[{"file":[{"date_updated":"2021-02-03T12:47:04Z","date_created":"2021-02-03T12:47:04Z","success":1,"checksum":"d9acbc502390ed7a97e631d23ae19ecd","file_id":"9074","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":398075,"file_name":"2021_PhysicalRevLett_DeNicola.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 126","title":"Entanglement view of dynamical quantum phase transitions","status":"public","ddc":["530"],"_id":"9048","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"4","abstract":[{"text":"The analogy between an equilibrium partition function and the return probability in many-body unitary dynamics has led to the concept of dynamical quantum phase transition (DQPT). DQPTs are defined by nonanalyticities in the return amplitude and are present in many models. In some cases, DQPTs can be related to equilibrium concepts, such as order parameters, yet their universal description is an open question. In this Letter, we provide first steps toward a classification of DQPTs by using a matrix product state description of unitary dynamics in the thermodynamic limit. This allows us to distinguish the two limiting cases of “precession” and “entanglement” DQPTs, which are illustrated using an analytical description in the quantum Ising model. While precession DQPTs are characterized by a large entanglement gap and are semiclassical in their nature, entanglement DQPTs occur near avoided crossings in the entanglement spectrum and can be distinguished by a complex pattern of nonlocal correlations. We demonstrate the existence of precession and entanglement DQPTs beyond Ising models, discuss observables that can distinguish them, and relate their interplay to complex DQPT phenomenology.","lang":"eng"}],"type":"journal_article","date_published":"2021-01-29T00:00:00Z","article_type":"original","citation":{"ista":"De Nicola S, Michailidis A, Serbyn M. 2021. Entanglement view of dynamical quantum phase transitions. Physical Review Letters. 126(4), 040602.","ieee":"S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement view of dynamical quantum phase transitions,” Physical Review Letters, vol. 126, no. 4. American Physical Society, 2021.","apa":"De Nicola, S., Michailidis, A., & Serbyn, M. (2021). Entanglement view of dynamical quantum phase transitions. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.126.040602","ama":"De Nicola S, Michailidis A, Serbyn M. Entanglement view of dynamical quantum phase transitions. Physical Review Letters. 2021;126(4). doi:10.1103/physrevlett.126.040602","chicago":"De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement View of Dynamical Quantum Phase Transitions.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/physrevlett.126.040602.","mla":"De Nicola, Stefano, et al. “Entanglement View of Dynamical Quantum Phase Transitions.” Physical Review Letters, vol. 126, no. 4, 040602, American Physical Society, 2021, doi:10.1103/physrevlett.126.040602.","short":"S. De Nicola, A. Michailidis, M. Serbyn, Physical Review Letters 126 (2021)."},"publication":"Physical Review Letters","article_processing_charge":"Yes","has_accepted_license":"1","day":"29","keyword":["General Physics and Astronomy"],"volume":126,"date_created":"2021-02-01T09:20:00Z","date_updated":"2023-09-05T12:08:58Z","author":[{"orcid":"0000-0002-4842-6671","id":"42832B76-F248-11E8-B48F-1D18A9856A87","last_name":"De Nicola","first_name":"Stefano","full_name":"De Nicola, Stefano"},{"full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","first_name":"Alexios"},{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}],"department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","acknowledgement":"S. D. N. acknowledges funding from the Institute of Science and Technology (IST) Austria and from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. A. M. and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 Research and\r\nInnovation Programme (Grant Agreement No. 850899).","year":"2021","ec_funded":1,"file_date_updated":"2021-02-03T12:47:04Z","article_number":"040602","language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.126.040602","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000613148200001"],"arxiv":["2008.04894"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"01"},{"_id":"9368","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 186","title":"mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth","status":"public","oa_version":"Published Version","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"The quality control system for messenger RNA (mRNA) is fundamental for cellular activities in eukaryotes. To elucidate the molecular mechanism of 3'-Phosphoinositide-Dependent Protein Kinase1 (PDK1), a master regulator that is essential throughout eukaryotic growth and development, we employed a forward genetic approach to screen for suppressors of the loss-of-function T-DNA insertion double mutant pdk1.1 pdk1.2 in Arabidopsis thaliana. Notably, the severe growth attenuation of pdk1.1 pdk1.2 was rescued by sop21 (suppressor of pdk1.1 pdk1.2), which harbours a loss-of-function mutation in PELOTA1 (PEL1). PEL1 is a homologue of mammalian PELOTA and yeast (Saccharomyces cerevisiae) DOM34p, which each form a heterodimeric complex with the GTPase HBS1 (HSP70 SUBFAMILY B SUPPRESSOR1, also called SUPERKILLER PROTEIN7, SKI7), a protein that is responsible for ribosomal rescue and thereby assures the quality and fidelity of mRNA molecules during translation. Genetic analysis further revealed that a dysfunctional PEL1-HBS1 complex failed to degrade the T-DNA-disrupted PDK1 transcripts, which were truncated but functional, and thus rescued the growth and developmental defects of pdk1.1 pdk1.2. Our studies demonstrated the functionality of a homologous PELOTA-HBS1 complex and identified its essential regulatory role in plants, providing insights into the mechanism of mRNA quality control."}],"citation":{"ama":"Kong W, Tan S, Zhao Q, et al. mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. 2021;186(4):2003-2020. doi:10.1093/plphys/kiab199","apa":"Kong, W., Tan, S., Zhao, Q., Lin, D., Xu, Z., Friml, J., & Xue, H. (2021). mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1093/plphys/kiab199","ieee":"W. Kong et al., “mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth,” Plant Physiology, vol. 186, no. 4. American Society of Plant Biologists, pp. 2003–2020, 2021.","ista":"Kong W, Tan S, Zhao Q, Lin D, Xu Z, Friml J, Xue H. 2021. mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. 186(4), 2003–2020.","short":"W. Kong, S. Tan, Q. Zhao, D. Lin, Z. Xu, J. Friml, H. Xue, Plant Physiology 186 (2021) 2003–2020.","mla":"Kong, W., et al. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein Kinase1 and Plant Growth.” Plant Physiology, vol. 186, no. 4, American Society of Plant Biologists, 2021, pp. 2003–20, doi:10.1093/plphys/kiab199.","chicago":"Kong, W, Shutang Tan, Q Zhao, DL Lin, ZH Xu, Jiří Friml, and HW Xue. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein Kinase1 and Plant Growth.” Plant Physiology. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plphys/kiab199."},"publication":"Plant Physiology","page":"2003-2020","article_type":"original","date_published":"2021-04-30T00:00:00Z","article_processing_charge":"No","day":"30","pmid":1,"acknowledgement":"We gratefully acknowledge the Arabidopsis Biological Resource Centre (ABRC) for providing T-DNA insertional mutants, and Prof. Remko Offringa for sharing published seeds. We thank Yuchuan Liu (Shanghai OE Biotech Co., Ltd) for help with proteomics data analysis, Xixi Zhang (IST Austria) for providing the pDONR-P4P1r-mCherry plasmid, and Yao Xiao (Technical University of Munich), Alexander Johnson (IST Austria) and Hana Semeradova (IST Austria) for helpful discussions. The study was supported by National Natural Science Foundation of China (NSFC, 31721001, 91954206, to H.-W. X.), “Ten-Thousand Talent Program” (to H.-W. X.) and Collaborative Innovation Center of Crop Stress Biology, Henan Province, and Austrian Science Fund (FWF): I 3630-B25 (to J. F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015).","year":"2021","department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","publication_status":"published","author":[{"last_name":"Kong","first_name":"W","full_name":"Kong, W"},{"first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"full_name":"Zhao, Q","first_name":"Q","last_name":"Zhao"},{"first_name":"DL","last_name":"Lin","full_name":"Lin, DL"},{"last_name":"Xu","first_name":"ZH","full_name":"Xu, ZH"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"full_name":"Xue, HW","last_name":"Xue","first_name":"HW"}],"volume":186,"date_updated":"2023-09-05T12:20:27Z","date_created":"2021-05-03T13:28:20Z","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"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/plphys/kiab199"}],"external_id":{"isi":["000703922000025"],"pmid":["33930167"]},"oa":1,"project":[{"name":"Long Term Fellowship","_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","doi":"10.1093/plphys/kiab199","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"month":"04"},{"article_type":"original","page":"942-963","publication":"Canadian Mathematical Bulletin","citation":{"chicago":"Ivanov, Grigory. “Tight Frames and Related Geometric Problems.” Canadian Mathematical Bulletin. Canadian Mathematical Society, 2021. https://doi.org/10.4153/s000843952000096x.","mla":"Ivanov, Grigory. “Tight Frames and Related Geometric Problems.” Canadian Mathematical Bulletin, vol. 64, no. 4, Canadian Mathematical Society, 2021, pp. 942–63, doi:10.4153/s000843952000096x.","short":"G. Ivanov, Canadian Mathematical Bulletin 64 (2021) 942–963.","ista":"Ivanov G. 2021. Tight frames and related geometric problems. Canadian Mathematical Bulletin. 64(4), 942–963.","apa":"Ivanov, G. (2021). Tight frames and related geometric problems. Canadian Mathematical Bulletin. Canadian Mathematical Society. https://doi.org/10.4153/s000843952000096x","ieee":"G. Ivanov, “Tight frames and related geometric problems,” Canadian Mathematical Bulletin, vol. 64, no. 4. Canadian Mathematical Society, pp. 942–963, 2021.","ama":"Ivanov G. Tight frames and related geometric problems. Canadian Mathematical Bulletin. 2021;64(4):942-963. doi:10.4153/s000843952000096x"},"date_published":"2021-12-18T00:00:00Z","keyword":["General Mathematics","Tight frame","Grassmannian","zonotope"],"scopus_import":"1","day":"18","article_processing_charge":"No","status":"public","title":"Tight frames and related geometric problems","intvolume":" 64","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10860","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"A tight frame is the orthogonal projection of some orthonormal basis of Rn onto Rk. We show that a set of vectors is a tight frame if and only if the set of all cross products of these vectors is a tight frame. We reformulate a range of problems on the volume of projections (or sections) of regular polytopes in terms of tight frames and write a first-order necessary condition for local extrema of these problems. As applications, we prove new results for the problem of maximization of the volume of zonotopes.","lang":"eng"}],"issue":"4","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.10055"}],"oa":1,"external_id":{"arxiv":["1804.10055"],"isi":["000730165300021"]},"language":[{"iso":"eng"}],"doi":"10.4153/s000843952000096x","month":"12","publication_identifier":{"issn":["0008-4395"],"eissn":["1496-4287"]},"publication_status":"published","publisher":"Canadian Mathematical Society","department":[{"_id":"UlWa"}],"year":"2021","acknowledgement":"The author was supported by the Swiss National Science Foundation grant 200021_179133. The author acknowledges the financial support from the Ministry of Education and Science of the Russian Federation in the framework of MegaGrant no. 075-15-2019-1926.","date_created":"2022-03-18T09:55:59Z","date_updated":"2023-09-05T12:43:09Z","volume":64,"author":[{"full_name":"Ivanov, Grigory","first_name":"Grigory","last_name":"Ivanov","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"}]},{"pmid":1,"acknowledgement":"We acknowledge Ben Scheres, Christian Luschnig, and Claus Schwechheimer for sharing published material. We thank Monika Hrtyan and Dorota Jaworska at IST Austria and Gerda Lamers and Ward de Winter at IBL Netherlands for technical assistance; Corinna Hartinger, Jakub Hajný, Lesia Rodriguez, Mingyue Li, and Lindy Abas for experimental support; and the Bioimaging Facility at IST Austria and the Bioimaging Core at VIB for imaging support. We are grateful to Christian Luschnig, Lindy Abas, and Roman Pleskot for valuable discussions. We also acknowledge the EMBO for supporting M.G. with a long-term fellowship ( ALTF 1005-2019 ) during the finalization and revision of this manuscript in the laboratory of B.D.R., and we thank R. Pierik for allowing K.V.G. to work on this manuscript during a postdoc in his laboratory at Utrecht University. This work was supported by grants from the European Research Council under the European Union’s Seventh Framework Programme (ERC grant agreements 742985 to J.F., 714055 to B.D.R., and 803048 to M.F.), the Austrian Science Fund (FWF; I 3630-B25 to J.F.), Chemical Sciences (partly) financed by the Dutch Research Council (NWO-CW TOP 700.58.301 to R.O.), the Dutch Research Council (NWO-VICI 865.17.002 to R. Pierik), Grants-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology, Japan (KAKENHI grant 17K17595 to S.N.), the Ministry of Education, Youth and Sports of the Czech Republic (MŠMT project NPUI-LO1417 ), and a China Scholarship Council (to X.W.).","year":"2021","publisher":"Elsevier","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"full_name":"Glanc, Matous","last_name":"Glanc","first_name":"Matous","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"last_name":"Van Gelderen","first_name":"K","full_name":"Van Gelderen, K"},{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","first_name":"Lukas","last_name":"Hörmayer","full_name":"Hörmayer, Lukas"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan","full_name":"Tan, Shutang"},{"full_name":"Naramoto, S","last_name":"Naramoto","first_name":"S"},{"full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi","last_name":"Zhang"},{"full_name":"Domjan, David","last_name":"Domjan","first_name":"David","orcid":"0000-0003-2267-106X","id":"C684CD7A-257E-11EA-9B6F-D8588B4F947F"},{"first_name":"L","last_name":"Vcelarova","full_name":"Vcelarova, L"},{"last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","first_name":"Alexander J"},{"last_name":"de Koning","first_name":"E","full_name":"de Koning, E"},{"first_name":"M","last_name":"van Dop","full_name":"van Dop, M"},{"full_name":"Rademacher, E","last_name":"Rademacher","first_name":"E"},{"full_name":"Janson, S","last_name":"Janson","first_name":"S"},{"full_name":"Wei, X","first_name":"X","last_name":"Wei"},{"id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","last_name":"Molnar","full_name":"Molnar, Gergely"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych","full_name":"Fendrych, Matyas"},{"full_name":"De Rybel, B","first_name":"B","last_name":"De Rybel"},{"last_name":"Offringa","first_name":"R","full_name":"Offringa, R"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"volume":31,"date_updated":"2023-09-05T13:03:34Z","date_created":"2021-03-26T12:09:33Z","ec_funded":1,"file_date_updated":"2021-04-01T10:53:42Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000653077800004"],"pmid":["33705718"]},"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"}],"quality_controlled":"1","isi":1,"doi":"10.1016/j.cub.2021.02.028","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"month":"03","_id":"9290","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 31","ddc":["580"],"title":"AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells","status":"public","file":[{"date_created":"2021-04-01T10:53:42Z","date_updated":"2021-04-01T10:53:42Z","success":1,"checksum":"b1723040ecfd8c81194185472eb62546","file_id":"9303","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":4324371,"file_name":"2021_CurrentBiology_Glanc.