[{"title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","ddc":["570"],"status":"public","intvolume":" 41","_id":"12106","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_size":12040976,"content_type":"application/pdf","creator":"dernst","file_name":"2023_NatureBioTech_Yeung.pdf","access_level":"open_access","date_created":"2023-08-16T11:30:45Z","date_updated":"2023-08-16T11:30:45Z","checksum":"668447a1c8d360b68f8aaf9e08ed644f","success":1,"relation":"main_file","file_id":"14066"}],"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"}],"article_type":"original","page":"813–823","publication":"Nature Biotechnology","citation":{"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.","ieee":"J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823, 2023.","apa":"Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., & Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-022-01560-3","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"},"date_published":"2023-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","department":[{"_id":"ScienComp"}],"publisher":"Springer Nature","year":"2023","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.","date_created":"2023-01-08T23:00:53Z","date_updated":"2023-08-16T11:32:33Z","volume":41,"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","first_name":"Maria","last_name":"Florescu"},{"first_name":"Peter","last_name":"Zeller","full_name":"Zeller, Peter"},{"last_name":"De Barbanson","first_name":"Buys Anton","full_name":"De Barbanson, Buys Anton"},{"last_name":"Wellenstein","first_name":"Max D.","full_name":"Wellenstein, Max D."},{"last_name":"Van Oudenaarden","first_name":"Alexander","full_name":"Van Oudenaarden, Alexander"}],"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2023-08-16T11:30:45Z","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":["000909067600003"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41587-022-01560-3","month":"06","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]}},{"department":[{"_id":"RoSe"}],"publisher":"Springer Nature","publication_status":"published","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","volume":24,"date_created":"2023-01-15T23:00:52Z","date_updated":"2023-08-16T11:34:03Z","author":[{"full_name":"Boccato, Chiara","last_name":"Boccato","first_name":"Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"ec_funded":1,"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,"oa":1,"external_id":{"isi":["000910751800002"],"arxiv":["2205.15284"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2205.15284"}],"language":[{"iso":"eng"}],"doi":"10.1007/s00023-022-01252-3","publication_identifier":{"issn":["1424-0637"]},"month":"05","intvolume":" 24","title":"The Bose Gas in a box with Neumann boundary conditions","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12183","oa_version":"Preprint","type":"journal_article","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"}],"page":"1505-1560","article_type":"original","citation":{"chicago":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01252-3.","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.","ista":"Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 24, 1505–1560.","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","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.","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"},"publication":"Annales Henri Poincare","date_published":"2023-05-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"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"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2023_JCIM_Koehl.pdf","access_level":"open_access","creator":"dernst","file_size":8069223,"content_type":"application/pdf","file_id":"14070","relation":"main_file","date_updated":"2023-08-16T12:21:13Z","date_created":"2023-08-16T12:21:13Z","success":1,"checksum":"7d20562269edff1e31b9d6019d4983b0"}],"intvolume":" 63","ddc":["510","540"],"status":"public","title":"Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives","_id":"12544","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","article_processing_charge":"No","day":"13","scopus_import":"1","date_published":"2023-02-13T00:00:00Z","page":"973-985","article_type":"original","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","ec_funded":1,"file_date_updated":"2023-08-16T12:21:13Z","volume":63,"date_created":"2023-02-12T23:00:59Z","date_updated":"2023-08-16T12:22:07Z","author":[{"last_name":"Koehl","first_name":"Patrice","full_name":"Koehl, Patrice"},{"last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"}],"department":[{"_id":"HeEd"}],"publisher":"American Chemical Society","publication_status":"published","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).","publication_identifier":{"issn":["1549-9596"],"eissn":["1549-960X"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1021/acs.jcim.2c01346","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"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":["000920370700001"],"pmid":["36638318"]}},{"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":"14069","relation":"main_file","success":1,"checksum":"8244f4650a0e7aeea488d1bcd4a31702","date_updated":"2023-08-16T11:54:59Z","date_created":"2023-08-16T11:54:59Z","access_level":"open_access","file_name":"2023_NatureEcoEvo_Stock.pdf","creator":"dernst","content_type":"application/pdf","file_size":1600499}],"title":"Pathogen evasion of social immunity","status":"public","ddc":["570"],"intvolume":" 7","_id":"12543","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-03-01T00:00:00Z","article_type":"original","page":"450-460","publication":"Nature Ecology and Evolution","citation":{"short":"M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N. Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution 7 (2023) 450–460.","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.","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."},"file_date_updated":"2023-08-16T11:54:59Z","ec_funded":1,"date_updated":"2023-08-16T11:55:48Z","date_created":"2023-02-12T23:00:59Z","volume":7,"author":[{"full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","last_name":"Stock"},{"full_name":"Milutinovic, Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8214-4758","first_name":"Barbara","last_name":"Milutinovic"},{"full_name":"Hönigsberger, Michaela","first_name":"Michaela","last_name":"Hönigsberger","id":"953894f3-25bd-11ec-8556-f70a9d38ef60"},{"full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V"},{"first_name":"Florian","last_name":"Wiesenhofer","id":"39523C54-F248-11E8-B48F-1D18A9856A87","full_name":"Wiesenhofer, Florian"},{"full_name":"Kampleitner, Niklas","first_name":"Niklas","last_name":"Kampleitner","id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","first_name":"Madhumitha","orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schmitt, Thomas","first_name":"Thomas","last_name":"Schmitt"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/"}]},"publication_status":"published","department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"publisher":"Springer Nature","acknowledgement":"We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team at ISTA for ant collection and experimental help, in particular H. Leitner, and the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the Social Immunity team for comments on the manuscript. The study was funded by the German Research Foundation (CR118/3-1) within the Framework of the Priority Program SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.","year":"2023","pmid":1,"month":"03","publication_identifier":{"eissn":["2397-334X"]},"acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41559-023-01981-6","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Epidemics in ant societies on a chip","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"},{"name":"Host-Parasite Coevolution","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["36732670"],"isi":["000924572800001"]}},{"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","article_type":"original","citation":{"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.","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","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."},"publication":"Evolution Letters","date_published":"2023-02-01T00:00:00Z","type":"journal_article","issue":"1","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"}],"intvolume":" 7","title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12521","oa_version":"Published Version","file":[{"file_id":"14068","relation":"main_file","date_created":"2023-08-16T11:43:33Z","date_updated":"2023-08-16T11:43:33Z","success":1,"checksum":"a240a041cb9b9b7c8ba93a4706674a3f","file_name":"2023_EvLetters_Mrnjavac.pdf","access_level":"open_access","creator":"dernst","file_size":2592189,"content_type":"application/pdf"}],"publication_identifier":{"issn":["2056-3744"]},"month":"02","project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37065438"],"isi":["001021692200001"]},"language":[{"iso":"eng"}],"doi":"10.1093/evlett/qrac004","article_number":"qrac004","ec_funded":1,"file_date_updated":"2023-08-16T11:43:33Z","publisher":"Oxford University Press","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"publication_status":"published","pmid":1,"year":"2023","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).","volume":7,"date_updated":"2023-08-16T11:44:32Z","date_created":"2023-02-06T13:59:12Z","author":[{"last_name":"Mrnjavac","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","full_name":"Mrnjavac, Andrea"},{"orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","first_name":"Kseniia","full_name":"Khudiakova, Kseniia"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12679","intvolume":" 79","ddc":["570"],"status":"public","title":"Principles of neural stem cell lineage progression: Insights from developing cerebral cortex","file":[{"access_level":"open_access","file_name":"2023_CurrentOpinionNeurobio_Hippenmeyer.pdf","content_type":"application/pdf","file_size":1787894,"creator":"dernst","relation":"main_file","file_id":"14071","checksum":"4d11c4ca87e6cbc4d2ac46d3225ea615","success":1,"date_updated":"2023-08-16T12:29:06Z","date_created":"2023-08-16T12:29:06Z"}],"oa_version":"Published Version","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":{"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).","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.","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","ista":"Hippenmeyer S. 2023. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4), 102695.","apa":"Hippenmeyer, S. (2023). Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2023.102695","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."},"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","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","publisher":"Elsevier","department":[{"_id":"SiHi"}],"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","external_id":{"pmid":["36842274"],"isi":["000953497700001"]},"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":[{"grant_number":"F07805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1016/j.conb.2023.102695","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0959-4388"]},"month":"04"},{"language":[{"iso":"eng"}],"doi":"10.1002/mana.202100192","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000914134900001"],"arxiv":["2104.05063"]},"publication_identifier":{"issn":["0025-584X"],"eissn":["1522-2616"]},"month":"04","volume":296,"date_created":"2023-01-29T23:00:59Z","date_updated":"2023-08-16T11:41:42Z","author":[{"first_name":"Antonio","last_name":"Agresti","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio"},{"last_name":"Lindemulder","first_name":"Nick","full_name":"Lindemulder, Nick"},{"last_name":"Veraar","first_name":"Mark","full_name":"Veraar, Mark"}],"department":[{"_id":"JuFi"}],"publisher":"Wiley","publication_status":"published","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).","year":"2023","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2023-08-16T11:40:02Z","date_published":"2023-04-01T00:00:00Z","page":"1319-1350","article_type":"original","citation":{"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.","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.","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","ista":"Agresti A, Lindemulder N, Veraar M. 2023. On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. 296(4), 1319–1350.","apa":"Agresti, A., Lindemulder, N., & Veraar, M. (2023). On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. Wiley. https://doi.org/10.1002/mana.202100192","ieee":"A. Agresti, N. Lindemulder, and M. Veraar, “On the trace embedding and its applications to evolution equations,” Mathematische Nachrichten, vol. 296, no. 4. Wiley, pp. 1319–1350, 2023."},"publication":"Mathematische Nachrichten","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":449280,"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","intvolume":" 296","status":"public","title":"On the trace embedding and its applications to evolution equations","ddc":["510"],"_id":"12429","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","abstract":[{"lang":"eng","text":"In this paper, we consider traces at initial times for functions with mixed time-space smoothness. Such results are often needed in the theory of evolution equations. Our result extends and unifies many previous results. Our main improvement is that we can allow general interpolation couples. The abstract results are applied to regularity problems for fractional evolution equations and stochastic evolution equations, where uniform trace estimates on the half-line are shown."