128","ista":"Farag NL, Jethwa RB, Beardmore AE, Insinna T, O’Keefe CA, Klusener PAA, Grey CP, Wright DS. 2023. Triarylamines as catholytes in aqueous organic redox flow batteries. ChemSusChem. 16(13), e202300128.","ama":"Farag NL, Jethwa RB, Beardmore AE, et al. Triarylamines as catholytes in aqueous organic redox flow batteries. ChemSusChem. 2023;16(13). doi:10.1002/cssc.202300128","chicago":"Farag, Nadia L., Rajesh B Jethwa, Alice E. Beardmore, Teresa Insinna, Christopher A. O’Keefe, Peter A.A. Klusener, Clare P. Grey, and Dominic S. Wright. “Triarylamines as Catholytes in Aqueous Organic Redox Flow Batteries.” ChemSusChem. Wiley, 2023. https://doi.org/10.1002/cssc.202300128.","short":"N.L. Farag, R.B. Jethwa, A.E. Beardmore, T. Insinna, C.A. O’Keefe, P.A.A. Klusener, C.P. Grey, D.S. Wright, ChemSusChem 16 (2023).","mla":"Farag, Nadia L., et al. “Triarylamines as Catholytes in Aqueous Organic Redox Flow Batteries.” ChemSusChem, vol. 16, no. 13, e202300128, Wiley, 2023, doi:10.1002/cssc.202300128."},"publication":"ChemSusChem","date_published":"2023-07-06T00:00:00Z"},{"volume":19,"date_created":"2023-06-04T22:01:02Z","date_updated":"2023-11-14T12:58:31Z","related_material":{"link":[{"relation":"erratum","url":"10.1038/s41567-023-02130-3"}]},"author":[{"first_name":"J.-A.","last_name":"Hernandez","full_name":"Hernandez, J.-A."},{"id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","orcid":"0000-0002-1838-2129","first_name":"Mandy","last_name":"Bethkenhagen","full_name":"Bethkenhagen, Mandy"},{"full_name":"Ninet, S.","last_name":"Ninet","first_name":"S."},{"full_name":"French, M.","first_name":"M.","last_name":"French"},{"last_name":"Benuzzi-Mounaix","first_name":"A.","full_name":"Benuzzi-Mounaix, A."},{"first_name":"F.","last_name":"Datchi","full_name":"Datchi, F."},{"last_name":"Guarguaglini","first_name":"M.","full_name":"Guarguaglini, M."},{"full_name":"Lefevre, F.","first_name":"F.","last_name":"Lefevre"},{"last_name":"Occelli","first_name":"F.","full_name":"Occelli, F."},{"last_name":"Redmer","first_name":"R.","full_name":"Redmer, R."},{"first_name":"T.","last_name":"Vinci","full_name":"Vinci, T."},{"first_name":"A.","last_name":"Ravasio","full_name":"Ravasio, A."}],"department":[{"_id":"BiCh"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"We acknowledge the crucial contribution of the LULI2000 laser and support teams to the success of the experiments. We also thank S. Brygoo and P. Loubeyre for useful discussions. This research was supported by the French National Research Agency (ANR) through the projects POMPEI (grant no. ANR-16-CE31-0008) and SUPER-ICES (grant ANR-15-CE30-008-01), and by the PLAS@PAR Federation. M.F. and R.R. gratefully acknowledge support by the DFG within the Research Unit FOR 2440. M.B. was supported by the European Union within the Marie Skłodowska-Curie actions (xICE grant 894725) and the NOMIS foundation. The DFT-MD calculations were performed at the North-German Supercomputing Alliance facilities.","year":"2023","language":[{"iso":"eng"}],"doi":"10.1038/s41567-023-02074-8","quality_controlled":"1","isi":1,"external_id":{"isi":["000996921200001"]},"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"month":"09","oa_version":"None","intvolume":" 19","status":"public","title":"Melting curve of superionic ammonia at planetary interior conditions","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13118","abstract":[{"text":"Under high pressures and temperatures, molecular systems with substantial polarization charges, such as ammonia and water, are predicted to form superionic phases and dense fluid states with dissociating molecules and high electrical conductivity. This behaviour potentially plays a role in explaining the origin of the multipolar magnetic fields of Uranus and Neptune, whose mantles are thought to result from a mixture of H2O, NH3 and CH4 ices. Determining the stability domain, melting curve and electrical conductivity of these superionic phases is therefore crucial for modelling planetary interiors and dynamos. Here we report the melting curve of superionic ammonia up to 300 GPa from laser-driven shock compression of pre-compressed samples and atomistic calculations. We show that ammonia melts at lower temperatures than water above 100 GPa and that fluid ammonia’s electrical conductivity exceeds that of water at conditions predicted by hot, super-adiabatic models for Uranus and Neptune, and enhances the conductivity in their fluid water-rich dynamo layers.","lang":"eng"}],"type":"journal_article","date_published":"2023-09-01T00:00:00Z","page":"1280-1285","article_type":"original","citation":{"mla":"Hernandez, J. A., et al. “Melting Curve of Superionic Ammonia at Planetary Interior Conditions.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1280–85, doi:10.1038/s41567-023-02074-8.","short":"J.-A. Hernandez, M. Bethkenhagen, S. Ninet, M. French, A. Benuzzi-Mounaix, F. Datchi, M. Guarguaglini, F. Lefevre, F. Occelli, R. Redmer, T. Vinci, A. Ravasio, Nature Physics 19 (2023) 1280–1285.","chicago":"Hernandez, J.-A., Mandy Bethkenhagen, S. Ninet, M. French, A. Benuzzi-Mounaix, F. Datchi, M. Guarguaglini, et al. “Melting Curve of Superionic Ammonia at Planetary Interior Conditions.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02074-8.","ama":"Hernandez J-A, Bethkenhagen M, Ninet S, et al. Melting curve of superionic ammonia at planetary interior conditions. Nature Physics. 2023;19:1280-1285. doi:10.1038/s41567-023-02074-8","ista":"Hernandez J-A, Bethkenhagen M, Ninet S, French M, Benuzzi-Mounaix A, Datchi F, Guarguaglini M, Lefevre F, Occelli F, Redmer R, Vinci T, Ravasio A. 2023. Melting curve of superionic ammonia at planetary interior conditions. Nature Physics. 19, 1280–1285.","ieee":"J.-A. Hernandez et al., “Melting curve of superionic ammonia at planetary interior conditions,” Nature Physics, vol. 19. Springer Nature, pp. 1280–1285, 2023.","apa":"Hernandez, J.-A., Bethkenhagen, M., Ninet, S., French, M., Benuzzi-Mounaix, A., Datchi, F., … Ravasio, A. (2023). Melting curve of superionic ammonia at planetary interior conditions. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02074-8"},"publication":"Nature Physics","article_processing_charge":"No","day":"01","scopus_import":"1"},{"month":"06","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41586-023-06018-3","quality_controlled":"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"},"external_id":{"isi":["001001139300008"]},"oa":1,"file_date_updated":"2023-11-14T13:00:19Z","date_updated":"2023-11-14T13:02:50Z","date_created":"2023-06-04T22:01:03Z","volume":618,"author":[{"full_name":"Helson, Victor","first_name":"Victor","last_name":"Helson"},{"first_name":"Timo","last_name":"Zwettler","full_name":"Zwettler, Timo"},{"last_name":"Mivehvar","first_name":"Farokh","full_name":"Mivehvar, Farokh"},{"first_name":"Elvia","last_name":"Colella","full_name":"Colella, Elvia"},{"full_name":"Roux, Kevin Etienne Robert","last_name":"Roux","first_name":"Kevin Etienne Robert","id":"53f93ea2-803f-11ed-ab7e-b283135794ef"},{"full_name":"Konishi, Hideki","last_name":"Konishi","first_name":"Hideki"},{"last_name":"Ritsch","first_name":"Helmut","full_name":"Ritsch, Helmut"},{"full_name":"Brantut, Jean Philippe","last_name":"Brantut","first_name":"Jean Philippe"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GeKa"}],"acknowledgement":"Open access funding provided by EPFL Lausanne.We acknowledge discussions with T. Donner and T. Esslinger. We thank G. del Pace and T. Bühler for their assistance in the final stages of the experiment. We acknowledge funding from the European Research Council under the European Union Horizon 2020 Research and Innovation Programme (Grant no. 714309) and the Swiss National Science Foundation (Grant no. 184654). F.M. acknowledges financial support from the Austrian Science Fund (Stand-Alone Project P 35891-N).","year":"2023","day":"22","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2023-06-22T00:00:00Z","article_type":"original","page":"716-720","publication":"Nature","citation":{"chicago":"Helson, Victor, Timo Zwettler, Farokh Mivehvar, Elvia Colella, Kevin Etienne Robert Roux, Hideki Konishi, Helmut Ritsch, and Jean Philippe Brantut. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06018-3.","mla":"Helson, Victor, et al. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” Nature, vol. 618, Springer Nature, 2023, pp. 716–20, doi:10.1038/s41586-023-06018-3.","short":"V. Helson, T. Zwettler, F. Mivehvar, E. Colella, K.E.R. Roux, H. Konishi, H. Ritsch, J.P. Brantut, Nature 618 (2023) 716–720.","ista":"Helson V, Zwettler T, Mivehvar F, Colella E, Roux KER, Konishi H, Ritsch H, Brantut JP. 2023. Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. Nature. 618, 716–720.","apa":"Helson, V., Zwettler, T., Mivehvar, F., Colella, E., Roux, K. E. R., Konishi, H., … Brantut, J. P. (2023). Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06018-3","ieee":"V. Helson et al., “Density-wave ordering in a unitary Fermi gas with photon-mediated interactions,” Nature, vol. 618. Springer Nature, pp. 716–720, 2023.","ama":"Helson V, Zwettler T, Mivehvar F, et al. Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. Nature. 2023;618:716-720. doi:10.1038/s41586-023-06018-3"},"abstract":[{"text":"A density wave (DW) is a fundamental type of long-range order in quantum matter tied to self-organization into a crystalline structure. The interplay of DW order with superfluidity can lead to complex scenarios that pose a great challenge to theoretical analysis. In the past decades, tunable quantum Fermi gases have served as model systems for exploring the physics of strongly interacting fermions, including most notably magnetic ordering1, pairing and superfluidity2, and the crossover from a Bardeen–Cooper–Schrieffer superfluid to a Bose–Einstein condensate3. Here, we realize a Fermi gas featuring both strong, tunable contact interactions and photon-mediated, spatially structured long-range interactions in a transversely driven high-finesse optical cavity. Above a critical long-range interaction strength, DW order is stabilized in the system, which we identify via its superradiant light-scattering properties. We quantitatively measure the variation of the onset of DW order as the contact interaction is varied across the Bardeen–Cooper–Schrieffer superfluid and Bose–Einstein condensate crossover, in qualitative agreement with a mean-field theory. The atomic DW susceptibility varies over an order of magnitude upon tuning the strength and the sign of the long-range interactions below the self-ordering threshold, demonstrating independent and simultaneous control over the contact and long-range interactions. Therefore, our experimental setup provides a fully tunable and microscopically controllable platform for the experimental study of the interplay of superfluidity and DW order.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2023-11-14T13:00:19Z","date_created":"2023-11-14T13:00:19Z","success":1,"checksum":"4887a296e3b6f54e8c0b946cbfd24f49","file_id":"14534","relation":"main_file","creator":"dernst","file_size":8156497,"content_type":"application/pdf","file_name":"2023_Nature_Helson.pdf","access_level":"open_access"}],"status":"public","ddc":["530"],"title":"Density-wave ordering in a unitary Fermi gas with photon-mediated interactions","intvolume":" 618","_id":"13119","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12911","intvolume":" 285","status":"public","title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","issue":"4","abstract":[{"text":"This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground-state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.","lang":"eng"}],"type":"journal_article","date_published":"2023-08-15T00:00:00Z","citation":{"chicago":"Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” Journal of Functional Analysis. Elsevier, 2023. https://doi.org/10.1016/j.jfa.2023.109963.","short":"D. Feliciangeli, A. Gerolin, L. Portinale, Journal of Functional Analysis 285 (2023).","mla":"Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” Journal of Functional Analysis, vol. 285, no. 4, 109963, Elsevier, 2023, doi:10.1016/j.jfa.2023.109963.","ieee":"D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” Journal of Functional Analysis, vol. 285, no. 4. Elsevier, 2023.","apa":"Feliciangeli, D., Gerolin, A., & Portinale, L. (2023). A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2023.109963","ista":"Feliciangeli D, Gerolin A, Portinale L. 2023. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. Journal of Functional Analysis. 285(4), 109963.","ama":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. Journal of Functional Analysis. 