[{"language":[{"iso":"eng"}],"doi":"10.1021/acs.chemmater.2c03542","isi":1,"quality_controlled":"1","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000914749700001"]},"month":"01","publication_identifier":{"issn":["0897-4756"],"eissn":["1520-5002"]},"date_created":"2023-01-22T23:00:55Z","date_updated":"2023-08-14T12:57:44Z","volume":35,"author":[{"full_name":"Wang, Siqi","first_name":"Siqi","last_name":"Wang"},{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","first_name":"Cheng","last_name":"Chang","full_name":"Chang, Cheng"},{"last_name":"Bai","first_name":"Shulin","full_name":"Bai, Shulin"},{"full_name":"Qin, Bingchao","first_name":"Bingchao","last_name":"Qin"},{"last_name":"Zhu","first_name":"Yingcai","full_name":"Zhu, Yingcai"},{"full_name":"Zhan, Shaoping","first_name":"Shaoping","last_name":"Zhan"},{"full_name":"Zheng, Junqing","first_name":"Junqing","last_name":"Zheng"},{"full_name":"Tang, Shuwei","first_name":"Shuwei","last_name":"Tang"},{"full_name":"Zhao, Li Dong","last_name":"Zhao","first_name":"Li Dong"}],"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"MaIb"}],"acknowledgement":"The National Key Research and Development Program of China (2018YFA0702100), the Basic Science Center Project of the National Natural Science Foundation of China (51788104), the National Natural Science Foundation of China (51571007 and 51772012), the Beijing Natural Science Foundation (JQ18004), the 111 Project (B17002), the National Science Fund for Distinguished Young Scholars (51925101), and the FWF “Lise Meitner Fellowship” (grant agreement M2889-N). Open Access is funded by the Austrian Science Fund (FWF).","year":"2023","file_date_updated":"2023-08-14T12:57:25Z","date_published":"2023-01-24T00:00:00Z","article_type":"original","page":"755-763","publication":"Chemistry of Materials","citation":{"ama":"Wang S, Chang C, Bai S, et al. Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. 2023;35(2):755-763. doi:10.1021/acs.chemmater.2c03542","ieee":"S. Wang et al., “Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe,” Chemistry of Materials, vol. 35, no. 2. American Chemical Society, pp. 755–763, 2023.","apa":"Wang, S., Chang, C., Bai, S., Qin, B., Zhu, Y., Zhan, S., … Zhao, L. D. (2023). Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/acs.chemmater.2c03542","ista":"Wang S, Chang C, Bai S, Qin B, Zhu Y, Zhan S, Zheng J, Tang S, Zhao LD. 2023. Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. 35(2), 755–763.","short":"S. Wang, C. Chang, S. Bai, B. Qin, Y. Zhu, S. Zhan, J. Zheng, S. Tang, L.D. Zhao, Chemistry of Materials 35 (2023) 755–763.","mla":"Wang, Siqi, et al. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials, vol. 35, no. 2, American Chemical Society, 2023, pp. 755–63, doi:10.1021/acs.chemmater.2c03542.","chicago":"Wang, Siqi, Cheng Chang, Shulin Bai, Bingchao Qin, Yingcai Zhu, Shaoping Zhan, Junqing Zheng, Shuwei Tang, and Li Dong Zhao. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials. American Chemical Society, 2023. https://doi.org/10.1021/acs.chemmater.2c03542."},"day":"24","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"14055","relation":"main_file","date_created":"2023-08-14T12:57:25Z","date_updated":"2023-08-14T12:57:25Z","success":1,"checksum":"b21dca2aa7a80c068bc256bdd1fea9df","file_name":"2023_ChemistryMaterials_Wang.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2961043}],"title":"Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe","ddc":["540"],"status":"public","intvolume":" 35","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12331","abstract":[{"lang":"eng","text":"High carrier mobility is critical to improving thermoelectric performance over a broad temperature range. However, traditional doping inevitably deteriorates carrier mobility. Herein, we develop a strategy for fine tuning of defects to improve carrier mobility. To begin, n-type PbTe is created by compensating for the intrinsic Pb vacancy in bare PbTe. Excess Pb2+ reduces vacancy scattering, resulting in a high carrier mobility of ∼3400 cm2 V–1 s–1. Then, excess Ag is introduced to compensate for the remaining intrinsic Pb vacancies. We find that excess Ag exhibits a dynamic doping process with increasing temperatures, increasing both the carrier concentration and carrier mobility throughout a wide temperature range; specifically, an ultrahigh carrier mobility ∼7300 cm2 V–1 s–1 is obtained for Pb1.01Te + 0.002Ag at 300 K. Moreover, the dynamic doping-induced high carrier concentration suppresses the bipolar thermal conductivity at high temperatures. The final step is using iodine to optimize the carrier concentration to ∼1019 cm–3. Ultimately, a maximum ZT value of ∼1.5 and a large average ZTave value of ∼1.0 at 300–773 K are obtained for Pb1.01Te0.998I0.002 + 0.002Ag. These findings demonstrate that fine tuning of defects with <0.5% impurities can remarkably enhance carrier mobility and improve thermoelectric performance."}],"issue":"2","type":"journal_article"},{"abstract":[{"text":"A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP-complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ, it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.","lang":"eng"}],"type":"journal_article","file":[{"file_size":1002218,"content_type":"application/pdf","creator":"alisjak","file_name":"2022_DiscreteandComputionalGeometry_Arroyo.pdf","access_level":"open_access","date_updated":"2022-08-29T11:23:15Z","date_created":"2022-08-29T11:23:15Z","checksum":"def7ae3b28d9fd6aec16450e40090302","success":1,"relation":"main_file","file_id":"12006"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11999","intvolume":" 69","title":"Inserting one edge into a simple drawing is hard","status":"public","ddc":["510"],"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2023-04-01T00:00:00Z","citation":{"ama":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 2023;69:745–770. doi:10.1007/s00454-022-00394-9","ista":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. 2023. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 69, 745–770.","apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R., & Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00394-9","ieee":"A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” Discrete and Computational Geometry, vol. 69. Springer Nature, pp. 745–770, 2023.","mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry, vol. 69, Springer Nature, 2023, pp. 745–770, doi:10.1007/s00454-022-00394-9.","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770.","chicago":"Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber, Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00394-9."},"publication":"Discrete and Computational Geometry","page":"745–770","article_type":"original","ec_funded":1,"file_date_updated":"2022-08-29T11:23:15Z","author":[{"full_name":"Arroyo Guevara, Alan M","orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","last_name":"Arroyo Guevara","first_name":"Alan M"},{"full_name":"Klute, Fabian","first_name":"Fabian","last_name":"Klute"},{"first_name":"Irene","last_name":"Parada","full_name":"Parada, Irene"},{"first_name":"Birgit","last_name":"Vogtenhuber","full_name":"Vogtenhuber, Birgit"},{"full_name":"Seidel, Raimund","last_name":"Seidel","first_name":"Raimund"},{"full_name":"Wiedera, Tilo","first_name":"Tilo","last_name":"Wiedera"}],"volume":69,"date_updated":"2023-08-14T12:51:25Z","date_created":"2022-08-28T22:02:01Z","acknowledgement":"This work was started during the 6th Austrian–Japanese–Mexican–Spanish Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants for the good atmosphere as well as discussions on the topic. Also, we thank Jan Kynčl for sending us remarks on a preliminary version of this work and an anonymous referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie grant agreement No 754411. Fabian Klute was partially supported by the Netherlands Organisation for Scientific Research (NWO) under project no. 612.001.651 and by the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was also partially supported by the Independent Research Fund Denmark grant 2020-2023 (9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded by the Ministry of Universities of Spain and the European Union (NextGenerationEU). Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.","year":"2023","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"month":"04","doi":"10.1007/s00454-022-00394-9","language":[{"iso":"eng"}],"external_id":{"arxiv":["1909.07347"],"isi":["000840292800001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1"},{"language":[{"iso":"eng"}],"doi":"10.1007/s00446-022-00441-x","quality_controlled":"1","isi":1,"external_id":{"arxiv":["2008.01009"],"isi":["000913424000001"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2008.01009"}],"month":"09","publication_identifier":{"eissn":["1432-0452"],"issn":["0178-2770"]},"date_created":"2023-01-22T23:00:55Z","date_updated":"2023-08-14T12:54:32Z","volume":36,"author":[{"full_name":"Aksenov, Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87","first_name":"Vitalii","last_name":"Aksenov"},{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Drozdova","first_name":"Alexandra","full_name":"Drozdova, Alexandra"},{"last_name":"Mohtashami","first_name":"Amirkeivan","full_name":"Mohtashami, Amirkeivan"}],"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Springer Nature","year":"2023","date_published":"2023-09-01T00:00:00Z","article_type":"original","page":"395-418","publication":"Distributed Computing","citation":{"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.","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.","short":"V. Aksenov, D.-A. Alistarh, A. Drozdova, A. Mohtashami, Distributed Computing 36 (2023) 395–418.","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.","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.","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","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"},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","status":"public","title":"The splay-list: A distribution-adaptive concurrent skip-list","intvolume":" 36","_id":"12330","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}],"type":"journal_article"},{"intvolume":" 32","ddc":["570"],"status":"public","title":"On the origin and structure of haplotype blocks","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12159","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_MolecularEcology_Shipilina.pdf","file_size":7144607,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14062","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","success":1,"date_created":"2023-08-16T08:15:41Z","date_updated":"2023-08-16T08:15:41Z"}],"type":"journal_article","issue":"6","abstract":[{"lang":"eng","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."}],"page":"1441-1457","article_type":"original","citation":{"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","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.","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.","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","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.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 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."},"publication":"Molecular Ecology","date_published":"2023-03-01T00:00:00Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","pmid":1,"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).","year":"2023","volume":32,"date_updated":"2023-08-16T08:18:47Z","date_created":"2023-01-12T12:09:17Z","author":[{"first_name":"Daria","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria"},{"last_name":"Pal","first_name":"Arka","orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","full_name":"Pal, Arka"},{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Chan, Yingguang Frank","last_name":"Chan","first_name":"Yingguang Frank"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"file_date_updated":"2023-08-16T08:15:41Z","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"The maintenance of alternative adaptive peaks in snapdragons"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000900762000001"],"pmid":["36433653"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/mec.16793","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"month":"03"},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["Structural Biology"],"date_published":"2023-01-01T00:00:00Z","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.","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).","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.","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","ista":"Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.","apa":"Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079","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."},"publication":"Journal of Structural Biology: X","article_type":"original","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"}],"type":"journal_article","file":[{"date_updated":"2023-08-16T09:36:28Z","date_created":"2023-08-16T09:36:28Z","checksum":"b4b1c10a31018aafe053b7d55a470e54","success":1,"relation":"main_file","file_id":"14064","content_type":"application/pdf","file_size":5132322,"creator":"dernst","file_name":"2023_JourStrucBiologyX_Gauto.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12114","intvolume":" 7","title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","ddc":["570"],"status":"public","publication_identifier":{"issn":["2590-1524"]},"month":"01","doi":"10.1016/j.yjsbx.2022.100079","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["36578472"]},"oa":1,"quality_controlled":"1","file_date_updated":"2023-08-16T09:36:28Z","article_number":"100079","author":[{"last_name":"Gauto","first_name":"Diego F.","full_name":"Gauto, Diego F."},{"full_name":"Lebedenko, Olga O.","last_name":"Lebedenko","first_name":"Olga O."},{"last_name":"Becker","first_name":"Lea Marie","orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","full_name":"Becker, Lea Marie"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"full_name":"Lichtenecker, Roman","last_name":"Lichtenecker","first_name":"Roman"},{"full_name":"Skrynnikov, Nikolai R.","first_name":"Nikolai R.","last_name":"Skrynnikov"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul"}],"volume":7,"date_created":"2023-01-12T11:55:38Z","date_updated":"2023-08-16T09:37:25Z","pmid":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”.","year":"2023","publisher":"Elsevier","department":[{"_id":"PaSc"}],"publication_status":"published"},{"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"scopus_import":"1","date_published":"2023-03-01T00:00:00Z","page":"762-777","article_type":"review","citation":{"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.","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","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.","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","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.","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.","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777."},"publication":"FEBS Letters","issue":"6","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."}],"type":"journal_article","file":[{"file_name":"2023_FEBSLetters_Loose.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":3148143,"file_id":"14063","relation":"main_file","date_created":"2023-08-16T08:31:04Z","date_updated":"2023-08-16T08:31:04Z","success":1,"checksum":"7492244d3f9c5faa1347ef03f6e5bc84"}],"oa_version":"Published Version","intvolume":" 597","ddc":["570"],"status":"public","title":"In vitro reconstitution of small GTPase regulation","_id":"12163","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0014-5793"],"eissn":["1873-3468"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1002/1873-3468.14540","isi":1,"quality_controlled":"1","external_id":{"isi":["000891573000001"],"pmid":["36448231"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"file_date_updated":"2023-08-16T08:31:04Z","volume":597,"date_updated":"2023-08-16T08:32:29Z","date_created":"2023-01-12T12:09:58Z","author":[{"last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"},{"full_name":"Auer, Albert","orcid":"0000-0002-3580-2906","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","last_name":"Auer","first_name":"Albert"},{"id":"D96FFDA0-A884-11E9-9968-DC26E6697425","last_name":"Brognara","first_name":"Gabriel","full_name":"Brognara, Gabriel"},{"full_name":"Budiman, Hanifatul R","first_name":"Hanifatul R","last_name":"Budiman","id":"55380f95-15b2-11ec-abd3-aff8e230696b"},{"full_name":"Kowalski, Lukasz M","id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2","last_name":"Kowalski","first_name":"Lukasz M"},{"full_name":"Matijevic, Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","first_name":"Ivana","last_name":"Matijevic"}],"publisher":"Wiley","department":[{"_id":"MaLo"}],"publication_status":"published","pmid":1,"year":"2023","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."},{"article_type":"original","page":"29-43","publication":"Distributed Computing","citation":{"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","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.","ista":"Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 36, 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","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.","short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023) 29–43.","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."},"date_published":"2023-03-01T00:00:00Z","keyword":["Computational Theory and Mathematics","Computer Networks and Communications","Hardware and Architecture","Theoretical Computer Science"],"scopus_import":"1","day":"01","article_processing_charge":"No","title":"Long-lived counters with polylogarithmic amortized step complexity","status":"public","intvolume":" 36","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12164","oa_version":"Preprint","type":"journal_article","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"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000890138700001"]},"main_file_link":[{"open_access":"1","url":"https://drops.dagstuhl.de/opus/volltexte/2019/11310/"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00446-022-00439-5","month":"03","publication_identifier":{"eissn":["1432-0452"],"issn":["0178-2770"]},"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer Nature","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).","year":"2023","date_updated":"2023-08-16T08:39:36Z","date_created":"2023-01-12T12:10:08Z","volume":36,"author":[{"full_name":"Baig, Mirza Ahad","last_name":"Baig","first_name":"Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425"},{"full_name":"Hendler, Danny","last_name":"Hendler","first_name":"Danny"},{"full_name":"Milani, Alessia","last_name":"Milani","first_name":"Alessia"},{"last_name":"Travers","first_name":"Corentin","full_name":"Travers, Corentin"}]},{"article_number":"1097467","file_date_updated":"2023-02-06T07:56:14Z","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Frontiers","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.","year":"2023","pmid":1,"date_updated":"2023-08-16T11:37:52Z","date_created":"2023-02-05T23:01:00Z","volume":16,"author":[{"first_name":"Irene","last_name":"Ortiz-Leal","full_name":"Ortiz-Leal, Irene"},{"first_name":"Mateo V.","last_name":"Torres","full_name":"Torres, Mateo V."},{"last_name":"Vargas Barroso","first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M"},{"full_name":"Fidalgo, Luis Eusebio","first_name":"Luis Eusebio","last_name":"Fidalgo"},{"first_name":"Ana María","last_name":"López-Beceiro","full_name":"López-Beceiro, Ana María"},{"full_name":"Larriva-Sahd, Jorge A.","first_name":"Jorge A.","last_name":"Larriva-Sahd"},{"first_name":"Pablo","last_name":"Sánchez-Quinteiro","full_name":"Sánchez-Quinteiro, Pablo"}],"month":"01","publication_identifier":{"eissn":["1662-5129"]},"quality_controlled":"1","isi":1,"external_id":{"isi":["000919786900001"],"pmid":["36704406"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3389/fnana.2022.1097467","type":"journal_article","abstract":[{"lang":"eng","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."}],"status":"public","ddc":["570"],"title":"The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway","intvolume":" 16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12515","oa_version":"Published Version","file":[{"checksum":"49cd40f3bda6f267079427042e7d15e3","success":1,"date_updated":"2023-02-06T07:56:14Z","date_created":"2023-02-06T07:56:14Z","relation":"main_file","file_id":"12518","content_type":"application/pdf","file_size":21943473,"creator":"dernst","access_level":"open_access","file_name":"2022_FrontiersNeuroanatomy_OrtizLeal.pdf"}],"scopus_import":"1","day":"10","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Frontiers in Neuroanatomy","citation":{"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.","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.","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","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.","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.","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)."},"date_published":"2023-01-10T00:00:00Z"},{"page":"813–823","article_type":"original","citation":{"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","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.","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.","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","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.","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.","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."},"publication":"Nature Biotechnology","date_published":"2023-06-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","intvolume":" 41","title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12106","oa_version":"Published Version","file":[{"file_name":"2023_NatureBioTech_Yeung.pdf","access_level":"open_access","creator":"dernst","file_size":12040976,"content_type":"application/pdf","file_id":"14066","relation":"main_file","date_created":"2023-08-16T11:30:45Z","date_updated":"2023-08-16T11:30:45Z","success":1,"checksum":"668447a1c8d360b68f8aaf9e08ed644f"}],"type":"journal_article","abstract":[{"text":"Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.","lang":"eng"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000909067600003"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41587-022-01560-3","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"month":"06","department":[{"_id":"ScienComp"}],"publisher":"Springer Nature","publication_status":"published","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.","year":"2023","volume":41,"date_created":"2023-01-08T23:00:53Z","date_updated":"2023-08-16T11:32:33Z","author":[{"full_name":"Yeung, Jake","last_name":"Yeung","first_name":"Jake","orcid":"0000-0003-1732-1559","id":"123012b2-db30-11eb-b4d8-a35840c0551b"},{"full_name":"Florescu, Maria","last_name":"Florescu","first_name":"Maria"},{"full_name":"Zeller, Peter","first_name":"Peter","last_name":"Zeller"},{"full_name":"De Barbanson, Buys Anton","last_name":"De Barbanson","first_name":"Buys Anton"},{"last_name":"Wellenstein","first_name":"Max D.","full_name":"Wellenstein, Max D."},{"full_name":"Van Oudenaarden, Alexander","first_name":"Alexander","last_name":"Van Oudenaarden"}],"file_date_updated":"2023-08-16T11:30:45Z"},{"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"}],"type":"journal_article","oa_version":"Preprint","_id":"12183","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 24","title":"The Bose Gas in a box with Neumann boundary conditions","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2023-05-01T00:00:00Z","citation":{"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","ista":"Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 24, 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.","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","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.","short":"C. Boccato, R. Seiringer, Annales Henri Poincare 24 (2023) 1505–1560.","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."},"publication":"Annales Henri Poincare","page":"1505-1560","article_type":"original","ec_funded":1,"author":[{"id":"342E7E22-F248-11E8-B48F-1D18A9856A87","first_name":"Chiara","last_name":"Boccato","full_name":"Boccato, Chiara"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"volume":24,"date_updated":"2023-08-16T11:34:03Z","date_created":"2023-01-15T23:00:52Z","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged.","year":"2023","department":[{"_id":"RoSe"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"issn":["1424-0637"]},"month":"05","doi":"10.1007/s00023-022-01252-3","language":[{"iso":"eng"}],"external_id":{"isi":["000910751800002"],"arxiv":["2205.15284"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2205.15284","open_access":"1"}],"oa":1,"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"13","citation":{"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.","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","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.","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","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.","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.","short":"P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and Modeling 63 (2023) 973–985."},"publication":"Journal of Chemical Information and Modeling","page":"973-985","article_type":"original","date_published":"2023-02-13T00:00:00Z","type":"journal_article","issue":"3","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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12544","intvolume":" 63","title":"Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives","ddc":["510","540"],"status":"public","file":[{"file_name":"2023_JCIM_Koehl.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":8069223,"file_id":"14070","relation":"main_file","date_updated":"2023-08-16T12:21:13Z","date_created":"2023-08-16T12:21:13Z","success":1,"checksum":"7d20562269edff1e31b9d6019d4983b0"}],"oa_version":"Published Version","publication_identifier":{"issn":["1549-9596"],"eissn":["1549-960X"]},"month":"02","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000920370700001"],"pmid":["36638318"]},"project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"doi":"10.1021/acs.jcim.2c01346","language":[{"iso":"eng"}],"ec_funded":1,"file_date_updated":"2023-08-16T12:21:13Z","pmid":1,"year":"2023","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).","publisher":"American Chemical Society","department":[{"_id":"HeEd"}],"publication_status":"published","author":[{"first_name":"Patrice","last_name":"Koehl","full_name":"Koehl, Patrice"},{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy"},{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"volume":63,"date_updated":"2023-08-16T12:22:07Z","date_created":"2023-02-12T23:00:59Z"},{"acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41559-023-01981-6","quality_controlled":"1","isi":1,"project":[{"grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip","call_identifier":"H2020"},{"name":"Host-Parasite Coevolution","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000924572800001"],"pmid":["36732670"]},"month":"03","publication_identifier":{"eissn":["2397-334X"]},"date_created":"2023-02-12T23:00:59Z","date_updated":"2023-08-16T11:55:48Z","volume":7,"author":[{"full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","last_name":"Stock","first_name":"Miriam"},{"full_name":"Milutinovic, Barbara","first_name":"Barbara","last_name":"Milutinovic","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8214-4758"},{"full_name":"Hönigsberger, Michaela","id":"953894f3-25bd-11ec-8556-f70a9d38ef60","first_name":"Michaela","last_name":"Hönigsberger"},{"full_name":"Grasse, Anna V","first_name":"Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wiesenhofer, Florian","last_name":"Wiesenhofer","first_name":"Florian","id":"39523C54-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kampleitner, Niklas","last_name":"Kampleitner","first_name":"Niklas","id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671"},{"full_name":"Schmitt, Thomas","last_name":"Schmitt","first_name":"Thomas"},{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/","relation":"press_release","description":"News on ISTA website"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"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.","year":"2023","pmid":1,"file_date_updated":"2023-08-16T11:54:59Z","ec_funded":1,"date_published":"2023-03-01T00:00:00Z","article_type":"original","page":"450-460","publication":"Nature Ecology and Evolution","citation":{"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","ieee":"M. Stock et al., “Pathogen evasion of social immunity,” Nature Ecology and Evolution, vol. 7. Springer Nature, pp. 450–460, 2023.","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","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.","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.","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.","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."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"14069","relation":"main_file","success":1,"checksum":"8244f4650a0e7aeea488d1bcd4a31702","date_created":"2023-08-16T11:54:59Z","date_updated":"2023-08-16T11:54:59Z","access_level":"open_access","file_name":"2023_NatureEcoEvo_Stock.pdf","creator":"dernst","file_size":1600499,"content_type":"application/pdf"}],"status":"public","title":"Pathogen evasion of social immunity","ddc":["570"],"intvolume":" 7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12543","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"}],"type":"journal_article"},{"oa_version":"Published Version","file":[{"file_id":"14068","relation":"main_file","success":1,"checksum":"a240a041cb9b9b7c8ba93a4706674a3f","date_created":"2023-08-16T11:43:33Z","date_updated":"2023-08-16T11:43:33Z","access_level":"open_access","file_name":"2023_EvLetters_Mrnjavac.pdf","creator":"dernst","content_type":"application/pdf","file_size":2592189}],"status":"public","ddc":["570"],"title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","intvolume":" 7","_id":"12521","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"}],"issue":"1","type":"journal_article","date_published":"2023-02-01T00:00:00Z","article_type":"original","publication":"Evolution Letters","citation":{"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","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.","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.","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","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.","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."},"day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","date_created":"2023-02-06T13:59:12Z","date_updated":"2023-08-16T11:44:32Z","volume":7,"author":[{"full_name":"Mrnjavac, Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea","last_name":"Mrnjavac"},{"full_name":"Khudiakova, Kseniia","first_name":"Kseniia","last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"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).","year":"2023","pmid":1,"file_date_updated":"2023-08-16T11:43:33Z","ec_funded":1,"article_number":"qrac004","language":[{"iso":"eng"}],"doi":"10.1093/evlett/qrac004","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001021692200001"],"pmid":["37065438"]},"month":"02","publication_identifier":{"issn":["2056-3744"]}},{"pmid":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.","year":"2023","department":[{"_id":"SiHi"}],"publisher":"Elsevier","publication_status":"published","author":[{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"volume":79,"date_updated":"2023-08-16T12:30:25Z","date_created":"2023-02-26T12:24:21Z","article_number":"102695","ec_funded":1,"file_date_updated":"2023-08-16T12:29:06Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["36842274"],"isi":["000953497700001"]},"project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"doi":"10.1016/j.conb.2023.102695","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0959-4388"]},"month":"04","_id":"12679","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 79","title":"Principles of neural stem cell lineage progression: Insights from developing cerebral cortex","ddc":["570"],"status":"public","oa_version":"Published Version","file":[{"file_size":1787894,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_CurrentOpinionNeurobio_Hippenmeyer.pdf","checksum":"4d11c4ca87e6cbc4d2ac46d3225ea615","success":1,"date_updated":"2023-08-16T12:29:06Z","date_created":"2023-08-16T12:29:06Z","relation":"main_file","file_id":"14071"}],"type":"journal_article","issue":"4","abstract":[{"lang":"eng","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."}],"citation":{"ista":"Hippenmeyer S. 2023. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4), 102695.","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.","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","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","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.","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.","short":"S. Hippenmeyer, Current Opinion in Neurobiology 79 (2023)."},"publication":"Current Opinion in Neurobiology","article_type":"review","date_published":"2023-04-01T00:00:00Z","scopus_import":"1","keyword":["General Neuroscience"],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01"},{"file_date_updated":"2023-08-16T11:40:02Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","author":[{"full_name":"Agresti, Antonio","last_name":"Agresti","first_name":"Antonio","orcid":"0000-0002-9573-2962","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72"},{"full_name":"Lindemulder, Nick","first_name":"Nick","last_name":"Lindemulder"},{"full_name":"Veraar, Mark","last_name":"Veraar","first_name":"Mark"}],"volume":296,"date_updated":"2023-08-16T11:41:42Z","date_created":"2023-01-29T23:00:59Z","year":"2023","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).","publisher":"Wiley","department":[{"_id":"JuFi"}],"publication_status":"published","publication_identifier":{"eissn":["1522-2616"],"issn":["0025-584X"]},"month":"04","doi":"10.1002/mana.202100192","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"arxiv":["2104.05063"],"isi":["000914134900001"]},"isi":1,"quality_controlled":"1","issue":"4","abstract":[{"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.","lang":"eng"}],"type":"journal_article","file":[{"file_size":449280,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_MathNachrichten_Agresti.pdf","checksum":"6f099f1d064173784d1a27716a2cc795","success":1,"date_created":"2023-08-16T11:40:02Z","date_updated":"2023-08-16T11:40:02Z","relation":"main_file","file_id":"14067"}],"oa_version":"Published Version","_id":"12429","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 296","ddc":["510"],"title":"On the trace embedding and its applications to evolution equations","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2023-04-01T00:00:00Z","citation":{"ista":"Agresti A, Lindemulder N, Veraar M. 2023. On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. 296(4), 1319–1350.","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.","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","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","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.","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.","short":"A. Agresti, N. Lindemulder, M. Veraar, Mathematische Nachrichten 296 (2023) 1319–1350."},"publication":"Mathematische Nachrichten","page":"1319-1350","article_type":"original"},{"oa_version":"Preprint","status":"public","title":"Bogoliubov dynamics and higher-order corrections for the regularized Nelson model","intvolume":" 35","_id":"12430","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"}],"issue":"4","type":"journal_article","date_published":"2023-01-09T00:00:00Z","article_type":"original","publication":"Reviews in Mathematical Physics","citation":{"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.","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.","short":"M. Falconi, N.K. Leopold, D.J. Mitrouskas, S.P. Petrat, Reviews in Mathematical Physics 35 (2023).","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.","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","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.","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"},"day":"09","article_processing_charge":"No","scopus_import":"1","date_created":"2023-01-29T23:00:59Z","date_updated":"2023-08-16T11:47:27Z","volume":35,"author":[{"full_name":"Falconi, Marco","first_name":"Marco","last_name":"Falconi"},{"full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","last_name":"Leopold","first_name":"Nikolai K"},{"id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","last_name":"Mitrouskas","first_name":"David Johannes","full_name":"Mitrouskas, David Johannes"},{"full_name":"Petrat, Sören P","first_name":"Sören P","last_name":"Petrat","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9166-5889"}],"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"World Scientific Publishing","year":"2023","article_number":"2350006","language":[{"iso":"eng"}],"doi":"10.1142/S0129055X2350006X","isi":1,"quality_controlled":"1","external_id":{"arxiv":["2110.00458"],"isi":["000909760300001"]},"oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2110.00458"}],"month":"01","publication_identifier":{"issn":["0129-055X"]}},{"language":[{"iso":"eng"}],"doi":"10.1038/s43588-023-00410-9","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015","name":"Efficient coding with biophysical realism"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2108.06686"]},"month":"03","publication_identifier":{"eissn":["2662-8457"]},"date_updated":"2023-08-16T12:41:53Z","date_created":"2023-03-26T22:01:08Z","volume":3,"author":[{"last_name":"Lombardi","first_name":"Fabrizio","orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","full_name":"Lombardi, Fabrizio"},{"full_name":"Pepic, Selver","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425","last_name":"Pepic","first_name":"Selver"},{"full_name":"Shriki, Oren","last_name":"Shriki","first_name":"Oren"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","first_name":"Daniele","full_name":"De Martino, Daniele"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GaTk"},{"_id":"GradSch"}],"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.).","year":"2023","file_date_updated":"2023-08-16T12:39:57Z","ec_funded":1,"date_published":"2023-03-20T00:00:00Z","article_type":"original","page":"254-263","publication":"Nature Computational Science","citation":{"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.","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","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.","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263.","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.","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."},"day":"20","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"date_created":"2023-08-16T12:39:57Z","date_updated":"2023-08-16T12:39:57Z","checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","success":1,"relation":"main_file","file_id":"14073","content_type":"application/pdf","file_size":4474284,"creator":"dernst","file_name":"2023_NatureCompScience_Lombardi.pdf","access_level":"open_access"}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","intvolume":" 3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12762","abstract":[{"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.","lang":"eng"}],"type":"journal_article"},{"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Paderborn, Germany","start_date":"2023-07-10","end_date":"2023-07-14"},"doi":"10.4230/LIPIcs.ICALP.2023.69","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"unknown":["2211.09606"]},"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer"}],"month":"07","publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]},"author":[{"first_name":"Gramoz","last_name":"Goranci","full_name":"Goranci, Gramoz"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"}],"date_updated":"2023-08-21T07:00:49Z","date_created":"2023-08-20T22:01:14Z","volume":261,"year":"2023","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (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.","publication_status":"published","department":[{"_id":"MoHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2023-08-21T06:59:05Z","ec_funded":1,"article_number":"69","date_published":"2023-07-01T00:00:00Z","publication":"50th International Colloquium on Automata, Languages, and Programming","citation":{"short":"G. Goranci, M.H. Henzinger, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","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.","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.","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","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","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."},"day":"01","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","file":[{"file_name":"2023_LIPIcsICALP_Goranci.pdf","access_level":"open_access","creator":"dernst","file_size":875910,"content_type":"application/pdf","file_id":"14089","relation":"main_file","date_created":"2023-08-21T06:59:05Z","date_updated":"2023-08-21T06:59:05Z","success":1,"checksum":"074177e815a1656de5d4071c7a3dffa6"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14085","ddc":["000"],"status":"public","title":"Efficient data structures for incremental exact and approximate maximum flow","intvolume":" 261","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"}],"type":"conference","alternative_title":["LIPIcs"]},{"_id":"14084","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Parameter estimation for Gibbs distributions","status":"public","ddc":["000","510"],"intvolume":" 261","file":[{"date_created":"2023-08-21T06:45:16Z","date_updated":"2023-08-21T06:45:16Z","checksum":"6dee0684245bb1c524b9c955db1e933d","success":1,"relation":"main_file","file_id":"14088","file_size":917791,"content_type":"application/pdf","creator":"dernst","file_name":"2023_LIPIcsICALP_Harris.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","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."}],"publication":"50th International Colloquium on Automata, Languages, and Programming","citation":{"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.","short":"D.G. Harris, V. Kolmogorov, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","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.","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","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.","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.","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"},"date_published":"2023-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","year":"2023","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.","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"VlKo"}],"author":[{"first_name":"David G.","last_name":"Harris","full_name":"Harris, David G."