}],"type":"journal_article"},{"scopus_import":"1","day":"09","article_processing_charge":"No","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.","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.","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","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"},"article_type":"original","date_published":"2023-01-09T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12430","title":"Bogoliubov dynamics and higher-order corrections for the regularized Nelson model","status":"public","intvolume":" 35","oa_version":"Preprint","month":"01","publication_identifier":{"issn":["0129-055X"]},"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2110.00458"}],"oa":1,"external_id":{"isi":["000909760300001"],"arxiv":["2110.00458"]},"quality_controlled":"1","isi":1,"doi":"10.1142/S0129055X2350006X","language":[{"iso":"eng"}],"article_number":"2350006","year":"2023","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"World Scientific Publishing","author":[{"last_name":"Falconi","first_name":"Marco","full_name":"Falconi, Marco"},{"last_name":"Leopold","first_name":"Nikolai K","orcid":"0000-0002-0495-6822","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","full_name":"Leopold, Nikolai K"},{"full_name":"Mitrouskas, David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","last_name":"Mitrouskas","first_name":"David Johannes"},{"first_name":"Sören P","last_name":"Petrat","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9166-5889","full_name":"Petrat, Sören P"}],"date_updated":"2023-08-16T11:47:27Z","date_created":"2023-01-29T23:00:59Z","volume":35},{"ec_funded":1,"file_date_updated":"2023-08-16T12:39:57Z","publisher":"Springer Nature","department":[{"_id":"GaTk"},{"_id":"GradSch"}],"publication_status":"published","year":"2023","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.).","volume":3,"date_updated":"2023-08-16T12:41:53Z","date_created":"2023-03-26T22:01:08Z","author":[{"first_name":"Fabrizio","last_name":"Lombardi","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio"},{"full_name":"Pepic, Selver","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425","first_name":"Selver","last_name":"Pepic"},{"full_name":"Shriki, Oren","first_name":"Oren","last_name":"Shriki"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"},{"last_name":"De Martino","first_name":"Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele"}],"publication_identifier":{"eissn":["2662-8457"]},"month":"03","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"}],"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":["2108.06686"]},"language":[{"iso":"eng"}],"doi":"10.1038/s43588-023-00410-9","type":"journal_article","abstract":[{"lang":"eng","text":"Neurons in the brain are wired into adaptive networks that exhibit collective dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches. Although existing models account for oscillations and avalanches separately, they typically do not explain both phenomena, are too complex to analyze analytically or intractable to infer from data rigorously. Here we propose a feedback-driven Ising-like class of neural networks that captures avalanches and oscillations simultaneously and quantitatively. In the simplest yet fully microscopic model version, we can analytically compute the phase diagram and make direct contact with human brain resting-state activity recordings via tractable inference of the model’s two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor oscillations to collective behaviors of extreme events and neuronal avalanches. Importantly, the inferred parameters indicate that the co-existence of scale-specific (oscillations) and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations."}],"intvolume":" 3","status":"public","ddc":["570"],"title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12762","file":[{"file_id":"14073","relation":"main_file","success":1,"checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","date_created":"2023-08-16T12:39:57Z","date_updated":"2023-08-16T12:39:57Z","access_level":"open_access","file_name":"2023_NatureCompScience_Lombardi.pdf","creator":"dernst","file_size":4474284,"content_type":"application/pdf"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"20","page":"254-263","article_type":"original","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","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","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.","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."},"publication":"Nature Computational Science","date_published":"2023-03-20T00:00:00Z"},{"has_accepted_license":"1","article_processing_charge":"No","day":"05","date_published":"2023-05-05T00:00:00Z","citation":{"apa":"Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12891","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:10.15479/at:ista:12891","chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12891.","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.","mla":"Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12891."},"page":"190","abstract":[{"text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"file_name":"Thesis_Schauer_final.pdf","embargo_to":"open_access","access_level":"closed","creator":"aschauer","file_size":31434230,"content_type":"application/pdf","file_id":"12907","embargo":"2024-05-05","relation":"main_file","date_updated":"2023-05-05T13:01:14Z","date_created":"2023-05-05T13:01:14Z","checksum":"59b0303dc483f40a96a610a90aab7ee9"},{"file_size":43809109,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"aschauer","file_name":"Thesis_Schauer_final.docx","access_level":"closed","date_updated":"2023-05-05T13:04:15Z","date_created":"2023-05-05T13:04:15Z","checksum":"25f54e12479b6adaabd129a20568e6c1","relation":"source_file","file_id":"12908"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12891","status":"public","title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","ddc":["570"],"publication_identifier":{"issn":["2663 - 337X"]},"month":"05","doi":"10.15479/at:ista:12891","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"supervisor":[{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues"}],"ec_funded":1,"file_date_updated":"2023-05-05T13:04:15Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8966"},{"status":"public","relation":"part_of_dissertation","id":"7888"}]},"author":[{"full_name":"Schauer, Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","first_name":"Alexandra","last_name":"Schauer"}],"date_created":"2023-05-05T08:48:20Z","date_updated":"2023-08-21T06:25:48Z","year":"2023","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published"},{"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.ICALP.2023.69","conference":{"location":"Paderborn, Germany","start_date":"2023-07-10","end_date":"2023-07-14","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"project":[{"call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 "}],"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":{"unknown":["2211.09606"]},"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772785"]},"month":"07","volume":261,"date_updated":"2023-08-21T07:00:49Z","date_created":"2023-08-20T22:01:14Z","author":[{"full_name":"Goranci, Gramoz","last_name":"Goranci","first_name":"Gramoz"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"department":[{"_id":"MoHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","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.","ec_funded":1,"file_date_updated":"2023-08-21T06:59:05Z","article_number":"69","date_published":"2023-07-01T00:00:00Z","citation":{"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.","ieee":"G. Goranci and M. H. Henzinger, “Efficient data structures for incremental exact and approximate maximum flow,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","apa":"Goranci, G., & Henzinger, M. H. (2023). Efficient data structures for incremental exact and approximate maximum flow. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.69","ama":"Goranci G, Henzinger MH. Efficient data structures for incremental exact and approximate maximum flow. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.69","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.","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.","short":"G. Goranci, M.H. Henzinger, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023."},"publication":"50th International Colloquium on Automata, Languages, and Programming","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":875910,"creator":"dernst","file_name":"2023_LIPIcsICALP_Goranci.pdf","access_level":"open_access","date_created":"2023-08-21T06:59:05Z","date_updated":"2023-08-21T06:59:05Z","checksum":"074177e815a1656de5d4071c7a3dffa6","success":1,"relation":"main_file","file_id":"14089"}],"oa_version":"Published Version","intvolume":" 261","title":"Efficient data structures for incremental exact and approximate maximum flow","ddc":["000"],"status":"public","_id":"14085","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","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."}],"alternative_title":["LIPIcs"],"type":"conference"},{"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772785"]},"month":"07","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":["2007.10824"]},"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.ICALP.2023.72","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","start_date":"2023-07-10","location":"Paderborn, Germany","end_date":"2023-07-14"},"article_number":"72","file_date_updated":"2023-08-21T06:45:16Z","department":[{"_id":"VlKo"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","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.","year":"2023","volume":261,"date_updated":"2023-08-21T06:49:11Z","date_created":"2023-08-20T22:01:14Z","author":[{"full_name":"Harris, David G.","last_name":"Harris","first_name":"David G."},{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","citation":{"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.","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.","ama":"Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.72","apa":"Harris, D. G., & Kolmogorov, V. (2023). Parameter estimation for Gibbs distributions. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.72","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."},"publication":"50th International Colloquium on Automata, Languages, and Programming","date_published":"2023-07-01T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"A central problem in computational statistics is to convert a procedure for sampling combinatorial objects into a procedure for counting those objects, and vice versa. We will consider sampling problems which come from Gibbs distributions, which are families of probability distributions over a discrete space Ω with probability mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max] and H(ω) ∈ {0} ∪ [1, n].\r\nThe partition function is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the log partition ratio is defined as q = (log Z(β_max))/Z(β_min)\r\nWe develop a number of algorithms to estimate the counts c_x using roughly Õ(q/ε²) samples for general Gibbs distributions and Õ(n²/ε²) samples for integer-valued distributions (ignoring some second-order terms and parameters), We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs and perfect matchings in a graph.","lang":"eng"}],"intvolume":" 261","title":"Parameter estimation for Gibbs distributions","status":"public","ddc":["000","510"],"_id":"14084","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"checksum":"6dee0684245bb1c524b9c955db1e933d","success":1,"date_created":"2023-08-21T06:45:16Z","date_updated":"2023-08-21T06:45:16Z","relation":"main_file","file_id":"14088","file_size":917791,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_LIPIcsICALP_Harris.pdf"}]},{"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":["2305.00122"]},"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","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 "}],"quality_controlled":"1","doi":"10.4230/LIPIcs.ICALP.2023.74","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","start_date":"2023-07-10","location":"Paderborn, Germany","end_date":"2023-07-14"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["18688969"],"isbn":["9783959772785"]},"month":"07","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","department":[{"_id":"MoHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","author":[{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"full_name":"Liu, Paul","first_name":"Paul","last_name":"Liu"},{"full_name":"Vondrák, Jan","last_name":"Vondrák","first_name":"Jan"},{"full_name":"Zheng, Da Wei","first_name":"Da Wei","last_name":"Zheng"}],"volume":261,"date_updated":"2023-08-21T07:05:47Z","date_created":"2023-08-20T22:01:14Z","article_number":"74","ec_funded":1,"file_date_updated":"2023-08-21T07:04:36Z","citation":{"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","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.","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.","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."