2023;285(4). doi:10.1016/j.jfa.2023.109963"},"publication":"Journal of Functional Analysis","article_type":"original","article_processing_charge":"No","day":"15","scopus_import":"1","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9792"}]},"author":[{"full_name":"Feliciangeli, Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","first_name":"Dario","last_name":"Feliciangeli"},{"full_name":"Gerolin, Augusto","first_name":"Augusto","last_name":"Gerolin"},{"full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo","last_name":"Portinale"}],"volume":285,"date_created":"2023-05-07T22:01:02Z","date_updated":"2023-11-14T13:21:01Z","year":"2023","acknowledgement":"This work started when A.G. was visiting the Erwin Schrödinger Institute and then continued when D.F. and L.P visited the Theoretical Chemistry Department of the Vrije Universiteit Amsterdam. The authors thank the hospitality of both places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature suggestions in the early state of the project. The authors also thank J. Maas and R. Seiringer for their feedback and useful comments to a first draft of the article. Finally, we acknowledge the high quality review done by the anonymous referee of our paper, who we would like to thank for the excellent work and constructive feedback.\r\nD.F acknowledges support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreements No 716117 and No 694227). A.G. acknowledges funding by the HORIZON EUROPE European Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942] as well as partial support of his research by the Canada Research Chairs Program (ID 2021-00234) and Natural Sciences and Engineering Research Council of Canada, RGPIN-2022-05207. L.P. acknowledges support by the Austrian Science Fund (FWF), grants No W1245 and No F65, and by the Deutsche Forschungsgemeinschaft (DFG) - Project number 390685813.","publisher":"Elsevier","department":[{"_id":"RoSe"},{"_id":"JaMa"}],"publication_status":"published","ec_funded":1,"article_number":"109963","doi":"10.1016/j.jfa.2023.109963","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000990804300001"],"arxiv":["2106.11217"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2106.11217"}],"project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"},{"grant_number":" F06504","_id":"260482E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Taming Complexity in Partial Di erential Systems"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"month":"08"},{"date_created":"2023-07-02T22:00:43Z","date_updated":"2023-11-14T13:07:09Z","volume":151,"author":[{"last_name":"Hua","first_name":"Bobo","full_name":"Hua, Bobo"},{"first_name":"Matthias","last_name":"Keller","full_name":"Keller, Matthias"},{"last_name":"Schwarz","first_name":"Michael","full_name":"Schwarz, Michael"},{"first_name":"Melchior","last_name":"Wirth","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","full_name":"Wirth, Melchior"}],"publication_status":"published","publisher":"American Mathematical Society","department":[{"_id":"JaMa"}],"acknowledgement":"The second author was supported by the priority program SPP2026 of the German Research Foundation (DFG). The fourth author was supported by the German Academic Scholarship Foundation (Studienstiftung des deutschen Volkes) and by the German Research Foundation (DFG) via RTG 1523/2.","year":"2023","month":"08","publication_identifier":{"eissn":["1088-6826"],"issn":["0002-9939"]},"language":[{"iso":"eng"}],"doi":"10.1090/proc/14361","quality_controlled":"1","isi":1,"external_id":{"isi":["000988204400001"],"arxiv":["1804.08353"]},"oa":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1804.08353","open_access":"1"}],"abstract":[{"text":"In this note we study the eigenvalue growth of infinite graphs with discrete spectrum. We assume that the corresponding Dirichlet forms satisfy certain Sobolev-type inequalities and that the total measure is finite. In this sense, the associated operators on these graphs display similarities to elliptic operators on bounded domains in the continuum. Specifically, we prove lower bounds on the eigenvalue growth and show by examples that corresponding upper bounds cannot be established.","lang":"eng"}],"issue":"8","type":"journal_article","oa_version":"Preprint","title":"Sobolev-type inequalities and eigenvalue growth on graphs with finite measure","status":"public","intvolume":" 151","_id":"13177","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2023-08-01T00:00:00Z","article_type":"original","page":"3401-3414","publication":"Proceedings of the American Mathematical Society","citation":{"ista":"Hua B, Keller M, Schwarz M, Wirth M. 2023. Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. Proceedings of the American Mathematical Society. 151(8), 3401–3414.","apa":"Hua, B., Keller, M., Schwarz, M., & Wirth, M. (2023). Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/14361","ieee":"B. Hua, M. Keller, M. Schwarz, and M. Wirth, “Sobolev-type inequalities and eigenvalue growth on graphs with finite measure,” Proceedings of the American Mathematical Society, vol. 151, no. 8. American Mathematical Society, pp. 3401–3414, 2023.","ama":"Hua B, Keller M, Schwarz M, Wirth M. Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. Proceedings of the American Mathematical Society. 2023;151(8):3401-3414. doi:10.1090/proc/14361","chicago":"Hua, Bobo, Matthias Keller, Michael Schwarz, and Melchior Wirth. “Sobolev-Type Inequalities and Eigenvalue Growth on Graphs with Finite Measure.” Proceedings of the American Mathematical Society. American Mathematical Society, 2023. https://doi.org/10.1090/proc/14361.","mla":"Hua, Bobo, et al. “Sobolev-Type Inequalities and Eigenvalue Growth on Graphs with Finite Measure.” Proceedings of the American Mathematical Society, vol. 151, no. 8, American Mathematical Society, 2023, pp. 3401–14, doi:10.1090/proc/14361.","short":"B. Hua, M. Keller, M. Schwarz, M. Wirth, Proceedings of the American Mathematical Society 151 (2023) 3401–3414."}},{"type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"n the dynamic minimum set cover problem, the challenge is to minimize the update time while guaranteeing a close-to-optimal min{O(log n), f} approximation factor. (Throughout, n, m, f , and C are parameters denoting the maximum number of elements, the number of sets, the frequency, and the cost range.) In the high-frequency range, when f = Ω(log n) , this was achieved by a deterministic O(log n) -approximation algorithm with O(f log n) amortized update time by Gupta et al. [Online and dynamic algorithms for set cover, in Proceedings STOC 2017, ACM, pp. 537–550]. In this paper we consider the low-frequency range, when f = O(log n) , and obtain deterministic algorithms with a (1 + ∈)f -approximation ratio and the following guarantees on the update time. (1) O ((f/∈)-log(Cn)) amortized update time: Prior to our work, the best approximation ratio guaranteed by deterministic algorithms was O(f2) of Bhattacharya, Henzinger, and Italiano [Design of dynamic algorithms via primal-dual method, in Proceedings ICALP 2015, Springer, pp. 206–218]. In contrast, the only result with O(f) -approximation was that of Abboud et al. [Dynamic set cover: Improved algorithms and lower bounds, in Proceedings STOC 2019, ACM, pp. 114–125], who designed a randomized (1+∈)f -approximation algorithm with amortized update time. (2) O(f2/∈3 + (f/∈2).logC) amortized update time: This result improves the above update time bound for most values of f\r\n in the low-frequency range, i.e., f=o(log n) . It is also the first result that is independent of m\r\n and n. It subsumes the constant amortized update time of Bhattacharya and Kulkarni [Deterministically maintaining a (2 + ∈) -approximate minimum vertex cover in O(1/∈2) amortized update time, in Proceedings SODA 2019, SIAM, pp. 1872–1885] for unweighted dynamic vertex cover (i.e., when f = 2 and C = 1). (3) O((f/∈3).log2(Cn)) worst-case update time: No nontrivial worst-case update time was previously known for the dynamic set cover problem. Our bound subsumes and improves by a logarithmic factor the O(log3n/poly (∈)) \r\n worst-case update time for the unweighted dynamic vertex cover problem (i.e., when f = 2\r\n and C =1) of Bhattacharya, Henzinger, and Nanongkai [Fully dynamic approximate maximum matching and minimum vertex cover in O(log3)n worst case update time, in Proceedings SODA 2017, SIAM, pp. 470–489]. We achieve our results via the primal-dual approach, by maintaining a fractional packing solution as a dual certificate. Prior work in dynamic algorithms that employs the primal-dual approach uses a local update scheme that maintains relaxed complementary slackness conditions for every set. For our first result we use instead a global update scheme that does not always maintain complementary slackness conditions. For our second result we combine the global and the local update schema. To achieve our third result we use a hierarchy of background schedulers. It is an interesting open question whether this background scheduler technique can also be used to transform algorithms with amortized running time bounds into algorithms with worst-case running time bounds."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14558","intvolume":" 52","status":"public","title":"Deterministic near-optimal approximation algorithms for dynamic set cover","oa_version":"None","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"mla":"Bhattacharya, Sayan, et al. “Deterministic Near-Optimal Approximation Algorithms for Dynamic Set Cover.” SIAM Journal on Computing, vol. 52, no. 5, Society for Industrial and Applied Mathematics, 2023, pp. 1132–92, doi:10.1137/21M1428649.","short":"S. Bhattacharya, M.H. Henzinger, D. Nanongkai, X. Wu, SIAM Journal on Computing 52 (2023) 1132–1192.","chicago":"Bhattacharya, Sayan, Monika H Henzinger, Danupon Nanongkai, and Xiaowei Wu. “Deterministic Near-Optimal Approximation Algorithms for Dynamic Set Cover.” SIAM Journal on Computing. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/21M1428649.","ama":"Bhattacharya S, Henzinger MH, Nanongkai D, Wu X. Deterministic near-optimal approximation algorithms for dynamic set cover. SIAM Journal on Computing. 2023;52(5):1132-1192. doi:10.1137/21M1428649","ista":"Bhattacharya S, Henzinger MH, Nanongkai D, Wu X. 2023. Deterministic near-optimal approximation algorithms for dynamic set cover. SIAM Journal on Computing. 52(5), 1132–1192.","apa":"Bhattacharya, S., Henzinger, M. H., Nanongkai, D., & Wu, X. (2023). Deterministic near-optimal approximation algorithms for dynamic set cover. SIAM Journal on Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/21M1428649","ieee":"S. Bhattacharya, M. H. Henzinger, D. Nanongkai, and X. Wu, “Deterministic near-optimal approximation algorithms for dynamic set cover,” SIAM Journal on Computing, vol. 52, no. 5. Society for Industrial and Applied Mathematics, pp. 1132–1192, 2023."},"publication":"SIAM Journal on Computing","page":"1132-1192","article_type":"original","date_published":"2023-10-01T00:00:00Z","ec_funded":1,"year":"2023","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grants 715672 and\r\n101019564 ``The Design of Modern Fully Dynamic Data Structures (MoDynStruct)\"\") and from the Engineering and Physical Sciences Research Council, UK (EPSRC) under grant EP/S03353X/1. The second author was also supported by the Austrian Science Fund (FWF) project ``Fast Algorithms for a Reactive Network Layer (ReactNet),\"\" P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020--2024, project ``Static and Dynamic Hierarchical Graph Decompositions,\"\"I 5982-N, and project Z 422-N. The third author was also supported by the Swedish Research Council (Reg. No. 2015-04659). The fourth author was also supported by the Science and Technology Development Fund (FDCT), Macau SAR (file 0014/2022/AFJ, 0085/2022/A, 0143/2020/A3, and SKL-IOTSC-2021-2023).","department":[{"_id":"MoHe"}],"publisher":"Society for Industrial and Applied Mathematics","publication_status":"published","author":[{"full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya","first_name":"Sayan"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"},{"full_name":"Wu, Xiaowei","first_name":"Xiaowei","last_name":"Wu"}],"volume":52,"date_created":"2023-11-19T23:00:56Z","date_updated":"2023-11-20T08:21:07Z","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"month":"10","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"},{"grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Wittgenstein Award - Monika Henzinger"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"}],"quality_controlled":"1","doi":"10.1137/21M1428649","language":[{"iso":"eng"}]},{"abstract":[{"text":"We consider the problem of learning control policies in discrete-time stochastic systems which guarantee that the system stabilizes within some specified stabilization region with probability 1. Our approach is based on the novel notion of stabilizing ranking supermartingales (sRSMs) that we introduce in this work. Our sRSMs overcome the limitation of methods proposed in previous works whose applicability is restricted to systems in which the stabilizing region cannot be left once entered under any control policy. We present a learning procedure that learns a control policy together with an sRSM that formally certifies probability 1 stability, both learned as neural networks. We show that this procedure can also be adapted to formally verifying that, under a given Lipschitz continuous control policy, the stochastic system stabilizes within some stabilizing region with probability 1. Our experimental evaluation shows that our learning procedure can successfully learn provably stabilizing policies in practice.