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"9","abstract":[{"text":"Polar subcellular localization of the PIN exporters of the phytohormone auxin is a key determinant of directional, intercellular auxin transport and thus a central topic of both plant cell and developmental biology. Arabidopsis mutants lacking PID, a kinase that phosphorylates PINs, or the MAB4/MEL proteins of unknown molecular function display PIN polarity defects and phenocopy pin mutants, but mechanistic insights into how these factors convey PIN polarity are missing. Here, by combining protein biochemistry with quantitative live-cell imaging, we demonstrate that PINs, MAB4/MELs, and AGC kinases interact in the same complex at the plasma membrane. MAB4/MELs are recruited to the plasma membrane by the PINs and in concert with the AGC kinases maintain PIN polarity through limiting lateral diffusion-based escape of PINs from the polar domain. The PIN-MAB4/MEL-PID protein complex has self-reinforcing properties thanks to positive feedback between AGC kinase-mediated PIN phosphorylation and MAB4/MEL recruitment. We thus uncover the molecular mechanism by which AGC kinases and MAB4/MEL proteins regulate PIN localization and plant development.","lang":"eng"}],"citation":{"short":"M. Glanc, K. Van Gelderen, L. Hörmayer, S. Tan, S. Naramoto, X. Zhang, D. Domjan, L. Vcelarova, R. Hauschild, A.J. Johnson, E. de Koning, M. van Dop, E. Rademacher, S. Janson, X. Wei, G. Molnar, M. Fendrych, B. De Rybel, R. Offringa, J. Friml, Current Biology 31 (2021) 1918–1930.","mla":"Glanc, Matous, et al. “AGC Kinases and MAB4/MEL Proteins Maintain PIN Polarity by Limiting Lateral Diffusion in Plant Cells.” Current Biology, vol. 31, no. 9, Elsevier, 2021, pp. 1918–30, doi:10.1016/j.cub.2021.02.028.","chicago":"Glanc, Matous, K Van Gelderen, Lukas Hörmayer, Shutang Tan, S Naramoto, Xixi Zhang, David Domjan, et al. “AGC Kinases and MAB4/MEL Proteins Maintain PIN Polarity by Limiting Lateral Diffusion in Plant Cells.” Current Biology. Elsevier, 2021. https://doi.org/10.1016/j.cub.2021.02.028.","ama":"Glanc M, Van Gelderen K, Hörmayer L, et al. AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Current Biology. 2021;31(9):1918-1930. doi:10.1016/j.cub.2021.02.028","ieee":"M. Glanc et al., “AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells,” Current Biology, vol. 31, no. 9. Elsevier, pp. 1918–1930, 2021.","apa":"Glanc, M., Van Gelderen, K., Hörmayer, L., Tan, S., Naramoto, S., Zhang, X., … Friml, J. (2021). AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2021.02.028","ista":"Glanc M, Van Gelderen K, Hörmayer L, Tan S, Naramoto S, Zhang X, Domjan D, Vcelarova L, Hauschild R, Johnson AJ, de Koning E, van Dop M, Rademacher E, Janson S, Wei X, Molnar G, Fendrych M, De Rybel B, Offringa R, Friml J. 2021. AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Current Biology. 31(9), 1918–1930."},"publication":"Current Biology","page":"1918-1930","article_type":"original","date_published":"2021-03-10T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"10"},{"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1, 2, 3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1, 2, 3, 4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7, 8, 9, 10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface."}],"_id":"8824","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 31","status":"public","ddc":["570"],"title":"Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism","file":[{"relation":"main_file","file_id":"9090","checksum":"30b3393d841fb2b1e2b22fb42b5c8fff","success":1,"date_created":"2021-02-04T11:37:50Z","date_updated":"2021-02-04T11:37:50Z","access_level":"open_access","file_name":"2021_CurrentBiology_MarquesBueno.pdf","content_type":"application/pdf","file_size":3458646,"creator":"dernst"}],"oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"11","citation":{"ama":"Marquès-Bueno M, Armengot L, Noack L, et al. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. 2021;31(1). doi:10.1016/j.cub.2020.10.011","ista":"Marquès-Bueno M, Armengot L, Noack L, Bareille J, Rodriguez Solovey L, Platre M, Bayle V, Liu M, Opdenacker D, Vanneste S, Möller B, Nimchuk Z, Beeckman T, Caño-Delgado A, Friml J, Jaillais Y. 2021. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. 31(1).","apa":"Marquès-Bueno, M., Armengot, L., Noack, L., Bareille, J., Rodriguez Solovey, L., Platre, M., … Jaillais, Y. (2021). Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2020.10.011","ieee":"M. Marquès-Bueno et al., “Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism,” Current Biology, vol. 31, no. 1. Elsevier, 2021.","mla":"Marquès-Bueno, MM, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.” Current Biology, vol. 31, no. 1, Elsevier, 2021, doi:10.1016/j.cub.2020.10.011.","short":"M. Marquès-Bueno, L. Armengot, L. Noack, J. Bareille, L. Rodriguez Solovey, M. Platre, V. Bayle, M. Liu, D. Opdenacker, S. Vanneste, B. Möller, Z. Nimchuk, T. Beeckman, A. Caño-Delgado, J. Friml, Y. Jaillais, Current Biology 31 (2021).","chicago":"Marquès-Bueno, MM, L Armengot, LC Noack, J Bareille, Lesia Rodriguez Solovey, MP Platre, V Bayle, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.” Current Biology. Elsevier, 2021. https://doi.org/10.1016/j.cub.2020.10.011."},"publication":"Current Biology","article_type":"original","date_published":"2021-01-11T00:00:00Z","file_date_updated":"2021-02-04T11:37:50Z","pmid":1,"year":"2021","acknowledgement":"We thank the SiCE group for discussions and comments; S. Yalovsky, B. Scheres, and the NASC/ABRC collection for providing transgenic Arabidopsis lines and plasmids; L. Kalmbach and M. Barberon for the gift of pLOK180_pFR7m34GW; A. Lacroix, J. Berger, and P. Bolland for plant care; and M. Fendrych for help with microfluidics in the J.F. lab. We acknowledge\r\nthe contribution of the SFR Biosciences (UMS3444/CNRS, US8/Inser m, ENS de Lyon, UCBL) facilities: C. Lionet, E. Chatre, and J. Brocard at LBIPLATIM-MICROSCOPY for assistance with imaging, and V. GuegenChaignon and A. Page at the Protein Science Facility (PSF) for assistance with protein purification and mass spectrometry. Y.J. was funded by ERC\r\ngrant 3363360-APPL under FP/2007–2013. Y.J. and Z.L.N. were funded by an ANR- and NSF-supported ERA-CAPS project (SICOPID: ANR-17-CAPS0003-01/NSF PGRP IOS-1841917). A.I.C.-D. is funded by an ERC consolidator grant (ERC-2015-CoG–683163) and BIO2016-78955 grant from the Spanish Ministry of Economy and Competitiveness. Exchanges between the Y.J. and T.B. laboratories were funded by Tournesol grant 35656NB. B.K.M. was\r\nfunded by the Omics@vib Marie Curie COFUND and Research Foundation Flanders for a postdoctoral fellowship.","department":[{"_id":"JiFr"}],"publisher":"Elsevier","publication_status":"published","author":[{"last_name":"Marquès-Bueno","first_name":"MM","full_name":"Marquès-Bueno, MM"},{"full_name":"Armengot, L","first_name":"L","last_name":"Armengot"},{"full_name":"Noack, LC","last_name":"Noack","first_name":"LC"},{"first_name":"J","last_name":"Bareille","full_name":"Bareille, J"},{"full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237"},{"full_name":"Platre, MP","first_name":"MP","last_name":"Platre"},{"full_name":"Bayle, V","first_name":"V","last_name":"Bayle"},{"last_name":"Liu","first_name":"M","full_name":"Liu, M"},{"full_name":"Opdenacker, D","last_name":"Opdenacker","first_name":"D"},{"full_name":"Vanneste, S","first_name":"S","last_name":"Vanneste"},{"first_name":"BK","last_name":"Möller","full_name":"Möller, BK"},{"full_name":"Nimchuk, ZL","last_name":"Nimchuk","first_name":"ZL"},{"first_name":"T","last_name":"Beeckman","full_name":"Beeckman, T"},{"last_name":"Caño-Delgado","first_name":"AI","full_name":"Caño-Delgado, AI"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"last_name":"Jaillais","first_name":"Y","full_name":"Jaillais, Y"}],"volume":31,"date_updated":"2023-09-05T13:03:15Z","date_created":"2020-12-01T13:39:46Z","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"month":"01","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":["33157019"],"isi":["000614361000039"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1016/j.cub.2020.10.011","language":[{"iso":"eng"}]},{"day":"06","article_processing_charge":"No","keyword":["small-angle X-ray scattering","oxygen reduction","disproportionation","Li-air battery"],"date_published":"2021-04-06T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","citation":{"ama":"Prehal C, Samojlov A, Nachtnebel M, et al. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. 2021;118(14). doi:10.1073/pnas.2021893118","ieee":"C. Prehal et al., “In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes,” Proceedings of the National Academy of Sciences, vol. 118, no. 14. National Academy of Sciences, 2021.","apa":"Prehal, C., Samojlov, A., Nachtnebel, M., Lovicar, L., Kriechbaum, M., Amenitsch, H., & Freunberger, S. A. (2021). In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2021893118","ista":"Prehal C, Samojlov A, Nachtnebel M, Lovicar L, Kriechbaum M, Amenitsch H, Freunberger SA. 2021. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. 118(14), e2021893118.","short":"C. Prehal, A. Samojlov, M. Nachtnebel, L. Lovicar, M. Kriechbaum, H. Amenitsch, S.A. Freunberger, Proceedings of the National Academy of Sciences 118 (2021).","mla":"Prehal, Christian, et al. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences, vol. 118, no. 14, e2021893118, National Academy of Sciences, 2021, doi:10.1073/pnas.2021893118.","chicago":"Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Ludek Lovicar, Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2021893118."},"article_type":"original","abstract":[{"text":"Electrodepositing insulating lithium peroxide (Li2O2) is the key process during discharge of aprotic Li–O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and dissolved lithium superoxide governs whether Li2O2 grows as a conformal surface film or larger particles, leading to low or high capacities, respectively. However, better understanding governing factors for Li2O2 packing density and capacity requires structural sensitive in situ metrologies. Here, we establish in situ small- and wide-angle X-ray scattering (SAXS/WAXS) as a suitable method to record the Li2O2 phase evolution with atomic to submicrometer resolution during cycling a custom-built in situ Li–O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative structural information from complex multiphase systems. Surprisingly, we find that features are absent that would point at a Li2O2 surface film formed via two consecutive electron transfers, even in poorly solvating electrolytes thought to be prototypical for surface growth. All scattering data can be modeled by stacks of thin Li2O2 platelets potentially forming large toroidal particles. Li2O2 solution growth is further justified by rotating ring-disk electrode measurements and electron microscopy. Higher discharge overpotentials lead to smaller Li2O2 particles, but there is no transition to an electronically passivating, conformal Li2O2 coating. Hence, mass transport of reactive species rather than electronic transport through a Li2O2 film limits the discharge capacity. Provided that species mobilities and carbon surface areas are high, this allows for high discharge capacities even in weakly solvating electrolytes. The currently accepted Li–O2 reaction mechanism ought to be reconsidered.","lang":"eng"}],"issue":"14","type":"journal_article","oa_version":"Preprint","_id":"9301","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes","status":"public","intvolume":" 118","month":"04","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.2021893118","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv.11447775"}],"external_id":{"isi":["000637398300050"]},"isi":1,"quality_controlled":"1","article_number":"e2021893118","author":[{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"last_name":"Samojlov","first_name":"Aleksej","full_name":"Samojlov, Aleksej"},{"last_name":"Nachtnebel","first_name":"Manfred","full_name":"Nachtnebel, Manfred"},{"full_name":"Lovicar, Ludek","last_name":"Lovicar","first_name":"Ludek","orcid":"0000-0001-6206-4200","id":"36DB3A20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kriechbaum, Manfred","first_name":"Manfred","last_name":"Kriechbaum"},{"full_name":"Amenitsch, Heinz","first_name":"Heinz","last_name":"Amenitsch"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander"}],"date_updated":"2023-09-05T13:27:18Z","date_created":"2021-03-31T07:00:01Z","volume":118,"year":"2021","acknowledgement":"S.A.F. and C.P. are indebted to the European Research Council under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 636069), the Austrian Federal Ministry of Science, Research and Economy, and the Austrian Research Promotion Agency (Grant No. 845364). We acknowledge A. Zankel and H. Schroettner for support with SEM measurements. C.P. thanks N. Kostoglou, C. Koczwara, M. Hartmann, and M. Burian for discussions on gas sorption analysis, C++ programming, Monte Carlo modeling, and in situ SAXS experiments, respectively. We thank S. Stadlbauer for help with Karl Fischer titration, R. Riccò for gas sorption measurements, and acknowledge Graz University of Technology for support through the Lead Project LP-03. Likewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. S.A.F. is indebted to Institute of Science and Technology Austria (IST Austria) for support. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility.","publication_status":"published","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"publisher":"National Academy of Sciences"},{"volume":220,"date_created":"2021-02-05T10:08:04Z","date_updated":"2023-09-05T13:57:53Z","author":[{"full_name":"Leithner, Alexander F","last_name":"Leithner","first_name":"Alexander F","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Altenburger","first_name":"LM","full_name":"Altenburger, LM"},{"last_name":"Hauschild","first_name":"R","full_name":"Hauschild, R"},{"last_name":"Assen","first_name":"Frank P","orcid":"0000-0003-3470-6119","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","full_name":"Assen, Frank P"},{"first_name":"K","last_name":"Rottner","full_name":"Rottner, K"},{"last_name":"TEB","first_name":"Stradal","full_name":"TEB, Stradal"},{"first_name":"A","last_name":"Diz-Muñoz","full_name":"Diz-Muñoz, A"},{"last_name":"Stein","first_name":"JV","full_name":"Stein, JV"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"department":[{"_id":"MiSi"}],"publisher":"Rockefeller University Press","publication_status":"published","pmid":1,"year":"2021","file_date_updated":"2022-05-12T14:16:21Z","article_number":"e202006081","language":[{"iso":"eng"}],"doi":"10.1083/jcb.202006081","quality_controlled":"1","isi":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)"},"external_id":{"pmid":["33533935"],"isi":["000626365700001"]},"oa":1,"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"month":"04","file":[{"file_id":"11367","relation":"main_file","success":1,"checksum":"843ebc153847c8626e13c9c5ce71d533","date_updated":"2022-05-12T14:16:21Z","date_created":"2022-05-12T14:16:21Z","access_level":"open_access","file_name":"2021_JournCellBiology_Leithner.pdf","creator":"dernst","content_type":"application/pdf","file_size":5102328}],"oa_version":"Published Version","intvolume":" 220","ddc":["570"],"title":"Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9094","issue":"4","abstract":[{"text":"Dendritic cells (DCs) are crucial for the priming of naive T cells and the initiation of adaptive immunity. Priming is initiated at a heterologous cell–cell contact, the immunological synapse (IS). While it is established that F-actin dynamics regulates signaling at the T cell side of the contact, little is known about the cytoskeletal contribution on the DC side. Here, we show that the DC actin cytoskeleton is decisive for the formation of a multifocal synaptic structure, which correlates with T cell priming efficiency. DC actin at the IS appears in transient foci that are dynamized by the WAVE regulatory complex (WRC). The absence of the WRC in DCs leads to stabilized contacts with T cells, caused by an increase in ICAM1-integrin–mediated cell–cell adhesion. This results in lower numbers of activated and proliferating T cells, demonstrating an important role for DC actin in the regulation of immune synapse functionality.","lang":"eng"}],"type":"journal_article","date_published":"2021-04-05T00:00:00Z","article_type":"original","citation":{"chicago":"Leithner, Alexander F, LM Altenburger, R Hauschild, Frank P Assen, K Rottner, Stradal TEB, A Diz-Muñoz, JV Stein, and Michael K Sixt. “Dendritic Cell Actin Dynamics Control Contact Duration and Priming Efficiency at the Immunological Synapse.” Journal of Cell Biology. Rockefeller University Press, 2021. https://doi.org/10.1083/jcb.202006081.","mla":"Leithner, Alexander F., et al. “Dendritic Cell Actin Dynamics Control Contact Duration and Priming Efficiency at the Immunological Synapse.” Journal of Cell Biology, vol. 220, no. 4, e202006081, Rockefeller University Press, 2021, doi:10.1083/jcb.202006081.","short":"A.F. Leithner, L. Altenburger, R. Hauschild, F.P. Assen, K. Rottner, S. TEB, A. Diz-Muñoz, J. Stein, M.K. Sixt, Journal of Cell Biology 220 (2021).","ista":"Leithner AF, Altenburger L, Hauschild R, Assen FP, Rottner K, TEB S, Diz-Muñoz A, Stein J, Sixt MK. 2021. Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. Journal of Cell Biology. 220(4), e202006081.","ieee":"A. F. Leithner et al., “Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse,” Journal of Cell Biology, vol. 220, no. 4. Rockefeller University Press, 2021.","apa":"Leithner, A. F., Altenburger, L., Hauschild, R., Assen, F. P., Rottner, K., TEB, S., … Sixt, M. K. (2021). Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202006081","ama":"Leithner AF, Altenburger L, Hauschild R, et al. Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. Journal of Cell Biology. 2021;220(4). doi:10.1083/jcb.202006081"},"publication":"Journal of Cell Biology","has_accepted_license":"1","article_processing_charge":"No","day":"05","scopus_import":"1"},{"project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000616763400002"],"pmid":["33431633"]},"language":[{"iso":"eng"}],"doi":"10.1523/jneurosci.1655-20.2020","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"month":"02","publisher":"Society for Neuroscience","department":[{"_id":"SiHi"}],"publication_status":"published","pmid":1,"year":"2021","acknowledgement":"Work in the I.L.H.-O. laboratory was supported by European Research Council Grant ERC-2015-CoG 681577 and German Research Foundation Ha 4466/10-1, Ha4466/11-1, Ha4466/12-1, SPP 1665, and SFB 936B5. Work in the S.J.B.B. laboratory was supported by Biotechnology and Biological Sciences Research Council BB/P003796/1, Medical Research Council MR/K004387/1 and MR/T033320/1, Wellcome Trust 215199/Z/19/Z and 102386/Z/13/Z, and John Fell Fund. Work in the S.H. laboratory was supported by European Research Council Grants ERC-2016-CoG 725780 LinPro and FWF SFB F78. This work was supported by National Institutes of Health Grant NIMH 1R01MH110553 to N.V.D.M.G. Work in the J.A.C. laboratory was supported by the Ludwig Family Foundation, Simons Foundation SFARI Research Award, and National Institutes of Health/National Institute of Mental Health R01 MH102365 and R01MH113852. The B.V. laboratory was supported by Whitehall Foundation 2017-12-73, National Science Foundation 1736028, National Institutes of Health, National Institute of General Medical Sciences R01GM134363-01, and Halıcıoğlu Data Science Institute Fellowship. This work was supported by the University of California San Diego School of Medicine.","volume":41,"date_created":"2021-02-03T12:23:51Z","date_updated":"2023-09-05T14:03:17Z","author":[{"full_name":"Hanganu-Opatz, Ileana L.","first_name":"Ileana L.","last_name":"Hanganu-Opatz"},{"first_name":"Simon J. B.","last_name":"Butt","full_name":"Butt, Simon J. B."},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"full_name":"De Marco García, Natalia V.","first_name":"Natalia V.","last_name":"De Marco García"},{"last_name":"Cardin","first_name":"Jessica A.","full_name":"Cardin, Jessica A."},{"full_name":"Voytek, Bradley","first_name":"Bradley","last_name":"Voytek"},{"full_name":"Muotri, Alysson R.","last_name":"Muotri","first_name":"Alysson R."}],"ec_funded":1,"file_date_updated":"2022-05-27T06:59:55Z","page":"813-822","article_type":"original","citation":{"ista":"Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, De Marco García NV, Cardin JA, Voytek B, Muotri AR. 2021. The logic of developing neocortical circuits in health and disease. The Journal of Neuroscience. 41(5), 813–822.","apa":"Hanganu-Opatz, I. L., Butt, S. J. B., Hippenmeyer, S., De Marco García, N. V., Cardin, J. A., Voytek, B., & Muotri, A. R. (2021). The logic of developing neocortical circuits in health and disease. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/jneurosci.1655-20.2020","ieee":"I. L. Hanganu-Opatz et al., “The logic of developing neocortical circuits in health and disease,” The Journal of Neuroscience, vol. 41, no. 5. Society for Neuroscience, pp. 813–822, 2021.","ama":"Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, et al. The logic of developing neocortical circuits in health and disease. The Journal of Neuroscience. 2021;41(5):813-822. doi:10.1523/jneurosci.1655-20.2020","chicago":"Hanganu-Opatz, Ileana L., Simon J. B. Butt, Simon Hippenmeyer, Natalia V. De Marco García, Jessica A. Cardin, Bradley Voytek, and Alysson R. Muotri. “The Logic of Developing Neocortical Circuits in Health and Disease.” The Journal of Neuroscience. Society for Neuroscience, 2021. https://doi.org/10.1523/jneurosci.1655-20.2020.","mla":"Hanganu-Opatz, Ileana L., et al. “The Logic of Developing Neocortical Circuits in Health and Disease.” The Journal of Neuroscience, vol. 41, no. 5, Society for Neuroscience, 2021, pp. 813–22, doi:10.1523/jneurosci.1655-20.2020.","short":"I.L. Hanganu-Opatz, S.J.B. Butt, S. Hippenmeyer, N.V. De Marco García, J.A. Cardin, B. Voytek, A.R. Muotri, The Journal of Neuroscience 41 (2021) 813–822."},"publication":"The Journal of Neuroscience","date_published":"2021-02-03T00:00:00Z","keyword":["General Neuroscience"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"03","intvolume":" 41","ddc":["570"],"status":"public","title":"The logic of developing neocortical circuits in health and disease","_id":"9073","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"checksum":"578fd7ed1a0aef74bce61bea2d987b33","success":1,"date_updated":"2022-05-27T06:59:55Z","date_created":"2022-05-27T06:59:55Z","relation":"main_file","file_id":"11414","file_size":1031150,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2021_JourNeuroscience_Hanganu.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"5","abstract":[{"text":"The sensory and cognitive abilities of the mammalian neocortex are underpinned by intricate columnar and laminar circuits formed from an array of diverse neuronal populations. One approach to determining how interactions between these circuit components give rise to complex behavior is to investigate the rules by which cortical circuits are formed and acquire functionality during development. This review summarizes recent research on the development of the neocortex, from genetic determination in neural stem cells through to the dynamic role that specific neuronal populations play in the earliest circuits of neocortex, and how they contribute to emergent function and cognition. While many of these endeavors take advantage of model systems, consideration will also be given to advances in our understanding of activity in nascent human circuits. Such cross-species perspective is imperative when investigating the mechanisms underlying the dysfunction of early neocortical circuits in neurodevelopmental disorders, so that one can identify targets amenable to therapeutic intervention.","lang":"eng"}]},{"abstract":[{"text":"We study the problem of recovering an unknown signal 𝑥𝑥 given measurements obtained from a generalized linear model with a Gaussian sensing matrix. Two popular solutions are based on a linear estimator 𝑥𝑥^L and a spectral estimator 𝑥𝑥^s. The former is a data-dependent linear combination of the columns of the measurement matrix, and its analysis is quite simple. The latter is the principal eigenvector of a data-dependent matrix, and a recent line of work has studied its performance. In this paper, we show how to optimally combine 𝑥𝑥^L and 𝑥𝑥^s. At the heart of our analysis is the exact characterization of the empirical joint distribution of (𝑥𝑥,𝑥𝑥^L,𝑥𝑥^s) in the high-dimensional limit. This allows us to compute the Bayes-optimal combination of 𝑥𝑥^L and 𝑥𝑥^s, given the limiting distribution of the signal 𝑥𝑥. When the distribution of the signal is Gaussian, then the Bayes-optimal combination has the form 𝜃𝑥𝑥^L+𝑥𝑥^s and we derive the optimal combination coefficient. In order to establish the limiting distribution of (𝑥𝑥,𝑥𝑥^L,𝑥𝑥^s), we design and analyze an approximate message passing algorithm whose iterates give 𝑥𝑥^L and approach 𝑥𝑥^s. Numerical simulations demonstrate the improvement of the proposed combination with respect to the two methods considered separately.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"10542","relation":"main_file","date_updated":"2021-12-13T15:47:54Z","date_created":"2021-12-13T15:47:54Z","success":1,"checksum":"9ea12dd8045a0678000a3a59295221cb","file_name":"2021_Springer_Mondelli.pdf","access_level":"open_access","creator":"alisjak","file_size":2305731,"content_type":"application/pdf"}],"ddc":["510"],"title":"Optimal combination of linear and spectral estimators for generalized linear models","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10211","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"17","keyword":["Applied Mathematics","Computational Theory and Mathematics","Computational Mathematics","Analysis"],"scopus_import":"1","date_published":"2021-08-17T00:00:00Z","article_type":"original","citation":{"chicago":"Mondelli, Marco, Christos Thrampoulidis, and Ramji Venkataramanan. “Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models.” Foundations of Computational Mathematics. Springer, 2021. https://doi.org/10.1007/s10208-021-09531-x.","short":"M. Mondelli, C. Thrampoulidis, R. Venkataramanan, Foundations of Computational Mathematics (2021).","mla":"Mondelli, Marco, et al. “Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models.” Foundations of Computational Mathematics, Springer, 2021, doi:10.1007/s10208-021-09531-x.","apa":"Mondelli, M., Thrampoulidis, C., & Venkataramanan, R. (2021). Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-021-09531-x","ieee":"M. Mondelli, C. Thrampoulidis, and R. Venkataramanan, “Optimal combination of linear and spectral estimators for generalized linear models,” Foundations of Computational Mathematics. Springer, 2021.","ista":"Mondelli M, Thrampoulidis C, Venkataramanan R. 2021. Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics.","ama":"Mondelli M, Thrampoulidis C, Venkataramanan R. Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics. 2021. doi:10.1007/s10208-021-09531-x"},"publication":"Foundations of Computational Mathematics","file_date_updated":"2021-12-13T15:47:54Z","date_created":"2021-11-03T10:59:08Z","date_updated":"2023-09-05T14:13:57Z","author":[{"first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"full_name":"Thrampoulidis, Christos","first_name":"Christos","last_name":"Thrampoulidis"},{"full_name":"Venkataramanan, Ramji","last_name":"Venkataramanan","first_name":"Ramji"}],"department":[{"_id":"MaMo"}],"publisher":"Springer","publication_status":"published","acknowledgement":"M. Mondelli would like to thank Andrea Montanari for helpful discussions. All the authors would like to thank the anonymous reviewers for their helpful comments.","year":"2021","publication_identifier":{"issn":["1615-3375"],"eissn":["1615-3383"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1007/s10208-021-09531-x","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["2008.03326"],"isi":["000685721000001"]},"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},{"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","keyword":["Theoretical Computer Science","Computational Theory and Mathematics","Geometry and Topology","Discrete Mathematics and Combinatorics"],"date_published":"2021-07-01T00:00:00Z","citation":{"short":"J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, Discrete & Computational Geometry 66 (2021) 386–434.","mla":"Boissonnat, Jean-Daniel, et al. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” Discrete & Computational Geometry, vol. 66, no. 1, Springer Nature, 2021, pp. 386–434, doi:10.1007/s00454-020-00250-8.","chicago":"Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” Discrete & Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00250-8.","ama":"Boissonnat J-D, Kachanovich S, Wintraecken M. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete & Computational Geometry. 2021;66(1):386-434. doi:10.1007/s00454-020-00250-8","apa":"Boissonnat, J.-D., Kachanovich, S., & Wintraecken, M. (2021). Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00250-8","ieee":"J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Triangulating submanifolds: An elementary and quantified version of Whitney’s method,” Discrete & Computational Geometry, vol. 66, no. 1. Springer Nature, pp. 386–434, 2021.","ista":"Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete & Computational Geometry. 