},"publication":"50th International Colloquium on Automata, Languages, and Programming","date_published":"2023-07-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","_id":"14086","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 261","title":"Faster submodular maximization for several classes of matroids","ddc":["000"],"status":"public","file":[{"file_size":930943,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_LIPIcsICALP_HenzingerM.pdf","checksum":"a5eef225014e003efbfbe4830fdd23cb","success":1,"date_updated":"2023-08-21T07:04:36Z","date_created":"2023-08-21T07:04:36Z","relation":"main_file","file_id":"14090"}],"oa_version":"Published Version","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"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.","lang":"eng"}]},{"file_date_updated":"2023-08-21T07:23:18Z","article_number":"99","volume":261,"date_updated":"2023-08-21T07:26:01Z","date_created":"2023-08-20T22:01:13Z","author":[{"full_name":"Resch, Nicolas","first_name":"Nicolas","last_name":"Resch"},{"full_name":"Yuan, Chen","first_name":"Chen","last_name":"Yuan"},{"full_name":"Zhang, Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258","first_name":"Yihan","last_name":"Zhang"}],"department":[{"_id":"MaMo"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","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.","year":"2023","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772785"]},"month":"07","language":[{"iso":"eng"}],"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"},"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":["2210.07754"]},"abstract":[{"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.","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","file":[{"file_id":"14091","relation":"main_file","date_updated":"2023-08-21T07:23:18Z","date_created":"2023-08-21T07:23:18Z","success":1,"checksum":"a449143fec3fbebb092cb8ef3b53c226","file_name":"2023_LIPIcsICALP_Resch.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1141497}],"oa_version":"Published Version","intvolume":" 261","title":"Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery","status":"public","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14083","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2023-07-01T00:00:00Z","citation":{"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.","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.","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.","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"},"publication":"50th International Colloquium on Automata, Languages, and Programming"},{"type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"9","title":"Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media","ddc":["530","537"],"status":"public","intvolume":" 130","_id":"12697","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"checksum":"c4f2f6eea0408811f8f4898e15890355","date_updated":"2023-02-28T12:20:27Z","date_created":"2023-02-28T12:20:27Z","file_id":"12698","relation":"main_file","creator":"ggrosjea","file_size":2301864,"content_type":"application/pdf","access_level":"open_access","file_name":"Main_Preprint.pdf"},{"file_name":"Suppl_info.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1138625,"creator":"ggrosjea","relation":"main_file","file_id":"12699","date_updated":"2023-02-28T12:20:55Z","date_created":"2023-02-28T12:20:55Z","checksum":"6af6ed6c97a977f923de4162294b43c4","success":1},{"relation":"main_file","file_id":"12700","checksum":"3f20365fb9515bdba3a111d912c8d8b4","success":1,"date_updated":"2023-02-28T12:37:54Z","date_created":"2023-02-28T12:37:54Z","access_level":"open_access","file_name":"Suppl_vid1.mp4","content_type":"video/mp4","file_size":793449,"creator":"ggrosjea"},{"content_type":"video/mp4","file_size":455925,"creator":"ggrosjea","file_name":"Suppl_vid2.mp4","access_level":"open_access","date_updated":"2023-02-28T12:37:54Z","date_created":"2023-02-28T12:37:54Z","checksum":"90cecacbe0e2f9dea11f91a4ba20c32e","success":1,"relation":"main_file","file_id":"12701"}],"oa_version":"Preprint","keyword":["General Physics","Electrostatics","Triboelectricity","Soft Matter","Acoustic Levitation","Granular Materials"],"day":"03","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Physical Review Letters","citation":{"mla":"Grosjean, Galien M., and Scott R. Waitukaitis. “Single-Collision Statistics Reveal a Global Mechanism Driven by Sample History for Contact Electrification in Granular Media.” Physical Review Letters, vol. 130, no. 9, 098202, American Physical Society, 2023, doi:10.1103/physrevlett.130.098202.","short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Letters 130 (2023).","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","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.","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"},"date_published":"2023-03-03T00:00:00Z","article_number":"098202","file_date_updated":"2023-02-28T12:37:54Z","ec_funded":1,"publication_status":"published","department":[{"_id":"ScWa"}],"publisher":"American Physical Society","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","date_created":"2023-02-28T12:14:46Z","date_updated":"2023-08-22T08:41:32Z","volume":130,"author":[{"full_name":"Grosjean, Galien M","first_name":"Galien M","last_name":"Grosjean","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","orcid":"0000-0001-5154-417X"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R"}],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"8101"}]},"month":"03","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"quality_controlled":"1","isi":1,"project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","call_identifier":"H2020","grant_number":"949120","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"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":["000946178200008"],"arxiv":["2211.02488"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2211.02488"}],"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.130.098202"},{"author":[{"full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","first_name":"Rishabh","last_name":"Sahu"}],"related_material":{"record":[{"relation":"old_edition","status":"public","id":"12900"},{"status":"public","relation":"part_of_dissertation","id":"10924"},{"relation":"part_of_dissertation","status":"public","id":"9114"}]},"date_updated":"2023-08-24T11:16:35Z","date_created":"2023-06-30T08:07:43Z","year":"2023","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-07-06T11:35:15Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","doi":"10.15479/at:ista:13175","supervisor":[{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"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)"},"project":[{"grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"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"}],"month":"05","publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-030-5"]},"file":[{"file_name":"thesis_pdfa.pdf","access_level":"open_access","file_size":18688376,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"13176","date_created":"2023-06-30T08:17:25Z","date_updated":"2023-06-30T08:17:25Z","checksum":"7d03f1a5a5258ee43dfc3323dea4e08f","success":1},{"file_name":"thesis.zip","access_level":"closed","content_type":"application/x-zip-compressed","file_size":37847025,"creator":"cchlebak","relation":"source_file","file_id":"13196","date_updated":"2023-07-06T11:35:15Z","date_created":"2023-07-06T11:35:15Z","checksum":"c3b45317ae58e0527533f98c202d81b7"}],"oa_version":"Published Version","_id":"13175","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["537","535","539"],"status":"public","title":"Cavity quantum electrooptics","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"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2023-05-05T00:00:00Z","citation":{"chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13175.","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.","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.","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:13175"},"page":"202","day":"05","article_processing_charge":"No","has_accepted_license":"1","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"]},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. "}],"title":"Cavity quantum electrooptics","status":"public","ddc":["537","535","539"],"_id":"12900","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_size":36767177,"content_type":"application/x-zip-compressed","creator":"rsahu","access_level":"closed","embargo_to":"open_access","file_name":"thesis.zip","checksum":"8cbdab9c37ee55e591092a6f66b272c4","date_created":"2023-05-09T08:45:14Z","date_updated":"2023-06-06T22:30:03Z","relation":"source_file","file_id":"12928"},{"file_id":"12929","relation":"main_file","date_updated":"2023-07-06T11:37:40Z","date_created":"2023-05-09T08:51:17Z","checksum":"439659ead46618147309be39d9dd5a8c","file_name":"thesis_pdfa_final.pdf","access_level":"closed","creator":"rsahu","file_size":17501990,"content_type":"application/pdf"}],"oa_version":"Published Version","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"article_processing_charge":"No","has_accepted_license":"1","day":"05","page":"190","citation":{"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:12900","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:12900","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12900.","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:12900."},"date_published":"2023-05-05T00:00:00Z","ec_funded":1,"file_date_updated":"2023-07-06T11:37:40Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"publication_status":"published","year":"2023","date_updated":"2023-08-24T11:16:35Z","date_created":"2023-05-05T11:08:50Z","related_material":{"record":[{"relation":"new_edition","status":"public","id":"13175"},{"relation":"part_of_dissertation","status":"public","id":"10924"},{"relation":"part_of_dissertation","status":"public","id":"9114"}]},"author":[{"full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","first_name":"Rishabh","last_name":"Sahu"}],"publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-030-5"]},"month":"05","project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354","call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"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)"},"language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"supervisor":[{"full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/at:ista:12900"},{"date_published":"2023-06-26T00:00:00Z","citation":{"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.","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.","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.","apa":"Lechner, M., Zikelic, D., Chatterjee, K., Henzinger, T. A., & Rus, D. (2023). Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. In Proceedings of the 37th AAAI Conference on Artificial Intelligence (Vol. 37, pp. 14964–14973). Washington, DC, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v37i12.26747","ieee":"M. Lechner, D. Zikelic, K. Chatterjee, T. A. Henzinger, and D. Rus, “Quantization-aware interval bound propagation for training certifiably robust quantized neural networks,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence, Washington, DC, United States, 2023, vol. 37, no. 12, pp. 14964–14973.","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.","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"},"publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","page":"14964-14973","article_processing_charge":"No","day":"26","scopus_import":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14242","intvolume":" 37","title":"Quantization-aware interval bound propagation for training certifiably robust quantized neural networks","status":"public","issue":"12","abstract":[{"lang":"eng","text":"We study the problem of training and certifying adversarially robust quantized neural networks (QNNs). Quantization is a technique for making neural networks more efficient by running them using low-bit integer arithmetic and is therefore commonly adopted in industry. Recent work has shown that floating-point neural networks that have been verified to be robust can become vulnerable to adversarial attacks after quantization, and certification of the quantized representation is necessary to guarantee robustness. In this work, we present quantization-aware interval bound propagation (QA-IBP), a novel method for training robust QNNs. Inspired by advances in robust learning of non-quantized networks, our training algorithm computes the gradient of an abstract representation of the actual network. Unlike existing approaches, our method can handle the discrete semantics of QNNs. Based on QA-IBP, we also develop a complete verification procedure for verifying the adversarial robustness of QNNs, which is guaranteed to terminate and produce a correct answer. Compared to existing approaches, the key advantage of our verification procedure is that it runs entirely on GPU or other accelerator devices. We demonstrate experimentally that our approach significantly outperforms existing methods and establish the new state-of-the-art for training and certifying the robustness of QNNs."}],"type":"conference","doi":"10.1609/aaai.v37i12.26747","conference":{"name":"AAAI: Conference on Artificial Intelligence","end_date":"2023-02-14","start_date":"2023-02-07","location":"Washington, DC, United States"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2211.16187"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.16187","open_access":"1"}],"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"},{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"quality_controlled":"1","publication_identifier":{"isbn":["9781577358800"]},"month":"06","author":[{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner"},{"full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"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":"Rus, Daniela","first_name":"Daniela","last_name":"Rus"}],"volume":37,"date_created":"2023-08-27T22:01:17Z","date_updated":"2023-09-05T07:06:14Z","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.","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Association for the Advancement of Artificial Intelligence","publication_status":"published","ec_funded":1},{"page":"5464-5471","publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","citation":{"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.","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","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.","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."