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14559","title":"Learning provably stabilizing neural controllers for discrete-time stochastic systems","status":"public","intvolume":" 14215","day":"22","article_processing_charge":"No","scopus_import":"1","date_published":"2023-10-22T00:00:00Z","publication":"21st International Symposium on Automated Technology for Verification and Analysis","citation":{"ama":"Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. Learning provably stabilizing neural controllers for discrete-time stochastic systems. In: 21st International Symposium on Automated Technology for Verification and Analysis. Vol 14215. Springer Nature; 2023:357-379. doi:10.1007/978-3-031-45329-8_17","ista":"Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. Learning provably stabilizing neural controllers for discrete-time stochastic systems. 21st International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 14215, 357–379.","apa":"Ansaripour, M., Chatterjee, K., Henzinger, T. A., Lechner, M., & Zikelic, D. (2023). Learning provably stabilizing neural controllers for discrete-time stochastic systems. In 21st International Symposium on Automated Technology for Verification and Analysis (Vol. 14215, pp. 357–379). Singapore, Singapore: Springer Nature. https://doi.org/10.1007/978-3-031-45329-8_17","ieee":"M. Ansaripour, K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “Learning provably stabilizing neural controllers for discrete-time stochastic systems,” in 21st International Symposium on Automated Technology for Verification and Analysis, Singapore, Singapore, 2023, vol. 14215, pp. 357–379.","mla":"Ansaripour, Matin, et al. “Learning Provably Stabilizing Neural Controllers for Discrete-Time Stochastic Systems.” 21st International Symposium on Automated Technology for Verification and Analysis, vol. 14215, Springer Nature, 2023, pp. 357–79, doi:10.1007/978-3-031-45329-8_17.","short":"M. Ansaripour, K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, 21st International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2023, pp. 357–379.","chicago":"Ansaripour, Matin, Krishnendu Chatterjee, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “Learning Provably Stabilizing Neural Controllers for Discrete-Time Stochastic Systems.” In 21st International Symposium on Automated Technology for Verification and Analysis, 14215:357–79. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-45329-8_17."},"page":"357-379","ec_funded":1,"author":[{"first_name":"Matin","last_name":"Ansaripour","full_name":"Ansaripour, Matin"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zikelic, Dorde","last_name":"Zikelic","first_name":"Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-11-20T08:30:20Z","date_created":"2023-11-19T23:00:56Z","volume":14215,"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","year":"2023","publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Springer Nature","month":"10","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031453281"],"issn":["0302-9743"]},"conference":{"name":"ATVA: Automated Technology for Verification and Analysis","location":"Singapore, Singapore","start_date":"2023-10-24","end_date":"2023-10-27"},"doi":"10.1007/978-3-031-45329-8_17","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}]},{"publication_identifier":{"issn":["2822-7840"],"eissn":["2804-7214"]},"month":"09","doi":"10.1051/m2an/2023077","language":[{"iso":"eng"}],"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"},"oa":1,"project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","ec_funded":1,"file_date_updated":"2023-11-20T08:34:57Z","related_material":{"link":[{"url":"https://github.com/tonyshardlow/RIDK-FD","relation":"software"}]},"author":[{"full_name":"Cornalba, Federico","id":"2CEB641C-A400-11E9-A717-D712E6697425","orcid":"0000-0002-6269-5149","first_name":"Federico","last_name":"Cornalba"},{"full_name":"Shardlow, Tony","last_name":"Shardlow","first_name":"Tony"}],"volume":57,"date_created":"2023-11-19T23:00:55Z","date_updated":"2023-11-20T08:38:47Z","year":"2023","acknowledgement":"The authors thank the anonymous referees for their careful reading of the manuscript and their\r\nvaluable suggestions. FC gratefully acknowledges funding from the Austrian Science Fund (FWF) through the project F65, and from the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No. 754411 (the latter funding source covered the first part of this project).","publisher":"EDP Sciences","department":[{"_id":"JuFi"}],"publication_status":"published","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2023-09-01T00:00:00Z","citation":{"ama":"Cornalba F, Shardlow T. The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. 2023;57(5):3061-3090. doi:10.1051/m2an/2023077","ieee":"F. Cornalba and T. Shardlow, “The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime,” ESAIM: Mathematical Modelling and Numerical Analysis, vol. 57, no. 5. EDP Sciences, pp. 3061–3090, 2023.","apa":"Cornalba, F., & Shardlow, T. (2023). The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences. https://doi.org/10.1051/m2an/2023077","ista":"Cornalba F, Shardlow T. 2023. The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. 57(5), 3061–3090.","short":"F. Cornalba, T. Shardlow, ESAIM: Mathematical Modelling and Numerical Analysis 57 (2023) 3061–3090.","mla":"Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.” ESAIM: Mathematical Modelling and Numerical Analysis, vol. 57, no. 5, EDP Sciences, 2023, pp. 3061–90, doi:10.1051/m2an/2023077.","chicago":"Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.” ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences, 2023. https://doi.org/10.1051/m2an/2023077."},"publication":"ESAIM: Mathematical Modelling and Numerical Analysis","page":"3061-3090","article_type":"original","issue":"5","abstract":[{"text":"The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations around the meanfield limit for large-scale particle systems in both particle density and momentum density. We focus on the following two aspects. Firstly, we set up a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide suitable definitions of numerical fluxes at the interface of the mesh elements which are consistent with the wave-type nature of the RIDK model and grant stability of the simulations, and we quantify the rate of convergence in mean square to the continuous RIDK model. Secondly, we introduce modifications of the RIDK model in order to preserve positivity of the density (such a feature only holds in a “high-probability sense” for the original RIDK model). By means of numerical simulations, we show that the modifications lead to physically realistic and positive density profiles. In one case, subject to additional regularity constraints, we also prove positivity. Finally, we present an application of our methodology to a system of diffusing and reacting particles. Our Python code is available in open-source format.","lang":"eng"}],"type":"journal_article","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1508534,"file_name":"2023_ESAIM_Cornalba.pdf","access_level":"open_access","date_created":"2023-11-20T08:34:57Z","date_updated":"2023-11-20T08:34:57Z","success":1,"checksum":"3aef1475b1882c8dec112df9a5167c39","file_id":"14560","relation":"main_file"}],"oa_version":"Published Version","_id":"14554","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 57","ddc":["510"],"status":"public","title":"The regularised inertial Dean' Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime"},{"ddc":["570"],"title":"How chromosomal inversions reorient the evolutionary process","status":"public","_id":"14556","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach."}],"article_type":"review","publication":"Journal of Evolutionary Biology","citation":{"ieee":"E. L. Berdan et al., “How chromosomal inversions reorient the evolutionary process,” Journal of Evolutionary Biology. Wiley, 2023.","apa":"Berdan, E. L., Barton, N. H., Butlin, R., Charlesworth, B., Faria, R., Fragata, I., … Flatt, T. (2023). How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14242","ista":"Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology., 14242.","ama":"Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. 2023. doi:10.1111/jeb.14242","chicago":"Berdan, Emma L., Nicholas H Barton, Roger Butlin, Brian Charlesworth, Rui Faria, Inês Fragata, Kimberly J. Gilbert, et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” Journal of Evolutionary Biology. Wiley, 2023. https://doi.org/10.1111/jeb.14242.","short":"E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata, K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell, M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson, T. Flatt, Journal of Evolutionary Biology (2023).","mla":"Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” Journal of Evolutionary Biology, 14242, Wiley, 2023, doi:10.1111/jeb.14242."},"date_published":"2023-11-08T00:00:00Z","scopus_import":"1","day":"08","has_accepted_license":"1","article_processing_charge":"No","publication_status":"epub_ahead","publisher":"Wiley","department":[{"_id":"NiBa"}],"year":"2023","acknowledgement":"We are grateful to two referees and Luke Holman for valuable comments on a previous version of our manuscript. This paper was conceived at the ESEB Progress Meeting ‘Disentangling neutral versus adaptive evolution in chromosomal inversions’, organized by ELB, KJ and TF and held at Tjärnö Marine Laboratory (Sweden) between 28 February and 3 March 2022. We are indebted to ESEB for sponsoring our workshop and to the following funding bodies for supporting our research: ERC AdG 101055327 to NHB; Swedish Research Council (VR) 2018-03695 and Leverhulme Trust RPG-2021-141 to RKB; Fundação para a Ciência e a Tecnologia (FCT) contract 2020.00275.CEECIND and research project PTDC/BIA-1232 EVL/1614/2021 to RF; Fundação para a Ciência e a Tecnologia (FCT) junior researcher contract CEECIND/02616/2018 to IF; Swiss National Science Foundation (SNSF) Ambizione #PZ00P3_185952 to KJG; National Science Foundation NSF-OCE 2043905 and NSF-DEB 1655701 to KEL; Swiss National Science Foundation (SNSF) 310030_204681 to CLP; Swedish Research Council (VR) 2021-05243 to MR; Norwegian Research Council grant 315287 to AMW; Swiss National Science Foundation (SNSF) 31003A-182262 and FZEB-0-214654 to TF. We also thank Luca Ferretti for the discussion and Eliane Zinn (Flatt lab) for help with reference formatting.","date_created":"2023-11-19T23:00:55Z","date_updated":"2023-11-20T08:51:09Z","author":[{"full_name":"Berdan, Emma L.","first_name":"Emma L.","last_name":"Berdan"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"last_name":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"},{"last_name":"Charlesworth","first_name":"Brian","full_name":"Charlesworth, Brian"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Inês","last_name":"Fragata","full_name":"Fragata, Inês"},{"full_name":"Gilbert, Kimberly J.","first_name":"Kimberly J.","last_name":"Gilbert"},{"full_name":"Jay, Paul","last_name":"Jay","first_name":"Paul"},{"first_name":"Martin","last_name":"Kapun","full_name":"Kapun, Martin"},{"full_name":"Lotterhos, Katie E.","last_name":"Lotterhos","first_name":"Katie E."},{"full_name":"Mérot, Claire","first_name":"Claire","last_name":"Mérot"},{"first_name":"Esra","last_name":"Durmaz Mitchell","full_name":"Durmaz Mitchell, Esra"},{"full_name":"Pascual, Marta","first_name":"Marta","last_name":"Pascual"},{"full_name":"Peichel, Catherine L.","first_name":"Catherine L.","last_name":"Peichel"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Schaeffer, Stephen W.","last_name":"Schaeffer","first_name":"Stephen W."