[{"title":"The splay-list: A distribution-adaptive concurrent skip-list","external_id":{"isi":["000913424000001"],"arxiv":["2008.01009"]},"article_processing_charge":"No","author":[{"first_name":"Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87","full_name":"Aksenov, Vitalii","last_name":"Aksenov"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"Alexandra","full_name":"Drozdova, Alexandra","last_name":"Drozdova"},{"last_name":"Mohtashami","full_name":"Mohtashami, Amirkeivan","first_name":"Amirkeivan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. 2023. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 36, 395–418.","chicago":"Aksenov, Vitalii, Dan-Adrian Alistarh, Alexandra Drozdova, and Amirkeivan Mohtashami. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00441-x.","ama":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 2023;36:395-418. doi:10.1007/s00446-022-00441-x","apa":"Aksenov, V., Alistarh, D.-A., Drozdova, A., & Mohtashami, A. (2023). The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00441-x","short":"V. Aksenov, D.-A. Alistarh, A. Drozdova, A. Mohtashami, Distributed Computing 36 (2023) 395–418.","ieee":"V. Aksenov, D.-A. Alistarh, A. Drozdova, and A. Mohtashami, “The splay-list: A distribution-adaptive concurrent skip-list,” Distributed Computing, vol. 36. Springer Nature, pp. 395–418, 2023.","mla":"Aksenov, Vitalii, et al. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 395–418, doi:10.1007/s00446-022-00441-x."},"date_created":"2023-01-22T23:00:55Z","date_published":"2023-09-01T00:00:00Z","doi":"10.1007/s00446-022-00441-x","page":"395-418","publication":"Distributed Computing","day":"01","year":"2023","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer Nature","department":[{"_id":"DaAl"}],"date_updated":"2023-08-14T12:54:32Z","status":"public","type":"journal_article","article_type":"original","_id":"12330","volume":36,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0452"],"issn":["0178-2770"]},"intvolume":" 36","month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2008.01009"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"The design and implementation of efficient concurrent data structures has seen significant attention. However, most of this work has focused on concurrent data structures providing good worst-case guarantees, although, in real workloads, objects are often accessed at different rates. Efficient distribution-adaptive data structures, such as splay-trees, are known in the sequential case; however, they often are hard to translate efficiently to the concurrent case. We investigate distribution-adaptive concurrent data structures, and propose a new design called the splay-list. At a high level, the splay-list is similar to a standard skip-list, with the key distinction that the height of each element adapts dynamically to its access rate: popular elements “move up,” whereas rarely-accessed elements decrease in height. We show that the splay-list provides order-optimal amortized complexity bounds for a subset of operations, while being amenable to efficient concurrent implementation. Experiments show that the splay-list can leverage distribution-adaptivity for performance, and can outperform the only previously-known distribution-adaptive concurrent design in certain workloads."}]},{"citation":{"chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.","ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023). On the origin and structure of haplotype blocks. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16793","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” Molecular Ecology, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria"},{"last_name":"Pal","orcid":"0000-0002-4530-8469","full_name":"Pal, Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka"},{"full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"last_name":"Chan","full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["36433653"],"isi":["000900762000001"]},"title":"On the origin and structure of haplotype blocks","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"The maintenance of alternative adaptive peaks in snapdragons"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"isi":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"Molecular Ecology","page":"1441-1457","date_published":"2023-03-01T00:00:00Z","doi":"10.1111/mec.16793","date_created":"2023-01-12T12:09:17Z","acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","publisher":"Wiley","quality_controlled":"1","oa":1,"date_updated":"2023-08-16T08:18:47Z","ddc":["570"],"department":[{"_id":"NiBa"}],"file_date_updated":"2023-08-16T08:15:41Z","_id":"12159","type":"journal_article","article_type":"original","tmp":{"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)","short":"CC BY (4.0)"},"status":"public","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"publication_status":"published","file":[{"file_size":7144607,"date_updated":"2023-08-16T08:15:41Z","creator":"dernst","file_name":"2023_MolecularEcology_Shipilina.pdf","date_created":"2023-08-16T08:15:41Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14062","checksum":"b10e0f8fa3dc4d72aaf77a557200978a"}],"language":[{"iso":"eng"}],"volume":32,"issue":"6","license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 32"},{"oa":1,"publisher":"Elsevier","quality_controlled":"1","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”.","date_created":"2023-01-12T11:55:38Z","date_published":"2023-01-01T00:00:00Z","doi":"10.1016/j.yjsbx.2022.100079","publication":"Journal of Structural Biology: X","day":"01","year":"2023","has_accepted_license":"1","article_number":"100079","title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","article_processing_charge":"No","external_id":{"pmid":["36578472"]},"author":[{"first_name":"Diego F.","full_name":"Gauto, Diego F.","last_name":"Gauto"},{"full_name":"Lebedenko, Olga O.","last_name":"Lebedenko","first_name":"Olga O."},{"full_name":"Becker, Lea Marie","orcid":"0000-0002-6401-5151","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"first_name":"Roman","full_name":"Lichtenecker, Roman","last_name":"Lichtenecker"},{"first_name":"Nikolai R.","last_name":"Skrynnikov","full_name":"Skrynnikov, Nikolai R."},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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.","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."},"intvolume":" 7","month":"01","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":7,"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-08-16T09:36:28Z","file_size":5132322,"date_created":"2023-08-16T09:36:28Z","file_name":"2023_JourStrucBiologyX_Gauto.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14064","checksum":"b4b1c10a31018aafe053b7d55a470e54","success":1}],"publication_status":"published","publication_identifier":{"issn":["2590-1524"]},"keyword":["Structural Biology"],"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","_id":"12114","file_date_updated":"2023-08-16T09:36:28Z","department":[{"_id":"PaSc"}],"ddc":["570"],"date_updated":"2023-08-16T09:37:25Z"},{"file_date_updated":"2023-08-16T08:31:04Z","department":[{"_id":"MaLo"}],"date_updated":"2023-08-16T08:32:29Z","ddc":["570"],"article_type":"review","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"_id":"12163","issue":"6","volume":597,"publication_identifier":{"eissn":["1873-3468"],"issn":["0014-5793"]},"publication_status":"published","file":[{"date_created":"2023-08-16T08:31:04Z","file_name":"2023_FEBSLetters_Loose.pdf","creator":"dernst","date_updated":"2023-08-16T08:31:04Z","file_size":3148143,"file_id":"14063","checksum":"7492244d3f9c5faa1347ef03f6e5bc84","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 597","abstract":[{"lang":"eng","text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time."}],"pmid":1,"oa_version":"Published Version","author":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"},{"last_name":"Auer","full_name":"Auer, Albert","orcid":"0000-0002-3580-2906","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","first_name":"Albert"},{"id":"D96FFDA0-A884-11E9-9968-DC26E6697425","first_name":"Gabriel","full_name":"Brognara, Gabriel","last_name":"Brognara"},{"last_name":"Budiman","full_name":"Budiman, Hanifatul R","first_name":"Hanifatul R","id":"55380f95-15b2-11ec-abd3-aff8e230696b"},{"last_name":"Kowalski","full_name":"Kowalski, Lukasz M","first_name":"Lukasz M","id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2"},{"first_name":"Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","full_name":"Matijevic, Ivana","last_name":"Matijevic"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000891573000001"],"pmid":["36448231"]},"title":"In vitro reconstitution of small GTPase regulation","citation":{"chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters. Wiley, 2023. https://doi.org/10.1002/1873-3468.14540.","ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.","mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:10.1002/1873-3468.14540.","ieee":"M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” FEBS Letters, vol. 597, no. 6. Wiley, pp. 762–777, 2023.","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777.","apa":"Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., & Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. FEBS Letters. Wiley. https://doi.org/10.1002/1873-3468.14540","ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. FEBS Letters. 2023;597(6):762-777. doi:10.1002/1873-3468.14540"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"762-777","date_published":"2023-03-01T00:00:00Z","doi":"10.1002/1873-3468.14540","date_created":"2023-01-12T12:09:58Z","has_accepted_license":"1","isi":1,"year":"2023","day":"01","publication":"FEBS Letters","quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"The authors acknowledge support from IST Austria and helpful comments from the anonymous reviewers that helped to improve this manuscript. We apologize to the authors of primary literature and outstanding research not cited here due to space restraints."},{"isi":1,"year":"2023","day":"01","publication":"Distributed Computing","page":"29-43","doi":"10.1007/s00446-022-00439-5","date_published":"2023-03-01T00:00:00Z","date_created":"2023-01-12T12:10:08Z","acknowledgement":"A preliminary version of this work appeared in DISC’19. Mirza Ahad Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported by the Israel Science Foundation (Grants 380/18 and 1425/22).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"citation":{"mla":"Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 29–43, doi:10.1007/s00446-022-00439-5.","ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with polylogarithmic amortized step complexity,” Distributed Computing, vol. 36. Springer Nature, pp. 29–43, 2023.","short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023) 29–43.","ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 2023;36:29-43. doi:10.1007/s00446-022-00439-5","apa":"Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2023). Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00439-5","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00439-5.","ista":"Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 36, 29–43."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","first_name":"Mirza Ahad","last_name":"Baig","full_name":"Baig, Mirza Ahad"},{"first_name":"Danny","full_name":"Hendler, Danny","last_name":"Hendler"},{"first_name":"Alessia","last_name":"Milani","full_name":"Milani, Alessia"},{"first_name":"Corentin","full_name":"Travers, Corentin","last_name":"Travers"}],"article_processing_charge":"No","external_id":{"isi":["000890138700001"]},"title":"Long-lived counters with polylogarithmic amortized step complexity","publication_identifier":{"issn":["0178-2770"],"eissn":["1432-0452"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":36,"abstract":[{"text":"A shared-memory counter is a widely-used and well-studied concurrent object. It supports two operations: An Inc operation that increases its value by 1 and a Read operation that returns its current value. In Jayanti et al (SIAM J Comput, 30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case step complexity of obstruction-free implementations, from read-write registers, of a large class of shared objects that includes counters. The lower bound leaves open the question of finding counter implementations with sub-linear amortized step complexity. In this work, we address this gap. We show that n-process, wait-free and linearizable counters can be implemented from read-write registers with O(log2n) amortized step complexity. This is the first counter algorithm from read-write registers that provides sub-linear amortized step complexity in executions of arbitrary length. Since a logarithmic lower bound on the amortized step complexity of obstruction-free counter implementations exists, our upper bound is within a logarithmic factor of the optimal. The worst-case step complexity of the construction remains linear, which is optimal. This is obtained thanks to a new max register construction with O(logn) amortized step complexity in executions of arbitrary length in which the value stored in the register does not grow too quickly. We then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel [1] in which we “plug” our max register implementation to show that it remains linearizable while achieving O(log2n) amortized step complexity.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://drops.dagstuhl.de/opus/volltexte/2019/11310/"}],"month":"03","intvolume":" 36","date_updated":"2023-08-16T08:39:36Z","department":[{"_id":"KrPi"}],"_id":"12164","article_type":"original","type":"journal_article","status":"public","keyword":["Computational Theory and Mathematics","Computer Networks and Communications","Hardware and Architecture","Theoretical Computer Science"]},{"title":"Experimental analysis of Cascade CSTRs with step and pulse inputs","article_processing_charge":"No","author":[{"first_name":"Bushra","last_name":"Khatoon","full_name":"Khatoon, Bushra"},{"id":"185a19af-dc7d-11ea-9b2f-8eb2201959e9","first_name":"Shoaib","full_name":"Kamil, Shoaib","last_name":"Kamil"},{"full_name":"Babu, Hitesh","last_name":"Babu","first_name":"Hitesh"},{"first_name":"M.","full_name":"Siraj Alam, M.","last_name":"Siraj Alam"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Khatoon, Bushra, Shoaib Kamil, Hitesh Babu, and M. Siraj Alam. “Experimental Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings. Elsevier, 2023. https://doi.org/10.1016/j.matpr.2022.11.037.","ista":"Khatoon B, Kamil S, Babu H, Siraj Alam M. 2023. Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 78(Part 1), 40–47.","mla":"Khatoon, Bushra, et al. “Experimental Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings, vol. 78, no. Part 1, Elsevier, 2023, pp. 40–47, doi:10.1016/j.matpr.2022.11.037.","apa":"Khatoon, B., Kamil, S., Babu, H., & Siraj Alam, M. (2023). Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. Elsevier. https://doi.org/10.1016/j.matpr.2022.11.037","ama":"Khatoon B, Kamil S, Babu H, Siraj Alam M. Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 2023;78(Part 1):40-47. doi:10.1016/j.matpr.2022.11.037","short":"B. Khatoon, S. Kamil, H. Babu, M. Siraj Alam, Materials Today: Proceedings 78 (2023) 40–47.","ieee":"B. Khatoon, S. Kamil, H. Babu, and M. Siraj Alam, “Experimental analysis of Cascade CSTRs with step and pulse inputs,” Materials Today: Proceedings, vol. 78, no. Part 1. Elsevier, pp. 40–47, 2023."},"date_created":"2023-01-12T12:11:26Z","doi":"10.1016/j.matpr.2022.11.037","date_published":"2023-03-20T00:00:00Z","page":"40-47","publication":"Materials Today: Proceedings","day":"20","year":"2023","quality_controlled":"1","publisher":"Elsevier","department":[{"_id":"BjHo"}],"date_updated":"2023-08-16T09:08:11Z","keyword":["General Medicine"],"status":"public","article_type":"original","type":"journal_article","_id":"12172","volume":78,"issue":"Part 1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2214-7853"]},"intvolume":" 78","month":"03","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"In industrial reactors and equipment, non-ideality is quite a common phenomenon rather than an exception. These deviations from ideality impact the process's overall efficiency and the effectiveness of the equipment. To recognize the associated non-ideality, one needs to have enough understanding of the formulation of the equations and in-depth knowledge of the residence time distribution (RTD) data of real reactors. In the current work, step input and pulse input were used to create RTD data for Cascade continuous stirred tank reactors (CSTRs). For the aforementioned configuration, experiments were run at various flow rates to validate the developed characteristic equations. To produce RTD data, distilled water was utilized as the flowing fluid, and NaOH was the tracer substance. The ideal behavior of tracer concentration exits age distribution, and cumulative fraction for each setup and each input was plotted and experimental results were compared with perfect behavior. Deviation of concentration exit age distribution and cumulative fractional distribution from ideal behavior is more in pulse input as compared to a step input. For ideal cases, the exit age distribution curve and cumulative fraction curves are independent of the type of input. But a significant difference was observed for the two cases, which may be due to non-measurable fluctuations in volumetric flow rate, non-achievement of instant injection of tracer in case of pulse input, and slight variations in the sampling period. Further, with increasing flow rate, concentration, exit age, and cumulative fractional curves shifted upward, and this behavior matches with the actual case."}]},{"_id":"12515","status":"public","tmp":{"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)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["570"],"date_updated":"2023-08-16T11:37:52Z","department":[{"_id":"PeJo"}],"file_date_updated":"2023-02-06T07:56:14Z","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents.\r\nMethods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques.\r\nResults: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity.\r\nDiscussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues.","lang":"eng"}],"intvolume":" 16","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2023-02-06T07:56:14Z","file_name":"2022_FrontiersNeuroanatomy_OrtizLeal.pdf","date_updated":"2023-02-06T07:56:14Z","file_size":21943473,"creator":"dernst","checksum":"49cd40f3bda6f267079427042e7d15e3","file_id":"12518","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"eissn":["1662-5129"]},"volume":16,"article_number":"1097467","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Ortiz-Leal, Irene, Mateo V. Torres, Victor M Vargas Barroso, Luis Eusebio Fidalgo, Ana María López-Beceiro, Jorge A. Larriva-Sahd, and Pablo Sánchez-Quinteiro. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy. Frontiers, 2023. https://doi.org/10.3389/fnana.2022.1097467.","ista":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, Fidalgo LE, López-Beceiro AM, Larriva-Sahd JA, Sánchez-Quinteiro P. 2023. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 16, 1097467.","mla":"Ortiz-Leal, Irene, et al. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy, vol. 16, 1097467, Frontiers, 2023, doi:10.3389/fnana.2022.1097467.","ama":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, et al. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 2023;16. doi:10.3389/fnana.2022.1097467","apa":"Ortiz-Leal, I., Torres, M. V., Vargas Barroso, V. M., Fidalgo, L. E., López-Beceiro, A. M., Larriva-Sahd, J. A., & Sánchez-Quinteiro, P. (2023). The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. Frontiers. https://doi.org/10.3389/fnana.2022.1097467","ieee":"I. Ortiz-Leal et al., “The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway,” Frontiers in Neuroanatomy, vol. 16. Frontiers, 2023.","short":"I. Ortiz-Leal, M.V. Torres, V.M. Vargas Barroso, L.E. Fidalgo, A.M. López-Beceiro, J.A. Larriva-Sahd, P. Sánchez-Quinteiro, Frontiers in Neuroanatomy 16 (2023)."},"title":"The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway","article_processing_charge":"No","external_id":{"isi":["000919786900001"],"pmid":["36704406"]},"author":[{"first_name":"Irene","full_name":"Ortiz-Leal, Irene","last_name":"Ortiz-Leal"},{"first_name":"Mateo V.","last_name":"Torres","full_name":"Torres, Mateo V."},{"id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","first_name":"Victor M","last_name":"Vargas Barroso","full_name":"Vargas Barroso, Victor M"},{"last_name":"Fidalgo","full_name":"Fidalgo, Luis Eusebio","first_name":"Luis Eusebio"},{"first_name":"Ana María","full_name":"López-Beceiro, Ana María","last_name":"López-Beceiro"},{"first_name":"Jorge A.","full_name":"Larriva-Sahd, Jorge A.","last_name":"Larriva-Sahd"},{"first_name":"Pablo","full_name":"Sánchez-Quinteiro, Pablo","last_name":"Sánchez-Quinteiro"}],"acknowledgement":"This work was partially supported by a grant from “Consello Social Universidade de Santiago de Compostela” 2022-PU004.We would like to show special gratitude to Prof. Ludwig Wagner (Medical University, Vienna) for kindly providing us with the secretagogin antibody. We thank the Wildlife Recovery Centres of Galicia, Dirección Xeral de Patrimonio Natural (Xunta de Galicia, Spain), and Federación Galega de Caza for providing the red foxes used in this study.","oa":1,"quality_controlled":"1","publisher":"Frontiers","publication":"Frontiers in Neuroanatomy","day":"10","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-02-05T23:01:00Z","doi":"10.3389/fnana.2022.1097467","date_published":"2023-01-10T00:00:00Z"},{"page":"813–823","date_created":"2023-01-08T23:00:53Z","doi":"10.1038/s41587-022-01560-3","date_published":"2023-06-01T00:00:00Z","year":"2023","has_accepted_license":"1","isi":1,"publication":"Nature Biotechnology","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer Nature","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.","article_processing_charge":"No","external_id":{"isi":["000909067600003"]},"author":[{"first_name":"Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b","orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake","last_name":"Yeung"},{"first_name":"Maria","last_name":"Florescu","full_name":"Florescu, Maria"},{"last_name":"Zeller","full_name":"Zeller, Peter","first_name":"Peter"},{"full_name":"De Barbanson, Buys Anton","last_name":"De Barbanson","first_name":"Buys Anton"},{"first_name":"Max D.","full_name":"Wellenstein, Max D.","last_name":"Wellenstein"},{"first_name":"Alexander","full_name":"Van Oudenaarden, Alexander","last_name":"Van Oudenaarden"}],"title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","citation":{"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.","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","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","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":41,"publication_status":"published","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"668447a1c8d360b68f8aaf9e08ed644f","file_id":"14066","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_NatureBioTech_Yeung.pdf","date_created":"2023-08-16T11:30:45Z","creator":"dernst","file_size":12040976,"date_updated":"2023-08-16T11:30:45Z"}],"scopus_import":"1","intvolume":" 41","month":"06","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","department":[{"_id":"ScienComp"}],"file_date_updated":"2023-08-16T11:30:45Z","date_updated":"2023-08-16T11:32:33Z","ddc":["570"],"tmp":{"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)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"12106"},{"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01252-3.","ista":"Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 24, 1505–1560.","mla":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare, vol. 24, Springer Nature, 2023, pp. 1505–60, doi:10.1007/s00023-022-01252-3.","ama":"Boccato C, Seiringer R. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 2023;24:1505-1560. doi:10.1007/s00023-022-01252-3","apa":"Boccato, C., & Seiringer, R. (2023). The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01252-3","short":"C. Boccato, R. Seiringer, Annales Henri Poincare 24 (2023) 1505–1560.","ieee":"C. Boccato and R. Seiringer, “The Bose Gas in a box with Neumann boundary conditions,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 1505–1560, 2023."