},"date_published":"2023-06-27T00:00:00Z","scopus_import":"1","day":"27","article_processing_charge":"No","title":"Bidding graph games with partially-observable budgets","status":"public","intvolume":" 37","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14243","oa_version":"Published Version","type":"conference","abstract":[{"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.","lang":"eng"}],"issue":"5","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"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1609/aaai.v37i5.25679"}],"external_id":{"arxiv":["2211.13626"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2023-02-14","location":"Washington, DC, United States","start_date":"2023-02-07","name":"AAAI: Conference on Artificial Intelligence"},"doi":"10.1609/aaai.v37i5.25679","month":"06","publication_identifier":{"isbn":["9781577358800"]},"publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"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.","date_updated":"2023-09-05T08:37:00Z","date_created":"2023-08-27T22:01:18Z","volume":37,"author":[{"orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy","full_name":"Avni, Guy"},{"last_name":"Jecker","first_name":"Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","full_name":"Jecker, Ismael R"},{"full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde"}],"ec_funded":1},{"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"}],"type":"conference","oa_version":"Preprint","title":"Stealth shaper: Reflectivity optimization as surface stylization","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14241","article_processing_charge":"No","day":"23","scopus_import":"1","date_published":"2023-07-23T00:00:00Z","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.","mla":"Tojo, Kenji, et al. “Stealth Shaper: Reflectivity Optimization as Surface Stylization.” SIGGRAPH 2023 Conference Proceedings, 20, Association for Computing Machinery, 2023, doi:10.1145/3588432.3591542.","short":"K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH 2023 Conference Proceedings, Association for Computing Machinery, 2023.","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.","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","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.","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"},"publication":"SIGGRAPH 2023 Conference Proceedings","article_number":"20","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"},{"last_name":"Shamir","first_name":"Ariel","full_name":"Shamir, Ariel"},{"full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"full_name":"Umetani, Nobuyuki","first_name":"Nobuyuki","last_name":"Umetani"}],"department":[{"_id":"BeBi"}],"publisher":"Association for Computing Machinery","publication_status":"published","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","publication_identifier":{"isbn":["9798400701597"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1145/3588432.3591542","conference":{"location":"Los Angeles, CA, United States","start_date":"2023-08-06","end_date":"2023-08-10","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference"},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.05944"}],"oa":1,"external_id":{"arxiv":["2305.05944"]}},{"_id":"12562","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons","intvolume":" 129","oa_version":"None","type":"journal_article","abstract":[{"text":"Presynaptic inputs determine the pattern of activation of postsynaptic neurons in a neural circuit. Molecular and genetic pathways that regulate the selective formation of subsets of presynaptic inputs are largely unknown, despite significant understanding of the general process of synaptogenesis. In this study, we have begun to identify such factors using the spinal monosynaptic stretch reflex circuit as a model system. In this neuronal circuit, Ia proprioceptive afferents establish monosynaptic connections with spinal motor neurons that project to the same muscle (termed homonymous connections) or muscles with related or synergistic function. However, monosynaptic connections are not formed with motor neurons innervating muscles with antagonistic functions. The ETS transcription factor ER81 (also known as ETV1) is expressed by all proprioceptive afferents, but only a small set of motor neuron pools in the lumbar spinal cord of the mouse. Here we use conditional mouse genetic techniques to eliminate Er81 expression selectively from motor neurons. We find that ablation of Er81 in motor neurons reduces synaptic inputs from proprioceptive afferents conveying information from homonymous and synergistic muscles, with no change observed in the connectivity pattern from antagonistic proprioceptive afferents. In summary, these findings suggest a role for ER81 in defined motor neuron pools to control the assembly of specific presynaptic inputs and thereby influence the profile of activation of these motor neurons.","lang":"eng"}],"issue":"3","publication":"Journal of Neurophysiology","citation":{"ama":"Ladle DR, Hippenmeyer S. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 2023;129(3):501-512. doi:10.1152/jn.00172.2022","ista":"Ladle DR, Hippenmeyer S. 2023. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 129(3), 501–512.","apa":"Ladle, D. R., & Hippenmeyer, S. (2023). Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. American Physiological Society. https://doi.org/10.1152/jn.00172.2022","ieee":"D. R. Ladle and S. Hippenmeyer, “Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons,” Journal of Neurophysiology, vol. 129, no. 3. American Physiological Society, pp. 501–512, 2023.","mla":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal of Neurophysiology, vol. 129, no. 3, American Physiological Society, 2023, pp. 501–12, doi:10.1152/jn.00172.2022.","short":"D.R. Ladle, S. Hippenmeyer, Journal of Neurophysiology 129 (2023) 501–512.","chicago":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal of Neurophysiology. American Physiological Society, 2023. https://doi.org/10.1152/jn.00172.2022."},"article_type":"original","page":"501-512","date_published":"2023-03-01T00:00:00Z","keyword":["Physiology","General Neuroscience"],"day":"01","article_processing_charge":"No","acknowledgement":"The authors gratefully thank Dr. Silvia Arber, University of Basel and Friedrich Miescher Institute for Biomedical Research, for support and in whose lab the data were collected. For advice on statistical analysis, we thank Michael Bottomley from the Statistical Consulting Center, College of Science and Mathematics, Wright State University.","year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"American Physiological Society","author":[{"last_name":"Ladle","first_name":"David R.","full_name":"Ladle, David R."},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"date_updated":"2023-09-05T12:13:34Z","date_created":"2023-02-15T14:46:14Z","volume":129,"external_id":{"isi":["000957721600001"],"pmid":["36695533"]},"quality_controlled":"1","isi":1,"doi":"10.1152/jn.00172.2022","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["0022-3077"],"eissn":["1522-1598"]}},{"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"18","date_published":"2023-07-18T00:00:00Z","citation":{"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.","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.","short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification, Springer Nature, 2023, pp. 358–382.","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.","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","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.","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"},"publication":"Computer Aided Verification","page":"358–382","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."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Published Version","file":[{"creator":"dernst","file_size":647760,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_LNCS_CAV_HenzingerT.pdf","success":1,"checksum":"ccaf94bf7d658ba012c016e11869b54c","date_updated":"2023-07-31T08:11:20Z","date_created":"2023-07-31T08:11:20Z","file_id":"13327","relation":"main_file"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"13310","intvolume":" 13965","title":"Monitoring algorithmic fairness","ddc":["000"],"status":"public","publication_identifier":{"isbn":["9783031377020"],"eissn":["1611-3349"],"eisbn":["9783031377037"],"issn":["0302-9743"]},"month":"07","doi":"10.1007/978-3-031-37703-7_17","conference":{"end_date":"2023-07-22","location":"Paris, France","start_date":"2023-07-17","name":"CAV: Computer Aided Verification"},"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":["2305.15979"]},"oa":1,"project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"quality_controlled":"1","ec_funded":1,"file_date_updated":"2023-07-31T08:11:20Z","author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"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","last_name":"Kueffner","first_name":"Konstantin","orcid":"0000-0001-8974-2542","id":"8121a2d0-dc85-11ea-9058-af578f3b4515"},{"full_name":"Mallik, Kaushik","first_name":"Kaushik","last_name":"Mallik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","orcid":"0000-0001-9864-7475"}],"volume":13965,"date_updated":"2023-09-05T15:14:00Z","date_created":"2023-07-25T18:32:40Z","acknowledgement":"This work is supported by the European Research Council under Grant No.: ERC-2020-AdG101020093.","year":"2023","publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publication_status":"published"},{"related_material":{"record":[{"status":"public","relation":"other","id":"12115"}]},"author":[{"full_name":"Glajzer, Jacek","last_name":"Glajzer","first_name":"Jacek"},{"full_name":"Castillo-Tong, Dan Cacsire","last_name":"Castillo-Tong","first_name":"Dan Cacsire"},{"full_name":"Richter, Rolf","first_name":"Rolf","last_name":"Richter"},{"full_name":"Vergote, Ignace","last_name":"Vergote","first_name":"Ignace"},{"first_name":"Hagen","last_name":"Kulbe","full_name":"Kulbe, Hagen"},{"first_name":"Adriaan","last_name":"Vanderstichele","full_name":"Vanderstichele, Adriaan"},{"first_name":"Ilary","last_name":"Ruscito","full_name":"Ruscito, Ilary"},{"first_name":"Fabian","last_name":"Trillsch","full_name":"Trillsch, Fabian"},{"full_name":"Mustea, Alexander","last_name":"Mustea","first_name":"Alexander"},{"full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gourley","first_name":"Charlie","full_name":"Gourley, Charlie"},{"full_name":"Gabra, Hani","first_name":"Hani","last_name":"Gabra"},{"full_name":"Taube, Eliane T.","first_name":"Eliane T.","last_name":"Taube"},{"first_name":"Oliver","last_name":"Dorigo","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"},{"last_name":"Angelotti","first_name":"Timothy","full_name":"Angelotti, Timothy"},{"full_name":"Sehouli, Jalid","first_name":"Jalid","last_name":"Sehouli"},{"full_name":"Braicu, Elena Ioana","first_name":"Elena Ioana","last_name":"Braicu"}],"volume":30,"date_updated":"2023-09-05T15:18:37Z","date_created":"2023-01-16T09:44:36Z","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.","year":"2023","publisher":"Springer Nature","department":[{"_id":"JoDa"}],"publication_status":"published","file_date_updated":"2023-02-02T13:01:20Z","doi":"10.1245/s10434-022-12459-3","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"},"oa":1,"external_id":{"isi":["000852125500006"]},"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1534-4681"],"issn":["1068-9265"]},"month":"01","file":[{"file_size":365865,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_AnnalsSurgicalOncology_Glajzer.pdf","checksum":"36a1200e1011f4b2155a8041d0308f34","success":1,"date_created":"2023-02-02T13:01:20Z","date_updated":"2023-02-02T13:01:20Z","relation":"main_file","file_id":"12490"}],"oa_version":"Published Version","_id":"12205","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 30","status":"public","ddc":["610"],"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","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","date_published":"2023-01-01T00:00:00Z","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."},"publication":"Annals of Surgical Oncology","page":"35-45","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","keyword":["Oncology","Surgery"]},{"quality_controlled":"1","isi":1,"external_id":{"isi":["000879151800001"]},"main_file_link":[{"url":"https://doi.org/10.1245/s10434-022-12681-z","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1245/s10434-022-12681-z","month":"01","publication_identifier":{"issn":["1068-9265"],"eissn":["1534-4681"]},"publication_status":"published","department":[{"_id":"JoDa"}],"publisher":"Springer Nature","acknowledgement":"This work was supported by European Commission’s Seventh Framework Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).","year":"2023","date_created":"2023-01-12T11:56:22Z","date_updated":"2023-09-05T15:18:36Z","volume":30,"author":[{"last_name":"Glajzer","first_name":"Jacek","full_name":"Glajzer, Jacek"},{"first_name":"Dan Cacsire","last_name":"Castillo-Tong","full_name":"Castillo-Tong, Dan Cacsire"},{"full_name":"Richter, Rolf","first_name":"Rolf","last_name":"Richter"},{"first_name":"Ignace","last_name":"Vergote","full_name":"Vergote, Ignace"},{"full_name":"Kulbe, Hagen","last_name":"Kulbe","first_name":"Hagen"},{"first_name":"Adriaan","last_name":"Vanderstichele","full_name":"Vanderstichele, Adriaan"},{"first_name":"Ilary","last_name":"Ruscito","full_name":"Ruscito, Ilary"},{"first_name":"Fabian","last_name":"Trillsch","full_name":"Trillsch, Fabian"},{"full_name":"Mustea, Alexander","first_name":"Alexander","last_name":"Mustea"},{"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"},{"last_name":"Gabra","first_name":"Hani","full_name":"Gabra, Hani"},{"first_name":"Eliane T.","last_name":"Taube","full_name":"Taube, Eliane T."