},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Flatt, Thomas","last_name":"Flatt","first_name":"Thomas"}],"article_number":"14242","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"main_file_link":[{"url":"https://doi.org/10.1111/jeb.14242","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/jeb.14242","month":"11","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]}},{"abstract":[{"text":"The intricate regulatory processes behind actin polymerization play a crucial role in cellular biology, including essential mechanisms such as cell migration or cell division. However, the self-organizing principles governing actin polymerization are still poorly understood. In this perspective article, we compare the Belousov-Zhabotinsky (BZ) reaction, a classic and well understood chemical oscillator known for its self-organizing spatiotemporal dynamics, with the excitable dynamics of polymerizing actin. While the BZ reaction originates from the domain of inorganic chemistry, it shares remarkable similarities with actin polymerization, including the characteristic propagating waves, which are influenced by geometry and external fields, and the emergent collective behavior. Starting with a general description of emerging patterns, we elaborate on single droplets or cell-level dynamics, the influence of geometric confinements and conclude with collective interactions. Comparing these two systems sheds light on the universal nature of self-organization principles in both living and inanimate systems.","lang":"eng"}],"type":"journal_article","file":[{"creator":"dernst","content_type":"application/pdf","file_size":2047622,"file_name":"2023_FrontiersCellDevBio_Riedl.pdf","access_level":"open_access","date_created":"2023-11-20T08:41:15Z","date_updated":"2023-11-20T08:41:15Z","success":1,"checksum":"61857fc3ebf019354932e7ee684658ce","file_id":"14561","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14555","title":"The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction","status":"public","ddc":["570"],"intvolume":" 11","day":"31","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2023-10-31T00:00:00Z","publication":"Frontiers in Cell and Developmental Biology","citation":{"apa":"Riedl, M., & Sixt, M. K. (2023). The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. Frontiers. https://doi.org/10.3389/fcell.2023.1287420","ieee":"M. Riedl and M. K. Sixt, “The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction,” Frontiers in Cell and Developmental Biology, vol. 11. Frontiers, 2023.","ista":"Riedl M, Sixt MK. 2023. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. 11, 1287420.","ama":"Riedl M, Sixt MK. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. 2023;11. doi:10.3389/fcell.2023.1287420","chicago":"Riedl, Michael, and Michael K Sixt. “The Excitable Nature of Polymerizing Actin and the Belousov-Zhabotinsky Reaction.” Frontiers in Cell and Developmental Biology. Frontiers, 2023. https://doi.org/10.3389/fcell.2023.1287420.","short":"M. Riedl, M.K. Sixt, Frontiers in Cell and Developmental Biology 11 (2023).","mla":"Riedl, Michael, and Michael K. Sixt. “The Excitable Nature of Polymerizing Actin and the Belousov-Zhabotinsky Reaction.” Frontiers in Cell and Developmental Biology, vol. 11, 1287420, Frontiers, 2023, doi:10.3389/fcell.2023.1287420."},"article_type":"original","file_date_updated":"2023-11-20T08:41:15Z","article_number":"1287420","author":[{"orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","last_name":"Riedl","first_name":"Michael","full_name":"Riedl, Michael"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"date_created":"2023-11-19T23:00:55Z","date_updated":"2023-11-20T08:44:17Z","volume":11,"year":"2023","acknowledgement":"The author(s) declare that no financial support was received for the research, authorship, and/or publication of this article.","publication_status":"published","publisher":"Frontiers","department":[{"_id":"MiSi"}],"month":"10","publication_identifier":{"eissn":["2296-634X"]},"doi":"10.3389/fcell.2023.1287420","language":[{"iso":"eng"}],"oa":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"},"quality_controlled":"1"},{"title":"Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders","status":"public","_id":"14543","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders."}],"article_type":"original","publication":"Brain","citation":{"ista":"Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2023. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain., awad380.","apa":"Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W., Godwin, A., … Maroofian, R. (2023). Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. Oxford University Press. https://doi.org/10.1093/brain/awad380","ieee":"R. Kaiyrzhanov et al., “Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders,” Brain. Oxford University Press, 2023.","ama":"Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 2023. doi:10.1093/brain/awad380","chicago":"Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella, Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain. Oxford University Press, 2023. https://doi.org/10.1093/brain/awad380.","mla":"Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain, awad380, Oxford University Press, 2023, doi:10.1093/brain/awad380.","short":"R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A. Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani, M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M. Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun, A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M. Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P. Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa, W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed, M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço, T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro, M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A. Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski, J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino, M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain (2023)."},"date_published":"2023-11-10T00:00:00Z","keyword":["Neurology (clinical)"],"scopus_import":"1","day":"10","article_processing_charge":"No","publication_status":"epub_ahead","department":[{"_id":"GradSch"}],"publisher":"Oxford University Press","year":"2023","date_updated":"2023-11-20T10:17:32Z","date_created":"2023-11-16T12:36:51Z","author":[{"full_name":"Kaiyrzhanov, Rauan","first_name":"Rauan","last_name":"Kaiyrzhanov"},{"full_name":"Rad, Aboulfazl","first_name":"Aboulfazl","last_name":"Rad"},{"full_name":"Lin, Sheng-Jia","last_name":"Lin","first_name":"Sheng-Jia"},{"full_name":"Bertoli-Avella, Aida","first_name":"Aida","last_name":"Bertoli-Avella"},{"full_name":"Kallemeijn, Wouter W","first_name":"Wouter W","last_name":"Kallemeijn"},{"last_name":"Godwin","first_name":"Annie","full_name":"Godwin, Annie"},{"full_name":"Zaki, Maha S","last_name":"Zaki","first_name":"Maha S"},{"id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","orcid":"0000-0002-2512-7812","first_name":"Kevin","last_name":"Huang","full_name":"Huang, Kevin"},{"full_name":"Lau, Tracy","first_name":"Tracy","last_name":"Lau"},{"first_name":"Cassidy","last_name":"Petree","full_name":"Petree, Cassidy"},{"full_name":"Efthymiou, Stephanie","last_name":"Efthymiou","first_name":"Stephanie"},{"full_name":"Ghayoor Karimiani, Ehsan","last_name":"Ghayoor Karimiani","first_name":"Ehsan"},{"full_name":"Hempel, Maja","last_name":"Hempel","first_name":"Maja"},{"full_name":"Normand, Elizabeth A","last_name":"Normand","first_name":"Elizabeth A"},{"last_name":"Rudnik-Schöneborn","first_name":"Sabine","full_name":"Rudnik-Schöneborn, Sabine"},{"full_name":"Schatz, Ulrich A","last_name":"Schatz","first_name":"Ulrich A"},{"full_name":"Baggelaar, Marc P","first_name":"Marc P","last_name":"Baggelaar"},{"last_name":"Ilyas","first_name":"Muhammad","full_name":"Ilyas, Muhammad"},{"full_name":"Sultan, Tipu","last_name":"Sultan","first_name":"Tipu"},{"full_name":"Alvi, Javeria Raza","first_name":"Javeria Raza","last_name":"Alvi"},{"full_name":"Ganieva, Manizha","last_name":"Ganieva","first_name":"Manizha"},{"full_name":"Fowler, Ben","first_name":"Ben","last_name":"Fowler"},{"last_name":"Aanicai","first_name":"Ruxandra","full_name":"Aanicai, Ruxandra"},{"full_name":"Akay Tayfun, Gulsen","first_name":"Gulsen","last_name":"Akay Tayfun"},{"full_name":"Al Saman, Abdulaziz","first_name":"Abdulaziz","last_name":"Al Saman"},{"first_name":"Abdulrahman","last_name":"Alswaid","full_name":"Alswaid, Abdulrahman"},{"full_name":"Amiri, Nafise","first_name":"Nafise","last_name":"Amiri"},{"first_name":"Nilufar","last_name":"Asilova","full_name":"Asilova, Nilufar"},{"full_name":"Shotelersuk, Vorasuk","first_name":"Vorasuk","last_name":"Shotelersuk"},{"first_name":"Patra","last_name":"Yeetong","full_name":"Yeetong, Patra"},{"full_name":"Azam, Matloob","last_name":"Azam","first_name":"Matloob"},{"first_name":"Meisam","last_name":"Babaei","full_name":"Babaei, Meisam"},{"full_name":"Bahrami Monajemi, Gholamreza","last_name":"Bahrami Monajemi","first_name":"Gholamreza"},{"last_name":"Mohammadi","first_name":"Pouria","full_name":"Mohammadi, Pouria"},{"full_name":"Samie, Saeed","last_name":"Samie","first_name":"Saeed"},{"last_name":"Banu","first_name":"Selina Husna","full_name":"Banu, Selina Husna"},{"first_name":"Jorge Pinto","last_name":"Basto","full_name":"Basto, Jorge Pinto"},{"last_name":"Kortüm","first_name":"Fanny","full_name":"Kortüm, Fanny"},{"last_name":"Bauer","first_name":"Mislen","full_name":"Bauer, Mislen"},{"full_name":"Bauer, Peter","last_name":"Bauer","first_name":"Peter"},{"full_name":"Beetz, Christian","last_name":"Beetz","first_name":"Christian"},{"first_name":"Masoud","last_name":"Garshasbi","full_name":"Garshasbi, Masoud"},{"first_name":"Awatif","last_name":"Hameed Issa","full_name":"Hameed Issa, Awatif"},{"full_name":"Eyaid, Wafaa","last_name":"Eyaid","first_name":"Wafaa"},{"last_name":"Ahmed","first_name":"Hind","full_name":"Ahmed, Hind"},{"first_name":"Narges","last_name":"Hashemi","full_name":"Hashemi, Narges"},{"first_name":"Kazem","last_name":"Hassanpour","full_name":"Hassanpour, Kazem"},{"first_name":"Isabella","last_name":"Herman","full_name":"Herman, Isabella"},{"full_name":"Ibrohimov, Sherozjon","last_name":"Ibrohimov","first_name":"Sherozjon"},{"full_name":"Abdul-Majeed, Ban A","last_name":"Abdul-Majeed","first_name":"Ban A"},{"first_name":"Maria","last_name":"Imdad","full_name":"Imdad, Maria"},{"full_name":"Isrofilov, Maksudjon","first_name":"Maksudjon","last_name":"Isrofilov"},{"first_name":"Qassem","last_name":"Kaiyal","full_name":"Kaiyal, Qassem"},{"last_name":"Khan","first_name":"Suliman","full_name":"Khan, Suliman"},{"full_name":"Kirmse, Brian","first_name":"Brian","last_name":"Kirmse"},{"last_name":"Koster","first_name":"Janet","full_name":"Koster, Janet"},{"full_name":"Lourenço, Charles Marques","last_name":"Lourenço","first_name":"Charles Marques"},{"full_name":"Mitani, Tadahiro","first_name":"Tadahiro","last_name":"Mitani"},{"full_name":"Moldovan, Oana","last_name":"Moldovan","first_name":"Oana"},{"last_name":"Murphy","first_name":"David","full_name":"Murphy, David"},{"last_name":"Najafi","first_name":"Maryam","full_name":"Najafi, Maryam"},{"full_name":"Pehlivan, Davut","last_name":"Pehlivan","first_name":"Davut"},{"first_name":"Maria Eugenia","last_name":"Rocha","full_name":"Rocha, Maria Eugenia"},{"full_name":"Salpietro, Vincenzo","first_name":"Vincenzo","last_name":"Salpietro"},{"last_name":"Schmidts","first_name":"Miriam","full_name":"Schmidts, Miriam"},{"full_name":"Shalata, Adel","first_name":"Adel","last_name":"Shalata"},{"full_name":"Mahroum, Mohammad","first_name":"Mohammad","last_name":"Mahroum"},{"last_name":"Talbeya","first_name":"Jawabreh Kassem","full_name":"Talbeya, Jawabreh Kassem"},{"full_name":"Taylor, Robert W","last_name":"Taylor","first_name":"Robert W"},{"first_name":"Dayana","last_name":"Vazquez","full_name":"Vazquez, Dayana"},{"full_name":"Vetro, Annalisa","first_name":"Annalisa","last_name":"Vetro"},{"full_name":"Waterham, Hans R","first_name":"Hans R","last_name":"Waterham"},{"first_name":"Mashaya","last_name":"Zaman","full_name":"Zaman, Mashaya"},{"full_name":"Schrader, Tina A","first_name":"Tina A","last_name":"Schrader"},{"last_name":"Chung","first_name":"Wendy K","full_name":"Chung, Wendy K"},{"full_name":"Guerrini, Renzo","first_name":"Renzo","last_name":"Guerrini"},{"first_name":"James R","last_name":"Lupski","full_name":"Lupski, James R"},{"first_name":"Joseph","last_name":"Gleeson","full_name":"Gleeson, Joseph"},{"last_name":"Suri","first_name":"Mohnish","full_name":"Suri, Mohnish"},{"full_name":"Jamshidi, Yalda","first_name":"Yalda","last_name":"Jamshidi"},{"last_name":"Bhatia","first_name":"Kailash P","full_name":"Bhatia, Kailash P"},{"full_name":"Vona, Barbara","last_name":"Vona","first_name":"Barbara"},{"full_name":"Schrader, Michael","first_name":"Michael","last_name":"Schrader"},{"first_name":"Mariasavina","last_name":"Severino","full_name":"Severino, Mariasavina"},{"first_name":"Matthew","last_name":"Guille","full_name":"Guille, Matthew"},{"full_name":"Tate, Edward W","last_name":"Tate","first_name":"Edward W"},{"full_name":"Varshney, Gaurav K","last_name":"Varshney","first_name":"Gaurav K"},{"last_name":"Houlden","first_name":"Henry","full_name":"Houlden, Henry"},{"first_name":"Reza","last_name":"Maroofian","full_name":"Maroofian, Reza"}],"article_number":"awad380","extern":"1","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/brain/awad380"}],"language":[{"iso":"eng"}],"doi":"10.1093/brain/awad380","month":"11","publication_identifier":{"eissn":["1460-2156"],"issn":["0006-8950"]}},{"publication":"Reviews in Mathematical Physics","citation":{"mla":"Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics, 2360005, World Scientific Publishing, 2023, doi:10.1142/s0129055x2360005x.","short":"S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics (2023).","chicago":"Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics. World Scientific Publishing, 2023. https://doi.org/10.1142/s0129055x2360005x.","ama":"Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. 