[{"day":"11","related_material":{"record":[{"status":"public","id":"14274","relation":"used_in_publication"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","month":"07","oa_version":"Published Version","date_updated":"2023-10-03T11:42:58Z","ddc":["570"],"oa":1,"has_accepted_license":"1","abstract":[{"lang":"eng","text":"The zip file includes source data used in the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript.\r\nA sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt."}],"date_published":"2023-07-11T00:00:00Z","author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C","first_name":"Mehmet C","last_name":"Ucar","orcid":"0000-0003-0506-4217"}],"license":"https://creativecommons.org/licenses/by/4.0/","_id":"14279","doi":"10.5281/ZENODO.8133960","date_created":"2023-09-06T08:39:25Z","department":[{"_id":"EdHa"}],"publisher":"Zenodo","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133960","open_access":"1"}],"citation":{"ista":"Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, 10.5281/ZENODO.8133960.","ieee":"M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023.","ama":"Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” 2023. doi:10.5281/ZENODO.8133960","short":"M.C. Ucar, (2023).","chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133960.","apa":"Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. https://doi.org/10.5281/ZENODO.8133960","mla":"Ucar, Mehmet C. Source Data for the Manuscript “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Zenodo, 2023, doi:10.5281/ZENODO.8133960."},"article_processing_charge":"No","status":"public","type":"research_data_reference","title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"file":[{"date_updated":"2023-10-04T10:28:35Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhD Thesis_Philipp Radler_20231004.docx","file_size":114932847,"access_level":"closed","file_id":"14390","date_created":"2023-10-04T10:11:53Z","creator":"pradler","checksum":"87eef11fbc5c7df0826f12a3a629b444","relation":"source_file"},{"date_created":"2023-10-04T10:11:21Z","creator":"pradler","checksum":"3253e099b7126469d941fd9419d68b4f","relation":"main_file","file_id":"14391","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","access_level":"closed","file_size":37838778,"date_updated":"2023-10-04T10:28:35Z","content_type":"application/pdf","embargo_to":"open_access","embargo":"2024-10-04"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin"}],"project":[{"grant_number":"679239","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"name":"Understanding bacterial cell division by in vitro\r\nreconstitution","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"},{"grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"_id":"259B655A-B435-11E9-9278-68D0E5697425","name":"Reconstitution of bacterial cell wall sythesis","grant_number":"LT000824/2016"}],"date_created":"2023-09-06T10:58:25Z","file_date_updated":"2023-10-04T10:28:35Z","abstract":[{"lang":"eng","text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation."}],"date_published":"2023-09-25T00:00:00Z","author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","last_name":"Radler","first_name":"Philipp"}],"day":"25","year":"2023","language":[{"iso":"eng"}],"keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_processing_charge":"No","citation":{"ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","apa":"Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280","mla":"Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280.","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:10.15479/at:ista:14280"},"type":"dissertation","status":"public","title":"Spatiotemporal signaling during assembly of the bacterial divisome","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"_id":"14280","page":"156","doi":"10.15479/at:ista:14280","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"relation":"part_of_dissertation","id":"11373","status":"public"},{"id":"7387","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"10934","relation":"research_data"}]},"month":"09","oa_version":"Published Version","date_updated":"2024-02-21T12:35:18Z","ddc":["572"],"publication_identifier":{"isbn":["978-3-99078-033-6"],"issn":["2663-337X"]},"publication_status":"published"},{"publisher":"Oxford Academic","main_file_link":[{"url":"https://arxiv.org/abs/1901.08503","open_access":"1"}],"article_type":"original","date_created":"2021-01-22T09:31:09Z","author":[{"id":"560601DA-8D36-11E9-A136-7AC1E5697425","full_name":"Wilsch, Florian Alexander","last_name":"Wilsch","first_name":"Florian Alexander","orcid":"0000-0001-7302-8256"}],"volume":2023,"abstract":[{"text":"We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors.","lang":"eng"}],"date_published":"2023-04-01T00:00:00Z","issue":"8","publication":"International Mathematics Research Notices","day":"01","year":"2023","language":[{"iso":"eng"}],"title":"Integral points of bounded height on a log Fano threefold","status":"public","type":"journal_article","citation":{"chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices. Oxford Academic, 2023. https://doi.org/10.1093/imrn/rnac048.","short":"F.A. Wilsch, International Mathematics Research Notices 2023 (2023) 6780–6808.","ama":"Wilsch FA. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023;2023(8):6780-6808. doi:10.1093/imrn/rnac048","mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices, vol. 2023, no. 8, Oxford Academic, 2023, pp. 6780–808, doi:10.1093/imrn/rnac048.","apa":"Wilsch, F. A. (2023). Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. Oxford Academic. https://doi.org/10.1093/imrn/rnac048","ieee":"F. A. Wilsch, “Integral points of bounded height on a log Fano threefold,” International Mathematics Research Notices, vol. 2023, no. 8. Oxford Academic, pp. 6780–6808, 2023.","ista":"Wilsch FA. 2023. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023(8), 6780–6808."},"article_processing_charge":"No","isi":1,"acknowledgement":"This work was supported by the German Academic Exchange Service. Parts of this article were prepared at the Institut de Mathémathiques de Jussieu—Paris Rive Gauche. I wish to thank Antoine Chambert-Loir for his remarks and the institute for its hospitality, as well as the anonymous referee for several useful remarks and suggestions for improvements.","quality_controlled":"1","department":[{"_id":"TiBr"}],"doi":"10.1093/imrn/rnac048","external_id":{"isi":["000773116000001"],"arxiv":["1901.08503"]},"page":"6780-6808","_id":"9034","intvolume":" 2023","arxiv":1,"oa":1,"publication_status":"published","date_updated":"2023-08-01T12:23:55Z","publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"month":"04","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"quality_controlled":"1","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was started while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35. It was continued when the first named author was employed at University of Leipzig and the second named author was employed at Institute of Science and Technology of Austria, where he was supported by an IST Fellowship.","department":[{"_id":"UlWa"}],"external_id":{"isi":["001105681500001"],"arxiv":["2102.13046"]},"doi":"10.1007/s10711-023-00862-3","_id":"9651","title":"Divergence of separated nets with respect to displacement equivalence","status":"public","type":"journal_article","citation":{"ista":"Dymond M, Kaluza V. 2023. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata., 15.","ieee":"M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement equivalence,” Geometriae Dedicata. Springer Nature, 2023.","mla":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata, 15, Springer Nature, 2023, doi:10.1007/s10711-023-00862-3.","apa":"Dymond, M., & Kaluza, V. (2023). Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. Springer Nature. https://doi.org/10.1007/s10711-023-00862-3","chicago":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata. Springer Nature, 2023. https://doi.org/10.1007/s10711-023-00862-3.","short":"M. Dymond, V. Kaluza, Geometriae Dedicata (2023).","ama":"Dymond M, Kaluza V. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 2023. doi:10.1007/s10711-023-00862-3"},"article_processing_charge":"Yes (via OA deal)","isi":1,"publication_status":"epub_ahead","oa":1,"publication_identifier":{"issn":["0046-5755"],"eissn":["1572-9168"]},"date_updated":"2024-01-11T13:06:32Z","oa_version":"Published Version","month":"11","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"15","arxiv":1,"article_type":"original","date_created":"2021-07-14T07:01:27Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s10711-023-00862-3"}],"publisher":"Springer Nature","publication":"Geometriae Dedicata","year":"2023","language":[{"iso":"eng"}],"day":"17","author":[{"full_name":"Dymond, Michael","first_name":"Michael","last_name":"Dymond"},{"last_name":"Kaluza","first_name":"Vojtech","orcid":"0000-0002-2512-8698","full_name":"Kaluza, Vojtech","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E"}],"date_published":"2023-11-17T00:00:00Z","abstract":[{"text":"We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence.","lang":"eng"}]},{"file":[{"content_type":"application/pdf","date_updated":"2021-07-14T07:41:50Z","file_size":900422,"access_level":"open_access","file_name":"separated_nets.pdf","file_id":"9653","relation":"main_file","checksum":"6fa0a3207dd1d6467c309fd1bcc867d1","creator":"vkaluza","date_created":"2021-07-14T07:41:50Z"}],"publisher":"Springer Nature","scopus_import":"1","date_created":"2021-07-14T07:01:28Z","article_type":"original","file_date_updated":"2021-07-14T07:41:50Z","date_published":"2023-03-01T00:00:00Z","abstract":[{"lang":"eng","text":"In 1998 Burago and Kleiner and (independently) McMullen gave examples of separated nets in Euclidean space which are non-bilipschitz equivalent to the integer lattice. We study weaker notions of equivalence of separated nets and demonstrate that such notions also give rise to distinct equivalence classes. Put differently, we find occurrences of particularly strong divergence of separated nets from the integer lattice. Our approach generalises that of Burago and Kleiner and McMullen which takes place largely in a continuous setting. Existence of irregular separated nets is verified via the existence of non-realisable density functions ρ:[0,1]d→(0,∞). In the present work we obtain stronger types of non-realisable densities."}],"volume":253,"author":[{"full_name":"Dymond, Michael","first_name":"Michael","last_name":"Dymond"},{"full_name":"Kaluza, Vojtech","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","orcid":"0000-0002-2512-8698","first_name":"Vojtech","last_name":"Kaluza"}],"language":[{"iso":"eng"}],"year":"2023","day":"01","publication":"Israel Journal of Mathematics","keyword":["Lipschitz","bilipschitz","bounded displacement","modulus of continuity","separated net","non-realisable density","Burago--Kleiner construction"],"isi":1,"citation":{"short":"M. Dymond, V. Kaluza, Israel Journal of Mathematics 253 (2023) 501–554.","ama":"Dymond M, Kaluza V. Highly irregular separated nets. Israel Journal of Mathematics. 2023;253:501-554. doi:10.1007/s11856-022-2448-6","chicago":"Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-022-2448-6.","mla":"Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel Journal of Mathematics, vol. 253, Springer Nature, 2023, pp. 501–54, doi:10.1007/s11856-022-2448-6.","apa":"Dymond, M., & Kaluza, V. (2023). Highly irregular separated nets. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-022-2448-6","ieee":"M. Dymond and V. Kaluza, “Highly irregular separated nets,” Israel Journal of Mathematics, vol. 253. Springer Nature, pp. 501–554, 2023.","ista":"Dymond M, Kaluza V. 2023. Highly irregular separated nets. Israel Journal of Mathematics. 253, 501–554."},"article_processing_charge":"No","type":"journal_article","status":"public","title":"Highly irregular separated nets","intvolume":" 253","_id":"9652","page":"501-554","external_id":{"isi":["000904950300003"],"arxiv":["1903.05923"]},"doi":"10.1007/s11856-022-2448-6","department":[{"_id":"UlWa"}],"quality_controlled":"1","acknowledgement":"This work was done while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35.","arxiv":1,"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","month":"03","publication_identifier":{"eissn":["1565-8511"]},"ddc":["515","516"],"date_updated":"2023-08-14T11:26:34Z","oa":1,"publication_status":"published"},{"arxiv":1,"has_accepted_license":"1","date_updated":"2023-10-04T09:19:12Z","ddc":["510"],"publication_identifier":{"eissn":["1572-929X"],"issn":["0926-2601"]},"oa":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"03","status":"public","type":"journal_article","title":"Ergodic decomposition of Dirichlet forms via direct integrals and applications","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"article_processing_charge":"Yes (via OA deal)","citation":{"mla":"Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct Integrals and Applications.” Potential Analysis, vol. 58, Springer Nature, 2023, pp. 573–615, doi:10.1007/s11118-021-09951-y.","apa":"Dello Schiavo, L. (2023). Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. Springer Nature. https://doi.org/10.1007/s11118-021-09951-y","chicago":"Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct Integrals and Applications.” Potential Analysis. Springer Nature, 2023. https://doi.org/10.1007/s11118-021-09951-y.","ama":"Dello Schiavo L. Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. 2023;58:573-615. doi:10.1007/s11118-021-09951-y","short":"L. Dello Schiavo, Potential Analysis 58 (2023) 573–615.","ieee":"L. Dello Schiavo, “Ergodic decomposition of Dirichlet forms via direct integrals and applications,” Potential Analysis, vol. 58. Springer Nature, pp. 573–615, 2023.","ista":"Dello Schiavo L. 2023. Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. 58, 573–615."},"department":[{"_id":"JaMa"}],"acknowledgement":"The author is grateful to Professors Sergio Albeverio and Andreas Eberle, and to Dr. Kohei Suzuki, for fruitful conversations on the subject of the present work, and for respectively pointing out the references [1, 13], and [3, 20]. Finally, he is especially grateful to an anonymous Reviewer for their very careful reading and their suggestions which improved the readability of the paper.","quality_controlled":"1","_id":"10145","page":"573-615","intvolume":" 58","doi":"10.1007/s11118-021-09951-y","external_id":{"isi":["000704213400001"],"arxiv":["2003.01366"]},"abstract":[{"text":"We study direct integrals of quadratic and Dirichlet forms. We show that each quasi-regular Dirichlet space over a probability space admits a unique representation as a direct integral of irreducible Dirichlet spaces, quasi-regular for the same underlying topology. The same holds for each quasi-regular strongly local Dirichlet space over a metrizable Luzin σ-finite Radon measure space, and admitting carré du champ operator. In this case, the representation is only projectively unique.","lang":"eng"}],"volume":58,"date_published":"2023-03-01T00:00:00Z","author":[{"id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","full_name":"Dello Schiavo, Lorenzo","orcid":"0000-0002-9881-6870","last_name":"Dello Schiavo","first_name":"Lorenzo"}],"file_date_updated":"2023-10-04T09:18:59Z","ec_funded":1,"day":"01","year":"2023","language":[{"iso":"eng"}],"publication":"Potential Analysis","scopus_import":"1","file":[{"success":1,"date_created":"2023-10-04T09:18:59Z","creator":"dernst","checksum":"625526482be300ca7281c91c30d41725","relation":"main_file","file_id":"14387","file_name":"2023_PotentialAnalysis_DelloSchiavo.pdf","file_size":806391,"access_level":"open_access","date_updated":"2023-10-04T09:18:59Z","content_type":"application/pdf"}],"publisher":"Springer Nature","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","call_identifier":"H2020"}],"article_type":"original","date_created":"2021-10-17T22:01:17Z"},{"date_created":"2021-10-23T10:50:22Z","article_type":"original","scopus_import":"1","file":[{"success":1,"file_name":"2023_StochPartialDiffEquations_Clozeau.pdf","file_size":1635193,"access_level":"open_access","date_updated":"2023-08-14T11:51:04Z","content_type":"application/pdf","date_created":"2023-08-14T11:51:04Z","creator":"dernst","checksum":"f83dcaecdbd3ace862c4ed97a20e8501","relation":"main_file","file_id":"14052"}],"publisher":"Springer