},{"last_name":"Dorigo","first_name":"Oliver","full_name":"Dorigo, Oliver"},{"full_name":"Horst, David","first_name":"David","last_name":"Horst"},{"first_name":"Carlotta","last_name":"Keunecke","full_name":"Keunecke, Carlotta"},{"first_name":"Joanna","last_name":"Baum","full_name":"Baum, Joanna"},{"full_name":"Angelotti, Timothy","first_name":"Timothy","last_name":"Angelotti"},{"full_name":"Sehouli, Jalid","first_name":"Jalid","last_name":"Sehouli"},{"last_name":"Braicu","first_name":"Elena Ioana","full_name":"Braicu, Elena Ioana"}],"related_material":{"record":[{"id":"12205","status":"public","relation":"other"}]},"article_type":"original","page":"46-47","publication":"Annals of Surgical Oncology","citation":{"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.","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.","ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:46-47. doi:10.1245/s10434-022-12681-z","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12681-z","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."},"date_published":"2023-01-01T00:00:00Z","keyword":["Oncology","Surgery"],"scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium","intvolume":" 30","_id":"12115","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","type":"journal_article"},{"department":[{"_id":"RySh"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"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.).","year":"2023","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."},{"last_name":"Ribeiro-Silva","first_name":"Luisa","full_name":"Ribeiro-Silva, Luisa"},{"full_name":"Kirmiz, Michael","last_name":"Kirmiz","first_name":"Michael"},{"last_name":"Van Der List","first_name":"Deborah","full_name":"Van Der List, Deborah"},{"orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","first_name":"Pradeep","full_name":"Bhandari, Pradeep"},{"first_name":"Olivia A.","last_name":"Mack","full_name":"Mack, Olivia A."},{"first_name":"James","last_name":"Carroll","full_name":"Carroll, James"},{"full_name":"Le Monnier, Elodie","first_name":"Elodie","last_name":"Le Monnier","id":"3B59276A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aicher, Sue A.","last_name":"Aicher","first_name":"Sue A."},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"first_name":"James S.","last_name":"Trimmer","full_name":"Trimmer, James S."}],"article_number":"5231","file_date_updated":"2023-09-06T06:50:07Z","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,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-40930-6","publication_identifier":{"eissn":["2041-1723"]},"month":"08","intvolume":" 14","title":"Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling","ddc":["570"],"status":"public","_id":"14253","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"14270","relation":"main_file","date_created":"2023-09-06T06:50:07Z","date_updated":"2023-09-06T06:50:07Z","success":1,"checksum":"6ab8aab4e957f626a09a1c73db3388fb","file_name":"2023_NatureComm_Vierra.pdf","access_level":"open_access","creator":"dernst","file_size":9412549,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","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."}],"article_type":"original","citation":{"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","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.","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","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.","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).","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.","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."},"publication":"Nature Communications","date_published":"2023-08-26T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"26"},{"type":"conference","alternative_title":["LNCS"],"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"}],"_id":"14259","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"title":"Guessing winning policies in LTL synthesis by semantic learning","status":"public","intvolume":" 13964","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":428354,"access_level":"open_access","file_name":"2023_LNCS_CAV_Kretinsky.pdf","success":1,"checksum":"ed66278b61bb869e1baba3d9b9081271","date_updated":"2023-09-06T08:25:50Z","date_created":"2023-09-06T08:25:50Z","file_id":"14276","relation":"main_file"}],"scopus_import":"1","day":"17","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","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.","short":"J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414.","mla":"Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” 35th International Conference on Computer Aided Verification , vol. 13964, Springer Nature, 2023, pp. 390–414, doi:10.1007/978-3-031-37706-8_20.","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","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.","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.","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"},"page":"390-414","date_published":"2023-07-17T00:00:00Z","file_date_updated":"2023-09-06T08:25:50Z","year":"2023","acknowledgement":"This research was funded in part by the German Research Foundation (DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","author":[{"full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky"},{"full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","first_name":"Tobias","last_name":"Meggendorfer"},{"last_name":"Prokop","first_name":"Maximilian","full_name":"Prokop, Maximilian"},{"first_name":"Sabine","last_name":"Rieder","full_name":"Rieder, Sabine"}],"date_updated":"2023-09-06T08:27:33Z","date_created":"2023-09-03T22:01:16Z","volume":13964,"month":"07","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377051"]},"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","conference":{"name":"CAV: Computer Aided Verification","end_date":"2023-07-22","location":"Paris, France","start_date":"2023-07-17"},"doi":"10.1007/978-3-031-37706-8_20","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"doi":"10.1051/0004-6361/202346832","isi":1,"quality_controlled":"1","external_id":{"isi":["001046037700007"],"arxiv":["2306.11587"]},"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":"08","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"date_updated":"2023-09-06T11:05:58Z","date_created":"2023-09-03T22:01:15Z","volume":676,"author":[{"full_name":"Mathis, S.","first_name":"S.","last_name":"Mathis"},{"id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","last_name":"Bugnet","full_name":"Bugnet, Lisa Annabelle"}],"publication_status":"published","department":[{"_id":"LiBu"}],"publisher":"EDP Sciences","acknowledgement":"The authors are grateful to the referee for her/his detailed and constructive report, which has allowed us to improve our article. S. M. acknowledges support from the CNES GOLF-SOHO and PLATO grants at CEA/DAp and PNPS (CNRS/INSU). We thank R. A. Garcia for fruitful discussions and suggestions.","year":"2023","file_date_updated":"2023-09-06T07:13:19Z","article_number":"L9","date_published":"2023-08-01T00:00:00Z","article_type":"letter_note","publication":"Astronomy and Astrophysics","citation":{"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","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","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.","short":"S. Mathis, L.A. Bugnet, Astronomy and Astrophysics 676 (2023).","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.","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."},"day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2023_AstronomyAstrophysics_Mathis.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":458120,"file_id":"14271","relation":"main_file","date_created":"2023-09-06T07:13:19Z","date_updated":"2023-09-06T07:13:19Z","success":1,"checksum":"7b30d26fb2b7bcb5b5be1414950615f9"}],"title":"Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields","status":"public","ddc":["520"],"intvolume":" 676","_id":"14256","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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"},{"volume":14,"date_updated":"2023-09-06T11:04:31Z","date_created":"2023-09-03T22:01:16Z","author":[{"first_name":"Jakob","last_name":"Gamper","full_name":"Gamper, Jakob"},{"first_name":"Florian","last_name":"Kluibenschedl","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","full_name":"Kluibenschedl, Florian"},{"first_name":"Alexander K.H.","last_name":"Weiss","full_name":"Weiss, Alexander K.H."},{"last_name":"Hofer","first_name":"Thomas S.","full_name":"Hofer, Thomas S."}],"department":[{"_id":"GradSch"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"acknowledgement":"Financial supports for this work via a PhD scholarship for J. Gamper issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike Tanzer) are gratefully acknowledged. The computational results presented have been achieved (in part) using the HPC infrastructure of the University of Innsbruck.","year":"2023","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"},"oa":1,"external_id":{"isi":["001048165800001"],"pmid":["37566743"]},"publication_identifier":{"eissn":["1948-7185"]},"month":"08","oa_version":"Published Version","file":[{"file_size":4986859,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_JourPhysChemistry_Gamper.pdf","checksum":"637454e2b3a357498d8d622d241c4bf6","success":1,"date_updated":"2023-09-06T07:32:39Z","date_created":"2023-09-06T07:32:39Z","relation":"main_file","file_id":"14272"}],"intvolume":" 14","status":"public","ddc":["530","540"],"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","_id":"14261","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"33","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2023-08-11T00:00:00Z","page":"7395-7403","article_type":"original","citation":{"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.","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.","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","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.","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","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."},"publication":"Journal of Physical Chemistry Letters","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"11","scopus_import":"1"},{"type":"journal_article","issue":"1","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."}],"intvolume":" 1","status":"public","ddc":["570"],"title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","_id":"14277","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_PRXLife_Boocock.pdf","creator":"dernst","file_size":2559520,"content_type":"application/pdf","file_id":"14335","relation":"main_file","success":1,"checksum":"f881d98c89eb9f1aa136d7b781511553","date_created":"2023-09-15T06:30:50Z","date_updated":"2023-09-15T06:30:50Z"}],"article_processing_charge":"Yes","has_accepted_license":"1","day":"20","article_type":"original","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)."},"publication":"PRX Life","date_published":"2023-07-20T00:00:00Z","article_number":"013001","ec_funded":1,"file_date_updated":"2023-09-15T06:30:50Z","department":[{"_id":"EdHa"}],"publisher":"American Physical Society","publication_status":"published","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","volume":1,"date_updated":"2023-09-15T06:39:17Z","date_created":"2023-09-06T08:30:59Z","author":[{"full_name":"Boocock, Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1585-2631","first_name":"Daniel R","last_name":"Boocock"},{"full_name":"Hirashima, Tsuyoshi","first_name":"Tsuyoshi","last_name":"Hirashima"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2835-8279"]},"month":"07","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-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":"10.1103/prxlife.1.013001"},{"publication_identifier":{"eissn":["2211-1247"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2023.113015","project":[{"name":"Inter-and intracellular signalling in schizophrenia","call_identifier":"FP7","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","grant_number":"607616"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37632747"]},"ec_funded":1,"file_date_updated":"2023-09-15T07:12:46Z","article_number":"113015","volume":42,"date_created":"2023-09-10T22:01:11Z","date_updated":"2023-09-15T07:14:12Z","author":[{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","first_name":"Michele","last_name":"Nardin","full_name":"Nardin, Michele"},{"full_name":"Käfer, Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola","last_name":"Käfer"},{"full_name":"Stella, Federico","first_name":"Federico","last_name":"Stella","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9439-3148"},{"first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"publisher":"Elsevier","department":[{"_id":"JoCs"}],"publication_status":"published","pmid":1,"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).","article_processing_charge":"Yes","has_accepted_license":"1","day":"26","scopus_import":"1","date_published":"2023-09-26T00:00:00Z","article_type":"original","citation":{"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","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.","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."},"publication":"Cell Reports","issue":"9","abstract":[{"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.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2023_CellPress_Nardin.