},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-21T06:49:11Z","date_created":"2023-08-20T22:01:14Z","volume":261,"article_number":"72","file_date_updated":"2023-08-21T06:45:16Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2007.10824"]},"quality_controlled":"1","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Paderborn, Germany","start_date":"2023-07-10","end_date":"2023-07-14"},"doi":"10.4230/LIPIcs.ICALP.2023.72","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]}},{"month":"07","publication_identifier":{"isbn":["9783959772785"],"issn":["18688969"]},"quality_controlled":"1","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2305.00122"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2023-07-14","location":"Paderborn, Germany","start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"doi":"10.4230/LIPIcs.ICALP.2023.74","article_number":"74","file_date_updated":"2023-08-21T07:04:36Z","ec_funded":1,"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"MoHe"}],"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.","year":"2023","date_created":"2023-08-20T22:01:14Z","date_updated":"2023-08-21T07:05:47Z","volume":261,"author":[{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"full_name":"Liu, Paul","first_name":"Paul","last_name":"Liu"},{"last_name":"Vondrák","first_name":"Jan","full_name":"Vondrák, Jan"},{"full_name":"Zheng, Da Wei","last_name":"Zheng","first_name":"Da Wei"}],"scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","publication":"50th International Colloquium on Automata, Languages, and Programming","citation":{"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.","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.","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.","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.","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.","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"},"date_published":"2023-07-01T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","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."}],"ddc":["000"],"status":"public","title":"Faster submodular maximization for several classes of matroids","intvolume":" 261","_id":"14086","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_created":"2023-08-21T07:04:36Z","date_updated":"2023-08-21T07:04:36Z","success":1,"checksum":"a5eef225014e003efbfbe4830fdd23cb","file_id":"14090","relation":"main_file","creator":"dernst","file_size":930943,"content_type":"application/pdf","file_name":"2023_LIPIcsICALP_HenzingerM.pdf","access_level":"open_access"}]},{"has_accepted_license":"1","article_processing_charge":"Yes","day":"01","scopus_import":"1","date_published":"2023-07-01T00:00:00Z","citation":{"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","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.","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.","short":"N. Resch, C. Yuan, Y. Zhang, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","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.","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."},"publication":"50th International Colloquium on Automata, Languages, and Programming","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."}],"type":"conference","alternative_title":["LIPIcs"],"file":[{"file_name":"2023_LIPIcsICALP_Resch.pdf","access_level":"open_access","creator":"dernst","file_size":1141497,"content_type":"application/pdf","file_id":"14091","relation":"main_file","date_created":"2023-08-21T07:23:18Z","date_updated":"2023-08-21T07:23:18Z","success":1,"checksum":"a449143fec3fbebb092cb8ef3b53c226"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14083","intvolume":" 261","status":"public","ddc":["000"],"title":"Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772785"]},"month":"07","doi":"10.4230/LIPIcs.ICALP.2023.99","conference":{"end_date":"2023-07-14","location":"Paderborn, Germany","start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2210.07754"]},"quality_controlled":"1","file_date_updated":"2023-08-21T07:23:18Z","article_number":"99","author":[{"last_name":"Resch","first_name":"Nicolas","full_name":"Resch, Nicolas"},{"last_name":"Yuan","first_name":"Chen","full_name":"Yuan, Chen"},{"first_name":"Yihan","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258","full_name":"Zhang, Yihan"}],"volume":261,"date_updated":"2023-08-21T07:26:01Z","date_created":"2023-08-20T22:01:13Z","year":"2023","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.","department":[{"_id":"MaMo"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published"},{"issue":"9","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"}],"type":"journal_article","file":[{"checksum":"c4f2f6eea0408811f8f4898e15890355","success":1,"date_created":"2023-02-28T12:20:27Z","date_updated":"2023-02-28T12:20:27Z","relation":"main_file","file_id":"12698","content_type":"application/pdf","file_size":2301864,"creator":"ggrosjea","access_level":"open_access","file_name":"Main_Preprint.pdf"},{"relation":"main_file","file_id":"12699","checksum":"6af6ed6c97a977f923de4162294b43c4","success":1,"date_updated":"2023-02-28T12:20:55Z","date_created":"2023-02-28T12:20:55Z","access_level":"open_access","file_name":"Suppl_info.pdf","file_size":1138625,"content_type":"application/pdf","creator":"ggrosjea"},{"file_size":793449,"content_type":"video/mp4","creator":"ggrosjea","access_level":"open_access","file_name":"Suppl_vid1.mp4","checksum":"3f20365fb9515bdba3a111d912c8d8b4","success":1,"date_created":"2023-02-28T12:37:54Z","date_updated":"2023-02-28T12:37:54Z","relation":"main_file","file_id":"12700"},{"success":1,"checksum":"90cecacbe0e2f9dea11f91a4ba20c32e","date_created":"2023-02-28T12:37:54Z","date_updated":"2023-02-28T12:37:54Z","file_id":"12701","relation":"main_file","creator":"ggrosjea","file_size":455925,"content_type":"video/mp4","access_level":"open_access","file_name":"Suppl_vid2.mp4"}],"oa_version":"Preprint","intvolume":" 130","title":"Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media","ddc":["530","537"],"status":"public","_id":"12697","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","has_accepted_license":"1","day":"03","keyword":["General Physics","Electrostatics","Triboelectricity","Soft Matter","Acoustic Levitation","Granular Materials"],"date_published":"2023-03-03T00:00:00Z","article_type":"original","citation":{"short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Letters 130 (2023).","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.","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.","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","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","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."},"publication":"Physical Review Letters","ec_funded":1,"file_date_updated":"2023-02-28T12:37:54Z","article_number":"098202","volume":130,"date_updated":"2023-08-22T08:41:32Z","date_created":"2023-02-28T12:14:46Z","related_material":{"record":[{"id":"8101","status":"public","relation":"research_paper"}]},"author":[{"id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","orcid":"0000-0001-5154-417X","first_name":"Galien M","last_name":"Grosjean","full_name":"Grosjean, Galien M"},{"full_name":"Waitukaitis, Scott R","first_name":"Scott R","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176"}],"department":[{"_id":"ScWa"}],"publisher":"American Physical Society","publication_status":"published","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.","year":"2023","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.130.098202","project":[{"grant_number":"949120","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2211.02488"],"isi":["000946178200008"]},"main_file_link":[{"url":"https://arxiv.org/abs/2211.02488","open_access":"1"}]},{"publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-030-5"]},"month":"05","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:13175","project":[{"grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020"},{"grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"file_date_updated":"2023-07-06T11:35:15Z","date_updated":"2023-08-24T11:16:35Z","date_created":"2023-06-30T08:07:43Z","related_material":{"record":[{"id":"12900","relation":"old_edition","status":"public"},{"id":"10924","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"9114"}]},"author":[{"full_name":"Sahu, Rishabh","first_name":"Rishabh","last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162"}],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2023","has_accepted_license":"1","article_processing_charge":"No","day":"05","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"date_published":"2023-05-05T00:00:00Z","page":"202","citation":{"short":"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:13175.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13175.","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:13175","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","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria."},"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"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"file_size":18688376,"content_type":"application/pdf","creator":"cchlebak","file_name":"thesis_pdfa.pdf","access_level":"open_access","date_created":"2023-06-30T08:17:25Z","date_updated":"2023-06-30T08:17:25Z","checksum":"7d03f1a5a5258ee43dfc3323dea4e08f","success":1,"relation":"main_file","file_id":"13176"},{"access_level":"closed","file_name":"thesis.zip","content_type":"application/x-zip-compressed","file_size":37847025,"creator":"cchlebak","relation":"source_file","file_id":"13196","checksum":"c3b45317ae58e0527533f98c202d81b7","date_created":"2023-07-06T11:35:15Z","date_updated":"2023-07-06T11:35:15Z"}],"oa_version":"Published Version","title":"Cavity quantum electrooptics","status":"public","ddc":["537","535","539"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"13175"},{"publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","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.","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.","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","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.","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.","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"},"page":"14964-14973","date_published":"2023-06-26T00:00:00Z","scopus_import":"1","day":"26","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14242","title":"Quantization-aware interval bound propagation for training certifiably robust quantized neural networks","status":"public","intvolume":" 37","oa_version":"Preprint","type":"conference","abstract":[{"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.","lang":"eng"}],"issue":"12","external_id":{"arxiv":["2211.16187"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.16187","open_access":"1"}],"quality_controlled":"1","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"},{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"conference":{"start_date":"2023-02-07","location":"Washington, DC, United States","end_date":"2023-02-14","name":"AAAI: Conference on Artificial Intelligence"},"doi":"10.1609/aaai.v37i12.26747","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"isbn":["9781577358800"]},"year":"2023","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.","publication_status":"published","publisher":"Association for the Advancement of Artificial Intelligence","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"author":[{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner"},{"last_name":"Zikelic","first_name":"Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"first_name":"Daniela","last_name":"Rus","full_name":"Rus, Daniela"}],"date_created":"2023-08-27T22:01:17Z","date_updated":"2023-09-05T07:06:14Z","volume":37,"ec_funded":1},{"ec_funded":1,"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published","year":"2023","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.","volume":37,"date_created":"2023-08-27T22:01:18Z","date_updated":"2023-09-05T08:37:00Z","author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy"},{"first_name":"Ismael R","last_name":"Jecker","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","full_name":"Jecker, Ismael R"},{"first_name":"Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde"}],"publication_identifier":{"isbn":["9781577358800"]},"month":"06","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"quality_controlled":"1","external_id":{"arxiv":["2211.13626"]},"main_file_link":[{"url":"https://doi.org/10.1609/aaai.v37i5.25679","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1609/aaai.v37i5.25679","conference":{"name":"AAAI: Conference on Artificial Intelligence","end_date":"2023-02-14","location":"Washington, DC, United States","start_date":"2023-02-07"},"type":"conference","issue":"5","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."}],"intvolume":" 37","title":"Bidding graph games with partially-observable budgets","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14243","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"27","page":"5464-5471","citation":{"short":"G. Avni, I.R. Jecker, D. Zikelic, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, 2023, 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.","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","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.","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","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."},"publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","date_published":"2023-06-27T00:00:00Z"},{"type":"conference","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"}],"title":"Stealth shaper: Reflectivity optimization as surface stylization","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14241","oa_version":"Preprint","scopus_import":"1","day":"23","article_processing_charge":"No","publication":"SIGGRAPH 2023 Conference Proceedings","citation":{"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.","short":"K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH 2023 Conference Proceedings, Association for Computing Machinery, 2023.","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.","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","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.","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"},"date_published":"2023-07-23T00:00:00Z","article_number":"20","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"BeBi"}],"year":"2023","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","date_created":"2023-08-27T22:01:17Z","date_updated":"2023-09-05T07:22:03Z","author":[{"first_name":"Kenji","last_name":"Tojo","full_name":"Tojo, Kenji"},{"first_name":"Ariel","last_name":"Shamir","full_name":"Shamir, Ariel"},{"full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Umetani, Nobuyuki","first_name":"Nobuyuki","last_name":"Umetani"}],"month":"07","publication_identifier":{"isbn":["9798400701597"]},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.05944"}],"external_id":{"arxiv":["2305.05944"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2023-08-10","start_date":"2023-08-06","location":"Los Angeles, CA, United States","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference"},"doi":"10.1145/3588432.3591542"},{"abstract":[{"lang":"eng","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."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Published Version","file":[{"file_id":"13327","relation":"main_file","date_created":"2023-07-31T08:11:20Z","date_updated":"2023-07-31T08:11:20Z","success":1,"checksum":"ccaf94bf7d658ba012c016e11869b54c","file_name":"2023_LNCS_CAV_HenzingerT.pdf","access_level":"open_access","creator":"dernst","file_size":647760,"content_type":"application/pdf"}],"intvolume":" 13965","ddc":["000"],"title":"Monitoring algorithmic fairness","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"13310","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"18","date_published":"2023-07-18T00:00:00Z","page":"358–382","citation":{"short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification, Springer Nature, 2023, 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.","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.","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","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.","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","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."},"publication":"Computer Aided Verification","ec_funded":1,"file_date_updated":"2023-07-31T08:11:20Z","volume":13965,"date_updated":"2023-09-05T15:14:00Z","date_created":"2023-07-25T18:32:40Z","author":[{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"first_name":"Mahyar","last_name":"Karimi","id":"f1dedef5-2f78-11ee-989a-c4c97bccf506","orcid":"0009-0005-0820-1696","full_name":"Karimi, Mahyar"},{"full_name":"Kueffner, Konstantin","first_name":"Konstantin","last_name":"Kueffner","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","orcid":"0000-0001-8974-2542"},{"full_name":"Mallik, Kaushik","last_name":"Mallik","first_name":"Kaushik","orcid":"0000-0001-9864-7475","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598"}],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","acknowledgement":"This work is supported by the European Research Council under Grant No.: ERC-2020-AdG101020093.","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783031377037"],"isbn":["9783031377020"],"eissn":["1611-3349"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-37703-7_17","conference":{"name":"CAV: Computer Aided Verification","end_date":"2023-07-22","location":"Paris, France","start_date":"2023-07-17"},"project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2305.15979"]}},{"date_published":"2023-01-01T00:00:00Z","publication":"Annals of Surgical Oncology","citation":{"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","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.","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","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.","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."},"article_type":"original","page":"35-45","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","keyword":["Oncology","Surgery"],"file":[{"file_id":"12490","relation":"main_file","date_created":"2023-02-02T13:01:20Z","date_updated":"2023-02-02T13:01:20Z","success":1,"checksum":"36a1200e1011f4b2155a8041d0308f34","file_name":"2023_AnnalsSurgicalOncology_Glajzer.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":365865}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"12205","ddc":["610"],"status":"public","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","intvolume":" 30","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"}],"type":"journal_article","doi":"10.1245/s10434-022-12459-3","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000852125500006"]},"isi":1,"quality_controlled":"1","month":"01","publication_identifier":{"eissn":["1534-4681"],"issn":["1068-9265"]},"author":[{"first_name":"Jacek","last_name":"Glajzer","full_name":"Glajzer, Jacek"},{"first_name":"Dan Cacsire","last_name":"Castillo-Tong","full_name":"Castillo-Tong, Dan Cacsire"},{"first_name":"Rolf","last_name":"Richter","full_name":"Richter, Rolf"},{"full_name":"Vergote, Ignace","last_name":"Vergote","first_name":"Ignace"},{"full_name":"Kulbe, Hagen","first_name":"Hagen","last_name":"Kulbe"},{"full_name":"Vanderstichele, Adriaan","last_name":"Vanderstichele","first_name":"Adriaan"},{"full_name":"Ruscito, Ilary","first_name":"Ilary","last_name":"Ruscito"},{"last_name":"Trillsch","first_name":"Fabian","full_name":"Trillsch, Fabian"},{"full_name":"Mustea, Alexander","last_name":"Mustea","first_name":"Alexander"},{"full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Kreuzinger"},{"full_name":"Gourley, Charlie","first_name":"Charlie","last_name":"Gourley"},{"first_name":"Hani","last_name":"Gabra","full_name":"Gabra, Hani"},{"full_name":"Taube, Eliane T.","last_name":"Taube","first_name":"Eliane T."},{"last_name":"Dorigo","first_name":"Oliver","full_name":"Dorigo, Oliver"},{"full_name":"Horst, David","first_name":"David","last_name":"Horst"},{"last_name":"Keunecke","first_name":"Carlotta","full_name":"Keunecke, Carlotta"},{"full_name":"Baum, Joanna","last_name":"Baum","first_name":"Joanna"},{"full_name":"Angelotti, Timothy","last_name":"Angelotti","first_name":"Timothy"},{"first_name":"Jalid","last_name":"Sehouli","full_name":"Sehouli, Jalid"},{"full_name":"Braicu, Elena Ioana","first_name":"Elena Ioana","last_name":"Braicu"}],"related_material":{"record":[{"id":"12115","status":"public","relation":"other"}]},"date_created":"2023-01-16T09:44:36Z","date_updated":"2023-09-05T15:18:37Z","volume":30,"year":"2023","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.","publication_status":"published","department":[{"_id":"JoDa"}],"publisher":"Springer Nature","file_date_updated":"2023-02-02T13:01:20Z"},{"scopus_import":"1","keyword":["Oncology","Surgery"],"day":"01","article_processing_charge":"No","publication":"Annals of Surgical Oncology","citation":{"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","ieee":"J. Glajzer et al., “ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 46–47, 2023.","ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 46–47.","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","chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12681-z.","short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 46–47.","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."},"article_type":"original","page":"46-47","date_published":"2023-01-01T00:00:00Z","type":"journal_article","_id":"12115","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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","status":"public","intvolume":" 30","oa_version":"Published Version","month":"01","publication_identifier":{"issn":["1068-9265"],"eissn":["1534-4681"]},"external_id":{"isi":["000879151800001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1245/s10434-022-12681-z"}],"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1245/s10434-022-12681-z","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by European Commission’s Seventh Framework Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).","year":"2023","publication_status":"published","department":[{"_id":"JoDa"}],"publisher":"Springer Nature","author":[{"full_name":"Glajzer, Jacek","last_name":"Glajzer","first_name":"Jacek"},{"full_name":"Castillo-Tong, Dan Cacsire","first_name":"Dan Cacsire","last_name":"Castillo-Tong"},{"last_name":"Richter","first_name":"Rolf","full_name":"Richter, Rolf"},{"last_name":"Vergote","first_name":"Ignace","full_name":"Vergote, Ignace"},{"first_name":"Hagen","last_name":"Kulbe","full_name":"Kulbe, Hagen"},{"first_name":"Adriaan","last_name":"Vanderstichele","full_name":"Vanderstichele, Adriaan"},{"last_name":"Ruscito","first_name":"Ilary","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","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"},{"first_name":"Charlie","last_name":"Gourley","full_name":"Gourley, Charlie"},{"first_name":"Hani","last_name":"Gabra","full_name":"Gabra, Hani"},{"full_name":"Taube, Eliane T.","first_name":"Eliane T.","last_name":"Taube"},{"last_name":"Dorigo","first_name":"Oliver","full_name":"Dorigo, Oliver"},{"full_name":"Horst, David","last_name":"Horst","first_name":"David"},{"first_name":"Carlotta","last_name":"Keunecke","full_name":"Keunecke, Carlotta"},{"first_name":"Joanna","last_name":"Baum","full_name":"Baum, Joanna"},{"last_name":"Angelotti","first_name":"Timothy","full_name":"Angelotti, Timothy"},{"last_name":"Sehouli","first_name":"Jalid","full_name":"Sehouli, Jalid"},{"first_name":"Elena Ioana","last_name":"Braicu","full_name":"Braicu, Elena Ioana"}],"related_material":{"record":[{"id":"12205","status":"public","relation":"other"}]},"date_created":"2023-01-12T11:56:22Z","date_updated":"2023-09-05T15:18:36Z","volume":30},{"file":[{"success":1,"checksum":"6ab8aab4e957f626a09a1c73db3388fb","date_updated":"2023-09-06T06:50:07Z","date_created":"2023-09-06T06:50:07Z","file_id":"14270","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":9412549,"access_level":"open_access","file_name":"2023_NatureComm_Vierra.pdf"}],"oa_version":"Published Version","intvolume":" 14","ddc":["570"],"title":"Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling","status":"public","_id":"14253","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2023-08-26T00:00:00Z","article_type":"original","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.","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","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","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.","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.","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)."},"publication":"Nature Communications","has_accepted_license":"1","article_processing_charge":"Yes","day":"26","scopus_import":"1","volume":14,"date_updated":"2023-09-06T06:53:32Z","date_created":"2023-09-03T22:01:14Z","author":[{"first_name":"Nicholas C.","last_name":"Vierra","full_name":"Vierra, Nicholas C."},{"first_name":"Luisa","last_name":"Ribeiro-Silva","full_name":"Ribeiro-Silva, Luisa"},{"full_name":"Kirmiz, Michael","last_name":"Kirmiz","first_name":"Michael"},{"first_name":"Deborah","last_name":"Van Der List","full_name":"Van Der List, Deborah"},{"full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","first_name":"Pradeep"},{"full_name":"Mack, Olivia A.","last_name":"Mack","first_name":"Olivia A."},{"full_name":"Carroll, James","last_name":"Carroll","first_name":"James"},{"full_name":"Le Monnier, Elodie","last_name":"Le Monnier","first_name":"Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aicher, Sue A.","first_name":"Sue A.","last_name":"Aicher"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"full_name":"Trimmer, James S.","first_name":"James S.","last_name":"Trimmer"}],"publisher":"Springer Nature","department":[{"_id":"RySh"}],"publication_status":"published","pmid":1,"year":"2023","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.).","file_date_updated":"2023-09-06T06:50:07Z","article_number":"5231","language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-40930-6","quality_controlled":"1","external_id":{"pmid":["37633939"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["2041-1723"]},"month":"08"},{"month":"07","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377051"]},"language":[{"iso":"eng"}],"conference":{"location":"Paris, France","start_date":"2023-07-17","end_date":"2023-07-22","name":"CAV: Computer Aided Verification"},"doi":"10.1007/978-3-031-37706-8_20","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2023-09-06T08:25:50Z","date_updated":"2023-09-06T08:27:33Z","date_created":"2023-09-03T22:01:16Z","volume":13964,"author":[{"full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer","first_name":"Tobias","orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"},{"full_name":"Prokop, Maximilian","first_name":"Maximilian","last_name":"Prokop"},{"full_name":"Rieder, Sabine","last_name":"Rieder","first_name":"Sabine"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"year":"2023","acknowledgement":"This research was funded in part by the German Research Foundation (DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).","day":"17","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","date_published":"2023-07-17T00:00:00Z","page":"390-414","publication":"35th International Conference on Computer Aided Verification ","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.","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.","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.","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.","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","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"},"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"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Published Version","file":[{"file_id":"14276","relation":"main_file","date_updated":"2023-09-06T08:25:50Z","date_created":"2023-09-06T08:25:50Z","success":1,"checksum":"ed66278b61bb869e1baba3d9b9081271","file_name":"2023_LNCS_CAV_Kretinsky.pdf","access_level":"open_access","creator":"dernst","file_size":428354,"content_type":"application/pdf"}],"ddc":["000"],"title":"Guessing winning policies in LTL synthesis by semantic learning","status":"public","intvolume":" 13964","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14259"},{"date_published":"2023-08-01T00:00:00Z","citation":{"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.","short":"S. Mathis, L.A. Bugnet, Astronomy and Astrophysics 676 (2023).","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.","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","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.","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.","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"},"publication":"Astronomy and Astrophysics","article_type":"letter_note","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":458120,"access_level":"open_access","file_name":"2023_AstronomyAstrophysics_Mathis.pdf","success":1,"checksum":"7b30d26fb2b7bcb5b5be1414950615f9","date_created":"2023-09-06T07:13:19Z","date_updated":"2023-09-06T07:13:19Z","file_id":"14271","relation":"main_file"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"14256","intvolume":" 676","title":"Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields","status":"public","ddc":["520"],"abstract":[{"lang":"eng","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."}],"type":"journal_article","doi":"10.1051/0004-6361/202346832","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001046037700007"],"arxiv":["2306.11587"]},"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"month":"08","author":[{"full_name":"Mathis, S.","first_name":"S.","last_name":"Mathis"},{"last_name":"Bugnet","first_name":"Lisa Annabelle","orcid":"0000-0003-0142-4000","id":"d9edb345-f866-11ec-9b37-d119b5234501","full_name":"Bugnet, Lisa Annabelle"}],"volume":676,"date_updated":"2023-09-06T11:05:58Z","date_created":"2023-09-03T22:01:15Z","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.","year":"2023","publisher":"EDP Sciences","department":[{"_id":"LiBu"}],"publication_status":"published","file_date_updated":"2023-09-06T07:13:19Z","article_number":"L9"},{"file":[{"access_level":"open_access","file_name":"2023_JourPhysChemistry_Gamper.pdf","content_type":"application/pdf","file_size":4986859,"creator":"dernst","relation":"main_file","file_id":"14272","checksum":"637454e2b3a357498d8d622d241c4bf6","success":1,"date_created":"2023-09-06T07:32:39Z","date_updated":"2023-09-06T07:32:39Z"}],"oa_version":"Published Version","intvolume":" 14","status":"public","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","ddc":["530","540"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"14261","issue":"33","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"}],"type":"journal_article","date_published":"2023-08-11T00:00:00Z","page":"7395-7403","article_type":"original","citation":{"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.","short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403.","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.","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","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.","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.","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"},"publication":"Journal of Physical Chemistry Letters","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"11","scopus_import":"1","volume":14,"date_updated":"2023-09-06T11:04:31Z","date_created":"2023-09-03T22:01:16Z","author":[{"full_name":"Gamper, Jakob","last_name":"Gamper","first_name":"Jakob"},{"id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","last_name":"Kluibenschedl","first_name":"Florian","full_name":"Kluibenschedl, Florian"},{"first_name":"Alexander K.H.","last_name":"Weiss","full_name":"Weiss, Alexander K.H."},{"full_name":"Hofer, Thomas S.","last_name":"Hofer","first_name":"Thomas S."}],"department":[{"_id":"GradSch"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2023","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","language":[{"iso":"eng"}],"doi":"10.1021/acs.jpclett.3c01707","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001048165800001"],"pmid":["37566743"]},"oa":1,"publication_identifier":{"eissn":["1948-7185"]},"month":"08"},{"language":[{"iso":"eng"}],"doi":"10.1103/prxlife.1.013001","quality_controlled":"1","project":[{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"07","publication_identifier":{"issn":["2835-8279"]},"date_created":"2023-09-06T08:30:59Z","date_updated":"2023-09-15T06:39:17Z","volume":1,"author":[{"full_name":"Boocock, Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1585-2631","first_name":"Daniel R","last_name":"Boocock"},{"last_name":"Hirashima","first_name":"Tsuyoshi","full_name":"Hirashima, Tsuyoshi"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"}],"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"American Physical Society","acknowledgement":"We thank all members of the Hannezo group for discussions and suggestions, as well as Sound Wai Phow for technical assistance. This work received funding from the European Research Council under the EU Horizon 2020 research and innovation program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and the Ministry of Education under the Research Centres of Excellence program through the MBI at NUS.","year":"2023","file_date_updated":"2023-09-15T06:30:50Z","ec_funded":1,"article_number":"013001","date_published":"2023-07-20T00:00:00Z","article_type":"original","publication":"PRX Life","citation":{"ista":"Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.","ieee":"D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers,” PRX Life, vol. 1, no. 1. American Physical Society, 2023.","apa":"Boocock, D. R., Hirashima, T., & Hannezo, E. B. (2023). Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. American Physical Society. https://doi.org/10.1103/prxlife.1.013001","ama":"Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 2023;1(1). doi:10.1103/prxlife.1.013001","chicago":"Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” PRX Life. American Physical Society, 2023. https://doi.org/10.1103/prxlife.1.013001.","mla":"Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” PRX Life, vol. 1, no. 1, 013001, American Physical Society, 2023, doi:10.1103/prxlife.1.013001.","short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023)."},"day":"20","has_accepted_license":"1","article_processing_charge":"Yes","file":[{"relation":"main_file","file_id":"14335","date_updated":"2023-09-15T06:30:50Z","date_created":"2023-09-15T06:30:50Z","checksum":"f881d98c89eb9f1aa136d7b781511553","success":1,"file_name":"2023_PRXLife_Boocock.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2559520,"creator":"dernst"}],"oa_version":"Published Version","ddc":["570"],"title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","status":"public","intvolume":" 1","_id":"14277","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Living tissues are characterized by an intrinsically mechanochemical interplay of active physical forces and complex biochemical signaling pathways. Either feature alone can give rise to complex emergent phenomena, for example, mechanically driven glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion instabilities. An important question is how to quantitatively assess the contribution of these different cues to the large-scale dynamics of biological materials. We address this in Madin-Darby canine kidney (MDCK) monolayers, considering both mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling activity and cellular density as well as a mechanically active tissue rheology via a self-propelled vertex model. We show that the relative strength of active migration forces to mechanochemical couplings controls a transition from a uniform active glass to periodic spatiotemporal waves. We parametrize the model from published experimental data sets on MDCK monolayers and use it to make new predictions on the correlation functions of cellular dynamics and the dynamics of topological defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers are best described by an intermediary parameter region in which both mechanochemical couplings and noisy active propulsion have a strong influence on the dynamics. Finally, we study how tissue rheology and ERK waves produce feedback on one another and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical waves at both the local and global levels."}],"issue":"1","type":"journal_article"},{"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Inter-and intracellular signalling in schizophrenia","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","grant_number":"607616"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37632747"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2023.113015","month":"09","publication_identifier":{"eissn":["2211-1247"]},"publication_status":"published","publisher":"Elsevier","department":[{"_id":"JoCs"}],"year":"2023","acknowledgement":"We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS (grant 607616).","pmid":1,"date_created":"2023-09-10T22:01:11Z","date_updated":"2023-09-15T07:14:12Z","volume":42,"author":[{"first_name":"Michele","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele"},{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola","last_name":"Käfer","full_name":"Käfer, Karola"},{"full_name":"Stella, Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9439-3148","first_name":"Federico","last_name":"Stella"},{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"article_number":"113015","file_date_updated":"2023-09-15T07:12:46Z","ec_funded":1,"article_type":"original","publication":"Cell Reports","citation":{"ieee":"M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions,” Cell Reports, vol. 42, no. 9. Elsevier, 2023.","apa":"Nardin, M., Käfer, K., Stella, F., & Csicsvari, J. L. (2023). Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113015","ista":"Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9), 113015.","ama":"Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 2023;42(9). doi:10.1016/j.celrep.2023.113015","chicago":"Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.113015.","short":"M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).","mla":"Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” Cell Reports, vol. 42, no. 9, 113015, Elsevier, 2023, doi:10.1016/j.celrep.2023.113015."},"date_published":"2023-09-26T00:00:00Z","scopus_import":"1","day":"26","has_accepted_license":"1","article_processing_charge":"Yes","title":"Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions","status":"public","ddc":["570"],"intvolume":" 42","_id":"14314","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_updated":"2023-09-15T07:12:46Z","date_created":"2023-09-15T07:12:46Z","success":1,"checksum":"ca77a304fb813c292550b8604b0fb41d","file_id":"14337","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":4879455,"file_name":"2023_CellPress_Nardin.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations."}],"issue":"9"},{"month":"09","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.89066","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["37665327"]},"file_date_updated":"2023-09-15T06:59:10Z","article_number":"RP89066","date_created":"2023-09-10T22:01:11Z","date_updated":"2023-09-15T07:07:10Z","volume":12,"author":[{"full_name":"Cho, Ukrae H.","last_name":"Cho","first_name":"Ukrae H."},{"first_name":"Martin W","last_name":"Hetzer","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"Hetzer, Martin W"}],"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"MaHe"}],"acknowledgement":"We thank the members of the Hetzer laboratory, Tony Hunter (Salk), Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital) for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin (Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH), and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC). This work was also supported by the Mass Spectrometry Core of the Salk Institute with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine. We thank Jolene Diedrich and Antonio Pinto for technical support.","year":"2023","pmid":1,"day":"04","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2023-09-04T00:00:00Z","article_type":"original","publication":"eLife","citation":{"mla":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife, vol. 12, RP89066, eLife Sciences Publications, 2023, doi:10.7554/eLife.89066.","short":"U.H. Cho, M. Hetzer, ELife 12 (2023).","chicago":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife. eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.89066.","ama":"Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 2023;12. doi:10.7554/eLife.89066","ista":"Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.","apa":"Cho, U. H., & Hetzer, M. (2023). Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.89066","ieee":"U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress,” eLife, vol. 12. eLife Sciences Publications, 2023."},"abstract":[{"text":"During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels.","lang":"eng"}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2023_eLife_Cho.pdf","creator":"dernst","file_size":3703097,"content_type":"application/pdf","file_id":"14336","relation":"main_file","success":1,"checksum":"db24bf3d595507387b48d3799c33e289","date_updated":"2023-09-15T06:59:10Z","date_created":"2023-09-15T06:59:10Z"}],"oa_version":"Published Version","status":"public","title":"Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress","ddc":["570"],"intvolume":" 12","_id":"14315","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Published Version","file":[{"creator":"dernst","file_size":247917,"content_type":"application/pdf","file_name":"2023_elecJournCombinatorics_Anastos.pdf","access_level":"open_access","date_updated":"2023-09-15T08:02:09Z","date_created":"2023-09-15T08:02:09Z","success":1,"checksum":"52c46c8cb329f9aaee9ade01525f317b","file_id":"14338","relation":"main_file"}],"_id":"14319","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 30","status":"public","title":"Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets","ddc":["510"],"issue":"3","abstract":[{"lang":"eng","text":"We study multigraphs whose edge-sets are the union of three perfect matchings, M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6 n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2 f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture however that if G is bipartite, the same result holds with n - 2 replaced by n - 1. We give a construction that shows such a result would be tight. We\r\nalso make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities."}],"type":"journal_article","date_published":"2023-07-28T00:00:00Z","citation":{"mla":"Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” Electronic Journal of Combinatorics, vol. 30, no. 3, P3.10, Electronic Journal of Combinatorics, 2023, doi:10.37236/11714.","short":"M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics 30 (2023).","chicago":"Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11714.","ama":"Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. 2023;30(3). doi:10.37236/11714","ista":"Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. 30(3), P3.10.","apa":"Anastos, M., Fabian, D., Müyesser, A., & Szabó, T. (2023). Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11714","ieee":"M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets,” Electronic Journal of Combinatorics, vol. 30, no. 3. Electronic Journal of Combinatorics, 2023."},"publication":"Electronic Journal of Combinatorics","article_type":"original","article_processing_charge":"Yes","has_accepted_license":"1","day":"28","scopus_import":"1","author":[{"first_name":"Michael","last_name":"Anastos","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","full_name":"Anastos, Michael"},{"full_name":"Fabian, David","first_name":"David","last_name":"Fabian"},{"last_name":"Müyesser","first_name":"Alp","full_name":"Müyesser, Alp"},{"full_name":"Szabó, Tibor","first_name":"Tibor","last_name":"Szabó"}],"volume":30,"date_created":"2023-09-10T22:01:12Z","date_updated":"2023-09-15T08:12:30Z","acknowledgement":"Anastos has received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Sk lodowska-Curie grant agreement No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft (DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434).","year":"2023","department":[{"_id":"MaKw"}],"publisher":"Electronic Journal of Combinatorics","publication_status":"published","ec_funded":1,"file_date_updated":"2023-09-15T08:02:09Z","license":"https://creativecommons.org/licenses/by-nd/4.0/","article_number":"P3.10","doi":"10.37236/11714","language":[{"iso":"eng"}],"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"external_id":{"arxiv":["2212.03100"]},"oa":1,"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"quality_controlled":"1","publication_identifier":{"eissn":["1077-8926"]},"month":"07"},{"date_published":"2023-07-17T00:00:00Z","page":"16-39","publication":"Computer Aided Verification","citation":{"short":"Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification, Springer Nature, 2023, pp. 16–39.","mla":"Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” Computer Aided Verification, vol. 13966, Springer Nature, 2023, pp. 16–39, doi:10.1007/978-3-031-37709-9_2.","chicago":"Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In Computer Aided Verification, 13966:16–39. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_2.","ama":"Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic recurrence relations. In: Computer Aided Verification. Vol 13966. Springer Nature; 2023:16-39. doi:10.1007/978-3-031-37709-9_2","apa":"Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2023). Automated tail bound analysis for probabilistic recurrence relations. In Computer Aided Verification (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_2","ieee":"Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound analysis for probabilistic recurrence relations,” in Computer Aided Verification, Paris, France, 2023, vol. 13966, pp. 16–39.","ista":"Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 16–39."},"day":"17","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","oa_version":"Published Version","file":[{"date_updated":"2023-09-20T08:24:47Z","date_created":"2023-09-20T08:24:47Z","success":1,"checksum":"42917e086f8c7699f3bccf84f74fe000","file_id":"14348","relation":"main_file","creator":"dernst","file_size":624647,"content_type":"application/pdf","file_name":"2023_LNCS_Sun.pdf","access_level":"open_access"}],"ddc":["000"],"title":"Automated tail bound analysis for probabilistic recurrence relations","status":"public","intvolume":" 13966","_id":"14318","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Probabilistic recurrence relations (PRRs) are a standard formalism for describing the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem, the classical and most well-known approach is the cookbook method by Karp (JACM 1994), while other approaches are mostly limited to deriving tail bounds of specific PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing time and random passed sizes observe discrete or (piecewise) uniform distribution and whose recursive call is either a single procedure call or a divide-and-conquer. We first establish a theoretical approach via Markov’s inequality, and then instantiate the theoretical approach with a template-based algorithmic approach via a refined treatment of exponentiation. Experimental evaluation shows that our algorithmic approach is capable of deriving tail bounds that are (i) asymptotically tighter than Karp’s method, (ii) match the best-known manually-derived asymptotic tail bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor) than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover, our algorithmic approach handles all examples (including realistic PRRs such as QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing that our approach is efficient in practice.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"conference":{"end_date":"2023-07-22","start_date":"2023-07-17","location":"Paris, France","name":"CAV: Computer Aided Verification"},"doi":"10.1007/978-3-031-37709-9_2","quality_controlled":"1","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"07","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377082"]},"date_updated":"2023-09-20T08:25:57Z","date_created":"2023-09-10T22:01:12Z","volume":13966,"author":[{"first_name":"Yican","last_name":"Sun","full_name":"Sun, Yican"},{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"}],"related_material":{"link":[{"url":"https://github.com/boyvolcano/PRR","relation":"software"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"acknowledgement":"We thank Prof. Bican Xia for valuable information on the exponential theory of reals. The work is partially supported by the National Natural Science Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt), the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.","year":"2023","file_date_updated":"2023-09-20T08:24:47Z","ec_funded":1},{"department":[{"_id":"KrCh"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","acknowledgement":"This work was supported in part 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 as well as DST/CEFIPRA/INRIA project EQuaVE and SERB Matrices grant MTR/2018/00074.","volume":13966,"date_created":"2023-09-10T22:01:12Z","date_updated":"2023-09-20T09:04:40Z","author":[{"first_name":"S.","last_name":"Akshay","full_name":"Akshay, S."},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","first_name":"Tobias"},{"full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","first_name":"Dorde","last_name":"Zikelic"}],"ec_funded":1,"file_date_updated":"2023-09-20T08:46:43Z","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-37709-9_5","conference":{"location":"Paris, France","start_date":"2023-07-17","end_date":"2023-07-22","name":"CAV: Computer Aided Verification"},"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031377082"],"issn":["0302-9743"]},"month":"07","intvolume":" 13966","ddc":["000"],"status":"public","title":"MDPs as distribution transformers: Affine invariant synthesis for safety objectives","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14317","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":531745,"creator":"dernst","file_name":"2023_LNCS_Akshay.pdf","access_level":"open_access","date_updated":"2023-09-20T08:46:43Z","date_created":"2023-09-20T08:46:43Z","checksum":"f143c8eedf609f20f2aad2eeb496d53f","success":1,"relation":"main_file","file_id":"14349"}],"alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Markov decision processes can be viewed as transformers of probability distributions. While this view is useful from a practical standpoint to reason about trajectories of distributions, basic reachability and safety problems are known to be computationally intractable (i.e., Skolem-hard) to solve in such models. Further, we show that even for simple examples of MDPs, strategies for safety objectives over distributions can require infinite memory and randomization.\r\nIn light of this, we present a novel overapproximation approach to synthesize strategies in an MDP, such that a safety objective over the distributions is met. More precisely, we develop a new framework for template-based synthesis of certificates as affine distributional and inductive invariants for safety objectives in MDPs. We provide two algorithms within this framework. One can only synthesize memoryless strategies, but has relative completeness guarantees, while the other can synthesize general strategies. The runtime complexity of both algorithms is in PSPACE. We implement these algorithms and show that they can solve several non-trivial examples."}],"page":"86-112","citation":{"chicago":"Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” In International Conference on Computer Aided Verification, 13966:86–112. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_5.","mla":"Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” International Conference on Computer Aided Verification, vol. 13966, Springer Nature, 2023, pp. 86–112, doi:10.1007/978-3-031-37709-9_5.","short":"S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.","ista":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 86–112.","ieee":"S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution transformers: Affine invariant synthesis for safety objectives,” in International Conference on Computer Aided Verification, Paris, France, 2023, vol. 13966, pp. 86–112.","apa":"Akshay, S., Chatterjee, K., Meggendorfer, T., & Zikelic, D. (2023). MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In International Conference on Computer Aided Verification (Vol. 13966, pp. 86–112). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_5","ama":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In: International Conference on Computer Aided Verification. Vol 13966. Springer Nature; 2023:86-112. doi:10.1007/978-3-031-37709-9_5"},"publication":"International Conference on Computer Aided Verification","date_published":"2023-07-17T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"17"},{"month":"09","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"language":[{"iso":"eng"}],"doi":"10.1242/jcs.261448","quality_controlled":"1","oa":1,"external_id":{"pmid":["37539494"]},"main_file_link":[{"url":"https://doi.org/10.1101/2023.03.27.534325","open_access":"1"}],"article_number":"jcs261448","date_created":"2023-09-10T22:01:12Z","date_updated":"2023-09-20T09:14:15Z","volume":136,"author":[{"last_name":"Nagano","first_name":"Makoto","full_name":"Nagano, Makoto"},{"full_name":"Aoshima, Kaito","last_name":"Aoshima","first_name":"Kaito"},{"full_name":"Shimamura, Hiroki","first_name":"Hiroki","last_name":"Shimamura"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E"},{"last_name":"Toshima","first_name":"Junko Y.","full_name":"Toshima, Junko Y."},{"full_name":"Toshima, Jiro","first_name":"Jiro","last_name":"Toshima"}],"publication_status":"published","publisher":"The Company of Biologists","department":[{"_id":"DaSi"}],"year":"2023","pmid":1,"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2023-09-01T00:00:00Z","article_type":"original","publication":"Journal of Cell Science","citation":{"short":"M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Science 136 (2023).","mla":"Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of Cell Science, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:10.1242/jcs.261448.","chicago":"Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.261448.","ama":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 2023;136(17). doi:10.1242/jcs.261448","apa":"Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., & Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.261448","ieee":"M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J. Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway,” Journal of Cell Science, vol. 136, no. 17. The Company of Biologists, 2023.","ista":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 136(17), jcs261448."},"abstract":[{"lang":"eng","text":"Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport. In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted to generate distinct transport vesicles at the trans-Golgi network (TGN), and the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories for these adaptors. Recently, we showed that vesicle transport from the TGN is crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However, these observations were incompatible with previous studies showing that these adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall mechanism responsible for regulation of Vps21p activity remains ambiguous. Here, we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and Ypt32p were found to have partially overlapping functions for recruitment of AP-1 and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors for Vps21p activation in the TGN–endosome trafficking pathway."}],"issue":"17","type":"journal_article","oa_version":"Preprint","title":"Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway","status":"public","intvolume":" 136","_id":"14316","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Preprint","intvolume":" 108","status":"public","title":"Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14320","issue":"12","abstract":[{"text":"The development of two-dimensional materials has resulted in a diverse range of novel, high-quality compounds with increasing complexity. A key requirement for a comprehensive quantitative theory is the accurate determination of these materials' band structure parameters. However, this task is challenging due to the intricate band structures and the indirect nature of experimental probes. In this work, we introduce a general framework to derive band structure parameters from experimental data using deep neural networks. We applied our method to the penetration field capacitance measurement of trilayer graphene, an effective probe of its density of states. First, we demonstrate that a trained deep network gives accurate predictions for the penetration field capacitance as a function of tight-binding parameters. Next, we use the fast and accurate predictions from the trained network to automatically determine tight-binding parameters directly from experimental data, with extracted parameters being in a good agreement with values in the literature. We conclude by discussing potential applications of our method to other materials and experimental techniques beyond penetration field capacitance.","lang":"eng"}],"type":"journal_article","date_published":"2023-09-15T00:00:00Z","article_type":"original","citation":{"chicago":"Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young, and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.125411.","short":"P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical Review B 108 (2023).","mla":"Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” Physical Review B, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:10.1103/physrevb.108.125411.","ieee":"P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn, “Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene,” Physical Review B, vol. 108, no. 12. American Physical Society, 2023.","apa":"Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., & Serbyn, M. (2023). Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.108.125411","ista":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. 108(12), 125411.","ama":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. 2023;108(12). doi:10.1103/physrevb.108.125411"},"publication":"Physical Review B","article_processing_charge":"No","day":"15","scopus_import":"1","volume":108,"date_updated":"2023-09-20T09:38:24Z","date_created":"2023-09-12T07:12:12Z","author":[{"first_name":"Paul M","last_name":"Henderson","id":"13C09E74-18D9-11E9-8878-32CFE5697425","orcid":"0000-0002-5198-7445","full_name":"Henderson, Paul M"},{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan"},{"full_name":"Zibrov, Alexander A.","last_name":"Zibrov","first_name":"Alexander A."},{"full_name":"Young, Andrea F.","last_name":"Young","first_name":"Andrea F."},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"}],"publisher":"American Physical Society","department":[{"_id":"MaSe"},{"_id":"ChLa"},{"_id":"MiLe"}],"publication_status":"published","acknowledgement":"A.F.Y. acknowledges primary support from the Department of Energy under award DE-SC0020043, and additional support from the Gordon and Betty Moore Foundation under award GBMF9471 for group operations.","year":"2023","article_number":"125411","language":[{"iso":"eng"}],"doi":"10.1103/physrevb.108.125411","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2210.06310","open_access":"1"}],"external_id":{"arxiv":["2210.06310"]},"oa":1,"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"09"},{"page":"158","citation":{"mla":"Brighi, Pietro. Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12732.","short":"P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023.","chicago":"Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12732.","ama":"Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:10.15479/at:ista:12732","ista":"Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria.","apa":"Brighi, P. (2023). Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12732","ieee":"P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023."},"date_published":"2023-03-21T00:00:00Z","day":"21","article_processing_charge":"No","has_accepted_license":"1","ddc":["530"],"status":"public","title":"Ergodicity breaking in disordered and kinetically constrained quantum many-body systems","_id":"12732","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"None","file":[{"checksum":"5d2de651ef9449c1b8dc27148ca74777","date_updated":"2023-03-23T16:42:56Z","date_created":"2023-03-23T16:42:56Z","file_id":"12753","relation":"source_file","creator":"pbrighi","content_type":"application/zip","file_size":42167561,"access_level":"closed","file_name":"Thesis_sub_PBrighi.zip"},{"file_name":"Thesis_PBrighi.pdf","access_level":"open_access","file_size":13977000,"content_type":"application/pdf","creator":"pbrighi","relation":"main_file","file_id":"12754","date_created":"2023-03-23T16:43:14Z","date_updated":"2023-03-23T16:43:14Z","checksum":"7caa153d4a5b0873a79358787d2dfe1e","success":1}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices.\r\nGoing beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models.\r\nIn particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models.\r\nUsing tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods.\r\nIn this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges.\r\nInspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model.\r\nThe system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping.\r\nWe show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon.\r\nWe further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density.\r\nThis feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies.\r\nThe time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities.\r\nOur results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the topic of many-body localization proximity effect.\r\nWe study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons.\r\nThe interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong.\r\nWe furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings.","lang":"eng"}],"project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12732","month":"03","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"publisher":"Institute of Science and Technology Austria","year":"2023","date_updated":"2023-09-20T10:44:12Z","date_created":"2023-03-17T13:30:48Z","author":[{"last_name":"Brighi","first_name":"Pietro","orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","full_name":"Brighi, Pietro"}],"related_material":{"record":[{"id":"11470","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8308"},{"id":"11469","status":"public","relation":"part_of_dissertation"},{"id":"12750","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2023-03-23T16:43:14Z","ec_funded":1},{"keyword":["General Physics and Astronomy"],"article_processing_charge":"No","has_accepted_license":"1","day":"13","article_type":"original","citation":{"short":"P. Brighi, M. Ljubotina, M. Serbyn, SciPost Physics 15 (2023).","mla":"Brighi, Pietro, et al. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” SciPost Physics, vol. 15, no. 3, 093, SciPost Foundation, 2023, doi:10.21468/scipostphys.15.3.093.","chicago":"Brighi, Pietro, Marko Ljubotina, and Maksym Serbyn. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” SciPost Physics. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.15.3.093.","ama":"Brighi P, Ljubotina M, Serbyn M. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. 2023;15(3). doi:10.21468/scipostphys.15.3.093","ieee":"P. Brighi, M. Ljubotina, and M. Serbyn, “Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models,” SciPost Physics, vol. 15, no. 3. SciPost Foundation, 2023.","apa":"Brighi, P., Ljubotina, M., & Serbyn, M. (2023). Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.15.3.093","ista":"Brighi P, Ljubotina M, Serbyn M. 2023. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. 15(3), 093."},"publication":"SciPost Physics","date_published":"2023-09-13T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Quantum kinetically constrained models have recently attracted significant attention due to their anomalous dynamics and thermalization. In this work, we introduce a hitherto unexplored family of kinetically constrained models featuring conserved particle number and strong inversion-symmetry breaking due to facilitated hopping. We demonstrate that these models provide a generic example of so-called quantum Hilbert space fragmentation, that is manifested in disconnected sectors in the Hilbert space that are not apparent in the computational basis. Quantum Hilbert space fragmentation leads to an exponential in system size number of eigenstates with exactly zero entanglement entropy across several bipartite cuts. These eigenstates can be probed dynamically using quenches from simple initial product states. In addition, we study the particle spreading under unitary dynamics launched from the domain wall state, and find faster than diffusive dynamics at high particle densities, that crosses over into logarithmically slow relaxation at smaller densities. Using a classically simulable cellular automaton, we reproduce the logarithmic dynamics observed in the quantum case. Our work suggests that particle conserving constrained models with inversion symmetry breaking realize so far unexplored dynamical behavior and invite their further theoretical and experimental studies."}],"intvolume":" 15","status":"public","ddc":["530"],"title":"Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models","_id":"14334","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"2023_SciPostPhysics_Brighi.pdf","creator":"dernst","content_type":"application/pdf","file_size":4866506,"file_id":"14350","relation":"main_file","success":1,"checksum":"4cef6a8021f6b6c47ab2f2f2b1387ac2","date_created":"2023-09-20T10:46:10Z","date_updated":"2023-09-20T10:46:10Z"}],"oa_version":"Published Version","publication_identifier":{"issn":["2542-4653"]},"month":"09","project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"quality_controlled":"1","external_id":{"arxiv":["2210.15607"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.21468/scipostphys.15.3.093","article_number":"093","ec_funded":1,"file_date_updated":"2023-09-20T10:46:10Z","department":[{"_id":"MaSe"}],"publisher":"SciPost Foundation","publication_status":"published","year":"2023","acknowledgement":"We would like to thank Raimel A. Medina, Hansveer Singh, and Dmitry Abanin for useful\r\ndiscussions.The authors acknowledge support by the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). We acknowledge support by the Erwin Schrödinger International\r\nInstitute for Mathematics and Physics (ESI).","volume":15,"date_created":"2023-09-14T13:08:23Z","date_updated":"2023-09-20T10:46:29Z","related_material":{"record":[{"id":"12750","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Brighi, Pietro","last_name":"Brighi","first_name":"Pietro","orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ljubotina, Marko","orcid":"0000-0003-0038-7068","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina","first_name":"Marko"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym"}]},{"_id":"14321","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 159","title":"Achiral dipoles on a ferromagnet can affect its magnetization direction","status":"public","ddc":["530"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14322","checksum":"507ab65ab29e2c987c94cabad7c5370b","success":1,"date_updated":"2023-09-13T09:34:20Z","date_created":"2023-09-13T09:34:20Z","access_level":"open_access","file_name":"104103_1_5.0165806.pdf","content_type":"application/pdf","file_size":5749653,"creator":"acappell"}],"type":"journal_article","issue":"10","abstract":[{"text":"We demonstrate the possibility of a coupling between the magnetization direction of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate the mechanism of the coupling, we analyze a minimal Stoner model that includes Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet. The proposed mechanism allows us to study magnetic anisotropy of the system with an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can change magnetocrystalline anisotropy of the substrate. Our research aims to motivate further experimental studies of the current-free chirality induced spin selectivity effect involving both enantiomers.","lang":"eng"}],"citation":{"ama":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 2023;159(10). doi:10.1063/5.0165806","ista":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 159(10), 104103.","ieee":"R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles on a ferromagnet can affect its magnetization direction,” The Journal of Chemical Physics, vol. 159, no. 10. AIP Publishing, 2023.","apa":"Al Hyder, R., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0165806","mla":"Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” The Journal of Chemical Physics, vol. 159, no. 10, 104103, AIP Publishing, 2023, doi:10.1063/5.0165806.","short":"R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical Physics 159 (2023).","chicago":"Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” The Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0165806."},"publication":"The Journal of Chemical Physics","article_type":"original","date_published":"2023-09-11T00:00:00Z","scopus_import":"1","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"11","pmid":1,"year":"2023","acknowledgement":"We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan, and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot.","department":[{"_id":"MiLe"}],"publisher":"AIP Publishing","publication_status":"published","author":[{"full_name":"Al Hyder, Ragheed","first_name":"Ragheed","last_name":"Al Hyder","id":"d1c405be-ae15-11ed-8510-ccf53278162e"},{"full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro","first_name":"Alberto"},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"}],"volume":159,"date_updated":"2023-09-20T09:48:12Z","date_created":"2023-09-13T09:25:09Z","article_number":"104103","ec_funded":1,"file_date_updated":"2023-09-13T09:34:20Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["37694742"],"arxiv":["2306.17592"]},"project":[{"name":"Non-equilibrium Field Theory of Molecular Rotations","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338","grant_number":"101062862"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"quality_controlled":"1","doi":"10.1063/5.0165806","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"month":"09"},{"publication_identifier":{"issn":["0003-6951"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1063/5.0161713","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2306.09043"]},"oa":1,"file_date_updated":"2023-09-20T11:36:16Z","article_number":"091104","volume":123,"date_updated":"2023-09-20T11:50:06Z","date_created":"2023-09-17T22:01:09Z","author":[{"last_name":"Lorenc","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan"},{"full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87"}],"publisher":"AIP Publishing","department":[{"_id":"ZhAl"}],"publication_status":"published","year":"2023","acknowledgement":"The work was supported by IST Austria. The authors would like to gratefully acknowledge the help and assistance of Professor John M. Dudley.","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"28","scopus_import":"1","date_published":"2023-08-28T00:00:00Z","article_type":"original","citation":{"mla":"Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics Letters, vol. 123, no. 9, 091104, AIP Publishing, 2023, doi:10.1063/5.0161713.","short":"D. Lorenc, Z. Alpichshev, Applied Physics Letters 123 (2023).","chicago":"Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics Letters. AIP Publishing, 2023. https://doi.org/10.1063/5.0161713.","ama":"Lorenc D, Alpichshev Z. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. 2023;123(9). doi:10.1063/5.0161713","ista":"Lorenc D, Alpichshev Z. 2023. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. 123(9), 091104.","apa":"Lorenc, D., & Alpichshev, Z. (2023). Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. AIP Publishing. https://doi.org/10.1063/5.0161713","ieee":"D. Lorenc and Z. Alpichshev, “Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam,” Applied Physics Letters, vol. 123, no. 9. AIP Publishing, 2023."},"publication":"Applied Physics Letters","issue":"9","abstract":[{"text":"We propose a simple method to measure nonlinear Kerr refractive index in mid-infrared frequency range that avoids using sophisticated infrared detectors. Our approach is based on using a near-infrared probe beam which interacts with a mid-IR beam via wavelength-non-degenerate cross-phase modulation (XPM). By carefully measuring XPM-induced spectral modifications in the probe beam and comparing the experimental data with simulation results, we extract the value for the non-degenerate Kerr index. Finally, in order to obtain the value of degenerate mid-IR Kerr index, we use the well-established two-band formalism of Sheik-Bahae et al., which is shown to become particularly simple in the limit of low frequencies. The proposed technique is complementary to the conventional techniques, such as z-scan, and has the advantage of not requiring any mid-infrared detectors.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2023-09-20T11:36:16Z","date_created":"2023-09-20T11:36:16Z","success":1,"checksum":"89a1b604d58b209fec66c6b6f919ac98","file_id":"14353","relation":"main_file","creator":"dernst","file_size":1486715,"content_type":"application/pdf","file_name":"2023_ApplPhysLetter_Lorenc.pdf","access_level":"open_access"}],"intvolume":" 123","ddc":["530"],"title":"Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam","status":"public","_id":"14342","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"year":"2023","acknowledgement":"Jasmin Blanchette: This research has received funding from the Netherlands Organization\r\nfor Scientific Research (NWO) under the Vidi program (project No. 016.Vidi.189.037, Lean Forward).\r\n__\r\nWe thank Vladimir Kolmogorov for making this collaboration possible. We\r\nthank Václav Končický for discussing ideas about the Kleene star construction. We thank Patrick Johnson, Floris van Doorn, and Damiano Testa for their small yet very valuable contributions to our code. We thank Eric Wieser for simplifying one of our proofs. We thank Mark Summerfield for suggesting textual improvements. We thank the anonymous reviewers for very helpful comments. Finally, we thank the Lean community for helping us with various technical issues and answering many questions. ","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"publication_status":"published","related_material":{"link":[{"url":"https://github.com/madvorak/grammars/tree/publish","relation":"software"}]},"author":[{"id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","orcid":"0000-0001-5293-214X","first_name":"Martin","last_name":"Dvorak","full_name":"Dvorak, Martin"},{"last_name":"Blanchette","first_name":"Jasmin","full_name":"Blanchette, Jasmin"}],"volume":268,"date_created":"2023-06-05T07:29:05Z","date_updated":"2023-09-25T11:04:29Z","article_number":"15","file_date_updated":"2023-08-07T11:55:43Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2302.06420"]},"quality_controlled":"1","doi":"10.4230/LIPIcs.ITP.2023.15","conference":{"name":"ITP: International Conference on Interactive Theorem Proving","end_date":"2023-08-04","start_date":"2023-07-31","location":"Bialystok, Poland"},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772846"]},"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13120","intvolume":" 268","status":"public","title":"Closure properties of general grammars - formally verified","ddc":["000"],"oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":715976,"file_name":"2023_LIPIcS_Dvorak.pdf","access_level":"open_access","date_updated":"2023-08-07T11:55:43Z","date_created":"2023-08-07T11:55:43Z","success":1,"checksum":"773a0197f05b67feaa6cb1e17ec3642d","file_id":"13982","relation":"main_file"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"We formalized general (i.e., type-0) grammars using the Lean 3 proof assistant. We defined basic notions of rewrite rules and of words derived by a grammar, and used grammars to show closure of the class of type-0 languages under four operations: union, reversal, concatenation, and the Kleene star. The literature mostly focuses on Turing machine arguments, which are possibly more difficult to formalize. For the Kleene star, we could not follow the literature and came up with our own grammar-based construction."}],"citation":{"chicago":"Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” In 14th International Conference on Interactive Theorem Proving, Vol. 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ITP.2023.15.","short":"M. Dvorak, J. Blanchette, in:, 14th International Conference on Interactive Theorem Proving, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","mla":"Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” 14th International Conference on Interactive Theorem Proving, vol. 268, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ITP.2023.15.","ieee":"M. Dvorak and J. Blanchette, “Closure properties of general grammars - formally verified,” in 14th International Conference on Interactive Theorem Proving, Bialystok, Poland, 2023, vol. 268.","apa":"Dvorak, M., & Blanchette, J. (2023). Closure properties of general grammars - formally verified. In 14th International Conference on Interactive Theorem Proving (Vol. 268). Bialystok, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITP.2023.15","ista":"Dvorak M, Blanchette J. 2023. Closure properties of general grammars - formally verified. 14th International Conference on Interactive Theorem Proving. ITP: International Conference on Interactive Theorem Proving, LIPIcs, vol. 268, 15.","ama":"Dvorak M, Blanchette J. Closure properties of general grammars - formally verified. In: 14th International Conference on Interactive Theorem Proving. Vol 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ITP.2023.15"},"publication":"14th International Conference on Interactive Theorem Proving","date_published":"2023-07-27T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"27"},{"date_published":"2023-07-01T00:00:00Z","publication":"Journal of Graph Algorithms and Applications","citation":{"short":"A.M. Arroyo Guevara, S. Felsner, Journal of Graph Algorithms and Applications 27 (2023) 433–457.","mla":"Arroyo Guevara, Alan M., and Stefan Felsner. “Approximating the Bundled Crossing Number.” Journal of Graph Algorithms and Applications, vol. 27, no. 6, Brown University, 2023, pp. 433–57, doi:10.7155/jgaa.00629.","chicago":"Arroyo Guevara, Alan M, and Stefan Felsner. “Approximating the Bundled Crossing Number.” Journal of Graph Algorithms and Applications. Brown University, 2023. https://doi.org/10.7155/jgaa.00629.","ama":"Arroyo Guevara AM, Felsner S. Approximating the bundled crossing number. Journal of Graph Algorithms and Applications. 2023;27(6):433-457. doi:10.7155/jgaa.00629","ieee":"A. M. Arroyo Guevara and S. Felsner, “Approximating the bundled crossing number,” Journal of Graph Algorithms and Applications, vol. 27, no. 6. Brown University, pp. 433–457, 2023.","apa":"Arroyo Guevara, A. M., & Felsner, S. (2023). Approximating the bundled crossing number. Journal of Graph Algorithms and Applications. Brown University. https://doi.org/10.7155/jgaa.00629","ista":"Arroyo Guevara AM, Felsner S. 2023. Approximating the bundled crossing number. Journal of Graph Algorithms and Applications. 27(6), 433–457."},"article_type":"original","page":"433-457","day":"01","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"13979","date_created":"2023-08-07T08:00:48Z","date_updated":"2023-08-07T08:00:48Z","checksum":"9c30d2b8e324cc1c904f2aeec92013a3","success":1,"file_name":"2023_JourGraphAlgorithms_Arroyo.pdf","access_level":"open_access","file_size":865774,"content_type":"application/pdf","creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13969","status":"public","title":"Approximating the bundled crossing number","ddc":["510"],"intvolume":" 27","abstract":[{"lang":"eng","text":"Bundling crossings is a strategy which can enhance the readability\r\nof graph drawings. In this paper we consider good drawings, i.e., we require that\r\nany two edges have at most one common point which can be a common vertex or a\r\ncrossing. Our main result is that there is a polynomial-time algorithm to compute an\r\n8-approximation of the bundled crossing number of a good drawing with no toothed\r\nhole. In general the number of toothed holes has to be added to the 8-approximation.\r\nIn the special case of circular drawings the approximation factor is 8, this improves\r\nupon the 10-approximation of Fink et al. [14]. Our approach also works with the same\r\napproximation factor for families of pseudosegments, i.e., curves intersecting at most\r\nonce. We also show how to compute a 9/2-approximation when the intersection graph of\r\nthe pseudosegments is bipartite and has no toothed hole."}],"issue":"6","type":"journal_article","doi":"10.7155/jgaa.00629","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2109.14892"]},"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"month":"07","publication_identifier":{"issn":["1526-1719"]},"author":[{"full_name":"Arroyo Guevara, Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2401-8670","first_name":"Alan M","last_name":"Arroyo Guevara"},{"last_name":"Felsner","first_name":"Stefan","full_name":"Felsner, Stefan"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"11185"}]},"date_created":"2023-08-06T22:01:11Z","date_updated":"2023-09-25T10:56:10Z","volume":27,"acknowledgement":"This work was initiated during the Workshop on Geometric Graphs in November 2019 in Strobl, Austria. We would like to thank Oswin Aichholzer, Fabian Klute, Man-Kwun Chiu, Martin Balko, Pavel Valtr for their avid discussions during the workshop. The first author has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No 754411. The second author has been supported by the German Research Foundation DFG Project FE 340/12-1. An extended abstract of this paper has been published in the proceedings of WALCOM 2022 in the Springer LNCS series, vol. 13174, pages 383–395.","year":"2023","publication_status":"published","publisher":"Brown University","department":[{"_id":"UlWa"}],"file_date_updated":"2023-08-07T08:00:48Z","ec_funded":1},{"author":[{"full_name":"Anastos, Michael","first_name":"Michael","last_name":"Anastos","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb"}],"date_updated":"2023-09-25T09:13:41Z","date_created":"2023-09-17T22:01:10Z","volume":2023,"year":"2023","publication_status":"published","department":[{"_id":"MaKw"}],"publisher":"Society for Industrial and Applied Mathematics","conference":{"end_date":"2023-01-25","start_date":"2023-01-22","location":"Florence, Italy","name":"SODA: Symposium on Discrete Algorithms"},"doi":"10.1137/1.9781611977554.ch88","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2111.14759","open_access":"1"}],"external_id":{"arxiv":["2111.14759"]},"oa":1,"quality_controlled":"1","month":"01","publication_identifier":{"isbn":["9781611977554"]},"oa_version":"Preprint","_id":"14344","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Fast algorithms for solving the Hamilton cycle problem with high probability","status":"public","intvolume":" 2023","abstract":[{"text":"We study the Hamilton cycle problem with input a random graph G ~ G(n,p) in two different settings. In the first one, G is given to us in the form of randomly ordered adjacency lists while in the second one, we are given the adjacency matrix of G. In each of the two settings we derive a deterministic algorithm that w.h.p. either finds a Hamilton cycle or returns a certificate that such a cycle does not exist for p = p(n) ≥ 0. The running times of our algorithms are O(n) and respectively, each being best possible in its own setting.","lang":"eng"}],"type":"conference","date_published":"2023-01-01T00:00:00Z","publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","citation":{"chicago":"Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, 2023:2286–2323. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/1.9781611977554.ch88.","mla":"Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2023, Society for Industrial and Applied Mathematics, 2023, pp. 2286–323, doi:10.1137/1.9781611977554.ch88.","short":"M. Anastos, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 2286–2323.","ista":"Anastos M. 2023. Fast algorithms for solving the Hamilton cycle problem with high probability. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2023, 2286–2323.","ieee":"M. Anastos, “Fast algorithms for solving the Hamilton cycle problem with high probability,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy, 2023, vol. 2023, pp. 2286–2323.","apa":"Anastos, M. (2023). Fast algorithms for solving the Hamilton cycle problem with high probability. In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2023, pp. 2286–2323). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch88","ama":"Anastos M. Fast algorithms for solving the Hamilton cycle problem with high probability. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. Vol 2023. Society for Industrial and Applied Mathematics; 2023:2286-2323. doi:10.1137/1.9781611977554.ch88"},"page":"2286-2323","day":"01","article_processing_charge":"No","scopus_import":"1"},{"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":2898063,"creator":"dernst","access_level":"open_access","file_name":"2023_AdvancedMaterials_Schamberger.pdf","checksum":"5c04d68130e97a0ecd1ca27fbc15a246","success":1,"date_created":"2023-09-26T10:51:56Z","date_updated":"2023-09-26T10:51:56Z","relation":"main_file","file_id":"14373"}],"intvolume":" 35","ddc":["570"],"title":"Curvature in biological systems: Its quantification, emergence, and implications across the scales","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12710","issue":"13","abstract":[{"text":"Surface curvature both emerges from, and influences the behavior of, living objects at length scales ranging from cell membranes to single cells to tissues and organs. The relevance of surface curvature in biology is supported by numerous experimental and theoretical investigations in recent years. In this review, first, a brief introduction to the key ideas of surface curvature in the context of biological systems is given and the challenges that arise when measuring surface curvature are discussed. Giving an overview of the emergence of curvature in biological systems, its significance at different length scales becomes apparent. On the other hand, summarizing current findings also shows that both single cells and entire cell sheets, tissues or organisms respond to curvature by modulating their shape and their migration behavior. Finally, the interplay between the distribution of morphogens or micro-organisms and the emergence of curvature across length scales is addressed with examples demonstrating these key mechanistic principles of morphogenesis. Overall, this review highlights that curved interfaces are not merely a passive by-product of the chemical, biological, and mechanical processes but that curvature acts also as a signal that co-determines these processes.","lang":"eng"}],"type":"journal_article","date_published":"2023-03-29T00:00:00Z","article_type":"review","citation":{"ista":"Schamberger B, Ziege R, Anselme K, Ben Amar M, Bykowski M, Castro APG, Cipitria A, Coles RA, Dimova R, Eder M, Ehrig S, Escudero LM, Evans ME, Fernandes PR, Fratzl P, Geris L, Gierlinger N, Hannezo EB, Iglič A, Kirkensgaard JJK, Kollmannsberger P, Kowalewska Ł, Kurniawan NA, Papantoniou I, Pieuchot L, Pires THV, Renner LD, Sageman-Furnas AO, Schröder-Turk GE, Sengupta A, Sharma VR, Tagua A, Tomba C, Trepat X, Waters SL, Yeo EF, Roschger A, Bidan CM, Dunlop JWC. 2023. Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. 35(13), 2206110.","apa":"Schamberger, B., Ziege, R., Anselme, K., Ben Amar, M., Bykowski, M., Castro, A. P. G., … Dunlop, J. W. C. (2023). Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202206110","ieee":"B. Schamberger et al., “Curvature in biological systems: Its quantification, emergence, and implications across the scales,” Advanced Materials, vol. 35, no. 13. Wiley, 2023.","ama":"Schamberger B, Ziege R, Anselme K, et al. Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. 2023;35(13). doi:10.1002/adma.202206110","chicago":"Schamberger, Barbara, Ricardo Ziege, Karine Anselme, Martine Ben Amar, Michał Bykowski, André P.G. Castro, Amaia Cipitria, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” Advanced Materials. Wiley, 2023. https://doi.org/10.1002/adma.202206110.","mla":"Schamberger, Barbara, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” Advanced Materials, vol. 35, no. 13, 2206110, Wiley, 2023, doi:10.1002/adma.202206110.","short":"B. Schamberger, R. Ziege, K. Anselme, M. Ben Amar, M. Bykowski, A.P.G. Castro, A. Cipitria, R.A. Coles, R. Dimova, M. Eder, S. Ehrig, L.M. Escudero, M.E. Evans, P.R. Fernandes, P. Fratzl, L. Geris, N. Gierlinger, E.B. Hannezo, A. Iglič, J.J.K. Kirkensgaard, P. Kollmannsberger, Ł. Kowalewska, N.A. Kurniawan, I. Papantoniou, L. Pieuchot, T.H.V. Pires, L.D. Renner, A.O. Sageman-Furnas, G.E. Schröder-Turk, A. Sengupta, V.R. Sharma, A. Tagua, C. Tomba, X. Trepat, S.L. Waters, E.F. Yeo, A. Roschger, C.M. Bidan, J.W.C. Dunlop, Advanced Materials 35 (2023)."},"publication":"Advanced Materials","article_processing_charge":"No","has_accepted_license":"1","day":"29","scopus_import":"1","volume":35,"date_created":"2023-03-05T23:01:06Z","date_updated":"2023-09-26T10:56:46Z","author":[{"full_name":"Schamberger, Barbara","first_name":"Barbara","last_name":"Schamberger"},{"first_name":"Ricardo","last_name":"Ziege","full_name":"Ziege, Ricardo"},{"full_name":"Anselme, Karine","first_name":"Karine","last_name":"Anselme"},{"full_name":"Ben Amar, Martine","first_name":"Martine","last_name":"Ben Amar"},{"first_name":"Michał","last_name":"Bykowski","full_name":"Bykowski, Michał"},{"full_name":"Castro, André P.G.","first_name":"André P.G.","last_name":"Castro"},{"full_name":"Cipitria, Amaia","first_name":"Amaia","last_name":"Cipitria"},{"full_name":"Coles, Rhoslyn A.","last_name":"Coles","first_name":"Rhoslyn A."},{"full_name":"Dimova, Rumiana","last_name":"Dimova","first_name":"Rumiana"},{"full_name":"Eder, Michaela","last_name":"Eder","first_name":"Michaela"},{"first_name":"Sebastian","last_name":"Ehrig","full_name":"Ehrig, Sebastian"},{"full_name":"Escudero, Luis M.","last_name":"Escudero","first_name":"Luis M."},{"full_name":"Evans, Myfanwy E.","last_name":"Evans","first_name":"Myfanwy E."},{"first_name":"Paulo R.","last_name":"Fernandes","full_name":"Fernandes, Paulo R."},{"last_name":"Fratzl","first_name":"Peter","full_name":"Fratzl, Peter"},{"full_name":"Geris, Liesbet","first_name":"Liesbet","last_name":"Geris"},{"full_name":"Gierlinger, Notburga","last_name":"Gierlinger","first_name":"Notburga"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"last_name":"Iglič","first_name":"Aleš","full_name":"Iglič, Aleš"},{"full_name":"Kirkensgaard, Jacob J.K.","last_name":"Kirkensgaard","first_name":"Jacob J.K."},{"first_name":"Philip","last_name":"Kollmannsberger","full_name":"Kollmannsberger, Philip"},{"full_name":"Kowalewska, Łucja","last_name":"Kowalewska","first_name":"Łucja"},{"full_name":"Kurniawan, Nicholas A.","first_name":"Nicholas A.","last_name":"Kurniawan"},{"last_name":"Papantoniou","first_name":"Ioannis","full_name":"Papantoniou, Ioannis"},{"last_name":"Pieuchot","first_name":"Laurent","full_name":"Pieuchot, Laurent"},{"full_name":"Pires, Tiago H.V.","last_name":"Pires","first_name":"Tiago H.V."},{"first_name":"Lars D.","last_name":"Renner","full_name":"Renner, Lars D."},{"first_name":"Andrew O.","last_name":"Sageman-Furnas","full_name":"Sageman-Furnas, Andrew O."},{"full_name":"Schröder-Turk, Gerd E.","first_name":"Gerd E.","last_name":"Schröder-Turk"},{"full_name":"Sengupta, Anupam","last_name":"Sengupta","first_name":"Anupam"},{"full_name":"Sharma, Vikas R.","first_name":"Vikas R.","last_name":"Sharma"},{"first_name":"Antonio","last_name":"Tagua","full_name":"Tagua, Antonio"},{"last_name":"Tomba","first_name":"Caterina","full_name":"Tomba, Caterina"},{"first_name":"Xavier","last_name":"Trepat","full_name":"Trepat, Xavier"},{"last_name":"Waters","first_name":"Sarah L.","full_name":"Waters, Sarah L."},{"last_name":"Yeo","first_name":"Edwina F.","full_name":"Yeo, Edwina F."},{"full_name":"Roschger, Andreas","first_name":"Andreas","last_name":"Roschger"},{"full_name":"Bidan, Cécile M.","first_name":"Cécile M.","last_name":"Bidan"},{"last_name":"Dunlop","first_name":"John W.C.","full_name":"Dunlop, John W.C."}],"publisher":"Wiley","department":[{"_id":"EdHa"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"B.S. and A.R. contributed equally to this work. A.P.G.C. and P.R.F. acknowledge the funding from Fundação para a Ciência e Tecnologia (Portugal), through IDMEC, under LAETA project UIDB/50022/2020. T.H.V.P. acknowledges the funding from Fundação para a Ciência e Tecnologia (Portugal), through Ph.D. Grant 2020.04417.BD. A.S. acknowledges that this work was partially supported by the ATTRACT Investigator Grant (no. A17/MS/11572821/MBRACE, to A.S.) from the Luxembourg National Research Fund. The author thanks Gerardo Ceada for his help in the graphical representations. N.A.K. acknowledges support from the European Research Council (grant 851960) and the Gravitation Program “Materials Driven Regeneration,” funded by the Netherlands Organization for Scientific Research (024.003.013). M.B.A. acknowledges support from the French National Research Agency (grant ANR-201-8-CE1-3-0008 for the project “Epimorph”). G.E.S.T. acknowledges funding by the Australian Research Council through project DP200102593. A.C. acknowledges the funding from the Deutsche Forschungsgemeinschaft (DFG) Emmy Noether Grant CI 203/-2 1, the Spanish Ministry of Science and Innovation (PID2021-123013O-BI00) and the IKERBASQUE Basque Foundation for Science.","file_date_updated":"2023-09-26T10:51:56Z","article_number":"2206110","language":[{"iso":"eng"}],"doi":"10.1002/adma.202206110","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["36461812"],"isi":["000941068900001"]},"oa":1,"publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"month":"03"},{"language":[{"iso":"eng"}],"doi":"10.1126/science.adh9059","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.26434/chemrxiv-2023-gq2h0","open_access":"1"}],"oa":1,"month":"09","publication_identifier":{"eissn":["1095-9203"]},"date_updated":"2023-10-03T08:11:26Z","date_created":"2023-08-01T08:26:15Z","volume":381,"author":[{"full_name":"Gemen, Julius","last_name":"Gemen","first_name":"Julius"},{"full_name":"Church, Jonathan R.","last_name":"Church","first_name":"Jonathan R."},{"first_name":"Tero-Petri","last_name":"Ruoko","full_name":"Ruoko, Tero-Petri"},{"full_name":"Durandin, Nikita","last_name":"Durandin","first_name":"Nikita"},{"full_name":"Białek, Michał J.","last_name":"Białek","first_name":"Michał J."},{"first_name":"Maren","last_name":"Weissenfels","full_name":"Weissenfels, Maren"},{"full_name":"Feller, Moran","first_name":"Moran","last_name":"Feller"},{"full_name":"Kazes, Miri","first_name":"Miri","last_name":"Kazes"},{"first_name":"Veniamin A.","last_name":"Borin","full_name":"Borin, Veniamin A."},{"full_name":"Odaybat, Magdalena","last_name":"Odaybat","first_name":"Magdalena"},{"first_name":"Rishir","last_name":"Kalepu","full_name":"Kalepu, Rishir"},{"full_name":"Diskin-Posner, Yael","last_name":"Diskin-Posner","first_name":"Yael"},{"full_name":"Oron, Dan","first_name":"Dan","last_name":"Oron"},{"full_name":"Fuchter, Matthew J.","last_name":"Fuchter","first_name":"Matthew J."},{"full_name":"Priimagi, Arri","first_name":"Arri","last_name":"Priimagi"},{"full_name":"Schapiro, Igor","last_name":"Schapiro","first_name":"Igor"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"}],"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"RaKl"}],"acknowledgement":"We acknowledge funding from the European Union’s Horizon 2020 Research and Innovation Program [European Research Council grants 820008 (Ra.K.) and 101045223 (A.P.) and Marie Skłodowska-Curie grants 812868 (J.G.) and 101022777 (T.-P.R.)], the Academy of Finland [Center of Excellence Programme LIBER grant 346107 (A.P.), Flagship Programme PREIN grant 320165 (A.P.), and Postdoctoral Researcher grant 340103 (T.-P.R.)], Zuckerman STEM Leadership Program Fellowship (J.R.C.), President’s PhD Scholarship (M.O.), and the EPSRC [Established Career Fellowship grant EP/R00188X/1 (M.J.F.)].","year":"2023","date_published":"2023-09-22T00:00:00Z","article_type":"original","page":"1357-1363","publication":"Science","citation":{"short":"J. Gemen, J.R. Church, T.-P. Ruoko, N. Durandin, M.J. Białek, M. Weissenfels, M. Feller, M. Kazes, V.A. Borin, M. Odaybat, R. Kalepu, Y. Diskin-Posner, D. Oron, M.J. Fuchter, A. Priimagi, I. Schapiro, R. Klajn, Science 381 (2023) 1357–1363.","mla":"Gemen, Julius, et al. “Disequilibrating Azoarenes by Visible-Light Sensitization under Confinement.” Science, vol. 381, no. 6664, American Association for the Advancement of Science, 2023, pp. 1357–63, doi:10.1126/science.adh9059.","chicago":"Gemen, Julius, Jonathan R. Church, Tero-Petri Ruoko, Nikita Durandin, Michał J. Białek, Maren Weissenfels, Moran Feller, et al. “Disequilibrating Azoarenes by Visible-Light Sensitization under Confinement.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adh9059.","ama":"Gemen J, Church JR, Ruoko T-P, et al. Disequilibrating azoarenes by visible-light sensitization under confinement. Science. 2023;381(6664):1357-1363. doi:10.1126/science.adh9059","ieee":"J. Gemen et al., “Disequilibrating azoarenes by visible-light sensitization under confinement,” Science, vol. 381, no. 6664. American Association for the Advancement of Science, pp. 1357–1363, 2023.","apa":"Gemen, J., Church, J. R., Ruoko, T.-P., Durandin, N., Białek, M. J., Weissenfels, M., … Klajn, R. (2023). Disequilibrating azoarenes by visible-light sensitization under confinement. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adh9059","ista":"Gemen J, Church JR, Ruoko T-P, Durandin N, Białek MJ, Weissenfels M, Feller M, Kazes M, Borin VA, Odaybat M, Kalepu R, Diskin-Posner Y, Oron D, Fuchter MJ, Priimagi A, Schapiro I, Klajn R. 2023. Disequilibrating azoarenes by visible-light sensitization under confinement. Science. 381(6664), 1357–1363."},"day":"22","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Disequilibrating azoarenes by visible-light sensitization under confinement","status":"public","intvolume":" 381","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13340","abstract":[{"lang":"eng","text":"Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E-to-Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E-azobenzenes to the Z state. In this way, the host–photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation."}],"issue":"6664","type":"journal_article"},{"article_number":"074905","volume":158,"date_created":"2023-03-05T23:01:05Z","date_updated":"2023-10-03T11:31:51Z","author":[{"full_name":"Sorichetti, Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","orcid":"0000-0002-9645-6576","first_name":"Valerio","last_name":"Sorichetti"},{"first_name":"Andrea","last_name":"Ninarello","full_name":"Ninarello, Andrea"},{"first_name":"José","last_name":"Ruiz-Franco","full_name":"Ruiz-Franco, José"},{"last_name":"Hugouvieux","first_name":"Virginie","full_name":"Hugouvieux, Virginie"},{"full_name":"Zaccarelli, Emanuela","first_name":"Emanuela","last_name":"Zaccarelli"},{"full_name":"Micheletti, Cristian","first_name":"Cristian","last_name":"Micheletti"},{"first_name":"Walter","last_name":"Kob","full_name":"Kob, Walter"},{"full_name":"Rovigatti, Lorenzo","last_name":"Rovigatti","first_name":"Lorenzo"}],"department":[{"_id":"AnSa"}],"publisher":"American Institute of Physics","publication_status":"published","pmid":1,"acknowledgement":"We thank Michael Lang for helpful discussions. We acknowledge financial support from the European Research Council (ERC Consolidator Grant No. 681597, MIMIC) and from LabEx NUMEV (Grant No. ANR-10-LABX-20) funded by the “Investissements d’Avenir” French Government program, managed by the French National Research Agency (ANR). W.K. is a senior member of the Institut Universitaire de France.","year":"2023","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1063/5.0134271","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04810"}],"external_id":{"pmid":["36813705"],"isi":["000936943800002"],"arxiv":["2211.04810"]},"issue":"7","abstract":[{"text":"The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 158","title":"Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks","status":"public","_id":"12705","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"21","scopus_import":"1","date_published":"2023-02-21T00:00:00Z","article_type":"original","citation":{"mla":"Sorichetti, Valerio, et al. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” Journal of Chemical Physics, vol. 158, no. 7, 074905, American Institute of Physics, 2023, doi:10.1063/5.0134271.","short":"V. Sorichetti, A. Ninarello, J. Ruiz-Franco, V. Hugouvieux, E. Zaccarelli, C. Micheletti, W. Kob, L. Rovigatti, Journal of Chemical Physics 158 (2023).","chicago":"Sorichetti, Valerio, Andrea Ninarello, José Ruiz-Franco, Virginie Hugouvieux, Emanuela Zaccarelli, Cristian Micheletti, Walter Kob, and Lorenzo Rovigatti. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0134271.","ama":"Sorichetti V, Ninarello A, Ruiz-Franco J, et al. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. 2023;158(7). doi:10.1063/5.0134271","ista":"Sorichetti V, Ninarello A, Ruiz-Franco J, Hugouvieux V, Zaccarelli E, Micheletti C, Kob W, Rovigatti L. 2023. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. 158(7), 074905.","apa":"Sorichetti, V., Ninarello, A., Ruiz-Franco, J., Hugouvieux, V., Zaccarelli, E., Micheletti, C., … Rovigatti, L. (2023). Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/5.0134271","ieee":"V. Sorichetti et al., “Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks,” Journal of Chemical Physics, vol. 158, no. 7. American Institute of Physics, 2023."},"publication":"Journal of Chemical Physics"},{"ec_funded":1,"publication_status":"epub_ahead","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","year":"2023","acknowledgement":"Tobias Winkler and Joost-Pieter Katoen are supported by the DFG RTG 2236 UnRAVeL and the innovation programme under the Marie Skłodowska-Curie grant agreement No. 101008233 (Mission). Krishnendu Chatterjee is supported by the ERC CoG 863818 (ForM-SMArt) and the Vienna Science and Technology Fund (WWTF) Project ICT15-003. Maximilian Weininger is supported by the DFG projects 383882557 Statistical Unbounded Verification (SUV) and 427755713 Group-By Objectives in Probabilistic Verification (GOPro). Stefanie Mohr is supported by the DFG RTG 2428 CONVEY. Open Access funding enabled and organized by Projekt DEAL.","date_created":"2023-03-19T23:00:59Z","date_updated":"2023-10-03T11:36:13Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Joost P","last_name":"Katoen","id":"4524F760-F248-11E8-B48F-1D18A9856A87","full_name":"Katoen, Joost P"},{"first_name":"Stefanie","last_name":"Mohr","full_name":"Mohr, Stefanie"},{"first_name":"Maximilian","last_name":"Weininger","full_name":"Weininger, Maximilian"},{"last_name":"Winkler","first_name":"Tobias","full_name":"Winkler, Tobias"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"8272"}]},"month":"03","publication_identifier":{"eissn":["1572-8102"]},"quality_controlled":"1","isi":1,"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.1007/s10703-023-00411-4","open_access":"1"}],"external_id":{"isi":["000946174300001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s10703-023-00411-4","type":"journal_article","abstract":[{"text":"We study turn-based stochastic zero-sum games with lexicographic preferences over objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as controllable and adversarial non-determinism. Lexicographic order allows one to consider multiple objectives with a strict preference order. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. For a mixture of reachability and safety objectives, we show that deterministic lexicographically optimal strategies exist and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP, matching the current known bound for single objectives; and in general the decision problem is PSPACE-hard and can be solved in NEXPTIME∩coNEXPTIME. We present an algorithm that computes the lexicographically optimal strategies via a reduction to the computation of optimal strategies in a sequence of single-objectives games. For omega-regular objectives, we restrict our analysis to one-player games, also known as Markov decision processes. We show that lexicographically optimal strategies exist and need either randomization or finite memory. We present an algorithm that solves the relevant decision problem in polynomial time. We have implemented our algorithms and report experimental results on various case studies.","lang":"eng"}],"status":"public","ddc":["000"],"title":"Stochastic games with lexicographic objectives","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12738","oa_version":"Published Version","scopus_import":"1","day":"08","article_processing_charge":"No","article_type":"original","publication":"Formal Methods in System Design","citation":{"apa":"Chatterjee, K., Katoen, J. P., Mohr, S., Weininger, M., & Winkler, T. (2023). Stochastic games with lexicographic objectives. Formal Methods in System Design. Springer Nature. https://doi.org/10.1007/s10703-023-00411-4","ieee":"K. Chatterjee, J. P. Katoen, S. Mohr, M. Weininger, and T. Winkler, “Stochastic games with lexicographic objectives,” Formal Methods in System Design. Springer Nature, 2023.","ista":"Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. 2023. Stochastic games with lexicographic objectives. Formal Methods in System Design.","ama":"Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. Stochastic games with lexicographic objectives. Formal Methods in System Design. 2023. doi:10.1007/s10703-023-00411-4","chicago":"Chatterjee, Krishnendu, Joost P Katoen, Stefanie Mohr, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Objectives.” Formal Methods in System Design. Springer Nature, 2023. https://doi.org/10.1007/s10703-023-00411-4.","short":"K. Chatterjee, J.P. Katoen, S. Mohr, M. Weininger, T. Winkler, Formal Methods in System Design (2023).","mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Objectives.” Formal Methods in System Design, Springer Nature, 2023, doi:10.1007/s10703-023-00411-4."},"date_published":"2023-03-08T00:00:00Z"},{"day":"11","month":"07","article_processing_charge":"No","has_accepted_license":"1","date_published":"2023-07-11T00:00:00Z","doi":"10.5281/ZENODO.8133960","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133960","open_access":"1"}],"citation":{"short":"M.C. Ucar, (2023).","mla":"Ucar, Mehmet C. Source Data for the Manuscript “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Zenodo, 2023, doi:10.5281/ZENODO.8133960.","chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133960.","ama":"Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” 2023. doi:10.5281/ZENODO.8133960","apa":"Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. https://doi.org/10.5281/ZENODO.8133960","ieee":"M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023.","ista":"Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, 10.5281/ZENODO.8133960."},"abstract":[{"text":"The zip file includes source data used in the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript.\r\nA sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt.","lang":"eng"}],"type":"research_data_reference","author":[{"full_name":"Ucar, Mehmet C","first_name":"Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217"}],"related_material":{"record":[{"id":"14274","status":"public","relation":"used_in_publication"}]},"date_created":"2023-09-06T08:39:25Z","date_updated":"2023-10-03T11:42:58Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14279","year":"2023","ddc":["570"],"status":"public","title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","publisher":"Zenodo","department":[{"_id":"EdHa"}]},{"author":[{"orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","first_name":"Giorgio","full_name":"Cipolloni, Giorgio"},{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","first_name":"Dominik J","last_name":"Schröder"}],"date_created":"2021-12-05T23:01:41Z","date_updated":"2023-10-04T09:22:55Z","volume":76,"year":"2023","acknowledgement":"L.E. would like to thank Nathanaël Berestycki and D.S.would like to thank Nina Holden for valuable discussions on the Gaussian freefield.G.C. and L.E. are partially supported by ERC Advanced Grant No. 338804.G.C. received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Skłodowska-Curie Grant Agreement No.665385. D.S. is supported by Dr. Max Rössler, the Walter Haefner Foundation, and the ETH Zürich Foundation.","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Wiley","file_date_updated":"2023-10-04T09:21:48Z","ec_funded":1,"doi":"10.1002/cpa.22028","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000724652500001"],"arxiv":["1912.04100"]},"isi":1,"quality_controlled":"1","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"month":"05","publication_identifier":{"issn":["0010-3640"],"eissn":["1097-0312"]},"file":[{"file_id":"14388","relation":"main_file","date_created":"2023-10-04T09:21:48Z","date_updated":"2023-10-04T09:21:48Z","success":1,"checksum":"8346bc2642afb4ccb7f38979f41df5d9","file_name":"2023_CommPureMathematics_Cipolloni.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":803440}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10405","status":"public","ddc":["510"],"title":"Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices","intvolume":" 76","abstract":[{"text":"We consider large non-Hermitian random matrices X with complex, independent, identically distributed centred entries and show that the linear statistics of their eigenvalues are asymptotically Gaussian for test functions having 2+ϵ derivatives. Previously this result was known only for a few special cases; either the test functions were required to be analytic [72], or the distribution of the matrix elements needed to be Gaussian [73], or at least match the Gaussian up to the first four moments [82, 56]. We find the exact dependence of the limiting variance on the fourth cumulant that was not known before. The proof relies on two novel ingredients: (i) a local law for a product of two resolvents of the Hermitisation of X with different spectral parameters and (ii) a coupling of several weakly dependent Dyson Brownian motions. These methods are also the key inputs for our analogous results on the linear eigenvalue statistics of real matrices X that are presented in the companion paper [32]. ","lang":"eng"}],"issue":"5","type":"journal_article","date_published":"2023-05-01T00:00:00Z","publication":"Communications on Pure and Applied Mathematics","citation":{"mla":"Cipolloni, Giorgio, et al. “Central Limit Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” Communications on Pure and Applied Mathematics, vol. 76, no. 5, Wiley, 2023, pp. 946–1034, doi:10.1002/cpa.22028.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications on Pure and Applied Mathematics 76 (2023) 946–1034.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Central Limit Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” Communications on Pure and Applied Mathematics. Wiley, 2023. https://doi.org/10.1002/cpa.22028.","ama":"Cipolloni G, Erdös L, Schröder DJ. Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. 2023;76(5):946-1034. doi:10.1002/cpa.22028","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. 76(5), 946–1034.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices,” Communications on Pure and Applied Mathematics, vol. 76, no. 5. Wiley, pp. 946–1034, 2023.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.22028"},"article_type":"original","page":"946-1034","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1"},{"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"external_id":{"isi":["000753777100001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s13235-022-00425-3","month":"03","publication_identifier":{"eissn":["2153-0793"],"issn":["2153-0785"]},"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","acknowledgement":"The authors would like to acknowledge stimulating email discussions with Dr Wayne Lobb of W.A. Lobb LLC on the topic of evolutionary games. We also thank Dr Thomas Taimre for his input to the material in Sect. 3.\r\nThe authors would like to acknowledge partial support from the Australian Research Council under the Discovery grant DP180101602 and support by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411.","year":"2023","date_created":"2022-02-20T23:01:32Z","date_updated":"2023-10-04T09:24:30Z","volume":13,"author":[{"full_name":"Graham, Thomas","last_name":"Graham","first_name":"Thomas"},{"full_name":"Kleshnina, Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Kleshnina"},{"full_name":"Filar, Jerzy A.","first_name":"Jerzy A.","last_name":"Filar"}],"file_date_updated":"2022-02-21T08:54:17Z","ec_funded":1,"article_type":"original","page":"231-264","publication":"Dynamic Games and Applications","citation":{"ista":"Graham T, Kleshnina M, Filar JA. 2023. Where do mistakes lead? A survey of games with incompetent players. Dynamic Games and Applications. 13, 231–264.","apa":"Graham, T., Kleshnina, M., & Filar, J. A. (2023). Where do mistakes lead? A survey of games with incompetent players. Dynamic Games and Applications. Springer Nature. https://doi.org/10.1007/s13235-022-00425-3","ieee":"T. Graham, M. Kleshnina, and J. A. Filar, “Where do mistakes lead? A survey of games with incompetent players,” Dynamic Games and Applications, vol. 13. Springer Nature, pp. 231–264, 2023.","ama":"Graham T, Kleshnina M, Filar JA. Where do mistakes lead? A survey of games with incompetent players. Dynamic Games and Applications. 2023;13:231-264. doi:10.1007/s13235-022-00425-3","chicago":"Graham, Thomas, Maria Kleshnina, and Jerzy A. Filar. “Where Do Mistakes Lead? A Survey of Games with Incompetent Players.” Dynamic Games and Applications. Springer Nature, 2023. https://doi.org/10.1007/s13235-022-00425-3.","mla":"Graham, Thomas, et al. “Where Do Mistakes Lead? A Survey of Games with Incompetent Players.” Dynamic Games and Applications, vol. 13, Springer Nature, 2023, pp. 231–64, doi:10.1007/s13235-022-00425-3.","short":"T. Graham, M. Kleshnina, J.A. Filar, Dynamic Games and Applications 13 (2023) 231–264."},"date_published":"2023-03-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","status":"public","ddc":["000"],"title":"Where do mistakes lead? A survey of games with incompetent players","intvolume":" 13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10770","file":[{"access_level":"open_access","file_name":"2022_DynamicGamesApplic_Graham.pdf","creator":"dernst","file_size":1890512,"content_type":"application/pdf","file_id":"10781","relation":"main_file","success":1,"checksum":"cd53b07e96f9030ddb348f305e5b58c7","date_updated":"2022-02-21T08:54:17Z","date_created":"2022-02-21T08:54:17Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Mathematical models often aim to describe a complicated mechanism in a cohesive and simple manner. However, reaching perfect balance between being simple enough or overly simplistic is a challenging task. Frequently, game-theoretic models have an underlying assumption that players, whenever they choose to execute a specific action, do so perfectly. In fact, it is rare that action execution perfectly coincides with intentions of individuals, giving rise to behavioural mistakes. The concept of incompetence of players was suggested to address this issue in game-theoretic settings. Under the assumption of incompetence, players have non-zero probabilities of executing a different strategy from the one they chose, leading to stochastic outcomes of the interactions. In this article, we survey results related to the concept of incompetence in classic as well as evolutionary game theory and provide several new results. We also suggest future extensions of the model and argue why it is important to take into account behavioural mistakes when analysing interactions among players in both economic and biological settings.","lang":"eng"}]},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000704213400001"],"arxiv":["2003.01366"]},"isi":1,"quality_controlled":"1","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"}],"doi":"10.1007/s11118-021-09951-y","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["1572-929X"],"issn":["0926-2601"]},"year":"2023","acknowledgement":"The author is grateful to Professors Sergio Albeverio and Andreas Eberle, and to Dr. Kohei Suzuki, for fruitful conversations on the subject of the present work, and for respectively pointing out the references [1, 13], and [3, 20]. Finally, he is especially grateful to an anonymous Reviewer for their very careful reading and their suggestions which improved the readability of the paper.","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JaMa"}],"author":[{"full_name":"Dello Schiavo, Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","orcid":"0000-0002-9881-6870","first_name":"Lorenzo","last_name":"Dello Schiavo"}],"date_created":"2021-10-17T22:01:17Z","date_updated":"2023-10-04T09:19:12Z","volume":58,"file_date_updated":"2023-10-04T09:18:59Z","ec_funded":1,"publication":"Potential Analysis","citation":{"ama":"Dello Schiavo L. Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. 2023;58:573-615. doi:10.1007/s11118-021-09951-y","ista":"Dello Schiavo L. 2023. Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. 58, 573–615.","ieee":"L. Dello Schiavo, “Ergodic decomposition of Dirichlet forms via direct integrals and applications,” Potential Analysis, vol. 58. Springer Nature, pp. 573–615, 2023.","apa":"Dello Schiavo, L. (2023). Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. Springer Nature. https://doi.org/10.1007/s11118-021-09951-y","mla":"Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct Integrals and Applications.” Potential Analysis, vol. 58, Springer Nature, 2023, pp. 573–615, doi:10.1007/s11118-021-09951-y.","short":"L. Dello Schiavo, Potential Analysis 58 (2023) 573–615.","chicago":"Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct Integrals and Applications.” Potential Analysis. Springer Nature, 2023. https://doi.org/10.1007/s11118-021-09951-y."},"article_type":"original","page":"573-615","date_published":"2023-03-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","_id":"10145","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["510"],"title":"Ergodic decomposition of Dirichlet forms via direct integrals and applications","intvolume":" 58","oa_version":"Published Version","file":[{"file_name":"2023_PotentialAnalysis_DelloSchiavo.pdf","access_level":"open_access","file_size":806391,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14387","date_updated":"2023-10-04T09:18:59Z","date_created":"2023-10-04T09:18:59Z","checksum":"625526482be300ca7281c91c30d41725","success":1}],"type":"journal_article","abstract":[{"lang":"eng","text":"We study direct integrals of quadratic and Dirichlet forms. We show that each quasi-regular Dirichlet space over a probability space admits a unique representation as a direct integral of irreducible Dirichlet spaces, quasi-regular for the same underlying topology. The same holds for each quasi-regular strongly local Dirichlet space over a metrizable Luzin σ-finite Radon measure space, and admitting carré du champ operator. In this case, the representation is only projectively unique."}]},{"doi":"10.1002/rsa.21106","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000828530400001"]},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1098-2418"],"issn":["1042-9832"]},"month":"07","author":[{"full_name":"Liebenau, Anita","first_name":"Anita","last_name":"Liebenau"},{"last_name":"Mattos","first_name":"Letícia","full_name":"Mattos, Letícia"},{"full_name":"Mendonca Dos Santos, Walner","first_name":"Walner","last_name":"Mendonca Dos Santos","id":"12c6bd4d-2cd0-11ec-a0da-e28f42f65ebd"},{"full_name":"Skokan, Jozef","first_name":"Jozef","last_name":"Skokan"}],"volume":62,"date_created":"2022-07-31T22:01:49Z","date_updated":"2023-10-04T09:38:45Z","year":"2023","acknowledgement":"This work was started at the thematic program GRAPHS@IMPA (January–March 2018), in Rio de Janeiro. We thank IMPA and the organisers for the hospitality and for providing a pleasant research environment. We thank Rob Morris for helpful discussions, and the anonymous referees for their careful reading and many helpful suggestions. Open Access funding enabled and organized by Projekt DEAL.\r\nA. Liebenau was supported by an ARC DECRA Fellowship Grant DE170100789. L. Mattos was supported by CAPES and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – The Berlin Mathematics Research Center MATH+ (EXC-2046/1, project ID: 390685689). W. Mendonça was supported by CAPES project 88882.332408/2010-01.","publisher":"Wiley","department":[{"_id":"MaKw"}],"publication_status":"published","file_date_updated":"2023-10-04T09:37:26Z","date_published":"2023-07-01T00:00:00Z","citation":{"chicago":"Liebenau, Anita, Letícia Mattos, Walner Mendonca dos Santos, and Jozef Skokan. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” Random Structures and Algorithms. Wiley, 2023. https://doi.org/10.1002/rsa.21106.","short":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, J. Skokan, Random Structures and Algorithms 62 (2023) 1035–1055.","mla":"Liebenau, Anita, et al. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” Random Structures and Algorithms, vol. 62, no. 4, Wiley, 2023, pp. 1035–55, doi:10.1002/rsa.21106.","apa":"Liebenau, A., Mattos, L., Mendonca dos Santos, W., & Skokan, J. (2023). Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. Wiley. https://doi.org/10.1002/rsa.21106","ieee":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, and J. Skokan, “Asymmetric Ramsey properties of random graphs involving cliques and cycles,” Random Structures and Algorithms, vol. 62, no. 4. Wiley, pp. 1035–1055, 2023.","ista":"Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. 2023. Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. 62(4), 1035–1055.","ama":"Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. 2023;62(4):1035-1055. doi:10.1002/rsa.21106"},"publication":"Random Structures and Algorithms","page":"1035-1055","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","scopus_import":"1","file":[{"date_updated":"2023-10-04T09:37:26Z","date_created":"2023-10-04T09:37:26Z","success":1,"checksum":"3a5969d0c512aef01c30f3dc81c6d59b","file_id":"14389","relation":"main_file","creator":"dernst","file_size":1362334,"content_type":"application/pdf","file_name":"2023_RandomStructureAlgorithms_Liebenau.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11706","intvolume":" 62","ddc":["510"],"title":"Asymmetric Ramsey properties of random graphs involving cliques and cycles","status":"public","issue":"4","abstract":[{"text":"We say that (Formula presented.) if, in every edge coloring (Formula presented.), we can find either a 1-colored copy of (Formula presented.) or a 2-colored copy of (Formula presented.). The well-known states that the threshold for the property (Formula presented.) is equal to (Formula presented.), where (Formula presented.) is given by (Formula presented.) for any pair of graphs (Formula presented.) and (Formula presented.) with (Formula presented.). In this article, we show the 0-statement of the Kohayakawa–Kreuter conjecture for every pair of cycles and cliques. ","lang":"eng"}],"type":"journal_article"},{"volume":29,"date_created":"2023-03-05T23:01:05Z","date_updated":"2023-10-04T10:21:07Z","author":[{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"full_name":"Xu, Yuanyuan","last_name":"Xu","first_name":"Yuanyuan","orcid":"0000-0003-1559-1205","id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3"}],"publisher":"Bernoulli Society for Mathematical Statistics and Probability","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2023","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.3150/22-BEJ1490","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2112.12093","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2112.12093 "],"isi":["000947270100008"]},"publication_identifier":{"issn":["1350-7265"]},"month":"05","oa_version":"Preprint","intvolume":" 29","title":"Small deviation estimates for the largest eigenvalue of Wigner matrices","status":"public","_id":"12707","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","abstract":[{"text":"We establish precise right-tail small deviation estimates for the largest eigenvalue of real symmetric and complex Hermitian matrices whose entries are independent random variables with uniformly bounded moments. The proof relies on a Green function comparison along a continuous interpolating matrix flow for a long time. Less precise estimates are also obtained in the left tail.","lang":"eng"}],"type":"journal_article","date_published":"2023-05-01T00:00:00Z","page":"1063-1079","article_type":"original","citation":{"chicago":"Erdös, László, and Yuanyuan Xu. “Small Deviation Estimates for the Largest Eigenvalue of Wigner Matrices.” Bernoulli. Bernoulli Society for Mathematical Statistics and Probability, 2023. https://doi.org/10.3150/22-BEJ1490.","mla":"Erdös, László, and Yuanyuan Xu. “Small Deviation Estimates for the Largest Eigenvalue of Wigner Matrices.” Bernoulli, vol. 29, no. 2, Bernoulli Society for Mathematical Statistics and Probability, 2023, pp. 1063–79, doi:10.3150/22-BEJ1490.","short":"L. Erdös, Y. Xu, Bernoulli 29 (2023) 1063–1079.","ista":"Erdös L, Xu Y. 2023. Small deviation estimates for the largest eigenvalue of Wigner matrices. Bernoulli. 29(2), 1063–1079.","apa":"Erdös, L., & Xu, Y. (2023). Small deviation estimates for the largest eigenvalue of Wigner matrices. Bernoulli. Bernoulli Society for Mathematical Statistics and Probability. https://doi.org/10.3150/22-BEJ1490","ieee":"L. Erdös and Y. Xu, “Small deviation estimates for the largest eigenvalue of Wigner matrices,” Bernoulli, vol. 29, no. 2. Bernoulli Society for Mathematical Statistics and Probability, pp. 1063–1079, 2023.","ama":"Erdös L, Xu Y. Small deviation estimates for the largest eigenvalue of Wigner matrices. Bernoulli. 2023;29(2):1063-1079. doi:10.3150/22-BEJ1490"},"publication":"Bernoulli","article_processing_charge":"No","day":"01","scopus_import":"1"},{"ec_funded":1,"file_date_updated":"2023-10-04T11:13:28Z","department":[{"_id":"EdHa"},{"_id":"AnKi"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"We thank S. Hippenmeyer for the reagents and C. P. Heisenberg, J. Briscoe and K. Page for comments on the manuscript. This work was supported by IST Austria; the European Research Council under Horizon 2020 research and innovation programme grant no. 680037 and Horizon Europe grant 101044579 (A.K.); Austrian Science Fund (FWF): F78 (Stem Cell Modulation) (A.K.); ISTFELLOW postdoctoral program (A.S.); Narodowe Centrum Nauki, Poland SONATA, 2017/26/D/NZ2/00454 (M.Z.); and the Polish National Agency for Academic Exchange (M.Z.).","year":"2023","volume":19,"date_updated":"2023-10-04T11:14:05Z","date_created":"2023-04-16T22:01:09Z","related_material":{"record":[{"id":"13081","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Bocanegra, Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87","last_name":"Bocanegra","first_name":"Laura"},{"id":"76250f9f-3a21-11eb-9a80-a6180a0d7958","last_name":"Singh","first_name":"Amrita","full_name":"Singh, Amrita"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","first_name":"Marcin P","last_name":"Zagórski","full_name":"Zagórski, Marcin P"},{"full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"month":"07","project":[{"grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord"},{"name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F07802","name":"Morphogen control of growth and pattern in the spinal cord"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000964029300003"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41567-023-01977-w","type":"journal_article","abstract":[{"lang":"eng","text":"As developing tissues grow in size and undergo morphogenetic changes, their material properties may be altered. Such changes result from tension dynamics at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms controlling the physical state of growing tissues are unclear. We found that at early developmental stages, the epithelium in the developing mouse spinal cord maintains both high junctional tension and high fluidity. This is achieved via a mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the cell proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification uncovered here resembles a glass transition that depends on the dynamical stresses generated by proliferation and differentiation. Our finding that the fluidity of developing epithelia is linked to interkinetic nuclear movements and the dynamics of growth is likely to be relevant to multiple developing tissues."