},"title":"The Bose Gas in a box with Neumann boundary conditions","author":[{"id":"342E7E22-F248-11E8-B48F-1D18A9856A87","first_name":"Chiara","full_name":"Boccato, Chiara","last_name":"Boccato"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"external_id":{"isi":["000910751800002"],"arxiv":["2205.15284"]},"article_processing_charge":"No","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"01","publication":"Annales Henri Poincare","isi":1,"year":"2023","date_published":"2023-05-01T00:00:00Z","doi":"10.1007/s00023-022-01252-3","date_created":"2023-01-15T23:00:52Z","page":"1505-1560","_id":"12183","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-16T11:34:03Z","department":[{"_id":"RoSe"}],"oa_version":"Preprint","abstract":[{"text":"We consider a gas of n bosonic particles confined in a box [−ℓ/2,ℓ/2]3 with Neumann boundary conditions. We prove Bose–Einstein condensation in the Gross–Pitaevskii regime, with an optimal bound on the condensate depletion. Moreover, our lower bound for the ground state energy in a small box [−ℓ/2,ℓ/2]3 implies (via Neumann bracketing) a lower bound for the ground state energy of N bosons in a large box [−L/2,L/2]3 with density ρ=N/L3 in the thermodynamic limit.","lang":"eng"}],"month":"05","intvolume":" 24","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2205.15284","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1424-0637"]},"publication_status":"published","volume":24,"ec_funded":1},{"type":"journal_article","article_type":"original","tmp":{"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)","short":"CC BY (4.0)"},"status":"public","_id":"12544","file_date_updated":"2023-08-16T12:21:13Z","department":[{"_id":"HeEd"}],"date_updated":"2023-08-16T12:22:07Z","ddc":["510","540"],"scopus_import":"1","month":"02","intvolume":" 63","abstract":[{"text":"Geometry is crucial in our efforts to comprehend the structures and dynamics of biomolecules. For example, volume, surface area, and integrated mean and Gaussian curvature of the union of balls representing a molecule are used to quantify its interactions with the water surrounding it in the morphometric implicit solvent models. The Alpha Shape theory provides an accurate and reliable method for computing these geometric measures. In this paper, we derive homogeneous formulas for the expressions of these measures and their derivatives with respect to the atomic coordinates, and we provide algorithms that implement them into a new software package, AlphaMol. The only variables in these formulas are the interatomic distances, making them insensitive to translations and rotations. AlphaMol includes a sequential algorithm and a parallel algorithm. In the parallel version, we partition the atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented by a buffer zone to account for atoms whose ball representations may partially cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up compared to an independent serial implementation when using 32 processors. For instance, it takes 31 s to compute the geometric measures and derivatives of each atom in a viral capsid with more than 26 million atoms on 32 Intel processors running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant computations, which ultimately limit the impact of using multiple processors. AlphaMol is available as an OpenSource software.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":63,"issue":"3","ec_funded":1,"publication_identifier":{"eissn":["1549-960X"],"issn":["1549-9596"]},"publication_status":"published","file":[{"file_id":"14070","checksum":"7d20562269edff1e31b9d6019d4983b0","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-08-16T12:21:13Z","file_name":"2023_JCIM_Koehl.pdf","creator":"dernst","date_updated":"2023-08-16T12:21:13Z","file_size":8069223}],"language":[{"iso":"eng"}],"project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","name":"The Wittgenstein Prize"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"author":[{"last_name":"Koehl","full_name":"Koehl, Patrice","first_name":"Patrice"},{"last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000920370700001"],"pmid":["36638318"]},"title":"Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives","citation":{"chicago":"Koehl, Patrice, Arseniy Akopyan, and Herbert Edelsbrunner. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information and Modeling. American Chemical Society, 2023. https://doi.org/10.1021/acs.jcim.2c01346.","ista":"Koehl P, Akopyan A, Edelsbrunner H. 2023. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 63(3), 973–985.","mla":"Koehl, Patrice, et al. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information and Modeling, vol. 63, no. 3, American Chemical Society, 2023, pp. 973–85, doi:10.1021/acs.jcim.2c01346.","ieee":"P. Koehl, A. Akopyan, and H. Edelsbrunner, “Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives,” Journal of Chemical Information and Modeling, vol. 63, no. 3. American Chemical Society, pp. 973–985, 2023.","short":"P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and Modeling 63 (2023) 973–985.","ama":"Koehl P, Akopyan A, Edelsbrunner H. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 2023;63(3):973-985. doi:10.1021/acs.jcim.2c01346","apa":"Koehl, P., Akopyan, A., & Edelsbrunner, H. (2023). Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. American Chemical Society. https://doi.org/10.1021/acs.jcim.2c01346"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"acknowledgement":"P.K. acknowledges support from the University of California Multicampus Research Programs and Initiatives (Grant No. M21PR3267) and from the NSF (Grant No.1760485). H.E. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program, 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.\r\nOpen Access is funded by the Austrian Science Fund (FWF).","page":"973-985","date_published":"2023-02-13T00:00:00Z","doi":"10.1021/acs.jcim.2c01346","date_created":"2023-02-12T23:00:59Z","has_accepted_license":"1","isi":1,"year":"2023","day":"13","publication":"Journal of Chemical Information and Modeling"},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team at ISTA for ant collection and experimental help, in particular H. Leitner, and the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the Social Immunity team for comments on the manuscript. The study was funded by the German Research Foundation (CR118/3-1) within the Framework of the Priority Program SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.","date_created":"2023-02-12T23:00:59Z","doi":"10.1038/s41559-023-01981-6","date_published":"2023-03-01T00:00:00Z","page":"450-460","publication":"Nature Ecology and Evolution","day":"01","year":"2023","has_accepted_license":"1","isi":1,"project":[{"name":"Epidemics in ant societies on a chip","grant_number":"771402","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"},{"name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"}],"title":"Pathogen evasion of social immunity","external_id":{"pmid":["36732670"],"isi":["000924572800001"]},"article_processing_charge":"No","author":[{"last_name":"Stock","full_name":"Stock, Miriam","first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","last_name":"Milutinovic","first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michaela","id":"953894f3-25bd-11ec-8556-f70a9d38ef60","full_name":"Hönigsberger, Michaela","last_name":"Hönigsberger"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","full_name":"Grasse, Anna V"},{"id":"39523C54-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Wiesenhofer, Florian","last_name":"Wiesenhofer"},{"last_name":"Kampleitner","full_name":"Kampleitner, Niklas","first_name":"Niklas","id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Narasimhan","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha"},{"first_name":"Thomas","last_name":"Schmitt","full_name":"Schmitt, Thomas"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N. Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution 7 (2023) 450–460.","ieee":"M. Stock et al., “Pathogen evasion of social immunity,” Nature Ecology and Evolution, vol. 7. Springer Nature, pp. 450–460, 2023.","ama":"Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity. Nature Ecology and Evolution. 2023;7:450-460. doi:10.1038/s41559-023-01981-6","apa":"Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F., Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-023-01981-6","mla":"Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution, vol. 7, Springer Nature, 2023, pp. 450–60, doi:10.1038/s41559-023-01981-6.","ista":"Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity. Nature Ecology and Evolution. 7, 450–460.","chicago":"Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse, Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt, and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution. Springer Nature, 2023. https://doi.org/10.1038/s41559-023-01981-6."},"intvolume":" 7","month":"03","scopus_import":"1","oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"text":"Treating sick group members is a hallmark of collective disease defence in vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness and epidemiology, it is still largely unknown how pathogens react to the selection pressure imposed by care intervention. Using social insects and pathogenic fungi, we here performed a serial passage experiment in the presence or absence of colony members, which provide social immunity by grooming off infectious spores from exposed individuals. We found specific effects on pathogen diversity, virulence and transmission. Under selection of social immunity, pathogens invested into higher spore production, but spores were less virulent. Notably, they also elicited a lower grooming response in colony members, compared with spores from the individual host selection lines. Chemical spore analysis suggested that the spores from social selection lines escaped the caregivers’ detection by containing lower levels of ergosterol, a key fungal membrane component. Experimental application of chemically pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated cue triggering host social immunity against fungal pathogens. By reducing this detection cue, pathogens were able to evade the otherwise very effective collective disease defences of their social hosts.","lang":"eng"}],"ec_funded":1,"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/","description":"News on ISTA website"}]},"volume":7,"language":[{"iso":"eng"}],"file":[{"date_created":"2023-08-16T11:54:59Z","file_name":"2023_NatureEcoEvo_Stock.pdf","date_updated":"2023-08-16T11:54:59Z","file_size":1600499,"creator":"dernst","file_id":"14069","checksum":"8244f4650a0e7aeea488d1bcd4a31702","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"eissn":["2397-334X"]},"status":"public","tmp":{"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)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"12543","department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"file_date_updated":"2023-08-16T11:54:59Z","ddc":["570"],"date_updated":"2023-08-16T11:55:48Z"},{"article_number":"qrac004","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"},{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"citation":{"ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004.","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 2023;7(1). doi:10.1093/evlett/qrac004","ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” Evolution Letters, vol. 7, no. 1. Oxford University Press, 2023.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["37065438"],"isi":["001021692200001"]},"author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"},{"first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","year":"2023","isi":1,"has_accepted_license":"1","publication":"Evolution Letters","day":"01","date_created":"2023-02-06T13:59:12Z","date_published":"2023-02-01T00:00:00Z","doi":"10.1093/evlett/qrac004","_id":"12521","tmp":{"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)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"status":"public","date_updated":"2023-08-16T11:44:32Z","ddc":["570"],"file_date_updated":"2023-08-16T11:43:33Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"abstract":[{"text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 7","month":"02","publication_status":"published","publication_identifier":{"issn":["2056-3744"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":2592189,"date_updated":"2023-08-16T11:43:33Z","file_name":"2023_EvLetters_Mrnjavac.pdf","date_created":"2023-08-16T11:43:33Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14068","checksum":"a240a041cb9b9b7c8ba93a4706674a3f"}],"ec_funded":1,"volume":7,"issue":"1"},{"month":"04","intvolume":" 79","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"How to generate a brain of correct size and with appropriate cell-type diversity during development is a major question in Neuroscience. In the developing neocortex, radial glial progenitor (RGP) cells are the main neural stem cells that produce cortical excitatory projection neurons, glial cells, and establish the prospective postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated developmental program that when disrupted can result in severe cortical malformations such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms instructing faithful RGP lineage progression are however not well understood. This review will summarize recent conceptual advances that contribute to our understanding of the general principles of RGP lineage progression.","lang":"eng"}],"issue":"4","volume":79,"ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"4d11c4ca87e6cbc4d2ac46d3225ea615","file_id":"14071","file_size":1787894,"date_updated":"2023-08-16T12:29:06Z","creator":"dernst","file_name":"2023_CurrentOpinionNeurobio_Hippenmeyer.pdf","date_created":"2023-08-16T12:29:06Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0959-4388"]},"publication_status":"published","status":"public","keyword":["General Neuroscience"],"article_type":"review","type":"journal_article","tmp":{"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)","short":"CC BY (4.0)"},"_id":"12679","file_date_updated":"2023-08-16T12:29:06Z","department":[{"_id":"SiHi"}],"ddc":["570"],"date_updated":"2023-08-16T12:30:25Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"I wish to thank all current and past members of the Hippenmeyer laboratory at ISTA for exciting discussions on the subject of this review. I apologize to colleagues whose work I could not cite and/or discuss in the frame of the available space. Work in the Hippenmeyer laboratory on the\r\ndiscussed topic is supported by ISTA institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agree-ment no. 725780 LinPro) to SH.","doi":"10.1016/j.conb.2023.102695","date_published":"2023-04-01T00:00:00Z","date_created":"2023-02-26T12:24:21Z","day":"01","publication":"Current Opinion in Neurobiology","isi":1,"has_accepted_license":"1","year":"2023","project":[{"grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"article_number":"102695","title":"Principles of neural stem cell lineage progression: Insights from developing cerebral cortex","author":[{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000953497700001"],"pmid":["36842274"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology. Elsevier, 2023. https://doi.org/10.1016/j.conb.2023.102695.","ista":"Hippenmeyer S. 2023. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4), 102695.","mla":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology, vol. 79, no. 4, 102695, Elsevier, 2023, doi:10.1016/j.conb.2023.102695.","ama":"Hippenmeyer S. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 2023;79(4). doi:10.1016/j.conb.2023.102695","apa":"Hippenmeyer, S. (2023). Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2023.102695","short":"S. Hippenmeyer, Current Opinion in Neurobiology 79 (2023).","ieee":"S. Hippenmeyer, “Principles of neural stem cell lineage progression: Insights from developing cerebral cortex,” Current Opinion in Neurobiology, vol. 79, no. 4. Elsevier, 2023."}},{"citation":{"ama":"Agresti A, Lindemulder N, Veraar M. On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. 2023;296(4):1319-1350. doi:10.1002/mana.202100192","apa":"Agresti, A., Lindemulder, N., & Veraar, M. (2023). On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. Wiley. https://doi.org/10.1002/mana.202100192","ieee":"A. Agresti, N. Lindemulder, and M. Veraar, “On the trace embedding and its applications to evolution equations,” Mathematische Nachrichten, vol. 296, no. 4. Wiley, pp. 1319–1350, 2023.","short":"A. Agresti, N. Lindemulder, M. Veraar, Mathematische Nachrichten 296 (2023) 1319–1350.","mla":"Agresti, Antonio, et al. “On the Trace Embedding and Its Applications to Evolution Equations.” Mathematische Nachrichten, vol. 296, no. 4, Wiley, 2023, pp. 1319–50, doi:10.1002/mana.202100192.","ista":"Agresti A, Lindemulder N, Veraar M. 2023. On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. 296(4), 1319–1350.","chicago":"Agresti, Antonio, Nick Lindemulder, and Mark Veraar. “On the Trace Embedding and Its Applications to Evolution Equations.” Mathematische Nachrichten. Wiley, 2023. https://doi.org/10.1002/mana.202100192."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio","last_name":"Agresti","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio"},{"full_name":"Lindemulder, Nick","last_name":"Lindemulder","first_name":"Nick"},{"full_name":"Veraar, Mark","last_name":"Veraar","first_name":"Mark"}],"article_processing_charge":"No","external_id":{"isi":["000914134900001"],"arxiv":["2104.05063"]},"title":"On the trace embedding and its applications to evolution equations","acknowledgement":"The first author has been partially supported by the Nachwuchsring—Network for the promotion of young scientists—at TU Kaiserslautern. The second and third authors were supported by the Vidi subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO).","quality_controlled":"1","publisher":"Wiley","oa":1,"has_accepted_license":"1","isi":1,"year":"2023","day":"01","publication":"Mathematische Nachrichten","page":"1319-1350","date_published":"2023-04-01T00:00:00Z","doi":"10.1002/mana.202100192","date_created":"2023-01-29T23:00:59Z","_id":"12429","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","date_updated":"2023-08-16T11:41:42Z","ddc":["510"],"file_date_updated":"2023-08-16T11:40:02Z","department":[{"_id":"JuFi"}],"abstract":[{"lang":"eng","text":"In this paper, we consider traces at initial times for functions with mixed time-space smoothness. Such results are often needed in the theory of evolution equations. Our result extends and unifies many previous results. Our main improvement is that we can allow general interpolation couples. The abstract results are applied to regularity problems for fractional evolution equations and stochastic evolution equations, where uniform trace estimates on the half-line are shown."}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 296","publication_identifier":{"eissn":["1522-2616"],"issn":["0025-584X"]},"publication_status":"published","file":[{"file_id":"14067","checksum":"6f099f1d064173784d1a27716a2cc795","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-08-16T11:40:02Z","file_name":"2023_MathNachrichten_Agresti.pdf","creator":"dernst","date_updated":"2023-08-16T11:40:02Z","file_size":449280}],"language":[{"iso":"eng"}],"issue":"4","volume":296,"license":"https://creativecommons.org/licenses/by-nc/4.0/"},{"publisher":"World Scientific Publishing","quality_controlled":"1","oa":1,"isi":1,"year":"2023","day":"09","publication":"Reviews in Mathematical Physics","date_published":"2023-01-09T00:00:00Z","doi":"10.1142/S0129055X2350006X","date_created":"2023-01-29T23:00:59Z","article_number":"2350006","citation":{"ama":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. 2023;35(4). doi:10.1142/S0129055X2350006X","apa":"Falconi, M., Leopold, N. K., Mitrouskas, D. J., & Petrat, S. P. (2023). Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X2350006X","short":"M. Falconi, N.K. Leopold, D.J. Mitrouskas, S.P. Petrat, Reviews in Mathematical Physics 35 (2023).","ieee":"M. Falconi, N. K. Leopold, D. J. Mitrouskas, and S. P. Petrat, “Bogoliubov dynamics and higher-order corrections for the regularized Nelson model,” Reviews in Mathematical Physics, vol. 35, no. 4. World Scientific Publishing, 2023.","mla":"Falconi, Marco, et al. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” Reviews in Mathematical Physics, vol. 35, no. 4, 2350006, World Scientific Publishing, 2023, doi:10.1142/S0129055X2350006X.","ista":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. 2023. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. 35(4), 2350006.","chicago":"Falconi, Marco, Nikolai K Leopold, David Johannes Mitrouskas, and Sören P Petrat. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” Reviews in Mathematical Physics. World Scientific Publishing, 2023. https://doi.org/10.1142/S0129055X2350006X."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Falconi, Marco","last_name":"Falconi","first_name":"Marco"},{"id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K","last_name":"Leopold","full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822"},{"last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes"},{"last_name":"Petrat","full_name":"Petrat, Sören P","orcid":"0000-0002-9166-5889","first_name":"Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["2110.00458"],"isi":["000909760300001"]},"article_processing_charge":"No","title":"Bogoliubov dynamics and higher-order corrections for the regularized Nelson model","abstract":[{"text":"We study the time evolution of the Nelson model in a mean-field limit in which N nonrelativistic bosons weakly couple (with respect to the particle number) to a positive or zero mass quantized scalar field. Our main result is the derivation of the Bogoliubov dynamics and higher-order corrections. More precisely, we prove the convergence of the approximate wave function to the many-body wave function in norm, with a convergence rate proportional to the number of corrections taken into account in the approximation. We prove an analogous result for the unitary propagator. As an application, we derive a simple system of partial differential equations describing the time evolution of the first- and second-order approximations to the one-particle reduced density matrices of the particles and the quantum field, respectively.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2110.00458"}],"month":"01","intvolume":" 35","publication_identifier":{"issn":["0129-055X"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":35,"issue":"4","_id":"12430","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-16T11:47:27Z","department":[{"_id":"RoSe"}]},{"department":[{"_id":"GaTk"},{"_id":"GradSch"}],"file_date_updated":"2023-08-16T12:39:57Z","date_updated":"2023-08-16T12:41:53Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"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)","short":"CC BY (4.0)"},"status":"public","_id":"12762","volume":3,"ec_funded":1,"publication_identifier":{"eissn":["2662-8457"]},"publication_status":"published","file":[{"date_updated":"2023-08-16T12:39:57Z","file_size":4474284,"creator":"dernst","date_created":"2023-08-16T12:39:57Z","file_name":"2023_NatureCompScience_Lombardi.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","file_id":"14073","success":1}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 3","abstract":[{"lang":"eng","text":"Neurons in the brain are wired into adaptive networks that exhibit collective dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches. Although existing models account for oscillations and avalanches separately, they typically do not explain both phenomena, are too complex to analyze analytically or intractable to infer from data rigorously. Here we propose a feedback-driven Ising-like class of neural networks that captures avalanches and oscillations simultaneously and quantitatively. In the simplest yet fully microscopic model version, we can analytically compute the phase diagram and make direct contact with human brain resting-state activity recordings via tractable inference of the model’s two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor oscillations to collective behaviors of extreme events and neuronal avalanches. Importantly, the inferred parameters indicate that the co-existence of scale-specific (oscillations) and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations."}],"oa_version":"Published Version","author":[{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio","last_name":"Lombardi","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249"},{"last_name":"Pepic","full_name":"Pepic, Selver","first_name":"Selver","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425"},{"full_name":"Shriki, Oren","last_name":"Shriki","first_name":"Oren"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik"},{"orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"}],"external_id":{"arxiv":["2108.06686"]},"article_processing_charge":"No","title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","citation":{"mla":"Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63, doi:10.1038/s43588-023-00410-9.","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (2023). Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-023-00410-9","ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9","ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” Nature Computational Science, vol. 3. Springer Nature, pp. 254–263, 2023.","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263.","chicago":"Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9.","ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 3, 254–263."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"page":"254-263","doi":"10.1038/s43588-023-00410-9","date_published":"2023-03-20T00:00:00Z","date_created":"2023-03-26T22:01:08Z","has_accepted_license":"1","year":"2023","day":"20","publication":"Nature Computational Science","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"This research was funded in whole, or in part, by the Austrian Science Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie action (grant agreement No. 754411 to F.L.)."},{"related_material":{"record":[{"relation":"part_of_dissertation","id":"8966","status":"public"},{"relation":"part_of_dissertation","id":"7888","status":"public"}]},"ec_funded":1,"file":[{"checksum":"59b0303dc483f40a96a610a90aab7ee9","file_id":"12907","embargo":"2024-05-05","access_level":"closed","relation":"main_file","content_type":"application/pdf","embargo_to":"open_access","date_created":"2023-05-05T13:01:14Z","file_name":"Thesis_Schauer_final.pdf","creator":"aschauer","date_updated":"2023-05-05T13:01:14Z","file_size":31434230},{"file_size":43809109,"date_updated":"2023-05-05T13:04:15Z","creator":"aschauer","file_name":"Thesis_Schauer_final.docx","date_created":"2023-05-05T13:04:15Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"12908","checksum":"25f54e12479b6adaabd129a20568e6c1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","month":"05","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context."}],"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"file_date_updated":"2023-05-05T13:04:15Z","ddc":["570"],"supervisor":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-21T06:25:48Z","status":"public","type":"dissertation","_id":"12891","doi":"10.15479/at:ista:12891","date_published":"2023-05-05T00:00:00Z","date_created":"2023-05-05T08:48:20Z","page":"190","day":"05","has_accepted_license":"1","year":"2023","publisher":"Institute of Science and Technology Austria","title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","author":[{"full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","last_name":"Schauer","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12891.","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","mla":"Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12891.","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:10.15479/at:ista:12891","apa":"Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12891","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023."},"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues"}]},{"ddc":["000"],"date_updated":"2023-08-21T07:00:49Z","department":[{"_id":"MoHe"}],"file_date_updated":"2023-08-21T06:59:05Z","_id":"14085","status":"public","type":"conference","tmp":{"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)","short":"CC BY (4.0)"},"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","end_date":"2023-07-14","location":"Paderborn, Germany","start_date":"2023-07-10"},"file":[{"success":1,"file_id":"14089","checksum":"074177e815a1656de5d4071c7a3dffa6","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_LIPIcsICALP_Goranci.pdf","date_created":"2023-08-21T06:59:05Z","file_size":875910,"date_updated":"2023-08-21T06:59:05Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772785"]},"publication_status":"published","volume":261,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"We show an (1+ϵ)-approximation algorithm for maintaining maximum s-t flow under m edge insertions in m1/2+o(1)ϵ−1/2 amortized update time for directed, unweighted graphs. This constitutes the first sublinear dynamic maximum flow algorithm in general sparse graphs with arbitrarily good approximation guarantee.","lang":"eng"}],"month":"07","intvolume":" 261","alternative_title":["LIPIcs"],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"G. Goranci, M.H. Henzinger, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"G. Goranci and M. H. Henzinger, “Efficient data structures for incremental exact and approximate maximum flow,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","apa":"Goranci, G., & Henzinger, M. H. (2023). Efficient data structures for incremental exact and approximate maximum flow. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.69","ama":"Goranci G, Henzinger MH. Efficient data structures for incremental exact and approximate maximum flow. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.69","mla":"Goranci, Gramoz, and Monika H. Henzinger. “Efficient Data Structures for Incremental Exact and Approximate Maximum Flow.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 69, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.69.","ista":"Goranci G, Henzinger MH. 2023. Efficient data structures for incremental exact and approximate maximum flow. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 69.","chicago":"Goranci, Gramoz, and Monika H Henzinger. “Efficient Data Structures for Incremental Exact and Approximate Maximum Flow.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.69."},"title":"Efficient data structures for incremental exact and approximate maximum flow","author":[{"first_name":"Gramoz","last_name":"Goranci","full_name":"Goranci, Gramoz"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"article_processing_charge":"Yes","external_id":{"unknown":["2211.09606"]},"article_number":"69","project":[{"name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer"}],"day":"01","publication":"50th International Colloquium on Automata, Languages, and Programming","has_accepted_license":"1","year":"2023","date_published":"2023-07-01T00:00:00Z","doi":"10.4230/LIPIcs.ICALP.2023.69","date_created":"2023-08-20T22:01:14Z","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No.\r\n101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the\r\nAustrian Science Fund (FWF) project “Static and Dynamic Hierarchical Graph Decompositions”,\r\nI 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nThis work was done in part while Gramoz Goranci was at Institute for Theoretical Studies, ETH Zurich, Switzerland. There, he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation. We also thank Richard Peng, Thatchaphol Saranurak, Sebastian Forster and Sushant Sachdeva for helpful discussions, and the anonymous reviewers for their insightful comments.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1},{"date_updated":"2023-08-21T06:49:11Z","ddc":["000","510"],"department":[{"_id":"VlKo"}],"file_date_updated":"2023-08-21T06:45:16Z","_id":"14084","type":"conference","conference":{"end_date":"2023-07-14","location":"Paderborn, Germany","start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"tmp":{"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)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]},"publication_status":"published","file":[{"file_name":"2023_LIPIcsICALP_Harris.pdf","date_created":"2023-08-21T06:45:16Z","creator":"dernst","file_size":917791,"date_updated":"2023-08-21T06:45:16Z","success":1,"checksum":"6dee0684245bb1c524b9c955db1e933d","file_id":"14088","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":261,"abstract":[{"text":"A central problem in computational statistics is to convert a procedure for sampling combinatorial objects into a procedure for counting those objects, and vice versa. We will consider sampling problems which come from Gibbs distributions, which are families of probability distributions over a discrete space Ω with probability mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max] and H(ω) ∈ {0} ∪ [1, n].\r\nThe partition function is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the log partition ratio is defined as q = (log Z(β_max))/Z(β_min)\r\nWe develop a number of algorithms to estimate the counts c_x using roughly Õ(q/ε²) samples for general Gibbs distributions and Õ(n²/ε²) samples for integer-valued distributions (ignoring some second-order terms and parameters), We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs and perfect matchings in a graph.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"scopus_import":"1","month":"07","intvolume":" 261","citation":{"ama":"Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.72","apa":"Harris, D. G., & Kolmogorov, V. (2023). Parameter estimation for Gibbs distributions. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.72","short":"D.G. Harris, V. Kolmogorov, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","mla":"Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 72, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.72.","ista":"Harris DG, Kolmogorov V. 2023. Parameter estimation for Gibbs distributions. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 72.","chicago":"Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.72."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Harris, David G.","last_name":"Harris","first_name":"David G."},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"}],"article_processing_charge":"Yes","external_id":{"arxiv":["2007.10824"]},"title":"Parameter estimation for Gibbs distributions","article_number":"72","has_accepted_license":"1","year":"2023","day":"01","publication":"50th International Colloquium on Automata, Languages, and Programming","doi":"10.4230/LIPIcs.ICALP.2023.72","date_published":"2023-07-01T00:00:00Z","date_created":"2023-08-20T22:01:14Z","acknowledgement":"We thank Heng Guo for helpful explanations of algorithms for sampling connected subgraphs and matchings, Maksym Serbyn for bringing to our attention the Wang-Landau algorithm and its use in physics.","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1},{"article_number":"74","project":[{"name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Henzinger MH, Liu P, Vondrák J, Zheng DW. 2023. Faster submodular maximization for several classes of matroids. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 74.","chicago":"Henzinger, Monika H, Paul Liu, Jan Vondrák, and Da Wei Zheng. “Faster Submodular Maximization for Several Classes of Matroids.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.74.","ama":"Henzinger MH, Liu P, Vondrák J, Zheng DW. Faster submodular maximization for several classes of matroids. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.74","apa":"Henzinger, M. H., Liu, P., Vondrák, J., & Zheng, D. W. (2023). Faster submodular maximization for several classes of matroids. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.74","ieee":"M. H. Henzinger, P. Liu, J. Vondrák, and D. W. Zheng, “Faster submodular maximization for several classes of matroids,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","short":"M.H. Henzinger, P. Liu, J. Vondrák, D.W. Zheng, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","mla":"Henzinger, Monika H., et al. “Faster Submodular Maximization for Several Classes of Matroids.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 74, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.74."},"title":"Faster submodular maximization for several classes of matroids","author":[{"last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"last_name":"Liu","full_name":"Liu, Paul","first_name":"Paul"},{"full_name":"Vondrák, Jan","last_name":"Vondrák","first_name":"Jan"},{"full_name":"Zheng, Da Wei","last_name":"Zheng","first_name":"Da Wei"}],"article_processing_charge":"Yes","external_id":{"arxiv":["2305.00122"]},"acknowledgement":" Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. Jan Vondrák: Supported by NSF Award 2127781.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"day":"01","publication":"50th International Colloquium on Automata, Languages, and Programming","has_accepted_license":"1","year":"2023","date_published":"2023-07-01T00:00:00Z","doi":"10.4230/LIPIcs.ICALP.2023.74","date_created":"2023-08-20T22:01:14Z","_id":"14086","status":"public","type":"conference","conference":{"location":"Paderborn, Germany","end_date":"2023-07-14","start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"tmp":{"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)","short":"CC BY (4.0)"},"ddc":["000"],"date_updated":"2023-08-21T07:05:47Z","department":[{"_id":"MoHe"}],"file_date_updated":"2023-08-21T07:04:36Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The maximization of submodular functions have found widespread application in areas such as machine learning, combinatorial optimization, and economics, where practitioners often wish to enforce various constraints; the matroid constraint has been investigated extensively due to its algorithmic properties and expressive power. Though tight approximation algorithms for general matroid constraints exist in theory, the running times of such algorithms typically scale quadratically, and are not practical for truly large scale settings. Recent progress has focused on fast algorithms for important classes of matroids given in explicit form. Currently, nearly-linear time algorithms only exist for graphic and partition matroids [Alina Ene and Huy L. Nguyen, 2019]. In this work, we develop algorithms for monotone submodular maximization constrained by graphic, transversal matroids, or laminar matroids in time near-linear in the size of their representation. Our algorithms achieve an optimal approximation of 1-1/e-ε and both generalize and accelerate the results of Ene and Nguyen [Alina Ene and Huy L. Nguyen, 2019]. In fact, the running time of our algorithm cannot be improved within the fast continuous greedy framework of Badanidiyuru and Vondrák [Ashwinkumar Badanidiyuru and Jan Vondrák, 2014].\r\nTo achieve near-linear running time, we make use of dynamic data structures that maintain bases with approximate maximum cardinality and weight under certain element updates. These data structures need to support a weight decrease operation and a novel Freeze operation that allows the algorithm to freeze elements (i.e. force to be contained) in its basis regardless of future data structure operations. For the laminar matroid, we present a new dynamic data structure using the top tree interface of Alstrup, Holm, de Lichtenberg, and Thorup [Stephen Alstrup et al., 2005] that maintains the maximum weight basis under insertions and deletions of elements in O(log n) time. This data structure needs to support certain subtree query and path update operations that are performed every insertion and deletion that are non-trivial to handle in conjunction. For the transversal matroid the Freeze operation corresponds to requiring the data structure to keep a certain set S of vertices matched, a property that we call S-stability. While there is a large body of work on dynamic matching algorithms, none are S-stable and maintain an approximate maximum weight matching under vertex updates. We give the first such algorithm for bipartite graphs with total running time linear (up to log factors) in the number of edges."}],"month":"07","intvolume":" 261","alternative_title":["LIPIcs"],"scopus_import":"1","file":[{"file_id":"14090","checksum":"a5eef225014e003efbfbe4830fdd23cb","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-08-21T07:04:36Z","file_name":"2023_LIPIcsICALP_HenzingerM.pdf","creator":"dernst","date_updated":"2023-08-21T07:04:36Z","file_size":930943}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783959772785"],"issn":["18688969"]},"publication_status":"published","volume":261,"ec_funded":1},{"abstract":[{"lang":"eng","text":"In this work we consider the list-decodability and list-recoverability of arbitrary q-ary codes, for all integer values of q ≥ 2. A code is called (p,L)_q-list-decodable if every radius pn Hamming ball contains less than L codewords; (p,𝓁,L)_q-list-recoverability is a generalization where we place radius pn Hamming balls on every point of a combinatorial rectangle with side length 𝓁 and again stipulate that there be less than L codewords.\r\nOur main contribution is to precisely calculate the maximum value of p for which there exist infinite families of positive rate (p,𝓁,L)_q-list-recoverable codes, the quantity we call the zero-rate threshold. Denoting this value by p_*, we in fact show that codes correcting a p_*+ε fraction of errors must have size O_ε(1), i.e., independent of n. Such a result is typically referred to as a \"Plotkin bound.\" To complement this, a standard random code with expurgation construction shows that there exist positive rate codes correcting a p_*-ε fraction of errors. We also follow a classical proof template (typically attributed to Elias and Bassalygo) to derive from the zero-rate threshold other tradeoffs between rate and decoding radius for list-decoding and list-recovery.\r\nTechnically, proving the Plotkin bound boils down to demonstrating the Schur convexity of a certain function defined on the q-simplex as well as the convexity of a univariate function derived from it. We remark that an earlier argument claimed similar results for q-ary list-decoding; however, we point out that this earlier proof is flawed."}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LIPIcs"],"month":"07","intvolume":" 261","publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14091","checksum":"a449143fec3fbebb092cb8ef3b53c226","file_size":1141497,"date_updated":"2023-08-21T07:23:18Z","creator":"dernst","file_name":"2023_LIPIcsICALP_Resch.pdf","date_created":"2023-08-21T07:23:18Z"}],"language":[{"iso":"eng"}],"volume":261,"_id":"14083","type":"conference","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","end_date":"2023-07-14","location":"Paderborn, Germany","start_date":"2023-07-10"},"tmp":{"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)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-21T07:26:01Z","ddc":["000"],"department":[{"_id":"MaMo"}],"file_date_updated":"2023-08-21T07:23:18Z","acknowledgement":"Nicolas Resch: Research supported in part by ERC H2020 grant No.74079 (ALGSTRONGCRYPTO). Chen Yuan: Research supported in part by the National Key Research and Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the National Natural Science Foundation of China under Grant 12101403 and Grant 12031011.\r\nAcknowledgements YZ is grateful to Shashank Vatedka, Diyuan Wu and Fengxing Zhu for inspiring discussions.","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"50th International Colloquium on Automata, Languages, and Programming","doi":"10.4230/LIPIcs.ICALP.2023.99","date_published":"2023-07-01T00:00:00Z","date_created":"2023-08-20T22:01:13Z","article_number":"99","citation":{"ista":"Resch N, Yuan C, Zhang Y. 2023. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 99.","chicago":"Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.99.","ama":"Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.99","apa":"Resch, N., Yuan, C., & Zhang, Y. (2023). Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.99","short":"N. Resch, C. Yuan, Y. Zhang, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","mla":"Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.99."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Nicolas","last_name":"Resch","full_name":"Resch, Nicolas"},{"first_name":"Chen","last_name":"Yuan","full_name":"Yuan, Chen"},{"orcid":"0000-0002-6465-6258","full_name":"Zhang, Yihan","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","first_name":"Yihan"}],"external_id":{"arxiv":["2210.07754"]},"article_processing_charge":"Yes","title":"Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery"},{"_id":"12922","keyword":["General Chemistry","Catalysis"],"status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2023-08-21T09:18:12Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The influence of structural modifications on the catalytic activity of carbon materials is poorly understood. A collection of carbonaceous materials with different pore networks and high nitrogen content was characterized and used to catalyze four reactions to deduce structure–activity relationships. The CO2 cycloaddition and Knoevenagel reaction depend on Lewis basic sites (electron-rich nitrogen species). The absence of large conjugated carbon domains resulting from the introduction of large amounts of nitrogen in the carbon network is responsible for poor redox activity, as observed through the catalytic reduction of nitrobenzene with hydrazine and the catalytic oxidation of 3,3′,5,5′-tetramethylbenzidine using hydroperoxide. The material with the highest activity towards Lewis acid catalysis (in the hydrolysis of (dimethoxymethyl)benzene to benzaldehyde) is the most effective for small molecule activation and presents the highest concentration of electron-poor nitrogen species."}],"intvolume":" 62","month":"01","main_file_link":[{"url":"https://doi.org/10.1002/anie.202211663","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"issue":"2","volume":62,"article_number":"e202211663","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"E. Lepre, S. Rat, C. Cavedon, P.H. Seeberger, B. Pieber, M. Antonietti, N. López‐Salas, Angewandte Chemie International Edition 62 (2023).","ieee":"E. Lepre et al., “Catalytic properties of high nitrogen content carbonaceous materials,” Angewandte Chemie International Edition, vol. 62, no. 2. Wiley, 2023.","ama":"Lepre E, Rat S, Cavedon C, et al. Catalytic properties of high nitrogen content carbonaceous materials. Angewandte Chemie International Edition. 2023;62(2). doi:10.1002/anie.202211663","apa":"Lepre, E., Rat, S., Cavedon, C., Seeberger, P. H., Pieber, B., Antonietti, M., & López‐Salas, N. (2023). Catalytic properties of high nitrogen content carbonaceous materials. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202211663","mla":"Lepre, Enrico, et al. “Catalytic Properties of High Nitrogen Content Carbonaceous Materials.” Angewandte Chemie International Edition, vol. 62, no. 2, e202211663, Wiley, 2023, doi:10.1002/anie.202211663.","ista":"Lepre E, Rat S, Cavedon C, Seeberger PH, Pieber B, Antonietti M, López‐Salas N. 2023. Catalytic properties of high nitrogen content carbonaceous materials. Angewandte Chemie International Edition. 62(2), e202211663.","chicago":"Lepre, Enrico, Sylvain Rat, Cristian Cavedon, Peter H. Seeberger, Bartholomäus Pieber, Markus Antonietti, and Nieves López‐Salas. “Catalytic Properties of High Nitrogen Content Carbonaceous Materials.” Angewandte Chemie International Edition. Wiley, 2023. https://doi.org/10.1002/anie.202211663."},"title":"Catalytic properties of high nitrogen content carbonaceous materials","article_processing_charge":"No","author":[{"first_name":"Enrico","full_name":"Lepre, Enrico","last_name":"Lepre"},{"full_name":"Rat, Sylvain","last_name":"Rat","first_name":"Sylvain"},{"first_name":"Cristian","last_name":"Cavedon","full_name":"Cavedon, Cristian"},{"full_name":"Seeberger, Peter H.","last_name":"Seeberger","first_name":"Peter H."