Nature","publication":"Stochastics and Partial Differential Equations: Analysis and Computations","year":"2023","language":[{"iso":"eng"}],"day":"01","author":[{"id":"fea1b376-906f-11eb-847d-b2c0cf46455b","full_name":"Clozeau, Nicolas","first_name":"Nicolas","last_name":"Clozeau"}],"date_published":"2023-09-01T00:00:00Z","volume":11,"abstract":[{"text":"We study the large scale behavior of elliptic systems with stationary random coefficient that have only slowly decaying correlations. To this aim we analyze the so-called corrector equation, a degenerate elliptic equation posed in the probability space. In this contribution, we use a parabolic approach and optimally quantify the time decay of the semigroup. For the theoretical point of view, we prove an optimal decay estimate of the gradient and flux of the corrector when spatially averaged over a scale R larger than 1. For the numerical point of view, our results provide convenient tools for the analysis of various numerical methods.","lang":"eng"}],"file_date_updated":"2023-08-14T11:51:04Z","quality_controlled":"1","acknowledgement":"I would like to thank my advisor Antoine Gloria for suggesting this problem to me, as well for many interesting discussions and suggestions.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","department":[{"_id":"JuFi"}],"external_id":{"isi":["000799715600001"],"arxiv":["2102.07452"]},"doi":"10.1007/s40072-022-00254-w","intvolume":" 11","_id":"10173","page":"1254–1378","title":"Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","type":"journal_article","citation":{"ieee":"N. Clozeau, “Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields,” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 11. Springer Nature, pp. 1254–1378, 2023.","ista":"Clozeau N. 2023. Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. 11, 1254–1378.","mla":"Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization for Correlated Coefficient Fields.” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 11, Springer Nature, 2023, pp. 1254–1378, doi:10.1007/s40072-022-00254-w.","apa":"Clozeau, N. (2023). Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-022-00254-w","chicago":"Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization for Correlated Coefficient Fields.” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2023. https://doi.org/10.1007/s40072-022-00254-w.","short":"N. Clozeau, Stochastics and Partial Differential Equations: Analysis and Computations 11 (2023) 1254–1378.","ama":"Clozeau N. Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. 2023;11:1254–1378. doi:10.1007/s40072-022-00254-w"},"article_processing_charge":"Yes (via OA deal)","isi":1,"oa":1,"publication_status":"published","publication_identifier":{"issn":["2194-0401"]},"date_updated":"2023-08-14T11:51:47Z","ddc":["510"],"month":"09","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","arxiv":1},{"ddc":["510"],"date_updated":"2023-10-04T09:22:55Z","publication_identifier":{"eissn":["1097-0312"],"issn":["0010-3640"]},"oa":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","oa_version":"Published Version","arxiv":1,"has_accepted_license":"1","department":[{"_id":"LaEr"}],"acknowledgement":"L.E. would like to thank Nathanaël Berestycki and D.S.would like to thank Nina Holden for valuable discussions on the Gaussian freefield.G.C. and L.E. are partially supported by ERC Advanced Grant No. 338804.G.C. received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Skłodowska-Curie Grant Agreement No.665385. D.S. is supported by Dr. Max Rössler, the Walter Haefner Foundation, and the ETH Zürich Foundation.","quality_controlled":"1","_id":"10405","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","page":"946-1034","intvolume":" 76","doi":"10.1002/cpa.22028","external_id":{"arxiv":["1912.04100"],"isi":["000724652500001"]},"type":"journal_article","status":"public","title":"Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"isi":1,"citation":{"apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.22028","mla":"Cipolloni, Giorgio, et al. “Central Limit Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” Communications on Pure and Applied Mathematics, vol. 76, no. 5, Wiley, 2023, pp. 946–1034, doi:10.1002/cpa.22028.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Central Limit Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” Communications on Pure and Applied Mathematics. Wiley, 2023. https://doi.org/10.1002/cpa.22028.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications on Pure and Applied Mathematics 76 (2023) 946–1034.","ama":"Cipolloni G, Erdös L, Schröder DJ. Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. 2023;76(5):946-1034. doi:10.1002/cpa.22028","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices,” Communications on Pure and Applied Mathematics, vol. 76, no. 5. Wiley, pp. 946–1034, 2023.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. 76(5), 946–1034."},"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"day":"01","year":"2023","language":[{"iso":"eng"}],"publication":"Communications on Pure and Applied Mathematics","volume":76,"abstract":[{"text":"We consider large non-Hermitian random matrices X with complex, independent, identically distributed centred entries and show that the linear statistics of their eigenvalues are asymptotically Gaussian for test functions having 2+ϵ derivatives. Previously this result was known only for a few special cases; either the test functions were required to be analytic [72], or the distribution of the matrix elements needed to be Gaussian [73], or at least match the Gaussian up to the first four moments [82, 56]. We find the exact dependence of the limiting variance on the fourth cumulant that was not known before. The proof relies on two novel ingredients: (i) a local law for a product of two resolvents of the Hermitisation of X with different spectral parameters and (ii) a coupling of several weakly dependent Dyson Brownian motions. These methods are also the key inputs for our analogous results on the linear eigenvalue statistics of real matrices X that are presented in the companion paper [32]. ","lang":"eng"}],"date_published":"2023-05-01T00:00:00Z","author":[{"full_name":"Cipolloni, Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","last_name":"Cipolloni","first_name":"Giorgio"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0002-2904-1856","first_name":"Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J"}],"issue":"5","file_date_updated":"2023-10-04T09:21:48Z","date_created":"2021-12-05T23:01:41Z","article_type":"original","project":[{"call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"scopus_import":"1","publisher":"Wiley","file":[{"success":1,"file_id":"14388","creator":"dernst","date_created":"2023-10-04T09:21:48Z","relation":"main_file","checksum":"8346bc2642afb4ccb7f38979f41df5d9","date_updated":"2023-10-04T09:21:48Z","content_type":"application/pdf","file_name":"2023_CommPureMathematics_Cipolloni.pdf","access_level":"open_access","file_size":803440}]},{"scopus_import":"1","file":[{"date_updated":"2023-06-19T07:33:53Z","content_type":"application/pdf","file_name":"2023_JourNonlinearScience_Fellner.pdf","access_level":"open_access","file_size":742315,"file_id":"13149","date_created":"2023-06-19T07:33:53Z","creator":"dernst","relation":"main_file","checksum":"f3f0f0886098e31c81116cff8183750b","success":1}],"publisher":"Springer Nature","date_created":"2021-12-16T12:15:35Z","article_type":"original","author":[{"first_name":"Klemens","last_name":"Fellner","full_name":"Fellner, Klemens"},{"orcid":"0000-0002-0479-558X","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L"},{"full_name":"Kniely, Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Kniely","orcid":"0000-0001-5645-4333"},{"first_name":"Bao Quoc","last_name":"Tang","full_name":"Tang, Bao Quoc"}],"volume":33,"abstract":[{"lang":"eng","text":"The global existence of renormalised solutions and convergence to equilibrium for reaction-diffusion systems with non-linear diffusion are investigated. The system is assumed to have quasi-positive non-linearities and to satisfy an entropy inequality. The difficulties in establishing global renormalised solutions caused by possibly degenerate diffusion are overcome by introducing a new class of weighted truncation functions. By means of the obtained global renormalised solutions, we study the large-time behaviour of complex balanced systems arising from chemical reaction network theory with non-linear diffusion. When the reaction network does not admit boundary equilibria, the complex balanced equilibrium is shown, by using the entropy method, to exponentially attract all renormalised solutions in the same compatibility class. This convergence extends even to a range of non-linear diffusion, where global existence is an open problem, yet we are able to show that solutions to approximate systems converge exponentially to equilibrium uniformly in the regularisation parameter."