}],"intvolume":" 19","title":"Cell cycle dynamics control fluidity of the developing mouse neuroepithelium","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12837","file":[{"creator":"dernst","file_size":5532285,"content_type":"application/pdf","file_name":"2023_NaturePhysics_Boncanegra.pdf","access_level":"open_access","date_updated":"2023-10-04T11:13:28Z","date_created":"2023-10-04T11:13:28Z","success":1,"checksum":"858225a4205b74406e5045006cdd853f","file_id":"14392","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"1050-1058","article_type":"original","citation":{"chicago":"Bocanegra, Laura, Amrita Singh, Edouard B Hannezo, Marcin P Zagórski, and Anna Kicheva. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-01977-w.","mla":"Bocanegra, Laura, et al. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1050–58, doi:10.1038/s41567-023-01977-w.","short":"L. Bocanegra, A. Singh, E.B. Hannezo, M.P. Zagórski, A. Kicheva, Nature Physics 19 (2023) 1050–1058.","ista":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. 2023. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. 19, 1050–1058.","ieee":"L. Bocanegra, A. Singh, E. B. Hannezo, M. P. Zagórski, and A. Kicheva, “Cell cycle dynamics control fluidity of the developing mouse neuroepithelium,” Nature Physics, vol. 19. Springer Nature, pp. 1050–1058, 2023.","apa":"Bocanegra, L., Singh, A., Hannezo, E. B., Zagórski, M. P., & Kicheva, A. (2023). Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-01977-w","ama":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. 2023;19:1050-1058. doi:10.1038/s41567-023-01977-w"},"publication":"Nature Physics","date_published":"2023-07-01T00:00:00Z"},{"type":"journal_article","issue":"13","abstract":[{"lang":"eng","text":"Coherent control and manipulation of quantum degrees of freedom such as spins forms the basis of emerging quantum technologies. In this context, the robust valley degree of freedom and the associated valley pseudospin found in two-dimensional transition metal dichalcogenides is a highly attractive platform. Valley polarization and coherent superposition of valley states have been observed in these systems even up to room temperature. Control of valley coherence is an important building block for the implementation of valley qubit. Large magnetic fields or high-power lasers have been used in the past to demonstrate the control (initialization and rotation) of the valley coherent states. Here, the control of layer–valley coherence via strong coupling of valley excitons in bilayer WS2 to microcavity photons is demonstrated by exploiting the pseudomagnetic field arising in optical cavities owing to the transverse electric–transverse magnetic (TE–TM)mode splitting. The use of photonic structures to generate pseudomagnetic fields which can be used to manipulate exciton-polaritons presents an attractive approach to control optical responses without the need for large magnets or high-intensity optical pump powers."}],"intvolume":" 11","status":"public","title":"Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12836","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"04","article_type":"original","citation":{"ama":"Khatoniar M, Yama N, Ghazaryan A, et al. Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities. Advanced Optical Materials. 2023;11(13). doi:10.1002/adom.202202631","ieee":"M. Khatoniar et al., “Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities,” Advanced Optical Materials, vol. 11, no. 13. Wiley, 2023.","apa":"Khatoniar, M., Yama, N., Ghazaryan, A., Guddala, S., Ghaemi, P., Majumdar, K., & Menon, V. (2023). Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities. Advanced Optical Materials. Wiley. https://doi.org/10.1002/adom.202202631","ista":"Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Majumdar K, Menon V. 2023. Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities. Advanced Optical Materials. 11(13), 2202631.","short":"M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, K. Majumdar, V. Menon, Advanced Optical Materials 11 (2023).","mla":"Khatoniar, Mandeep, et al. “Optical Manipulation of Layer–Valley Coherence via Strong Exciton–Photon Coupling in Microcavities.” Advanced Optical Materials, vol. 11, no. 13, 2202631, Wiley, 2023, doi:10.1002/adom.202202631.","chicago":"Khatoniar, Mandeep, Nicholas Yama, Areg Ghazaryan, Sriram Guddala, Pouyan Ghaemi, Kausik Majumdar, and Vinod Menon. “Optical Manipulation of Layer–Valley Coherence via Strong Exciton–Photon Coupling in Microcavities.” Advanced Optical Materials. Wiley, 2023. https://doi.org/10.1002/adom.202202631."},"publication":"Advanced Optical Materials","date_published":"2023-07-04T00:00:00Z","article_number":"2202631","publisher":"Wiley","department":[{"_id":"MiLe"}],"publication_status":"published","acknowledgement":"The authors acknowledge insightful discussions with Prof. Wang Yao and graphics by Rezlind Bushati. M.K. and N.Y. acknowledge support from NSF grants NSF DMR-1709996 and NSF OMA 1936276. S.G. was supported by the Army Research Office Multidisciplinary University Research Initiative program (W911NF-17-1-0312) and V.M.M. by the Army Research Office grant (W911NF-22-1-0091). K.M acknowledges the SPARC program that supported his collaboration with the CUNY team. The authors acknowledge the Nanofabrication facility at the CUNY Advanced Science Research Center where the cavity devices were fabricated.","year":"2023","volume":11,"date_updated":"2023-10-04T11:15:17Z","date_created":"2023-04-16T22:01:09Z","author":[{"last_name":"Khatoniar","first_name":"Mandeep","full_name":"Khatoniar, Mandeep"},{"full_name":"Yama, Nicholas","last_name":"Yama","first_name":"Nicholas"},{"last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg"},{"last_name":"Guddala","first_name":"Sriram","full_name":"Guddala, Sriram"},{"last_name":"Ghaemi","first_name":"Pouyan","full_name":"Ghaemi, Pouyan"},{"last_name":"Majumdar","first_name":"Kausik","full_name":"Majumdar, Kausik"},{"first_name":"Vinod","last_name":"Menon","full_name":"Menon, Vinod"}],"publication_identifier":{"eissn":["2195-1071"]},"month":"07","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000963866700001"],"arxiv":["2211.08755"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.08755"}],"language":[{"iso":"eng"}],"doi":"10.1002/adom.202202631"},{"type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"This paper deals with the large-scale behaviour of dynamical optimal transport on Zd\r\n-periodic graphs with general lower semicontinuous and convex energy densities. Our main contribution is a homogenisation result that describes the effective behaviour of the discrete problems in terms of a continuous optimal transport problem. The effective energy density can be explicitly expressed in terms of a cell formula, which is a finite-dimensional convex programming problem that depends non-trivially on the local geometry of the discrete graph and the discrete energy density. Our homogenisation result is derived from a Γ\r\n-convergence result for action functionals on curves of measures, which we prove under very mild growth conditions on the energy density. We investigate the cell formula in several cases of interest, including finite-volume discretisations of the Wasserstein distance, where non-trivial limiting behaviour occurs."}],"intvolume":" 62","status":"public","title":"Homogenisation of dynamical optimal transport on periodic graphs","ddc":["510"],"_id":"12959","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_updated":"2023-10-04T11:34:10Z","date_created":"2023-10-04T11:34:10Z","success":1,"checksum":"359bee38d94b7e0aa73925063cb8884d","file_id":"14393","relation":"main_file","creator":"dernst","file_size":1240995,"content_type":"application/pdf","file_name":"2023_CalculusEquations_Gladbach.pdf","access_level":"open_access"}],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"28","article_type":"original","citation":{"mla":"Gladbach, Peter, et al. “Homogenisation of Dynamical Optimal Transport on Periodic Graphs.” Calculus of Variations and Partial Differential Equations, vol. 62, no. 5, 143, Springer Nature, 2023, doi:10.1007/s00526-023-02472-z.","short":"P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Calculus of Variations and Partial Differential Equations 62 (2023).","chicago":"Gladbach, Peter, Eva Kopfer, Jan Maas, and Lorenzo Portinale. “Homogenisation of Dynamical Optimal Transport on Periodic Graphs.” Calculus of Variations and Partial Differential Equations. Springer Nature, 2023. https://doi.org/10.1007/s00526-023-02472-z.","ama":"Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of dynamical optimal transport on periodic graphs. Calculus of Variations and Partial Differential Equations. 2023;62(5). doi:10.1007/s00526-023-02472-z","ista":"Gladbach P, Kopfer E, Maas J, Portinale L. 2023. Homogenisation of dynamical optimal transport on periodic graphs. Calculus of Variations and Partial Differential Equations. 62(5), 143.","ieee":"P. Gladbach, E. Kopfer, J. Maas, and L. Portinale, “Homogenisation of dynamical optimal transport on periodic graphs,” Calculus of Variations and Partial Differential Equations, vol. 62, no. 5. Springer Nature, 2023.","apa":"Gladbach, P., Kopfer, E., Maas, J., & Portinale, L. (2023). Homogenisation of dynamical optimal transport on periodic graphs. Calculus of Variations and Partial Differential Equations. Springer Nature. https://doi.org/10.1007/s00526-023-02472-z"},"publication":"Calculus of Variations and Partial Differential Equations","date_published":"2023-04-28T00:00:00Z","article_number":"143","ec_funded":1,"file_date_updated":"2023-10-04T11:34:10Z","publisher":"Springer Nature","department":[{"_id":"JaMa"}],"publication_status":"published","acknowledgement":"J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117). J.M and L.P. also acknowledge support from the Austrian Science Fund (FWF), grants No F65 and W1245. E.K. gratefully acknowledges support by the German Research Foundation through the Hausdorff Center for Mathematics and the Collaborative Research Center 1060. P.G. is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—350398276. We thank the anonymous reviewer for the careful reading and for useful suggestions. Open access funding provided by Austrian Science Fund (FWF).","year":"2023","volume":62,"date_updated":"2023-10-04T11:34:49Z","date_created":"2023-05-14T22:01:00Z","author":[{"first_name":"Peter","last_name":"Gladbach","full_name":"Gladbach, Peter"},{"first_name":"Eva","last_name":"Kopfer","full_name":"Kopfer, Eva"},{"first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan"},{"full_name":"Portinale, Lorenzo","first_name":"Lorenzo","last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["0944-2669"],"eissn":["1432-0835"]},"month":"04","project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000980588900001"],"arxiv":["2110.15321"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00526-023-02472-z"},{"ec_funded":1,"author":[{"first_name":"Jacopo","last_name":"De Simoi","full_name":"De Simoi, Jacopo"},{"full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim"},{"first_name":"Martin","last_name":"Leguil","full_name":"Leguil, Martin"}],"volume":233,"date_created":"2023-04-30T22:01:05Z","date_updated":"2023-10-04T11:25:37Z","year":"2023","acknowledgement":"J.D.S. and M.L. have been partially supported by the NSERC Discovery grant, reference number 502617-2017. M.L. was also supported by the ERC project 692925 NUHGD of Sylvain Crovisier, by the ANR AAPG 2021 PRC CoSyDy: Conformally symplectic dynamics, beyond symplectic dynamics (ANR-CE40-0014), and by the ANR JCJC PADAWAN: Parabolic dynamics, bifurcations and wandering domains (ANR-21-CE40-0012). V.K. acknowledges partial support of the NSF grant DMS-1402164 and ERC Grant # 885707.","publisher":"Springer Nature","department":[{"_id":"VaKa"}],"publication_status":"published","publication_identifier":{"eissn":["1432-1297"],"issn":["0020-9910"]},"month":"08","doi":"10.1007/s00222-023-01191-8","language":[{"iso":"eng"}],"external_id":{"arxiv":["1905.00890"],"isi":["000978887600001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1905.00890"}],"oa":1,"project":[{"call_identifier":"H2020","name":"Spectral rigidity and integrability for billiards and geodesic flows","grant_number":"885707","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A"}],"isi":1,"quality_controlled":"1","abstract":[{"text":"We consider billiards obtained by removing from the plane finitely many strictly convex analytic obstacles satisfying the non-eclipse condition. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift, which provides a natural labeling of periodic orbits. We show that under suitable symmetry and genericity assumptions, the Marked Length Spectrum determines the geometry of the billiard table.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"12877","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 233","title":"Marked Length Spectral determination of analytic chaotic billiards with axial symmetries","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2023-08-01T00:00:00Z","citation":{"apa":"De Simoi, J., Kaloshin, V., & Leguil, M. (2023). Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. Inventiones Mathematicae. Springer Nature. https://doi.org/10.1007/s00222-023-01191-8","ieee":"J. De Simoi, V. Kaloshin, and M. Leguil, “Marked Length Spectral determination of analytic chaotic billiards with axial symmetries,” Inventiones Mathematicae, vol. 233. Springer Nature, pp. 829–901, 2023.","ista":"De Simoi J, Kaloshin V, Leguil M. 2023. Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. Inventiones Mathematicae. 233, 829–901.","ama":"De Simoi J, Kaloshin V, Leguil M. Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. Inventiones Mathematicae. 2023;233:829-901. doi:10.1007/s00222-023-01191-8","chicago":"De Simoi, Jacopo, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectral Determination of Analytic Chaotic Billiards with Axial Symmetries.” Inventiones Mathematicae. Springer Nature, 2023. https://doi.org/10.1007/s00222-023-01191-8.","short":"J. De Simoi, V. Kaloshin, M. Leguil, Inventiones Mathematicae 233 (2023) 829–901.","mla":"De Simoi, Jacopo, et al. “Marked Length Spectral Determination of Analytic Chaotic Billiards with Axial Symmetries.” Inventiones Mathematicae, vol. 233, Springer Nature, 2023, pp. 829–901, doi:10.1007/s00222-023-01191-8."},"publication":"Inventiones Mathematicae","page":"829-901","article_type":"original"},{"ec_funded":1,"file_date_updated":"2023-10-04T11:40:51Z","related_material":{"record":[{"id":"12370","relation":"research_data","status":"public"}]},"author":[{"id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7400-6665","first_name":"Divyansh","last_name":"Gupta","full_name":"Gupta, Divyansh"},{"full_name":"Mlynarski, Wiktor F","first_name":"Wiktor F","last_name":"Mlynarski","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"id":"3320A096-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4792-1881","first_name":"Anton L","last_name":"Sumser","full_name":"Sumser, Anton L"},{"orcid":"0000-0003-2012-9947","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","first_name":"Olga","full_name":"Symonova, Olga"},{"full_name":"Svaton, Jan","last_name":"Svaton","first_name":"Jan","orcid":"0000-0002-6198-2939","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch","full_name":"Jösch, Maximilian A"}],"volume":26,"date_created":"2023-01-23T14:14:19Z","date_updated":"2023-10-04T11:41:05Z","pmid":1,"acknowledgement":"We thank Hiroki Asari for sharing the dataset of naturalistic images, Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings. We also thank Gasper Tkacik and members of the Neuroethology group for their comments on the manuscript. This research was supported by the Scientific Service Units of IST Austria through resources provided by Scientific Computing, the Preclinical Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 (DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European Research Council Starting Grant 756502 (MJ).","year":"2023","publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publication_status":"published","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"month":"04","doi":"10.1038/s41593-023-01280-0","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"Bio"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000955258300002"],"pmid":["36959418"]},"oa":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"},{"name":"Circuits of Visual Attention","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502"},{"grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus"},{"name":"Connecting sensory with motor processing in the superior colliculus","_id":"264FEA02-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1098-2017"}],"isi":1,"quality_controlled":"1","abstract":[{"text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types.","lang":"eng"}],"type":"journal_article","file":[{"creator":"dernst","file_size":6144866,"content_type":"application/pdf","file_name":"2023_NatureNeuroscience_Gupta.pdf","access_level":"open_access","date_updated":"2023-10-04T11:40:51Z","date_created":"2023-10-04T11:40:51Z","success":1,"checksum":"a33d91e398e548f34003170e10988368","file_id":"14395","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12349","intvolume":" 26","ddc":["570"],"status":"public","title":"Panoramic visual statistics shape retina-wide organization of receptive fields","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","scopus_import":"1","date_published":"2023-04-01T00:00:00Z","citation":{"ieee":"D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A. Jösch, “Panoramic visual statistics shape retina-wide organization of receptive fields,” Nature Neuroscience, vol. 26. Springer Nature, pp. 606–614, 2023.","apa":"Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., & Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-023-01280-0","ista":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 26, 606–614.","ama":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 2023;26:606-614. doi:10.1038/s41593-023-01280-0","chicago":"Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Nature Neuroscience. Springer Nature, 2023. https://doi.org/10.1038/s41593-023-01280-0.","short":"D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch, Nature Neuroscience 26 (2023) 606–614.","mla":"Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Nature Neuroscience, vol. 26, Springer Nature, 2023, pp. 606–14, doi:10.1038/s41593-023-01280-0."},"publication":"Nature Neuroscience","page":"606-614","article_type":"original"},{"file_date_updated":"2023-01-26T10:51:34Z","abstract":[{"lang":"eng","text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. "}],"ec_funded":1,"type":"research_data","author":[{"id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7400-6665","first_name":"Divyansh","last_name":"Gupta","full_name":"Gupta, Divyansh"},{"full_name":"Sumser, Anton L","last_name":"Sumser","first_name":"Anton L","orcid":"0000-0002-4792-1881","id":"3320A096-F248-11E8-B48F-1D18A9856A87"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch","full_name":"Jösch, Maximilian A"}],"related_material":{"record":[{"id":"12349","status":"public","relation":"used_in_publication"}]},"contributor":[{"first_name":"Olga","last_name":"Symonova","contributor_type":"researcher","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Mlynarski","first_name":"Wiktor F"},{"first_name":"Jan","last_name":"Svaton","contributor_type":"researcher","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2"}],"date_created":"2023-01-25T12:45:18Z","date_updated":"2023-10-04T11:41:04Z","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12396","checksum":"172cd1c315cbf063c122298396bc17a7","success":1,"date_created":"2023-01-26T10:51:34Z","date_updated":"2023-01-26T10:51:34Z","access_level":"open_access","file_name":"readme_exvivo.txt","content_type":"text/plain","file_size":1917,"creator":"dgupta"},{"file_name":"readme_invivo.txt","access_level":"open_access","creator":"dgupta","file_size":1585,"content_type":"text/plain","file_id":"12397","relation":"main_file","date_updated":"2023-01-26T10:50:50Z","date_created":"2023-01-26T10:50:50Z","success":1,"checksum":"d3cecda51cad86b1182195731c01a14f"},{"file_name":"exvivo_RFs.mat","access_level":"open_access","content_type":"application/octet-stream","file_size":5019459775,"creator":"dgupta","relation":"main_file","file_id":"12398","date_updated":"2023-01-26T10:43:30Z","date_created":"2023-01-26T10:43:30Z","checksum":"b85018b27f2c43a6d94ee0e8b841220d","success":1},{"file_name":"RGC_in_vivo_RFs_selected.mat","access_level":"open_access","creator":"dgupta","content_type":"application/octet-stream","file_size":94999721,"file_id":"12399","relation":"main_file","date_updated":"2023-01-26T10:40:35Z","date_created":"2023-01-26T10:40:35Z","success":1,"checksum":"f75dccd96a3f837cdeed65b5134e697e"},{"file_id":"12382","relation":"main_file","date_updated":"2023-01-25T16:03:49Z","date_created":"2023-01-25T16:03:49Z","success":1,"checksum":"d41836ffe03ea0efb677de31287c8d2e","file_name":"invivo_BL6-eyeGC8m-dC-3_210924_1534_Result.mat","access_level":"open_access","creator":"dgupta","content_type":"application/octet-stream","file_size":720893739},{"file_id":"12383","relation":"main_file","success":1,"checksum":"0a0cba5208241a95f9bb7684d0a43afa","date_created":"2023-01-25T16:03:30Z","date_updated":"2023-01-25T16:03:30Z","access_level":"open_access","file_name":"invivo_BL6-eyeGC8m-dC-3_211026_1235_Result.mat","creator":"dgupta","content_type":"application/octet-stream","file_size":248122209},{"file_id":"12384","relation":"main_file","date_updated":"2023-01-25T16:04:54Z","date_created":"2023-01-25T16:04:54Z","success":1,"checksum":"cf72c1f325631212f305ff1a6d342bc3","file_name":"invivo_BL6-eyeGC8m-dC-3_211202_1505_Result.mat","access_level":"open_access","creator":"dgupta","file_size":1757729346,"content_type":"application/octet-stream"},{"access_level":"open_access","file_name":"invivo_BL6-eyeGC8m-dC-3_211208_1738_Result.mat","file_size":1177344595,"content_type":"application/octet-stream","creator":"dgupta","relation":"main_file","file_id":"12385","checksum":"f4cd25f37d433a7dced3aa8cc326c755","success":1,"date_updated":"2023-01-25T16:04:41Z","date_created":"2023-01-25T16:04:41Z"},{"success":1,"checksum":"8c31637d447f2088fdb5ba1c6775f243","date_updated":"2023-01-25T16:06:22Z","date_created":"2023-01-25T16:06:22Z","file_id":"12386","relation":"main_file","creator":"dgupta","file_size":2246592895,"content_type":"application/octet-stream","access_level":"open_access","file_name":"invivo_BL6-eyeGC8m-dC-3_220111_1735_Result.mat"},{"creator":"dgupta","file_size":2151341770,"content_type":"application/octet-stream","file_name":"invivo_BL6-eyeGC8m-dC-4_220216_0950_Result.mat","access_level":"open_access","date_created":"2023-01-25T16:07:41Z","date_updated":"2023-01-25T16:07:41Z","success":1,"checksum":"246d660ef06a9151c59b74490d991460","file_id":"12387","relation":"main_file"},{"file_name":"invivo_BL6-eyeGC8m-dC-4_220428_1351_Result.mat","access_level":"open_access","creator":"dgupta","file_size":3719145736,"content_type":"application/octet-stream","file_id":"12393","relation":"main_file","date_created":"2023-01-26T10:19:02Z","date_updated":"2023-01-26T10:19:02Z","success":1,"checksum":"b32987dd4589d05b9dfadb93d4178c0d"},{"date_created":"2023-01-26T10:34:46Z","date_updated":"2023-01-26T10:34:46Z","checksum":"6c88ca7d1df405f04002146d251dc22e","success":1,"relation":"main_file","file_id":"12395","content_type":"application/octet-stream","file_size":5818789752,"creator":"dgupta","file_name":"invivo_BL6-eyeGC8m-dC-4_220502_1357_Result.mat","access_level":"open_access"},{"creator":"dgupta","file_size":2614677996,"content_type":"application/octet-stream","file_name":"invivo_BL6-eyeGC8m-dC-4_220524_1726_Result.mat","access_level":"open_access","date_updated":"2023-01-26T10:23:19Z","date_created":"2023-01-26T10:23:19Z","success":1,"checksum":"494057076bb0b0a28e4b7146bb50113c","file_id":"12394","relation":"main_file"},{"date_created":"2023-01-25T16:20:51Z","date_updated":"2023-01-25T16:20:51Z","success":1,"checksum":"e51015d43ede6b1628803c58e424f99f","file_id":"12388","relation":"main_file","creator":"dgupta","file_size":1840481462,"content_type":"application/octet-stream","file_name":"invivo_BL6-eyeGC8m-dC-5_220613_1750_Result.mat","access_level":"open_access"},{"relation":"main_file","file_id":"12389","date_updated":"2023-01-25T16:23:02Z","date_created":"2023-01-25T16:23:02Z","checksum":"9483686a44e69eadea428b705c33a9a2","success":1,"file_name":"invivo_BL6-eyeGC8m-dC-5_220630_1518_Result.mat","access_level":"open_access","file_size":1617777136,"content_type":"application/octet-stream","creator":"dgupta"}],"_id":"12370","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["571"],"title":"Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"month":"01","day":"26","article_processing_charge":"No","has_accepted_license":"1","doi":"10.15479/AT:ISTA:12370","date_published":"2023-01-26T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"citation":{"chicago":"Gupta, Divyansh, Anton L Sumser, and Maximilian A Jösch. “Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12370.","mla":"Gupta, Divyansh, et al. Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12370.","short":"D. Gupta, A.L. Sumser, M.A. Jösch, (2023).","ista":"Gupta D, Sumser AL, Jösch MA. 2023. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12370.","apa":"Gupta, D., Sumser, A. L., & Jösch, M. A. (2023). Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12370","ieee":"D. Gupta, A. L. Sumser, and M. A. Jösch, “Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields.” Institute of Science and Technology Austria, 2023.","ama":"Gupta D, Sumser AL, Jösch MA. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. 2023. doi:10.15479/AT:ISTA:12370"},"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"},{"call_identifier":"H2020","name":"Circuits of Visual Attention","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017","_id":"264FEA02-B435-11E9-9278-68D0E5697425"}]},{"file_date_updated":"2023-10-04T11:46:24Z","author":[{"id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","orcid":"0000-0001-7841-0091","first_name":"Hana","last_name":"Kourimska","full_name":"Kourimska, Hana"}],"date_updated":"2023-10-04T11:46:48Z","date_created":"2023-03-26T22:01:09Z","volume":70,"acknowledgement":"Open access funding provided by the Austrian Science Fund (FWF). This research was supported by the FWF grant, Project number I4245-N35, and by the Deutsche Forschungsgemeinschaft (DFG - German Research Foundation) - Project-ID 195170736 - TRR109.","year":"2023","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"month":"07","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"doi":"10.1007/s00454-023-00484-2","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000948148000001"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Algebraic Footprints of Geometric Features in Homology","grant_number":"I04245","_id":"26AD5D90-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"We study a new discretization of the Gaussian curvature for polyhedral surfaces. This discrete Gaussian curvature is defined on each conical singularity of a polyhedral surface as the quotient of the angle defect and the area of the Voronoi cell corresponding to the singularity. We divide polyhedral surfaces into discrete conformal classes using a generalization of discrete conformal equivalence pioneered by Feng Luo. We subsequently show that, in every discrete conformal class, there exists a polyhedral surface with constant discrete Gaussian curvature. We also provide explicit examples to demonstrate that this surface is in general not unique.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"cdbf90ba4a7ddcb190d37b9e9d4cb9d3","date_updated":"2023-10-04T11:46:24Z","date_created":"2023-10-04T11:46:24Z","file_id":"14396","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1026683,"access_level":"open_access","file_name":"2023_DiscreteGeometry_Kourimska.pdf"}],"_id":"12764","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510"],"status":"public","title":"Discrete yamabe problem for polyhedral surfaces","intvolume":" 70","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2023-07-01T00:00:00Z","publication":"Discrete and Computational Geometry","citation":{"ama":"Kourimska H. Discrete yamabe problem for polyhedral surfaces. Discrete and Computational Geometry. 2023;70:123-153. doi:10.1007/s00454-023-00484-2","ista":"Kourimska H. 2023. Discrete yamabe problem for polyhedral surfaces. Discrete and Computational Geometry. 70, 123–153.","ieee":"H. Kourimska, “Discrete yamabe problem for polyhedral surfaces,” Discrete and Computational Geometry, vol. 70. Springer Nature, pp. 123–153, 2023.","apa":"Kourimska, H. (2023). Discrete yamabe problem for polyhedral surfaces. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-023-00484-2","mla":"Kourimska, Hana. “Discrete Yamabe Problem for Polyhedral Surfaces.” Discrete and Computational Geometry, vol. 70, Springer Nature, 2023, pp. 123–53, doi:10.1007/s00454-023-00484-2.","short":"H. Kourimska, Discrete and Computational Geometry 70 (2023) 123–153.","chicago":"Kourimska, Hana. “Discrete Yamabe Problem for Polyhedral Surfaces.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-023-00484-2."},"article_type":"original","page":"123-153"},{"doi":"10.15479/at:ista:13331","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"}],"degree_awarded":"MS","oa":1,"publication_identifier":{"issn":["2791-4585"]},"month":"07","related_material":{"record":[{"id":"12680","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Köse, Seyda","first_name":"Seyda","last_name":"Köse","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb"}],"date_updated":"2023-10-04T11:54:56Z","date_created":"2023-07-31T10:20:55Z","year":"2023","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","file_date_updated":"2023-08-03T15:28:55Z","date_published":"2023-07-31T00:00:00Z","citation":{"ama":"Köse S. Exterior algebra and combinatorics. 2023. doi:10.15479/at:ista:13331","apa":"Köse, S. (2023). Exterior algebra and combinatorics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13331","ieee":"S. Köse, “Exterior algebra and combinatorics,” Institute of Science and Technology Austria, 2023.","ista":"Köse S. 2023. Exterior algebra and combinatorics. Institute of Science and Technology Austria.","short":"S. Köse, Exterior Algebra and Combinatorics, Institute of Science and Technology Austria, 2023.","mla":"Köse, Seyda. Exterior Algebra and Combinatorics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13331.","chicago":"Köse, Seyda. “Exterior Algebra and Combinatorics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13331."},"page":"26","article_processing_charge":"No","has_accepted_license":"1","day":"31","file":[{"creator":"skoese","content_type":"application/x-zip-compressed","file_size":28684,"access_level":"closed","file_name":"Exterior Algebra and Combinatorics.zip","checksum":"96ee518d796d02af71395622c45de03c","date_created":"2023-07-31T10:16:32Z","date_updated":"2023-07-31T10:16:32Z","file_id":"13333","relation":"source_file"},{"access_level":"open_access","file_name":"thesis-pdfa.pdf","file_size":4953418,"content_type":"application/pdf","creator":"skoese","relation":"main_file","file_id":"13480","checksum":"f610f4713f88bc477de576aaa46b114e","success":1,"date_created":"2023-08-03T15:28:55Z","date_updated":"2023-08-03T15:28:55Z"}],"oa_version":"Published Version","_id":"13331","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Exterior algebra and combinatorics","ddc":["510","516"],"status":"public","abstract":[{"text":"The extension of extremal combinatorics to the setting of exterior algebra is a work\r\nin progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms.\r\n","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Master's Thesis"]},{"_id":"12680","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Erdős-Ko-Rado and Hilton-Milner theorems for two-forms","status":"public","intvolume":" 346","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"The celebrated Erdős–Ko–Rado theorem about the maximal size of an intersecting family of r-element subsets of was extended to the setting of exterior algebra in [5, Theorem 2.3] and in [6, Theorem 1.4]. However, the equality case has not been settled yet. In this short note, we show that the extension of the Erdős–Ko–Rado theorem and the characterization of the equality case therein, as well as those of the Hilton–Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms follow from a folklore puzzle about possible arrangements of an intersecting family of lines.","lang":"eng"}],"issue":"6","publication":"Discrete Mathematics","citation":{"chicago":"Ivanov, Grigory, and Seyda Köse. “Erdős-Ko-Rado and Hilton-Milner Theorems for Two-Forms.” Discrete Mathematics. Elsevier, 2023. https://doi.org/10.1016/j.disc.2023.113363.","mla":"Ivanov, Grigory, and Seyda Köse. “Erdős-Ko-Rado and Hilton-Milner Theorems for Two-Forms.” Discrete Mathematics, vol. 346, no. 6, 113363, Elsevier, 2023, doi:10.1016/j.disc.2023.113363.","short":"G. Ivanov, S. Köse, Discrete Mathematics 346 (2023).","ista":"Ivanov G, Köse S. 2023. Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. Discrete Mathematics. 346(6), 113363.","ieee":"G. Ivanov and S. Köse, “Erdős-Ko-Rado and Hilton-Milner theorems for two-forms,” Discrete Mathematics, vol. 346, no. 6. Elsevier, 2023.","apa":"Ivanov, G., & Köse, S. (2023). Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2023.113363","ama":"Ivanov G, Köse S. Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. Discrete Mathematics. 2023;346(6). doi:10.1016/j.disc.2023.113363"},"article_type":"letter_note","date_published":"2023-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","year":"2023","publication_status":"published","department":[{"_id":"UlWa"},{"_id":"GradSch"}],"publisher":"Elsevier","author":[{"first_name":"Grigory","last_name":"Ivanov","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","full_name":"Ivanov, Grigory"},{"full_name":"Köse, Seyda","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb","last_name":"Köse","first_name":"Seyda"}],"related_material":{"record":[{"id":"13331","relation":"dissertation_contains","status":"public"}]},"date_updated":"2023-10-04T11:54:57Z","date_created":"2023-02-26T23:01:00Z","volume":346,"article_number":"113363","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2201.10892","open_access":"1"}],"external_id":{"arxiv":["2201.10892"]},"oa":1,"quality_controlled":"1","doi":"10.1016/j.disc.2023.113363","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"issn":["0012-365X"]}},{"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2023-07-01T00:00:00Z","page":"1665-1700","article_type":"original","citation":{"short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics 401 (2023) 1665–1700.","mla":"Cipolloni, Giorgio, et al. “On the Spectral Form Factor for Random Matrices.” Communications in Mathematical Physics, vol. 401, Springer Nature, 2023, pp. 1665–700, doi:10.1007/s00220-023-04692-y.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “On the Spectral Form Factor for Random Matrices.” Communications in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s00220-023-04692-y.","ama":"Cipolloni G, Erdös L, Schröder DJ. On the spectral form factor for random matrices. Communications in Mathematical Physics. 2023;401:1665-1700. doi:10.1007/s00220-023-04692-y","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “On the spectral form factor for random matrices,” Communications in Mathematical Physics, vol. 401. Springer Nature, pp. 1665–1700, 2023.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). On the spectral form factor for random matrices. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-023-04692-y","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. On the spectral form factor for random matrices. Communications in Mathematical Physics. 401, 1665–1700."},"publication":"Communications in Mathematical Physics","abstract":[{"text":"In the physics literature the spectral form factor (SFF), the squared Fourier transform of the empirical eigenvalue density, is the most common tool to test universality for disordered quantum systems, yet previous mathematical results have been restricted only to two exactly solvable models (Forrester in J Stat Phys 183:33, 2021. https://doi.org/10.1007/s10955-021-02767-5, Commun Math Phys 387:215–235, 2021. https://doi.org/10.1007/s00220-021-04193-w). We rigorously prove the physics prediction on SFF up to an intermediate time scale for a large class of random matrices using a robust method, the multi-resolvent local laws. Beyond Wigner matrices we also consider the monoparametric ensemble and prove that universality of SFF can already be triggered by a single random parameter, supplementing the recently proven Wigner–Dyson universality (Cipolloni et al. in Probab Theory Relat Fields, 2021. https://doi.org/10.1007/s00440-022-01156-7) to larger spectral scales. Remarkably, extensive numerics indicates that our formulas correctly predict the SFF in the entire slope-dip-ramp regime, as customarily called in physics.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"14397","relation":"main_file","success":1,"checksum":"72057940f76654050ca84a221f21786c","date_created":"2023-10-04T12:09:18Z","date_updated":"2023-10-04T12:09:18Z","access_level":"open_access","file_name":"2023_CommMathPhysics_Cipolloni.pdf","creator":"dernst","file_size":859967,"content_type":"application/pdf"}],"oa_version":"Published Version","intvolume":" 401","status":"public","ddc":["510"],"title":"On the spectral form factor for random matrices","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12792","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1007/s00220-023-04692-y","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000957343500001"]},"ec_funded":1,"file_date_updated":"2023-10-04T12:09:18Z","volume":401,"date_created":"2023-04-02T22:01:11Z","date_updated":"2023-10-04T12:10:31Z","author":[{"full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","first_name":"Giorgio"},{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","first_name":"Dominik J"}],"department":[{"_id":"LaEr"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","acknowledgement":"We are grateful to the authors of [25] for sharing with us their insights and preliminary numerical results. We are especially thankful to Stephen Shenker for very valuable advice over several email communications. Helpful comments on the manuscript from Peter Forrester and from the anonymous referees are also acknowledged.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).\r\nLászló Erdős: Partially supported by ERC Advanced Grant \"RMTBeyond\" No. 101020331. Dominik Schröder: Supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation."},{"file_date_updated":"2023-03-07T14:40:14Z","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","acknowledgement":"We thank the anonymous reviewers for many helpful comments and suggestions, which led to substantial improvements of the paper. The first two authors were supported by the Austrian Science Fund (FWF) grant number P 29984-N35 and W1230. The first author was partly supported by an Austrian Marshall Plan Scholarship, and by the Brummer & Partners MathDataLab. A conference version of this paper was presented at the 37th International Symposium on Computational Geometry (SoCG 2021). Open access funding provided by the Royal Institute of Technology.","year":"2023","date_updated":"2023-10-04T12:03:40Z","date_created":"2023-03-05T23:01:06Z","volume":70,"author":[{"last_name":"Corbet","first_name":"René","full_name":"Corbet, René"},{"full_name":"Kerber, Michael","last_name":"Kerber","first_name":"Michael","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lesnick, Michael","first_name":"Michael","last_name":"Lesnick"},{"orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","first_name":"Georg F","full_name":"Osang, Georg F"}],"related_material":{"record":[{"id":"9605","relation":"earlier_version","status":"public"}]},"month":"09","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2103.07823"],"isi":["000936496800001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00454-022-00476-8","type":"journal_article","abstract":[{"lang":"eng","text":"Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness."}],"ddc":["000"],"status":"public","title":"Computing the multicover bifiltration","intvolume":" 70","_id":"12709","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"71ce7e59f7ee4620acc704fecca620c2","success":1,"date_created":"2023-03-07T14:40:14Z","date_updated":"2023-03-07T14:40:14Z","relation":"main_file","file_id":"12715","content_type":"application/pdf","file_size":1359323,"creator":"cchlebak","access_level":"open_access","file_name":"2023_DisCompGeo_Corbet.pdf"}],"oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","article_type":"original","page":"376-405","publication":"Discrete and Computational Geometry","citation":{"chicago":"Corbet, René, Michael Kerber, Michael Lesnick, and Georg F Osang. “Computing the Multicover Bifiltration.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00476-8.","short":"R. Corbet, M. Kerber, M. Lesnick, G.F. Osang, Discrete and Computational Geometry 70 (2023) 376–405.","mla":"Corbet, René, et al. “Computing the Multicover Bifiltration.” Discrete and Computational Geometry, vol. 70, Springer Nature, 2023, pp. 376–405, doi:10.1007/s00454-022-00476-8.","apa":"Corbet, R., Kerber, M., Lesnick, M., & Osang, G. F. (2023). Computing the multicover bifiltration. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00476-8","ieee":"R. Corbet, M. Kerber, M. Lesnick, and G. F. Osang, “Computing the multicover bifiltration,” Discrete and Computational Geometry, vol. 70. Springer Nature, pp. 376–405, 2023.","ista":"Corbet R, Kerber M, Lesnick M, Osang GF. 2023. Computing the multicover bifiltration. Discrete and Computational Geometry. 70, 376–405.","ama":"Corbet R, Kerber M, Lesnick M, Osang GF. Computing the multicover bifiltration. Discrete and Computational Geometry. 