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4879455,"creator":"dernst","relation":"main_file","file_id":"14337","date_updated":"2023-09-15T07:12:46Z","date_created":"2023-09-15T07:12:46Z","checksum":"ca77a304fb813c292550b8604b0fb41d","success":1}],"oa_version":"Published Version","intvolume":" 42","title":"Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions","ddc":["570"],"status":"public","_id":"14314","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_processing_charge":"Yes","has_accepted_license":"1","day":"04","scopus_import":"1","date_published":"2023-09-04T00:00:00Z","article_type":"original","citation":{"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.","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).","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.","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"},"publication":"eLife","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","oa_version":"Published Version","file":[{"date_created":"2023-09-15T06:59:10Z","date_updated":"2023-09-15T06:59:10Z","checksum":"db24bf3d595507387b48d3799c33e289","success":1,"relation":"main_file","file_id":"14336","content_type":"application/pdf","file_size":3703097,"creator":"dernst","file_name":"2023_eLife_Cho.pdf","access_level":"open_access"}],"intvolume":" 12","ddc":["570"],"status":"public","title":"Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress","_id":"14315","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2050-084X"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.7554/eLife.89066","quality_controlled":"1","external_id":{"pmid":["37665327"]},"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":"2023-09-15T06:59:10Z","article_number":"RP89066","volume":12,"date_updated":"2023-09-15T07:07:10Z","date_created":"2023-09-10T22:01:11Z","author":[{"full_name":"Cho, Ukrae H.","last_name":"Cho","first_name":"Ukrae H."},{"full_name":"Hetzer, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","first_name":"Martin W","last_name":"Hetzer"}],"publisher":"eLife Sciences Publications","department":[{"_id":"MaHe"}],"publication_status":"published","pmid":1,"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"},{"department":[{"_id":"MaKw"}],"publisher":"Electronic Journal of Combinatorics","publication_status":"published","year":"2023","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).","volume":30,"date_created":"2023-09-10T22:01:12Z","date_updated":"2023-09-15T08:12:30Z","author":[{"full_name":"Anastos, Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","last_name":"Anastos","first_name":"Michael"},{"first_name":"David","last_name":"Fabian","full_name":"Fabian, David"},{"full_name":"Müyesser, Alp","last_name":"Müyesser","first_name":"Alp"},{"full_name":"Szabó, Tibor","last_name":"Szabó","first_name":"Tibor"}],"article_number":"P3.10","license":"https://creativecommons.org/licenses/by-nd/4.0/","ec_funded":1,"file_date_updated":"2023-09-15T08:02:09Z","project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"quality_controlled":"1","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"},"oa":1,"external_id":{"arxiv":["2212.03100"]},"language":[{"iso":"eng"}],"doi":"10.37236/11714","publication_identifier":{"eissn":["1077-8926"]},"month":"07","intvolume":" 30","ddc":["510"],"title":"Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets","status":"public","_id":"14319","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"14338","checksum":"52c46c8cb329f9aaee9ade01525f317b","success":1,"date_created":"2023-09-15T08:02:09Z","date_updated":"2023-09-15T08:02:09Z","access_level":"open_access","file_name":"2023_elecJournCombinatorics_Anastos.pdf","content_type":"application/pdf","file_size":247917,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","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."}],"article_type":"original","citation":{"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.","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.","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","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."},"publication":"Electronic Journal of Combinatorics","date_published":"2023-07-28T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"28"},{"oa_version":"Published Version","file":[{"creator":"dernst","file_size":624647,"content_type":"application/pdf","file_name":"2023_LNCS_Sun.pdf","access_level":"open_access","date_updated":"2023-09-20T08:24:47Z","date_created":"2023-09-20T08:24:47Z","success":1,"checksum":"42917e086f8c7699f3bccf84f74fe000","file_id":"14348","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14318","title":"Automated tail bound analysis for probabilistic recurrence relations","status":"public","ddc":["000"],"intvolume":" 13966","abstract":[{"lang":"eng","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."}],"type":"conference","alternative_title":["LNCS"],"date_published":"2023-07-17T00:00:00Z","publication":"Computer Aided Verification","citation":{"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.","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.","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.","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"},"page":"16-39","day":"17","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","author":[{"first_name":"Yican","last_name":"Sun","full_name":"Sun, Yican"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/boyvolcano/PRR"}]},"date_created":"2023-09-10T22:01:12Z","date_updated":"2023-09-20T08:25:57Z","volume":13966,"year":"2023","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.","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"file_date_updated":"2023-09-20T08:24:47Z","ec_funded":1,"conference":{"name":"CAV: Computer Aided Verification","end_date":"2023-07-22","start_date":"2023-07-17","location":"Paris, France"},"doi":"10.1007/978-3-031-37709-9_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,"quality_controlled":"1","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"month":"07","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377082"]}},{"publication_identifier":{"issn":["0302-9743"],"isbn":["9783031377082"],"eissn":["1611-3349"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-37709-9_5","conference":{"end_date":"2023-07-22","location":"Paris, France","start_date":"2023-07-17","name":"CAV: Computer Aided Verification"},"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"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,"ec_funded":1,"file_date_updated":"2023-09-20T08:46:43Z","volume":13966,"date_created":"2023-09-10T22:01:12Z","date_updated":"2023-09-20T09:04:40Z","author":[{"full_name":"Akshay, S.","last_name":"Akshay","first_name":"S."},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Meggendorfer","first_name":"Tobias","orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias"},{"last_name":"Zikelic","first_name":"Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde"}],"publisher":"Springer Nature","department":[{"_id":"KrCh"}],"publication_status":"published","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.","year":"2023","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"17","scopus_import":"1","date_published":"2023-07-17T00:00:00Z","page":"86-112","citation":{"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","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."},"publication":"International Conference on Computer Aided Verification","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."}],"alternative_title":["LNCS"],"type":"conference","file":[{"file_name":"2023_LNCS_Akshay.pdf","access_level":"open_access","creator":"dernst","file_size":531745,"content_type":"application/pdf","file_id":"14349","relation":"main_file","date_updated":"2023-09-20T08:46:43Z","date_created":"2023-09-20T08:46:43Z","success":1,"checksum":"f143c8eedf609f20f2aad2eeb496d53f"}],"oa_version":"Published Version","intvolume":" 13966","title":"MDPs as distribution transformers: Affine invariant synthesis for safety objectives","ddc":["000"],"status":"public","_id":"14317","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14316","intvolume":" 136","status":"public","title":"Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway","oa_version":"Preprint","type":"journal_article","issue":"17","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."}],"citation":{"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.","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."},"publication":"Journal of Cell Science","article_type":"original","date_published":"2023-09-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","pmid":1,"year":"2023","publisher":"The Company of Biologists","department":[{"_id":"DaSi"}],"publication_status":"published","author":[{"full_name":"Nagano, Makoto","first_name":"Makoto","last_name":"Nagano"},{"last_name":"Aoshima","first_name":"Kaito","full_name":"Aoshima, Kaito"},{"full_name":"Shimamura, Hiroki","last_name":"Shimamura","first_name":"Hiroki"},{"full_name":"Siekhaus, Daria E","first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353"},{"full_name":"Toshima, Junko Y.","first_name":"Junko Y.","last_name":"Toshima"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"volume":136,"date_created":"2023-09-10T22:01:12Z","date_updated":"2023-09-20T09:14:15Z","article_number":"jcs261448","oa":1,"external_id":{"pmid":["37539494"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.03.27.534325"}],"quality_controlled":"1","doi":"10.1242/jcs.261448","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"month":"09"},{"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1103/physrevb.108.125411","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2210.06310","open_access":"1"}],"external_id":{"arxiv":["2210.06310"]},"article_number":"125411","volume":108,"date_created":"2023-09-12T07:12:12Z","date_updated":"2023-09-20T09:38:24Z","author":[{"last_name":"Henderson","first_name":"Paul M","orcid":"0000-0002-5198-7445","id":"13C09E74-18D9-11E9-8878-32CFE5697425","full_name":"Henderson, Paul M"},{"orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg","full_name":"Ghazaryan, Areg"},{"last_name":"Zibrov","first_name":"Alexander A.","full_name":"Zibrov, Alexander A."},{"full_name":"Young, Andrea F.","first_name":"Andrea F.","last_name":"Young"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym"}],"department":[{"_id":"MaSe"},{"_id":"ChLa"},{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","year":"2023","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.","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2023-09-15T00:00:00Z","article_type":"original","citation":{"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","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."},"publication":"Physical Review B","issue":"12","abstract":[{"lang":"eng","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."}],"type":"journal_article","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"},{"file_date_updated":"2023-03-23T16:43:14Z","ec_funded":1,"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"},{"status":"public","relation":"part_of_dissertation","id":"8308"},{"id":"11469","status":"public","relation":"part_of_dissertation"},{"id":"12750","status":"public","relation":"part_of_dissertation"}]},"date_created":"2023-03-17T13:30:48Z","date_updated":"2023-09-20T10:44:12Z","year":"2023","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"publisher":"Institute of Science and Technology Austria","month":"03","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:12732","acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"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)"},"project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"abstract":[{"lang":"eng","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."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"date_created":"2023-03-23T16:42:56Z","date_updated":"2023-03-23T16:42:56Z","checksum":"5d2de651ef9449c1b8dc27148ca74777","file_id":"12753","relation":"source_file","creator":"pbrighi","content_type":"application/zip","file_size":42167561,"file_name":"Thesis_sub_PBrighi.zip","access_level":"closed"},{"relation":"main_file","file_id":"12754","checksum":"7caa153d4a5b0873a79358787d2dfe1e","success":1,"date_created":"2023-03-23T16:43:14Z","date_updated":"2023-03-23T16:43:14Z","access_level":"open_access","file_name":"Thesis_PBrighi.pdf","file_size":13977000,"content_type":"application/pdf","creator":"pbrighi"}],"oa_version":"None","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12732","status":"public","title":"Ergodicity breaking in disordered and kinetically constrained quantum many-body systems","ddc":["530"],"day":"21","has_accepted_license":"1","article_processing_charge":"No","date_published":"2023-03-21T00:00:00Z","citation":{"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.","ama":"Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:10.15479/at:ista:12732","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.","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."