},{"first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus","last_name":"Pieber"},{"full_name":"Antonietti, Markus","last_name":"Antonietti","first_name":"Markus"},{"first_name":"Nieves","full_name":"López‐Salas, Nieves","last_name":"López‐Salas"}],"oa":1,"publisher":"Wiley","quality_controlled":"1","publication":"Angewandte Chemie International Edition","day":"09","year":"2023","date_created":"2023-05-08T08:28:14Z","doi":"10.1002/anie.202211663","date_published":"2023-01-09T00:00:00Z"},{"date_updated":"2023-08-21T12:07:05Z","extern":"1","article_type":"original","type":"journal_article","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"_id":"13450","volume":943,"issue":"1","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.3847/1538-4357/aca655","open_access":"1"}],"month":"01","intvolume":" 943","abstract":[{"lang":"eng","text":"In previous work, we identified a population of 38 cool and luminous variable stars in the Magellanic Clouds and examined 11 in detail in order to classify them as either Thorne–Żytkow objects (TŻOs; red supergiants with a neutron star cores) or super-asymptotic giant branch (sAGB) stars (the most massive stars that will not undergo core collapse). This population includes HV 2112, a peculiar star previously considered in other works to be either a TŻO or high-mass asymptotic giant branch (AGB) star. Here we continue this investigation, using the kinematic and radio environments and local star formation history of these stars to place constraints on the age of the progenitor systems and the presence of past supernovae. These stars are not associated with regions of recent star formation, and we find no evidence of past supernovae at their locations. Finally, we also assess the presence of heavy elements and lithium in their spectra compared to red supergiants. We find strong absorption in Li and s-process elements compared to RSGs in most of the sample, consistent with sAGB nucleosynthesis, while HV 2112 shows additional strong lines associated with TŻO nucleosynthesis. Coupled with our previous mass estimates, the results are consistent with the stars being massive (∼4–6.5 M⊙) or sAGB (∼6.5–12 M⊙) stars in the thermally pulsing phase, providing crucial observations of the transition between low- and high-mass stellar populations. HV 2112 is more ambiguous; it could either be a maximally massive sAGB star, or a TŻO if the minimum mass for stability extends down to ≲13 M⊙."}],"oa_version":"Published Version","author":[{"last_name":"O‘Grady","full_name":"O‘Grady, Anna J. G.","first_name":"Anna J. G."},{"first_name":"Maria R.","full_name":"Drout, Maria R.","last_name":"Drout"},{"full_name":"Gaensler, B. M.","last_name":"Gaensler","first_name":"B. M."},{"full_name":"Kochanek, C. S.","last_name":"Kochanek","first_name":"C. S."},{"full_name":"Neugent, Kathryn F.","last_name":"Neugent","first_name":"Kathryn F."},{"last_name":"Doherty","full_name":"Doherty, Carolyn L.","first_name":"Carolyn L."},{"first_name":"Joshua S.","full_name":"Speagle, Joshua S.","last_name":"Speagle"},{"first_name":"B. J.","last_name":"Shappee","full_name":"Shappee, B. J."},{"last_name":"Rauch","full_name":"Rauch, Michael","first_name":"Michael"},{"id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter","last_name":"Götberg","full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911"},{"first_name":"Bethany","last_name":"Ludwig","full_name":"Ludwig, Bethany"},{"full_name":"Thompson, Todd A.","last_name":"Thompson","first_name":"Todd A."}],"external_id":{"arxiv":["2211.12438"]},"article_processing_charge":"No","title":"Cool, luminous, and highly variable stars in the Magellanic Clouds. II. Spectroscopic and environmental analysis of Thorne–Żytkow object and super-AGB star candidates","citation":{"ista":"O‘Grady AJG, Drout MR, Gaensler BM, Kochanek CS, Neugent KF, Doherty CL, Speagle JS, Shappee BJ, Rauch M, Götberg YLL, Ludwig B, Thompson TA. 2023. Cool, luminous, and highly variable stars in the Magellanic Clouds. II. Spectroscopic and environmental analysis of Thorne–Żytkow object and super-AGB star candidates. The Astrophysical Journal. 943(1), 18.","chicago":"O‘Grady, Anna J. G., Maria R. Drout, B. M. Gaensler, C. S. Kochanek, Kathryn F. Neugent, Carolyn L. Doherty, Joshua S. Speagle, et al. “Cool, Luminous, and Highly Variable Stars in the Magellanic Clouds. II. Spectroscopic and Environmental Analysis of Thorne–Żytkow Object and Super-AGB Star Candidates.” The Astrophysical Journal. American Astronomical Society, 2023. https://doi.org/10.3847/1538-4357/aca655.","apa":"O‘Grady, A. J. G., Drout, M. R., Gaensler, B. M., Kochanek, C. S., Neugent, K. F., Doherty, C. L., … Thompson, T. A. (2023). Cool, luminous, and highly variable stars in the Magellanic Clouds. II. Spectroscopic and environmental analysis of Thorne–Żytkow object and super-AGB star candidates. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/aca655","ama":"O‘Grady AJG, Drout MR, Gaensler BM, et al. Cool, luminous, and highly variable stars in the Magellanic Clouds. II. Spectroscopic and environmental analysis of Thorne–Żytkow object and super-AGB star candidates. The Astrophysical Journal. 2023;943(1). doi:10.3847/1538-4357/aca655","short":"A.J.G. O‘Grady, M.R. Drout, B.M. Gaensler, C.S. Kochanek, K.F. Neugent, C.L. Doherty, J.S. Speagle, B.J. Shappee, M. Rauch, Y.L.L. Götberg, B. Ludwig, T.A. Thompson, The Astrophysical Journal 943 (2023).","ieee":"A. J. G. O‘Grady et al., “Cool, luminous, and highly variable stars in the Magellanic Clouds. II. Spectroscopic and environmental analysis of Thorne–Żytkow object and super-AGB star candidates,” The Astrophysical Journal, vol. 943, no. 1. American Astronomical Society, 2023.","mla":"O‘Grady, Anna J. G., et al. “Cool, Luminous, and Highly Variable Stars in the Magellanic Clouds. II. Spectroscopic and Environmental Analysis of Thorne–Żytkow Object and Super-AGB Star Candidates.” The Astrophysical Journal, vol. 943, no. 1, 18, American Astronomical Society, 2023, doi:10.3847/1538-4357/aca655."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"18","doi":"10.3847/1538-4357/aca655","date_published":"2023-01-20T00:00:00Z","date_created":"2023-08-03T10:10:12Z","year":"2023","day":"20","publication":"The Astrophysical Journal","quality_controlled":"1","publisher":"American Astronomical Society","oa":1},{"oa":1,"publisher":"IOP Publishing","quality_controlled":"1","publication":"Publications of the Astronomical Society of the Pacific","day":"09","year":"2023","date_created":"2023-08-03T10:09:57Z","date_published":"2023-03-09T00:00:00Z","doi":"10.1088/1538-3873/acb6b5","article_number":"021001","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Geen, Sam, Poojan Agrawal, Paul A. Crowther, B. W. Keller, Alex de Koter, Zsolt Keszthelyi, Freeke van de Voort, et al. “Bringing Stellar Evolution and Feedback Together: Summary of Proposals from the Lorentz Center Workshop.” Publications of the Astronomical Society of the Pacific. IOP Publishing, 2023. https://doi.org/10.1088/1538-3873/acb6b5.","ista":"Geen S, Agrawal P, Crowther PA, Keller BW, de Koter A, Keszthelyi Z, van de Voort F, Ali AA, Backs F, Bonne L, Brugaletta V, Derkink A, Ekström S, Fichtner YA, Grassitelli L, Götberg YLL, Higgins ER, Laplace E, You Liow K, Lorenzo M, McLeod AF, Meynet G, Newsome M, André Oliva G, Ramachandran V, Rey MP, Rieder S, Romano-Díaz E, Sabhahit G, Sander AAC, Sarwar R, Stinshoff H, Stoop M, Szécsi D, Trebitsch M, Vink JS, Winch E. 2023. Bringing stellar evolution and feedback together: Summary of proposals from the Lorentz Center workshop. Publications of the Astronomical Society of the Pacific. 135(1044), 021001.","mla":"Geen, Sam, et al. “Bringing Stellar Evolution and Feedback Together: Summary of Proposals from the Lorentz Center Workshop.” Publications of the Astronomical Society of the Pacific, vol. 135, no. 1044, 021001, IOP Publishing, 2023, doi:10.1088/1538-3873/acb6b5.","ama":"Geen S, Agrawal P, Crowther PA, et al. Bringing stellar evolution and feedback together: Summary of proposals from the Lorentz Center workshop. Publications of the Astronomical Society of the Pacific. 2023;135(1044). doi:10.1088/1538-3873/acb6b5","apa":"Geen, S., Agrawal, P., Crowther, P. A., Keller, B. W., de Koter, A., Keszthelyi, Z., … Winch, E. (2023). Bringing stellar evolution and feedback together: Summary of proposals from the Lorentz Center workshop. Publications of the Astronomical Society of the Pacific. IOP Publishing. https://doi.org/10.1088/1538-3873/acb6b5","short":"S. Geen, P. Agrawal, P.A. Crowther, B.W. Keller, A. de Koter, Z. Keszthelyi, F. van de Voort, A.A. Ali, F. Backs, L. Bonne, V. Brugaletta, A. Derkink, S. Ekström, Y.A. Fichtner, L. Grassitelli, Y.L.L. Götberg, E.R. Higgins, E. Laplace, K. You Liow, M. Lorenzo, A.F. McLeod, G. Meynet, M. Newsome, G. André Oliva, V. Ramachandran, M.P. Rey, S. Rieder, E. Romano-Díaz, G. Sabhahit, A.A.C. Sander, R. Sarwar, H. Stinshoff, M. Stoop, D. Szécsi, M. Trebitsch, J.S. Vink, E. Winch, Publications of the Astronomical Society of the Pacific 135 (2023).","ieee":"S. Geen et al., “Bringing stellar evolution and feedback together: Summary of proposals from the Lorentz Center workshop,” Publications of the Astronomical Society of the Pacific, vol. 135, no. 1044. IOP Publishing, 2023."},"title":"Bringing stellar evolution and feedback together: Summary of proposals from the Lorentz Center workshop","article_processing_charge":"No","external_id":{"arxiv":["2301.13611"]},"author":[{"first_name":"Sam","full_name":"Geen, Sam","last_name":"Geen"},{"full_name":"Agrawal, Poojan","last_name":"Agrawal","first_name":"Poojan"},{"first_name":"Paul A.","full_name":"Crowther, Paul A.","last_name":"Crowther"},{"last_name":"Keller","full_name":"Keller, B. W.","first_name":"B. W."},{"last_name":"de Koter","full_name":"de Koter, Alex","first_name":"Alex"},{"last_name":"Keszthelyi","full_name":"Keszthelyi, Zsolt","first_name":"Zsolt"},{"first_name":"Freeke","full_name":"van de Voort, Freeke","last_name":"van de Voort"},{"first_name":"Ahmad A.","full_name":"Ali, Ahmad A.","last_name":"Ali"},{"first_name":"Frank","last_name":"Backs","full_name":"Backs, Frank"},{"full_name":"Bonne, Lars","last_name":"Bonne","first_name":"Lars"},{"first_name":"Vittoria","full_name":"Brugaletta, Vittoria","last_name":"Brugaletta"},{"first_name":"Annelotte","full_name":"Derkink, Annelotte","last_name":"Derkink"},{"first_name":"Sylvia","last_name":"Ekström","full_name":"Ekström, Sylvia"},{"first_name":"Yvonne A.","full_name":"Fichtner, Yvonne A.","last_name":"Fichtner"},{"full_name":"Grassitelli, Luca","last_name":"Grassitelli","first_name":"Luca"},{"last_name":"Götberg","orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"first_name":"Erin R.","last_name":"Higgins","full_name":"Higgins, Erin R."},{"last_name":"Laplace","full_name":"Laplace, Eva","first_name":"Eva"},{"first_name":"Kong","full_name":"You Liow, Kong","last_name":"You Liow"},{"last_name":"Lorenzo","full_name":"Lorenzo, Marta","first_name":"Marta"},{"last_name":"McLeod","full_name":"McLeod, Anna F.","first_name":"Anna F."},{"first_name":"Georges","last_name":"Meynet","full_name":"Meynet, Georges"},{"last_name":"Newsome","full_name":"Newsome, Megan","first_name":"Megan"},{"first_name":"G.","full_name":"André Oliva, G.","last_name":"André Oliva"},{"full_name":"Ramachandran, Varsha","last_name":"Ramachandran","first_name":"Varsha"},{"first_name":"Martin P.","last_name":"Rey","full_name":"Rey, Martin P."},{"full_name":"Rieder, Steven","last_name":"Rieder","first_name":"Steven"},{"first_name":"Emilio","last_name":"Romano-Díaz","full_name":"Romano-Díaz, Emilio"},{"last_name":"Sabhahit","full_name":"Sabhahit, Gautham","first_name":"Gautham"},{"full_name":"Sander, Andreas A. C.","last_name":"Sander","first_name":"Andreas A. C."},{"first_name":"Rafia","full_name":"Sarwar, Rafia","last_name":"Sarwar"},{"first_name":"Hanno","full_name":"Stinshoff, Hanno","last_name":"Stinshoff"},{"full_name":"Stoop, Mitchel","last_name":"Stoop","first_name":"Mitchel"},{"first_name":"Dorottya","last_name":"Szécsi","full_name":"Szécsi, Dorottya"},{"last_name":"Trebitsch","full_name":"Trebitsch, Maxime","first_name":"Maxime"},{"last_name":"Vink","full_name":"Vink, Jorick S.","first_name":"Jorick S."},{"last_name":"Winch","full_name":"Winch, Ethan","first_name":"Ethan"}],"oa_version":"Published Version","abstract":[{"text":"Stars strongly impact their environment, and shape structures on all scales throughout the universe, in a process known as \"feedback.\" Due to the complexity of both stellar evolution and the physics of larger astrophysical structures, there remain many unanswered questions about how feedback operates and what we can learn about stars by studying their imprint on the wider universe. In this white paper, we summarize discussions from the Lorentz Center meeting \"Bringing Stellar Evolution and Feedback Together\" in 2022 April and identify key areas where further dialog can bring about radical changes in how we view the relationship between stars and the universe they live in.","lang":"eng"}],"intvolume":" 135","month":"03","main_file_link":[{"url":"https://doi.org/10.1088/1538-3873/acb6b5","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0004-6280"],"eissn":["1538-3873"]},"volume":135,"issue":"1044","_id":"13449","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2023-08-21T12:09:14Z"},{"quality_controlled":"1","publisher":"Oxford University Press","oa":1,"year":"2023","day":"01","publication":"Monthly Notices of the Royal Astronomical Society","page":"1692-1709","date_published":"2023-09-01T00:00:00Z","doi":"10.1093/mnras/stad1977","date_created":"2023-08-21T10:13:56Z","citation":{"ista":"Farmer R, Renzo M, Götberg YLL, Bellinger E, Justham S, de Mink SE. 2023. Observational predictions for Thorne–Żytkow objects. Monthly Notices of the Royal Astronomical Society. 524(2), 1692–1709.","chicago":"Farmer, R, M Renzo, Ylva Louise Linsdotter Götberg, E Bellinger, S Justham, and S E de Mink. “Observational Predictions for Thorne–Żytkow Objects.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2023. https://doi.org/10.1093/mnras/stad1977.","ama":"Farmer R, Renzo M, Götberg YLL, Bellinger E, Justham S, de Mink SE. Observational predictions for Thorne–Żytkow objects. Monthly Notices of the Royal Astronomical Society. 2023;524(2):1692-1709. doi:10.1093/mnras/stad1977","apa":"Farmer, R., Renzo, M., Götberg, Y. L. L., Bellinger, E., Justham, S., & de Mink, S. E. (2023). Observational predictions for Thorne–Żytkow objects. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stad1977","short":"R. Farmer, M. Renzo, Y.L.L. Götberg, E. Bellinger, S. Justham, S.E. de Mink, Monthly Notices of the Royal Astronomical Society 524 (2023) 1692–1709.","ieee":"R. Farmer, M. Renzo, Y. L. L. Götberg, E. Bellinger, S. Justham, and S. E. de Mink, “Observational predictions for Thorne–Żytkow objects,” Monthly Notices of the Royal Astronomical Society, vol. 524, no. 2. Oxford University Press, pp. 1692–1709, 2023.","mla":"Farmer, R., et al. “Observational Predictions for Thorne–Żytkow Objects.” Monthly Notices of the Royal Astronomical Society, vol. 524, no. 2, Oxford University Press, 2023, pp. 1692–709, doi:10.1093/mnras/stad1977."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Farmer","full_name":"Farmer, R","first_name":"R"},{"last_name":"Renzo","full_name":"Renzo, M","first_name":"M"},{"last_name":"Götberg","full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter"},{"full_name":"Bellinger, E","last_name":"Bellinger","first_name":"E"},{"first_name":"S","last_name":"Justham","full_name":"Justham, S"},{"first_name":"S E","full_name":"de Mink, S E","last_name":"de Mink"}],"article_processing_charge":"No","external_id":{"arxiv":["2305.07337"]},"title":"Observational predictions for Thorne–Żytkow objects","abstract":[{"text":"Thorne–Żytkow objects (TŻO) are potential end products of the merger of a neutron star with a non-degenerate star. In this work, we have computed the first grid of evolutionary models of TŻOs with the MESA stellar evolution code. With these models, we predict several observational properties of TŻOs, including their surface temperatures and luminosities, pulsation periods, and nucleosynthetic products. We expand the range of possible TŻO solutions to cover 3.45≲log(Teff/K)≲3.65 and 4.85≲log(L/L⊙)≲5.5. Due to the much higher densities our TŻOs reach compared to previous models, if TŻOs form we expect them to be stable over a larger mass range than previously predicted, without exhibiting a gap in their mass distribution. Using the GYRE stellar pulsation code we show that TŻOs should have fundamental pulsation periods of 1000–2000 d, and period ratios of ≈0.2–0.3. Models computed with a large 399 isotope fully coupled nuclear network show a nucleosynthetic signal that is different to previously predicted. We propose a new nucleosynthetic signal to determine a star’s status as a TŻO: the isotopologues 44TiO2 and 44TiO, which will have a shift in their spectral features as compared to stable titanium-containing molecules. We find that in the local Universe (∼SMC metallicities and above) TŻOs show little heavy metal enrichment, potentially explaining the difficulty in finding TŻOs to-date.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2305.07337"}],"month":"09","intvolume":" 524","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"2","volume":524,"_id":"14104","article_type":"original","type":"journal_article","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"date_updated":"2023-08-21T12:12:48Z","extern":"1"},{"date_updated":"2023-08-22T06:50:04Z","extern":"1","_id":"13989","article_type":"original","type":"journal_article","status":"public","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":14,"abstract":[{"text":"Characterizing and controlling entanglement in quantum materials is crucial for the development of next-generation quantum technologies. However, defining a quantifiable figure of merit for entanglement in macroscopic solids is theoretically and experimentally challenging. At equilibrium the presence of entanglement can be diagnosed by extracting entanglement witnesses from spectroscopic observables and a nonequilibrium extension of this method could lead to the discovery of novel dynamical phenomena. Here, we propose a systematic approach to quantify the time-dependent quantum Fisher information and entanglement depth of transient states of quantum materials with time-resolved resonant inelastic x-ray scattering. Using a quarter-filled extended Hubbard model as an example, we benchmark the efficiency of this approach and predict a light-enhanced many-body entanglement due to the proximity to a phase boundary. Our work sets the stage for experimentally witnessing and controlling entanglement in light-driven quantum materials via ultrafast spectroscopic measurements.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-023-38540-3"}],"month":"06","intvolume":" 14","citation":{"mla":"Hales, Jordyn, et al. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” Nature Communications, vol. 14, 3512, Springer Nature, 2023, doi:10.1038/s41467-023-38540-3.","apa":"Hales, J., Bajpai, U., Liu, T., Baykusheva, D. R., Li, M., Mitrano, M., & Wang, Y. (2023). Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38540-3","ama":"Hales J, Bajpai U, Liu T, et al. Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. Nature Communications. 2023;14. doi:10.1038/s41467-023-38540-3","short":"J. Hales, U. Bajpai, T. Liu, D.R. Baykusheva, M. Li, M. Mitrano, Y. Wang, Nature Communications 14 (2023).","ieee":"J. Hales et al., “Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering,” Nature Communications, vol. 14. Springer Nature, 2023.","chicago":"Hales, Jordyn, Utkarsh Bajpai, Tongtong Liu, Denitsa Rangelova Baykusheva, Mingda Li, Matteo Mitrano, and Yao Wang. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38540-3.","ista":"Hales J, Bajpai U, Liu T, Baykusheva DR, Li M, Mitrano M, Wang Y. 2023. Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. Nature Communications. 14, 3512."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jordyn","last_name":"Hales","full_name":"Hales, Jordyn"},{"first_name":"Utkarsh","full_name":"Bajpai, Utkarsh","last_name":"Bajpai"},{"first_name":"Tongtong","full_name":"Liu, Tongtong","last_name":"Liu"},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova"},{"first_name":"Mingda","last_name":"Li","full_name":"Li, Mingda"},{"first_name":"Matteo","full_name":"Mitrano, Matteo","last_name":"Mitrano"},{"first_name":"Yao","last_name":"Wang","full_name":"Wang, Yao"}],"article_processing_charge":"No","external_id":{"arxiv":["2209.02283"],"pmid":["37316515"]},"title":"Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering","article_number":"3512","year":"2023","day":"14","publication":"Nature Communications","date_published":"2023-06-14T00:00:00Z","doi":"10.1038/s41467-023-38540-3","date_created":"2023-08-09T13:06:59Z","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"10","volume":130,"abstract":[{"lang":"eng","text":"Many-body entanglement in condensed matter systems can be diagnosed from equilibrium response functions through the use of entanglement witnesses and operator-specific quantum bounds. Here, we investigate the applicability of this approach for detecting entangled states in quantum systems driven out of equilibrium. We use a multipartite entanglement witness, the quantum Fisher information, to study the dynamics of a paradigmatic fermion chain undergoing a time-dependent change of the Coulomb interaction. Our results show that the quantum Fisher information is able to witness distinct signatures of multipartite entanglement both near and far from equilibrium that are robust against decoherence. We discuss implications of these findings for probing entanglement in light-driven quantum materials with time-resolved optical and x-ray scattering methods."}],"oa_version":"Preprint","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2209.02081"}],"month":"03","intvolume":" 130","date_updated":"2023-08-22T07:18:01Z","extern":"1","_id":"13990","article_type":"original","type":"journal_article","status":"public","keyword":["General Physics and Astronomy"],"year":"2023","day":"10","publication":"Physical Review Letters","doi":"10.1103/physrevlett.130.106902","date_published":"2023-03-10T00:00:00Z","date_created":"2023-08-09T13:07:24Z","quality_controlled":"1","publisher":"American Physical Society","oa":1,"citation":{"short":"D.R. Baykusheva, M.H. Kalthoff, D. Hofmann, M. Claassen, D.M. Kennes, M.A. Sentef, M. Mitrano, Physical Review Letters 130 (2023).","ieee":"D. R. Baykusheva et al., “Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.","ama":"Baykusheva DR, Kalthoff MH, Hofmann D, et al. Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain. Physical Review Letters. 2023;130(10). doi:10.1103/physrevlett.130.106902","apa":"Baykusheva, D. R., Kalthoff, M. H., Hofmann, D., Claassen, M., Kennes, D. M., Sentef, M. A., & Mitrano, M. (2023). Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.106902","mla":"Baykusheva, Denitsa Rangelova, et al. “Witnessing Nonequilibrium Entanglement Dynamics in a Strongly Correlated Fermionic Chain.” Physical Review Letters, vol. 130, no. 10, 106902, American Physical Society, 2023, doi:10.1103/physrevlett.130.106902.","ista":"Baykusheva DR, Kalthoff MH, Hofmann D, Claassen M, Kennes DM, Sentef MA, Mitrano M. 2023. Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain. Physical Review Letters. 130(10), 106902.","chicago":"Baykusheva, Denitsa Rangelova, Mona H. Kalthoff, Damian Hofmann, Martin Claassen, Dante M. Kennes, Michael A. Sentef, and Matteo Mitrano. “Witnessing Nonequilibrium Entanglement Dynamics in a Strongly Correlated Fermionic Chain.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106902."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"first_name":"Mona H.","full_name":"Kalthoff, Mona H.","last_name":"Kalthoff"},{"full_name":"Hofmann, Damian","last_name":"Hofmann","first_name":"Damian"},{"first_name":"Martin","last_name":"Claassen","full_name":"Claassen, Martin"},{"full_name":"Kennes, Dante M.","last_name":"Kennes","first_name":"Dante M."},{"first_name":"Michael A.","last_name":"Sentef","full_name":"Sentef, Michael A."},{"first_name":"Matteo","full_name":"Mitrano, Matteo","last_name":"Mitrano"}],"article_processing_charge":"No","external_id":{"arxiv":["2209.02081"],"pmid":["36962013"]},"title":"Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain","article_number":"106902"},{"abstract":[{"text":"Models for same-material contact electrification in granular media often rely on a local charge-driving parameter whose spatial variations lead to a stochastic origin for charge exchange. Measuring the charge transfer from individual granular spheres after contacts with substrates of the same material, we find instead a “global” charging behavior, coherent over the sample’s whole surface. Cleaning and baking samples fully resets charging magnitude and direction, which indicates the underlying global parameter is not intrinsic to the material, but acquired from its history. Charging behavior is randomly and irreversibly affected by changes in relative humidity, hinting at a mechanism where adsorbates, in particular, water, are fundamental to the charge-transfer process.