2023;70:376-405. doi:10.1007/s00454-022-00476-8"},"date_published":"2023-09-01T00:00:00Z"},{"language":[{"iso":"eng"}],"doi":"10.1007/s41468-023-00116-x","quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses"}],"oa":1,"main_file_link":[{"url":"https://inserm.hal.science/INRIA-SACLAY/hal-04083524v1","open_access":"1"}],"month":"09","publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"date_updated":"2023-10-04T12:07:18Z","date_created":"2023-03-26T22:01:08Z","volume":7,"author":[{"last_name":"Boissonnat","first_name":"Jean Daniel","full_name":"Boissonnat, Jean Daniel"},{"full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","first_name":"Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","year":"2023","acknowledgement":"We thank Eddie Aamari, David Cohen-Steiner, Isa Costantini, Fred Chazal, Ramsay Dyer, André Lieutier, and Alef Sterk for discussion and Pierre Pansu for encouragement. We further acknowledge the anonymous reviewers whose comments helped improve the exposition.\r\nThe research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement No. 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions). The first author is further supported by the French government, through the 3IA Côte d’Azur Investments in the Future project managed by the National Research Agency (ANR) with the reference number ANR-19-P3IA-0002. The second author is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Austrian science fund (FWF) M-3073.","ec_funded":1,"date_published":"2023-09-01T00:00:00Z","article_type":"original","page":"619-641","publication":"Journal of Applied and Computational Topology","citation":{"ama":"Boissonnat JD, Wintraecken M. The reach of subsets of manifolds. Journal of Applied and Computational Topology. 2023;7:619-641. doi:10.1007/s41468-023-00116-x","ista":"Boissonnat JD, Wintraecken M. 2023. The reach of subsets of manifolds. Journal of Applied and Computational Topology. 7, 619–641.","apa":"Boissonnat, J. D., & Wintraecken, M. (2023). The reach of subsets of manifolds. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-023-00116-x","ieee":"J. D. Boissonnat and M. Wintraecken, “The reach of subsets of manifolds,” Journal of Applied and Computational Topology, vol. 7. Springer Nature, pp. 619–641, 2023.","mla":"Boissonnat, Jean Daniel, and Mathijs Wintraecken. “The Reach of Subsets of Manifolds.” Journal of Applied and Computational Topology, vol. 7, Springer Nature, 2023, pp. 619–41, doi:10.1007/s41468-023-00116-x.","short":"J.D. Boissonnat, M. Wintraecken, Journal of Applied and Computational Topology 7 (2023) 619–641.","chicago":"Boissonnat, Jean Daniel, and Mathijs Wintraecken. “The Reach of Subsets of Manifolds.” Journal of Applied and Computational Topology. Springer Nature, 2023. https://doi.org/10.1007/s41468-023-00116-x."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","status":"public","title":"The reach of subsets of manifolds","intvolume":" 7","_id":"12763","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Kleinjohann (Archiv der Mathematik 35(1):574–582, 1980; Mathematische Zeitschrift 176(3), 327–344, 1981) and Bangert (Archiv der Mathematik 38(1):54–57, 1982) extended the reach rch(S) from subsets S of Euclidean space to the reach rchM(S) of subsets S of Riemannian manifolds M, where M is smooth (we’ll assume at least C3). Bangert showed that sets of positive reach in Euclidean space and Riemannian manifolds are very similar. In this paper we introduce a slight variant of Kleinjohann’s and Bangert’s extension and quantify the similarity between sets of positive reach in Euclidean space and Riemannian manifolds in a new way: Given p∈M and q∈S, we bound the local feature size (a local version of the reach) of its lifting to the tangent space via the inverse exponential map (exp−1p(S)) at q, assuming that rchM(S) and the geodesic distance dM(p,q) are bounded. These bounds are motivated by the importance of the reach and local feature size to manifold learning, topological inference, and triangulating manifolds and the fact that intrinsic approaches circumvent the curse of dimensionality.","lang":"eng"}],"type":"journal_article"},{"article_number":"17","ec_funded":1,"file_date_updated":"2023-07-14T12:03:48Z","year":"2023","acknowledgement":"We thank Christof Löding for pointing us to some results on PSpace-hardess of universality problems and the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science Foundation grant 2410/22.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publication_status":"published","author":[{"first_name":"Udi","last_name":"Boker","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien","last_name":"Mazzocchi","id":"b26baa86-3308-11ec-87b0-8990f34baa85"},{"full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac","first_name":"Naci E"}],"volume":279,"date_updated":"2023-10-09T07:14:03Z","date_created":"2023-07-14T10:00:15Z","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772990"]},"month":"09","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2307.06016"]},"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"quality_controlled":"1","doi":"10.4230/LIPIcs.CONCUR.2023.17","conference":{"name":"CONCUR: Conference on Concurrency Theory","start_date":"2023-09-18","location":"Antwerp, Belgium","end_date":"2023-09-23"},"language":[{"iso":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"The safety-liveness dichotomy is a fundamental concept in formal languages which plays a key role in verification. Recently, this dichotomy has been lifted to quantitative properties, which are arbitrary functions from infinite words to partially-ordered domains. We look into harnessing the dichotomy for the specific classes of quantitative properties expressed by quantitative automata. These automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totallyordered domain of real numbers. In this automata-theoretic setting, we establish a connection between quantitative safety and topological continuity and provide an alternative characterization of quantitative safety and liveness in terms of their boolean counterparts. For all common value functions, we show how the safety closure of a quantitative automaton can be constructed in PTime, and we provide PSpace-complete checks of whether a given quantitative automaton is safe or live, with the exception of LimInfAvg and LimSupAvg automata, for which the safety check is in ExpSpace. Moreover, for deterministic Sup, LimInf, and LimSup automata, we give PTime decompositions into safe and live automata. These decompositions enable the separation of techniques for safety and liveness verification for quantitative specifications.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13221","intvolume":" 279","status":"public","ddc":["000"],"title":"Safety and liveness of quantitative automata","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"CONCUR23.pdf","creator":"esarac","file_size":755529,"content_type":"application/pdf","file_id":"13224","relation":"main_file","success":1,"checksum":"d40e57a04448ea5c77d7e1cfb9590a81","date_created":"2023-07-14T12:03:48Z","date_updated":"2023-07-14T12:03:48Z"}],"has_accepted_license":"1","article_processing_charge":"No","day":"01","citation":{"ieee":"U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness of quantitative automata,” in 34th International Conference on Concurrency Theory, Antwerp, Belgium, 2023, vol. 279.","apa":"Boker, U., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023). Safety and liveness of quantitative automata. In 34th International Conference on Concurrency Theory (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2023.17","ista":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Safety and liveness of quantitative automata. 34th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 279, 17.","ama":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative automata. In: 34th International Conference on Concurrency Theory. Vol 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.CONCUR.2023.17","chicago":"Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Safety and Liveness of Quantitative Automata.” In 34th International Conference on Concurrency Theory, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.CONCUR.2023.17.","short":"U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 34th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","mla":"Boker, Udi, et al. “Safety and Liveness of Quantitative Automata.” 34th International Conference on Concurrency Theory, vol. 279, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.CONCUR.2023.17."},"publication":"34th International Conference on Concurrency Theory","date_published":"2023-09-01T00:00:00Z"},{"date_published":"2023-09-01T00:00:00Z","publication":"Physical Review B","citation":{"ista":"Babkin S, Karcher JF, Burmistrov IS, Mirlin AD. 2023. Generalized surface multifractality in two-dimensional disordered systems. Physical Review B. 108(10), 104205.","ieee":"S. Babkin, J. F. Karcher, I. S. Burmistrov, and A. D. Mirlin, “Generalized surface multifractality in two-dimensional disordered systems,” Physical Review B, vol. 108, no. 10. American Physical Society, 2023.","apa":"Babkin, S., Karcher, J. F., Burmistrov, I. S., & Mirlin, A. D. (2023). Generalized surface multifractality in two-dimensional disordered systems. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.104205","ama":"Babkin S, Karcher JF, Burmistrov IS, Mirlin AD. Generalized surface multifractality in two-dimensional disordered systems. Physical Review B. 2023;108(10). doi:10.1103/PhysRevB.108.104205","chicago":"Babkin, Serafim, Jonas F. Karcher, Igor S. Burmistrov, and Alexander D. Mirlin. “Generalized Surface Multifractality in Two-Dimensional Disordered Systems.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.104205.","mla":"Babkin, Serafim, et al. “Generalized Surface Multifractality in Two-Dimensional Disordered Systems.” Physical Review B, vol. 108, no. 10, 104205, American Physical Society, 2023, doi:10.1103/PhysRevB.108.104205.","short":"S. Babkin, J.F. Karcher, I.S. Burmistrov, A.D. Mirlin, Physical Review B 108 (2023)."},"article_type":"original","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14406","title":"Generalized surface multifractality in two-dimensional disordered systems","status":"public","intvolume":" 108","abstract":[{"lang":"eng","text":"Recently, a concept of generalized multifractality, which characterizes fluctuations and correlations of critical eigenstates, was introduced and explored for all 10 symmetry classes of disordered systems. Here, by using the nonlinear sigma-model (\r\nNL\r\nσ\r\nM\r\n) field theory, we extend the theory of generalized multifractality to boundaries of systems at criticality. Our numerical simulations on two-dimensional systems of symmetry classes A, C, and AII fully confirm the analytical predictions of pure-scaling observables and Weyl symmetry relations between critical exponents of surface generalized multifractality. This demonstrates the validity of the \r\nNL\r\nσ\r\nM\r\n for the description of Anderson-localization critical phenomena, not only in the bulk but also on the boundary. The critical exponents strongly violate generalized parabolicity, in analogy with earlier results for the bulk, corroborating the conclusion that the considered Anderson-localization critical points are not described by conformal field theories. We further derive relations between generalized surface multifractal spectra and linear combinations of Lyapunov exponents of a strip in quasi-one-dimensional geometry, which hold under the assumption of invariance with respect to a logarithmic conformal map. Our numerics demonstrate that these relations hold with an excellent accuracy. Taken together, our results indicate an intriguing situation: the conformal invariance is broken but holds partially at critical points of Anderson localization."}],"issue":"10","type":"journal_article","doi":"10.1103/PhysRevB.108.104205","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2306.09455"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.09455"}],"quality_controlled":"1","month":"09","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"author":[{"first_name":"Serafim","last_name":"Babkin","id":"41e64307-6672-11ee-b9ad-cc7a0075a479","orcid":"0009-0003-7382-8036","full_name":"Babkin, Serafim"},{"last_name":"Karcher","first_name":"Jonas F.","full_name":"Karcher, Jonas F."},{"first_name":"Igor S.","last_name":"Burmistrov","full_name":"Burmistrov, Igor S."},{"last_name":"Mirlin","first_name":"Alexander D.","full_name":"Mirlin, Alexander D."}],"date_updated":"2023-10-09T07:09:30Z","date_created":"2023-10-08T22:01:17Z","volume":108,"year":"2023","acknowledgement":"We thank Ilya Gruzberg for many illuminating discussions. S.S.B., J.F.K., and A.D.M. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) via the Grant\r\nNo. MI 658/14-1. I.S.B. acknowledges support from Russian Science Foundation (Grant No. 22-42-04416).","publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","article_number":"104205"},{"date_published":"2023-09-01T00:00:00Z","citation":{"mla":"Bartocci, Ezio, et al. “Hypernode Automata.” 34th International Conference on Concurrency Theory, vol. 279, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.CONCUR.2023.21.","short":"E. Bartocci, T.A. Henzinger, D. Nickovic, A. Oliveira da Costa, in:, 34th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","chicago":"Bartocci, Ezio, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira da Costa. “Hypernode Automata.” In 34th International Conference on Concurrency Theory, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.CONCUR.2023.21.","ama":"Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. Hypernode automata. In: 34th International Conference on Concurrency Theory. Vol 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.CONCUR.2023.21","ista":"Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. 2023. Hypernode automata. 34th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 279, 21.","apa":"Bartocci, E., Henzinger, T. A., Nickovic, D., & Oliveira da Costa, A. (2023). Hypernode automata. In 34th International Conference on Concurrency Theory (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2023.21","ieee":"E. Bartocci, T. A. Henzinger, D. Nickovic, and A. Oliveira da Costa, “Hypernode automata,” in 34th International Conference on Concurrency Theory, Antwerp, Belgium, 2023, vol. 279."},"publication":"34th International Conference on Concurrency Theory","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"date_updated":"2023-10-09T07:42:45Z","date_created":"2023-10-09T07:42:45Z","success":1,"checksum":"215765e40454d806174ac0a223e8d6fa","file_id":"14413","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":795790,"file_name":"2023_LIPcs_Bartocci.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 279","title":"Hypernode automata","ddc":["000"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14405","abstract":[{"text":"We introduce hypernode automata as a new specification formalism for hyperproperties of concurrent systems. They are finite automata with nodes labeled with hypernode logic formulas and transitions labeled with actions. A hypernode logic formula specifies relations between sequences of variable values in different system executions. Unlike HyperLTL, hypernode logic takes an asynchronous view on execution traces by constraining the values and the order of value changes of each variable without correlating the timing of the changes. Different execution traces are synchronized solely through the transitions of hypernode automata. Hypernode automata naturally combine asynchronicity at the node level with synchronicity at the transition level. We show that the model-checking problem for hypernode automata is decidable over action-labeled Kripke structures, whose actions induce transitions of the specification automata. For this reason, hypernode automaton is a suitable formalism for specifying and verifying asynchronous hyperproperties, such as declassifying observational determinism in multi-threaded programs.","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.CONCUR.2023.21","conference":{"name":"CONCUR: Conference on Concurrency Theory","end_date":"2023-09-22","start_date":"2023-09-19","location":"Antwerp, Belgium"},"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2305.02836"]},"publication_identifier":{"isbn":["9783959772990"],"issn":["18688969"]},"month":"09","volume":279,"date_updated":"2023-10-09T07:43:44Z","date_created":"2023-10-08T22:01:16Z","author":[{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Nickovic, Dejan","first_name":"Dejan","last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ana","last_name":"Oliveira da Costa","id":"f347ec37-6676-11ee-b395-a888cb7b4fb4","orcid":"0000-0002-8741-5799","full_name":"Oliveira da Costa, Ana"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}],"publication_status":"published","acknowledgement":"This work was supported in part by the Austrian Science Fund (FWF) SFB project\r\nSpyCoDe F8502, by the FWF projects ZK-35 and W1255-N23, and by the ERC Advanced Grant\r\nVAMOS 101020093.","year":"2023","ec_funded":1,"file_date_updated":"2023-10-09T07:42:45Z","article_number":"21"},{"author":[{"orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","first_name":"Giorgio","full_name":"Cipolloni, Giorgio"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"},{"full_name":"Schröder, Dominik J","first_name":"Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856"}],"oa_version":"Preprint","date_created":"2023-10-08T22:01:17Z","date_updated":"2023-10-09T07:19:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14408","acknowledgement":"The authors are grateful to Joscha Henheik for his help with the formulas in Appendix B.","year":"2023","publisher":"Springer Nature","department":[{"_id":"LaEr"}],"status":"public","title":"Mesoscopic central limit theorem for non-Hermitian random matrices","publication_status":"epub_ahead","abstract":[{"lang":"eng","text":"We prove that the mesoscopic linear statistics ∑if(na(σi−z0)) of the eigenvalues {σi}i of large n×n non-Hermitian random matrices with complex centred i.i.d. entries are asymptotically Gaussian for any H20-functions f around any point z0 in the bulk of the spectrum on any mesoscopic scale 0Probability Theory and Related Fields. Springer Nature, 2023. https://doi.org/10.1007/s00440-023-01229-1.","mla":"Cipolloni, Giorgio, et al. “Mesoscopic Central Limit Theorem for Non-Hermitian Random Matrices.” Probability Theory and Related Fields, Springer Nature, 2023, doi:10.1007/s00440-023-01229-1.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields (2023).","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Mesoscopic central limit theorem for non-Hermitian random matrices. Probability Theory and Related Fields.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Mesoscopic central limit theorem for non-Hermitian random matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-023-01229-1","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Mesoscopic central limit theorem for non-Hermitian random matrices,” Probability Theory and Related Fields. Springer Nature, 2023.","ama":"Cipolloni G, Erdös L, Schröder DJ. Mesoscopic central limit theorem for non-Hermitian random matrices. Probability Theory and Related Fields. 2023. doi:10.1007/s00440-023-01229-1"},"publication":"Probability Theory and Related Fields","article_type":"original","quality_controlled":"1","publication_identifier":{"issn":["0178-8051"],"eissn":["1432-2064"]},"article_processing_charge":"No","day":"28","month":"09","scopus_import":"1"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2307.06611"]},"project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"quality_controlled":"1","doi":"10.4230/LIPIcs.MFCS.2023.15","conference":{"end_date":"2023-09-01","location":"Bordeaux, France","start_date":"2023-08-28","name":"MFCS: Symposium on Mathematical Foundations of Computer Science"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783959772921"],"eissn":["1868-8969"]},"month":"08","year":"2023","acknowledgement":"This work was partly funded by the ERC CoG 863818 (ForM-SMArt), the DFG Grant\r\n389792660 as part of TRR 248 (Foundations of Perspicuous Software Systems), the Cluster of\r\nExcellence EXC 2050/1 (CeTI, project ID 390696704, as part of Germany’s Excellence Strategy), and the DFG projects BA-1679/11-1 and BA-1679/12-1.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"publication_status":"published","author":[{"last_name":"Baier","first_name":"Christel","full_name":"Baier, Christel"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Meggendorfer, Tobias","first_name":"Tobias","last_name":"Meggendorfer","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165"},{"full_name":"Piribauer, Jakob","last_name":"Piribauer","first_name":"Jakob"}],"volume":272,"date_updated":"2023-10-09T09:22:37Z","date_created":"2023-10-09T09:21:05Z","article_number":"15","ec_funded":1,"file_date_updated":"2023-10-09T09:19:11Z","citation":{"ista":"Baier C, Chatterjee K, Meggendorfer T, Piribauer J. 2023. Entropic risk for turn-based stochastic games. 48th International Symposium on Mathematical Foundations of Computer Science. MFCS: Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 272, 15.","apa":"Baier, C., Chatterjee, K., Meggendorfer, T., & Piribauer, J. (2023). Entropic risk for turn-based stochastic games. In 48th International Symposium on Mathematical Foundations of Computer Science (Vol. 272). Bordeaux, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2023.15","ieee":"C. Baier, K. Chatterjee, T. Meggendorfer, and J. Piribauer, “Entropic risk for turn-based stochastic games,” in 48th International Symposium on Mathematical Foundations of Computer Science, Bordeaux, France, 2023, vol. 272.","ama":"Baier C, Chatterjee K, Meggendorfer T, Piribauer J. Entropic risk for turn-based stochastic games. In: 48th International Symposium on Mathematical Foundations of Computer Science. Vol 272. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.MFCS.2023.15","chicago":"Baier, Christel, Krishnendu Chatterjee, Tobias Meggendorfer, and Jakob Piribauer. “Entropic Risk for Turn-Based Stochastic Games.” In 48th International Symposium on Mathematical Foundations of Computer Science, Vol. 272. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.MFCS.2023.15.","mla":"Baier, Christel, et al. “Entropic Risk for Turn-Based Stochastic Games.” 48th International Symposium on Mathematical Foundations of Computer Science, vol. 272, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.MFCS.2023.15.","short":"C. Baier, K. Chatterjee, T. Meggendorfer, J. Piribauer, in:, 48th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023."},"publication":"48th International Symposium on Mathematical Foundations of Computer Science","date_published":"2023-08-21T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14417","intvolume":" 272","ddc":["000"],"status":"public","title":"Entropic risk for turn-based stochastic games","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_LIPIcsMFCS_Baier.pdf","file_size":826843,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14418","checksum":"402281b17ed669bbf149d0fdf68ac201","success":1,"date_created":"2023-10-09T09:19:11Z","date_updated":"2023-10-09T09:19:11Z"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"Entropic risk (ERisk) is an established risk measure in finance, quantifying risk by an exponential re-weighting of rewards. We study ERisk for the first time in the context of turn-based stochastic games with the total reward objective. This gives rise to an objective function that demands the control of systems in a risk-averse manner. We show that the resulting games are determined and, in particular, admit optimal memoryless deterministic strategies. This contrasts risk measures that previously have been considered in the special case of Markov decision processes and that require randomization and/or memory. We provide several results on the decidability and the computational complexity of the threshold problem, i.e. whether the optimal value of ERisk exceeds a given threshold. In the most general case, the problem is decidable subject to Shanuel’s conjecture. If all inputs are rational, the resulting threshold problem can be solved using algebraic numbers, leading to decidability via a polynomial-time reduction to the existential theory of the reals. Further restrictions on the encoding of the input allow the solution of the threshold problem in NP∩coNP. Finally, an approximation algorithm for the optimal value of ERisk is provided.","lang":"eng"}]},{"publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1137/21M1412918","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073"}],"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://hal-emse.ccsd.cnrs.fr/3IA-COTEDAZUR/hal-04083489v1"}],"external_id":{"isi":["001013183000012"]},"oa":1,"ec_funded":1,"volume":52,"date_updated":"2023-10-10T07:34:35Z","date_created":"2023-05-14T22:01:00Z","related_material":{"record":[{"id":"9441","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Boissonnat, Jean Daniel","first_name":"Jean Daniel","last_name":"Boissonnat"},{"full_name":"Kachanovich, Siargey","first_name":"Siargey","last_name":"Kachanovich"},{"full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","first_name":"Mathijs"}],"department":[{"_id":"HeEd"}],"publisher":"Society for Industrial and Applied Mathematics","publication_status":"published","year":"2023","acknowledgement":"The authors have received funding from the European Research Council under the European Union's ERC grant greement 339025 GUDHI (Algorithmic Foundations of Geometric Un-derstanding in Higher Dimensions). The first author was supported by the French government,through the 3IA C\\^ote d'Azur Investments in the Future project managed by the National ResearchAgency (ANR) with the reference ANR-19-P3IA-0002. The third author was supported by the Eu-ropean Union's Horizon 2020 research and innovation programme under the Marie Sk\\lodowska-Curiegrant agreement 754411 and the FWF (Austrian Science Fund) grant M 3073.","article_processing_charge":"No","day":"30","scopus_import":"1","date_published":"2023-04-30T00:00:00Z","page":"452-486","article_type":"original","citation":{"ista":"Boissonnat JD, Kachanovich S, Wintraecken M. 2023. Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. SIAM Journal on Computing. 52(2), 452–486.","ieee":"J. D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations,” SIAM Journal on Computing, vol. 52, no. 2. Society for Industrial and Applied Mathematics, pp. 452–486, 2023.","apa":"Boissonnat, J. D., Kachanovich, S., & Wintraecken, M. (2023). Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. SIAM Journal on Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/21M1412918","ama":"Boissonnat JD, Kachanovich S, Wintraecken M. Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. SIAM Journal on Computing. 2023;52(2):452-486. doi:10.1137/21M1412918","chicago":"Boissonnat, Jean Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter–Freudenthal–Kuhn Triangulations.” SIAM Journal on Computing. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/21M1412918.","mla":"Boissonnat, Jean Daniel, et al. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter–Freudenthal–Kuhn Triangulations.” SIAM Journal on Computing, vol. 52, no. 2, Society for Industrial and Applied Mathematics, 2023, pp. 452–86, doi:10.1137/21M1412918.","short":"J.D. Boissonnat, S. Kachanovich, M. Wintraecken, SIAM Journal on Computing 52 (2023) 452–486."},"publication":"SIAM Journal on Computing","issue":"2","abstract":[{"lang":"eng","text":"Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e., submanifolds of Rd defined as the zero set of some multivariate multivalued smooth function f:Rd→Rd−n, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M=f−1(0) is to consider its piecewise linear (PL) approximation M^\r\n based on a triangulation T of the ambient space Rd. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ=1/D (and unavoidably exponential in n). Since it is known that for δ=Ω(d2.5), M^ is O(D2)-close and isotopic to M\r\n, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M^ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art. "}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 52","title":"Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12960"},{"oa_version":"Published Version","file":[{"date_created":"2023-07-12T10:22:04Z","date_updated":"2023-07-12T10:22:04Z","success":1,"checksum":"e07d5323f9c0e5cbd1ad6453f29440ab","file_id":"13219","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","file_size":3155843,"file_name":"2023_JACS_Bunting.pdf","access_level":"open_access"}],"_id":"13216","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 145","status":"public","ddc":["540"],"title":"Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane","issue":"27","abstract":[{"text":"Physical catalysts often have multiple sites where reactions can take place. One prominent example is single-atom alloys, where the reactive dopant atoms can preferentially locate in the bulk or at different sites on the surface of the nanoparticle. However, ab initio modeling of catalysts usually only considers one site of the catalyst, neglecting the effects of multiple sites. Here, nanoparticles of copper doped with single-atom rhodium or palladium are modeled for the dehydrogenation of propane. Single-atom alloy nanoparticles are simulated at 400–600 K, using machine learning potentials trained on density functional theory calculations, and then the occupation of different single-atom active sites is identified using a similarity kernel. Further, the turnover frequency for all possible sites is calculated for propane dehydrogenation to propene through microkinetic modeling using density functional theory calculations. The total turnover frequencies of the whole nanoparticle are then described from both the population and the individual turnover frequency of each site. Under operating conditions, rhodium as a dopant is found to almost exclusively occupy (111) surface sites while palladium as a dopant occupies a greater variety of facets. Undercoordinated dopant surface sites are found to tend to be more reactive for propane dehydrogenation compared to the (111) surface. It is found that considering the dynamics of the single-atom alloy nanoparticle has a profound effect on the calculated catalytic activity of single-atom alloys by several orders of magnitude.","lang":"eng"}],"type":"journal_article","date_published":"2023-06-30T00:00:00Z","citation":{"ama":"Bunting R, Wodaczek F, Torabi T, Cheng B. Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. Journal of the American Chemical Society. 2023;145(27):14894-14902. doi:10.1021/jacs.3c04030","ista":"Bunting R, Wodaczek F, Torabi T, Cheng B. 2023. Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. Journal of the American Chemical Society. 145(27), 14894–14902.","ieee":"R. Bunting, F. Wodaczek, T. Torabi, and B. Cheng, “Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane,” Journal of the American Chemical Society, vol. 145, no. 27. American Chemical Society, pp. 14894–14902, 2023.","apa":"Bunting, R., Wodaczek, F., Torabi, T., & Cheng, B. (2023). Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.3c04030","mla":"Bunting, Rhys, et al. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.” Journal of the American Chemical Society, vol. 145, no. 27, American Chemical Society, 2023, pp. 14894–902, doi:10.1021/jacs.3c04030.","short":"R. Bunting, F. Wodaczek, T. Torabi, B. Cheng, Journal of the American Chemical Society 145 (2023) 14894–14902.","chicago":"Bunting, Rhys, Felix Wodaczek, Tina Torabi, and Bingqing Cheng. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.3c04030."},"publication":"Journal of the American Chemical Society","page":"14894-14902","article_type":"original","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"30","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"author":[{"full_name":"Bunting, Rhys","orcid":"0000-0001-6928-074X","id":"91deeae8-1207-11ec-b130-c194ad5b50c6","last_name":"Bunting","first_name":"Rhys"},{"full_name":"Wodaczek, Felix","id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e","orcid":"0009-0000-1457-795X","first_name":"Felix","last_name":"Wodaczek"},{"full_name":"Torabi, Tina","first_name":"Tina","last_name":"Torabi"},{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing"}],"volume":145,"date_updated":"2023-10-11T08:45:10Z","date_created":"2023-07-12T09:16:40Z","pmid":1,"year":"2023","acknowledgement":"B.C. acknowledges resources provided by the Cambridge Tier2 system operated by the University of Cambridge Research\r\nComputing Service funded by EPSRC Tier-2 capital grant EP/\r\nP020259/1.","department":[{"_id":"MaIb"},{"_id":"BiCh"}],"publisher":"American Chemical Society","publication_status":"published","file_date_updated":"2023-07-12T10:22:04Z","doi":"10.1021/jacs.3c04030","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["37390457"],"isi":["001020623900001"]},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"month":"06"},{"publication":"PLoS Biology","citation":{"ieee":"I. A. Unterweger, J. Klepstad, E. B. Hannezo, P. R. Lundegaard, A. Trusina, and E. A. Ober, “Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics,” PLoS Biology, vol. 21, no. 10. Public Library of Science, 2023.","apa":"Unterweger, I. A., Klepstad, J., Hannezo, E. B., Lundegaard, P. R., Trusina, A., & Ober, E. A. (2023). Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3002315","ista":"Unterweger IA, Klepstad J, Hannezo EB, Lundegaard PR, Trusina A, Ober EA. 2023. Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. PLoS Biology. 21(10), e3002315.","ama":"Unterweger IA, Klepstad J, Hannezo EB, Lundegaard PR, Trusina A, Ober EA. Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. PLoS Biology. 2023;21(10). doi:10.1371/journal.pbio.3002315","chicago":"Unterweger, Iris A., Julie Klepstad, Edouard B Hannezo, Pia R. Lundegaard, Ala Trusina, and Elke A. Ober. “Lineage Tracing Identifies Heterogeneous Hepatoblast Contribution to Cell Lineages and Postembryonic Organ Growth Dynamics.” PLoS Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pbio.3002315.","short":"I.A. Unterweger, J. Klepstad, E.B. Hannezo, P.R. Lundegaard, A. Trusina, E.A. Ober, PLoS Biology 21 (2023).","mla":"Unterweger, Iris A., et al. “Lineage Tracing Identifies Heterogeneous Hepatoblast Contribution to Cell Lineages and Postembryonic Organ Growth Dynamics.” PLoS Biology, vol. 21, no. 10, e3002315, Public Library of Science, 2023, doi:10.1371/journal.pbio.3002315."},"article_type":"original","date_published":"2023-10-04T00:00:00Z","scopus_import":"1","day":"04","article_processing_charge":"No","has_accepted_license":"1","_id":"14426","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics","ddc":["570"],"intvolume":" 21","file":[{"success":1,"checksum":"40a2b11b41d70a0e5939f8a52b66e389","date_created":"2023-10-16T07:20:49Z","date_updated":"2023-10-16T07:20:49Z","file_id":"14431","relation":"main_file","creator":"dernst","file_size":6193110,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_PloSBiology_Unterweger.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"To meet the physiological demands of the body, organs need to establish a functional tissue architecture and adequate size as the embryo develops to adulthood. In the liver, uni- and bipotent progenitor differentiation into hepatocytes and biliary epithelial cells (BECs), and their relative proportions, comprise the functional architecture. Yet, the contribution of individual liver progenitors at the organ level to both fates, and their specific proportion, is unresolved. Combining mathematical modelling with organ-wide, multispectral FRaeppli-NLS lineage tracing in zebrafish, we demonstrate that a precise BEC-to-hepatocyte ratio is established (i) fast, (ii) solely by heterogeneous lineage decisions from uni- and bipotent progenitors, and (iii) independent of subsequent cell type–specific proliferation. Extending lineage tracing to adulthood determined that embryonic cells undergo spatially heterogeneous three-dimensional growth associated with distinct environments. Strikingly, giant clusters comprising almost half a ventral lobe suggest lobe-specific dominant-like growth behaviours. We show substantial hepatocyte polyploidy in juveniles representing another hallmark of postembryonic liver growth. Our findings uncover heterogeneous progenitor contributions to tissue architecture-defining cell type proportions and postembryonic organ growth as key mechanisms forming the adult liver."}],"issue":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"doi":"10.1371/journal.pbio.3002315","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["1545-7885"]},"year":"2023","acknowledgement":"We thank the Ober group for discussion and comments on the manuscript. We are grateful to\r\nDr. F. Lemaigre for feedback on the manuscript and Dr. T. Piotrowski for invaluable support.\r\nWe thank the department of experimental medicine (AEM) in Copenhagen for expert fish\r\ncare. We gratefully acknowledge the DanStem Imaging Platform (University of Copenhagen)\r\nfor support and assistance in this work.\r\nThis work is supported by Novo Nordisk Foundation grant NNF17CC0027852 (EAO);\r\nNordisk Foundation grant NNF19OC0058327 (EAO); Novo Nordisk Foundation grant\r\nNNF17OC0031204 (PRL); https://novonordiskfonden.dk/en/; Danish National\r\nResearch Foundation grant DNRF116 (EAO and AT); https://dg.dk/en/; John and Birthe Meyer\r\nFoundation (PRL) and European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement No. 851288 (EH).","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"EdHa"}],"author":[{"first_name":"Iris A.","last_name":"Unterweger","full_name":"Unterweger, Iris A."},{"full_name":"Klepstad, Julie","last_name":"Klepstad","first_name":"Julie"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"last_name":"Lundegaard","first_name":"Pia R.","full_name":"Lundegaard, Pia R."},{"last_name":"Trusina","first_name":"Ala","full_name":"Trusina, Ala"},{"full_name":"Ober, Elke A.","last_name":"Ober","first_name":"Elke A."}],"related_material":{"link":[{"relation":"software","url":"https://github.com/JulieKlepstad/LiverDevelopment"}]},"date_created":"2023-10-15T22:01:10Z","date_updated":"2023-10-16T07:25:48Z","volume":21,"article_number":"e3002315","file_date_updated":"2023-10-16T07:20:49Z","ec_funded":1},{"date_published":"2023-08-09T00:00:00Z","publication":"43rd Annual International Cryptology Conference","citation":{"apa":"Dodis, Y., Ferguson, N., Goldin, E., Hall, P., & Pietrzak, K. Z. (2023). Random oracle combiners: Breaking the concatenation barrier for collision-resistance. In 43rd Annual International Cryptology Conference (Vol. 14082, pp. 514–546). Santa Barbara, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-031-38545-2_17","ieee":"Y. Dodis, N. Ferguson, E. Goldin, P. Hall, and K. Z. Pietrzak, “Random oracle combiners: Breaking the concatenation barrier for collision-resistance,” in 43rd Annual International Cryptology Conference, Santa Barbara, CA, United States, 2023, vol. 14082, pp. 514–546.","ista":"Dodis Y, Ferguson N, Goldin E, Hall P, Pietrzak KZ. 2023. Random oracle combiners: Breaking the concatenation barrier for collision-resistance. 43rd Annual International Cryptology Conference. CRYPTO: Advances in Cryptology, LNCS, vol. 14082, 514–546.","ama":"Dodis Y, Ferguson N, Goldin E, Hall P, Pietrzak KZ. Random oracle combiners: Breaking the concatenation barrier for collision-resistance. In: 43rd Annual International Cryptology Conference. Vol 14082. Springer Nature; 2023:514-546. doi:10.1007/978-3-031-38545-2_17","chicago":"Dodis, Yevgeniy, Niels Ferguson, Eli Goldin, Peter Hall, and Krzysztof Z Pietrzak. “Random Oracle Combiners: Breaking the Concatenation Barrier for Collision-Resistance.” In 43rd Annual International Cryptology Conference, 14082:514–46. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-38545-2_17.","short":"Y. Dodis, N. Ferguson, E. Goldin, P. Hall, K.Z. Pietrzak, in:, 43rd Annual International Cryptology Conference, Springer Nature, 2023, pp. 514–546.","mla":"Dodis, Yevgeniy, et al. “Random Oracle Combiners: Breaking the Concatenation Barrier for Collision-Resistance.” 43rd Annual International Cryptology Conference, vol. 14082, Springer Nature, 2023, pp. 514–46, doi:10.1007/978-3-031-38545-2_17."},"page":"514-546","day":"09","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","_id":"14428","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Random oracle combiners: Breaking the concatenation barrier for collision-resistance","status":"public","intvolume":" 14082","abstract":[{"text":"Suppose we have two hash functions h1 and h2, but we trust the security of only one of them. To mitigate this worry, we wish to build a hash combiner Ch1,h2 which is secure so long as one of the underlying hash functions is. This question has been well-studied in the regime of collision resistance. In this case, concatenating the two hash function outputs clearly works. Unfortunately, a long series of works (Boneh and Boyen, CRYPTO’06; Pietrzak, Eurocrypt’07; Pietrzak, CRYPTO’08) showed no (noticeably) shorter combiner for collision resistance is possible.\r\nIn this work, we revisit this pessimistic state of affairs, motivated by the observation that collision-resistance is insufficient for many interesting applications of cryptographic hash functions anyway. We argue the right formulation of the “hash combiner” is to build what we call random oracle (RO) combiners, utilizing stronger assumptions for stronger constructions.\r\nIndeed, we circumvent the previous lower bounds for collision resistance by constructing a simple length-preserving RO combiner C˜h1,h2Z1,Z2(M)=h1(M,Z1)⊕h2(M,Z2),where Z1,Z2\r\n are random salts of appropriate length. We show that this extra randomness is necessary for RO combiners, and indeed our construction is somewhat tight with this lower bound.\r\nOn the negative side, we show that one cannot generically apply the composition theorem to further replace “monolithic” hash functions h1 and h2 by some simpler indifferentiable construction (such as the Merkle-Damgård transformation) from smaller components, such as fixed-length compression functions. Finally, despite this issue, we directly prove collision resistance of the Merkle-Damgård variant of our combiner, where h1 and h2 are replaced by iterative Merkle-Damgård hashes applied to a fixed-length compression function. Thus, we can still subvert the concatenation barrier for collision-resistance combiners while utilizing practically small fixed-length components underneath.