}],"date_published":"2023-06-07T00:00:00Z","file_date_updated":"2023-06-19T07:33:53Z","publication":"Journal of Nonlinear Science","day":"07","year":"2023","language":[{"iso":"eng"}],"title":"Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","type":"journal_article","citation":{"ama":"Fellner K, Fischer JL, Kniely M, Tang BQ. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 2023;33. doi:10.1007/s00332-023-09926-w","short":"K. Fellner, J.L. Fischer, M. Kniely, B.Q. Tang, Journal of Nonlinear Science 33 (2023).","chicago":"Fellner, Klemens, Julian L Fischer, Michael Kniely, and Bao Quoc Tang. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear Science. Springer Nature, 2023. https://doi.org/10.1007/s00332-023-09926-w.","apa":"Fellner, K., Fischer, J. L., Kniely, M., & Tang, B. Q. (2023). Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. Springer Nature. https://doi.org/10.1007/s00332-023-09926-w","mla":"Fellner, Klemens, et al. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear Science, vol. 33, 66, Springer Nature, 2023, doi:10.1007/s00332-023-09926-w.","ieee":"K. Fellner, J. L. Fischer, M. Kniely, and B. Q. Tang, “Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion,” Journal of Nonlinear Science, vol. 33. Springer Nature, 2023.","ista":"Fellner K, Fischer JL, Kniely M, Tang BQ. 2023. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 33, 66."},"article_processing_charge":"No","isi":1,"acknowledgement":"We thank the referees for their valuable comments and suggestions. A major part of this work was carried out when B. Q. Tang visited the Institute of Science and Technology Austria (ISTA). The hospitality of ISTA is greatly acknowledged. This work was partially supported by NAWI Graz.\r\nOpen access funding provided by University of Graz.","quality_controlled":"1","department":[{"_id":"JuFi"}],"doi":"10.1007/s00332-023-09926-w","external_id":{"arxiv":["2109.12019"],"isi":["001002343400002"]},"_id":"10550","intvolume":" 33","article_number":"66","has_accepted_license":"1","arxiv":1,"publication_status":"published","oa":1,"date_updated":"2023-08-01T14:40:33Z","ddc":["510"],"publication_identifier":{"issn":["0938-8974"],"eissn":["1432-1467"]},"month":"06","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"acknowledgement":"We thank the anonymous referee for his/her careful reading of the manuscript and valuable 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 Skłodowska-Curie Grant Agreement No. 754411.\r\nOpen access funding provided by Austrian Science Fund (FWF).","quality_controlled":"1","department":[{"_id":"JuFi"}],"doi":"10.1007/s00205-023-01903-7","external_id":{"arxiv":["2109.06500"],"isi":["001043086800001"]},"_id":"10551","intvolume":" 247","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles","status":"public","type":"journal_article","citation":{"apa":"Cornalba, F., & Fischer, J. L. (2023). The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-023-01903-7","mla":"Cornalba, Federico, and Julian L. Fischer. “The Dean-Kawasaki Equation and the Structure of Density Fluctuations in Systems of Diffusing Particles.” Archive for Rational Mechanics and Analysis, vol. 247, no. 5, 76, Springer Nature, 2023, doi:10.1007/s00205-023-01903-7.","short":"F. Cornalba, J.L. Fischer, Archive for Rational Mechanics and Analysis 247 (2023).","chicago":"Cornalba, Federico, and Julian L Fischer. “The Dean-Kawasaki Equation and the Structure of Density Fluctuations in Systems of Diffusing Particles.” Archive for Rational Mechanics and Analysis. Springer Nature, 2023. https://doi.org/10.1007/s00205-023-01903-7.","ama":"Cornalba F, Fischer JL. The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. Archive for Rational Mechanics and Analysis. 2023;247(5). doi:10.1007/s00205-023-01903-7","ieee":"F. Cornalba and J. L. Fischer, “The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles,” Archive for Rational Mechanics and Analysis, vol. 247, no. 5. Springer Nature, 2023.","ista":"Cornalba F, Fischer JL. 2023. The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. Archive for Rational Mechanics and Analysis. 247(5), 76."},"article_processing_charge":"Yes (via OA deal)","isi":1,"oa":1,"publication_status":"published","ddc":["510"],"date_updated":"2024-01-30T12:10:10Z","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"oa_version":"Published Version","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"76","has_accepted_license":"1","arxiv":1,"date_created":"2021-12-16T12:16:03Z","article_type":"original","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"scopus_import":"1","file":[{"file_id":"14904","creator":"dernst","date_created":"2024-01-30T12:09:34Z","relation":"main_file","checksum":"4529eeff170b6745a461d397ee611b5a","date_updated":"2024-01-30T12:09:34Z","content_type":"application/pdf","file_name":"2023_ArchiveRationalMech_Cornalba.pdf","file_size":1851185,"access_level":"open_access","success":1}],"publisher":"Springer Nature","ec_funded":1,"publication":"Archive for Rational Mechanics and Analysis","day":"04","language":[{"iso":"eng"}],"year":"2023","author":[{"full_name":"Cornalba, Federico","id":"2CEB641C-A400-11E9-A717-D712E6697425","first_name":"Federico","last_name":"Cornalba","orcid":"0000-0002-6269-5149"},{"orcid":"0000-0002-0479-558X","last_name":"Fischer","first_name":"Julian L","full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"The Dean–Kawasaki equation—a strongly singular SPDE—is a basic equation of fluctuating hydrodynamics; it has been proposed in the physics literature to describe the fluctuations of the density of N independent diffusing particles in the regime of large particle numbers N≫1. The singular nature of the Dean–Kawasaki equation presents a substantial challenge for both its analysis and its rigorous mathematical justification. Besides being non-renormalisable by the theory of regularity structures by Hairer et al., it has recently been shown to not even admit nontrivial martingale solutions. In the present work, we give a rigorous and fully quantitative justification of the Dean–Kawasaki equation by considering the natural regularisation provided by standard numerical discretisations: We show that structure-preserving discretisations of the Dean–Kawasaki equation may approximate the density fluctuations of N non-interacting diffusing particles to arbitrary order in N−1 (in suitable weak metrics). In other words, the Dean–Kawasaki equation may be interpreted as a “recipe” for accurate and efficient numerical simulations of the density fluctuations of independent diffusing particles.","lang":"eng"}],"volume":247,"date_published":"2023-08-04T00:00:00Z","file_date_updated":"2024-01-30T12:09:34Z","issue":"5"},{"ec_funded":1,"publication":"Discrete and Computational Geometry","day":"01","year":"2023","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0003-2401-8670","last_name":"Arroyo Guevara","first_name":"Alan M","full_name":"Arroyo Guevara, Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Klute","first_name":"Fabian","full_name":"Klute, Fabian"},{"last_name":"Parada","first_name":"Irene","full_name":"Parada, Irene"},{"last_name":"Vogtenhuber","first_name":"Birgit","full_name":"Vogtenhuber, Birgit"},{"full_name":"Seidel, Raimund","first_name":"Raimund","last_name":"Seidel"},{"first_name":"Tilo","last_name":"Wiedera","full_name":"Wiedera, Tilo"}],"volume":69,"abstract":[{"lang":"eng","text":"A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP-complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ, it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles."}],"date_published":"2023-04-01T00:00:00Z","file_date_updated":"2022-08-29T11:23:15Z","article_type":"original","date_created":"2022-08-28T22:02:01Z","project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"scopus_import":"1","file":[{"success":1,"file_size":1002218,"access_level":"open_access","file_name":"2022_DiscreteandComputionalGeometry_Arroyo.pdf","content_type":"application/pdf","date_updated":"2022-08-29T11:23:15Z","relation":"main_file","checksum":"def7ae3b28d9fd6aec16450e40090302","date_created":"2022-08-29T11:23:15Z","creator":"alisjak","file_id":"12006"}],"publisher":"Springer Nature","publication_status":"published","oa":1,"ddc":["510"],"date_updated":"2023-08-14T12:51:25Z","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"month":"04","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","arxiv":1,"acknowledgement":"This work was started during the 6th Austrian–Japanese–Mexican–Spanish Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants for the good atmosphere as well as discussions on the topic. Also, we thank Jan Kynčl for sending us remarks on a preliminary version of this work and an anonymous referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie grant agreement No 754411. Fabian Klute was partially supported by the Netherlands Organisation for Scientific Research (NWO) under project no. 612.001.651 and by the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was also partially supported by the Independent Research Fund Denmark grant 2020-2023 (9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded by the Ministry of Universities of Spain and the European Union (NextGenerationEU). Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.","quality_controlled":"1","department":[{"_id":"UlWa"}],"doi":"10.1007/s00454-022-00394-9","external_id":{"arxiv":["1909.07347"],"isi":["000840292800001"]},"_id":"11999","page":"745–770","intvolume":" 69","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Inserting one edge into a simple drawing is hard","status":"public","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","citation":{"ista":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. 2023. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 69, 745–770.","ieee":"A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” Discrete and Computational Geometry, vol. 69. Springer Nature, pp. 745–770, 2023.","apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R., & Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00394-9","mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry, vol. 69, Springer Nature, 2023, pp. 745–770, doi:10.1007/s00454-022-00394-9.","ama":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 2023;69:745–770. doi:10.1007/s00454-022-00394-9","chicago":"Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber, Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00394-9.","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770."},"isi":1},{"scopus_import":"1","file":[{"file_id":"12322","relation":"main_file","checksum":"71685ca5121f4c837f40c3f8eb50c915","creator":"dernst","date_created":"2023-01-20T10:02:48Z","content_type":"application/pdf","date_updated":"2023-01-20T10:02:48Z","access_level":"open_access","file_size":911017,"file_name":"2023_Algorithmica_Edelsbrunner.pdf","success":1}],"publisher":"Springer Nature","article_type":"original","project":[{"call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00342","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF"}],"date_created":"2022-09-11T22:01:57Z","author":[{"first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","first_name":"Georg F"}],"date_published":"2023-01-01T00:00:00Z","abstract":[{"text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets.","lang":"eng"}],"volume":85,"file_date_updated":"2023-01-20T10:02:48Z","ec_funded":1,"publication":"Algorithmica","year":"2023","language":[{"iso":"eng"}],"day":"01","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","type":"journal_article","status":"public","article_processing_charge":"Yes (via OA deal)","citation":{"short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.","ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 2023;85:277-295. doi:10.1007/s00453-022-01027-6","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica. Springer Nature, 2023. https://doi.org/10.1007/s00453-022-01027-6.","apa":"Edelsbrunner, H., & Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-022-01027-6","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica, vol. 85, Springer Nature, 2023, pp. 277–95, doi:10.1007/s00453-022-01027-6.","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” Algorithmica, vol. 85. Springer Nature, pp. 277–295, 2023.","ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295."},"isi":1,"quality_controlled":"1","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","department":[{"_id":"HeEd"}],"external_id":{"isi":["000846967100001"]},"doi":"10.1007/s00453-022-01027-6","intvolume":" 85","_id":"12086","page":"277-295","has_accepted_license":"1","publication_status":"published","oa":1,"publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"date_updated":"2023-06-27T12:53:43Z","ddc":["510"],"oa_version":"Published Version","month":"01","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"},{"has_accepted_license":"1","arxiv":1,"publication_status":"published","oa":1,"publication_identifier":{"issn":["1424-0637"]},"date_updated":"2023-08-14T11:39:28Z","ddc":["510"],"month":"03","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Curvature-dimension conditions for symmetric quantum Markov semigroups","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","type":"journal_article","citation":{"ista":"Wirth M, Zhang H. 2023. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 24, 717–750.","ieee":"M. Wirth and H. Zhang, “Curvature-dimension conditions for symmetric quantum Markov semigroups,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 717–750, 2023.","mla":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” Annales Henri Poincare, vol. 24, Springer Nature, 2023, pp. 717–50, doi:10.1007/s00023-022-01220-x.","apa":"Wirth, M., & Zhang, H. (2023). Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01220-x","ama":"Wirth M, Zhang H. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 2023;24:717-750. doi:10.1007/s00023-022-01220-x","short":"M. Wirth, H. Zhang, Annales Henri Poincare 24 (2023) 717–750.","chicago":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01220-x."},"article_processing_charge":"Yes (via OA deal)","isi":1,"quality_controlled":"1","acknowledgement":"H.Z. is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. M.W. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117) and from the Austrian Science Fund (FWF) through grant number F65. Both authors would like to thank Jan Maas for fruitful discussions and helpful comments. Open access funding provided by Austrian Science Fund (FWF).","department":[{"_id":"JaMa"}],"external_id":{"isi":["000837499800002"],"arxiv":["2105.08303"]},"doi":"10.1007/s00023-022-01220-x","intvolume":" 24","_id":"12087","page":"717-750","author":[{"orcid":"0000-0002-0519-4241","first_name":"Melchior","last_name":"Wirth","full_name":"Wirth, Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"},{"first_name":"Haonan","last_name":"Zhang","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","full_name":"Zhang, Haonan"}],"date_published":"2023-03-01T00:00:00Z","volume":24,"abstract":[{"lang":"eng","text":"Following up on the recent work on lower Ricci curvature bounds for quantum systems, we introduce two noncommutative versions of curvature-dimension bounds for symmetric quantum Markov semigroups over matrix algebras. Under suitable such curvature-dimension conditions, we prove a family of dimension-dependent functional inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power in the noncommutative setting. We also provide examples satisfying certain curvature-dimension conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers over group algebras and generalized depolarizing semigroups."