66(1), 386–434."},"publication":"Discrete & Computational Geometry","page":"386-434","article_type":"original","issue":"1","abstract":[{"lang":"eng","text":"We quantise Whitney’s construction to prove the existence of a triangulation for any C^2 manifold, so that we get an algorithm with explicit bounds. We also give a new elementary proof, which is completely geometric."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2021_DescreteCompGeopmetry_Boissonnat.pdf","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","file_size":983307,"file_id":"9795","relation":"main_file","date_created":"2021-08-06T09:52:29Z","date_updated":"2021-08-06T09:52:29Z","success":1,"checksum":"c848986091e56699dc12de85adb1e39c"}],"_id":"8940","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 66","ddc":["516"],"title":"Triangulating submanifolds: An elementary and quantified version of Whitney’s method","status":"public","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"month":"07","doi":"10.1007/s00454-020-00250-8","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000597770300001"]},"oa":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","ec_funded":1,"file_date_updated":"2021-08-06T09:52:29Z","author":[{"last_name":"Boissonnat","first_name":"Jean-Daniel","full_name":"Boissonnat, Jean-Daniel"},{"full_name":"Kachanovich, Siargey","last_name":"Kachanovich","first_name":"Siargey"},{"full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","first_name":"Mathijs"}],"volume":66,"date_updated":"2023-09-05T15:02:40Z","date_created":"2020-12-12T11:07:02Z","acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement Number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. Open access funding provided by the Institute of Science and Technology (IST Austria).","year":"2021","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"publication_status":"published"},{"intvolume":" 111","ddc":["510"],"status":"public","title":"The BCS energy gap at low density","_id":"9121","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_id":"9122","relation":"main_file","success":1,"checksum":"eaf1b3ff5026f120f0929a5c417dc842","date_created":"2021-02-15T09:31:07Z","date_updated":"2021-02-15T09:31:07Z","access_level":"open_access","file_name":"2021_LettersMathPhysics_Lauritsen.pdf","creator":"dernst","content_type":"application/pdf","file_size":329332}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"We show that the energy gap for the BCS gap equation is\r\nΞ=μ(8e−2+o(1))exp(π2μ−−√a)\r\nin the low density limit μ→0. Together with the similar result for the critical temperature by Hainzl and Seiringer (Lett Math Phys 84: 99–107, 2008), this shows that, in the low density limit, the ratio of the energy gap and critical temperature is a universal constant independent of the interaction potential V. The results hold for a class of potentials with negative scattering length a and no bound states."}],"article_type":"original","citation":{"ama":"Lauritsen AB. The BCS energy gap at low density. Letters in Mathematical Physics. 2021;111. doi:10.1007/s11005-021-01358-5","apa":"Lauritsen, A. B. (2021). The BCS energy gap at low density. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-021-01358-5","ieee":"A. B. Lauritsen, “The BCS energy gap at low density,” Letters in Mathematical Physics, vol. 111. Springer Nature, 2021.","ista":"Lauritsen AB. 2021. The BCS energy gap at low density. Letters in Mathematical Physics. 111, 20.","short":"A.B. Lauritsen, Letters in Mathematical Physics 111 (2021).","mla":"Lauritsen, Asbjørn Bækgaard. “The BCS Energy Gap at Low Density.” Letters in Mathematical Physics, vol. 111, 20, Springer Nature, 2021, doi:10.1007/s11005-021-01358-5.","chicago":"Lauritsen, Asbjørn Bækgaard. “The BCS Energy Gap at Low Density.” Letters in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s11005-021-01358-5."},"publication":"Letters in Mathematical Physics","date_published":"2021-02-12T00:00:00Z","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"12","department":[{"_id":"GradSch"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","acknowledgement":"Most of this work was done as part of the author’s master’s thesis. The author would like to thank Jan Philip Solovej for his supervision of this process.\r\nOpen Access funding provided by Institute of Science and Technology (IST Austria)","volume":111,"date_created":"2021-02-15T09:27:14Z","date_updated":"2023-09-05T15:17:16Z","author":[{"full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard"}],"article_number":"20","file_date_updated":"2021-02-15T09:31:07Z","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"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":["000617531900001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s11005-021-01358-5","publication_identifier":{"issn":["0377-9017"],"eissn":["1573-0530"]},"month":"02"},{"type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"In this paper, we present two new inertial projection-type methods for solving multivalued variational inequality problems in finite-dimensional spaces. We establish the convergence of the sequence generated by these methods when the multivalued mapping associated with the problem is only required to be locally bounded without any monotonicity assumption. Furthermore, the inertial techniques that we employ in this paper are quite different from the ones used in most papers. Moreover, based on the weaker assumptions on the inertial factor in our methods, we derive several special cases of our methods. Finally, we present some experimental results to illustrate the profits that we gain by introducing the inertial extrapolation steps."}],"intvolume":" 21","title":"New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity","status":"public","ddc":["510"],"_id":"9234","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"relation":"main_file","file_id":"9884","checksum":"22b4253a2e5da843622a2df713784b4c","success":1,"date_updated":"2021-08-11T12:44:16Z","date_created":"2021-08-11T12:44:16Z","access_level":"open_access","file_name":"2021_NetworksSpatialEconomics_Shehu.pdf","content_type":"application/pdf","file_size":834964,"creator":"kschuh"}],"oa_version":"Published Version","keyword":["Computer Networks and Communications","Software","Artificial Intelligence"],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","page":"291-323","article_type":"original","citation":{"chicago":"Izuchukwu, Chinedu, and Yekini Shehu. “New Inertial Projection Methods for Solving Multivalued Variational Inequality Problems beyond Monotonicity.” Networks and Spatial Economics. Springer Nature, 2021. https://doi.org/10.1007/s11067-021-09517-w.","short":"C. Izuchukwu, Y. Shehu, Networks and Spatial Economics 21 (2021) 291–323.","mla":"Izuchukwu, Chinedu, and Yekini Shehu. “New Inertial Projection Methods for Solving Multivalued Variational Inequality Problems beyond Monotonicity.” Networks and Spatial Economics, vol. 21, no. 2, Springer Nature, 2021, pp. 291–323, doi:10.1007/s11067-021-09517-w.","ieee":"C. Izuchukwu and Y. Shehu, “New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity,” Networks and Spatial Economics, vol. 21, no. 2. Springer Nature, pp. 291–323, 2021.","apa":"Izuchukwu, C., & Shehu, Y. (2021). New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity. Networks and Spatial Economics. Springer Nature. https://doi.org/10.1007/s11067-021-09517-w","ista":"Izuchukwu C, Shehu Y. 2021. New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity. Networks and Spatial Economics. 21(2), 291–323.","ama":"Izuchukwu C, Shehu Y. New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity. Networks and Spatial Economics. 2021;21(2):291-323. doi:10.1007/s11067-021-09517-w"},"publication":"Networks and Spatial Economics","date_published":"2021-06-01T00:00:00Z","ec_funded":1,"file_date_updated":"2021-08-11T12:44:16Z","department":[{"_id":"VlKo"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","acknowledgement":"The authors sincerely thank the Editor-in-Chief and anonymous referees for their careful reading, constructive comments and fruitful suggestions that help improve the manuscript. The research of the first author is supported by the National Research Foundation (NRF) South Africa (S& F-DSI/NRF Free Standing Postdoctoral Fellowship; Grant Number: 120784). The first author also acknowledges the financial support from DSI/NRF, South Africa Center of Excellence in Mathematical and Statistical Sciences (CoE-MaSS) Postdoctoral Fellowship. The second author has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160). Open Access funding provided by Institute of Science and Technology (IST Austria).","volume":21,"date_created":"2021-03-10T12:18:47Z","date_updated":"2023-09-05T15:32:32Z","author":[{"last_name":"Izuchukwu","first_name":"Chinedu","full_name":"Izuchukwu, Chinedu"},{"full_name":"Shehu, Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","first_name":"Yekini","last_name":"Shehu"}],"publication_identifier":{"eissn":["1572-9427"],"issn":["1566-113X"]},"month":"06","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000625002100001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s11067-021-09517-w"},{"month":"03","publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"external_id":{"arxiv":["1909.03488"]},"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":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"doi":"10.1007/s41468-020-00063-x","language":[{"iso":"eng"}],"file_date_updated":"2021-02-11T14:43:59Z","ec_funded":1,"acknowledgement":"AB was supported in part by the European Union’s Horizon 2020 research and innovation\r\nprogramme under the Marie Sklodowska-Curie GrantAgreement No. 754411 and NSF IIS-1513616. OB was supported in part by the Israel Science Foundation, Grant 1965/19. BW was supported in part by NSF IIS-1513616 and DBI-1661375. EM was supported in part by NSF CMMI-1800466, DMS-1800446, and CCF-1907591.We would like to thank the Institute for Mathematics and its Applications for hosting a workshop titled Bridging Statistics and Sheaves in May 2018, where this work was conceived.\r\nOpen Access funding provided by Institute of Science and Technology (IST Austria).","year":"2021","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","author":[{"full_name":"Brown, Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425","first_name":"Adam","last_name":"Brown"},{"full_name":"Bobrowski, Omer","first_name":"Omer","last_name":"Bobrowski"},{"full_name":"Munch, Elizabeth","last_name":"Munch","first_name":"Elizabeth"},{"first_name":"Bei","last_name":"Wang","full_name":"Wang, Bei"}],"date_created":"2021-02-11T14:41:02Z","date_updated":"2023-09-05T15:37:56Z","volume":5,"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"Journal of Applied and Computational Topology","citation":{"short":"A. Brown, O. Bobrowski, E. Munch, B. Wang, Journal of Applied and Computational Topology 5 (2021) 99–140.","mla":"Brown, Adam, et al. “Probabilistic Convergence and Stability of Random Mapper Graphs.” Journal of Applied and Computational Topology, vol. 5, no. 1, Springer Nature, 2021, pp. 99–140, doi:10.1007/s41468-020-00063-x.","chicago":"Brown, Adam, Omer Bobrowski, Elizabeth Munch, and Bei Wang. “Probabilistic Convergence and Stability of Random Mapper Graphs.” Journal of Applied and Computational Topology. Springer Nature, 2021. https://doi.org/10.1007/s41468-020-00063-x.","ama":"Brown A, Bobrowski O, Munch E, Wang B. Probabilistic convergence and stability of random mapper graphs. Journal of Applied and Computational Topology. 2021;5(1):99-140. doi:10.1007/s41468-020-00063-x","apa":"Brown, A., Bobrowski, O., Munch, E., & Wang, B. (2021). Probabilistic convergence and stability of random mapper graphs. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-020-00063-x","ieee":"A. Brown, O. Bobrowski, E. Munch, and B. Wang, “Probabilistic convergence and stability of random mapper graphs,” Journal of Applied and Computational Topology, vol. 5, no. 1. Springer Nature, pp. 99–140, 2021.","ista":"Brown A, Bobrowski O, Munch E, Wang B. 2021. Probabilistic convergence and stability of random mapper graphs. Journal of Applied and Computational Topology. 5(1), 99–140."},"article_type":"original","page":"99-140","date_published":"2021-03-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We study the probabilistic convergence between the mapper graph and the Reeb graph of a topological space X equipped with a continuous function f:X→R. We first give a categorification of the mapper graph and the Reeb graph by interpreting them in terms of cosheaves and stratified covers of the real line R. We then introduce a variant of the classic mapper graph of Singh et al. (in: Eurographics symposium on point-based graphics, 2007), referred to as the enhanced mapper graph, and demonstrate that such a construction approximates the Reeb graph of (X,f) when it is applied to points randomly sampled from a probability density function concentrated on (X,f). Our techniques are based on the interleaving distance of constructible cosheaves and topological estimation via kernel density estimates. Following Munch and Wang (In: 32nd international symposium on computational geometry, volume 51 of Leibniz international proceedings in informatics (LIPIcs), Dagstuhl, Germany, pp 53:1–53:16, 2016), we first show that the mapper graph of (X,f), a constructible R-space (with a fixed open cover), approximates the Reeb graph of the same space. We then construct an isomorphism between the mapper of (X,f) to the mapper of a super-level set of a probability density function concentrated on (X,f). Finally, building on the approach of Bobrowski et al. (Bernoulli 23(1):288–328, 2017b), we show that, with high probability, we can recover the mapper of the super-level set given a sufficiently large sample. Our work is the first to consider the mapper construction using the theory of cosheaves in a probabilistic setting. It is part of an ongoing effort to combine sheaf theory, probability, and statistics, to support topological data analysis with random data."}],"issue":"1","_id":"9111","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["510"],"title":"Probabilistic convergence and stability of random mapper graphs","status":"public","intvolume":" 5","file":[{"access_level":"open_access","file_name":"2020_JourApplCompTopology_Brown.pdf","content_type":"application/pdf","file_size":2090265,"creator":"dernst","relation":"main_file","file_id":"9112","checksum":"3f02e9d47c428484733da0f588a3c069","success":1,"date_created":"2021-02-11T14:43:59Z","date_updated":"2021-02-11T14:43:59Z"}],"oa_version":"Published Version"},{"file_date_updated":"2021-08-11T13:39:19Z","acknowledgement":"We thank the reviewers for their helpful comments, and also our colleagues, for illuminating discussions over the long gestation of this paper.","year":"2021","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","related_material":{"record":[{"id":"13062","relation":"research_data","status":"public"}]},"author":[{"full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","last_name":"Szep"},{"full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"volume":75,"date_updated":"2023-09-05T15:44:06Z","date_created":"2021-03-20T08:22:10Z","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"month":"05","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000636966300001"]},"isi":1,"quality_controlled":"1","doi":"10.1111/evo.14210","language":[{"iso":"eng"}],"type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"This paper analyses the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat‐dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments."}],"_id":"9252","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 75","status":"public","title":"Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model","ddc":["570"],"file":[{"success":1,"checksum":"b90fb5767d623602046fed03725e16ca","date_created":"2021-08-11T13:39:19Z","date_updated":"2021-08-11T13:39:19Z","file_id":"9886","relation":"main_file","creator":"kschuh","content_type":"application/pdf","file_size":734102,"access_level":"open_access","file_name":"2021_Evolution_Szep.pdf"}],"oa_version":"Published Version","scopus_import":"1","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","citation":{"chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14210.","short":"E. Szep, H. Sachdeva, N.H. Barton, Evolution 75 (2021) 1030–1045.","mla":"Szep, Eniko, et al. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 1030–45, doi:10.1111/evo.14210.","apa":"Szep, E., Sachdeva, H., & Barton, N. H. (2021). Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. Wiley. https://doi.org/10.1111/evo.14210","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model,” Evolution, vol. 75, no. 5. Wiley, pp. 1030–1045, 2021.","ista":"Szep E, Sachdeva H, Barton NH. 2021. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 75(5), 1030–1045.","ama":"Szep E, Sachdeva H, Barton NH. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 2021;75(5):1030-1045. doi:10.1111/evo.14210"},"publication":"Evolution","page":"1030-1045","article_type":"original","date_published":"2021-05-01T00:00:00Z"},{"type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"If there are no constraints on the process of speciation, then the number of species might be expected to match the number of available niches and this number might be indefinitely large. One possible constraint is the opportunity for allopatric divergence. In 1981, Felsenstein used a simple and elegant model to ask if there might also be genetic constraints. He showed that progress towards speciation could be described by the build‐up of linkage disequilibrium among divergently selected loci and between these loci and those contributing to other forms of reproductive isolation. Therefore, speciation is opposed by recombination, because it tends to break down linkage disequilibria. Felsenstein then introduced a crucial distinction between “two‐allele” models, which are subject to this effect, and “one‐allele” models, which are free from the recombination constraint. These fundamentally important insights have been the foundation for both empirical and theoretical studies of speciation ever since."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9374","intvolume":" 75","status":"public","title":"Homage to Felsenstein 1981, or why are there so few/many species?","oa_version":"Published Version","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"article_processing_charge":"No","day":"19","citation":{"chicago":"Butlin, Roger K., Maria R. Servedio, Carole M. Smadja, Claudia Bank, Nicholas H Barton, Samuel M. Flaxman, Tatiana Giraud, et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14235.","short":"R.K. Butlin, M.R. Servedio, C.M. Smadja, C. Bank, N.H. Barton, S.M. Flaxman, T. Giraud, R. Hopkins, E.L. Larson, M.E. Maan, J. Meier, R. Merrill, M.A.F. Noor, D. Ortiz‐Barrientos, A. Qvarnström, Evolution 75 (2021) 978–988.","mla":"Butlin, Roger K., et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 978–88, doi:10.1111/evo.14235.","ieee":"R. K. Butlin et al., “Homage to Felsenstein 1981, or why are there so few/many species?,” Evolution, vol. 75, no. 5. Wiley, pp. 978–988, 2021.","apa":"Butlin, R. K., Servedio, M. R., Smadja, C. M., Bank, C., Barton, N. H., Flaxman, S. M., … Qvarnström, A. (2021). Homage to Felsenstein 1981, or why are there so few/many species? Evolution. Wiley. https://doi.org/10.1111/evo.14235","ista":"Butlin RK, Servedio MR, Smadja CM, Bank C, Barton NH, Flaxman SM, Giraud T, Hopkins R, Larson EL, Maan ME, Meier J, Merrill R, Noor MAF, Ortiz‐Barrientos D, Qvarnström A. 2021. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 75(5), 978–988.","ama":"Butlin RK, Servedio MR, Smadja CM, et al. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 2021;75(5):978-988. doi:10.1111/evo.14235"},"publication":"Evolution","page":"978-988","article_type":"original","date_published":"2021-04-19T00:00:00Z","year":"2021","acknowledgement":"RKB was funded by the Natural Environment Research Council (NE/P012272/1 & NE/P001610/1), the European Research Council (693030 BARRIERS), and the Swedish Research Council (VR) (2018‐03695). MRS was funded by the National Science Foundation (Grant No. DEB1939290).","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."},{"full_name":"Servedio, Maria R.","first_name":"Maria R.","last_name":"Servedio"},{"first_name":"Carole M.","last_name":"Smadja","full_name":"Smadja, Carole M."},{"first_name":"Claudia","last_name":"Bank","full_name":"Bank, Claudia"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"full_name":"Flaxman, Samuel M.","last_name":"Flaxman","first_name":"Samuel M."},{"last_name":"Giraud","first_name":"Tatiana","full_name":"Giraud, Tatiana"},{"last_name":"Hopkins","first_name":"Robin","full_name":"Hopkins, Robin"},{"last_name":"Larson","first_name":"Erica L.","full_name":"Larson, Erica L."},{"last_name":"Maan","first_name":"Martine E.","full_name":"Maan, Martine E."},{"full_name":"Meier, Joana","last_name":"Meier","first_name":"Joana"},{"full_name":"Merrill, Richard","first_name":"Richard","last_name":"Merrill"},{"last_name":"Noor","first_name":"Mohamed A. F.","full_name":"Noor, Mohamed A. F."},{"full_name":"Ortiz‐Barrientos, Daniel","last_name":"Ortiz‐Barrientos","first_name":"Daniel"},{"first_name":"Anna","last_name":"Qvarnström","full_name":"Qvarnström, Anna"}],"volume":75,"date_created":"2021-05-06T04:34:47Z","date_updated":"2023-09-05T15:44:33Z","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"month":"04","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://onlinelibrary.wiley.com/doi/10.1111/evo.14235","open_access":"1"}],"oa":1,"external_id":{"isi":["000647224000001"]},"quality_controlled":"1","isi":1,"doi":"10.1111/evo.14235","language":[{"iso":"eng"}]},{"doi":"10.5061/DRYAD.8GTHT76P1","date_published":"2021-03-02T00:00:00Z","citation":{"chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model.” Dryad, 2021. https://doi.org/10.5061/DRYAD.8GTHT76P1.","short":"E. Szep, H. Sachdeva, N.H. Barton, (2021).","mla":"Szep, Eniko, et al. Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model. Dryad, 2021, doi:10.5061/DRYAD.8GTHT76P1.","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad, 2021.","apa":"Szep, E., Sachdeva, H., & Barton, N. H. (2021). Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. Dryad. https://doi.org/10.5061/DRYAD.8GTHT76P1","ista":"Szep E, Sachdeva H, Barton NH. 2021. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model, Dryad, 10.5061/DRYAD.8GTHT76P1.","ama":"Szep E, Sachdeva H, Barton NH. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. 2021. doi:10.5061/DRYAD.8GTHT76P1"},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.8gtht76p1"}],"day":"02","month":"03","article_processing_charge":"No","author":[{"full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","last_name":"Szep"},{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"9252"}]},"date_created":"2023-05-23T16:17:02Z","date_updated":"2023-09-05T15:44:05Z","oa_version":"Published Version","year":"2021","_id":"13062","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model","status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","abstract":[{"text":"This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.","lang":"eng"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"research_data_reference"},{"month":"08","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"language":[{"iso":"eng"}],"doi":"10.1111/mec.15861","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":{"pmid":["33638231"],"isi":["000669439700001"]},"oa":1,"file_date_updated":"2022-03-08T11:31:30Z","date_updated":"2023-09-05T16:02:19Z","date_created":"2022-03-08T11:28:32Z","volume":30,"author":[{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"publication_status":"published","publisher":"Wiley","department":[{"_id":"BeVi"}],"year":"2021","acknowledgement":"We thank everyone who helped with fieldwork, snail processing and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot, Mark Ravinet, Irena Senčić and Zuzanna Zagrodzka. We are also grateful to Edinburgh Genomics for library preparation and sequencing, to Stuart Baird and Mark Ravinet for helpful discussions, and to three anonymous reviewers for their constructive comments. This work was supported by the Natural Environment Research Council (NE/K014021/1), the European Research Council (AdG-693030-BARRIERS), Swedish Research Councils Formas and Vetenskapsrådet through a Linnaeus grant to the Centre for Marine Evolutionary Biology (217-2008-1719), the European Regional Development Fund (POCI-01-0145-FEDER-030628), and the Fundação para a iência e a Tecnologia,\r\nPortugal (PTDC/BIA-EVL/\r\n30628/2017). A.M.W. and R.F. were\r\nfunded by the European Union’s Horizon 2020 research and innovation\r\nprogramme under Marie Skłodowska-Curie\r\ngrant agreements\r\nno. 754411/797747 and no. 706376, respectively.","pmid":1,"day":"01","has_accepted_license":"1","article_processing_charge":"No","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","date_published":"2021-08-01T00:00:00Z","article_type":"original","page":"3797-3814","publication":"Molecular Ecology","citation":{"chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, and Roger Butlin. “Using Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15861.","mla":"Westram, Anja M., et al. “Using Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.” Molecular Ecology, vol. 30, no. 15, Wiley, 2021, pp. 3797–814, doi:10.1111/mec.15861.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, Molecular Ecology 30 (2021) 3797–3814.","ista":"Westram AM, Faria R, Johannesson K, Butlin R. 2021. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Molecular Ecology. 30(15), 3797–3814.","apa":"Westram, A. M., Faria, R., Johannesson, K., & Butlin, R. (2021). Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15861","ieee":"A. M. Westram, R. Faria, K. Johannesson, and R. Butlin, “Using replicate hybrid zones to understand the genomic basis of adaptive divergence,” Molecular Ecology, vol. 30, no. 15. Wiley, pp. 3797–3814, 2021.","ama":"Westram AM, Faria R, Johannesson K, Butlin R. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Molecular Ecology. 2021;30(15):3797-3814. doi:10.1111/mec.15861"},"abstract":[{"lang":"eng","text":"Combining hybrid zone analysis with genomic data is a promising approach to understanding the genomic basis of adaptive divergence. It allows for the identification of genomic regions underlying barriers to gene flow. It also provides insights into spatial patterns of allele frequency change, informing about the interplay between environmental factors, dispersal and selection. However, when only a single hybrid zone is analysed, it is difficult to separate patterns generated by selection from those resulting from chance. Therefore, it is beneficial to look for repeatable patterns across replicate hybrid zones in the same system. We applied this approach to the marine snail Littorina saxatilis, which contains two ecotypes, adapted to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous hybrid zones between ecotypes offered the opportunity to test for the repeatability of genomic architectures and spatial patterns of divergence. We sampled and phenotyped snails from seven replicate hybrid zones on the Swedish west coast and genotyped them for thousands of single nucleotide polymorphisms. Shell shape and size showed parallel clines across all zones. Many genomic regions showing steep clines and/or high differentiation were shared among hybrid zones, consistent with a common evolutionary history and extensive gene flow between zones, and supporting the importance of these regions for divergence. In particular, we found that several large putative inversions contribute to divergence in all locations. Additionally, we found evidence for consistent displacement of clines from the boulder–rock transition. Our results demonstrate patterns of spatial variation that would not be accessible without continuous spatial sampling, a large genomic data set and replicate hybrid zones."}],"issue":"15","type":"journal_article","file":[{"creator":"dernst","file_size":1726548,"content_type":"application/pdf","file_name":"2021_MolecularEcology_Westram.pdf","access_level":"open_access","date_updated":"2022-03-08T11:31:30Z","date_created":"2022-03-08T11:31:30Z","success":1,"checksum":"d5611f243ceb63a0e091d6662ebd9cda","file_id":"10839","relation":"main_file"}],"oa_version":"Published Version","status":"public","title":"Using replicate hybrid zones to understand the genomic basis of adaptive divergence","ddc":["570"],"intvolume":" 30","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10838"},{"date_published":"2021-03-17T00:00:00Z","page":"2275-2291","article_type":"original","citation":{"chicago":"El Houari, I, C Van Beirs, HE Arents, Huibin Han, A Chanoca, D Opdenacker, J Pollier, et al. “Seedling Developmental Defects upon Blocking CINNAMATE-4-HYDROXYLASE Are Caused by Perturbations in Auxin Transport.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17349.","short":"I. El Houari, C. Van Beirs, H. Arents, H. Han, A. Chanoca, D. Opdenacker, J. Pollier, V. Storme, W. Steenackers, M. Quareshy, R. Napier, T. Beeckman, J. Friml, B. De Rybel, W. Boerjan, B. Vanholme, New Phytologist 230 (2021) 2275–2291.","mla":"El Houari, I., et al. “Seedling Developmental Defects upon Blocking CINNAMATE-4-HYDROXYLASE Are Caused by Perturbations in Auxin Transport.” New Phytologist, vol. 230, no. 6, Wiley, 2021, pp. 2275–91, doi:10.1111/nph.17349.","ieee":"I. El Houari et al., “Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport,” New Phytologist, vol. 230, no. 6. Wiley, pp. 2275–2291, 2021.","apa":"El Houari, I., Van Beirs, C., Arents, H., Han, H., Chanoca, A., Opdenacker, D., … Vanholme, B. (2021). Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. New Phytologist. Wiley. https://doi.org/10.1111/nph.17349","ista":"El Houari I, Van Beirs C, Arents H, Han H, Chanoca A, Opdenacker D, Pollier J, Storme V, Steenackers W, Quareshy M, Napier R, Beeckman T, Friml J, De Rybel B, Boerjan W, Vanholme B. 2021. Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. New Phytologist. 230(6), 2275–2291.","ama":"El Houari I, Van Beirs C, Arents H, et al. Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. New Phytologist. 