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"conference":{"end_date":"2023-08-24","location":"Santa Barbara, CA, United States","start_date":"2023-08-20","name":"CRYPTO: Advances in Cryptology"},"doi":"10.1007/978-3-031-38545-2_17","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2023/1041"}],"quality_controlled":"1","month":"08","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031385445"],"eissn":["1611-3349"]},"author":[{"full_name":"Dodis, Yevgeniy","last_name":"Dodis","first_name":"Yevgeniy"},{"last_name":"Ferguson","first_name":"Niels","full_name":"Ferguson, Niels"},{"first_name":"Eli","last_name":"Goldin","full_name":"Goldin, Eli"},{"first_name":"Peter","last_name":"Hall","full_name":"Hall, Peter"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z"}],"date_updated":"2023-10-16T08:02:11Z","date_created":"2023-10-15T22:01:11Z","volume":14082,"year":"2023","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer Nature"},{"month":"01","publication_identifier":{"issn":["0065-1036"],"eissn":["1730-6264"]},"oa":1,"external_id":{"arxiv":["2103.08268"],"isi":["000912903000001"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2103.08268","open_access":"1"}],"isi":1,"quality_controlled":"1","doi":"10.4064/aa210830-24-11","language":[{"iso":"eng"}],"acknowledgement":"This article is a version the author’s master thesis at the University of Bonn. The author would like to thank his advisor Valentin Blomer for introducing the problem, and giving generous feedback and encouragement along the way, especially during the global pandemic.\r\nThe author thanks Edgar Assing for his lectures on analytic number theory. Finally, the author is grateful to the anonymous referees for their valuable time and comments.\r\n","year":"2023","publication_status":"published","publisher":"Instytut Matematyczny","department":[{"_id":"GradSch"}],"author":[{"last_name":"Diao","first_name":"Yijie","orcid":"0000-0002-4989-5330","id":"7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b","full_name":"Diao, Yijie"}],"date_created":"2023-01-26T21:17:04Z","date_updated":"2023-10-17T09:15:17Z","volume":207,"keyword":["Algebra","Number Theory"],"day":"09","article_processing_charge":"No","publication":"Acta Arithmetica","citation":{"ieee":"Y. Diao, “Density of the union of positive diagonal binary quadratic forms,” Acta Arithmetica, vol. 207. Instytut Matematyczny, pp. 1–17, 2023.","apa":"Diao, Y. (2023). Density of the union of positive diagonal binary quadratic forms. Acta Arithmetica. Instytut Matematyczny. https://doi.org/10.4064/aa210830-24-11","ista":"Diao Y. 2023. Density of the union of positive diagonal binary quadratic forms. Acta Arithmetica. 207, 1–17.","ama":"Diao Y. Density of the union of positive diagonal binary quadratic forms. Acta Arithmetica. 2023;207:1-17. doi:10.4064/aa210830-24-11","chicago":"Diao, Yijie. “Density of the Union of Positive Diagonal Binary Quadratic Forms.” Acta Arithmetica. Instytut Matematyczny, 2023. https://doi.org/10.4064/aa210830-24-11.","short":"Y. Diao, Acta Arithmetica 207 (2023) 1–17.","mla":"Diao, Yijie. “Density of the Union of Positive Diagonal Binary Quadratic Forms.” Acta Arithmetica, vol. 207, Instytut Matematyczny, 2023, pp. 1–17, doi:10.4064/aa210830-24-11."},"article_type":"original","page":"1-17","date_published":"2023-01-09T00:00:00Z","type":"journal_article","abstract":[{"text":"Let X be a sufficiently large positive integer. We prove that one may choose a subset S of primes with cardinality O(logX) such that a positive proportion of integers less than X can be represented by x2+py2 for at least one p∈S.","lang":"eng"}],"_id":"12406","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Density of the union of positive diagonal binary quadratic forms","status":"public","intvolume":" 207","oa_version":"Preprint"},{"author":[{"full_name":"Qiu, Liu","orcid":"0000-0003-4345-4267","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","last_name":"Qiu","first_name":"Liu"},{"full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","last_name":"Sahu","first_name":"Rishabh"},{"first_name":"William J","last_name":"Hease","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","full_name":"Hease, William J"},{"last_name":"Arnold","first_name":"Georg M","orcid":"0000-0003-1397-7876","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M"},{"full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"date_updated":"2023-10-17T11:46:12Z","date_created":"2023-07-09T22:01:11Z","volume":14,"year":"2023","acknowledgement":"This work was supported by the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 899354 (FETopen SuperQuLAN), and the Austrian Science Fund (FWF) through BeyondC (F7105). L.Q. acknowledges generous support from the ISTFELLOW programme. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.","pmid":1,"publication_status":"published","publisher":"Nature Research","department":[{"_id":"JoFi"}],"file_date_updated":"2023-07-10T10:10:54Z","ec_funded":1,"article_number":"3784","doi":"10.1038/s41467-023-39493-3","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2210.12443"],"isi":["001018100800002"],"pmid":["37355691"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"month":"06","publication_identifier":{"eissn":["2041-1723"]},"file":[{"file_name":"2023_NatureComms_Qiu.pdf","access_level":"open_access","creator":"alisjak","file_size":1349134,"content_type":"application/pdf","file_id":"13206","relation":"main_file","date_created":"2023-07-10T10:10:54Z","date_updated":"2023-07-10T10:10:54Z","success":1,"checksum":"ec7ccd2c08f90d59cab302fd0d7776a4"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13200","status":"public","ddc":["000"],"title":"Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action","intvolume":" 14","abstract":[{"text":"Recent quantum technologies have established precise quantum control of various microscopic systems using electromagnetic waves. Interfaces based on cryogenic cavity electro-optic systems are particularly promising, due to the direct interaction between microwave and optical fields in the quantum regime. Quantum optical control of superconducting microwave circuits has been precluded so far due to the weak electro-optical coupling as well as quasi-particles induced by the pump laser. Here we report the coherent control of a superconducting microwave cavity using laser pulses in a multimode electro-optical device at millikelvin temperature with near-unity cooperativity. Both the stationary and instantaneous responses of the microwave and optical modes comply with the coherent electro-optical interaction, and reveal only minuscule amount of excess back-action with an unanticipated time delay. Our demonstration enables wide ranges of applications beyond quantum transductions, from squeezing and quantum non-demolition measurements of microwave fields, to entanglement generation and hybrid quantum networks.","lang":"eng"}],"type":"journal_article","date_published":"2023-06-24T00:00:00Z","publication":"Nature Communications","citation":{"ieee":"L. Qiu, R. Sahu, W. J. Hease, G. M. Arnold, and J. M. Fink, “Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action,” Nature Communications, vol. 14. Nature Research, 2023.","apa":"Qiu, L., Sahu, R., Hease, W. J., Arnold, G. M., & Fink, J. M. (2023). Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-023-39493-3","ista":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. 2023. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. 14, 3784.","ama":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. 2023;14. doi:10.1038/s41467-023-39493-3","chicago":"Qiu, Liu, Rishabh Sahu, William J Hease, Georg M Arnold, and Johannes M Fink. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” Nature Communications. Nature Research, 2023. https://doi.org/10.1038/s41467-023-39493-3.","short":"L. Qiu, R. Sahu, W.J. Hease, G.M. Arnold, J.M. Fink, Nature Communications 14 (2023).","mla":"Qiu, Liu, et al. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” Nature Communications, vol. 14, 3784, Nature Research, 2023, doi:10.1038/s41467-023-39493-3."},"article_type":"original","day":"24","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"acknowledgement":"J.B. was funded by the European Union (ERC, CHORAL, project number 101039794). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. M.M. was supported by the 2019 Lopez-Loreta Prize. We would like to thank the reviewers for the insightful comments and, in particular, for suggesting the BAMP-inspired denoisers leading to AMP-AP.","year":"2023","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"MaMo"}],"author":[{"full_name":"Barbier, Jean","last_name":"Barbier","first_name":"Jean"},{"full_name":"Camilli, Francesco","last_name":"Camilli","first_name":"Francesco"},{"first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"full_name":"Sáenz, Manuel","first_name":"Manuel","last_name":"Sáenz"}],"related_material":{"link":[{"url":"https://github.com/fcamilli95/Structured-PCA-","relation":"software"}]},"date_updated":"2023-10-17T11:44:55Z","date_created":"2023-07-30T22:01:02Z","volume":120,"article_number":"e2302028120","file_date_updated":"2023-07-31T07:30:48Z","external_id":{"pmid":["37463204"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"doi":"10.1073/pnas.2302028120","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"eissn":["1091-6490"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13315","status":"public","title":"Fundamental limits in structured principal component analysis and how to reach them","ddc":["000"],"intvolume":" 120","file":[{"checksum":"1fc06228afdb3aa80cf8e7766bcf9dc5","success":1,"date_updated":"2023-07-31T07:30:48Z","date_created":"2023-07-31T07:30:48Z","relation":"main_file","file_id":"13323","content_type":"application/pdf","file_size":995933,"creator":"dernst","access_level":"open_access","file_name":"2023_PNAS_Barbier.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"How do statistical dependencies in measurement noise influence high-dimensional inference? To answer this, we study the paradigmatic spiked matrix model of principal components analysis (PCA), where a rank-one matrix is corrupted by additive noise. We go beyond the usual independence assumption on the noise entries, by drawing the noise from a low-order polynomial orthogonal matrix ensemble. The resulting noise correlations make the setting relevant for applications but analytically challenging. We provide characterization of the Bayes optimal limits of inference in this model. If the spike is rotation invariant, we show that standard spectral PCA is optimal. However, for more general priors, both PCA and the existing approximate message-passing algorithm (AMP) fall short of achieving the information-theoretic limits, which we compute using the replica method from statistical physics. We thus propose an AMP, inspired by the theory of adaptive Thouless–Anderson–Palmer equations, which is empirically observed to saturate the conjectured theoretical limit. This AMP comes with a rigorous state evolution analysis tracking its performance. Although we focus on specific noise distributions, our methodology can be generalized to a wide class of trace matrix ensembles at the cost of more involved expressions. Finally, despite the seemingly strong assumption of rotation-invariant noise, our theory empirically predicts algorithmic performance on real data, pointing at strong universality properties.","lang":"eng"}],"issue":"30","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ista":"Barbier J, Camilli F, Mondelli M, Sáenz M. 2023. Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. 120(30), e2302028120.","apa":"Barbier, J., Camilli, F., Mondelli, M., & Sáenz, M. (2023). Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2302028120","ieee":"J. Barbier, F. Camilli, M. Mondelli, and M. Sáenz, “Fundamental limits in structured principal component analysis and how to reach them,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 30. National Academy of Sciences, 2023.","ama":"Barbier J, Camilli F, Mondelli M, Sáenz M. Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(30). doi:10.1073/pnas.2302028120","chicago":"Barbier, Jean, Francesco Camilli, Marco Mondelli, and Manuel Sáenz. “Fundamental Limits in Structured Principal Component Analysis and How to Reach Them.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2302028120.","mla":"Barbier, Jean, et al. “Fundamental Limits in Structured Principal Component Analysis and How to Reach Them.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 30, e2302028120, National Academy of Sciences, 2023, doi:10.1073/pnas.2302028120.","short":"J. Barbier, F. Camilli, M. Mondelli, M. Sáenz, Proceedings of the National Academy of Sciences of the United States of America 120 (2023)."},"article_type":"original","date_published":"2023-07-25T00:00:00Z","scopus_import":"1","day":"25","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1"},{"article_number":"e2300828120","ec_funded":1,"file_date_updated":"2023-08-14T07:43:45Z","department":[{"_id":"MiLe"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"acknowledgement":"N.M.-S. acknowledges the support of the Ministry of Energy, Israel, as part of the scholarship program for graduate students in the fields of energy. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. acknowledges the support of the Ministry of Innovation, Science and Technology, Israel Grant No. 1001593872. Y.P acknowledges the support of the BSF-NSF 094 Grant No. 2022503.","year":"2023","volume":120,"date_created":"2023-08-13T22:01:12Z","date_updated":"2023-10-17T11:45:25Z","author":[{"first_name":"Ofek","last_name":"Vardi","full_name":"Vardi, Ofek"},{"full_name":"Maroudas-Sklare, Naama","last_name":"Maroudas-Sklare","first_name":"Naama"},{"last_name":"Kolodny","first_name":"Yuval","full_name":"Kolodny, Yuval"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"},{"full_name":"Saragovi, Amijai","last_name":"Saragovi","first_name":"Amijai"},{"last_name":"Galili","first_name":"Nir","full_name":"Galili, Nir"},{"first_name":"Stav","last_name":"Ferrera","full_name":"Ferrera, Stav"},{"full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Yuran","first_name":"Nir","full_name":"Yuran, Nir"},{"first_name":"Hagit P.","last_name":"Affek","full_name":"Affek, Hagit P."},{"last_name":"Luz","first_name":"Boaz","full_name":"Luz, Boaz"},{"first_name":"Yonaton","last_name":"Goldsmith","full_name":"Goldsmith, Yonaton"},{"full_name":"Keren, Nir","first_name":"Nir","last_name":"Keren"},{"full_name":"Yochelis, Shira","first_name":"Shira","last_name":"Yochelis"},{"first_name":"Itay","last_name":"Halevy","full_name":"Halevy, Itay"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"full_name":"Paltiel, Yossi","last_name":"Paltiel","first_name":"Yossi"}],"publication_identifier":{"eissn":["1091-6490"]},"month":"07","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["37523549"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2300828120","type":"journal_article","issue":"32","abstract":[{"lang":"eng","text":"Traditionally, nuclear spin is not considered to affect biological processes. Recently, this has changed as isotopic fractionation that deviates from classical mass dependence was reported both in vitro and in vivo. In these cases, the isotopic effect correlates with the nuclear magnetic spin. Here, we show nuclear spin effects using stable oxygen isotopes (16O, 17O, and 18O) in two separate setups: an artificial dioxygen production system and biological aquaporin channels in cells. We observe that oxygen dynamics in chiral environments (in particular its transport) depend on nuclear spin, suggesting future applications for controlled isotope separation to be used, for instance, in NMR. To demonstrate the mechanism behind our findings, we formulate theoretical models based on a nuclear-spin-enhanced switch between electronic spin states. Accounting for the role of nuclear spin in biology can provide insights into the role of quantum effects in living systems and help inspire the development of future biotechnology solutions."}],"intvolume":" 120","title":"Nuclear spin effects in biological processes","status":"public","ddc":["530"],"_id":"14037","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"2023_PNAS_Vardi.pdf","content_type":"application/pdf","file_size":1003092,"creator":"dernst","relation":"main_file","file_id":"14047","checksum":"a5ed64788a5acef9b9a300a26fa5a177","success":1,"date_updated":"2023-08-14T07:43:45Z","date_created":"2023-08-14T07:43:45Z"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"31","article_type":"original","citation":{"chicago":"Vardi, Ofek, Naama Maroudas-Sklare, Yuval Kolodny, Artem Volosniev, Amijai Saragovi, Nir Galili, Stav Ferrera, et al. “Nuclear Spin Effects in Biological Processes.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2300828120.","mla":"Vardi, Ofek, et al. “Nuclear Spin Effects in Biological Processes.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 32, e2300828120, National Academy of Sciences, 2023, doi:10.1073/pnas.2300828120.","short":"O. Vardi, N. Maroudas-Sklare, Y. Kolodny, A. Volosniev, A. Saragovi, N. Galili, S. Ferrera, A. Ghazaryan, N. Yuran, H.P. Affek, B. Luz, Y. Goldsmith, N. Keren, S. Yochelis, I. Halevy, M. Lemeshko, Y. Paltiel, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","ista":"Vardi O, Maroudas-Sklare N, Kolodny Y, Volosniev A, Saragovi A, Galili N, Ferrera S, Ghazaryan A, Yuran N, Affek HP, Luz B, Goldsmith Y, Keren N, Yochelis S, Halevy I, Lemeshko M, Paltiel Y. 2023. Nuclear spin effects in biological processes. Proceedings of the National Academy of Sciences of the United States of America. 120(32), e2300828120.","apa":"Vardi, O., Maroudas-Sklare, N., Kolodny, Y., Volosniev, A., Saragovi, A., Galili, N., … Paltiel, Y. (2023). Nuclear spin effects in biological processes. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2300828120","ieee":"O. Vardi et al., “Nuclear spin effects in biological processes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 32. National Academy of Sciences, 2023.","ama":"Vardi O, Maroudas-Sklare N, Kolodny Y, et al. Nuclear spin effects in biological processes. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(32). doi:10.1073/pnas.2300828120"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","date_published":"2023-07-31T00:00:00Z"},{"ec_funded":1,"file_date_updated":"2023-02-27T09:43:27Z","author":[{"full_name":"Dubach, Guillaume","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","orcid":"0000-0001-6892-8137","first_name":"Guillaume","last_name":"Dubach"},{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"Erdös, László"}],"volume":28,"date_created":"2023-02-26T23:01:01Z","date_updated":"2023-10-17T12:48:10Z","year":"2023","acknowledgement":"G. Dubach gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. L. Erdős is supported by ERC Advanced Grant “RMTBeyond” No. 101020331.","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"publication_status":"published","publication_identifier":{"eissn":["1083-589X"]},"month":"02","doi":"10.1214/23-ECP516","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000950650200005"],"arxiv":["2108.13694"]},"oa":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","abstract":[{"text":"We study the eigenvalue trajectories of a time dependent matrix Gt=H+itvv∗ for t≥0, where H is an N×N Hermitian random matrix and v is a unit vector. In particular, we establish that with high probability, an outlier can be distinguished at all times t>1+N−1/3+ϵ, for any ϵ>0. The study of this natural process combines elements of Hermitian and non-Hermitian analysis, and illustrates some aspects of the intrinsic instability of (even weakly) non-Hermitian matrices.","lang":"eng"}],"type":"journal_article","file":[{"content_type":"application/pdf","file_size":479105,"creator":"dernst","file_name":"2023_ElectCommProbability_Dubach.pdf","access_level":"open_access","date_created":"2023-02-27T09:43:27Z","date_updated":"2023-02-27T09:43:27Z","checksum":"a1c6f0a3e33688fd71309c86a9aad86e","success":1,"relation":"main_file","file_id":"12692"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12683","intvolume":" 28","ddc":["510"],"status":"public","title":"Dynamics of a rank-one perturbation of a Hermitian matrix","has_accepted_license":"1","article_processing_charge":"No","day":"08","scopus_import":"1","date_published":"2023-02-08T00:00:00Z","citation":{"chicago":"Dubach, Guillaume, and László Erdös. “Dynamics of a Rank-One Perturbation of a Hermitian Matrix.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/23-ECP516.","short":"G. Dubach, L. Erdös, Electronic Communications in Probability 28 (2023) 1–13.","mla":"Dubach, Guillaume, and László Erdös. “Dynamics of a Rank-One Perturbation of a Hermitian Matrix.” Electronic Communications in Probability, vol. 28, Institute of Mathematical Statistics, 2023, pp. 1–13, doi:10.1214/23-ECP516.","ieee":"G. Dubach and L. Erdös, “Dynamics of a rank-one perturbation of a Hermitian matrix,” Electronic Communications in Probability, vol. 28. Institute of Mathematical Statistics, pp. 1–13, 2023.","apa":"Dubach, G., & Erdös, L. (2023). Dynamics of a rank-one perturbation of a Hermitian matrix. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/23-ECP516","ista":"Dubach G, Erdös L. 2023. Dynamics of a rank-one perturbation of a Hermitian matrix. Electronic Communications in Probability. 28, 1–13.","ama":"Dubach G, Erdös L. Dynamics of a rank-one perturbation of a Hermitian matrix. Electronic Communications in Probability. 2023;28:1-13. doi:10.1214/23-ECP516"},"publication":"Electronic Communications in Probability","page":"1-13","article_type":"original"},{"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We consider the fluctuations of regular functions f of a Wigner matrix W viewed as an entire matrix f (W). Going beyond the well-studied tracial mode, Trf (W), which is equivalent to the customary linear statistics of eigenvalues, we show that Trf (W)A is asymptotically normal for any nontrivial bounded deterministic matrix A. We identify three different and asymptotically independent modes of this fluctuation, corresponding to the tracial part, the traceless diagonal part and the off-diagonal part of f (W) in the entire mesoscopic regime, where we find that the off-diagonal modes fluctuate on a much smaller scale than the tracial mode. As a main motivation to study CLT in such generality on small mesoscopic scales, we determine\r\nthe fluctuations in the eigenstate thermalization hypothesis (Phys. Rev. A 43 (1991) 2046–2049), that is, prove that the eigenfunction overlaps with any deterministic matrix are asymptotically Gaussian after a small spectral averaging. Finally, in the macroscopic regime our result also generalizes (Zh. Mat. Fiz. Anal. Geom. 9 (2013) 536–581, 611, 615) to complex W and to all crossover ensembles in between. The main technical inputs are the recent\r\nmultiresolvent local laws with traceless deterministic matrices from the companion paper (Comm. Math. Phys. 388 (2021) 1005–1048)."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12761","intvolume":" 33","status":"public","title":"Functional central limit theorems for Wigner matrices","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"mla":"Cipolloni, Giorgio, et al. “Functional Central Limit Theorems for Wigner Matrices.” Annals of Applied Probability, vol. 33, no. 1, Institute of Mathematical Statistics, 2023, pp. 447–89, doi:10.1214/22-AAP1820.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Applied Probability 33 (2023) 447–489.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Functional Central Limit Theorems for Wigner Matrices.” Annals of Applied Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-AAP1820.","ama":"Cipolloni G, Erdös L, Schröder DJ. Functional central limit theorems for Wigner matrices. Annals of Applied Probability. 2023;33(1):447-489. doi:10.1214/22-AAP1820","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Functional central limit theorems for Wigner matrices. Annals of Applied Probability. 33(1), 447–489.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Functional central limit theorems for Wigner matrices,” Annals of Applied Probability, vol. 33, no. 1. Institute of Mathematical Statistics, pp. 447–489, 2023.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Functional central limit theorems for Wigner matrices. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/22-AAP1820"},"publication":"Annals of Applied Probability","page":"447-489","article_type":"original","date_published":"2023-02-01T00:00:00Z","ec_funded":1,"acknowledgement":"The second author is partially funded by the ERC Advanced Grant “RMTBEYOND” No. 101020331. The third author is supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation.","year":"2023","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"publication_status":"published","author":[{"full_name":"Cipolloni, Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","first_name":"Giorgio","last_name":"Cipolloni"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"},{"orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","first_name":"Dominik J","full_name":"Schröder, Dominik J"}],"volume":33,"date_created":"2023-03-26T22:01:08Z","date_updated":"2023-10-17T12:48:52Z","publication_identifier":{"issn":["1050-5164"]},"month":"02","oa":1,"external_id":{"isi":["000946432400015"],"arxiv":["2012.13218"]},"main_file_link":[{"url":"https://arxiv.org/abs/2012.13218","open_access":"1"}],"project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"quality_controlled":"1","isi":1,"doi":"10.1214/22-AAP1820","language":[{"iso":"eng"}]},{"type":"journal_article","issue":"3","abstract":[{"text":"It is known that the Brauer--Manin obstruction to the Hasse principle is vacuous for smooth Fano hypersurfaces of dimension at least 3 over any number field. Moreover, for such varieties it follows from a general conjecture of Colliot-Thélène that the Brauer--Manin obstruction to the Hasse principle should be the only one, so that the Hasse principle is expected to hold. Working over the field of rational numbers and ordering Fano hypersurfaces of fixed degree and dimension by height, we prove that almost every such hypersurface satisfies the Hasse principle provided that the dimension is at least 3. This proves a conjecture of Poonen and Voloch in every case except for cubic surfaces.","lang":"eng"}],"intvolume":" 197","title":"The Hasse principle for random Fano hypersurfaces","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8682","oa_version":"Preprint","article_processing_charge":"No","day":"01","page":"1115-1203","article_type":"original","citation":{"apa":"Browning, T. D., Boudec, P. L., & Sawin, W. (2023). The Hasse principle for random Fano hypersurfaces. Annals of Mathematics. Princeton University. https://doi.org/10.4007/annals.2023.197.3.3","ieee":"T. D. Browning, P. L. Boudec, and W. Sawin, “The Hasse principle for random Fano hypersurfaces,” Annals of Mathematics, vol. 197, no. 3. Princeton University, pp. 1115–1203, 2023.","ista":"Browning TD, Boudec PL, Sawin W. 2023. The Hasse principle for random Fano hypersurfaces. Annals of Mathematics. 197(3), 1115–1203.","ama":"Browning TD, Boudec PL, Sawin W. The Hasse principle for random Fano hypersurfaces. Annals of Mathematics. 2023;197(3):1115-1203. doi:10.4007/annals.2023.197.3.3","chicago":"Browning, Timothy D, Pierre Le Boudec, and Will Sawin. “The Hasse Principle for Random Fano Hypersurfaces.” Annals of Mathematics. Princeton University, 2023. https://doi.org/10.4007/annals.2023.197.3.3.","short":"T.D. Browning, P.L. Boudec, W. Sawin, Annals of Mathematics 197 (2023) 1115–1203.","mla":"Browning, Timothy D., et al. “The Hasse Principle for Random Fano Hypersurfaces.” Annals of Mathematics, vol. 197, no. 3, Princeton University, 2023, pp. 1115–203, doi:10.4007/annals.2023.197.3.3."},"publication":"Annals of Mathematics","date_published":"2023-05-01T00:00:00Z","publisher":"Princeton University","department":[{"_id":"TiBr"}],"publication_status":"published","year":"2023","volume":197,"date_updated":"2023-10-17T12:47:43Z","date_created":"2020-10-19T14:28:50Z","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/when-is-necessary-sufficient/"}]},"author":[{"full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pierre Le","last_name":"Boudec","full_name":"Boudec, Pierre Le"},{"first_name":"Will","last_name":"Sawin","full_name":"Sawin, Will"}],"publication_identifier":{"issn":["0003-486X"]},"month":"05","quality_controlled":"1","isi":1,"external_id":{"isi":["000966611000003"],"arxiv":["2006.02356"]},"main_file_link":[{"url":"https://arxiv.org/abs/2006.02356","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.4007/annals.2023.197.3.3"},{"type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Allometric settings of population dynamics models are appealing due to their parsimonious nature and broad utility when studying system level effects. Here, we parameterise the size-scaled Rosenzweig-MacArthur differential equations to eliminate prey-mass dependency, facilitating an in depth analytic study of the equations which incorporates scaling parameters’ contributions to coexistence. We define the functional response term to match empirical findings, and examine situations where metabolic theory derivations and observation diverge. The dynamical properties of the Rosenzweig-MacArthur system, encompassing the distribution of size-abundance equilibria, the scaling of period and amplitude of population cycling, and relationships between predator and prey abundances, are consistent with empirical observation. Our parameterisation is an accurate minimal model across 15+ orders of mass magnitude."}],"intvolume":" 18","status":"public","title":"Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations","ddc":["000"],"_id":"12706","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"798ed5739a4117b03173e5d56e0534c9","success":1,"date_updated":"2023-03-07T10:26:45Z","date_created":"2023-03-07T10:26:45Z","relation":"main_file","file_id":"12712","content_type":"application/pdf","file_size":1257003,"creator":"cchlebak","access_level":"open_access","file_name":"2023_PLOSOne_Mckerral.pdf"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"27","page":"e0279838","article_type":"original","citation":{"short":"J.C. Mckerral, M. Kleshnina, V. Ejov, L. Bartle, J.G. Mitchell, J.A. Filar, PLoS One 18 (2023) e0279838.","mla":"Mckerral, Jody C., et al. “Empirical Parameterisation and Dynamical Analysis of the Allometric Rosenzweig-MacArthur Equations.” PLoS One, vol. 18, no. 2, Public Library of Science, 2023, p. e0279838, doi:10.1371/journal.pone.0279838.","chicago":"Mckerral, Jody C., Maria Kleshnina, Vladimir Ejov, Louise Bartle, James G. Mitchell, and Jerzy A. Filar. “Empirical Parameterisation and Dynamical Analysis of the Allometric Rosenzweig-MacArthur Equations.” PLoS One. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0279838.","ama":"Mckerral JC, Kleshnina M, Ejov V, Bartle L, Mitchell JG, Filar JA. Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. PLoS One. 2023;18(2):e0279838. doi:10.1371/journal.pone.0279838","ieee":"J. C. Mckerral, M. Kleshnina, V. Ejov, L. Bartle, J. G. Mitchell, and J. A. Filar, “Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations,” PLoS One, vol. 18, no. 2. Public Library of Science, p. e0279838, 2023.","apa":"Mckerral, J. C., Kleshnina, M., Ejov, V., Bartle, L., Mitchell, J. G., & Filar, J. A. (2023). Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0279838","ista":"Mckerral JC, Kleshnina M, Ejov V, Bartle L, Mitchell JG, Filar JA. 2023. Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. PLoS One. 18(2), e0279838."},"publication":"PLoS One","date_published":"2023-02-27T00:00:00Z","file_date_updated":"2023-03-07T10:26:45Z","publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"This research was supported by an Australian Government Research Training Program\r\n(RTP) Scholarship to JCM (https://www.dese.gov.au), and LB is supported by the Centre de\r\nrecherche sur le vieillissement Fellowship Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","volume":18,"date_created":"2023-03-05T23:01:05Z","date_updated":"2023-10-17T12:53:30Z","author":[{"full_name":"Mckerral, Jody C.","last_name":"Mckerral","first_name":"Jody C."},{"first_name":"Maria","last_name":"Kleshnina","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","full_name":"Kleshnina, Maria"},{"full_name":"Ejov, Vladimir","first_name":"Vladimir","last_name":"Ejov"},{"full_name":"Bartle, Louise","last_name":"Bartle","first_name":"Louise"},{"full_name":"Mitchell, James G.","last_name":"Mitchell","first_name":"James G."},{"full_name":"Filar, Jerzy A.","first_name":"Jerzy A.","last_name":"Filar"}],"publication_identifier":{"eissn":["1932-6203"]},"month":"02","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["36848357"],"isi":["000996122900022"]},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0279838"},{"month":"06","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"doi":"10.1523/JNEUROSCI.1514-22.2023","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"external_id":{"isi":["001020132100005"],"pmid":["37160366"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"793482","_id":"2659CC84-B435-11E9-9278-68D0E5697425","name":"Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission","call_identifier":"H2020"},{"grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020"}],"file_date_updated":"2023-07-10T09:04:58Z","ec_funded":1,"author":[{"full_name":"Eguchi, Kohgaku","first_name":"Kohgaku","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6170-2546"},{"full_name":"Le Monnier, Elodie","first_name":"Elodie","last_name":"Le Monnier","id":"3B59276A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-10-18T07:12:47Z","date_created":"2023-07-09T22:01:12Z","volume":43,"year":"2023","acknowledgement":"This work was supported by The Institute of Science and Technology (IST) Austria, the European Union's Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant Agreement No. 793482 (to K.E.) and by the European Research Council (ERC) Grant Agreement No. 694539 (to R.S.). We thank Nicoleta Condruz (IST Austria, Klosterneuburg, Austria) for technical assistance with sample preparation, the Electron Microscopy Facility of IST Austria (Klosterneuburg, Austria) for technical support with EM works, Natalia Baranova (University of Vienna, Vienna, Austria) and Martin Loose (IST Austria, Klosterneuburg, Austria) for advice on liposome preparation, and Yugo Fukazawa (University of Fukui, Fukui, Japan) for comments.","pmid":1,"publication_status":"published","publisher":"Society for Neuroscience","department":[{"_id":"RySh"}],"day":"07","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-06-07T00:00:00Z","publication":"The Journal of Neuroscience","citation":{"chicago":"Eguchi, Kohgaku, Elodie Le Monnier, and Ryuichi Shigemoto. “Nanoscale Phosphoinositide Distribution on Cell Membranes of Mouse Cerebellar Neurons.” The Journal of Neuroscience. Society for Neuroscience, 2023. https://doi.org/10.1523/JNEUROSCI.1514-22.2023.","short":"K. Eguchi, E. Le Monnier, R. Shigemoto, The Journal of Neuroscience 43 (2023) 4197–4216.","mla":"Eguchi, Kohgaku, et al. “Nanoscale Phosphoinositide Distribution on Cell Membranes of Mouse Cerebellar Neurons.” The Journal of Neuroscience, vol. 43, no. 23, Society for Neuroscience, 2023, pp. 4197–216, doi:10.1523/JNEUROSCI.1514-22.2023.","ieee":"K. Eguchi, E. Le Monnier, and R. Shigemoto, “Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons,” The Journal of Neuroscience, vol. 43, no. 23. Society for Neuroscience, pp. 4197–4216, 2023.","apa":"Eguchi, K., Le Monnier, E., & Shigemoto, R. (2023). Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1514-22.2023","ista":"Eguchi K, Le Monnier E, Shigemoto R. 2023. Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. 43(23), 4197–4216.","ama":"Eguchi K, Le Monnier E, Shigemoto R. Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. 2023;43(23):4197-4216. doi:10.1523/JNEUROSCI.1514-22.2023"},"article_type":"original","page":"4197-4216","abstract":[{"text":"Phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) plays an essential role in neuronal activities through interaction with various proteins involved in signaling at membranes. However, the distribution pattern of PI(4,5)P2 and the association with these proteins on the neuronal cell membranes remain elusive. In this study, we established a method for visualizing PI(4,5)P2 by SDS-digested freeze-fracture replica labeling (SDS-FRL) to investigate the quantitative nanoscale distribution of PI(4,5)P2 in cryo-fixed brain. We demonstrate that PI(4,5)P2 forms tiny clusters with a mean size of ∼1000 nm2 rather than randomly distributed in cerebellar neuronal membranes in male C57BL/6J mice. These clusters show preferential accumulation in specific membrane compartments of different cell types, in particular, in Purkinje cell (PC) spines and granule cell (GC) presynaptic active zones. Furthermore, we revealed extensive association of PI(4,5)P2 with CaV2.1 and GIRK3 across different membrane compartments, whereas its association with mGluR1α was compartment specific. These results suggest that our SDS-FRL method provides valuable insights into the physiological functions of PI(4,5)P2 in neurons.","lang":"eng"}],"issue":"23","type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2023-07-10T09:04:58Z","date_updated":"2023-07-10T09:04:58Z","checksum":"70b2141870e0bf1c94fd343e18fdbc32","success":1,"relation":"main_file","file_id":"13205","content_type":"application/pdf","file_size":7794425,"creator":"alisjak","file_name":"2023_JN_Eguchi.pdf","access_level":"open_access"}],"_id":"13202","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons","ddc":["570"],"status":"public","intvolume":" 43"},{"month":"02","publication_identifier":{"eissn":["2036-2145"],"issn":["0391-173X"]},"language":[{"iso":"eng"}],"doi":"10.2422/2036-2145.202010_018","quality_controlled":"1","oa":1,"external_id":{"arxiv":["2007.14182"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2007.14182","open_access":"1"}],"date_created":"2023-05-07T22:01:04Z","date_updated":"2023-10-18T06:54:30Z","volume":24,"author":[{"id":"6A459894-5FDD-11E9-AF35-BB24E6697425","first_name":"Dante","last_name":"Bonolis","full_name":"Bonolis, Dante"},{"last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D"}],"publication_status":"published","department":[{"_id":"TiBr"}],"publisher":"Scuola Normale Superiore - Edizioni della Normale","year":"2023","day":"16","article_processing_charge":"No","scopus_import":"1","date_published":"2023-02-16T00:00:00Z","article_type":"original","page":"173-204","publication":"Annali della Scuola Normale Superiore di Pisa - Classe di Scienze","citation":{"chicago":"Bonolis, Dante, and Timothy D Browning. “Uniform Bounds for Rational Points on Hyperelliptic Fibrations.” Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze. Scuola Normale Superiore - Edizioni della Normale, 2023. https://doi.org/10.2422/2036-2145.202010_018.","mla":"Bonolis, Dante, and Timothy D. Browning. “Uniform Bounds for Rational Points on Hyperelliptic Fibrations.” Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze, vol. 24, no. 1, Scuola Normale Superiore - Edizioni della Normale, 2023, pp. 173–204, doi:10.2422/2036-2145.202010_018.","short":"D. Bonolis, T.D. Browning, Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze 24 (2023) 173–204.","ista":"Bonolis D, Browning TD. 2023. Uniform bounds for rational points on hyperelliptic fibrations. Annali della Scuola Normale Superiore di Pisa - Classe di Scienze. 24(1), 173–204.","ieee":"D. Bonolis and T. D. Browning, “Uniform bounds for rational points on hyperelliptic fibrations,” Annali della Scuola Normale Superiore di Pisa - Classe di Scienze, vol. 24, no. 1. Scuola Normale Superiore - Edizioni della Normale, pp. 173–204, 2023.","apa":"Bonolis, D., & Browning, T. D. (2023). Uniform bounds for rational points on hyperelliptic fibrations. Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze. Scuola Normale Superiore - Edizioni della Normale. https://doi.org/10.2422/2036-2145.202010_018","ama":"Bonolis D, Browning TD. Uniform bounds for rational points on hyperelliptic fibrations. Annali della Scuola Normale Superiore di Pisa - Classe di Scienze. 2023;24(1):173-204. doi:10.2422/2036-2145.202010_018"},"abstract":[{"lang":"eng","text":"We apply a variant of the square-sieve to produce an upper bound for the number of rational points of bounded height on a family of surfaces that admit a fibration over P1 whose general fibre is a hyperelliptic curve. The implied constant does not depend on the coefficients of the polynomial defining the surface.\r\n"}],"issue":"1","type":"journal_article","oa_version":"Preprint","title":"Uniform bounds for rational points on hyperelliptic fibrations","status":"public","intvolume":" 24","_id":"12916","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"text":"Superconductivity has many important applications ranging from levitating trains over qubits to MRI scanners. The phenomenon is successfully modeled by Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory has been studied extensively for systems without boundary. However, little is known in the presence of boundaries. With the help of numerical methods physicists observed that the critical temperature may increase in the presence of a boundary. The goal of this thesis is to understand the influence of boundaries on the critical temperature in BCS theory and to give a first rigorous justification of these observations. On the way, we also study two-body Schrödinger operators on domains with boundaries and prove additional results for superconductors without boundary.\r\n\r\nBCS theory is based on a non-linear functional, where the minimizer indicates whether the system is superconducting or in the normal, non-superconducting state. By considering the Hessian of the BCS functional at the normal state, one can analyze whether the normal state is possibly a minimum of the BCS functional and estimate the critical temperature. The Hessian turns out to be a linear operator resembling a Schrödinger operator for two interacting particles, but with more complicated kinetic energy. As a first step, we study the two-body Schrödinger operator in the presence of boundaries.\r\nFor Neumann boundary conditions, we prove that the addition of a boundary can create new eigenvalues, which correspond to the two particles forming a bound state close to the boundary.\r\n\r\nSecond, we need to understand superconductivity in the translation invariant setting. While in three dimensions this has been extensively studied, there is no mathematical literature for the one and two dimensional cases. In dimensions one and two, we compute the weak coupling asymptotics of the critical temperature and the energy gap in the translation invariant setting. We also prove that their ratio is independent of the microscopic details of the model in the weak coupling limit; this property is referred to as universality.\r\n\r\nIn the third part, we study the critical temperature of superconductors in the presence of boundaries. We start by considering the one-dimensional case of a half-line with contact interaction. Then, we generalize the results to generic interactions and half-spaces in one, two and three dimensions. Finally, we compare the critical temperature of a quarter space in two dimensions to the critical temperatures of a half-space and of the full space.