2023. doi:10.1142/s0129055x2360005x","ista":"Henheik SJ, Lauritsen AB, Roos B. 2023. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics., 2360005.","ieee":"S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional BCS theory,” Reviews in Mathematical Physics. World Scientific Publishing, 2023.","apa":"Henheik, S. J., Lauritsen, A. B., & Roos, B. (2023). Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/s0129055x2360005x"},"article_type":"original","date_published":"2023-10-31T00:00:00Z","scopus_import":"1","day":"31","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","_id":"14542","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Universality in low-dimensional BCS theory","status":"public","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"It is a remarkable property of BCS theory that the ratio of the energy gap at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given by a universal constant, independent of the microscopic details of the fermionic interaction. This universality has rigorously been proven quite recently in three spatial dimensions and three different limiting regimes: weak coupling, low density and high density. The goal of this short note is to extend the universal behavior to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1142/S0129055X2360005X"}],"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"},"oa":1,"external_id":{"arxiv":["2301.05621"]},"quality_controlled":"1","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d"},{"name":"Mathematical Challenges in BCS Theory of Superconductivity","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427"}],"doi":"10.1142/s0129055x2360005x","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["0129-055X"],"eissn":["1793-6659"]},"acknowledgement":"We thank Robert Seiringer for comments on the paper. J. H. gratefully acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond”No. 101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber I6427.","year":"2023","publication_status":"epub_ahead","department":[{"_id":"GradSch"},{"_id":"LaEr"},{"_id":"RoSe"}],"publisher":"World Scientific Publishing","author":[{"orcid":"0000-0003-1106-327X","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","last_name":"Henheik","first_name":"Sven Joscha","full_name":"Henheik, Sven Joscha"},{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard","last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard"},{"full_name":"Roos, Barbara","last_name":"Roos","first_name":"Barbara","orcid":"0000-0002-9071-5880","id":"5DA90512-D80F-11E9-8994-2E2EE6697425"}],"date_created":"2023-11-15T23:48:14Z","date_updated":"2023-11-20T10:04:38Z","article_number":"2360005 ","ec_funded":1},{"article_processing_charge":"No","day":"30","scopus_import":"1","date_published":"2023-10-30T00:00:00Z","citation":{"chicago":"Fedotova, Ekaterina, Nikolai Kuznetsov, Egor Tiunov, A. E. Ulanov, and A. I. Lvovsky. “Continuous-Variable Quantum Tomography of High-Amplitude States.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.108.042430.","mla":"Fedotova, Ekaterina, et al. “Continuous-Variable Quantum Tomography of High-Amplitude States.” Physical Review A, vol. 108, no. 4, 042430, American Physical Society, 2023, doi:10.1103/PhysRevA.108.042430.","short":"E. Fedotova, N. Kuznetsov, E. Tiunov, A.E. Ulanov, A.I. Lvovsky, Physical Review A 108 (2023).","ista":"Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. 2023. Continuous-variable quantum tomography of high-amplitude states. Physical Review A. 108(4), 042430.","apa":"Fedotova, E., Kuznetsov, N., Tiunov, E., Ulanov, A. E., & Lvovsky, A. I. (2023). Continuous-variable quantum tomography of high-amplitude states. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.108.042430","ieee":"E. Fedotova, N. Kuznetsov, E. Tiunov, A. E. Ulanov, and A. I. Lvovsky, “Continuous-variable quantum tomography of high-amplitude states,” Physical Review A, vol. 108, no. 4. American Physical Society, 2023.","ama":"Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. Continuous-variable quantum tomography of high-amplitude states. Physical Review A. 2023;108(4). doi:10.1103/PhysRevA.108.042430"},"publication":"Physical Review A","article_type":"original","issue":"4","abstract":[{"text":"Quantum state tomography is an essential component of modern quantum technology. In application to continuous-variable harmonic-oscillator systems, such as the electromagnetic field, existing tomography methods typically reconstruct the state in discrete bases, and are hence limited to states with relatively low amplitudes and energies. Here, we overcome this limitation by utilizing a feed-forward neural network to obtain the density matrix directly in the continuous position basis. An important benefit of our approach is the ability to choose specific regions in the phase space for detailed reconstruction. This results in a relatively slow scaling of the amount of resources required for the reconstruction with the state amplitude, and hence allows us to dramatically increase the range of amplitudes accessible with our method.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14553","intvolume":" 108","title":"Continuous-variable quantum tomography of high-amplitude states","status":"public","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"month":"10","doi":"10.1103/PhysRevA.108.042430","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2212.07406","open_access":"1"}],"external_id":{"arxiv":["2212.07406"]},"oa":1,"quality_controlled":"1","article_number":"042430","author":[{"first_name":"Ekaterina","last_name":"Fedotova","id":"c1bea5e1-878e-11ee-9dff-d7404e4422ab","orcid":"0000-0001-7242-015X","full_name":"Fedotova, Ekaterina"},{"last_name":"Kuznetsov","first_name":"Nikolai","full_name":"Kuznetsov, Nikolai"},{"last_name":"Tiunov","first_name":"Egor","full_name":"Tiunov, Egor"},{"first_name":"A. E.","last_name":"Ulanov","full_name":"Ulanov, A. E."},{"first_name":"A. I.","last_name":"Lvovsky","full_name":"Lvovsky, A. I."}],"volume":108,"date_updated":"2023-11-20T10:26:51Z","date_created":"2023-11-19T23:00:54Z","year":"2023","publisher":"American Physical Society","department":[{"_id":"JoFi"}],"publication_status":"published"},{"date_published":"2023-11-01T00:00:00Z","citation":{"ista":"Dikranjan D, Giordano Bruno A, Zava N. 2023. Epimorphisms and closure operators of categories of semilattices. Quaestiones Mathematicae. 46(S1), 191–221.","apa":"Dikranjan, D., Giordano Bruno, A., & Zava, N. (2023). Epimorphisms and closure operators of categories of semilattices. Quaestiones Mathematicae. Taylor & Francis. https://doi.org/10.2989/16073606.2023.2247731","ieee":"D. Dikranjan, A. Giordano Bruno, and N. Zava, “Epimorphisms and closure operators of categories of semilattices,” Quaestiones Mathematicae, vol. 46, no. S1. Taylor & Francis, pp. 191–221, 2023.","ama":"Dikranjan D, Giordano Bruno A, Zava N. Epimorphisms and closure operators of categories of semilattices. Quaestiones Mathematicae. 2023;46(S1):191-221. doi:10.2989/16073606.2023.2247731","chicago":"Dikranjan, D., A. Giordano Bruno, and Nicolò Zava. “Epimorphisms and Closure Operators of Categories of Semilattices.” Quaestiones Mathematicae. Taylor & Francis, 2023. https://doi.org/10.2989/16073606.2023.2247731.","mla":"Dikranjan, D., et al. “Epimorphisms and Closure Operators of Categories of Semilattices.” Quaestiones Mathematicae, vol. 46, no. S1, Taylor & Francis, 2023, pp. 191–221, doi:10.2989/16073606.2023.2247731.","short":"D. Dikranjan, A. Giordano Bruno, N. Zava, Quaestiones Mathematicae 46 (2023) 191–221."},"publication":"Quaestiones Mathematicae","page":"191-221","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14557","intvolume":" 46","status":"public","title":"Epimorphisms and closure operators of categories of semilattices","issue":"S1","abstract":[{"lang":"eng","text":"Motivated by a problem posed in [10], we investigate the closure operators of the category SLatt of join semilattices and its subcategory SLattO of join semilattices with bottom element. In particular, we show that there are only finitely many closure operators of both categories, and provide a complete classification. We use this result to deduce the known fact that epimorphisms of SLatt and SLattO are surjective. We complement the paper with two different proofs of this result using either generators or Isbell’s zigzag theorem."}],"type":"journal_article","doi":"10.2989/16073606.2023.2247731","language":[{"iso":"eng"}],"project":[{"call_identifier":"FWF","name":"Algebraic Footprints of Geometric Features in Homology","grant_number":"I04245","_id":"26AD5D90-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publication_identifier":{"eissn":["1727-933X"],"issn":["1607-3606"]},"month":"11","author":[{"last_name":"Dikranjan","first_name":"D.","full_name":"Dikranjan, D."},{"last_name":"Giordano Bruno","first_name":"A.","full_name":"Giordano Bruno, A."},{"full_name":"Zava, Nicolò","orcid":"0000-0001-8686-1888","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","last_name":"Zava","first_name":"Nicolò"}],"volume":46,"date_updated":"2023-11-20T09:24:48Z","date_created":"2023-11-19T23:00:55Z","year":"2023","acknowledgement":"The first and second named authors are members of GNSAGA – INdAM.\r\nThe third named author was supported by the FWF Grant, Project number I4245–N35","publisher":"Taylor & Francis","department":[{"_id":"HeEd"}],"publication_status":"published"},{"doi":"10.1126/science.adh8830","language":[{"iso":"eng"}],"external_id":{"pmid":["37943897"]},"quality_controlled":"1","month":"11","publication_identifier":{"eissn":["1095-9203"]},"author":[{"last_name":"Robinson","first_name":"M. 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A."},{"full_name":"Sapir, Y.","first_name":"Y.","last_name":"Sapir"},{"full_name":"Sasal, Y.","first_name":"Y.","last_name":"Sasal"},{"first_name":"Y.","last_name":"Sato","full_name":"Sato, Y."},{"full_name":"Sawant, M.","last_name":"Sawant","first_name":"M."},{"full_name":"Schroeder, H.","first_name":"H.","last_name":"Schroeder"},{"first_name":"I.","last_name":"Schumann","full_name":"Schumann, I."},{"last_name":"Segoli","first_name":"M.","full_name":"Segoli, M."},{"first_name":"H.","last_name":"Segre","full_name":"Segre, H."},{"first_name":"O.","last_name":"Shelef","full_name":"Shelef, O."},{"full_name":"Shinohara, N.","first_name":"N.","last_name":"Shinohara"},{"full_name":"Singh, R. P.","first_name":"R. P.","last_name":"Singh"},{"full_name":"Smith, D. S.","last_name":"Smith","first_name":"D. S."},{"last_name":"Sobral","first_name":"M.","full_name":"Sobral, M."},{"last_name":"Stotz","first_name":"G. C.","full_name":"Stotz, G. C."},{"full_name":"Tack, A. J.M.","last_name":"Tack","first_name":"A. J.M."},{"first_name":"M.","last_name":"Tayal","full_name":"Tayal, M."},{"last_name":"Tooker","first_name":"J. F.","full_name":"Tooker, J. F."},{"last_name":"Torrico-Bazoberry","first_name":"D.","full_name":"Torrico-Bazoberry, D."},{"full_name":"Tougeron, K.","last_name":"Tougeron","first_name":"K."},{"full_name":"Trowbridge, A. M.","last_name":"Trowbridge","first_name":"A. M."},{"first_name":"S.","last_name":"Utsumi","full_name":"Utsumi, S."},{"first_name":"O.","last_name":"Uyi","full_name":"Uyi, O."},{"last_name":"Vaca-Uribe","first_name":"J. L.","full_name":"Vaca-Uribe, J. L."},{"first_name":"A.","last_name":"Valtonen","full_name":"Valtonen, A."},{"full_name":"Van Dijk, L. J.A.","first_name":"L. J.A.","last_name":"Van Dijk"},{"first_name":"V.","last_name":"Vandvik","full_name":"Vandvik, V."},{"full_name":"Villellas, J.","last_name":"Villellas","first_name":"J."},{"first_name":"L. P.","last_name":"Waller","full_name":"Waller, L. P."},{"full_name":"Weber, M. G.","last_name":"Weber","first_name":"M. G."},{"full_name":"Yamawo, A.","first_name":"A.","last_name":"Yamawo"},{"full_name":"Yim, S.","first_name":"S.","last_name":"Yim"},{"full_name":"Zarnetske, P. L.","last_name":"Zarnetske","first_name":"P. L."