2021;230(6):2275-2291. doi:10.1111/nph.17349"},"publication":"New Phytologist","article_processing_charge":"No","day":"17","scopus_import":"1","oa_version":"Published Version","intvolume":" 230","status":"public","title":"Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport","_id":"9288","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"6","abstract":[{"lang":"eng","text":"• The phenylpropanoid pathway serves a central role in plant metabolism, providing numerous compounds involved in diverse physiological processes. Most carbon entering the pathway is incorporated into lignin. Although several phenylpropanoid pathway mutants show seedling growth arrest, the role for lignin in seedling growth and development is unexplored.\r\n• We use complementary pharmacological and genetic approaches to block CINNAMATE‐4‐HYDROXYLASE (C4H) functionality in Arabidopsis seedlings and a set of molecular and biochemical techniques to investigate the underlying phenotypes.\r\n• Blocking C4H resulted in reduced lateral rooting and increased adventitious rooting apically in the hypocotyl. These phenotypes coincided with an inhibition in auxin transport. The upstream accumulation in cis‐cinnamic acid was found to likely cause polar auxin transport inhibition. Conversely, a downstream depletion in lignin perturbed phloem‐mediated auxin transport. Restoring lignin deposition effectively reestablished phloem transport and, accordingly, auxin homeostasis.\r\n• Our results show that the accumulation of bioactive intermediates and depletion in lignin jointly cause the aberrant phenotypes upon blocking C4H, and demonstrate that proper deposition of lignin is essential for the establishment of auxin distribution in seedlings. Our data position the phenylpropanoid pathway and lignin in a new physiological framework, consolidating their importance in plant growth and development."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1111/nph.17349","quality_controlled":"1","isi":1,"oa":1,"external_id":{"pmid":["33728703"],"isi":["000639552400001"]},"main_file_link":[{"open_access":"1","url":"https://biblio.ugent.be/publication/8703799/file/8703800.pdf"}],"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"month":"03","volume":230,"date_updated":"2023-09-05T15:46:55Z","date_created":"2021-03-26T12:09:01Z","author":[{"last_name":"El Houari","first_name":"I","full_name":"El Houari, I"},{"first_name":"C","last_name":"Van Beirs","full_name":"Van Beirs, C"},{"full_name":"Arents, HE","first_name":"HE","last_name":"Arents"},{"full_name":"Han, Huibin","first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"first_name":"A","last_name":"Chanoca","full_name":"Chanoca, A"},{"full_name":"Opdenacker, D","first_name":"D","last_name":"Opdenacker"},{"full_name":"Pollier, J","last_name":"Pollier","first_name":"J"},{"last_name":"Storme","first_name":"V","full_name":"Storme, V"},{"full_name":"Steenackers, W","last_name":"Steenackers","first_name":"W"},{"last_name":"Quareshy","first_name":"M","full_name":"Quareshy, M"},{"first_name":"R","last_name":"Napier","full_name":"Napier, R"},{"first_name":"T","last_name":"Beeckman","full_name":"Beeckman, T"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"last_name":"De Rybel","first_name":"B","full_name":"De Rybel, B"},{"full_name":"Boerjan, W","last_name":"Boerjan","first_name":"W"},{"full_name":"Vanholme, B","last_name":"Vanholme","first_name":"B"}],"publisher":"Wiley","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2021"},{"date_published":"2021-05-01T00:00:00Z","page":"1553-1556","article_type":"letter_note","citation":{"chicago":"Pranger, Christina L., Judit Singer, Verena K. Köhler, Isabella Pali‐Schöll, Alessandro Fiocchi, Sophia N. Karagiannis, Olatz Zenarruzabeitia, Francisco Borrego, and Erika Jensen‐Jarolim. “PIPE‐cloned Human IgE and IgG4 Antibodies: New Tools for Investigating Cow’s Milk Allergy and Tolerance.” Allergy. Wiley, 2021. https://doi.org/10.1111/all.14604.","short":"C.L. Pranger, J. Singer, V.K. Köhler, I. Pali‐Schöll, A. Fiocchi, S.N. Karagiannis, O. Zenarruzabeitia, F. Borrego, E. Jensen‐Jarolim, Allergy 76 (2021) 1553–1556.","mla":"Pranger, Christina L., et al. “PIPE‐cloned Human IgE and IgG4 Antibodies: New Tools for Investigating Cow’s Milk Allergy and Tolerance.” Allergy, vol. 76, no. 5, Wiley, 2021, pp. 1553–56, doi:10.1111/all.14604.","apa":"Pranger, C. L., Singer, J., Köhler, V. K., Pali‐Schöll, I., Fiocchi, A., Karagiannis, S. N., … Jensen‐Jarolim, E. (2021). PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. Allergy. Wiley. https://doi.org/10.1111/all.14604","ieee":"C. L. Pranger et al., “PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance,” Allergy, vol. 76, no. 5. Wiley, pp. 1553–1556, 2021.","ista":"Pranger CL, Singer J, Köhler VK, Pali‐Schöll I, Fiocchi A, Karagiannis SN, Zenarruzabeitia O, Borrego F, Jensen‐Jarolim E. 2021. PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. Allergy. 76(5), 1553–1556.","ama":"Pranger CL, Singer J, Köhler VK, et al. PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. Allergy. 2021;76(5):1553-1556. doi:10.1111/all.14604"},"publication":"Allergy","article_processing_charge":"No","has_accepted_license":"1","day":"01","keyword":["Immunology","Immunology and Allergy"],"scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_Allergy_Pranger.pdf","creator":"dernst","content_type":"application/pdf","file_size":626081,"file_id":"10837","relation":"main_file","success":1,"checksum":"9526f9554112fc027c9f7fa540c488cd","date_updated":"2022-03-08T11:23:16Z","date_created":"2022-03-08T11:23:16Z"}],"intvolume":" 76","status":"public","ddc":["570"],"title":"PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow's milk allergy and tolerance","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10836","issue":"5","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1111/all.14604","quality_controlled":"1","isi":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":["32990982"],"isi":["000577708800001"]},"publication_identifier":{"eissn":["1398-9995"],"issn":["0105-4538"]},"month":"05","volume":76,"date_updated":"2023-09-05T15:58:53Z","date_created":"2022-03-08T11:19:05Z","author":[{"first_name":"Christina L.","last_name":"Pranger","full_name":"Pranger, Christina L."},{"first_name":"Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit"},{"full_name":"Köhler, Verena K.","last_name":"Köhler","first_name":"Verena K."},{"full_name":"Pali‐Schöll, Isabella","first_name":"Isabella","last_name":"Pali‐Schöll"},{"full_name":"Fiocchi, Alessandro","first_name":"Alessandro","last_name":"Fiocchi"},{"last_name":"Karagiannis","first_name":"Sophia N.","full_name":"Karagiannis, Sophia N."},{"first_name":"Olatz","last_name":"Zenarruzabeitia","full_name":"Zenarruzabeitia, Olatz"},{"last_name":"Borrego","first_name":"Francisco","full_name":"Borrego, Francisco"},{"first_name":"Erika","last_name":"Jensen‐Jarolim","full_name":"Jensen‐Jarolim, Erika"}],"department":[{"_id":"Bio"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2021","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) grants MCCA W1248-B30 and SFB F4606-B28 to EJJ. CP received a short-term research fellowship of the European Federation of Immunological Societies (EFIS-IL) for a research visit at Biocruces Bizkaia Health Research Institute, Barakaldo, Spain. VKK received an EFIS-IL short-term research fellowship for a research visit at King’s College London. The research was funded by the National Institute for Health Research (NIHR) Biomedical Research Centre (BRC) based at Guy's and St Thomas' NHS Foundation Trust and King's College London (IS-BRC-1215-20006) (SNK). The authors acknowledge support by the Medical Research Council (MR/L023091/1) (SNK); Breast Cancer Now (147; KCL-BCN-Q3)(SNK); Cancer Research UK (C30122/A11527; C30122/A15774) (SNK); Cancer Research UK King's Health Partners Centre at King's College London (C604/A25135) (SNK); CRUK/NIHR in England/DoH for Scotland, Wales and Northern Ireland Experimental Cancer Medicine Centre (C10355/A15587) (SNK). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health. Additionally, this work was funded by Instituto de Salud Carlos III through the project \"PI16/01223\" (Co-funded by European Regional Development Fund; “A way to make Europe”) to FB and by the Department of Health, Basque Government through the project “2019111031” to OZ. OZ is recipient of a Sara Borrell 2017 post-doctoral contract “CD17/00128” funded by Instituto de Salud Carlos III (Co-funded by European Social Fund; “Investing in your future”).","file_date_updated":"2022-03-08T11:23:16Z"},{"file_date_updated":"2021-02-04T09:53:16Z","date_updated":"2023-09-05T16:06:24Z","date_created":"2020-10-05T12:45:36Z","volume":229,"author":[{"last_name":"Ke","first_name":"M","full_name":"Ke, M"},{"full_name":"Ma, Z","last_name":"Ma","first_name":"Z"},{"full_name":"Wang, D","last_name":"Wang","first_name":"D"},{"full_name":"Sun, Y","first_name":"Y","last_name":"Sun"},{"full_name":"Wen, C","first_name":"C","last_name":"Wen"},{"last_name":"Huang","first_name":"D","full_name":"Huang, D"},{"full_name":"Chen, Z","last_name":"Chen","first_name":"Z"},{"full_name":"Yang, L","first_name":"L","last_name":"Yang"},{"full_name":"Tan, Shutang","last_name":"Tan","first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Li","first_name":"R","full_name":"Li, R"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"first_name":"Y","last_name":"Miao","full_name":"Miao, Y"},{"full_name":"Chen, X","first_name":"X","last_name":"Chen"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Wiley","acknowledgement":"This work was supported by the National Key Research andDevelopment Programme of China (2017YFA0506100), theNational Natural Science Foundation of China (31870170 and31701168), and the Fok Ying Tung Education Foundation(161027) to XC; NTU startup grant (M4081533) and NIM/01/2016 (NTU, Singapore) to YM. We thank Lei Shi andZhongquan Lin for microscopy assistance.","year":"2021","pmid":1,"month":"01","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"language":[{"iso":"eng"}],"doi":"10.1111/nph.16915","quality_controlled":"1","isi":1,"external_id":{"pmid":["32901934"],"isi":["000573568000001"]},"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,"abstract":[{"lang":"eng","text":"To adapt to the diverse array of biotic and abiotic cues, plants have evolved sophisticated mechanisms to sense changes in environmental conditions and modulate their growth. Growth-promoting hormones and defence signalling fine tune plant development antagonistically. During host-pathogen interactions, this defence-growth trade-off is mediated by the counteractive effects of the defence hormone salicylic acid (SA) and the growth hormone auxin. Here we revealed an underlying mechanism of SA regulating auxin signalling by constraining the plasma membrane dynamics of PIN2 auxin efflux transporter in Arabidopsis thaliana roots. The lateral diffusion of PIN2 proteins is constrained by SA signalling, during which PIN2 proteins are condensed into hyperclusters depending on REM1.2-mediated nanodomain compartmentalisation. Furthermore, membrane nanodomain compartmentalisation by SA or Remorin (REM) assembly significantly suppressed clathrin-mediated endocytosis. Consequently, SA-induced heterogeneous surface condensation disrupted asymmetric auxin distribution and the resultant gravitropic response. Our results demonstrated a defence-growth trade-off mechanism by which SA signalling crosstalked with auxin transport by concentrating membrane-resident PIN2 into heterogeneous compartments."}],"issue":"2","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2021_NewPhytologist_Ke.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3674502,"creator":"dernst","relation":"main_file","file_id":"9085","date_updated":"2021-02-04T09:53:16Z","date_created":"2021-02-04T09:53:16Z","checksum":"d36b6a8c6fafab66264e0d27114dae63","success":1}],"status":"public","ddc":["580"],"title":"Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana","intvolume":" 229","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8608","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2021-01-01T00:00:00Z","article_type":"original","page":"963-978","publication":"New Phytologist","citation":{"chicago":"Ke, M, Z Ma, D Wang, Y Sun, C Wen, D Huang, Z Chen, et al. “Salicylic Acid Regulates PIN2 Auxin Transporter Hyper-Clustering and Root Gravitropic Growth via Remorin-Dependent Lipid Nanodomain Organization in Arabidopsis Thaliana.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.16915.","short":"M. Ke, Z. Ma, D. Wang, Y. Sun, C. Wen, D. Huang, Z. Chen, L. Yang, S. Tan, R. Li, J. Friml, Y. Miao, X. Chen, New Phytologist 229 (2021) 963–978.","mla":"Ke, M., et al. “Salicylic Acid Regulates PIN2 Auxin Transporter Hyper-Clustering and Root Gravitropic Growth via Remorin-Dependent Lipid Nanodomain Organization in Arabidopsis Thaliana.” New Phytologist, vol. 229, no. 2, Wiley, 2021, pp. 963–78, doi:10.1111/nph.16915.","apa":"Ke, M., Ma, Z., Wang, D., Sun, Y., Wen, C., Huang, D., … Chen, X. (2021). Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. New Phytologist. Wiley. https://doi.org/10.1111/nph.16915","ieee":"M. Ke et al., “Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana,” New Phytologist, vol. 229, no. 2. Wiley, pp. 963–978, 2021.","ista":"Ke M, Ma Z, Wang D, Sun Y, Wen C, Huang D, Chen Z, Yang L, Tan S, Li R, Friml J, Miao Y, Chen X. 2021. Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. New Phytologist. 229(2), 963–978.","ama":"Ke M, Ma Z, Wang D, et al. Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. New Phytologist. 2021;229(2):963-978. doi:10.1111/nph.16915"}},{"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","publication":"Reviews in Mathematical Physics","citation":{"ama":"Benedikter NP. Bosonic collective excitations in Fermi gases. Reviews in Mathematical Physics. 2021;33(1). doi:10.1142/s0129055x20600090","apa":"Benedikter, N. P. (2021). Bosonic collective excitations in Fermi gases. Reviews in Mathematical Physics. World Scientific. https://doi.org/10.1142/s0129055x20600090","ieee":"N. P. Benedikter, “Bosonic collective excitations in Fermi gases,” Reviews in Mathematical Physics, vol. 33, no. 1. World Scientific, 2021.","ista":"Benedikter NP. 2021. Bosonic collective excitations in Fermi gases. Reviews in Mathematical Physics. 33(1), 2060009.","short":"N.P. Benedikter, Reviews in Mathematical Physics 33 (2021).","mla":"Benedikter, Niels P. “Bosonic Collective Excitations in Fermi Gases.” Reviews in Mathematical Physics, vol. 33, no. 1, 2060009, World Scientific, 2021, doi:10.1142/s0129055x20600090.","chicago":"Benedikter, Niels P. “Bosonic Collective Excitations in Fermi Gases.” Reviews in Mathematical Physics. World Scientific, 2021. https://doi.org/10.1142/s0129055x20600090."