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2211.02488","open_access":"1"}],"month":"03","intvolume":" 130","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publication_status":"published","file":[{"file_id":"12698","checksum":"c4f2f6eea0408811f8f4898e15890355","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-02-28T12:20:27Z","file_name":"Main_Preprint.pdf","creator":"ggrosjea","date_updated":"2023-02-28T12:20:27Z","file_size":2301864},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"6af6ed6c97a977f923de4162294b43c4","file_id":"12699","creator":"ggrosjea","file_size":1138625,"date_updated":"2023-02-28T12:20:55Z","file_name":"Suppl_info.pdf","date_created":"2023-02-28T12:20:55Z"},{"file_name":"Suppl_vid1.mp4","date_created":"2023-02-28T12:37:54Z","creator":"ggrosjea","file_size":793449,"date_updated":"2023-02-28T12:37:54Z","success":1,"checksum":"3f20365fb9515bdba3a111d912c8d8b4","file_id":"12700","relation":"main_file","access_level":"open_access","content_type":"video/mp4"},{"checksum":"90cecacbe0e2f9dea11f91a4ba20c32e","file_id":"12701","success":1,"access_level":"open_access","relation":"main_file","content_type":"video/mp4","date_created":"2023-02-28T12:37:54Z","file_name":"Suppl_vid2.mp4","creator":"ggrosjea","date_updated":"2023-02-28T12:37:54Z","file_size":455925}],"language":[{"iso":"eng"}],"volume":130,"related_material":{"record":[{"status":"public","id":"8101","relation":"research_paper"}]},"issue":"9","ec_funded":1,"_id":"12697","type":"journal_article","article_type":"original","tmp":{"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)","short":"CC BY (4.0)"},"status":"public","keyword":["General Physics","Electrostatics","Triboelectricity","Soft Matter","Acoustic Levitation","Granular Materials"],"date_updated":"2023-08-22T08:41:32Z","ddc":["530","537"],"department":[{"_id":"ScWa"}],"file_date_updated":"2023-02-28T12:37:54Z","acknowledgement":"We would like to thank Troy Shinbrot, Victor Lee and Daniele Foresti for helpful discussions. This project has received funding from the European Research Council Grant Agreement No. 949120 and from the the Marie Sk lodowska-Curie Grant Agreement No. 754411 under\r\nthe European Union’s Horizon 2020 research and innovation program.","publisher":"American Physical Society","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2023","day":"03","publication":"Physical Review Letters","date_published":"2023-03-03T00:00:00Z","doi":"10.1103/physrevlett.130.098202","date_created":"2023-02-28T12:14:46Z","article_number":"098202","project":[{"call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"citation":{"mla":"Grosjean, Galien M., and Scott R. Waitukaitis. “Single-Collision Statistics Reveal a Global Mechanism Driven by Sample History for Contact Electrification in Granular Media.” Physical Review Letters, vol. 130, no. 9, 098202, American Physical Society, 2023, doi:10.1103/physrevlett.130.098202.","short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Letters 130 (2023).","ieee":"G. M. Grosjean and S. R. Waitukaitis, “Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media,” Physical Review Letters, vol. 130, no. 9. American Physical Society, 2023.","apa":"Grosjean, G. M., & Waitukaitis, S. R. (2023). Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.098202","ama":"Grosjean GM, Waitukaitis SR. Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. Physical Review Letters. 2023;130(9). doi:10.1103/physrevlett.130.098202","chicago":"Grosjean, Galien M, and Scott R Waitukaitis. “Single-Collision Statistics Reveal a Global Mechanism Driven by Sample History for Contact Electrification in Granular Media.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.098202.","ista":"Grosjean GM, Waitukaitis SR. 2023. Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. Physical Review Letters. 130(9), 098202."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0001-5154-417X","full_name":"Grosjean, Galien M","last_name":"Grosjean","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","first_name":"Galien M"},{"last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R"}],"article_processing_charge":"No","external_id":{"isi":["000946178200008"],"arxiv":["2211.02488"]},"title":"Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media"},{"date_updated":"2023-08-22T11:01:07Z","extern":"1","article_type":"original","type":"journal_article","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"_id":"14103","volume":675,"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/202245650"}],"month":"07","intvolume":" 675","abstract":[{"lang":"eng","text":"Observations of individual massive stars, super-luminous supernovae, gamma-ray bursts, and gravitational wave events involving spectacular black hole mergers indicate that the low-metallicity Universe is fundamentally different from our own Galaxy. Many transient phenomena will remain enigmatic until we achieve a firm understanding of the physics and evolution of massive stars at low metallicity (Z). The Hubble Space Telescope has devoted 500 orbits to observing ∼250 massive stars at low Z in the ultraviolet (UV) with the COS and STIS spectrographs under the ULLYSES programme. The complementary X-Shooting ULLYSES (XShootU) project provides an enhanced legacy value with high-quality optical and near-infrared spectra obtained with the wide-wavelength coverage X-shooter spectrograph at ESO’s Very Large Telescope. We present an overview of the XShootU project, showing that combining ULLYSES UV and XShootU optical spectra is critical for the uniform determination of stellar parameters such as effective temperature, surface gravity, luminosity, and abundances, as well as wind properties such as mass-loss rates as a function of Z. As uncertainties in stellar and wind parameters percolate into many adjacent areas of astrophysics, the data and modelling of the XShootU project is expected to be a game changer for our physical understanding of massive stars at low Z. To be able to confidently interpret James Webb Space Telescope spectra of the first stellar generations, the individual spectra of low-Z stars need to be understood, which is exactly where XShootU can deliver."}],"oa_version":"Published Version","author":[{"first_name":"Jorick S.","last_name":"Vink","full_name":"Vink, Jorick S."},{"full_name":"Mehner, A.","last_name":"Mehner","first_name":"A."},{"last_name":"Crowther","full_name":"Crowther, P. A.","first_name":"P. A."},{"first_name":"A.","last_name":"Fullerton","full_name":"Fullerton, A."},{"first_name":"M.","full_name":"Garcia, M.","last_name":"Garcia"},{"first_name":"F.","last_name":"Martins","full_name":"Martins, F."},{"first_name":"N.","last_name":"Morrell","full_name":"Morrell, N."},{"first_name":"L. M.","full_name":"Oskinova, L. M.","last_name":"Oskinova"},{"full_name":"St-Louis, N.","last_name":"St-Louis","first_name":"N."},{"first_name":"A.","full_name":"ud-Doula, A.","last_name":"ud-Doula"},{"first_name":"A. A. C.","full_name":"Sander, A. A. C.","last_name":"Sander"},{"full_name":"Sana, H.","last_name":"Sana","first_name":"H."},{"full_name":"Bouret, J.-C.","last_name":"Bouret","first_name":"J.-C."},{"first_name":"B.","last_name":"Kubátová","full_name":"Kubátová, B."},{"full_name":"Marchant, P.","last_name":"Marchant","first_name":"P."},{"first_name":"L. P.","last_name":"Martins","full_name":"Martins, L. P."},{"first_name":"A.","full_name":"Wofford, A.","last_name":"Wofford"},{"first_name":"J. Th.","last_name":"van Loon","full_name":"van Loon, J. Th."},{"first_name":"O.","full_name":"Grace Telford, O.","last_name":"Grace Telford"},{"first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","last_name":"Götberg","orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter"},{"last_name":"Bowman","full_name":"Bowman, D. M.","first_name":"D. M."},{"full_name":"Erba, C.","last_name":"Erba","first_name":"C."},{"full_name":"Kalari, V. M.","last_name":"Kalari","first_name":"V. M."},{"full_name":"Abdul-Masih, M.","last_name":"Abdul-Masih","first_name":"M."},{"first_name":"T.","full_name":"Alkousa, T.","last_name":"Alkousa"},{"full_name":"Backs, F.","last_name":"Backs","first_name":"F."},{"last_name":"Barbosa","full_name":"Barbosa, C. L.","first_name":"C. L."},{"last_name":"Berlanas","full_name":"Berlanas, S. R.","first_name":"S. R."},{"first_name":"M.","last_name":"Bernini-Peron","full_name":"Bernini-Peron, M."},{"full_name":"Bestenlehner, J. M.","last_name":"Bestenlehner","first_name":"J. M."},{"full_name":"Blomme, R.","last_name":"Blomme","first_name":"R."},{"full_name":"Bodensteiner, J.","last_name":"Bodensteiner","first_name":"J."},{"first_name":"S. A.","full_name":"Brands, S. A.","last_name":"Brands"},{"full_name":"Evans, C. J.","last_name":"Evans","first_name":"C. J."},{"first_name":"A.","full_name":"David-Uraz, A.","last_name":"David-Uraz"},{"first_name":"F. A.","last_name":"Driessen","full_name":"Driessen, F. A."},{"last_name":"Dsilva","full_name":"Dsilva, K.","first_name":"K."},{"first_name":"S.","full_name":"Geen, S.","last_name":"Geen"},{"first_name":"V. M. A.","full_name":"Gómez-González, V. M. A.","last_name":"Gómez-González"},{"first_name":"L.","last_name":"Grassitelli","full_name":"Grassitelli, L."},{"first_name":"W.-R.","last_name":"Hamann","full_name":"Hamann, W.-R."},{"full_name":"Hawcroft, C.","last_name":"Hawcroft","first_name":"C."},{"last_name":"Herrero","full_name":"Herrero, A.","first_name":"A."},{"last_name":"Higgins","full_name":"Higgins, E. R.","first_name":"E. R."},{"first_name":"D.","last_name":"John Hillier","full_name":"John Hillier, D."},{"first_name":"R.","last_name":"Ignace","full_name":"Ignace, R."},{"first_name":"A. G.","last_name":"Istrate","full_name":"Istrate, A. G."},{"first_name":"L.","full_name":"Kaper, L.","last_name":"Kaper"},{"full_name":"Kee, N. D.","last_name":"Kee","first_name":"N. D."},{"full_name":"Kehrig, C.","last_name":"Kehrig","first_name":"C."},{"first_name":"Z.","full_name":"Keszthelyi, Z.","last_name":"Keszthelyi"},{"last_name":"Klencki","full_name":"Klencki, J.","first_name":"J."},{"full_name":"de Koter, A.","last_name":"de Koter","first_name":"A."},{"full_name":"Kuiper, R.","last_name":"Kuiper","first_name":"R."},{"full_name":"Laplace, E.","last_name":"Laplace","first_name":"E."},{"full_name":"Larkin, C. J. K.","last_name":"Larkin","first_name":"C. J. K."},{"full_name":"Lefever, R. R.","last_name":"Lefever","first_name":"R. R."},{"full_name":"Leitherer, C.","last_name":"Leitherer","first_name":"C."},{"last_name":"Lennon","full_name":"Lennon, D. J.","first_name":"D. J."},{"first_name":"L.","full_name":"Mahy, L.","last_name":"Mahy"},{"first_name":"J.","full_name":"Maíz Apellániz, J.","last_name":"Maíz Apellániz"},{"full_name":"Maravelias, G.","last_name":"Maravelias","first_name":"G."},{"full_name":"Marcolino, W.","last_name":"Marcolino","first_name":"W."},{"last_name":"McLeod","full_name":"McLeod, A. F.","first_name":"A. F."},{"last_name":"de Mink","full_name":"de Mink, S. E.","first_name":"S. E."},{"first_name":"F.","last_name":"Najarro","full_name":"Najarro, F."},{"last_name":"Oey","full_name":"Oey, M. S.","first_name":"M. S."},{"first_name":"T. N.","last_name":"Parsons","full_name":"Parsons, T. N."},{"first_name":"D.","last_name":"Pauli","full_name":"Pauli, D."},{"full_name":"Pedersen, M. G.","last_name":"Pedersen","first_name":"M. G."},{"last_name":"Prinja","full_name":"Prinja, R. K.","first_name":"R. K."},{"first_name":"V.","full_name":"Ramachandran, V.","last_name":"Ramachandran"},{"last_name":"Ramírez-Tannus","full_name":"Ramírez-Tannus, M. C.","first_name":"M. C."},{"first_name":"G. N.","last_name":"Sabhahit","full_name":"Sabhahit, G. N."},{"full_name":"Schootemeijer, A.","last_name":"Schootemeijer","first_name":"A."},{"first_name":"S.","last_name":"Reyero Serantes","full_name":"Reyero Serantes, S."},{"last_name":"Shenar","full_name":"Shenar, T.","first_name":"T."},{"first_name":"G. S.","full_name":"Stringfellow, G. S.","last_name":"Stringfellow"},{"full_name":"Sudnik, N.","last_name":"Sudnik","first_name":"N."},{"full_name":"Tramper, F.","last_name":"Tramper","first_name":"F."},{"first_name":"L.","full_name":"Wang, L.","last_name":"Wang"}],"external_id":{"arxiv":["2305.06376"]},"article_processing_charge":"No","title":"X-shooting ULLYSES: Massive stars at low metallicity. I. Project description","citation":{"mla":"Vink, Jorick S., et al. “X-Shooting ULLYSES: Massive Stars at Low Metallicity. I. Project Description.” Astronomy & Astrophysics, vol. 675, A154, EDP Sciences, 2023, doi:10.1051/0004-6361/202245650.","ieee":"J. S. Vink et al., “X-shooting ULLYSES: Massive stars at low metallicity. I. Project description,” Astronomy & Astrophysics, vol. 675. EDP Sciences, 2023.","short":"J.S. Vink, A. Mehner, P.A. Crowther, A. Fullerton, M. Garcia, F. Martins, N. Morrell, L.M. Oskinova, N. St-Louis, A. ud-Doula, A.A.C. Sander, H. Sana, J.-C. Bouret, B. Kubátová, P. Marchant, L.P. Martins, A. Wofford, J.T. van Loon, O. Grace Telford, Y.L.L. Götberg, D.M. Bowman, C. Erba, V.M. Kalari, M. Abdul-Masih, T. Alkousa, F. Backs, C.L. Barbosa, S.R. Berlanas, M. Bernini-Peron, J.M. Bestenlehner, R. Blomme, J. Bodensteiner, S.A. Brands, C.J. Evans, A. David-Uraz, F.A. Driessen, K. Dsilva, S. Geen, V.M.A. Gómez-González, L. Grassitelli, W.-R. Hamann, C. Hawcroft, A. Herrero, E.R. Higgins, D. John Hillier, R. Ignace, A.G. Istrate, L. Kaper, N.D. Kee, C. Kehrig, Z. Keszthelyi, J. Klencki, A. de Koter, R. Kuiper, E. Laplace, C.J.K. Larkin, R.R. Lefever, C. Leitherer, D.J. Lennon, L. Mahy, J. Maíz Apellániz, G. Maravelias, W. Marcolino, A.F. McLeod, S.E. de Mink, F. Najarro, M.S. Oey, T.N. Parsons, D. Pauli, M.G. Pedersen, R.K. Prinja, V. Ramachandran, M.C. Ramírez-Tannus, G.N. Sabhahit, A. Schootemeijer, S. Reyero Serantes, T. Shenar, G.S. Stringfellow, N. Sudnik, F. Tramper, L. Wang, Astronomy & Astrophysics 675 (2023).","ama":"Vink JS, Mehner A, Crowther PA, et al. X-shooting ULLYSES: Massive stars at low metallicity. I. Project description. Astronomy & Astrophysics. 2023;675. doi:10.1051/0004-6361/202245650","apa":"Vink, J. S., Mehner, A., Crowther, P. A., Fullerton, A., Garcia, M., Martins, F., … Wang, L. (2023). X-shooting ULLYSES: Massive stars at low metallicity. I. Project description. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202245650","chicago":"Vink, Jorick S., A. Mehner, P. A. Crowther, A. Fullerton, M. Garcia, F. Martins, N. Morrell, et al. “X-Shooting ULLYSES: Massive Stars at Low Metallicity. I. Project Description.” Astronomy & Astrophysics. EDP Sciences, 2023. https://doi.org/10.1051/0004-6361/202245650.","ista":"Vink JS, Mehner A, Crowther PA, Fullerton A, Garcia M, Martins F, Morrell N, Oskinova LM, St-Louis N, ud-Doula A, Sander AAC, Sana H, Bouret J-C, Kubátová B, Marchant P, Martins LP, Wofford A, van Loon JT, Grace Telford O, Götberg YLL, Bowman DM, Erba C, Kalari VM, Abdul-Masih M, Alkousa T, Backs F, Barbosa CL, Berlanas SR, Bernini-Peron M, Bestenlehner JM, Blomme R, Bodensteiner J, Brands SA, Evans CJ, David-Uraz A, Driessen FA, Dsilva K, Geen S, Gómez-González VMA, Grassitelli L, Hamann W-R, Hawcroft C, Herrero A, Higgins ER, John Hillier D, Ignace R, Istrate AG, Kaper L, Kee ND, Kehrig C, Keszthelyi Z, Klencki J, de Koter A, Kuiper R, Laplace E, Larkin CJK, Lefever RR, Leitherer C, Lennon DJ, Mahy L, Maíz Apellániz J, Maravelias G, Marcolino W, McLeod AF, de Mink SE, Najarro F, Oey MS, Parsons TN, Pauli D, Pedersen MG, Prinja RK, Ramachandran V, Ramírez-Tannus MC, Sabhahit GN, Schootemeijer A, Reyero Serantes S, Shenar T, Stringfellow GS, Sudnik N, Tramper F, Wang L. 2023. X-shooting ULLYSES: Massive stars at low metallicity. I. Project description. Astronomy & Astrophysics. 675, A154."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"A154","doi":"10.1051/0004-6361/202245650","date_published":"2023-07-01T00:00:00Z","date_created":"2023-08-21T10:12:35Z","year":"2023","day":"01","publication":"Astronomy & Astrophysics","publisher":"EDP Sciences","quality_controlled":"1","oa":1},{"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-030-5"],"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"13176","checksum":"7d03f1a5a5258ee43dfc3323dea4e08f","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-06-30T08:17:25Z","file_name":"thesis_pdfa.pdf","date_updated":"2023-06-30T08:17:25Z","file_size":18688376,"creator":"cchlebak"},{"file_name":"thesis.zip","date_created":"2023-07-06T11:35:15Z","file_size":37847025,"date_updated":"2023-07-06T11:35:15Z","creator":"cchlebak","file_id":"13196","checksum":"c3b45317ae58e0527533f98c202d81b7","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"related_material":{"record":[{"relation":"old_edition","status":"public","id":"12900"},{"id":"10924","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9114"}]},"abstract":[{"lang":"eng","text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. "}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"05","date_updated":"2023-08-24T11:16:35Z","supervisor":[{"last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["537","535","539"],"file_date_updated":"2023-07-06T11:35:15Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"_id":"13175","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"status":"public","year":"2023","has_accepted_license":"1","day":"05","page":"202","date_created":"2023-06-30T08:07:43Z","doi":"10.15479/at:ista:13175","date_published":"2023-05-05T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","apa":"Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13175","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:13175","mla":"Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13175.","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13175."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh"}],"title":"Cavity quantum electrooptics","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}]},{"doi":"10.15479/at:ista:12900","date_published":"2023-05-05T00:00:00Z","date_created":"2023-05-05T11:08:50Z","page":"190","day":"05","has_accepted_license":"1","year":"2023","publisher":"Institute of Science and Technology Austria","title":"Cavity quantum electrooptics","author":[{"orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","last_name":"Sahu","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12900.","apa":"Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12900","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:12900","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","mla":"Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12900."},"project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"related_material":{"record":[{"id":"13175","status":"public","relation":"new_edition"},{"relation":"part_of_dissertation","status":"public","id":"10924"},{"relation":"part_of_dissertation","id":"9114","status":"public"}]},"ec_funded":1,"file":[{"file_name":"thesis.zip","date_created":"2023-05-09T08:45:14Z","creator":"rsahu","file_size":36767177,"date_updated":"2023-06-06T22:30:03Z","checksum":"8cbdab9c37ee55e591092a6f66b272c4","file_id":"12928","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/x-zip-compressed"},{"date_created":"2023-05-09T08:51:17Z","file_name":"thesis_pdfa_final.pdf","creator":"rsahu","date_updated":"2023-07-06T11:37:40Z","file_size":17501990,"file_id":"12929","checksum":"439659ead46618147309be39d9dd5a8c","access_level":"closed","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-030-5"]},"publication_status":"published","degree_awarded":"PhD","month":"05","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"abstract":[{"text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. ","lang":"eng"}],"file_date_updated":"2023-07-06T11:37:40Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"ddc":["537","535","539"],"supervisor":[{"last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-24T11:16:35Z","status":"public","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"_id":"12900"},{"project":[{"grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Lechner, Mathias, et al. “Quantization-Aware Interval Bound Propagation for Training Certifiably Robust Quantized Neural Networks.” Proceedings of the 37th AAAI Conference on Artificial Intelligence, vol. 37, no. 12, Association for the Advancement of Artificial Intelligence, 2023, pp. 14964–73, doi:10.1609/aaai.v37i12.26747.","ama":"Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. In: Proceedings of the 37th AAAI Conference on Artificial Intelligence. Vol 37. Association for the Advancement of Artificial Intelligence; 2023:14964-14973. doi:10.1609/aaai.v37i12.26747","apa":"Lechner, M., Zikelic, D., Chatterjee, K., Henzinger, T. A., & Rus, D. (2023). Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. In Proceedings of the 37th AAAI Conference on Artificial Intelligence (Vol. 37, pp. 14964–14973). Washington, DC, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v37i12.26747","ieee":"M. Lechner, D. Zikelic, K. Chatterjee, T. A. Henzinger, and D. Rus, “Quantization-aware interval bound propagation for training certifiably robust quantized neural networks,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence, Washington, DC, United States, 2023, vol. 37, no. 12, pp. 14964–14973.","short":"M. Lechner, D. Zikelic, K. Chatterjee, T.A. Henzinger, D. Rus, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2023, pp. 14964–14973.","chicago":"Lechner, Mathias, Dorde Zikelic, Krishnendu Chatterjee, Thomas A Henzinger, and Daniela Rus. “Quantization-Aware Interval Bound Propagation for Training Certifiably Robust Quantized Neural Networks.” In Proceedings of the 37th AAAI Conference on Artificial Intelligence, 37:14964–73. Association for the Advancement of Artificial Intelligence, 2023. https://doi.org/10.1609/aaai.v37i12.26747.","ista":"Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. 2023. Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 14964–14973."},"title":"Quantization-aware interval bound propagation for training certifiably robust quantized neural networks","external_id":{"arxiv":["2211.16187"]},"article_processing_charge":"No","author":[{"full_name":"Lechner, Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias"},{"first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniela","last_name":"Rus","full_name":"Rus, Daniela"}],"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Research was sponsored by the United\r\nStates Air Force Research Laboratory and the United States Air Force Artificial Intelligence Accelerator and was accomplished under Cooperative Agreement Number FA8750-19-2-\r\n1000. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied,\r\nof the United States Air Force or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright\r\nnotation herein. The research was also funded in part by the AI2050 program at Schmidt Futures (Grant G-22-63172) and Capgemini SE.","oa":1,"quality_controlled":"1","publisher":"Association for the Advancement of Artificial Intelligence","publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","day":"26","year":"2023","date_created":"2023-08-27T22:01:17Z","doi":"10.1609/aaai.v37i12.26747","date_published":"2023-06-26T00:00:00Z","page":"14964-14973","_id":"14242","status":"public","conference":{"location":"Washington, DC, United States","end_date":"2023-02-14","start_date":"2023-02-07","name":"AAAI: Conference on Artificial Intelligence"},"type":"conference","date_updated":"2023-09-05T07:06:14Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study the problem of training and certifying adversarially robust quantized neural networks (QNNs). Quantization is a technique for making neural networks more efficient by running them using low-bit integer arithmetic and is therefore commonly adopted in industry. Recent work has shown that floating-point neural networks that have been verified to be robust can become vulnerable to adversarial attacks after quantization, and certification of the quantized representation is necessary to guarantee robustness. In this work, we present quantization-aware interval bound propagation (QA-IBP), a novel method for training robust QNNs. Inspired by advances in robust learning of non-quantized networks, our training algorithm computes the gradient of an abstract representation of the actual network. Unlike existing approaches, our method can handle the discrete semantics of QNNs. Based on QA-IBP, we also develop a complete verification procedure for verifying the adversarial robustness of QNNs, which is guaranteed to terminate and produce a correct answer. Compared to existing approaches, the key advantage of our verification procedure is that it runs entirely on GPU or other accelerator devices. We demonstrate experimentally that our approach significantly outperforms existing methods and establish the new state-of-the-art for training and certifying the robustness of QNNs."}],"intvolume":" 37","month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.16187"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781577358800"]},"ec_funded":1,"issue":"12","volume":37},{"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Avni G, Jecker IR, Zikelic D. 2023. Bidding graph games with partially-observable budgets. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 5464–5471.","chicago":"Avni, Guy, Ismael R Jecker, and Dorde Zikelic. “Bidding Graph Games with Partially-Observable Budgets.” In Proceedings of the 37th AAAI Conference on Artificial Intelligence, 37:5464–71, 2023. https://doi.org/10.1609/aaai.v37i5.25679.","ama":"Avni G, Jecker IR, Zikelic D. Bidding graph games with partially-observable budgets. In: Proceedings of the 37th AAAI Conference on Artificial Intelligence. Vol 37. ; 2023:5464-5471. doi:10.1609/aaai.v37i5.25679","apa":"Avni, G., Jecker, I. R., & Zikelic, D. (2023). Bidding graph games with partially-observable budgets. In Proceedings of the 37th AAAI Conference on Artificial Intelligence (Vol. 37, pp. 5464–5471). Washington, DC, United States. https://doi.org/10.1609/aaai.v37i5.25679","short":"G. Avni, I.R. Jecker, D. Zikelic, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, 2023, pp. 5464–5471.","ieee":"G. Avni, I. R. Jecker, and D. Zikelic, “Bidding graph games with partially-observable budgets,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence, Washington, DC, United States, 2023, vol. 37, no. 5, pp. 5464–5471.","mla":"Avni, Guy, et al. “Bidding Graph Games with Partially-Observable Budgets.” Proceedings of the 37th AAAI Conference on Artificial Intelligence, vol. 37, no. 5, 2023, pp. 5464–71, doi:10.1609/aaai.v37i5.25679."},"title":"Bidding graph games with partially-observable budgets","author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy"},{"first_name":"Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","last_name":"Jecker","full_name":"Jecker, Ismael R"},{"orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde"}],"article_processing_charge":"No","external_id":{"arxiv":["2211.13626"]},"acknowledgement":"This research was supported in part by ISF grant no.1679/21, by the ERC CoG 863818 (ForM-SMArt), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","quality_controlled":"1","oa":1,"day":"27","publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","year":"2023","date_published":"2023-06-27T00:00:00Z","doi":"10.1609/aaai.v37i5.25679","date_created":"2023-08-27T22:01:18Z","page":"5464-5471","_id":"14243","status":"public","type":"conference","conference":{"start_date":"2023-02-07","end_date":"2023-02-14","location":"Washington, DC, United States","name":"AAAI: Conference on Artificial Intelligence"},"date_updated":"2023-09-05T08:37:00Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Two-player zero-sum \"graph games\" are central in logic, verification, and multi-agent systems. The game proceeds by placing a token on a vertex of a graph, and allowing the players to move it to produce an infinite path, which determines the winner or payoff of the game. Traditionally, the players alternate turns in moving the token. In \"bidding games\", however, the players have budgets and in each turn, an auction (bidding) determines which player moves the token. So far, bidding games have only been studied as full-information games. In this work we initiate the study of partial-information bidding games: we study bidding games in which a player's initial budget is drawn from a known probability distribution. We show that while for some bidding mechanisms and objectives, it is straightforward to adapt the results from the full-information setting to the partial-information setting, for others, the analysis is significantly more challenging, requires new techniques, and gives rise to interesting results. Specifically, we study games with \"mean-payoff\" objectives in combination with \"poorman\" bidding. We construct optimal strategies for a partially-informed player who plays against a fully-informed adversary. We show that, somewhat surprisingly, the \"value\" under pure strategies does not necessarily exist in such games."}],"month":"06","intvolume":" 37","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1609/aaai.v37i5.25679","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781577358800"]},"publication_status":"published","issue":"5","volume":37,"ec_funded":1},{"publication":"SIGGRAPH 2023 Conference Proceedings","day":"23","year":"2023","date_created":"2023-08-27T22:01:17Z","date_published":"2023-07-23T00:00:00Z","doi":"10.1145/3588432.3591542","acknowledgement":"The authors would like to thank Yuki Koyama and Takeo Igarashi for early discussions, and Yuta Yaguchi for support in 3D printing. This research is partially supported by the Israel Science Foundation grant number 1390/19.\r\n","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Tojo, Kenji, et al. “Stealth Shaper: Reflectivity Optimization as Surface Stylization.” SIGGRAPH 2023 Conference Proceedings, 20, Association for Computing Machinery, 2023, doi:10.1145/3588432.3591542.","short":"K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH 2023 Conference Proceedings, Association for Computing Machinery, 2023.","ieee":"K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Stealth shaper: Reflectivity optimization as surface stylization,” in SIGGRAPH 2023 Conference Proceedings, Los Angeles, CA, United States, 2023.","apa":"Tojo, K., Shamir, A., Bickel, B., & Umetani, N. (2023). Stealth shaper: Reflectivity optimization as surface stylization. In SIGGRAPH 2023 Conference Proceedings. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3588432.3591542","ama":"Tojo K, Shamir A, Bickel B, Umetani N. Stealth shaper: Reflectivity optimization as surface stylization. In: SIGGRAPH 2023 Conference Proceedings. Association for Computing Machinery; 2023. doi:10.1145/3588432.3591542","chicago":"Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Stealth Shaper: Reflectivity Optimization as Surface Stylization.” In SIGGRAPH 2023 Conference Proceedings. Association for Computing Machinery, 2023. https://doi.org/10.1145/3588432.3591542.","ista":"Tojo K, Shamir A, Bickel B, Umetani N. 2023. Stealth shaper: Reflectivity optimization as surface stylization. SIGGRAPH 2023 Conference Proceedings. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 20."},"title":"Stealth shaper: Reflectivity optimization as surface stylization","external_id":{"arxiv":["2305.05944"]},"article_processing_charge":"No","author":[{"first_name":"Kenji","last_name":"Tojo","full_name":"Tojo, Kenji"},{"first_name":"Ariel","last_name":"Shamir","full_name":"Shamir, Ariel"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Umetani","full_name":"Umetani, Nobuyuki","first_name":"Nobuyuki"}],"article_number":"20","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9798400701597"]},"oa_version":"Preprint","abstract":[{"text":"We present a technique to optimize the reflectivity of a surface while preserving its overall shape. The naïve optimization of the mesh vertices using the gradients of reflectivity simulations results in undesirable distortion. In contrast, our robust formulation optimizes the surface normal as an independent variable that bridges the reflectivity term with differential rendering, and the regularization term with as-rigid-as-possible elastic energy. We further adaptively subdivide the input mesh to improve the convergence. Consequently, our method can minimize the retroreflectivity of a wide range of input shapes, resulting in sharply creased shapes ubiquitous among stealth aircraft and Sci-Fi vehicles. Furthermore, by changing the reward for the direction of the outgoing light directions, our method can be applied to other reflectivity design tasks, such as the optimization of architectural walls to concentrate light in a specific region. We have tested the proposed method using light-transport simulations and real-world 3D-printed objects.","lang":"eng"}],"month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.05944"}],"scopus_import":"1","date_updated":"2023-09-05T07:22:03Z","department":[{"_id":"BeBi"}],"_id":"14241","status":"public","conference":{"start_date":"2023-08-06","location":"Los Angeles, CA, United States","end_date":"2023-08-10","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference"},"type":"conference"},{"month":"03","intvolume":" 129","abstract":[{"lang":"eng","text":"Presynaptic inputs determine the pattern of activation of postsynaptic neurons in a neural circuit. Molecular and genetic pathways that regulate the selective formation of subsets of presynaptic inputs are largely unknown, despite significant understanding of the general process of synaptogenesis. In this study, we have begun to identify such factors using the spinal monosynaptic stretch reflex circuit as a model system. In this neuronal circuit, Ia proprioceptive afferents establish monosynaptic connections with spinal motor neurons that project to the same muscle (termed homonymous connections) or muscles with related or synergistic function. However, monosynaptic connections are not formed with motor neurons innervating muscles with antagonistic functions. The ETS transcription factor ER81 (also known as ETV1) is expressed by all proprioceptive afferents, but only a small set of motor neuron pools in the lumbar spinal cord of the mouse. Here we use conditional mouse genetic techniques to eliminate Er81 expression selectively from motor neurons. We find that ablation of Er81 in motor neurons reduces synaptic inputs from proprioceptive afferents conveying information from homonymous and synergistic muscles, with no change observed in the connectivity pattern from antagonistic proprioceptive afferents. In summary, these findings suggest a role for ER81 in defined motor neuron pools to control the assembly of specific presynaptic inputs and thereby influence the profile of activation of these motor neurons."}],"oa_version":"None","pmid":1,"volume":129,"issue":"3","publication_identifier":{"eissn":["1522-1598"],"issn":["0022-3077"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","keyword":["Physiology","General Neuroscience"],"_id":"12562","department":[{"_id":"SiHi"}],"date_updated":"2023-09-05T12:13:34Z","publisher":"American Physiological Society","quality_controlled":"1","acknowledgement":"The authors gratefully thank Dr. Silvia Arber, University of Basel and Friedrich Miescher Institute for Biomedical Research, for support and in whose lab the data were collected. For advice on statistical analysis, we thank Michael Bottomley from the Statistical Consulting Center, College of Science and Mathematics, Wright State University.","page":"501-512","date_published":"2023-03-01T00:00:00Z","doi":"10.1152/jn.00172.2022","date_created":"2023-02-15T14:46:14Z","isi":1,"year":"2023","day":"01","publication":"Journal of Neurophysiology","author":[{"full_name":"Ladle, David R.","last_name":"Ladle","first_name":"David R."},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"}],"article_processing_charge":"No","external_id":{"isi":["000957721600001"],"pmid":["36695533"]},"title":"Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons","citation":{"ista":"Ladle DR, Hippenmeyer S. 2023. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 129(3), 501–512.","chicago":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal of Neurophysiology. American Physiological Society, 2023. https://doi.org/10.1152/jn.00172.2022.","short":"D.R. Ladle, S. Hippenmeyer, Journal of Neurophysiology 129 (2023) 501–512.","ieee":"D. R. Ladle and S. Hippenmeyer, “Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons,” Journal of Neurophysiology, vol. 129, no. 3. American Physiological Society, pp. 501–512, 2023.","apa":"Ladle, D. R., & Hippenmeyer, S. (2023). Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. American Physiological Society. https://doi.org/10.1152/jn.00172.2022","ama":"Ladle DR, Hippenmeyer S. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 2023;129(3):501-512. doi:10.1152/jn.00172.2022","mla":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal of Neurophysiology, vol. 129, no. 3, American Physiological Society, 2023, pp. 501–12, doi:10.1152/jn.00172.2022."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"citation":{"ista":"Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Monitoring algorithmic fairness. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13965, 358–382.","chicago":"Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Monitoring Algorithmic Fairness.” In Computer Aided Verification, 13965:358–382. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37703-7_17.","apa":"Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Monitoring algorithmic fairness. In Computer Aided Verification (Vol. 13965, pp. 358–382). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37703-7_17","ama":"Henzinger TA, Karimi M, Kueffner K, Mallik K. Monitoring algorithmic fairness. In: Computer Aided Verification. Vol 13965. Springer Nature; 2023:358–382. doi:10.1007/978-3-031-37703-7_17","short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification, Springer Nature, 2023, pp. 358–382.","ieee":"T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Monitoring algorithmic fairness,” in Computer Aided Verification, Paris, France, 2023, vol. 13965, pp. 358–382.","mla":"Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness.” Computer Aided Verification, vol. 13965, Springer Nature, 2023, pp. 358–382, doi:10.1007/978-3-031-37703-7_17."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Karimi, Mahyar","orcid":"0009-0005-0820-1696","last_name":"Karimi","first_name":"Mahyar","id":"f1dedef5-2f78-11ee-989a-c4c97bccf506"},{"id":"8121a2d0-dc85-11ea-9058-af578f3b4515","first_name":"Konstantin","last_name":"Kueffner","orcid":"0000-0001-8974-2542","full_name":"Kueffner, Konstantin"},{"last_name":"Mallik","full_name":"Mallik, Kaushik","orcid":"0000-0001-9864-7475","first_name":"Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598"}],"external_id":{"arxiv":["2305.15979"]},"article_processing_charge":"Yes (in subscription journal)","title":"Monitoring algorithmic fairness","project":[{"grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020"}],"has_accepted_license":"1","year":"2023","day":"18","publication":"Computer Aided Verification","page":"358–382","date_published":"2023-07-18T00:00:00Z","doi":"10.1007/978-3-031-37703-7_17","date_created":"2023-07-25T18:32:40Z","acknowledgement":"This work is supported by the European Research Council under Grant No.: ERC-2020-AdG101020093.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_updated":"2023-09-05T15:14:00Z","ddc":["000"],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"file_date_updated":"2023-07-31T08:11:20Z","_id":"13310","type":"conference","conference":{"location":"Paris, France","end_date":"2023-07-22","start_date":"2023-07-17","name":"CAV: Computer Aided Verification"},"tmp":{"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)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031377020"],"eissn":["1611-3349"],"eisbn":["9783031377037"]},"publication_status":"published","file":[{"date_created":"2023-07-31T08:11:20Z","file_name":"2023_LNCS_CAV_HenzingerT.pdf","date_updated":"2023-07-31T08:11:20Z","file_size":647760,"creator":"dernst","file_id":"13327","checksum":"ccaf94bf7d658ba012c016e11869b54c","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":13965,"ec_funded":1,"abstract":[{"text":"Machine-learned systems are in widespread use for making decisions about humans, and it is important that they are fair, i.e., not biased against individuals based on sensitive attributes. We present runtime verification of algorithmic fairness for systems whose models are unknown, but are assumed to have a Markov chain structure. We introduce a specification language that can model many common algorithmic fairness properties, such as demographic parity, equal opportunity, and social burden. We build monitors that observe a long sequence of events as generated by a given system, and output, after each observation, a quantitative estimate of how fair or biased the system was on that run until that point in time. The estimate is proven to be correct modulo a variable error bound and a given confidence level, where the error bound gets tighter as the observed sequence gets longer. Our monitors are of two types, and use, respectively, frequentist and Bayesian statistical inference techniques. While the frequentist monitors compute estimates that are objectively correct with respect to the ground truth, the Bayesian monitors compute estimates that are correct subject to a given prior belief about the system’s model. Using a prototype implementation, we show how we can monitor if a bank is fair in giving loans to applicants from different social backgrounds, and if a college is fair in admitting students while maintaining a reasonable financial burden on the society. Although they exhibit different theoretical complexities in certain cases, in our experiments, both frequentist and Bayesian monitors took less than a millisecond to update their verdicts after each observation.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["LNCS"],"month":"07","intvolume":" 13965"},{"keyword":["Oncology","Surgery"],"status":"public","tmp":{"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)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"12205","file_date_updated":"2023-02-02T13:01:20Z","department":[{"_id":"JoDa"}],"ddc":["610"],"date_updated":"2023-09-05T15:18:37Z","intvolume":" 30","month":"01","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Background: This study seeks to evaluate the impact of breast cancer (BRCA) gene status on tumor dissemination pattern, surgical outcome and survival in a multicenter cohort of paired primary ovarian cancer (pOC) and recurrent ovarian cancer (rOC).\r\n\r\nPatients and Methods: Medical records and follow-up data from 190 patients were gathered retrospectively. All patients had surgery at pOC and at least one further rOC surgery at four European high-volume centers. Patients were divided into one cohort with confirmed mutation for BRCA1 and/or BRCA2 (BRCAmut) and a second cohort with BRCA wild type or unknown (BRCAwt). Patterns of tumor presentation, surgical outcome and survival data were analyzed between the two groups.\r\n\r\nResults: Patients with BRCAmut disease were on average 4 years younger and had significantly more tumor involvement upon diagnosis. Patients with BRCAmut disease showed higher debulking rates at all stages. Multivariate analysis showed that only patient age had significant predictive value for complete tumor resection in pOC. At rOC, however, only BRCAmut status significantly correlated with optimal debulking. Patients with BRCAmut disease showed significantly prolonged overall survival (OS) by 24.3 months. Progression-free survival (PFS) was prolonged in the BRCAmut group at all stages as well, reaching statistical significance during recurrence.\r\n\r\nConclusions: Patients with BRCAmut disease showed a more aggressive course of disease with earlier onset and more extensive tumor dissemination at pOC. However, surgical outcome and OS were significantly better in patients with BRCAmut disease compared with patients with BRCAwt disease. We therefore propose to consider BRCAmut status in regard to patient selection for cytoreductive surgery, especially in rOC.","lang":"eng"}],"volume":30,"related_material":{"record":[{"relation":"other","status":"public","id":"12115"}]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":365865,"date_updated":"2023-02-02T13:01:20Z","file_name":"2023_AnnalsSurgicalOncology_Glajzer.pdf","date_created":"2023-02-02T13:01:20Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"36a1200e1011f4b2155a8041d0308f34","file_id":"12490"}],"publication_status":"published","publication_identifier":{"issn":["1068-9265"],"eissn":["1534-4681"]},"title":"Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium","external_id":{"isi":["000852125500006"]},"article_processing_charge":"No","author":[{"full_name":"Glajzer, Jacek","last_name":"Glajzer","first_name":"Jacek"},{"full_name":"Castillo-Tong, Dan Cacsire","last_name":"Castillo-Tong","first_name":"Dan Cacsire"},{"first_name":"Rolf","last_name":"Richter","full_name":"Richter, Rolf"},{"first_name":"Ignace","full_name":"Vergote, Ignace","last_name":"Vergote"},{"first_name":"Hagen","last_name":"Kulbe","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"},{"first_name":"Alexander","last_name":"Mustea","full_name":"Mustea, Alexander"},{"first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline"},{"first_name":"Charlie","last_name":"Gourley","full_name":"Gourley, Charlie"},{"first_name":"Hani","last_name":"Gabra","full_name":"Gabra, Hani"},{"first_name":"Eliane T.","full_name":"Taube, Eliane T.","last_name":"Taube"},{"first_name":"Oliver","last_name":"Dorigo","full_name":"Dorigo, Oliver"},{"first_name":"David","last_name":"Horst","full_name":"Horst, David"},{"last_name":"Keunecke","full_name":"Keunecke, Carlotta","first_name":"Carlotta"},{"first_name":"Joanna","last_name":"Baum","full_name":"Baum, Joanna"},{"full_name":"Angelotti, Timothy","last_name":"Angelotti","first_name":"Timothy"},{"last_name":"Sehouli","full_name":"Sehouli, Jalid","first_name":"Jalid"},{"first_name":"Elena Ioana","full_name":"Braicu, Elena Ioana","last_name":"Braicu"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12459-3.","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. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 35–45.","mla":"Glajzer, Jacek, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 35–45, doi:10.1245/s10434-022-12459-3.","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) 35–45.","ieee":"J. Glajzer et al., “Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 35–45, 2023.","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12459-3","ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:35-45. doi:10.1245/s10434-022-12459-3"},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"E.I.B. is a Feodor Lynen fellow of the Humboldt Foundation and a participant of the Charité Clinical Scientist Program funded by the Charité Universitätsmedizin Berlin and the Berlin Institute of Health. This work was supported by European Commission’s Seventh Framework Programme under grant agreement no. 279113 (OCTIPS; www.octips.eu).\r\nOpen Access funding enabled and organized by Projekt DEAL.","date_created":"2023-01-16T09:44:36Z","doi":"10.1245/s10434-022-12459-3","date_published":"2023-01-01T00:00:00Z","page":"35-45","publication":"Annals of Surgical Oncology","day":"01","year":"2023","isi":1,"has_accepted_license":"1"},{"_id":"12115","status":"public","keyword":["Oncology","Surgery"],"article_type":"original","type":"journal_article","date_updated":"2023-09-05T15:18:36Z","department":[{"_id":"JoDa"}],"oa_version":"Published Version","month":"01","intvolume":" 30","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1245/s10434-022-12681-z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1068-9265"],"eissn":["1534-4681"]},"publication_status":"published","volume":30,"related_material":{"record":[{"status":"public","id":"12205","relation":"other"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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","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","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.","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.","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.","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."},"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","author":[{"first_name":"Jacek","full_name":"Glajzer, Jacek","last_name":"Glajzer"},{"first_name":"Dan Cacsire","full_name":"Castillo-Tong, Dan Cacsire","last_name":"Castillo-Tong"},{"last_name":"Richter","full_name":"Richter, Rolf","first_name":"Rolf"},{"last_name":"Vergote","full_name":"Vergote, Ignace","first_name":"Ignace"},{"last_name":"Kulbe","full_name":"Kulbe, Hagen","first_name":"Hagen"},{"full_name":"Vanderstichele, Adriaan","last_name":"Vanderstichele","first_name":"Adriaan"},{"full_name":"Ruscito, Ilary","last_name":"Ruscito","first_name":"Ilary"},{"last_name":"Trillsch","full_name":"Trillsch, Fabian","first_name":"Fabian"},{"full_name":"Mustea, Alexander","last_name":"Mustea","first_name":"Alexander"},{"first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline"},{"first_name":"Charlie","full_name":"Gourley, Charlie","last_name":"Gourley"},{"first_name":"Hani","last_name":"Gabra","full_name":"Gabra, Hani"},{"last_name":"Taube","full_name":"Taube, Eliane T.","first_name":"Eliane T."