},"page":"158"},{"doi":"10.21468/scipostphys.15.3.093","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":{"arxiv":["2210.15607"]},"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"quality_controlled":"1","publication_identifier":{"issn":["2542-4653"]},"month":"09","related_material":{"record":[{"id":"12750","relation":"earlier_version","status":"public"}]},"author":[{"orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi","first_name":"Pietro","full_name":"Brighi, Pietro"},{"last_name":"Ljubotina","first_name":"Marko","orcid":"0000-0003-0038-7068","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","full_name":"Ljubotina, Marko"},{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}],"volume":15,"date_created":"2023-09-14T13:08:23Z","date_updated":"2023-09-20T10:46:29Z","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).","publisher":"SciPost Foundation","department":[{"_id":"MaSe"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2023-09-20T10:46:10Z","article_number":"093","date_published":"2023-09-13T00:00:00Z","citation":{"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.","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.","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","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.","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.","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"},"publication":"SciPost Physics","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"13","keyword":["General Physics and Astronomy"],"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_updated":"2023-09-20T10:46:10Z","date_created":"2023-09-20T10:46:10Z"}],"oa_version":"Published Version","_id":"14334","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 15","title":"Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models","ddc":["530"],"status":"public","issue":"3","abstract":[{"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.","lang":"eng"}],"type":"journal_article"},{"article_type":"original","publication":"The Journal of Chemical Physics","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","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","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.","short":"R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical Physics 159 (2023).","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.","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."},"date_published":"2023-09-11T00:00:00Z","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"scopus_import":"1","day":"11","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","ddc":["530"],"title":"Achiral dipoles on a ferromagnet can affect its magnetization direction","status":"public","intvolume":" 159","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14321","file":[{"content_type":"application/pdf","file_size":5749653,"creator":"acappell","access_level":"open_access","file_name":"104103_1_5.0165806.pdf","checksum":"507ab65ab29e2c987c94cabad7c5370b","success":1,"date_created":"2023-09-13T09:34:20Z","date_updated":"2023-09-13T09:34:20Z","relation":"main_file","file_id":"14322"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"10","quality_controlled":"1","project":[{"_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338","grant_number":"101062862","name":"Non-equilibrium Field Theory of Molecular Rotations"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"external_id":{"pmid":["37694742"],"arxiv":["2306.17592"]},"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":"10.1063/5.0165806","month":"09","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"AIP Publishing","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.","pmid":1,"date_created":"2023-09-13T09:25:09Z","date_updated":"2023-09-20T09:48:12Z","volume":159,"author":[{"full_name":"Al Hyder, Ragheed","first_name":"Ragheed","last_name":"Al Hyder","id":"d1c405be-ae15-11ed-8510-ccf53278162e"},{"orcid":"0000-0001-6110-2359","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro","first_name":"Alberto","full_name":"Cappellaro, Alberto"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}],"article_number":"104103","file_date_updated":"2023-09-13T09:34:20Z","ec_funded":1},{"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,"publication_identifier":{"issn":["0003-6951"]},"month":"08","volume":123,"date_updated":"2023-09-20T11:50:06Z","date_created":"2023-09-17T22:01:09Z","author":[{"full_name":"Lorenc, Dusan","last_name":"Lorenc","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","first_name":"Zhanybek","full_name":"Alpichshev, Zhanybek"}],"department":[{"_id":"ZhAl"}],"publisher":"AIP Publishing","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.","file_date_updated":"2023-09-20T11:36:16Z","article_number":"091104","date_published":"2023-08-28T00:00:00Z","article_type":"original","citation":{"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.","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."},"publication":"Applied Physics Letters","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"28","scopus_import":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1486715,"creator":"dernst","access_level":"open_access","file_name":"2023_ApplPhysLetter_Lorenc.pdf","checksum":"89a1b604d58b209fec66c6b6f919ac98","success":1,"date_updated":"2023-09-20T11:36:16Z","date_created":"2023-09-20T11:36:16Z","relation":"main_file","file_id":"14353"}],"intvolume":" 123","ddc":["530"],"status":"public","title":"Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14342","issue":"9","abstract":[{"lang":"eng","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."}],"type":"journal_article"},{"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"month":"09","project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"},{"name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","call_identifier":"FWF","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","grant_number":"I04188"}],"quality_controlled":"1","external_id":{"pmid":["37673988"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"doi":"10.1038/s41586-023-06399-5","publisher":"Springer Nature","department":[{"_id":"BjHo"}],"publication_status":"published","pmid":1,"acknowledgement":"We acknowledge the assistance of the Miba machine shop and the team of the ISTA-HPC cluster. We thank M. Quadrio for the discussions. The work was supported by the Simons Foundation (grant no. 662960) and by the Austrian Science Fund (grant no. I4188-N30), within Deutsche Forschungsgemeinschaft research unit FOR 2688.","year":"2023","volume":621,"date_updated":"2023-09-20T12:10:22Z","date_created":"2023-09-17T22:01:09Z","related_material":{"link":[{"url":"https://www.ista.ac.at/en/news/pumping-like-the-heart/","relation":"press_release","description":"News on ISTA website"}]},"author":[{"first_name":"Davide","last_name":"Scarselli","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271","full_name":"Scarselli, Davide"},{"last_name":"Lopez Alonso","first_name":"Jose M","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Alonso, Jose M"},{"first_name":"Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"scopus_import":"1","article_processing_charge":"No","day":"07","page":"71-74","article_type":"original","citation":{"ama":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. 2023;621(7977):71-74. doi:10.1038/s41586-023-06399-5","ieee":"D. Scarselli, J. M. Lopez Alonso, A. Varshney, and B. Hof, “Turbulence suppression by cardiac-cycle-inspired driving of pipe flow,” Nature, vol. 621, no. 7977. Springer Nature, pp. 71–74, 2023.","apa":"Scarselli, D., Lopez Alonso, J. M., Varshney, A., & Hof, B. (2023). Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06399-5","ista":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. 2023. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. 621(7977), 71–74.","short":"D. Scarselli, J.M. Lopez Alonso, A. Varshney, B. Hof, Nature 621 (2023) 71–74.","mla":"Scarselli, Davide, et al. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” Nature, vol. 621, no. 7977, Springer Nature, 2023, pp. 71–74, doi:10.1038/s41586-023-06399-5.","chicago":"Scarselli, Davide, Jose M Lopez Alonso, Atul Varshney, and Björn Hof. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06399-5."},"publication":"Nature","date_published":"2023-09-07T00:00:00Z","type":"journal_article","issue":"7977","abstract":[{"lang":"eng","text":"Flows through pipes and channels are, in practice, almost always turbulent, and the multiscale eddying motion is responsible for a major part of the encountered friction losses and pumping costs1. Conversely, for pulsatile flows, in particular for aortic blood flow, turbulence levels remain low despite relatively large peak velocities. For aortic blood flow, high turbulence levels are intolerable as they would damage the shear-sensitive endothelial cell layer2,3,4,5. Here we show that turbulence in ordinary pipe flow is diminished if the flow is driven in a pulsatile mode that incorporates all the key features of the cardiac waveform. At Reynolds numbers comparable to those of aortic blood flow, turbulence is largely inhibited, whereas at much higher speeds, the turbulent drag is reduced by more than 25%. This specific operation mode is more efficient when compared with steady driving, which is the present situation for virtually all fluid transport processes ranging from heating circuits to water, gas and oil pipelines."}],"intvolume":" 621","title":"Turbulence suppression by cardiac-cycle-inspired driving of pipe flow","status":"public","_id":"14341","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None"},{"oa_version":"Published Version","file":[{"success":1,"checksum":"773a0197f05b67feaa6cb1e17ec3642d","date_updated":"2023-08-07T11:55:43Z","date_created":"2023-08-07T11:55:43Z","file_id":"13982","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":715976,"access_level":"open_access","file_name":"2023_LIPIcS_Dvorak.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13120","intvolume":" 268","ddc":["000"],"status":"public","title":"Closure properties of general grammars - formally verified","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."}],"type":"conference","alternative_title":["LIPIcs"],"date_published":"2023-07-27T00:00:00Z","citation":{"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.","short":"M. Dvorak, J. Blanchette, in:, 14th International Conference on Interactive Theorem Proving, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","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.","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","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.","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"},"publication":"14th International Conference on Interactive Theorem Proving","article_processing_charge":"No","has_accepted_license":"1","day":"27","scopus_import":"1","related_material":{"link":[{"relation":"software","url":"https://github.com/madvorak/grammars/tree/publish"}]},"author":[{"orcid":"0000-0001-5293-214X","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","last_name":"Dvorak","first_name":"Martin","full_name":"Dvorak, Martin"},{"first_name":"Jasmin","last_name":"Blanchette","full_name":"Blanchette, Jasmin"}],"volume":268,"date_created":"2023-06-05T07:29:05Z","date_updated":"2023-09-25T11:04:29Z","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","file_date_updated":"2023-08-07T11:55:43Z","article_number":"15","doi":"10.4230/LIPIcs.ITP.2023.15","conference":{"end_date":"2023-08-04","start_date":"2023-07-31","location":"Bialystok, Poland","name":"ITP: International Conference on Interactive Theorem Proving"},"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":["2302.06420"]},"oa":1,"quality_controlled":"1","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772846"]},"month":"07"},{"ddc":["510"],"title":"Approximating the bundled crossing number","status":"public","intvolume":" 27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13969","file":[{"checksum":"9c30d2b8e324cc1c904f2aeec92013a3","success":1,"date_updated":"2023-08-07T08:00:48Z","date_created":"2023-08-07T08:00:48Z","relation":"main_file","file_id":"13979","content_type":"application/pdf","file_size":865774,"creator":"dernst","access_level":"open_access","file_name":"2023_JourGraphAlgorithms_Arroyo.pdf"}],"oa_version":"Published Version","type":"journal_article","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","article_type":"original","page":"433-457","publication":"Journal of Graph Algorithms and Applications","citation":{"ista":"Arroyo Guevara AM, Felsner S. 2023. Approximating the bundled crossing number. Journal of Graph Algorithms and Applications. 27(6), 433–457.","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","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.","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","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.","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.","short":"A.M. Arroyo Guevara, S. Felsner, Journal of Graph Algorithms and Applications 27 (2023) 433–457."},"date_published":"2023-07-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Brown University","year":"2023","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.","date_updated":"2023-09-25T10:56:10Z","date_created":"2023-08-06T22:01:11Z","volume":27,"author":[{"full_name":"Arroyo Guevara, Alan M","last_name":"Arroyo Guevara","first_name":"Alan M","orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Felsner","first_name":"Stefan","full_name":"Felsner, Stefan"}],"related_material":{"record":[{"id":"11185","status":"public","relation":"earlier_version"}]},"file_date_updated":"2023-08-07T08:00:48Z","ec_funded":1,"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"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"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7155/jgaa.00629","month":"07","publication_identifier":{"issn":["1526-1719"]}},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2023-01-01T00:00:00Z","page":"2286-2323","citation":{"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","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","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.","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."