},{"full_name":"Zehr, L. N.","first_name":"L. N.","last_name":"Zehr"},{"first_name":"Z.","last_name":"Zhong","full_name":"Zhong, Z."},{"full_name":"Wetzel, W. C.","first_name":"W. C.","last_name":"Wetzel"}],"related_material":{"record":[{"id":"14579","status":"public","relation":"research_data"}]},"date_updated":"2023-11-20T11:17:34Z","date_created":"2023-11-19T23:00:54Z","volume":382,"year":"2023","acknowledgement":"The authors acknowledge funding for central project coordination from NSF Research Coordination Network grant DEB-2203582; the Ecology, Evolution, and Behavior Program at Michigan State University; and AgBioResearch at Michigan State University. Site-specific funding is listed in the supplementary materials.","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"AAAS","date_published":"2023-11-09T00:00:00Z","publication":"Science","citation":{"ista":"Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 382(6671), 679–683.","ieee":"M. L. Robinson et al., “Plant size, latitude, and phylogeny explain within-population variability in herbivory,” Science, vol. 382, no. 6671. AAAS, pp. 679–683, 2023.","apa":"Robinson, M. L., Hahn, P. G., Inouye, B. D., Underwood, N., Whitehead, S. R., Abbott, K. C., … Wetzel, W. C. (2023). Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. AAAS. https://doi.org/10.1126/science.adh8830","ama":"Robinson ML, Hahn PG, Inouye BD, et al. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 2023;382(6671):679-683. doi:10.1126/science.adh8830","chicago":"Robinson, M. L., P. G. Hahn, B. D. Inouye, N. Underwood, S. R. Whitehead, K. C. Abbott, E. M. Bruna, et al. “Plant Size, Latitude, and Phylogeny Explain within-Population Variability in Herbivory.” Science. AAAS, 2023. https://doi.org/10.1126/science.adh8830.","mla":"Robinson, M. L., et al. “Plant Size, Latitude, and Phylogeny Explain within-Population Variability in Herbivory.” Science, vol. 382, no. 6671, AAAS, 2023, pp. 679–83, doi:10.1126/science.adh8830.","short":"M.L. Robinson, P.G. Hahn, B.D. Inouye, N. Underwood, S.R. Whitehead, K.C. Abbott, E.M. Bruna, N.I. Cacho, L.A. Dyer, L. Abdala-Roberts, W.J. Allen, J.F. Andrade, D.F. Angulo, D. Anjos, D.N. Anstett, R. Bagchi, S. Bagchi, M. Barbosa, S. Barrett, C. Baskett, E. Ben-Simchon, K.J. Bloodworth, J.L. Bronstein, Y.M. Buckley, K.T. Burghardt, C. Bustos-Segura, E.S. Calixto, R.L. Carvalho, B. Castagneyrol, M.C. Chiuffo, D. Cinoğlu, E. Cinto Mejía, M.C. Cock, R. Cogni, O.L. Cope, T. Cornelissen, D.R. Cortez, D.W. Crowder, C. Dallstream, W. Dáttilo, J.K. Davis, R.D. Dimarco, H.E. Dole, I.N. Egbon, M. Eisenring, A. Ejomah, B.D. Elderd, M.J. Endara, M.D. Eubanks, S.E. Everingham, K.N. Farah, R.P. Farias, A.P. Fernandes, G.W. Fernandes, M. Ferrante, A. Finn, G.A. Florjancic, M.L. Forister, Q.N. Fox, E. Frago, F.M. França, A.S. Getman-Pickering, Z. Getman-Pickering, E. Gianoli, B. Gooden, M.M. Gossner, K.A. Greig, S. Gripenberg, R. Groenteman, P. Grof-Tisza, N. Haack, L. Hahn, S.M. Haq, A.M. Helms, J. Hennecke, S.L. Hermann, L.M. Holeski, S. Holm, M.C. Hutchinson, E.E. Jackson, S. Kagiya, A. Kalske, M. Kalwajtys, R. Karban, R. Kariyat, T. Keasar, M.F. Kersch-Becker, H.M. Kharouba, T.N. Kim, D.M. Kimuyu, J. Kluse, S.E. Koerner, K.J. Komatsu, S. Krishnan, M. Laihonen, L. Lamelas-López, M.C. Lascaleia, N. Lecomte, C.R. Lehn, X. Li, R.L. Lindroth, E.F. Lopresti, M. Losada, A.M. Louthan, V.J. Luizzi, S.C. Lynch, J.S. Lynn, N.J. Lyon, L.F. Maia, R.A. Maia, T.L. Mannall, B.S. Martin, T.J. Massad, A.C. Mccall, K. Mcgurrin, A.C. Merwin, Z. Mijango-Ramos, C.H. Mills, A.T. Moles, C.M. Moore, X. Moreira, C.R. Morrison, M.C. Moshobane, A. Muola, R. Nakadai, K. Nakajima, S. Novais, C.O. Ogbebor, H. Ohsaki, V.S. Pan, N.A. Pardikes, M. Pareja, N. Parthasarathy, R.R. Pawar, Q. Paynter, I.S. Pearse, R.M. Penczykowski, A.A. Pepi, C.C. Pereira, S.S. Phartyal, F.I. Piper, K. Poveda, E.G. Pringle, J. Puy, T. Quijano, C. Quintero, S. Rasmann, C. Rosche, L.Y. Rosenheim, J.A. Rosenheim, J.B. Runyon, A. Sadeh, Y. Sakata, D.M. Salcido, C. Salgado-Luarte, B.A. Santos, Y. Sapir, Y. Sasal, Y. Sato, M. Sawant, H. Schroeder, I. Schumann, M. Segoli, H. Segre, O. Shelef, N. Shinohara, R.P. Singh, D.S. Smith, M. Sobral, G.C. Stotz, A.J.M. Tack, M. Tayal, J.F. Tooker, D. Torrico-Bazoberry, K. Tougeron, A.M. Trowbridge, S. Utsumi, O. Uyi, J.L. Vaca-Uribe, A. Valtonen, L.J.A. Van Dijk, V. Vandvik, J. Villellas, L.P. Waller, M.G. Weber, A. Yamawo, S. Yim, P.L. Zarnetske, L.N. Zehr, Z. Zhong, W.C. Wetzel, Science 382 (2023) 679–683."},"article_type":"original","page":"679-683","day":"09","article_processing_charge":"No","scopus_import":"1","oa_version":"None","_id":"14552","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Plant size, latitude, and phylogeny explain within-population variability in herbivory","intvolume":" 382","abstract":[{"text":"Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth.","lang":"eng"}],"issue":"6671","type":"journal_article"},{"file":[{"file_name":"2023_CellSystems_Briffa.pdf","access_level":"open_access","creator":"dernst","file_size":5587897,"content_type":"application/pdf","file_id":"14580","relation":"main_file","date_updated":"2023-11-20T11:22:52Z","date_created":"2023-11-20T11:22:52Z","success":1,"checksum":"101fdac59e6f1102d68ef91f2b5bd51a"}],"oa_version":"Published Version","intvolume":" 14","title":"Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14551","issue":"11","abstract":[{"lang":"eng","text":"Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale."}],"type":"journal_article","date_published":"2023-11-15T00:00:00Z","page":"953-967","article_type":"original","citation":{"short":"A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D. Zilberman, Cell Systems 14 (2023) 953–967.","mla":"Briffa, Amy, et al. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” Cell Systems, vol. 14, no. 11, Elsevier, 2023, pp. 953–67, doi:10.1016/j.cels.2023.10.007.","chicago":"Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” Cell Systems. Elsevier, 2023. https://doi.org/10.1016/j.cels.2023.10.007.","ama":"Briffa A, Hollwey E, Shahzad Z, et al. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 2023;14(11):953-967. doi:10.1016/j.cels.2023.10.007","ieee":"A. Briffa et al., “Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations,” Cell Systems, vol. 14, no. 11. Elsevier, pp. 953–967, 2023.","apa":"Briffa, A., Hollwey, E., Shahzad, Z., Moore, J. D., Lyons, D. B., Howard, M., & Zilberman, D. (2023). Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. Elsevier. https://doi.org/10.1016/j.cels.2023.10.007","ista":"Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D. 2023. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 14(11), 953–967."},"publication":"Cell Systems","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"15","scopus_import":"1","volume":14,"date_created":"2023-11-19T23:00:54Z","date_updated":"2023-11-20T11:24:34Z","author":[{"full_name":"Briffa, Amy","first_name":"Amy","last_name":"Briffa"},{"full_name":"Hollwey, Elizabeth","last_name":"Hollwey","first_name":"Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd"},{"full_name":"Shahzad, Zaigham","last_name":"Shahzad","first_name":"Zaigham"},{"first_name":"Jonathan D.","last_name":"Moore","full_name":"Moore, Jonathan D."},{"full_name":"Lyons, David B.","last_name":"Lyons","first_name":"David B."},{"full_name":"Howard, Martin","last_name":"Howard","first_name":"Martin"},{"full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"publisher":"Elsevier","department":[{"_id":"DaZi"}],"publication_status":"published","pmid":1,"acknowledgement":"We would like to thank Xiaoqi Feng, Ander Movilla Miangolarra, and Suzanne de Bruijn for discussions. This work was supported by BBSRC Institute Strategic Programme GEN (BB/P013511/1) to M.H. and D.Z. and by a European Research Council grant MaintainMeth (725746) to D.Z.","year":"2023","ec_funded":1,"file_date_updated":"2023-11-20T11:22:52Z","language":[{"iso":"eng"}],"doi":"10.1016/j.cels.2023.10.007","project":[{"_id":"62935a00-2b32-11ec-9570-eff30fa39068","grant_number":"725746","call_identifier":"H2020","name":"Quantitative analysis of DNA methylation maintenance with chromatin"}],"quality_controlled":"1","oa":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"},"external_id":{"pmid":["37944515"]},"publication_identifier":{"eissn":["2405-4720"],"issn":["2405-4712"]},"month":"11"},{"month":"07","day":"11","article_processing_charge":"No","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8133118"}],"citation":{"short":"W. Wetzel, (2023).","mla":"Wetzel, William. HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0. Zenodo, 2023, doi:10.5281/ZENODO.8133117.","chicago":"Wetzel, William. “HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133117.","ama":"Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:10.5281/ZENODO.8133117","ieee":"W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo, 2023.","apa":"Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo. https://doi.org/10.5281/ZENODO.8133117","ista":"Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo, 10.5281/ZENODO.8133117."},"date_published":"2023-07-11T00:00:00Z","doi":"10.5281/ZENODO.8133117","type":"research_data_reference","abstract":[{"text":"This is associated with our paper \"Plant size, latitude, and phylogeny explain within-population variability in herbivory\" published in Science.\r\n","lang":"eng"}],"year":"2023","_id":"14579","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0","ddc":["570"],"department":[{"_id":"NiBa"}],"publisher":"Zenodo","author":[{"first_name":"William","last_name":"Wetzel","full_name":"Wetzel, William"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14552"}]},"date_created":"2023-11-20T11:07:45Z","date_updated":"2023-11-20T11:17:33Z","oa_version":"Published Version"},{"type":"journal_article","issue":"3","abstract":[{"text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.","lang":"eng"}],"intvolume":" 9","status":"public","ddc":["570"],"title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","_id":"12334","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_size":1756234,"content_type":"application/pdf","creator":"dernst","file_name":"2023_ScienceAdvances_Faessler.pdf","access_level":"open_access","date_created":"2023-01-23T07:45:54Z","date_updated":"2023-01-23T07:45:54Z","checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e","success":1,"relation":"main_file","file_id":"12335"}],"keyword":["Multidisciplinary"],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"20","article_type":"original","citation":{"ama":"Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 2023;9(3). doi:10.1126/sciadv.add6495","ista":"Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V, Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 9(3), add6495.","apa":"Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A., … Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.add6495","ieee":"F. Fäßler et al., “ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning,” Science Advances, vol. 9, no. 3. American Association for the Advancement of Science, 2023.","mla":"Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” Science Advances, vol. 9, no. 3, add6495, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.add6495.","short":"F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V. Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).","chicago":"Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner, and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.add6495."