},{"first_name":"Oliver","last_name":"Dorigo","full_name":"Dorigo, Oliver"},{"last_name":"Horst","full_name":"Horst, David","first_name":"David"},{"first_name":"Carlotta","full_name":"Keunecke, Carlotta","last_name":"Keunecke"},{"last_name":"Baum","full_name":"Baum, Joanna","first_name":"Joanna"},{"first_name":"Timothy","full_name":"Angelotti, Timothy","last_name":"Angelotti"},{"last_name":"Sehouli","full_name":"Sehouli, Jalid","first_name":"Jalid"},{"first_name":"Elena Ioana","full_name":"Braicu, Elena Ioana","last_name":"Braicu"}],"external_id":{"isi":["000879151800001"]},"article_processing_charge":"No","acknowledgement":"This work was supported by European Commission’s Seventh Framework Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"01","publication":"Annals of Surgical Oncology","isi":1,"year":"2023","date_published":"2023-01-01T00:00:00Z","doi":"10.1245/s10434-022-12681-z","date_created":"2023-01-12T11:56:22Z","page":"46-47"},{"article_number":"5231","citation":{"ista":"Vierra NC, Ribeiro-Silva L, Kirmiz M, Van Der List D, Bhandari P, Mack OA, Carroll J, Le Monnier E, Aicher SA, Shigemoto R, Trimmer JS. 2023. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. 14, 5231.","chicago":"Vierra, Nicholas C., Luisa Ribeiro-Silva, Michael Kirmiz, Deborah Van Der List, Pradeep Bhandari, Olivia A. Mack, James Carroll, et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40930-6.","short":"N.C. Vierra, L. Ribeiro-Silva, M. Kirmiz, D. Van Der List, P. Bhandari, O.A. Mack, J. Carroll, E. Le Monnier, S.A. Aicher, R. Shigemoto, J.S. Trimmer, Nature Communications 14 (2023).","ieee":"N. C. Vierra et al., “Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling,” Nature Communications, vol. 14. Springer Nature, 2023.","ama":"Vierra NC, Ribeiro-Silva L, Kirmiz M, et al. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. 2023;14. doi:10.1038/s41467-023-40930-6","apa":"Vierra, N. C., Ribeiro-Silva, L., Kirmiz, M., Van Der List, D., Bhandari, P., Mack, O. A., … Trimmer, J. S. (2023). Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40930-6","mla":"Vierra, Nicholas C., et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” Nature Communications, vol. 14, 5231, Springer Nature, 2023, doi:10.1038/s41467-023-40930-6."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","external_id":{"pmid":["37633939"]},"author":[{"last_name":"Vierra","full_name":"Vierra, Nicholas C.","first_name":"Nicholas C."},{"first_name":"Luisa","full_name":"Ribeiro-Silva, Luisa","last_name":"Ribeiro-Silva"},{"last_name":"Kirmiz","full_name":"Kirmiz, Michael","first_name":"Michael"},{"last_name":"Van Der List","full_name":"Van Der List, Deborah","first_name":"Deborah"},{"last_name":"Bhandari","orcid":"0000-0003-0863-4481","full_name":"Bhandari, Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","first_name":"Pradeep"},{"full_name":"Mack, Olivia A.","last_name":"Mack","first_name":"Olivia A."},{"last_name":"Carroll","full_name":"Carroll, James","first_name":"James"},{"last_name":"Le Monnier","full_name":"Le Monnier, Elodie","first_name":"Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sue A.","full_name":"Aicher, Sue A.","last_name":"Aicher"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"full_name":"Trimmer, James S.","last_name":"Trimmer","first_name":"James S."}],"title":"Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling","acknowledgement":"We thank Kayla Templeton and Peter Turcanu for technical assistance, Michelle Salemi for assistance with LC-MS data acquisition and analysis, Dr. Belvin Gong for advice on monoclonal antibody generation, Drs. Maria Casas Prat and Eamonn Dickson for assistance with super-resolution TIRF microscopy, Dr. Oscar Cerda for assistance with the design of TAT-FFAT peptides, Dr. Fernando Santana for helpful discussions, and Dr. Jodi Nunnari for a careful reading of our manuscript. We also thank Dr. Alan Howe, Dr. Sohum Mehta, and Dr. Jin Zhang for providing plasmids used in this study. This project was funded by NIH Grants R01NS114210 and R21NS101648 (J.S.T.), and F32NS108519 (N.C.V.).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2023","has_accepted_license":"1","publication":"Nature Communications","day":"26","date_created":"2023-09-03T22:01:14Z","doi":"10.1038/s41467-023-40930-6","date_published":"2023-08-26T00:00:00Z","_id":"14253","tmp":{"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)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-06T06:53:32Z","ddc":["570"],"department":[{"_id":"RySh"}],"file_date_updated":"2023-09-06T06:50:07Z","abstract":[{"text":"Junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM) are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration of intracellular signaling machinery near ER-PM junctions allows these domains to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular compartmentalization of protein kinase A (PKA) signaling also regulates essential cellular functions, however, no specific association between PKA and ER-PM junctional domains is known. Here, we show that in brain neurons type I PKA is directed to Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and ER-resident VAP proteins results in the concentration of type I PKA between stacked ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome enables reciprocal regulation between PKA and Ca2+ signaling machinery to support Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal ER-PM junctions support a receptor-independent form of PKA signaling driven by membrane depolarization and intracellular Ca2+, allowing conversion of information encoded in electrical signals into biochemical changes universally recognized throughout the cell.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 14","month":"08","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"6ab8aab4e957f626a09a1c73db3388fb","file_id":"14270","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_NatureComm_Vierra.pdf","date_created":"2023-09-06T06:50:07Z","creator":"dernst","file_size":9412549,"date_updated":"2023-09-06T06:50:07Z"}],"volume":14},{"status":"public","conference":{"location":"Paris, France","end_date":"2023-07-22","start_date":"2023-07-17","name":"CAV: Computer Aided Verification"},"tmp":{"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)","short":"CC BY (4.0)"},"type":"conference","_id":"14259","file_date_updated":"2023-09-06T08:25:50Z","department":[{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2023-09-06T08:27:33Z","intvolume":" 13964","month":"07","scopus_import":"1","alternative_title":["LNCS"],"oa_version":"Published Version","abstract":[{"text":"We provide a learning-based technique for guessing a winning strategy in a parity game originating from an LTL synthesis problem. A cheaply obtained guess can be useful in several applications. Not only can the guessed strategy be applied as best-effort in cases where the game’s huge size prohibits rigorous approaches, but it can also increase the scalability of rigorous LTL synthesis in several ways. Firstly, checking whether a guessed strategy is winning is easier than constructing one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy iteration faster than constructing one from scratch. Thirdly, the guess can be used in on-the-fly approaches to prioritize exploration in the most fruitful directions.\r\nIn contrast to previous works, we (i) reflect the highly structured logical information in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata translations, and (ii) learn to reflect it properly by learning from previously solved games, bringing the solving process closer to human-like reasoning.","lang":"eng"}],"volume":13964,"language":[{"iso":"eng"}],"file":[{"file_name":"2023_LNCS_CAV_Kretinsky.pdf","date_created":"2023-09-06T08:25:50Z","creator":"dernst","file_size":428354,"date_updated":"2023-09-06T08:25:50Z","success":1,"checksum":"ed66278b61bb869e1baba3d9b9081271","file_id":"14276","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031377051"],"issn":["0302-9743"]},"title":"Guessing winning policies in LTL synthesis by semantic learning","article_processing_charge":"Yes (in subscription journal)","author":[{"orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165"},{"first_name":"Maximilian","full_name":"Prokop, Maximilian","last_name":"Prokop"},{"full_name":"Rieder, Sabine","last_name":"Rieder","first_name":"Sabine"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kretinsky, Jan, Tobias Meggendorfer, Maximilian Prokop, and Sabine Rieder. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” In 35th International Conference on Computer Aided Verification , 13964:390–414. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_20.","ista":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. 2023. Guessing winning policies in LTL synthesis by semantic learning. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 390–414.","mla":"Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” 35th International Conference on Computer Aided Verification , vol. 13964, Springer Nature, 2023, pp. 390–414, doi:10.1007/978-3-031-37706-8_20.","short":"J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414.","ieee":"J. Kretinsky, T. Meggendorfer, M. Prokop, and S. Rieder, “Guessing winning policies in LTL synthesis by semantic learning,” in 35th International Conference on Computer Aided Verification , Paris, France, 2023, vol. 13964, pp. 390–414.","ama":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. Guessing winning policies in LTL synthesis by semantic learning. In: 35th International Conference on Computer Aided Verification . Vol 13964. Springer Nature; 2023:390-414. doi:10.1007/978-3-031-37706-8_20","apa":"Kretinsky, J., Meggendorfer, T., Prokop, M., & Rieder, S. (2023). Guessing winning policies in LTL synthesis by semantic learning. In 35th International Conference on Computer Aided Verification (Vol. 13964, pp. 390–414). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_20"},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"This research was funded in part by the German Research Foundation (DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).","date_created":"2023-09-03T22:01:16Z","date_published":"2023-07-17T00:00:00Z","doi":"10.1007/978-3-031-37706-8_20","page":"390-414","publication":"35th International Conference on Computer Aided Verification ","day":"17","year":"2023","has_accepted_license":"1"},{"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Sinha S, Gehler P, Locatello F, Schiele B. 2023. TeST: Test-time Self-Training under distribution shift. 2023 IEEE/CVF Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision.","chicago":"Sinha, Samarth, Peter Gehler, Francesco Locatello, and Bernt Schiele. “TeST: Test-Time Self-Training under Distribution Shift.” In 2023 IEEE/CVF Winter Conference on Applications of Computer Vision. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/wacv56688.2023.00278.","ama":"Sinha S, Gehler P, Locatello F, Schiele B. TeST: Test-time Self-Training under distribution shift. In: 2023 IEEE/CVF Winter Conference on Applications of Computer Vision. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/wacv56688.2023.00278","apa":"Sinha, S., Gehler, P., Locatello, F., & Schiele, B. (2023). TeST: Test-time Self-Training under distribution shift. In 2023 IEEE/CVF Winter Conference on Applications of Computer Vision. Waikoloa, HI, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/wacv56688.2023.00278","ieee":"S. Sinha, P. Gehler, F. Locatello, and B. Schiele, “TeST: Test-time Self-Training under distribution shift,” in 2023 IEEE/CVF Winter Conference on Applications of Computer Vision, Waikoloa, HI, United States, 2023.","short":"S. Sinha, P. Gehler, F. Locatello, B. Schiele, in:, 2023 IEEE/CVF Winter Conference on Applications of Computer Vision, Institute of Electrical and Electronics Engineers, 2023.","mla":"Sinha, Samarth, et al. “TeST: Test-Time Self-Training under Distribution Shift.” 2023 IEEE/CVF Winter Conference on Applications of Computer Vision, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/wacv56688.2023.00278."},"date_updated":"2023-09-06T10:26:56Z","title":"TeST: Test-time Self-Training under distribution shift","department":[{"_id":"FrLo"}],"author":[{"first_name":"Samarth","last_name":"Sinha","full_name":"Sinha, Samarth"},{"last_name":"Gehler","full_name":"Gehler, Peter","first_name":"Peter"},{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"first_name":"Bernt","full_name":"Schiele, Bernt","last_name":"Schiele"}],"external_id":{"arxiv":["2209.11459"]},"article_processing_charge":"No","_id":"14105","status":"public","type":"conference","conference":{"name":"WACV: Winter Conference on Applications of Computer Vision","location":"Waikoloa, HI, United States","end_date":"2023-01-07","start_date":"2023-01-02"},"day":"06","language":[{"iso":"eng"}],"publication":"2023 IEEE/CVF Winter Conference on Applications of Computer Vision","publication_identifier":{"isbn":["9781665493475"],"eissn":["2642-9381"]},"publication_status":"published","year":"2023","doi":"10.1109/wacv56688.2023.00278","date_published":"2023-02-06T00:00:00Z","date_created":"2023-08-21T12:11:38Z","oa_version":"Preprint","abstract":[{"text":"Despite their recent success, deep neural networks continue to perform poorly when they encounter distribution shifts at test time. Many recently proposed approaches try to counter this by aligning the model to the new distribution prior to inference. With no labels available this requires unsupervised objectives to adapt the model on the observed test data. In this paper, we propose Test-Time SelfTraining (TeST): a technique that takes as input a model trained on some source data and a novel data distribution at test time, and learns invariant and robust representations using a student-teacher framework. We find that models adapted using TeST significantly improve over baseline testtime adaptation algorithms. TeST achieves competitive performance to modern domain adaptation algorithms [4, 43], while having access to 5-10x less data at time of adaption. We thoroughly evaluate a variety of baselines on two tasks:\r\nobject detection and image segmentation and find that models adapted with TeST. We find that TeST sets the new stateof-the art for test-time domain adaptation algorithms. ","lang":"eng"}],"month":"02","publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2209.11459"}],"oa":1},{"title":"Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields","external_id":{"isi":["001046037700007"],"arxiv":["2306.11587"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"S.","last_name":"Mathis","full_name":"Mathis, S."},{"orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle","last_name":"Bugnet","first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"S. Mathis, L.A. Bugnet, Astronomy and Astrophysics 676 (2023).","ieee":"S. Mathis and L. A. Bugnet, “Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields,” Astronomy and Astrophysics, vol. 676. EDP Sciences, 2023.","ama":"Mathis S, Bugnet LA. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. 2023;676. doi:10.1051/0004-6361/202346832","apa":"Mathis, S., & Bugnet, L. A. (2023). Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202346832","mla":"Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” Astronomy and Astrophysics, vol. 676, L9, EDP Sciences, 2023, doi:10.1051/0004-6361/202346832.","ista":"Mathis S, Bugnet LA. 2023. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. 676, L9.","chicago":"Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” Astronomy and Astrophysics. EDP Sciences, 2023. https://doi.org/10.1051/0004-6361/202346832."},"article_number":"L9","date_created":"2023-09-03T22:01:15Z","doi":"10.1051/0004-6361/202346832","date_published":"2023-08-01T00:00:00Z","publication":"Astronomy and Astrophysics","day":"01","year":"2023","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"EDP Sciences","acknowledgement":"The authors are grateful to the referee for her/his detailed and constructive report, which has allowed us to improve our article. S. M. acknowledges support from the CNES GOLF-SOHO and PLATO grants at CEA/DAp and PNPS (CNRS/INSU). We thank R. A. Garcia for fruitful discussions and suggestions.","department":[{"_id":"LiBu"}],"file_date_updated":"2023-09-06T07:13:19Z","ddc":["520"],"date_updated":"2023-09-06T11:05:58Z","status":"public","tmp":{"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)","short":"CC BY (4.0)"},"article_type":"letter_note","type":"journal_article","_id":"14256","volume":676,"language":[{"iso":"eng"}],"file":[{"file_name":"2023_AstronomyAstrophysics_Mathis.pdf","date_created":"2023-09-06T07:13:19Z","file_size":458120,"date_updated":"2023-09-06T07:13:19Z","creator":"dernst","success":1,"file_id":"14271","checksum":"7b30d26fb2b7bcb5b5be1414950615f9","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"intvolume":" 676","month":"08","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Context. Space asteroseismology is revolutionizing our knowledge of the internal structure and dynamics of stars. A breakthrough is ongoing with the recent discoveries of signatures of strong magnetic fields in the core of red giant stars. The key signature for such a detection is the asymmetry these fields induce in the frequency splittings of observed dipolar mixed gravito-acoustic modes.\r\nAims. We investigate the ability of the observed asymmetries of the frequency splittings of dipolar mixed modes to constrain the geometrical properties of deep magnetic fields.\r\nMethods. We used the powerful analytical Racah-Wigner algebra used in quantum mechanics to characterize the geometrical couplings of dipolar mixed oscillation modes with various realistically plausible topologies of fossil magnetic fields. We also computed the induced perturbation of their frequencies.\r\nResults. First, in the case of an oblique magnetic dipole, we provide the exact analytical expression of the asymmetry as a function of the angle between the rotation and magnetic axes. Its value provides a direct measure of this angle. Second, considering a combination of axisymmetric dipolar and quadrupolar fields, we show how the asymmetry is blind to the unraveling of the relative strength and sign of each component. Finally, in the case of a given multipole, we show that a negative asymmetry is a signature of non-axisymmetric topologies.\r\nConclusions. Asymmetries of dipolar mixed modes provide a key bit of information on the geometrical topology of deep fossil magnetic fields, but this is insufficient on its own. Asteroseismic constraints should therefore be combined with spectropolarimetric observations and numerical simulations, which aim to predict the more probable stable large-scale geometries.","lang":"eng"}]},{"author":[{"first_name":"Jakob","last_name":"Gamper","full_name":"Gamper, Jakob"},{"id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","first_name":"Florian","full_name":"Kluibenschedl, Florian","last_name":"Kluibenschedl"},{"full_name":"Weiss, Alexander K.H.","last_name":"Weiss","first_name":"Alexander K.H."},{"first_name":"Thomas S.","full_name":"Hofer, Thomas S.","last_name":"Hofer"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["37566743"],"isi":["001048165800001"]},"title":"Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems","citation":{"ista":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2023. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. 14(33), 7395–7403.","chicago":"Gamper, Jakob, Florian Kluibenschedl, Alexander K.H. Weiss, and Thomas S. Hofer. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” Journal of Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01707.","ieee":"J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems,” Journal of Physical Chemistry Letters, vol. 14, no. 33. American Chemical Society, pp. 7395–7403, 2023.","short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403.","ama":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. 2023;14(33):7395-7403. doi:10.1021/acs.jpclett.3c01707","apa":"Gamper, J., Kluibenschedl, F., Weiss, A. K. H., & Hofer, T. S. (2023). Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01707","mla":"Gamper, Jakob, et al. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” Journal of Physical Chemistry Letters, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403, doi:10.1021/acs.jpclett.3c01707."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"7395-7403","doi":"10.1021/acs.jpclett.3c01707","date_published":"2023-08-11T00:00:00Z","date_created":"2023-09-03T22:01:16Z","isi":1,"has_accepted_license":"1","year":"2023","day":"11","publication":"Journal of Physical Chemistry Letters","publisher":"American Chemical Society","quality_controlled":"1","oa":1,"acknowledgement":"Financial supports for this work via a PhD scholarship for J. Gamper issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike Tanzer) are gratefully acknowledged. The computational results presented have been achieved (in part) using the HPC infrastructure of the University of Innsbruck.","file_date_updated":"2023-09-06T07:32:39Z","department":[{"_id":"GradSch"}],"date_updated":"2023-09-06T11:04:31Z","ddc":["530","540"],"type":"journal_article","article_type":"original","tmp":{"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)","short":"CC BY (4.0)"},"status":"public","_id":"14261","issue":"33","volume":14,"publication_identifier":{"eissn":["1948-7185"]},"publication_status":"published","file":[{"file_name":"2023_JourPhysChemistry_Gamper.pdf","date_created":"2023-09-06T07:32:39Z","creator":"dernst","file_size":4986859,"date_updated":"2023-09-06T07:32:39Z","success":1,"file_id":"14272","checksum":"637454e2b3a357498d8d622d241c4bf6","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"08","intvolume":" 14","abstract":[{"text":"In this work, a generalized, adapted Numerov implementation capable of determining band structures of periodic quantum systems is outlined. Based on the input potential, the presented approach numerically solves the Schrödinger equation in position space at each momentum space point. Thus, in addition to the band structure, the method inherently provides information about the state functions and probability densities in position space at each momentum space point considered. The generalized, adapted Numerov framework provided reliable estimates for a variety of increasingly complex test suites in one, two, and three dimensions. The accuracy of the proposed methodology was benchmarked against results obtained for the analytically solvable Kronig-Penney model. Furthermore, the presented numerical solver was applied to a model potential representing a 2D optical lattice being a challenging application relevant, for example, in the field of quantum computing.","lang":"eng"}],"oa_version":"Published Version","pmid":1},{"abstract":[{"text":"This paper focuses on over-parameterized deep neural networks (DNNs) with ReLU activation functions and proves that when the data distribution is well-separated, DNNs can achieve Bayes-optimal test error for classification while obtaining (nearly) zero-training error under the lazy training regime. For this purpose, we unify three interrelated concepts of overparameterization, benign overfitting, and the Lipschitz constant of DNNs. Our results indicate that interpolating with smoother functions leads to better generalization. Furthermore, we investigate the special case where interpolating smooth ground-truth functions is performed by DNNs under the Neural Tangent Kernel (NTK) regime for generalization. Our result demonstrates that the generalization error converges to a constant order that only depends on label noise and initialization noise, which theoretically verifies benign overfitting. Our analysis provides a tight lower bound on the normalized margin under non-smooth activation functions, as well as the minimum eigenvalue of NTK under high-dimensional settings, which has its own interest in learning theory.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2305.19377","open_access":"1"}],"alternative_title":["PMLR"],"intvolume":" 202","month":"05","publication_status":"published","language":[{"iso":"eng"}],"volume":202,"_id":"14208","conference":{"name":"International Conference on Machine Learning","start_date":"2023-07-23","location":"Honolulu, Hawaii, United States","end_date":"2023-07-29"},"type":"conference","status":"public","date_updated":"2023-09-13T08:46:46Z","extern":"1","department":[{"_id":"FrLo"}],"oa":1,"publisher":"ML Research Press","quality_controlled":"1","year":"2023","publication":"Proceedings of the 40th International Conference on Machine Learning","day":"30","page":"43105-43128","date_created":"2023-08-22T14:18:18Z","date_published":"2023-05-30T00:00:00Z","citation":{"chicago":"Zhu, Zhenyu, Fanghui Liu, Grigorios G Chrysos, Francesco Locatello, and Volkan Cevher. “Benign Overfitting in Deep Neural Networks under Lazy Training.” In Proceedings of the 40th International Conference on Machine Learning, 202:43105–28. ML Research Press, 2023.","ista":"Zhu Z, Liu F, Chrysos GG, Locatello F, Cevher V. 2023. Benign overfitting in deep neural networks under lazy training. Proceedings of the 40th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 202, 43105–43128.","mla":"Zhu, Zhenyu, et al. “Benign Overfitting in Deep Neural Networks under Lazy Training.