},"publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","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","oa_version":"Preprint","intvolume":" 2023","title":"Fast algorithms for solving the Hamilton cycle problem with high probability","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14344","publication_identifier":{"isbn":["9781611977554"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1137/1.9781611977554.ch88","conference":{"name":"SODA: Symposium on Discrete Algorithms","location":"Florence, Italy","start_date":"2023-01-22","end_date":"2023-01-25"},"quality_controlled":"1","external_id":{"arxiv":["2111.14759"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2111.14759"}],"volume":2023,"date_created":"2023-09-17T22:01:10Z","date_updated":"2023-09-25T09:13:41Z","author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","last_name":"Anastos","first_name":"Michael","full_name":"Anastos, Michael"}],"department":[{"_id":"MaKw"}],"publisher":"Society for Industrial and Applied Mathematics","publication_status":"published","year":"2023"},{"_id":"12710","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 35","ddc":["570"],"title":"Curvature in biological systems: Its quantification, emergence, and implications across the scales","status":"public","oa_version":"Published Version","file":[{"checksum":"5c04d68130e97a0ecd1ca27fbc15a246","success":1,"date_created":"2023-09-26T10:51:56Z","date_updated":"2023-09-26T10:51:56Z","relation":"main_file","file_id":"14373","file_size":2898063,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_AdvancedMaterials_Schamberger.pdf"}],"type":"journal_article","issue":"13","abstract":[{"lang":"eng","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."}],"citation":{"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","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.","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.","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","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).","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."},"publication":"Advanced Materials","article_type":"review","date_published":"2023-03-29T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"29","pmid":1,"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.","year":"2023","publisher":"Wiley","department":[{"_id":"EdHa"}],"publication_status":"published","author":[{"full_name":"Schamberger, Barbara","first_name":"Barbara","last_name":"Schamberger"},{"full_name":"Ziege, Ricardo","first_name":"Ricardo","last_name":"Ziege"},{"first_name":"Karine","last_name":"Anselme","full_name":"Anselme, Karine"},{"last_name":"Ben Amar","first_name":"Martine","full_name":"Ben Amar, Martine"},{"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","last_name":"Cipitria","first_name":"Amaia"},{"last_name":"Coles","first_name":"Rhoslyn A.","full_name":"Coles, Rhoslyn A."},{"first_name":"Rumiana","last_name":"Dimova","full_name":"Dimova, Rumiana"},{"first_name":"Michaela","last_name":"Eder","full_name":"Eder, Michaela"},{"full_name":"Ehrig, Sebastian","last_name":"Ehrig","first_name":"Sebastian"},{"first_name":"Luis M.","last_name":"Escudero","full_name":"Escudero, Luis M."},{"full_name":"Evans, Myfanwy E.","first_name":"Myfanwy E.","last_name":"Evans"},{"full_name":"Fernandes, Paulo R.","last_name":"Fernandes","first_name":"Paulo R."},{"full_name":"Fratzl, Peter","first_name":"Peter","last_name":"Fratzl"},{"last_name":"Geris","first_name":"Liesbet","full_name":"Geris, Liesbet"},{"first_name":"Notburga","last_name":"Gierlinger","full_name":"Gierlinger, Notburga"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"full_name":"Iglič, Aleš","first_name":"Aleš","last_name":"Iglič"},{"last_name":"Kirkensgaard","first_name":"Jacob J.K.","full_name":"Kirkensgaard, Jacob J.K."},{"full_name":"Kollmannsberger, Philip","first_name":"Philip","last_name":"Kollmannsberger"},{"last_name":"Kowalewska","first_name":"Łucja","full_name":"Kowalewska, Łucja"},{"first_name":"Nicholas A.","last_name":"Kurniawan","full_name":"Kurniawan, Nicholas A."},{"first_name":"Ioannis","last_name":"Papantoniou","full_name":"Papantoniou, Ioannis"},{"full_name":"Pieuchot, Laurent","first_name":"Laurent","last_name":"Pieuchot"},{"full_name":"Pires, Tiago H.V.","last_name":"Pires","first_name":"Tiago H.V."},{"last_name":"Renner","first_name":"Lars D.","full_name":"Renner, Lars D."},{"full_name":"Sageman-Furnas, Andrew O.","first_name":"Andrew O.","last_name":"Sageman-Furnas"},{"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"},{"full_name":"Tagua, Antonio","last_name":"Tagua","first_name":"Antonio"},{"first_name":"Caterina","last_name":"Tomba","full_name":"Tomba, Caterina"},{"full_name":"Trepat, Xavier","last_name":"Trepat","first_name":"Xavier"},{"first_name":"Sarah L.","last_name":"Waters","full_name":"Waters, Sarah L."},{"full_name":"Yeo, Edwina F.","last_name":"Yeo","first_name":"Edwina F."},{"last_name":"Roschger","first_name":"Andreas","full_name":"Roschger, Andreas"},{"full_name":"Bidan, Cécile M.","last_name":"Bidan","first_name":"Cécile M."},{"last_name":"Dunlop","first_name":"John W.C.","full_name":"Dunlop, John W.C."}],"volume":35,"date_updated":"2023-09-26T10:56:46Z","date_created":"2023-03-05T23:01:06Z","article_number":"2206110","file_date_updated":"2023-09-26T10:51:56Z","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":["36461812"],"isi":["000941068900001"]},"quality_controlled":"1","isi":1,"doi":"10.1002/adma.202206110","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"month":"03"},{"_id":"13340","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 381","title":"Disequilibrating azoarenes by visible-light sensitization under confinement","status":"public","oa_version":"Preprint","type":"journal_article","issue":"6664","abstract":[{"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.","lang":"eng"}],"citation":{"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.","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.","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.","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.","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","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.","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"},"publication":"Science","page":"1357-1363","article_type":"original","date_published":"2023-09-22T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"22","year":"2023","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.)].","publisher":"American Association for the Advancement of Science","department":[{"_id":"RaKl"}],"publication_status":"published","author":[{"full_name":"Gemen, Julius","last_name":"Gemen","first_name":"Julius"},{"full_name":"Church, Jonathan R.","first_name":"Jonathan R.","last_name":"Church"},{"last_name":"Ruoko","first_name":"Tero-Petri","full_name":"Ruoko, Tero-Petri"},{"full_name":"Durandin, Nikita","last_name":"Durandin","first_name":"Nikita"},{"last_name":"Białek","first_name":"Michał J.","full_name":"Białek, Michał J."},{"full_name":"Weissenfels, Maren","last_name":"Weissenfels","first_name":"Maren"},{"full_name":"Feller, Moran","first_name":"Moran","last_name":"Feller"},{"last_name":"Kazes","first_name":"Miri","full_name":"Kazes, Miri"},{"first_name":"Veniamin A.","last_name":"Borin","full_name":"Borin, Veniamin A."},{"first_name":"Magdalena","last_name":"Odaybat","full_name":"Odaybat, Magdalena"},{"full_name":"Kalepu, Rishir","last_name":"Kalepu","first_name":"Rishir"},{"full_name":"Diskin-Posner, Yael","last_name":"Diskin-Posner","first_name":"Yael"},{"full_name":"Oron, Dan","last_name":"Oron","first_name":"Dan"},{"last_name":"Fuchter","first_name":"Matthew J.","full_name":"Fuchter, Matthew J."},{"full_name":"Priimagi, Arri","last_name":"Priimagi","first_name":"Arri"},{"full_name":"Schapiro, Igor","last_name":"Schapiro","first_name":"Igor"},{"last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal"}],"volume":381,"date_updated":"2023-10-03T08:11:26Z","date_created":"2023-08-01T08:26:15Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv-2023-gq2h0"}],"oa":1,"quality_controlled":"1","doi":"10.1126/science.adh9059","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"]},"month":"09"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04810"}],"oa":1,"external_id":{"pmid":["36813705"],"isi":["000936943800002"],"arxiv":["2211.04810"]},"isi":1,"quality_controlled":"1","doi":"10.1063/5.0134271","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"month":"02","pmid":1,"year":"2023","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.","publisher":"American Institute of Physics","department":[{"_id":"AnSa"}],"publication_status":"published","author":[{"full_name":"Sorichetti, Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","orcid":"0000-0002-9645-6576","first_name":"Valerio","last_name":"Sorichetti"},{"full_name":"Ninarello, Andrea","last_name":"Ninarello","first_name":"Andrea"},{"first_name":"José","last_name":"Ruiz-Franco","full_name":"Ruiz-Franco, José"},{"full_name":"Hugouvieux, Virginie","first_name":"Virginie","last_name":"Hugouvieux"},{"first_name":"Emanuela","last_name":"Zaccarelli","full_name":"Zaccarelli, Emanuela"},{"first_name":"Cristian","last_name":"Micheletti","full_name":"Micheletti, Cristian"},{"full_name":"Kob, Walter","first_name":"Walter","last_name":"Kob"},{"first_name":"Lorenzo","last_name":"Rovigatti","full_name":"Rovigatti, Lorenzo"}],"volume":158,"date_created":"2023-03-05T23:01:05Z","date_updated":"2023-10-03T11:31:51Z","article_number":"074905","citation":{"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.","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","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.","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)."},"publication":"Journal of Chemical Physics","article_type":"original","date_published":"2023-02-21T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"21","_id":"12705","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 158","status":"public","title":"Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks","oa_version":"Preprint","type":"journal_article","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"}]},{"article_processing_charge":"No","day":"08","scopus_import":"1","date_published":"2023-03-08T00:00:00Z","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."},"publication":"Formal Methods in System Design","article_type":"original","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Published Version","_id":"12738","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"status":"public","title":"Stochastic games with lexicographic objectives","publication_identifier":{"eissn":["1572-8102"]},"month":"03","doi":"10.1007/s10703-023-00411-4","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"},"main_file_link":[{"url":"https://doi.org/10.1007/s10703-023-00411-4","open_access":"1"}],"oa":1,"external_id":{"isi":["000946174300001"]},"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1","isi":1,"ec_funded":1,"related_material":{"record":[{"id":"8272","status":"public","relation":"earlier_version"}]},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Katoen","first_name":"Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","full_name":"Katoen, Joost P"},{"last_name":"Mohr","first_name":"Stefanie","full_name":"Mohr, Stefanie"},{"full_name":"Weininger, Maximilian","first_name":"Maximilian","last_name":"Weininger"},{"full_name":"Winkler, Tobias","first_name":"Tobias","last_name":"Winkler"}],"date_updated":"2023-10-03T11:36:13Z","date_created":"2023-03-19T23:00:59Z","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.","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"publication_status":"epub_ahead"},{"day":"11","month":"07","has_accepted_license":"1","article_processing_charge":"No","date_published":"2023-07-11T00:00:00Z","doi":"10.5281/ZENODO.8133960","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133960","open_access":"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":{"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.","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.","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.","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"},"oa":1,"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","relation":"used_in_publication","status":"public"}]},"date_created":"2023-09-06T08:39:25Z","date_updated":"2023-10-03T11:42:58Z","oa_version":"Published Version","_id":"14279","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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\"","department":[{"_id":"EdHa"}],"publisher":"Zenodo"},{"publication_identifier":{"eissn":["1097-0312"],"issn":["0010-3640"]},"month":"05","project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"arxiv":["1912.04100"],"isi":["000724652500001"]},"language":[{"iso":"eng"}],"doi":"10.1002/cpa.22028","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"file_date_updated":"2023-10-04T09:21:48Z","department":[{"_id":"LaEr"}],"publisher":"Wiley","publication_status":"published","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.","volume":76,"date_created":"2021-12-05T23:01:41Z","date_updated":"2023-10-04T09:22:55Z","author":[{"last_name":"Cipolloni","first_name":"Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","first_name":"Dominik J","last_name":"Schröder","full_name":"Schröder, Dominik J"}],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","page":"946-1034","article_type":"original","citation":{"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.","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","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.","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."},"publication":"Communications on Pure and Applied Mathematics","date_published":"2023-05-01T00:00:00Z","type":"journal_article","issue":"5","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"}],"intvolume":" 76","status":"public","ddc":["510"],"title":"Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices","_id":"10405","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14388","date_created":"2023-10-04T09:21:48Z","date_updated":"2023-10-04T09:21:48Z","checksum":"8346bc2642afb4ccb7f38979f41df5d9","success":1,"file_name":"2023_CommPureMathematics_Cipolloni.pdf","access_level":"open_access","content_type":"application/pdf","file_size":803440,"creator":"dernst"}]}]