},"publication":"Science Advances","date_published":"2023-01-20T00:00:00Z","article_number":"add6495","file_date_updated":"2023-01-23T07:45:54Z","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","year":"2023","acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nThis research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","volume":9,"date_updated":"2023-11-21T08:05:35Z","date_created":"2023-01-23T07:26:42Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"14562"}]},"author":[{"full_name":"Fäßler, Florian","last_name":"Fäßler","first_name":"Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath","last_name":"Javoor","full_name":"Javoor, Manjunath"},{"full_name":"Datler, Julia","first_name":"Julia","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580"},{"full_name":"Döring, Hermann","first_name":"Hermann","last_name":"Döring"},{"last_name":"Hofer","first_name":"Florian","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","full_name":"Hofer, Florian"},{"last_name":"Dimchev","first_name":"Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"full_name":"Faix, Jan","last_name":"Faix","first_name":"Jan"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM"}],"publication_identifier":{"issn":["2375-2548"]},"month":"01","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000964550100015"]},"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"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"doi":"10.1126/sciadv.add6495"},{"doi":"10.15479/AT:ISTA:14562","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"tmp":{"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)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"oa":1,"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"}],"month":"11","contributor":[{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","contributor_type":"researcher","first_name":"Florian"},{"id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath","contributor_type":"researcher","last_name":"Javoor"},{"orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Datler","first_name":"Julia"},{"first_name":"Hermann","contributor_type":"researcher","last_name":"Döring"},{"first_name":"Florian","last_name":"Hofer","contributor_type":"researcher","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6"},{"orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Dimchev","first_name":"Georgi A"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","contributor_type":"researcher","first_name":"Victor-Valentin"},{"first_name":"Jan","contributor_type":"researcher","last_name":"Faix"},{"contributor_type":"researcher","last_name":"Rottner","first_name":"Klemens"},{"last_name":"Schur","contributor_type":"researcher","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"12334"}]},"author":[{"full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"date_created":"2023-11-20T09:22:33Z","date_updated":"2023-11-21T08:05:34Z","acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nFunding: This research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","year":"2023","department":[{"_id":"FlSc"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-11-20T11:49:58Z","license":"https://creativecommons.org/licenses/by-sa/4.0/","date_published":"2023-11-21T00:00:00Z","citation":{"ama":"Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” 2023. doi:10.15479/AT:ISTA:14562","ieee":"F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.’” Institute of Science and Technology Austria, 2023.","apa":"Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14562","ista":"Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14562.","short":"F.K. Schur, (2023).","mla":"Schur, Florian KM. Research Data of the Publication “ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14562.","chicago":"Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’” Institute of Science and Technology Austria, 2023. 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An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.\r\n"}],"type":"research_data"},{"type":"software","file_date_updated":"2023-11-21T08:20:23Z","abstract":[{"lang":"eng","text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized fila- mentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner."}],"license":"https://choosealicense.com/licenses/agpl-3.0/","year":"2023","_id":"14502","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","ddc":["570"],"status":"public","department":[{"_id":"FlSc"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","first_name":"Georgi A","last_name":"Dimchev","full_name":"Dimchev, Georgi A"},{"full_name":"Amiri, Behnam","first_name":"Behnam","last_name":"Amiri"},{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","first_name":"Florian","last_name":"Fäßler","full_name":"Fäßler, Florian"},{"first_name":"Martin","last_name":"Falcke","full_name":"Falcke, Martin"},{"full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"10290","status":"public","relation":"used_for_analysis_in"}]},"date_created":"2023-11-08T19:40:54Z","date_updated":"2023-11-21T08:36:02Z","file":[{"relation":"main_file","file_id":"14503","date_updated":"2023-11-08T20:23:07Z","date_created":"2023-11-08T20:23:07Z","checksum":"a8b9adeb53a4109dea4d5e39fa1acccf","success":1,"file_name":"Computational_Toolbox_v1.2.zip","access_level":"open_access","file_size":347641117,"content_type":"application/zip","creator":"fschur"},{"date_created":"2023-11-21T08:20:23Z","date_updated":"2023-11-21T08:20:23Z","success":1,"checksum":"14db2addbfca61a085ba301ed6f2900b","file_id":"14586","relation":"main_file","creator":"dernst","file_size":1522,"content_type":"text/plain","file_name":"Readme.txt","access_level":"open_access"}],"keyword":["cryo-electron tomography","actin cytoskeleton","toolbox"],"day":"21","month":"11","has_accepted_license":"1","citation":{"chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14502.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023).","mla":"Dimchev, Georgi A., et al. Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14502.","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2023). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14502","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data.” Institute of Science and Technology Austria, 2023.","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14502.","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023. doi:10.15479/AT:ISTA:14502"},"tmp":{"short":"GNU AGPLv3 ","legal_code_url":"https://www.gnu.org/licenses/agpl-3.0.html","name":"GNU Affero General Public License v3.0"},"oa":1,"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"doi":"10.15479/AT:ISTA:14502","date_published":"2023-11-21T00:00:00Z"},{"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"21","scopus_import":"1","date_published":"2023-11-21T00:00:00Z","article_type":"original","citation":{"mla":"Kroll, Janina, et al. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” EMBO Journal, e114557, Embo Press, 2023, doi:10.15252/embj.2023114557.","short":"J. Kroll, R. Hauschild, A. Kuznetcov, K. Stefanowski, M.D. Hermann, J. Merrin, L.B. Shafeek, A. Müller-Taubenberger, J. Renkawitz, EMBO Journal (2023).","chicago":"Kroll, Janina, Robert Hauschild, Arthur Kuznetcov, Kasia Stefanowski, Monika D. Hermann, Jack Merrin, Lubuna B Shafeek, Annette Müller-Taubenberger, and Jörg Renkawitz. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” EMBO Journal. Embo Press, 2023. https://doi.org/10.15252/embj.2023114557.","ama":"Kroll J, Hauschild R, Kuznetcov A, et al. Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal. 2023. doi:10.15252/embj.2023114557","ista":"Kroll J, Hauschild R, Kuznetcov A, Stefanowski K, Hermann MD, Merrin J, Shafeek LB, Müller-Taubenberger A, Renkawitz J. 2023. Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal., e114557.","apa":"Kroll, J., Hauschild, R., Kuznetcov, A., Stefanowski, K., Hermann, M. D., Merrin, J., … Renkawitz, J. (2023). Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2023114557","ieee":"J. Kroll et al., “Adaptive pathfinding by nucleokinesis during amoeboid migration,” EMBO Journal. Embo Press, 2023."},"publication":"EMBO Journal","abstract":[{"lang":"eng","text":"Motile cells moving in multicellular organisms encounter microenvironments of locally heterogeneous mechanochemical composition. Individual compositional parameters like chemotactic signals, adhesiveness, and pore sizes are well known to be sensed by motile cells, providing individual guidance cues for cellular pathfinding. However, motile cells encounter diverse mechanochemical signals at the same time, raising the question of how cells respond to locally diverse and potentially competing signals on their migration routes. Here, we reveal that motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using mammalian immune cells and the amoebaDictyostelium discoideum, we discover that frequent, rapid and long-distance nucleokinesis is a basic component of amoeboid pathfinding, enabling cells to reorientate quickly between locally competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the ‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment. Our findings establish that nucleokinesis is required for amoeboid cell navigation. Given that motile single-cell amoebae, many immune cells, and some cancer cells utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis underlies cellular navigation during unicellular biology, immunity, and disease."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_size":4862497,"content_type":"application/pdf","creator":"dernst","file_name":"2023_EmboJournal_Kroll.pdf","access_level":"open_access","date_created":"2023-11-27T08:45:56Z","date_updated":"2023-11-27T08:45:56Z","checksum":"6261d0041c7e8d284c39712c40079730","success":1,"relation":"main_file","file_id":"14611"}],"ddc":["570"],"status":"public","title":"Adaptive pathfinding by nucleokinesis during amoeboid migration","_id":"13342","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.15252/embj.2023114557","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["37987147"]},"oa":1,"file_date_updated":"2023-11-27T08:45:56Z","article_number":"e114557","date_created":"2023-08-01T08:59:06Z","date_updated":"2023-11-27T08:47:45Z","author":[{"last_name":"Kroll","first_name":"Janina","full_name":"Kroll, Janina"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild"},{"last_name":"Kuznetcov","first_name":"Arthur","full_name":"Kuznetcov, Arthur"},{"full_name":"Stefanowski, Kasia","first_name":"Kasia","last_name":"Stefanowski"},{"full_name":"Hermann, Monika D.","last_name":"Hermann","first_name":"Monika D."},{"full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lubuna B","last_name":"Shafeek","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7180-6050","full_name":"Shafeek, Lubuna B"},{"last_name":"Müller-Taubenberger","first_name":"Annette","full_name":"Müller-Taubenberger, Annette"},{"last_name":"Renkawitz","first_name":"Jörg","orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg"}],"publisher":"Embo Press","department":[{"_id":"NanoFab"},{"_id":"Bio"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank Christoph Mayr and Bingzhi Wang for initial experiments on amoeboid nucleokinesis, Ana-Maria Lennon-Duménil and Aline Yatim for bone marrow from MyoIIA-Flox*CD11c-Cre mice, Michael Sixt and Aglaja Kopf for EMTB-mCherry, EB3-mCherry, Lifeact-GFP, Lfc knockout, and Myh9-GFP expressing HoxB8 cells, Malte Benjamin Braun, Mauricio Ruiz, and Madeleine T. Schmitt for critical reading of the manuscript, and the Core Facility Bioimaging, the Core Facility Flow Cytometry, and the Animal Core Facility of the Biomedical Center (BMC) for excellent support. This study was supported by the Peter Hans Hofschneider Professorship of the foundation “Stiftung Experimentelle Biomedizin” (to JR), the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to JR), and the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation; SFB914 project A12, to JR), and the CZI grant DAF2020-225401 (https://doi.org/10.37921/120055ratwvi) from the Chan Zuckerberg Initiative DAF (to RH; an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989)). Open Access funding enabled and organized by Projekt DEAL."},{"month":"11","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"external_id":{"pmid":["37968398"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41586-023-06726-w","open_access":"1"}],"quality_controlled":"1","doi":"10.1038/s41586-023-06726-w","language":[{"iso":"eng"}],"year":"2023","acknowledgement":"We thank the Human Embryonic Stem Cell Unit, Advanced Light Microscopy and High-throughput Screening facilities at the Crick for their support in various aspects of the work. We thank the laboratory of P. Anderson for providing the G3BP-DKO U2OS cells. The authors thank N. Chen for providing the purified glycinin protein; Z. Zhao for providing the microfluidic chip wafers; and M. Amaral and F. Frey for helpful discussions and valuable input regarding analysis methods. This work was supported by the Francis Crick Institute (to M.G.G.), which receives its core funding from Cancer Research UK (FC001092), the UK Medical Research Council (FC001092) and the Wellcome Trust (FC001092). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 772022 to M.G.G.). C.B. has received funding from the European Respiratory Society and the European Union’s H2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 713406. A.M. acknowledges support from Alexander von Humboldt Foundation and C.V.-C. acknowledges funding by the Royal Society and the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960 to A.S.). All simulations were carried out on the high-performance computing cluster at the Institute of Science and Technology Austria. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.