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 43105–28.","ieee":"Z. Zhu, F. Liu, G. G. Chrysos, F. Locatello, and V. Cevher, “Benign overfitting in deep neural networks under lazy training,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, United States, 2023, vol. 202, pp. 43105–43128.","short":"Z. Zhu, F. Liu, G.G. Chrysos, F. Locatello, V. Cevher, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 43105–43128.","ama":"Zhu Z, Liu F, Chrysos GG, Locatello F, Cevher V. Benign overfitting in deep neural networks under lazy training. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:43105-43128.","apa":"Zhu, Z., Liu, F., Chrysos, G. G., Locatello, F., & Cevher, V. (2023). Benign overfitting in deep neural networks under lazy training. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 43105–43128). Honolulu, Hawaii, United States: ML Research Press."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2305.19377"]},"article_processing_charge":"No","author":[{"full_name":"Zhu, Zhenyu","last_name":"Zhu","first_name":"Zhenyu"},{"last_name":"Liu","full_name":"Liu, Fanghui","first_name":"Fanghui"},{"last_name":"Chrysos","full_name":"Chrysos, Grigorios G","first_name":"Grigorios G"},{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"},{"full_name":"Cevher, Volkan","last_name":"Cevher","first_name":"Volkan"}],"title":"Benign overfitting in deep neural networks under lazy training"},{"month":"04","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2304.10253","open_access":"1"}],"oa":1,"oa_version":"Preprint","abstract":[{"text":"Diffusion models excel at generating photorealistic images from text-queries. Naturally, many approaches have been proposed to use these generative abilities to augment training datasets for downstream tasks, such as classification. However, diffusion models are themselves trained on large noisily supervised, but nonetheless, annotated datasets. It is an open question whether the generalization capabilities of diffusion models beyond using the additional data of the pre-training process for augmentation lead to improved downstream performance. We perform a systematic evaluation of existing methods to generate images from diffusion models and study new extensions to assess their benefit for data augmentation. While we find that personalizing diffusion models towards the target data outperforms simpler prompting strategies, we also show that using the training data of the diffusion model alone, via a simple nearest neighbor retrieval procedure, leads to even stronger downstream performance. Overall, our study probes the limitations of diffusion models for data augmentation but also highlights its potential in generating new training data to improve performance on simple downstream vision tasks.","lang":"eng"}],"date_published":"2023-04-20T00:00:00Z","doi":"10.48550/arXiv.2304.10253","date_created":"2023-08-22T14:18:43Z","day":"20","publication":"arXiv","language":[{"iso":"eng"}],"year":"2023","publication_status":"submitted","status":"public","type":"preprint","article_number":"2304.10253","_id":"14209","title":"A data augmentation perspective on diffusion models and retrieval","department":[{"_id":"FrLo"}],"author":[{"first_name":"Max F.","full_name":"Burg, Max F.","last_name":"Burg"},{"full_name":"Wenzel, Florian","last_name":"Wenzel","first_name":"Florian"},{"first_name":"Dominik","full_name":"Zietlow, Dominik","last_name":"Zietlow"},{"first_name":"Max","last_name":"Horn","full_name":"Horn, Max"},{"full_name":"Makansi, Osama","last_name":"Makansi","first_name":"Osama"},{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Chris","last_name":"Russell","full_name":"Russell, Chris"}],"external_id":{"arxiv":["2304.10253"]},"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Burg, Max F., Florian Wenzel, Dominik Zietlow, Max Horn, Osama Makansi, Francesco Locatello, and Chris Russell. “A Data Augmentation Perspective on Diffusion Models and Retrieval.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2304.10253.","ista":"Burg MF, Wenzel F, Zietlow D, Horn M, Makansi O, Locatello F, Russell C. A data augmentation perspective on diffusion models and retrieval. arXiv, 2304.10253.","mla":"Burg, Max F., et al. “A Data Augmentation Perspective on Diffusion Models and Retrieval.” ArXiv, 2304.10253, doi:10.48550/arXiv.2304.10253.","ama":"Burg MF, Wenzel F, Zietlow D, et al. A data augmentation perspective on diffusion models and retrieval. arXiv. doi:10.48550/arXiv.2304.10253","apa":"Burg, M. F., Wenzel, F., Zietlow, D., Horn, M., Makansi, O., Locatello, F., & Russell, C. (n.d.). A data augmentation perspective on diffusion models and retrieval. arXiv. https://doi.org/10.48550/arXiv.2304.10253","short":"M.F. Burg, F. Wenzel, D. Zietlow, M. Horn, O. Makansi, F. Locatello, C. Russell, ArXiv (n.d.).","ieee":"M. F. Burg et al., “A data augmentation perspective on diffusion models and retrieval,” arXiv. ."},"date_updated":"2023-09-13T08:51:56Z"},{"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-13T09:00:31Z","citation":{"ista":"Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. 2023. Causal discovery with score matching on additive models with arbitrary noise. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning.","chicago":"Montagna, Francesco, Nicoletta Noceti, Lorenzo Rosasco, Kun Zhang, and Francesco Locatello. “Causal Discovery with Score Matching on Additive Models with Arbitrary Noise.” In 2nd Conference on Causal Learning and Reasoning, 2023.","ieee":"F. Montagna, N. Noceti, L. Rosasco, K. Zhang, and F. Locatello, “Causal discovery with score matching on additive models with arbitrary noise,” in 2nd Conference on Causal Learning and Reasoning, Tübingen, Germany, 2023.","short":"F. Montagna, N. Noceti, L. Rosasco, K. Zhang, F. Locatello, in:, 2nd Conference on Causal Learning and Reasoning, 2023.","apa":"Montagna, F., Noceti, N., Rosasco, L., Zhang, K., & Locatello, F. (2023). Causal discovery with score matching on additive models with arbitrary noise. In 2nd Conference on Causal Learning and Reasoning. Tübingen, Germany.","ama":"Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. Causal discovery with score matching on additive models with arbitrary noise. In: 2nd Conference on Causal Learning and Reasoning. ; 2023.","mla":"Montagna, Francesco, et al. “Causal Discovery with Score Matching on Additive Models with Arbitrary Noise.” 2nd Conference on Causal Learning and Reasoning, 2023."},"title":"Causal discovery with score matching on additive models with arbitrary noise","department":[{"_id":"FrLo"}],"author":[{"last_name":"Montagna","full_name":"Montagna, Francesco","first_name":"Francesco"},{"first_name":"Nicoletta","last_name":"Noceti","full_name":"Noceti, Nicoletta"},{"full_name":"Rosasco, Lorenzo","last_name":"Rosasco","first_name":"Lorenzo"},{"first_name":"Kun","full_name":"Zhang, Kun","last_name":"Zhang"},{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"}],"external_id":{"arxiv":["2304.03265"]},"article_processing_charge":"No","_id":"14211","status":"public","type":"conference","conference":{"end_date":"2023-04-14","location":"Tübingen, Germany","start_date":"2023-04-11","name":"CLeaR: Conference on Causal Learning and Reasoning"},"day":"01","language":[{"iso":"eng"}],"publication":"2nd Conference on Causal Learning and Reasoning","publication_status":"published","year":"2023","date_published":"2023-04-01T00:00:00Z","date_created":"2023-08-22T14:19:21Z","oa_version":"Preprint","abstract":[{"text":"Causal discovery methods are intrinsically constrained by the set of assumptions needed to ensure structure identifiability. Moreover additional restrictions are often imposed in order to simplify the inference task: this is the case for the Gaussian noise assumption on additive non-linear models, which is common to many causal discovery approaches. In this paper we show the shortcomings of inference under this hypothesis, analyzing the risk of edge inversion under violation of Gaussianity of the noise terms. Then, we propose a novel method for inferring the topological ordering of the variables in the causal graph, from data generated according to an additive non-linear model with a generic noise distribution. This leads to NoGAM (Not only Gaussian Additive noise Models), a causal discovery algorithm with a minimal set of assumptions and state of the art performance, experimentally benchmarked on synthetic data.","lang":"eng"}],"month":"04","scopus_import":"1","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2304.03265","open_access":"1"}]},{"department":[{"_id":"FrLo"}],"title":"Scalable causal discovery with score matching","external_id":{"arxiv":["2304.03382"]},"article_processing_charge":"No","author":[{"full_name":"Montagna, Francesco","last_name":"Montagna","first_name":"Francesco"},{"first_name":"Nicoletta","full_name":"Noceti, Nicoletta","last_name":"Noceti"},{"first_name":"Lorenzo","last_name":"Rosasco","full_name":"Rosasco, Lorenzo"},{"last_name":"Zhang","full_name":"Zhang, Kun","first_name":"Kun"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2023-09-13T09:03:24Z","citation":{"ista":"Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. 2023. Scalable causal discovery with score matching. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning.","chicago":"Montagna, Francesco, Nicoletta Noceti, Lorenzo Rosasco, Kun Zhang, and Francesco Locatello. “Scalable Causal Discovery with Score Matching.” In 2nd Conference on Causal Learning and Reasoning, 2023.","apa":"Montagna, F., Noceti, N., Rosasco, L., Zhang, K., & Locatello, F. (2023). Scalable causal discovery with score matching. In 2nd Conference on Causal Learning and Reasoning. Tübingen, Germany.","ama":"Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. Scalable causal discovery with score matching. In: 2nd Conference on Causal Learning and Reasoning. ; 2023.","ieee":"F. Montagna, N. Noceti, L. Rosasco, K. Zhang, and F. Locatello, “Scalable causal discovery with score matching,” in 2nd Conference on Causal Learning and Reasoning, Tübingen, Germany, 2023.","short":"F. Montagna, N. Noceti, L. Rosasco, K. Zhang, F. Locatello, in:, 2nd Conference on Causal Learning and Reasoning, 2023.","mla":"Montagna, Francesco, et al. “Scalable Causal Discovery with Score Matching.” 2nd Conference on Causal Learning and Reasoning, 2023."},"status":"public","conference":{"name":"CLeaR: Conference on Causal Learning and Reasoning","location":"Tübingen, Germany","end_date":"2023-04-14","start_date":"2023-04-11"},"type":"conference","_id":"14212","date_created":"2023-08-22T14:19:40Z","date_published":"2023-04-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"2nd Conference on Causal Learning and Reasoning","day":"01","year":"2023","publication_status":"published","month":"04","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2304.03382","open_access":"1"}],"quality_controlled":"1","scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"This paper demonstrates how to discover the whole causal graph from the second derivative of the log-likelihood in observational non-linear additive Gaussian noise models. Leveraging scalable machine learning approaches to approximate the score function ∇logp(X), we extend the work of Rolland et al. (2022) that only recovers the topological order from the score and requires an expensive pruning step removing spurious edges among those admitted by the ordering. Our analysis leads to DAS (acronym for Discovery At Scale), a practical algorithm that reduces the complexity of the pruning by a factor proportional to the graph size. In practice, DAS achieves competitive accuracy with current state-of-the-art while being over an order of magnitude faster. Overall, our approach enables principled and scalable causal discovery, significantly lowering the compute bar.","lang":"eng"}]},{"conference":{"name":"CLeaR: Conference on Causal Learning and Reasoning","start_date":"2023-04-11","location":"Tübingen, Germany","end_date":"2023-04-14"},"type":"conference","status":"public","_id":"14214","article_processing_charge":"No","external_id":{"arxiv":["2301.05169"]},"author":[{"first_name":"Yuejiang","last_name":"Liu","full_name":"Liu, Yuejiang"},{"last_name":"Alahi","full_name":"Alahi, Alexandre","first_name":"Alexandre"},{"full_name":"Russell, Chris","last_name":"Russell","first_name":"Chris"},{"last_name":"Horn","full_name":"Horn, Max","first_name":"Max"},{"first_name":"Dominik","full_name":"Zietlow, Dominik","last_name":"Zietlow"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello"}],"title":"Causal triplet: An open challenge for intervention-centric causal representation learning","department":[{"_id":"FrLo"}],"citation":{"ista":"Liu Y, Alahi A, Russell C, Horn M, Zietlow D, Schölkopf B, Locatello F. 2023. Causal triplet: An open challenge for intervention-centric causal representation learning. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning.","chicago":"Liu, Yuejiang, Alexandre Alahi, Chris Russell, Max Horn, Dominik Zietlow, Bernhard Schölkopf, and Francesco Locatello. “Causal Triplet: An Open Challenge for Intervention-Centric Causal Representation Learning.” In 2nd Conference on Causal Learning and Reasoning, 2023.","ama":"Liu Y, Alahi A, Russell C, et al. Causal triplet: An open challenge for intervention-centric causal representation learning. In: 2nd Conference on Causal Learning and Reasoning. ; 2023.","apa":"Liu, Y., Alahi, A., Russell, C., Horn, M., Zietlow, D., Schölkopf, B., & Locatello, F. (2023). Causal triplet: An open challenge for intervention-centric causal representation learning. In 2nd Conference on Causal Learning and Reasoning. Tübingen, Germany.","ieee":"Y. Liu et al., “Causal triplet: An open challenge for intervention-centric causal representation learning,” in 2nd Conference on Causal Learning and Reasoning, Tübingen, Germany, 2023.","short":"Y. Liu, A. Alahi, C. Russell, M. Horn, D. Zietlow, B. Schölkopf, F. Locatello, in:, 2nd Conference on Causal Learning and Reasoning, 2023.","mla":"Liu, Yuejiang, et al. “Causal Triplet: An Open Challenge for Intervention-Centric Causal Representation Learning.” 2nd Conference on Causal Learning and Reasoning, 2023."},"date_updated":"2023-09-13T09:23:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.05169"}],"quality_controlled":"1","month":"04","abstract":[{"lang":"eng","text":"Recent years have seen a surge of interest in learning high-level causal representations from low-level image pairs under interventions. Yet, existing efforts are largely limited to simple synthetic settings that are far away from real-world problems. In this paper, we present Causal Triplet, a causal representation learning benchmark featuring not only visually more complex scenes, but also two crucial desiderata commonly overlooked in previous works: (i) an actionable counterfactual setting, where only certain object-level variables allow for counterfactual observations whereas others do not; (ii) an interventional downstream task with an emphasis on out-of-distribution robustness from the independent causal mechanisms principle. Through extensive experiments, we find that models built with the knowledge of disentangled or object-centric representations significantly outperform their distributed counterparts. However, recent causal representation learning methods still struggle to identify such latent structures, indicating substantial challenges and opportunities for future work."}],"oa_version":"Preprint","date_created":"2023-08-22T14:20:18Z","date_published":"2023-04-12T00:00:00Z","year":"2023","publication_status":"published","language":[{"iso":"eng"}],"publication":"2nd Conference on Causal Learning and Reasoning","day":"12"},{"title":"Relative representations enable zero-shot latent space communication","department":[{"_id":"FrLo"}],"author":[{"first_name":"Luca","full_name":"Moschella, Luca","last_name":"Moschella"},{"full_name":"Maiorca, Valentino","last_name":"Maiorca","first_name":"Valentino"},{"first_name":"Marco","last_name":"Fumero","full_name":"Fumero, Marco"},{"first_name":"Antonio","last_name":"Norelli","full_name":"Norelli, Antonio"},{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"first_name":"Emanuele","last_name":"Rodolà","full_name":"Rodolà, Emanuele"}],"external_id":{"arxiv":["2209.15430"]},"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-13T09:44:26Z","citation":{"chicago":"Moschella, Luca, Valentino Maiorca, Marco Fumero, Antonio Norelli, Francesco Locatello, and Emanuele Rodolà. “Relative Representations Enable Zero-Shot Latent Space Communication.” In The 11th International Conference on Learning Representations, 2023.","ista":"Moschella L, Maiorca V, Fumero M, Norelli A, Locatello F, Rodolà E. 2023. Relative representations enable zero-shot latent space communication. The 11th International Conference on Learning Representations. International Conference on Machine Learning Representations.","mla":"Moschella, Luca, et al. “Relative Representations Enable Zero-Shot Latent Space Communication.” The 11th International Conference on Learning Representations, 2023.","ieee":"L. Moschella, V. Maiorca, M. Fumero, A. Norelli, F. Locatello, and E. Rodolà, “Relative representations enable zero-shot latent space communication,” in The 11th International Conference on Learning Representations, Kigali, Rwanda, 2023.","short":"L. Moschella, V. Maiorca, M. Fumero, A. Norelli, F. Locatello, E. Rodolà, in:, The 11th International Conference on Learning Representations, 2023.","ama":"Moschella L, Maiorca V, Fumero M, Norelli A, Locatello F, Rodolà E. Relative representations enable zero-shot latent space communication. In: The 11th International Conference on Learning Representations. ; 2023.","apa":"Moschella, L., Maiorca, V., Fumero, M., Norelli, A., Locatello, F., & Rodolà, E. (2023). Relative representations enable zero-shot latent space communication. In The 11th International Conference on Learning Representations. Kigali, Rwanda."},"status":"public","type":"conference","conference":{"start_date":"2023-05-01","end_date":"2023-05-05","location":"Kigali, Rwanda","name":"International Conference on Machine Learning Representations"},"_id":"14217","date_published":"2023-05-01T00:00:00Z","date_created":"2023-08-22T14:22:20Z","day":"01","language":[{"iso":"eng"}],"publication":"The 11th International Conference on Learning Representations","publication_status":"published","year":"2023","month":"05","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2209.15430"}],"oa":1,"oa_version":"Preprint","abstract":[{"text":"Neural networks embed the geometric structure of a data manifold lying in a high-dimensional space into latent representations. Ideally, the distribution of the data points in the latent space should depend only on the task, the data, the loss, and other architecture-specific constraints. However, factors such as the random weights initialization, training hyperparameters, or other sources of randomness in the training phase may induce incoherent latent spaces that hinder any form of reuse. Nevertheless, we empirically observe that, under the same data and modeling choices, the angles between the encodings within distinct latent spaces do not change. In this work, we propose the latent similarity between each sample and a fixed set of anchors as an alternative data representation, demonstrating that it can enforce the desired invariances without any additional training. We show how neural architectures can leverage these relative representations to guarantee, in practice, invariance to latent isometries and rescalings, effectively enabling latent space communication: from zero-shot model stitching to latent space comparison between diverse settings. We extensively validate the generalization capability of our approach on different datasets, spanning various modalities (images, text, graphs), tasks (e.g., classification, reconstruction) and architectures (e.g., CNNs, GCNs, transformers).","lang":"eng"}]},{"publication":"2nd Conference on Causal Learning and Reasoning","language":[{"iso":"eng"}],"day":"15","year":"2023","publication_status":"published","date_created":"2023-08-22T14:23:54Z","date_published":"2023-04-15T00:00:00Z","oa_version":"Preprint","abstract":[{"text":"Learning generative object models from unlabelled videos is a long standing problem and required for causal scene modeling. We decompose this problem into three easier subtasks, and provide candidate solutions for each of them. Inspired by the Common Fate Principle of Gestalt Psychology, we first extract (noisy) masks of moving objects via unsupervised motion segmentation. Second, generative models are trained on the masks of the background and the moving objects, respectively. Third, background and foreground models are combined in a conditional \"dead leaves\" scene model to sample novel scene configurations where occlusions and depth layering arise naturally. To evaluate the individual stages, we introduce the Fishbowl dataset positioned between complex real-world scenes and common object-centric benchmarks of simplistic objects. We show that our approach allows learning generative models that generalize beyond the occlusions present in the input videos, and represent scenes in a modular fashion that allows sampling plausible scenes outside the training distribution by permitting, for instance, object numbers or densities not observed in the training set.","lang":"eng"}],"month":"04","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2110.06562","open_access":"1"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2023-09-13T11:31:14Z","citation":{"apa":"Tangemann, M., Schneider, S., Kügelgen, J. von, Locatello, F., Gehler, P., Brox, T., … Schölkopf, B. (2023). Unsupervised object learning via common fate. In 2nd Conference on Causal Learning and Reasoning. Tübingen, Germany.","ama":"Tangemann M, Schneider S, Kügelgen J von, et al. Unsupervised object learning via common fate. In: 2nd Conference on Causal Learning and Reasoning. ; 2023.","short":"M. Tangemann, S. Schneider, J. von Kügelgen, F. Locatello, P. Gehler, T. Brox, M. Kümmerer, M. Bethge, B. Schölkopf, in:, 2nd Conference on Causal Learning and Reasoning, 2023.","ieee":"M. Tangemann et al., “Unsupervised object learning via common fate,” in 2nd Conference on Causal Learning and Reasoning, Tübingen, Germany, 2023.","mla":"Tangemann, Matthias, et al. “Unsupervised Object Learning via Common Fate.” 2nd Conference on Causal Learning and Reasoning, 2110.06562, 2023.","ista":"Tangemann M, Schneider S, Kügelgen J von, Locatello F, Gehler P, Brox T, Kümmerer M, Bethge M, Schölkopf B. 2023. Unsupervised object learning via common fate. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning, 2110.06562.","chicago":"Tangemann, Matthias, Steffen Schneider, Julius von Kügelgen, Francesco Locatello, Peter Gehler, Thomas Brox, Matthias Kümmerer, Matthias Bethge, and Bernhard Schölkopf. “Unsupervised Object Learning via Common Fate.” In 2nd Conference on Causal Learning and Reasoning, 2023."},"department":[{"_id":"FrLo"}],"title":"Unsupervised object learning via common fate","external_id":{"arxiv":["2110.06562"]},"article_processing_charge":"No","author":[{"first_name":"Matthias","full_name":"Tangemann, Matthias","last_name":"Tangemann"},{"full_name":"Schneider, Steffen","last_name":"Schneider","first_name":"Steffen"},{"first_name":"Julius von","full_name":"Kügelgen, Julius von","last_name":"Kügelgen"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"},{"full_name":"Gehler, Peter","last_name":"Gehler","first_name":"Peter"},{"last_name":"Brox","full_name":"Brox, Thomas","first_name":"Thomas"},{"full_name":"Kümmerer, Matthias","last_name":"Kümmerer","first_name":"Matthias"},{"full_name":"Bethge, Matthias","last_name":"Bethge","first_name":"Matthias"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"}],"article_number":"2110.06562","_id":"14222","status":"public","conference":{"start_date":"2023-04-11","location":"Tübingen, Germany","end_date":"2023-04-14","name":"CLeaR: Conference on Causal Learning and Reasoning"},"type":"conference"}]