}],"file_date_updated":"2023-08-14T11:38:28Z","ec_funded":1,"publication":"Annales Henri Poincare","year":"2023","language":[{"iso":"eng"}],"day":"01","scopus_import":"1","file":[{"success":1,"date_created":"2023-08-14T11:38:28Z","creator":"dernst","relation":"main_file","checksum":"8c7b185eba5ccd92ef55c120f654222c","file_id":"14051","file_name":"2023_AnnalesHenriPoincare_Wirth.pdf","file_size":554871,"access_level":"open_access","date_updated":"2023-08-14T11:38:28Z","content_type":"application/pdf"}],"publisher":"Springer Nature","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"grant_number":"M03337","name":"Curvature-dimension in noncommutative analysis","_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6"},{"call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"article_type":"original","date_created":"2022-09-11T22:01:57Z"},{"project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020"},{"_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","name":"Configuration Spaces over Non-Smooth Spaces","grant_number":"E208"},{"grant_number":"ESP156_N","name":"Gradient flow techniques for quantum Markov semigroups","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833"}],"article_type":"original","date_created":"2023-01-08T23:00:53Z","publisher":"Springer Nature","file":[{"success":1,"checksum":"1f34f3e2cb521033de6154f274ea3a4e","relation":"main_file","creator":"dernst","date_created":"2023-01-20T10:45:06Z","file_id":"12325","access_level":"open_access","file_size":422612,"file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf","content_type":"application/pdf","date_updated":"2023-01-20T10:45:06Z"}],"scopus_import":"1","language":[{"iso":"eng"}],"year":"2023","day":"01","publication":"Journal of Evolution Equations","ec_funded":1,"issue":"1","file_date_updated":"2023-01-20T10:45:06Z","date_published":"2023-01-01T00:00:00Z","abstract":[{"text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces.","lang":"eng"}],"volume":23,"author":[{"orcid":"0000-0002-9881-6870","last_name":"Dello Schiavo","first_name":"Lorenzo","full_name":"Dello Schiavo, Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E"},{"first_name":"Melchior","last_name":"Wirth","orcid":"0000-0002-0519-4241","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","full_name":"Wirth, Melchior"}],"intvolume":" 23","_id":"12104","external_id":{"isi":["000906214600004"]},"doi":"10.1007/s00028-022-00859-7","department":[{"_id":"JaMa"}],"quality_controlled":"1","acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","isi":1,"article_processing_charge":"Yes (via OA deal)","citation":{"ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” Journal of Evolution Equations, vol. 23, no. 1. Springer Nature, 2023.","ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).","chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations. Springer Nature, 2023. https://doi.org/10.1007/s00028-022-00859-7.","ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 2023;23(1). doi:10.1007/s00028-022-00859-7","mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations, vol. 23, no. 1, 9, Springer Nature, 2023, doi:10.1007/s00028-022-00859-7.","apa":"Dello Schiavo, L., & Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. Springer Nature. https://doi.org/10.1007/s00028-022-00859-7"},"type":"journal_article","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"01","publication_identifier":{"eissn":["1424-3202"],"issn":["1424-3199"]},"date_updated":"2023-06-28T11:54:35Z","ddc":["510"],"oa":1,"publication_status":"published","has_accepted_license":"1","article_number":"9"},{"year":"2023","language":[{"iso":"eng"}],"day":"10","publication":"Journal of Fluid Mechanics","file_date_updated":"2023-02-02T12:34:54Z","date_published":"2023-01-10T00:00:00Z","volume":954,"abstract":[{"lang":"eng","text":"Data-driven dimensionality reduction methods such as proper orthogonal decomposition and dynamic mode decomposition have proven to be useful for exploring complex phenomena within fluid dynamics and beyond. A well-known challenge for these techniques is posed by the continuous symmetries, e.g. translations and rotations, of the system under consideration, as drifts in the data dominate the modal expansions without providing an insight into the dynamics of the problem. In the present study, we address this issue for fluid flows in rectangular channels by formulating a continuous symmetry reduction method that eliminates the translations in the streamwise and spanwise directions simultaneously. We demonstrate our method by computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity of the invariant solutions with translation symmetries, i.e. travelling waves and relative periodic orbits, whereas in the latter, our calculations reveal episodes of turbulent time evolution that can be approximated by a low-dimensional linear expansion."}],"author":[{"first_name":"Elena","last_name":"Marensi","full_name":"Marensi, Elena","id":"0BE7553A-1004-11EA-B805-18983DDC885E"},{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","full_name":"Yalniz, Gökhan","first_name":"Gökhan","last_name":"Yalniz","orcid":"0000-0002-8490-9312"},{"orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010"}],"project":[{"grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"date_created":"2023-01-08T23:00:53Z","article_type":"original","file":[{"date_updated":"2023-02-02T12:34:54Z","content_type":"application/pdf","file_name":"2023_JourFluidMechanics_Marensi.pdf","file_size":1931647,"access_level":"open_access","file_id":"12489","date_created":"2023-02-02T12:34:54Z","creator":"dernst","checksum":"9224f987caefe5dd85a70814d3cce65c","relation":"main_file","success":1}],"publisher":"Cambridge University Press","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","month":"01","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"ddc":["530"],"date_updated":"2023-08-01T12:53:23Z","publication_status":"published","oa":1,"arxiv":1,"has_accepted_license":"1","article_number":"A10","intvolume":" 954","_id":"12105","external_id":{"isi":["000903336600001"],"arxiv":["2101.07516"]},"doi":"10.1017/jfm.2022.1001","department":[{"_id":"BjHo"}],"quality_controlled":"1","acknowledgement":"E.M. acknowledges funding from the ISTplus fellowship programme. G.Y. and B.H. acknowledge\r\na grant from the Simons Foundation (662960, BH).","isi":1,"article_processing_charge":"Yes (via OA deal)","citation":{"ieee":"E. Marensi, G. Yalniz, B. Hof, and N. B. Budanur, “Symmetry-reduced dynamic mode decomposition of near-wall turbulence,” Journal of Fluid Mechanics, vol. 954. Cambridge University Press, 2023.","ista":"Marensi E, Yalniz G, Hof B, Budanur NB. 2023. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 954, A10.","ama":"Marensi E, Yalniz G, Hof B, Budanur NB. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 2023;954. doi:10.1017/jfm.2022.1001","short":"E. Marensi, G. Yalniz, B. Hof, N.B. Budanur, Journal of Fluid Mechanics 954 (2023).","chicago":"Marensi, Elena, Gökhan Yalniz, Björn Hof, and Nazmi B Budanur. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics. Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2022.1001.","apa":"Marensi, E., Yalniz, G., Hof, B., & Budanur, N. B. (2023). Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2022.1001","mla":"Marensi, Elena, et al. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics, vol. 954, A10, Cambridge University Press, 2023, doi:10.1017/jfm.2022.1001."},"status":"public","type":"journal_article","title":"Symmetry-reduced dynamic mode decomposition of near-wall turbulence","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"has_accepted_license":"1","oa_version":"Published Version","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publication_status":"published","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"date_updated":"2023-08-16T11:32:33Z","ddc":["570"],"citation":{"ista":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. 2023. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 41, 813–823.","ieee":"J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823, 2023.","apa":"Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., & Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-022-01560-3","mla":"Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology, vol. 41, Springer Nature, 2023, pp. 813–823, doi:10.1038/s41587-022-01560-3.","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.","chicago":"Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology. Springer Nature, 2023. https://doi.org/10.1038/s41587-022-01560-3.","ama":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 2023;41:813–823. doi:10.1038/s41587-022-01560-3"},"article_processing_charge":"No","isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","type":"journal_article","status":"public","external_id":{"isi":["000909067600003"]},"doi":"10.1038/s41587-022-01560-3","intvolume":" 41","_id":"12106","page":"813–823","quality_controlled":"1","acknowledgement":"We thank M. van Loenhout for experimental advice on purifying cell types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat and O. Stegle for discussions on multinomial distributions. This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001) and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is part of the Oncode Institute which is financed partly by the Dutch Cancer Society.","department":[{"_id":"ScienComp"}],"file_date_updated":"2023-08-16T11:30:45Z","author":[{"id":"123012b2-db30-11eb-b4d8-a35840c0551b","full_name":"Yeung, Jake","first_name":"Jake","last_name":"Yeung","orcid":"0000-0003-1732-1559"},{"full_name":"Florescu, Maria","last_name":"Florescu","first_name":"Maria"},{"full_name":"Zeller, Peter","last_name":"Zeller","first_name":"Peter"},{"full_name":"De Barbanson, Buys Anton","first_name":"Buys Anton","last_name":"De Barbanson"},{"first_name":"Max D.","last_name":"Wellenstein","full_name":"Wellenstein, Max D."},{"full_name":"Van Oudenaarden, Alexander","first_name":"Alexander","last_name":"Van Oudenaarden"}],"date_published":"2023-06-01T00:00:00Z","volume":41,"abstract":[{"text":"Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.","lang":"eng"}],"publication":"Nature Biotechnology","year":"2023","language":[{"iso":"eng"}],"day":"01","file":[{"file_id":"14066","date_created":"2023-08-16T11:30:45Z","creator":"dernst","relation":"main_file","checksum":"668447a1c8d360b68f8aaf9e08ed644f","date_updated":"2023-08-16T11:30:45Z","content_type":"application/pdf","file_name":"2023_NatureBioTech_Yeung.pdf","access_level":"open_access","file_size":12040976,"success":1}],"publisher":"Springer Nature","scopus_import":"1","date_created":"2023-01-08T23:00:53Z","article_type":"original"},{"publication":"Applied Surface Science","day":"15","language":[{"iso":"eng"}],"year":"2023","keyword":["Surfaces","Coatings and Films","Condensed Matter Physics","Surfaces and Interfaces","General Physics and Astronomy","General Chemistry"],"author":[{"last_name":"Zhang","first_name":"Li","full_name":"Zhang, Li"},{"full_name":"Liu, Xingyu","first_name":"Xingyu","last_name":"Liu"},{"first_name":"Ting","last_name":"Wu","full_name":"Wu, Ting"},{"last_name":"Xu","first_name":"Shengduo","id":"12ab8624-4c8a-11ec-9e11-e1ac2438f22f","full_name":"Xu, Shengduo"},{"full_name":"Suo, Guoquan","first_name":"Guoquan","last_name":"Suo"},{"full_name":"Ye, Xiaohui","last_name":"Ye","first_name":"Xiaohui"},{"full_name":"Hou, Xiaojiang","last_name":"Hou","first_name":"Xiaojiang"},{"first_name":"Yanling","last_name":"Yang","full_name":"Yang, Yanling"},{"last_name":"Liu","first_name":"Qingfeng","full_name":"Liu, Qingfeng"},{"last_name":"Wang","first_name":"Hongqiang","full_name":"Wang, Hongqiang"}],"volume":613,"abstract":[{"text":"The power factor of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) film can be significantly improved by optimizing the oxidation level of the film in oxidation and reduction processes. However, precise control over the oxidation and reduction effects in PEDOT:PSS remains a challenge, which greatly sacrifices both S and σ. Here, we propose a two-step post-treatment using a mixture of ethylene glycol (EG) and Arginine (Arg) and sulfuric acid (H2SO4) in sequence to engineer high-performance PEDOT:PSS thermoelectric films. The high-polarity EG dopant removes the excess non-ionized PSS and induces benzenoid-to-quinoid conformational change in the PEDOT:PSS films. In particular, basic amino acid Arg tunes the oxidation level of PEDOT:PSS and prevents the films from over-oxidation during H2SO4 post-treatment, leading to increased S. The following H2SO4 post-treatment further induces highly orientated lamellar stacking microstructures to increase σ, yielding a maximum power factor of 170.6 μW m−1 K−2 at 460 K. Moreover, a novel trigonal-shape thermoelectric device is designed and assembled by the as-prepared PEDOT:PSS films in order to harvest heat via a vertical temperature gradient. An output power density of 33 μW cm−2 is generated at a temperature difference of 40 K, showing the potential application for low-grade wearable electronic devices.","lang":"eng"}],"date_published":"2023-03-15T00:00:00Z","article_type":"original","date_created":"2023-01-12T11:55:02Z","publisher":"Elsevier","scopus_import":"1","oa_version":"None","month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"epub_ahead","date_updated":"2023-08-14T11:47:06Z","publication_identifier":{"issn":["0169-4332"]},"article_number":"156101","doi":"10.1016/j.apsusc.2022.156101","external_id":{"isi":["000911497000001"]},"_id":"12113","intvolume":" 613","acknowledgement":"Scientific Research Program Funded by Shaanxi Provincial Education Department (Program No.22JY012), Natural Science Basic Research Program of Shaanxi (Grant No.2022JZ-31), Young Talent fund of University Association for Science and Technology in Shaanxi, China (Grant No.20210411), China Postdoctoral Science Foundation (Grant No. 2021M692621), the Foundation of Shaanxi University of Science & Technology (Grant No. 2017GBJ-03), Open Foundation of Key Laboratory of Auxiliary Chemistry and Technology for Chemical Industry, Ministry of Education, Shaanxi University of Science and Technology (Grant No. KFKT2022-15), and Open Foundation of Shaanxi Collaborative Innovation Center of Industrial Auxiliary Chemistry and Technology, Shaanxi University of Science and Technology (Grant No. KFKT2022-15).","quality_controlled":"1","department":[{"_id":"MaIb"}],"article_processing_charge":"No","citation":{"ieee":"L. Zhang et al., “Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient,” Applied Surface Science, vol. 613. Elsevier, 2023.","ista":"Zhang L, Liu X, Wu T, Xu S, Suo G, Ye X, Hou X, Yang Y, Liu Q, Wang H. 2023. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 613, 156101.","short":"L. Zhang, X. Liu, T. Wu, S. Xu, G. Suo, X. Ye, X. Hou, Y. Yang, Q. Liu, H. Wang, Applied Surface Science 613 (2023).","ama":"Zhang L, Liu X, Wu T, et al. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 2023;613. doi:10.1016/j.apsusc.2022.156101","chicago":"Zhang, Li, Xingyu Liu, Ting Wu, Shengduo Xu, Guoquan Suo, Xiaohui Ye, Xiaojiang Hou, Yanling Yang, Qingfeng Liu, and Hongqiang Wang. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” Applied Surface Science. Elsevier, 2023. https://doi.org/10.1016/j.apsusc.2022.156101.","apa":"Zhang, L., Liu, X., Wu, T., Xu, S., Suo, G., Ye, X., … Wang, H. (2023). Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. Elsevier. https://doi.org/10.1016/j.apsusc.2022.156101","mla":"Zhang, Li, et al. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” Applied Surface Science, vol. 613, 156101, Elsevier, 2023, doi:10.1016/j.apsusc.2022.156101."},"isi":1,"title":"Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient","status":"public","type":"journal_article"},{"doi":"10.1016/j.yjsbx.2022.100079","external_id":{"pmid":["36578472"]},"_id":"12114","intvolume":" 7","acknowledgement":"The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg State University in a form of the grant 92425251 and the access to the MRR, MCT and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact that “tensor asymmetry” is better called “tensor biaxiality”.","quality_controlled":"1","department":[{"_id":"PaSc"}],"citation":{"ieee":"D. F. Gauto et al., “Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,” Journal of Structural Biology: X, vol. 7. Elsevier, 2023.","ista":"Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.","apa":"Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079","mla":"Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X, vol. 7, 100079, Elsevier, 2023, doi:10.1016/j.yjsbx.2022.100079.","short":"D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).","ama":"Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 2023;7. doi:10.1016/j.yjsbx.2022.100079","chicago":"Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X. Elsevier, 2023. https://doi.org/10.1016/j.yjsbx.2022.100079."