\r\nOpen Access funding provided by The Francis Crick Institute.","pmid":1,"publication_status":"epub_ahead","publisher":"Springer Nature","department":[{"_id":"AnSa"}],"author":[{"first_name":"Claudio","last_name":"Bussi","full_name":"Bussi, Claudio"},{"full_name":"Mangiarotti, Agustín","last_name":"Mangiarotti","first_name":"Agustín"},{"full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos","first_name":"Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714"},{"full_name":"Aylan, Beren","last_name":"Aylan","first_name":"Beren"},{"last_name":"Pellegrino","first_name":"Enrica","full_name":"Pellegrino, Enrica"},{"full_name":"Athanasiadi, Natalia","first_name":"Natalia","last_name":"Athanasiadi"},{"full_name":"Fearns, Antony","first_name":"Antony","last_name":"Fearns"},{"last_name":"Rodgers","first_name":"Angela","full_name":"Rodgers, Angela"},{"last_name":"Franzmann","first_name":"Titus M.","full_name":"Franzmann, Titus M."},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Dimova, Rumiana","last_name":"Dimova","first_name":"Rumiana"},{"full_name":"Gutierrez, Maximiliano G.","first_name":"Maximiliano G.","last_name":"Gutierrez"}],"related_material":{"record":[{"id":"14472","relation":"research_data","status":"public"}],"link":[{"url":"https://doi.org/10.1038/s41586-023-06882-z","relation":"erratum"}]},"date_updated":"2023-11-27T09:05:08Z","date_created":"2023-11-27T07:56:37Z","keyword":["Multidisciplinary"],"day":"15","article_processing_charge":"Yes (via OA deal)","publication":"Nature","citation":{"short":"C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino, N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G. Gutierrez, Nature (2023).","mla":"Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Nature, Springer Nature, 2023, doi:10.1038/s41586-023-06726-w.","chicago":"Bussi, Claudio, Agustín Mangiarotti, Christian Eduardo Vanhille-Campos, Beren Aylan, Enrica Pellegrino, Natalia Athanasiadi, Antony Fearns, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06726-w.","ama":"Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and stabilize damaged endolysosomal membranes. Nature. 2023. doi:10.1038/s41586-023-06726-w","ieee":"C. Bussi et al., “Stress granules plug and stabilize damaged endolysosomal membranes,” Nature. Springer Nature, 2023.","apa":"Bussi, C., Mangiarotti, A., Vanhille-Campos, C. E., Aylan, B., Pellegrino, E., Athanasiadi, N., … Gutierrez, M. G. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06726-w","ista":"Bussi C, Mangiarotti A, Vanhille-Campos CE, Aylan B, Pellegrino E, Athanasiadi N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. 2023. Stress granules plug and stabilize damaged endolysosomal membranes. Nature."},"article_type":"original","date_published":"2023-11-15T00:00:00Z","type":"journal_article","abstract":[{"text":"AbstractEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells1,2. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis3–7. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for Mycobacterium tuberculosis, a human pathogen that exploits endomembrane damage to survive within the host.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14610","status":"public","title":"Stress granules plug and stabilize damaged endolysosomal membranes","oa_version":"Published Version"},{"type":"research_data","file_date_updated":"2023-10-31T08:57:50Z","abstract":[{"text":"Data related to the following paper:\r\n\"Stress granules plug and stabilize damaged endolysosomal membranes\" (https://doi.org/10.1038/s41586-023-06726-w)\r\n\r\nAbstract: \r\nEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. In this work we use a minimal coarse-grained molecular dynamics system to explore how lipid vesicles undergoing poration in a protein-rich medium can be plugged and stabilised by condensate formation. The solution of proteins in and out of the vesicle is described by beads dispersed in implicit solvent. The membrane is described as a one-bead-thick fluid elastic layer of mechanical properties that mimic biological membranes. We tune the interactions between solution beads in the different compartments to capture the differences between the cytoplasmic and endosomal protein solutions and explore how the system responds to different degrees of membrane poration. We find that, in the right interaction regime, condensates form rapidly at the damage site upon solution mixing and act as a plug that prevents futher mixing and destabilisation of the vesicle. Further, when the condensate can interact with the membrane (wetting interactions) we find that it mediates pore sealing and membrane repair. This research is part of the work published in \"Stress granules plug and stabilize damaged endolysosomal membranes\", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14472","year":"2023","ddc":["570"],"status":"public","title":"Stress granules plug and stabilize damaged endolysosomal membranes","department":[{"_id":"AnSa"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"3adeca52-9313-11ed-b1ac-c170b2505714","first_name":"Christian Eduardo","last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian Eduardo"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14610"}]},"date_updated":"2023-11-27T09:05:07Z","date_created":"2023-10-30T16:38:32Z","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14473","date_created":"2023-10-30T16:31:08Z","date_updated":"2023-10-30T16:31:08Z","checksum":"a18706e952e8660c51ede52a167270b7","success":1,"file_name":"SGporecondensation-main.zip","access_level":"open_access","file_size":62821432,"content_type":"application/zip","creator":"ipalaia"},{"creator":"dernst","content_type":"text/plain","file_size":1697,"access_level":"open_access","file_name":"README.txt","success":1,"checksum":"389eab31c6509dbc05795017fb618758","date_created":"2023-10-31T08:57:50Z","date_updated":"2023-10-31T08:57:50Z","file_id":"14474","relation":"main_file"}],"day":"31","month":"10","has_accepted_license":"1","article_processing_charge":"No","oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ama":"Vanhille-Campos CE, Šarić A. Stress granules plug and stabilize damaged endolysosomal membranes. 2023. doi:10.15479/AT:ISTA:14472","ista":"Vanhille-Campos CE, Šarić A. 2023. Stress granules plug and stabilize damaged endolysosomal membranes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14472.","ieee":"C. E. Vanhille-Campos and A. Šarić, “Stress granules plug and stabilize damaged endolysosomal membranes.” Institute of Science and Technology Austria, 2023.","apa":"Vanhille-Campos, C. E., & Šarić, A. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14472","mla":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14472.","short":"C.E. Vanhille-Campos, A. Šarić, (2023).","chicago":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14472."},"doi":"10.15479/AT:ISTA:14472","date_published":"2023-10-31T00:00:00Z"},{"oa":1,"external_id":{"isi":["000992064000002"],"pmid":["36941451"]},"main_file_link":[{"url":"https://doi.org/10.1101/2022.03.02.482658","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s42255-023-00766-2","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["2522-5812"]},"acknowledgement":"The authors thank the participants and their families for participating in the study. We thank all members of our laboratories for helpful discussions. We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T. Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A. Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg, Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson (University of Iowa, Carver College of Medicine) for advice on muscle tissue handling. We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, and the City of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z 271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program (F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US National Institutes of Health. C.K. is supported by a grant from the Agence Nationale de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative 2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y. acknowledge the support of the Spastic Paraplegia Foundation.","year":"2023","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"Bio"}],"author":[{"full_name":"Cikes, Domagoj","first_name":"Domagoj","last_name":"Cikes"},{"last_name":"Elsayad","first_name":"Kareem","full_name":"Elsayad, Kareem"},{"full_name":"Sezgin, Erdinc","first_name":"Erdinc","last_name":"Sezgin"},{"last_name":"Koitai","first_name":"Erika","full_name":"Koitai, Erika"},{"last_name":"Ferenc","first_name":"Torma","full_name":"Ferenc, Torma"},{"first_name":"Michael","last_name":"Orthofer","full_name":"Orthofer, Michael"},{"last_name":"Yarwood","first_name":"Rebecca","full_name":"Yarwood, Rebecca"},{"first_name":"Leonhard X.","last_name":"Heinz","full_name":"Heinz, Leonhard X."},{"last_name":"Sedlyarov","first_name":"Vitaly","full_name":"Sedlyarov, Vitaly"},{"orcid":"0000-0002-8821-8236","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","last_name":"Darwish-Miranda","first_name":"Nasser","full_name":"Darwish-Miranda, Nasser"},{"full_name":"Taylor, Adrian","last_name":"Taylor","first_name":"Adrian"},{"first_name":"Sophie","last_name":"Grapentine","full_name":"Grapentine, Sophie"},{"full_name":"al-Murshedi, Fathiya","last_name":"al-Murshedi","first_name":"Fathiya"},{"full_name":"Abot, Anne","first_name":"Anne","last_name":"Abot"},{"full_name":"Weidinger, Adelheid","first_name":"Adelheid","last_name":"Weidinger"},{"last_name":"Kutchukian","first_name":"Candice","full_name":"Kutchukian, Candice"},{"first_name":"Colline","last_name":"Sanchez","full_name":"Sanchez, Colline"},{"last_name":"Cronin","first_name":"Shane J. F.","full_name":"Cronin, Shane J. F."},{"full_name":"Novatchkova, Maria","last_name":"Novatchkova","first_name":"Maria"},{"full_name":"Kavirayani, Anoop","last_name":"Kavirayani","first_name":"Anoop"},{"first_name":"Thomas","last_name":"Schuetz","full_name":"Schuetz, Thomas"},{"first_name":"Bernhard","last_name":"Haubner","full_name":"Haubner, Bernhard"},{"last_name":"Haas","first_name":"Lisa","full_name":"Haas, Lisa"},{"full_name":"Hagelkruys, Astrid","first_name":"Astrid","last_name":"Hagelkruys"},{"last_name":"Jackowski","first_name":"Suzanne","full_name":"Jackowski, Suzanne"},{"full_name":"Kozlov, Andrey","last_name":"Kozlov","first_name":"Andrey"},{"last_name":"Jacquemond","first_name":"Vincent","full_name":"Jacquemond, Vincent"},{"full_name":"Knauf, Claude","first_name":"Claude","last_name":"Knauf"},{"full_name":"Superti-Furga, Giulio","last_name":"Superti-Furga","first_name":"Giulio"},{"first_name":"Eric","last_name":"Rullman","full_name":"Rullman, Eric"},{"last_name":"Gustafsson","first_name":"Thomas","full_name":"Gustafsson, Thomas"},{"full_name":"McDermot, John","last_name":"McDermot","first_name":"John"},{"full_name":"Lowe, Martin","last_name":"Lowe","first_name":"Martin"},{"first_name":"Zsolt","last_name":"Radak","full_name":"Radak, Zsolt"},{"full_name":"Chamberlain, Jeffrey S.","first_name":"Jeffrey S.","last_name":"Chamberlain"},{"first_name":"Marica","last_name":"Bakovic","full_name":"Bakovic, Marica"},{"first_name":"Siddharth","last_name":"Banka","full_name":"Banka, Siddharth"},{"full_name":"Penninger, Josef M.","first_name":"Josef M.","last_name":"Penninger"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s42255-023-00791-1"}]},"date_created":"2023-03-23T12:58:43Z","date_updated":"2023-11-28T07:31:33Z","volume":5,"publication":"Nature Metabolism","citation":{"apa":"Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., … Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-023-00766-2","ieee":"D. Cikes et al., “PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing,” Nature Metabolism, vol. 5. Springer Nature, pp. 495–515, 2023.","ista":"Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.","ama":"Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 2023;5:495-515. doi:10.1038/s42255-023-00766-2","chicago":"Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc, Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” Nature Metabolism. Springer Nature, 2023. https://doi.org/10.1038/s42255-023-00766-2.","short":"D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood, L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi, A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova, A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A. Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson, J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger, Nature Metabolism 5 (2023) 495–515.","mla":"Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” Nature Metabolism, vol. 5, Springer Nature, 2023, pp. 495–515, doi:10.1038/s42255-023-00766-2."},"article_type":"original","page":"495-515","date_published":"2023-03-20T00:00:00Z","scopus_import":"1","keyword":["Cell Biology","Physiology (medical)","Endocrinology","Diabetes and Metabolism","Internal Medicine"],"day":"20","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12747","title":"PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing","status":"public","intvolume":" 5","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.","lang":"eng"}]}]