},"date_published":"2021-01-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Hartree–Fock theory has been justified as a mean-field approximation for fermionic systems. However, it suffers from some defects in predicting physical properties, making necessary a theory of quantum correlations. Recently, bosonization of many-body correlations has been rigorously justified as an upper bound on the correlation energy at high density with weak interactions. We review the bosonic approximation, deriving an effective Hamiltonian. We then show that for systems with Coulomb interaction this effective theory predicts collective excitations (plasmons) in accordance with the random phase approximation of Bohm and Pines, and with experimental observation.","lang":"eng"}],"issue":"1","title":"Bosonic collective excitations in Fermi gases","status":"public","intvolume":" 33","_id":"7900","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","month":"01","publication_identifier":{"eissn":["1793-6659"],"issn":["0129-055X"]},"isi":1,"quality_controlled":"1","project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["1910.08190"],"isi":["000613313200010"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1910.08190","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1142/s0129055x20600090","article_number":"2060009","ec_funded":1,"publication_status":"published","publisher":"World Scientific","department":[{"_id":"RoSe"}],"year":"2021","date_updated":"2023-09-05T16:07:40Z","date_created":"2020-05-28T16:47:55Z","volume":33,"author":[{"first_name":"Niels P","last_name":"Benedikter","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1071-6091","full_name":"Benedikter, Niels P"}]},{"volume":33,"date_updated":"2023-09-05T16:08:02Z","date_created":"2022-03-18T08:11:34Z","author":[{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"publisher":"World Scientific Publishing","department":[{"_id":"RoSe"}],"publication_status":"published","year":"2021","acknowledgement":"This work was supported by the European Research Council (ERC) under the Euro-pean Union’s Horizon 2020 research and innovation programme (grant agreementNo. 694227).","ec_funded":1,"article_number":"2060012","language":[{"iso":"eng"}],"doi":"10.1142/s0129055x20600120","project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1912.12509"],"isi":["000613313200013"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.12509"}],"publication_identifier":{"issn":["0129-055X"],"eissn":["1793-6659"]},"month":"02","oa_version":"Preprint","intvolume":" 33","title":"The polaron at strong coupling","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10852","issue":"01","abstract":[{"lang":"eng","text":" We review old and new results on the Fröhlich polaron model. The discussion includes the validity of the (classical) Pekar approximation in the strong coupling limit, quantum corrections to this limit, as well as the divergence of the effective polaron mass."}],"type":"journal_article","date_published":"2021-02-01T00:00:00Z","article_type":"original","citation":{"chicago":"Seiringer, Robert. “The Polaron at Strong Coupling.” Reviews in Mathematical Physics. World Scientific Publishing, 2021. https://doi.org/10.1142/s0129055x20600120.","short":"R. Seiringer, Reviews in Mathematical Physics 33 (2021).","mla":"Seiringer, Robert. “The Polaron at Strong Coupling.” Reviews in Mathematical Physics, vol. 33, no. 01, 2060012, World Scientific Publishing, 2021, doi:10.1142/s0129055x20600120.","apa":"Seiringer, R. (2021). The polaron at strong coupling. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/s0129055x20600120","ieee":"R. Seiringer, “The polaron at strong coupling,” Reviews in Mathematical Physics, vol. 33, no. 01. World Scientific Publishing, 2021.","ista":"Seiringer R. 2021. The polaron at strong coupling. Reviews in Mathematical Physics. 33(01), 2060012.","ama":"Seiringer R. The polaron at strong coupling. Reviews in Mathematical Physics. 2021;33(01). doi:10.1142/s0129055x20600120"},"publication":"Reviews in Mathematical Physics","article_processing_charge":"No","day":"01","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"scopus_import":"1"},{"oa_version":"Published Version","file":[{"content_type":"application/zip","file_size":13446994,"creator":"patrickd","file_name":"thesis_source.zip","access_level":"closed","date_created":"2021-02-02T14:09:25Z","date_updated":"2021-02-03T10:37:28Z","checksum":"bcf27986147cab0533b6abadd74e7629","relation":"source_file","file_id":"9063"},{"relation":"main_file","file_id":"9064","checksum":"9cc8af266579a464385bbe2aff6af606","success":1,"date_updated":"2021-02-02T14:09:18Z","date_created":"2021-02-02T14:09:18Z","access_level":"open_access","file_name":"thesis_pdfA2b.pdf","content_type":"application/pdf","file_size":5210329,"creator":"patrickd"}],"ddc":["006","514","516"],"title":"Multi-cover persistence and Delaunay mosaics","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9056","abstract":[{"text":"In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2021-02-01T00:00:00Z","page":"134","citation":{"ista":"Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.","apa":"Osang, G. F. (2021). Multi-cover persistence and Delaunay mosaics. Institute of Science and Technology Austria, Klosterneuburg. https://doi.org/10.15479/AT:ISTA:9056","ieee":"G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021.","ama":"Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:10.15479/AT:ISTA:9056","chicago":"Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9056.","mla":"Osang, Georg F. Multi-Cover Persistence and Delaunay Mosaics. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9056.","short":"G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","date_updated":"2023-09-07T13:29:01Z","date_created":"2021-02-02T14:11:06Z","author":[{"last_name":"Osang","first_name":"Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"187"},{"relation":"part_of_dissertation","status":"public","id":"8703"}]},"publication_status":"published","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","year":"2021","file_date_updated":"2021-02-03T10:37:28Z","place":"Klosterneuburg","supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:9056","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":"02","publication_identifier":{"issn":["2663-337X"]}},{"abstract":[{"lang":"eng","text":"In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.\r\nIn the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time\r\n(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result\r\nimproves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"file_id":"9043","relation":"main_file","date_created":"2021-01-25T14:19:03Z","date_updated":"2021-01-25T14:19:03Z","success":1,"checksum":"5a93658a5f19478372523ee232887e2b","file_name":"thesis.pdf","access_level":"open_access","creator":"gcipollo","file_size":4127796,"content_type":"application/pdf"},{"date_updated":"2021-01-25T14:19:10Z","date_created":"2021-01-25T14:19:10Z","checksum":"e8270eddfe6a988e92a53c88d1d19b8c","file_id":"9044","relation":"source_file","creator":"gcipollo","file_size":12775206,"content_type":"application/zip","file_name":"Thesis_files.zip","access_level":"closed"}],"oa_version":"Published Version","ddc":["510"],"status":"public","title":"Fluctuations in the spectrum of random matrices","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9022","day":"25","has_accepted_license":"1","article_processing_charge":"No","date_published":"2021-01-25T00:00:00Z","page":"380","citation":{"ama":"Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:10.15479/AT:ISTA:9022","ista":"Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria.","ieee":"G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute of Science and Technology Austria, 2021.","apa":"Cipolloni, G. (2021). Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9022","mla":"Cipolloni, Giorgio. Fluctuations in the Spectrum of Random Matrices. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9022.","short":"G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute of Science and Technology Austria, 2021.","chicago":"Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9022."},"file_date_updated":"2021-01-25T14:19:10Z","ec_funded":1,"date_updated":"2023-09-07T13:29:32Z","date_created":"2021-01-21T18:16:54Z","author":[{"first_name":"Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"publisher":"Institute of Science and Technology Austria","year":"2021","acknowledgement":"I gratefully acknowledge the financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and my advisor’s ERC Advanced Grant No. 338804.","month":"01","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","supervisor":[{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:9022","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"oa":1},{"language":[{"iso":"eng"}],"conference":{"name":" ICLR: International Conference on Learning Representations","end_date":"2021-05-07","location":"Virtual","start_date":"2021-05-03"},"date_published":"2021-05-01T00:00:00Z","quality_controlled":"1","publication":"9th International Conference on Learning Representations","main_file_link":[{"open_access":"1","url":"https://openreview.net/pdf?id=krz7T0xU9Z_"}],"oa":1,"citation":{"ama":"Phuong M, Lampert C. The inductive bias of ReLU networks on orthogonally separable data. In: 9th International Conference on Learning Representations. ; 2021.","ista":"Phuong M, Lampert C. 2021. The inductive bias of ReLU networks on orthogonally separable data. 9th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","apa":"Phuong, M., & Lampert, C. (2021). The inductive bias of ReLU networks on orthogonally separable data. In 9th International Conference on Learning Representations. Virtual.","ieee":"M. Phuong and C. Lampert, “The inductive bias of ReLU networks on orthogonally separable data,” in 9th International Conference on Learning Representations, Virtual, 2021.","mla":"Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on Orthogonally Separable Data.” 9th International Conference on Learning Representations, 2021.","short":"M. Phuong, C. Lampert, in:, 9th International Conference on Learning Representations, 2021.","chicago":"Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on Orthogonally Separable Data.” In 9th International Conference on Learning Representations, 2021."},"day":"01","month":"05","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_updated":"2023-09-07T13:29:50Z","date_created":"2021-05-24T11:16:46Z","oa_version":"Published Version","file":[{"file_id":"9417","relation":"main_file","checksum":"f34ff17017527db5ba6927f817bdd125","date_updated":"2021-05-24T11:15:57Z","date_created":"2021-05-24T11:15:57Z","access_level":"open_access","file_name":"iclr2021_conference.pdf","creator":"bphuong","file_size":502356,"content_type":"application/pdf"}],"author":[{"full_name":"Bui Thi Mai, Phuong","first_name":"Phuong","last_name":"Bui Thi Mai","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9418"}]},"status":"public","title":"The inductive bias of ReLU networks on orthogonally separable data","publication_status":"published","ddc":["000"],"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9416","year":"2021","abstract":[{"lang":"eng","text":"We study the inductive bias of two-layer ReLU networks trained by gradient flow. We identify a class of easy-to-learn (`orthogonally separable') datasets, and characterise the solution that ReLU networks trained on such datasets converge to. Irrespective of network width, the solution turns out to be a combination of two max-margin classifiers: one corresponding to the positive data subset and one corresponding to the negative data subset. The proof is based on the recently introduced concept of extremal sectors, for which we prove a number of properties in the context of orthogonal separability. In particular, we prove stationarity of activation patterns from some time onwards, which enables a reduction of the ReLU network to an ensemble of linear subnetworks."}],"file_date_updated":"2021-05-24T11:15:57Z","type":"conference"},{"article_number":"19","ec_funded":1,"file_date_updated":"2021-03-09T11:44:34Z","department":[{"_id":"RoSe"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC Grant Agreement No 694227 (D.F. and R.S.) and under the Marie Skłodowska-Curie Grant Agreement No. 754411 (S.R.) is gratefully acknowledged. Open Access funding provided by Institute of Science and Technology (IST Austria)","volume":111,"date_created":"2021-03-07T23:01:25Z","date_updated":"2023-09-07T13:30:11Z","related_material":{"record":[{"id":"9733","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Dario","last_name":"Feliciangeli","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario"},{"orcid":"0000-0001-5059-4466","id":"856966FE-A408-11E9-977E-802DE6697425","last_name":"Rademacher","first_name":"Simone Anna Elvira","full_name":"Rademacher, Simone Anna Elvira"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"publication_identifier":{"issn":["03779017"],"eissn":["15730530"]},"month":"02","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"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":{"isi":["000617195700001"]},"language":[{"iso":"eng"}],"doi":"10.1007/s11005-020-01350-5","type":"journal_article","abstract":[{"lang":"eng","text":"The Landau–Pekar equations describe the dynamics of a strongly coupled polaron.\r\nHere, we provide a class of initial data for which the associated effective Hamiltonian\r\nhas a uniform spectral gap for all times. For such initial data, this allows us to extend the\r\nresults on the adiabatic theorem for the Landau–Pekar equations and their derivation\r\nfrom the Fröhlich model obtained in previous works to larger times."}],"intvolume":" 111","title":"Persistence of the spectral gap for the Landau–Pekar equations","ddc":["510"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9225","oa_version":"Published Version","file":[{"file_name":"2021_LettersMathPhysics_Feliciangeli.pdf","access_level":"open_access","file_size":391205,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"9232","date_created":"2021-03-09T11:44:34Z","date_updated":"2021-03-09T11:44:34Z","checksum":"ffbfe1aad623bce7ff529c207e343b53","success":1}],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"11","article_type":"original","citation":{"short":"D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, Letters in Mathematical Physics 111 (2021).","mla":"Feliciangeli, Dario, et al. “Persistence of the Spectral Gap for the Landau–Pekar Equations.” Letters in Mathematical Physics, vol. 111, 19, Springer Nature, 2021, doi:10.1007/s11005-020-01350-5.","chicago":"Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer. “Persistence of the Spectral Gap for the Landau–Pekar Equations.” Letters in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s11005-020-01350-5.","ama":"Feliciangeli D, Rademacher SAE, Seiringer R. Persistence of the spectral gap for the Landau–Pekar equations. Letters in Mathematical Physics. 2021;111. doi:10.1007/s11005-020-01350-5","apa":"Feliciangeli, D., Rademacher, S. A. E., & Seiringer, R. (2021). Persistence of the spectral gap for the Landau–Pekar equations. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-020-01350-5","ieee":"D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “Persistence of the spectral gap for the Landau–Pekar equations,” Letters in Mathematical Physics, vol. 111. Springer Nature, 2021.","ista":"Feliciangeli D, Rademacher SAE, Seiringer R. 2021. Persistence of the spectral gap for the Landau–Pekar equations. Letters in Mathematical Physics. 111, 19."