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"checksum":"ef039ffc3de2cb8dee5b14110938e9b6","date_updated":"2023-10-06T11:35:56Z","date_created":"2023-10-06T11:35:56Z","relation":"main_file","file_id":"14398","file_size":2365702,"content_type":"application/pdf","creator":"broos","access_level":"open_access","file_name":"phd-thesis-draft_pdfa_acrobat.pdf"},{"date_created":"2023-10-06T11:38:01Z","date_updated":"2023-10-06T11:38:01Z","checksum":"81dcac33daeefaf0111db52f41bb1fd0","file_id":"14399","relation":"source_file","creator":"broos","file_size":4691734,"content_type":"application/x-zip-compressed","file_name":"Version5.zip","access_level":"closed"}],"_id":"14374","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["515","539"],"status":"public","title":"Boundary superconductivity in BCS theory","day":"30","article_processing_charge":"No","has_accepted_license":"1","date_published":"2023-09-30T00:00:00Z","citation":{"mla":"Roos, Barbara. Boundary Superconductivity in BCS Theory. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14374.","short":"B. Roos, Boundary Superconductivity in BCS Theory, Institute of Science and Technology Austria, 2023.","chicago":"Roos, Barbara. “Boundary Superconductivity in BCS Theory.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14374.","ama":"Roos B. Boundary superconductivity in BCS theory. 2023. doi:10.15479/at:ista:14374","ista":"Roos B. 2023. Boundary superconductivity in BCS theory. Institute of Science and Technology Austria.","ieee":"B. Roos, “Boundary superconductivity in BCS theory,” Institute of Science and Technology Austria, 2023.","apa":"Roos, B. (2023). Boundary superconductivity in BCS theory. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14374"},"page":"206","file_date_updated":"2023-10-06T11:38:01Z","ec_funded":1,"author":[{"full_name":"Roos, Barbara","last_name":"Roos","first_name":"Barbara","orcid":"0000-0002-9071-5880","id":"5DA90512-D80F-11E9-8994-2E2EE6697425"}],"related_material":{"record":[{"id":"13207","status":"public","relation":"part_of_dissertation"},{"id":"10850","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-10-27T10:37:30Z","date_created":"2023-09-28T14:23:04Z","year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"month":"09","publication_identifier":{"issn":["2663 - 337X"]},"doi":"10.15479/at:ista:14374","degree_awarded":"PhD","supervisor":[{"full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity"}]},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2201.08090"],"isi":["000997933500008"]},"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"quality_controlled":"1","isi":1,"doi":"10.4171/JST/439","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1664-0403"],"issn":["1664-039X"]},"month":"05","year":"2023","acknowledgement":"We thank Egor Babaev for encouraging us to study this problem, and Rupert Frank for many fruitful discussions. scussions. Funding. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 (Barbara Roos and Robert Seiringer) is gratefully acknowledged.","publisher":"EMS Press","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"publication_status":"published","related_material":{"record":[{"id":"14374","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Hainzl, Christian","last_name":"Hainzl","first_name":"Christian"},{"full_name":"Roos, Barbara","last_name":"Roos","first_name":"Barbara","orcid":"0000-0002-9071-5880","id":"5DA90512-D80F-11E9-8994-2E2EE6697425"},{"full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"volume":12,"date_created":"2023-07-10T16:35:45Z","date_updated":"2023-10-27T10:37:29Z","ec_funded":1,"file_date_updated":"2023-07-11T08:19:15Z","citation":{"chicago":"Hainzl, Christian, Barbara Roos, and Robert Seiringer. “Boundary Superconductivity in the BCS Model.” Journal of Spectral Theory. EMS Press, 2023. https://doi.org/10.4171/JST/439.","mla":"Hainzl, Christian, et al. “Boundary Superconductivity in the BCS Model.” Journal of Spectral Theory, vol. 12, no. 4, EMS Press, 2023, pp. 1507–1540, doi:10.4171/JST/439.","short":"C. Hainzl, B. Roos, R. Seiringer, Journal of Spectral Theory 12 (2023) 1507–1540.","ista":"Hainzl C, Roos B, Seiringer R. 2023. Boundary superconductivity in the BCS model. Journal of Spectral Theory. 12(4), 1507–1540.","apa":"Hainzl, C., Roos, B., & Seiringer, R. (2023). Boundary superconductivity in the BCS model. Journal of Spectral Theory. EMS Press. https://doi.org/10.4171/JST/439","ieee":"C. Hainzl, B. Roos, and R. Seiringer, “Boundary superconductivity in the BCS model,” Journal of Spectral Theory, vol. 12, no. 4. EMS Press, pp. 1507–1540, 2023.","ama":"Hainzl C, Roos B, Seiringer R. Boundary superconductivity in the BCS model. Journal of Spectral Theory. 2023;12(4):1507–1540. doi:10.4171/JST/439"},"publication":"Journal of Spectral Theory","page":"1507–1540","article_type":"original","date_published":"2023-05-18T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"18","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13207","intvolume":" 12","title":"Boundary superconductivity in the BCS model","ddc":["530"],"status":"public","file":[{"success":1,"checksum":"5501da33be010b5c81440438287584d5","date_created":"2023-07-11T08:19:15Z","date_updated":"2023-07-11T08:19:15Z","file_id":"13208","relation":"main_file","creator":"alisjak","file_size":304619,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_EMS_Hainzl.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"We consider the linear BCS equation, determining the BCS critical temperature, in the presence of a boundary, where Dirichlet boundary conditions are imposed. In the one-dimensional case with point interactions, we prove that the critical temperature is strictly larger than the bulk value, at least at weak coupling. In particular, the Cooper-pair wave function localizes near the boundary, an effect that cannot be modeled by effective Neumann boundary conditions on the order parameter as often imposed in Ginzburg–Landau theory. We also show that the relative shift in critical temperature vanishes if the coupling constant either goes to zero or to infinity."}]},{"article_type":"original","publication":"Genetics","citation":{"short":"N.H. Barton, A.M. Etheridge, A. Véber, Genetics 225 (2023).","mla":"Barton, Nicholas H., et al. “The Infinitesimal Model with Dominance.” Genetics, vol. 225, no. 2, iyad133, Oxford Academic, 2023, doi:10.1093/genetics/iyad133.","chicago":"Barton, Nicholas H, Alison M. Etheridge, and Amandine Véber. “The Infinitesimal Model with Dominance.” Genetics. Oxford Academic, 2023. https://doi.org/10.1093/genetics/iyad133.","ama":"Barton NH, Etheridge AM, Véber A. The infinitesimal model with dominance. Genetics. 2023;225(2). doi:10.1093/genetics/iyad133","apa":"Barton, N. H., Etheridge, A. M., & Véber, A. (2023). The infinitesimal model with dominance. Genetics. Oxford Academic. https://doi.org/10.1093/genetics/iyad133","ieee":"N. H. Barton, A. M. Etheridge, and A. Véber, “The infinitesimal model with dominance,” Genetics, vol. 225, no. 2. Oxford Academic, 2023.","ista":"Barton NH, Etheridge AM, Véber A. 2023. The infinitesimal model with dominance. Genetics. 225(2), iyad133."},"date_published":"2023-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","title":"The infinitesimal model with dominance","ddc":["570"],"status":"public","intvolume":" 225","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14452","file":[{"access_level":"open_access","file_name":"2023_Genetics_Barton.pdf","content_type":"application/pdf","file_size":1439032,"creator":"dernst","relation":"main_file","file_id":"14469","checksum":"3f65b1fbe813e2f4dbb5d2b5e891844a","success":1,"date_updated":"2023-10-30T12:57:53Z","date_created":"2023-10-30T12:57:53Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and an environmental component, and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the parental traits. In previous work, we showed that when trait values are determined by the sum of a large number of additive Mendelian factors, each of small effect, one can justify the infinitesimal model as a limit of Mendelian inheritance. In this paper, we show that this result extends to include dominance. We define the model in terms of classical quantities of quantitative genetics, before justifying it as a limit of Mendelian inheritance as the number, M, of underlying loci tends to infinity. As in the additive case, the multivariate normal distribution of trait values across the pedigree can be expressed in terms of variance components in an ancestral population and probabilities of identity by descent determined by the pedigree. Now, with just first-order dominance effects, we require two-, three-, and four-way identities. We also show that, even if we condition on parental trait values, the “shared” and “residual” components of trait values within each family will be asymptotically normally distributed as the number of loci tends to infinity, with an error of order 1/M−−√. We illustrate our results with some numerical examples.","lang":"eng"}],"issue":"2","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"},{"name":"Understanding the evolution of continuous genomes","grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2211.03515"]},"language":[{"iso":"eng"}],"doi":"10.1093/genetics/iyad133","month":"10","publication_identifier":{"issn":["0016-6731"],"eissn":["1943-2631"]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Oxford Academic","acknowledgement":"NHB was supported in part by ERC Grants 250152 and 101055327. AV was partly supported by the chaire Modélisation Mathématique et Biodiversité of Veolia Environment—Ecole Polytechnique—Museum National d’Histoire Naturelle—Fondation X.","year":"2023","date_updated":"2023-10-30T13:04:11Z","date_created":"2023-10-29T23:01:15Z","volume":225,"author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Alison M.","last_name":"Etheridge","full_name":"Etheridge, Alison M."},{"full_name":"Véber, Amandine","last_name":"Véber","first_name":"Amandine"}],"related_material":{"record":[{"id":"12949","relation":"research_data","status":"public"}]},"article_number":"iyad133","file_date_updated":"2023-10-30T12:57:53Z","ec_funded":1},{"project":[{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"mla":"Barton, Nicholas H. The Infinitesimal Model with Dominance. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12949.","short":"N.H. Barton, (2023).","chicago":"Barton, Nicholas H. “The Infinitesimal Model with Dominance.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12949.","ama":"Barton NH. The infinitesimal model with dominance. 2023. doi:10.15479/AT:ISTA:12949","ista":"Barton NH. 2023. The infinitesimal model with dominance, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12949.","ieee":"N. H. Barton, “The infinitesimal model with dominance.” Institute of Science and Technology Austria, 2023.","apa":"Barton, N. H. (2023). The infinitesimal model with dominance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12949"},"date_published":"2023-05-13T00:00:00Z","doi":"10.15479/AT:ISTA:12949","keyword":["Quantitative genetics","infinitesimal model"],"day":"13","month":"05","has_accepted_license":"1","article_processing_charge":"No","title":"The infinitesimal model with dominance","ddc":["576"],"status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"_id":"12949","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-30T13:04:11Z","date_created":"2023-05-13T09:49:09Z","oa_version":"Published Version","file":[{"file_name":"Neutral identities 16th Jan","access_level":"open_access","file_size":13662,"content_type":"application/octet-stream","creator":"nbarton","relation":"main_file","file_id":"12950","date_created":"2023-05-13T09:36:33Z","date_updated":"2023-05-13T09:36:33Z","checksum":"b0ce7d4b1ee7e7265430ceed36fc3336","success":1},{"checksum":"ad5035ad4f7d3b150a252c79884f6a83","success":1,"date_updated":"2023-05-13T09:38:17Z","date_created":"2023-05-13T09:38:17Z","relation":"main_file","file_id":"12951","content_type":"application/octet-stream","file_size":181619928,"creator":"nbarton","access_level":"open_access","file_name":"p, zA, zD, N=30 neutral III"},{"relation":"main_file","file_id":"12952","date_created":"2023-05-13T09:41:59Z","date_updated":"2023-05-13T09:41:59Z","checksum":"62182a1de796256edd6f4223704312ef","success":1,"file_name":"p, zA, zD, N=30 neutral IV","access_level":"open_access","content_type":"application/octet-stream","file_size":605902074,"creator":"nbarton"},{"relation":"main_file","file_id":"12953","date_updated":"2023-05-13T09:46:52Z","date_created":"2023-05-13T09:46:52Z","checksum":"af775dda5c4f6859cb1e5a81ec40a667","success":1,"file_name":"p, zA, zD, N=30 selected k=5","access_level":"open_access","file_size":1018238746,"content_type":"application/octet-stream","creator":"nbarton"},{"file_size":3197160,"content_type":"application/octet-stream","creator":"nbarton","file_name":"Pairwise F N=30 neutral II","access_level":"open_access","date_created":"2023-05-13T09:42:05Z","date_updated":"2023-05-13T09:42:05Z","checksum":"af26f3394c387d3ada14b434cd68b1e5","success":1,"relation":"main_file","file_id":"12954"},{"file_size":55492,"content_type":"application/octet-stream","creator":"nbarton","access_level":"open_access","file_name":"Pedigrees N=30 neutral II","checksum":"d5da7dc0e7282dd48222e26d12e34220","success":1,"date_updated":"2023-05-13T09:42:06Z","date_created":"2023-05-13T09:42:06Z","relation":"main_file","file_id":"12955"},{"relation":"main_file","file_id":"12956","date_updated":"2023-05-13T09:46:06Z","date_created":"2023-05-13T09:46:06Z","checksum":"00f386d80677590e29f6235d49cba58d","success":1,"file_name":"selected reps N=30 selected k=1,2 300 reps III","access_level":"open_access","file_size":474003467,"content_type":"application/octet-stream","creator":"nbarton"},{"relation":"main_file","file_id":"12957","checksum":"658cef3eaea6136a4d24da4f074191d7","success":1,"date_updated":"2023-05-13T09:46:08Z","date_created":"2023-05-13T09:46:08Z","access_level":"open_access","file_name":"Algorithm for caclulating identities.nb","file_size":121209,"content_type":"application/octet-stream","creator":"nbarton"},{"access_level":"open_access","file_name":"Infinitesimal with dominance.nb","file_size":1803898,"content_type":"application/octet-stream","creator":"nbarton","relation":"main_file","file_id":"12958","checksum":"db9b6dddd7a596d974e25f5e78f5c45c","success":1,"date_created":"2023-05-13T09:46:08Z","date_updated":"2023-05-13T09:46:08Z"},{"creator":"nbarton","content_type":"text/plain","file_size":990,"file_name":"ReadMe.txt","access_level":"open_access","date_created":"2023-05-16T04:09:08Z","date_updated":"2023-05-16T04:09:08Z","success":1,"checksum":"91f80a9fb58cae8eef2d8bf59fe30189","file_id":"12967","relation":"main_file"}],"author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"contributor":[{"contributor_type":"researcher","last_name":"Veber","first_name":"Amandine"},{"contributor_type":"researcher","last_name":"Etheridge","first_name":"Alison"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14452"}]},"type":"research_data","file_date_updated":"2023-05-16T04:09:08Z","abstract":[{"text":"The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed.","lang":"eng"}]},{"ec_funded":1,"author":[{"first_name":"Ilia","last_name":"Markov","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","full_name":"Markov, Ilia"},{"last_name":"Vladu","first_name":"Adrian","full_name":"Vladu, Adrian"},{"first_name":"Qi","last_name":"Guo","full_name":"Guo, Qi"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"}],"volume":202,"date_updated":"2023-10-31T09:40:45Z","date_created":"2023-10-29T23:01:17Z","year":"2023","acknowledgement":"The authors gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML), as well as experimental support from the IST Austria IT department, in particular Stefano Elefante, Andrei Hornoiu, and Alois Schloegl. AV acknowledges the support of the French Agence Nationale de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT), the support of Fondation Hadamard with a PRMO grant, and the support of CNRS with a CoopIntEER IEA grant (project ALFRED).","department":[{"_id":"DaAl"}],"publisher":"ML Research Press","publication_status":"published","publication_identifier":{"eissn":["2640-3498"]},"month":"07","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2023-07-23","location":"Honolulu, Hawaii, HI, United States","end_date":"2023-07-29"},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2302.02390"}],"oa":1,"external_id":{"arxiv":["2302.02390"]},"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Communication-reduction techniques are a popular way to improve scalability in data-parallel training of deep neural networks (DNNs). The recent emergence of large language models such as GPT has created the need for new approaches to exploit data-parallelism. Among these, fully-sharded data parallel (FSDP) training is highly popular, yet it still encounters scalability bottlenecks. One reason is that applying compression techniques to FSDP is challenging: as the vast majority of the communication involves the model’s weights, direct compression alters convergence and leads to accuracy loss. We present QSDP, a variant of FSDP which supports both gradient and weight quantization with theoretical guarantees, is simple to implement and has essentially no overheads. To derive QSDP we prove that a natural modification of SGD achieves convergence even when we only maintain quantized weights, and thus the domain over which we train consists of quantized points and is, therefore, highly non-convex. We validate this approach by training GPT-family models with up to 1.3 billion parameters on a multi-node cluster. Experiments show that QSDP preserves model accuracy, while completely removing the communication bottlenecks of FSDP, providing end-to-end speedups of up to 2.2x."}],"type":"conference","alternative_title":["PMLR"],"oa_version":"Preprint","_id":"14461","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 202","status":"public","title":"Quantized distributed training of large models with convergence guarantees","article_processing_charge":"No","day":"30","scopus_import":"1","date_published":"2023-07-30T00:00:00Z","citation":{"ama":"Markov I, Vladu A, Guo Q, Alistarh D-A. Quantized distributed training of large models with convergence guarantees. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:24020-24044.","apa":"Markov, I., Vladu, A., Guo, Q., & Alistarh, D.-A. (2023). Quantized distributed training of large models with convergence guarantees. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 24020–24044). Honolulu, Hawaii, HI, United States: ML Research Press.","ieee":"I. Markov, A. Vladu, Q. Guo, and D.-A. Alistarh, “Quantized distributed training of large models with convergence guarantees,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 24020–24044.","ista":"Markov I, Vladu A, Guo Q, Alistarh D-A. 2023. Quantized distributed training of large models with convergence guarantees. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 24020–24044.","short":"I. Markov, A. Vladu, Q. Guo, D.-A. Alistarh, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 24020–24044.","mla":"Markov, Ilia, et al. “Quantized Distributed Training of Large Models with Convergence Guarantees.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 24020–44.","chicago":"Markov, Ilia, Adrian Vladu, Qi Guo, and Dan-Adrian Alistarh. “Quantized Distributed Training of Large Models with Convergence Guarantees.” In Proceedings of the 40th International Conference on Machine Learning, 202:24020–44. ML Research Press, 2023."},"publication":"Proceedings of the 40th International Conference on Machine Learning","page":"24020-24044"},{"type":"conference","alternative_title":["PMLR"],"abstract":[{"lang":"eng","text":"We study fine-grained error bounds for differentially private algorithms for counting under continual observation. Our main insight is that the matrix mechanism when using lower-triangular matrices can be used in the continual observation model. More specifically, we give an explicit factorization for the counting matrix Mcount and upper bound the error explicitly. We also give a fine-grained analysis, specifying the exact constant in the upper bound. Our analysis is based on upper and lower bounds of the completely bounded norm (cb-norm) of Mcount\r\n. Along the way, we improve the best-known bound of 28 years by Mathias (SIAM Journal on Matrix Analysis and Applications, 1993) on the cb-norm of Mcount for a large range of the dimension of Mcount. Furthermore, we are the first to give concrete error bounds for various problems under continual observation such as binary counting, maintaining a histogram, releasing an approximately cut-preserving synthetic graph, many graph-based statistics, and substring and episode counting. Finally, we note that our result can be used to get a fine-grained error bound for non-interactive local learning and the first lower bounds on the additive error for (ϵ,δ)-differentially-private counting under continual observation. Subsequent to this work, Henzinger et al. (SODA, 2023) showed that our factorization also achieves fine-grained mean-squared error."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14462","intvolume":" 202","title":"Constant matters: Fine-grained error bound on differentially private continual observation","status":"public","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"30","citation":{"chicago":"Fichtenberger, Hendrik, Monika H Henzinger, and Jalaj Upadhyay. “Constant Matters: Fine-Grained Error Bound on Differentially Private Continual Observation.” In Proceedings of the 40th International Conference on Machine Learning, 202:10072–92. ML Research Press, 2023.","short":"H. Fichtenberger, M.H. Henzinger, J. Upadhyay, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 10072–10092.","mla":"Fichtenberger, Hendrik, et al. “Constant Matters: Fine-Grained Error Bound on Differentially Private Continual Observation.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 10072–92.","apa":"Fichtenberger, H., Henzinger, M. H., & Upadhyay, J. (2023). Constant matters: Fine-grained error bound on differentially private continual observation. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 10072–10092). Honolulu, Hawaii, HI, United States: ML Research Press.","ieee":"H. Fichtenberger, M. H. Henzinger, and J. Upadhyay, “Constant matters: Fine-grained error bound on differentially private continual observation,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 10072–10092.","ista":"Fichtenberger H, Henzinger MH, Upadhyay J. 2023. Constant matters: Fine-grained error bound on differentially private continual observation. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 10072–10092.","ama":"Fichtenberger H, Henzinger MH, Upadhyay J. Constant matters: Fine-grained error bound on differentially private continual observation. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:10072-10092."},"publication":"Proceedings of the 40th International Conference on Machine Learning","page":"10072-10092","date_published":"2023-07-30T00:00:00Z","ec_funded":1,"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 Austrian Science Fund (FWF) project Z 422-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. 2020–2024. JU’s research was funded by Decanal Research Grant. A part of this work was done when JU was visiting Indian Statistical Institute, Delhi. The authors would like to thank Rajat Bhatia, Aleksandar Nikolov, Shanta Laisharam, Vern Paulsen, Ryan Rogers, Abhradeep Thakurta, and Sarvagya Upadhyay for useful discussions.","year":"2023","publisher":"ML Research Press","department":[{"_id":"MoHe"}],"publication_status":"published","author":[{"first_name":"Hendrik","last_name":"Fichtenberger","full_name":"Fichtenberger, Hendrik"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"last_name":"Upadhyay","first_name":"Jalaj","full_name":"Upadhyay, Jalaj"}],"volume":202,"date_updated":"2023-10-31T09:54:05Z","date_created":"2023-10-29T23:01:17Z","publication_identifier":{"eissn":["2640-3498"]},"month":"07","oa":1,"main_file_link":[{"open_access":"1","url":"https://proceedings.mlr.press/v202/fichtenberger23a/fichtenberger23a.pdf"}],"project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures"},{"grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Wittgenstein Award - Monika Henzinger"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 "}],"quality_controlled":"1","conference":{"end_date":"2023-07-29","start_date":"2023-07-23","location":"Honolulu, Hawaii, HI, United States","name":"ICML: International Conference on Machine Learning"},"language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions."}],"type":"conference","alternative_title":["PMLR"],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14459","intvolume":" 202","title":"Fundamental limits of two-layer autoencoders, and achieving them with gradient methods","status":"public","article_processing_charge":"No","day":"30","scopus_import":"1","date_published":"2023-07-30T00:00:00Z","citation":{"ama":"Shevchenko A, Kögler K, Hassani H, Mondelli M. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:31151-31209.","apa":"Shevchenko, A., Kögler, K., Hassani, H., & Mondelli, M. (2023). Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 31151–31209). Honolulu, Hawaii, HI, United States: ML Research Press.","ieee":"A. Shevchenko, K. Kögler, H. Hassani, and M. Mondelli, “Fundamental limits of two-layer autoencoders, and achieving them with gradient methods,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 31151–31209.","ista":"Shevchenko A, Kögler K, Hassani H, Mondelli M. 2023. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 31151–31209.","short":"A. Shevchenko, K. Kögler, H. Hassani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 31151–31209.","mla":"Shevchenko, Aleksandr, et al. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 31151–209.","chicago":"Shevchenko, Aleksandr, Kevin Kögler, Hamed Hassani, and Marco Mondelli. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” In Proceedings of the 40th International Conference on Machine Learning, 202:31151–209. ML Research Press, 2023."},"publication":"Proceedings of the 40th International Conference on Machine Learning","page":"31151-31209","author":[{"first_name":"Aleksandr","last_name":"Shevchenko","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","full_name":"Shevchenko, Aleksandr"},{"full_name":"Kögler, Kevin","id":"94ec913c-dc85-11ea-9058-e5051ab2428b","last_name":"Kögler","first_name":"Kevin"},{"full_name":"Hassani, Hamed","last_name":"Hassani","first_name":"Hamed"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli","full_name":"Mondelli, Marco"}],"volume":202,"date_created":"2023-10-29T23:01:17Z","date_updated":"2023-10-31T08:52:28Z","year":"2023","acknowledgement":"Aleksandr Shevchenko, Kevin Kogler and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed Hassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","publisher":"ML Research Press","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"publication_status":"published","publication_identifier":{"eissn":["2640-3498"]},"month":"07","conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2023-07-29","start_date":"2023-07-23","location":"Honolulu, Hawaii, HI, United States"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2212.13468"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2212.13468","open_access":"1"}],"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"We provide an efficient implementation of the backpropagation algorithm, specialized to the case where the weights of the neural network being trained are sparse. Our algorithm is general, as it applies to arbitrary (unstructured) sparsity and common layer types (e.g., convolutional or linear). We provide a fast vectorized implementation on commodity CPUs, and show that it can yield speedups in end-to-end runtime experiments, both in transfer learning using already-sparsified networks, and in training sparse networks from scratch. Thus, our results provide the first support for sparse training on commodity hardware."}],"alternative_title":["PMLR"],"type":"conference","oa_version":"Preprint","status":"public","title":"SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge","intvolume":" 202","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14460","day":"30","article_processing_charge":"No","scopus_import":"1","date_published":"2023-07-30T00:00:00Z","page":"26215-26227","publication":"Proceedings of the 40th International Conference on Machine Learning","citation":{"chicago":"Nikdan, Mahdi, Tommaso Pegolotti, Eugenia B Iofinova, Eldar Kurtic, and Dan-Adrian Alistarh. “SparseProp: Efficient Sparse Backpropagation for Faster Training of Neural Networks at the Edge.” In Proceedings of the 40th International Conference on Machine Learning, 202:26215–27. ML Research Press, 2023.","mla":"Nikdan, Mahdi, et al. “SparseProp: Efficient Sparse Backpropagation for Faster Training of Neural Networks at the Edge.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 26215–27.","short":"M. Nikdan, T. Pegolotti, E.B. Iofinova, E. Kurtic, D.-A. Alistarh, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 26215–26227.","ista":"Nikdan M, Pegolotti T, Iofinova EB, Kurtic E, Alistarh D-A. 2023. SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 26215–26227.","ieee":"M. Nikdan, T. Pegolotti, E. B. Iofinova, E. Kurtic, and D.-A. Alistarh, “SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 26215–26227.","apa":"Nikdan, M., Pegolotti, T., Iofinova, E. B., Kurtic, E., & Alistarh, D.-A. (2023). SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 26215–26227). Honolulu, Hawaii, HI, United States: ML Research Press.","ama":"Nikdan M, Pegolotti T, Iofinova EB, Kurtic E, Alistarh D-A. SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:26215-26227."},"ec_funded":1,"date_updated":"2023-10-31T09:33:51Z","date_created":"2023-10-29T23:01:17Z","volume":202,"author":[{"first_name":"Mahdi","last_name":"Nikdan","id":"66374281-f394-11eb-9cf6-869147deecc0","full_name":"Nikdan, Mahdi"},{"full_name":"Pegolotti, Tommaso","last_name":"Pegolotti","first_name":"Tommaso"},{"id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","orcid":"0000-0002-7778-3221","first_name":"Eugenia B","last_name":"Iofinova","full_name":"Iofinova, Eugenia B"},{"last_name":"Kurtic","first_name":"Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","full_name":"Kurtic, Eldar"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"}],"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"ML Research Press","year":"2023","acknowledgement":"We would like to thank Elias Frantar for his valuable assistance and support at the outset of this project, and the anonymous ICML and SNN reviewers for very constructive feedback. EI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35. DA acknowledges generous ERC support, via Starting Grant 805223 ScaleML. ","month":"07","publication_identifier":{"eissn":["2640-3498"]},"language":[{"iso":"eng"}],"conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2023-07-29","start_date":"2023-07-23","location":"Honolulu, Hawaii, HI, United States"},"quality_controlled":"1","project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"oa":1,"external_id":{"arxiv":["2302.04852"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2302.04852","open_access":"1"}]},{"abstract":[{"lang":"eng","text":"Threshold secret sharing allows a dealer to split a secret s into n shares, such that any t shares allow for reconstructing s, but no t-1 shares reveal any information about s. Leakage-resilient secret sharing requires that the secret remains hidden, even when an adversary additionally obtains a limited amount of leakage from every share. Benhamouda et al. (CRYPTO’18) proved that Shamir’s secret sharing scheme is one bit leakage-resilient for reconstruction threshold t≥0.85n and conjectured that the same holds for t = c.n for any constant 0≤c≤1. Nielsen and Simkin (EUROCRYPT’20) showed that this is the best one can hope for by proving that Shamir’s scheme is not secure against one-bit leakage when t0c.n/log(n).\r\nIn this work, we strengthen the lower bound of Nielsen and Simkin. We consider noisy leakage-resilience, where a random subset of leakages is replaced by uniformly random noise. We prove a lower bound for Shamir’s secret sharing, similar to that of Nielsen and Simkin, which holds even when a constant fraction of leakages is replaced by random noise. To this end, we first prove a lower bound on the share size of any noisy-leakage-resilient sharing scheme. We then use this lower bound to show that there exist universal constants c1, c2, such that for sufficiently large n it holds that Shamir’s secret sharing scheme is not noisy-leakage-resilient for t≤c1.n/log(n), even when a c2 fraction of leakages are replaced by random noise.\r\n\r\n\r\n\r\n"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"14457","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Stronger lower bounds for leakage-resilient secret sharing","status":"public","intvolume":" 14168","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2023-10-01T00:00:00Z","publication":"8th International Conference on Cryptology and Information Security in Latin America","citation":{"apa":"Hoffmann, C., & Simkin, M. (2023). Stronger lower bounds for leakage-resilient secret sharing. In 8th International Conference on Cryptology and Information Security in Latin America (Vol. 14168, pp. 215–228). Quito, Ecuador: Springer Nature. https://doi.org/10.1007/978-3-031-44469-2_11","ieee":"C. Hoffmann and M. Simkin, “Stronger lower bounds for leakage-resilient secret sharing,” in 8th International Conference on Cryptology and Information Security in Latin America, Quito, Ecuador, 2023, vol. 14168, pp. 215–228.","ista":"Hoffmann C, Simkin M. 2023. Stronger lower bounds for leakage-resilient secret sharing. 8th International Conference on Cryptology and Information Security in Latin America. LATINCRYPT: Conference on Cryptology and Information Security in Latin America, LNCS, vol. 14168, 215–228.","ama":"Hoffmann C, Simkin M. Stronger lower bounds for leakage-resilient secret sharing. In: 8th International Conference on Cryptology and Information Security in Latin America. Vol 14168. Springer Nature; 2023:215-228. doi:10.1007/978-3-031-44469-2_11","chicago":"Hoffmann, Charlotte, and Mark Simkin. “Stronger Lower Bounds for Leakage-Resilient Secret Sharing.” In 8th International Conference on Cryptology and Information Security in Latin America, 14168:215–28. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-44469-2_11.","short":"C. Hoffmann, M. Simkin, in:, 8th International Conference on Cryptology and Information Security in Latin America, Springer Nature, 2023, pp. 215–228.","mla":"Hoffmann, Charlotte, and Mark Simkin. “Stronger Lower Bounds for Leakage-Resilient Secret Sharing.” 8th International Conference on Cryptology and Information Security in Latin America, vol. 14168, Springer Nature, 2023, pp. 215–28, doi:10.1007/978-3-031-44469-2_11."},"page":"215-228","author":[{"full_name":"Hoffmann, Charlotte","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","orcid":"0000-0003-2027-5549","first_name":"Charlotte","last_name":"Hoffmann"},{"full_name":"Simkin, Mark","first_name":"Mark","last_name":"Simkin"}],"date_created":"2023-10-29T23:01:16Z","date_updated":"2023-10-31T11:43:12Z","volume":14168,"year":"2023","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"month":"10","publication_identifier":{"isbn":["9783031444685"],"eissn":["1611-3349"],"issn":["0302-9743"]},"conference":{"name":"LATINCRYPT: Conference on Cryptology and Information Security in Latin America","start_date":"2023-10-03","location":"Quito, Ecuador","end_date":"2023-10-06"},"doi":"10.1007/978-3-031-44469-2_11","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://eprint.iacr.org/2023/1017","open_access":"1"}],"oa":1,"quality_controlled":"1"},{"alternative_title":["PMLR"],"type":"conference","abstract":[{"lang":"eng","text":"We show for the first time that large-scale generative pretrained transformer (GPT) family models can be pruned to at least 50% sparsity in one-shot, without any retraining, at minimal loss of accuracy. This is achieved via a new pruning method called SparseGPT, specifically designed to work efficiently and accurately on massive GPT-family models. We can execute SparseGPT on the largest available open-source models, OPT-175B and BLOOM-176B, in under 4.5 hours, and can reach 60% unstructured sparsity with negligible increase in perplexity: remarkably, more than 100 billion weights from these models can be ignored at inference time. SparseGPT generalizes to semi-structured (2:4 and 4:8) patterns, and is compatible with weight quantization approaches. The code is available at: https://github.com/IST-DASLab/sparsegpt."}],"intvolume":" 202","status":"public","title":"SparseGPT: Massive language models can be accurately pruned in one-shot","_id":"14458","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"30","page":"10323-10337","citation":{"ama":"Frantar E, Alistarh D-A. SparseGPT: Massive language models can be accurately pruned in one-shot. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:10323-10337.","ista":"Frantar E, Alistarh D-A. 2023. SparseGPT: Massive language models can be accurately pruned in one-shot. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 10323–10337.","apa":"Frantar, E., & Alistarh, D.-A. (2023). SparseGPT: Massive language models can be accurately pruned in one-shot. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 10323–10337). Honolulu, Hawaii, HI, United States: ML Research Press.","ieee":"E. Frantar and D.-A. Alistarh, “SparseGPT: Massive language models can be accurately pruned in one-shot,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 10323–10337.","mla":"Frantar, Elias, and Dan-Adrian Alistarh. “SparseGPT: Massive Language Models Can Be Accurately Pruned in One-Shot.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 10323–37.","short":"E. Frantar, D.-A. Alistarh, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 10323–10337.","chicago":"Frantar, Elias, and Dan-Adrian Alistarh. “SparseGPT: Massive Language Models Can Be Accurately Pruned in One-Shot.” In Proceedings of the 40th International Conference on Machine Learning, 202:10323–37. ML Research Press, 2023."},"publication":"Proceedings of the 40th International Conference on Machine Learning","date_published":"2023-07-30T00:00:00Z","ec_funded":1,"publisher":"ML Research Press","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2023","acknowledgement":"The authors gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement No. 805223 ScaleML), as well as experimental support from Eldar Kurtic, and from the IST Austria IT department, in particular Stefano Elefante, Andrei Hornoiu, and Alois Schloegl.","volume":202,"date_created":"2023-10-29T23:01:16Z","date_updated":"2023-10-31T09:59:42Z","author":[{"id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","first_name":"Elias","last_name":"Frantar","full_name":"Frantar, Elias"},{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"publication_identifier":{"eissn":["2640-3498"]},"month":"07","project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"quality_controlled":"1","external_id":{"arxiv":["2301.00774"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.00774"}],"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"conference":{"name":"ICML: International Conference on Machine Learning","location":"Honolulu, Hawaii, HI, United States","start_date":"2023-07-23","end_date":"2023-07-29"}},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00521-023-09033-7"}],"external_id":{"arxiv":["2203.04579"]},"quality_controlled":"1","project":[{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"doi":"10.1007/s00521-023-09033-7","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["1433-3058"],"issn":["0941-0643"]},"year":"2023","acknowledgement":"Open access funding provided by Università degli Studi di Trieste within the CRUI-CARE Agreement. Funding was provided by Austrian Science Fund (Grant No. F65), Horizon 2020 (Grant No. 754411) and Österreichische Forschungsförderungsgesellschaft.","publication_status":"epub_ahead","publisher":"Springer Nature","department":[{"_id":"JuFi"}],"author":[{"id":"2CEB641C-A400-11E9-A717-D712E6697425","orcid":"0000-0002-6269-5149","first_name":"Federico","last_name":"Cornalba","full_name":"Cornalba, Federico"},{"full_name":"Disselkamp, Constantin","last_name":"Disselkamp","first_name":"Constantin"},{"full_name":"Scassola, Davide","last_name":"Scassola","first_name":"Davide"},{"last_name":"Helf","first_name":"Christopher","full_name":"Helf, Christopher"}],"date_updated":"2023-10-31T10:58:28Z","date_created":"2023-10-22T22:01:16Z","ec_funded":1,"publication":"Neural Computing and Applications","citation":{"short":"F. Cornalba, C. Disselkamp, D. Scassola, C. Helf, Neural Computing and Applications (2023).","mla":"Cornalba, Federico, et al. “Multi-Objective Reward Generalization: Improving Performance of Deep Reinforcement Learning for Applications in Single-Asset Trading.” Neural Computing and Applications, Springer Nature, 2023, doi:10.1007/s00521-023-09033-7.","chicago":"Cornalba, Federico, Constantin Disselkamp, Davide Scassola, and Christopher Helf. “Multi-Objective Reward Generalization: Improving Performance of Deep Reinforcement Learning for Applications in Single-Asset Trading.” Neural Computing and Applications. Springer Nature, 2023. https://doi.org/10.1007/s00521-023-09033-7.","ama":"Cornalba F, Disselkamp C, Scassola D, Helf C. Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading. Neural Computing and Applications. 2023. doi:10.1007/s00521-023-09033-7","ieee":"F. Cornalba, C. Disselkamp, D. Scassola, and C. Helf, “Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading,” Neural Computing and Applications. Springer Nature, 2023.","apa":"Cornalba, F., Disselkamp, C., Scassola, D., & Helf, C. (2023). Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading. Neural Computing and Applications. Springer Nature. https://doi.org/10.1007/s00521-023-09033-7","ista":"Cornalba F, Disselkamp C, Scassola D, Helf C. 2023. Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading. Neural Computing and Applications."},"article_type":"original","date_published":"2023-10-05T00:00:00Z","scopus_import":"1","day":"05","article_processing_charge":"Yes (via OA deal)","_id":"14451","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading","status":"public","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"We investigate the potential of Multi-Objective, Deep Reinforcement Learning for stock and cryptocurrency single-asset trading: in particular, we consider a Multi-Objective algorithm which generalizes the reward functions and discount factor (i.e., these components are not specified a priori, but incorporated in the learning process). Firstly, using several important assets (BTCUSD, ETHUSDT, XRPUSDT, AAPL, SPY, NIFTY50), we verify the reward generalization property of the proposed Multi-Objective algorithm, and provide preliminary statistical evidence showing increased predictive stability over the corresponding Single-Objective strategy. Secondly, we show that the Multi-Objective algorithm has a clear edge over the corresponding Single-Objective strategy when the reward mechanism is sparse (i.e., when non-null feedback is infrequent over time). Finally, we discuss the generalization properties with respect to the discount factor. The entirety of our code is provided in open-source format.","lang":"eng"}]}]