},"article_processing_charge":"No","title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"type":"journal_article","status":"public","oa_version":"Published Version","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"date_updated":"2023-08-16T09:37:25Z","ddc":["570"],"publication_identifier":{"issn":["2590-1524"]},"has_accepted_license":"1","article_number":"100079","date_created":"2023-01-12T11:55:38Z","article_type":"original","publisher":"Elsevier","file":[{"file_id":"14064","creator":"dernst","date_created":"2023-08-16T09:36:28Z","checksum":"b4b1c10a31018aafe053b7d55a470e54","relation":"main_file","date_updated":"2023-08-16T09:36:28Z","content_type":"application/pdf","file_name":"2023_JourStrucBiologyX_Gauto.pdf","file_size":5132322,"access_level":"open_access","success":1}],"pmid":1,"scopus_import":"1","publication":"Journal of Structural Biology: X","day":"01","language":[{"iso":"eng"}],"year":"2023","keyword":["Structural Biology"],"file_date_updated":"2023-08-16T09:36:28Z","author":[{"full_name":"Gauto, Diego F.","first_name":"Diego F.","last_name":"Gauto"},{"last_name":"Lebedenko","first_name":"Olga O.","full_name":"Lebedenko, Olga O."},{"orcid":"0000-0002-6401-5151","first_name":"Lea Marie","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","full_name":"Becker, Lea Marie"},{"last_name":"Ayala","first_name":"Isabel","full_name":"Ayala, Isabel"},{"last_name":"Lichtenecker","first_name":"Roman","full_name":"Lichtenecker, Roman"},{"full_name":"Skrynnikov, Nikolai R.","last_name":"Skrynnikov","first_name":"Nikolai R."},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606"}],"abstract":[{"lang":"eng","text":"Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects."}],"volume":7,"date_published":"2023-01-01T00:00:00Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","id":"12205","relation":"other"}]},"oa_version":"Published Version","month":"01","date_updated":"2023-09-05T15:18:36Z","publication_identifier":{"issn":["1068-9265"],"eissn":["1534-4681"]},"publication_status":"published","oa":1,"isi":1,"citation":{"ieee":"J. Glajzer et al., “ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 46–47, 2023.","ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 46–47.","chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12681-z.","short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 46–47.","ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:46-47. doi:10.1245/s10434-022-12681-z","mla":"Glajzer, Jacek, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 46–47, doi:10.1245/s10434-022-12681-z.","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12681-z"},"article_processing_charge":"No","type":"journal_article","status":"public","title":"ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium","page":"46-47","_id":"12115","intvolume":" 30","doi":"10.1245/s10434-022-12681-z","external_id":{"isi":["000879151800001"]},"department":[{"_id":"JoDa"}],"acknowledgement":"This work was supported by European Commission’s Seventh Framework Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).","quality_controlled":"1","volume":30,"date_published":"2023-01-01T00:00:00Z","author":[{"first_name":"Jacek","last_name":"Glajzer","full_name":"Glajzer, Jacek"},{"full_name":"Castillo-Tong, Dan Cacsire","last_name":"Castillo-Tong","first_name":"Dan Cacsire"},{"full_name":"Richter, Rolf","last_name":"Richter","first_name":"Rolf"},{"last_name":"Vergote","first_name":"Ignace","full_name":"Vergote, Ignace"},{"last_name":"Kulbe","first_name":"Hagen","full_name":"Kulbe, Hagen"},{"full_name":"Vanderstichele, Adriaan","last_name":"Vanderstichele","first_name":"Adriaan"},{"first_name":"Ilary","last_name":"Ruscito","full_name":"Ruscito, Ilary"},{"full_name":"Trillsch, Fabian","last_name":"Trillsch","first_name":"Fabian"},{"full_name":"Mustea, Alexander","last_name":"Mustea","first_name":"Alexander"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline","first_name":"Caroline","last_name":"Kreuzinger"},{"last_name":"Gourley","first_name":"Charlie","full_name":"Gourley, Charlie"},{"first_name":"Hani","last_name":"Gabra","full_name":"Gabra, Hani"},{"full_name":"Taube, Eliane T.","first_name":"Eliane T.","last_name":"Taube"},{"last_name":"Dorigo","first_name":"Oliver","full_name":"Dorigo, Oliver"},{"first_name":"David","last_name":"Horst","full_name":"Horst, David"},{"first_name":"Carlotta","last_name":"Keunecke","full_name":"Keunecke, Carlotta"},{"last_name":"Baum","first_name":"Joanna","full_name":"Baum, Joanna"},{"last_name":"Angelotti","first_name":"Timothy","full_name":"Angelotti, Timothy"},{"last_name":"Sehouli","first_name":"Jalid","full_name":"Sehouli, Jalid"},{"last_name":"Braicu","first_name":"Elena Ioana","full_name":"Braicu, Elena Ioana"}],"day":"01","language":[{"iso":"eng"}],"year":"2023","publication":"Annals of Surgical Oncology","keyword":["Oncology","Surgery"],"publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1245/s10434-022-12681-z"}],"scopus_import":"1","date_created":"2023-01-12T11:56:22Z","article_type":"original"},{"date_created":"2023-01-12T12:09:09Z","article_type":"review","file":[{"success":1,"file_name":"2023_NatureGenetics_Zeller.pdf","file_size":21484855,"access_level":"open_access","date_updated":"2023-02-27T07:46:45Z","content_type":"application/pdf","date_created":"2023-02-27T07:46:45Z","creator":"dernst","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","relation":"main_file","file_id":"12688"}],"publisher":"Springer Nature","scopus_import":"1","publication":"Nature Genetics","day":"01","year":"2023","language":[{"iso":"eng"}],"keyword":["Genetics"],"file_date_updated":"2023-02-27T07:46:45Z","author":[{"full_name":"Zeller, Peter","last_name":"Zeller","first_name":"Peter"},{"first_name":"Jake","last_name":"Yeung","orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b"},{"full_name":"Viñas Gaza, Helena","last_name":"Viñas Gaza","first_name":"Helena"},{"full_name":"de Barbanson, Buys Anton","last_name":"de Barbanson","first_name":"Buys Anton"},{"full_name":"Bhardwaj, Vivek","first_name":"Vivek","last_name":"Bhardwaj"},{"first_name":"Maria","last_name":"Florescu","full_name":"Florescu, Maria"},{"last_name":"van der Linden","first_name":"Reinier","full_name":"van der Linden, Reinier"},{"full_name":"van Oudenaarden, Alexander","last_name":"van Oudenaarden","first_name":"Alexander"}],"volume":55,"abstract":[{"lang":"eng","text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages."}],"date_published":"2023-02-01T00:00:00Z","doi":"10.1038/s41588-022-01260-3","_id":"12158","page":"333-345","intvolume":" 55","acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","quality_controlled":"1","department":[{"_id":"ScienComp"}],"article_processing_charge":"No","citation":{"chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3.","short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345. doi:10.1038/s41588-022-01260-3","apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-022-01260-3","mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature, 2023, pp. 333–45, doi:10.1038/s41588-022-01260-3.","ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.","ieee":"P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature, pp. 333–345, 2023."},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","status":"public","type":"journal_article","oa_version":"Published Version","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publication_status":"published","ddc":["570","000"],"date_updated":"2023-02-27T07:48:24Z","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"has_accepted_license":"1"}]