},"publication":"Letters in Mathematical Physics","date_published":"2021-02-11T00:00:00Z"},{"language":[{"iso":"eng"}],"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2101.12566"}],"oa":1,"external_id":{"arxiv":["2101.12566"]},"month":"02","date_updated":"2023-09-07T13:30:10Z","date_created":"2021-08-06T08:25:57Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"10224"},{"id":"9733","status":"public","relation":"dissertation_contains"}]},"author":[{"last_name":"Feliciangeli","first_name":"Dario","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","full_name":"Feliciangeli, Dario"},{"full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"department":[{"_id":"RoSe"}],"publication_status":"submitted","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged. We would also like to thank Rupert Frank for many helpful discussions, especially related to the Gross coordinate transformation defined in Def. 4.1.\r\n","year":"2021","ec_funded":1,"article_number":"2101.12566","date_published":"2021-02-01T00:00:00Z","citation":{"chicago":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” ArXiv, n.d.","mla":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” ArXiv, 2101.12566.","short":"D. Feliciangeli, R. Seiringer, ArXiv (n.d.).","ista":"Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. arXiv, 2101.12566.","apa":"Feliciangeli, D., & Seiringer, R. (n.d.). The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. arXiv.","ieee":"D. Feliciangeli and R. Seiringer, “The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics,” arXiv. .","ama":"Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. arXiv."},"publication":"arXiv","has_accepted_license":"1","article_processing_charge":"No","day":"01","oa_version":"Preprint","ddc":["510"],"title":"The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics","status":"public","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"9787","abstract":[{"text":"We investigate the Fröhlich polaron model on a three-dimensional torus, and give a proof of the second-order quantum corrections to its ground-state energy in the strong-coupling limit. Compared to previous work in the confined case, the translational symmetry (and its breaking in the Pekar approximation) makes the analysis substantially more challenging.","lang":"eng"}],"type":"preprint"},{"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10199"}]},"author":[{"full_name":"Agarwal, Pratyush","last_name":"Agarwal","first_name":"Pratyush"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Pathak, Shreya","last_name":"Pathak","first_name":"Shreya"},{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"},{"last_name":"Toman","first_name":"Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","full_name":"Toman, Viktor"}],"volume":"12759 ","date_created":"2021-09-05T22:01:24Z","date_updated":"2023-09-07T13:30:27Z","year":"2021","acknowledgement":"The research was partially funded by the ERC CoG 863818 (ForM-SMArt) and the Vienna Science and Technology Fund (WWTF) through project ICT15-003.","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2022-05-13T07:00:20Z","doi":"10.1007/978-3-030-81685-8_16","conference":{"location":"Virtual","start_date":"2021-07-20","end_date":"2021-07-23","name":"CAV: Computer Aided Verification "},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2105.06424"],"isi":["000698732400016"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-030-81685-8"],"isbn":["978-3-030-81684-1"],"eissn":["1611-3349"]},"month":"07","file":[{"file_id":"11368","relation":"main_file","success":1,"checksum":"4b346e5fbaa8b9bdf107819c7b2aadee","date_updated":"2022-05-13T07:00:20Z","date_created":"2022-05-13T07:00:20Z","access_level":"open_access","file_name":"2021_LNCS_Agarwal.pdf","creator":"dernst","file_size":1516756,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9987","ddc":["000"],"title":"Stateless model checking under a reads-value-from equivalence","status":"public","abstract":[{"text":"Stateless model checking (SMC) is one of the standard approaches to the verification of concurrent programs. As scheduling non-determinism creates exponentially large spaces of thread interleavings, SMC attempts to partition this space into equivalence classes and explore only a few representatives from each class. The efficiency of this approach depends on two factors: (a) the coarseness of the partitioning, and (b) the time to generate representatives in each class. For this reason, the search for coarse partitionings that are efficiently explorable is an active research challenge. In this work we present RVF-SMC , a new SMC algorithm that uses a novel reads-value-from (RVF) partitioning. Intuitively, two interleavings are deemed equivalent if they agree on the value obtained in each read event, and read events induce consistent causal orderings between them. The RVF partitioning is provably coarser than recent approaches based on Mazurkiewicz and “reads-from” partitionings. Our experimental evaluation reveals that RVF is quite often a very effective equivalence, as the underlying partitioning is exponentially coarser than other approaches. Moreover, RVF-SMC generates representatives very efficiently, as the reduction in the partitioning is often met with significant speed-ups in the model checking task.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2021-07-15T00:00:00Z","citation":{"apa":"Agarwal, P., Chatterjee, K., Pathak, S., Pavlogiannis, A., & Toman, V. (2021). Stateless model checking under a reads-value-from equivalence. In 33rd International Conference on Computer-Aided Verification (Vol. 12759, pp. 341–366). Virtual: Springer Nature. https://doi.org/10.1007/978-3-030-81685-8_16","ieee":"P. Agarwal, K. Chatterjee, S. Pathak, A. Pavlogiannis, and V. Toman, “Stateless model checking under a reads-value-from equivalence,” in 33rd International Conference on Computer-Aided Verification , Virtual, 2021, vol. 12759, pp. 341–366.","ista":"Agarwal P, Chatterjee K, Pathak S, Pavlogiannis A, Toman V. 2021. Stateless model checking under a reads-value-from equivalence. 33rd International Conference on Computer-Aided Verification . CAV: Computer Aided Verification , LNCS, vol. 12759, 341–366.","ama":"Agarwal P, Chatterjee K, Pathak S, Pavlogiannis A, Toman V. Stateless model checking under a reads-value-from equivalence. In: 33rd International Conference on Computer-Aided Verification . Vol 12759. Springer Nature; 2021:341-366. doi:10.1007/978-3-030-81685-8_16","chicago":"Agarwal, Pratyush, Krishnendu Chatterjee, Shreya Pathak, Andreas Pavlogiannis, and Viktor Toman. “Stateless Model Checking under a Reads-Value-from Equivalence.” In 33rd International Conference on Computer-Aided Verification , 12759:341–66. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-81685-8_16.","short":"P. Agarwal, K. Chatterjee, S. Pathak, A. Pavlogiannis, V. Toman, in:, 33rd International Conference on Computer-Aided Verification , Springer Nature, 2021, pp. 341–366.","mla":"Agarwal, Pratyush, et al. “Stateless Model Checking under a Reads-Value-from Equivalence.” 33rd International Conference on Computer-Aided Verification , vol. 12759, Springer Nature, 2021, pp. 341–66, doi:10.1007/978-3-030-81685-8_16."},"publication":"33rd International Conference on Computer-Aided Verification ","page":"341-366","article_processing_charge":"Yes","has_accepted_license":"1","day":"15","scopus_import":"1"},{"month":"09","publication_identifier":{"issn":["2663-337X"]},"oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"call_identifier":"H2020","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819"}],"doi":"10.15479/at:ista:10007","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L","full_name":"Fischer, Julian L"}],"language":[{"iso":"eng"}],"file_date_updated":"2021-09-15T14:37:30Z","ec_funded":1,"year":"2021","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","first_name":"Sebastian","last_name":"Hensel","full_name":"Hensel, Sebastian"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10012"},{"status":"public","relation":"part_of_dissertation","id":"10013"},{"id":"7489","relation":"part_of_dissertation","status":"public"}]},"date_created":"2021-09-13T11:12:34Z","date_updated":"2023-09-07T13:30:45Z","day":"14","has_accepted_license":"1","article_processing_charge":"No","citation":{"ieee":"S. Hensel, “Curvature driven interface evolution: Uniqueness properties of weak solution concepts,” Institute of Science and Technology Austria, 2021.","apa":"Hensel, S. (2021). Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10007","ista":"Hensel S. 2021. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria.","ama":"Hensel S. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. 2021. doi:10.15479/at:ista:10007","chicago":"Hensel, Sebastian. “Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10007.","short":"S. Hensel, Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts, Institute of Science and Technology Austria, 2021.","mla":"Hensel, Sebastian. Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10007."},"page":"300","date_published":"2021-09-14T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The present thesis is concerned with the derivation of weak-strong uniqueness principles for curvature driven interface evolution problems not satisfying a comparison principle. The specific examples being treated are two-phase Navier-Stokes flow with surface tension, modeling the evolution of two incompressible, viscous and immiscible fluids separated by a sharp interface, and multiphase mean curvature flow, which serves as an idealized model for the motion of grain boundaries in an annealing polycrystalline material. Our main results - obtained in joint works with Julian Fischer, Tim Laux and Theresa M. Simon - state that prior to the formation of geometric singularities due to topology changes, the weak solution concept of Abels (Interfaces Free Bound. 9, 2007) to two-phase Navier-Stokes flow with surface tension and the weak solution concept of Laux and Otto (Calc. Var. Partial Differential Equations 55, 2016) to multiphase mean curvature flow (for networks in R^2 or double bubbles in R^3) represents the unique solution to these interface evolution problems within the class of classical solutions, respectively. To the best of the author's knowledge, for interface evolution problems not admitting a geometric comparison principle the derivation of a weak-strong uniqueness principle represented an open problem, so that the works contained in the present thesis constitute the first positive results in this direction. The key ingredient of our approach consists of the introduction of a novel concept of relative entropies for a class of curvature driven interface evolution problems, for which the associated energy contains an interfacial contribution being proportional to the surface area of the evolving (network of) interface(s). The interfacial part of the relative entropy gives sufficient control on the interface error between a weak and a classical solution, and its time evolution can be computed, at least in principle, for any energy dissipating weak solution concept. A resulting stability estimate for the relative entropy essentially entails the above mentioned weak-strong uniqueness principles. The present thesis contains a detailed introduction to our relative entropy approach, which in particular highlights potential applications to other problems in curvature driven interface evolution not treated in this thesis.","lang":"eng"}],"_id":"10007","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["515"],"title":"Curvature driven interface evolution: Uniqueness properties of weak solution concepts","status":"public","oa_version":"Published Version","file":[{"access_level":"closed","file_name":"thesis_final_Hensel.zip","file_size":15022154,"content_type":"application/x-zip-compressed","creator":"shensel","relation":"source_file","file_id":"10008","checksum":"c8475faaf0b680b4971f638f1db16347","date_updated":"2021-09-15T14:37:30Z","date_created":"2021-09-13T11:03:24Z"},{"relation":"main_file","file_id":"10014","date_updated":"2021-09-14T09:52:47Z","date_created":"2021-09-13T14:18:56Z","checksum":"1a609937aa5275452822f45f2da17f07","file_name":"thesis_final_Hensel.pdf","access_level":"open_access","file_size":6583638,"content_type":"application/pdf","creator":"shensel"}]},{"abstract":[{"lang":"eng","text":"In this work we solve the algorithmic problem of consistency verification for the TSO and PSO memory models given a reads-from map, denoted VTSO-rf and VPSO-rf, respectively. For an execution of n events over k threads and d variables, we establish novel bounds that scale as nk+1 for TSO and as nk+1· min(nk2, 2k· d) for PSO. Moreover, based on our solution to these problems, we develop an SMC algorithm under TSO and PSO that uses the RF equivalence. The algorithm is exploration-optimal, in the sense that it is guaranteed to explore each class of the RF partitioning exactly once, and spends polynomial time per class when k is bounded. Finally, we implement all our algorithms in the SMC tool Nidhugg, and perform a large number of experiments over benchmarks from existing literature. Our experimental results show that our algorithms for VTSO-rf and VPSO-rf provide significant scalability improvements over standard alternatives. Moreover, when used for SMC, the RF partitioning is often much coarser than the standard Shasha-Snir partitioning for TSO/PSO, which yields a significant speedup in the model checking task.\r\n\r\n"}],"issue":"OOPSLA","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2021_ProcACMPL_Bui.pdf","access_level":"open_access","creator":"cchlebak","file_size":2903485,"content_type":"application/pdf","file_id":"10215","relation":"main_file","date_updated":"2021-11-04T07:24:48Z","date_created":"2021-11-04T07:24:48Z","success":1,"checksum":"9d6dce7b611853c529bb7b1915ac579e"}],"_id":"10191","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"The reads-from equivalence for the TSO and PSO memory models","ddc":["000"],"intvolume":" 5","day":"15","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","keyword":["safety","risk","reliability and quality","software"],"date_published":"2021-10-15T00:00:00Z","publication":"Proceedings of the ACM on Programming Languages","citation":{"ieee":"T. L. Bui, K. Chatterjee, T. Gautam, A. Pavlogiannis, and V. Toman, “The reads-from equivalence for the TSO and PSO memory models,” Proceedings of the ACM on Programming Languages, vol. 5, no. OOPSLA. Association for Computing Machinery, 2021.","apa":"Bui, T. L., Chatterjee, K., Gautam, T., Pavlogiannis, A., & Toman, V. (2021). The reads-from equivalence for the TSO and PSO memory models. Proceedings of the ACM on Programming Languages. Association for Computing Machinery. https://doi.org/10.1145/3485541","ista":"Bui TL, Chatterjee K, Gautam T, Pavlogiannis A, Toman V. 2021. The reads-from equivalence for the TSO and PSO memory models. Proceedings of the ACM on Programming Languages. 5(OOPSLA), 164.","ama":"Bui TL, Chatterjee K, Gautam T, Pavlogiannis A, Toman V. The reads-from equivalence for the TSO and PSO memory models. Proceedings of the ACM on Programming Languages. 2021;5(OOPSLA). doi:10.1145/3485541","chicago":"Bui, Truc Lam, Krishnendu Chatterjee, Tushar Gautam, Andreas Pavlogiannis, and Viktor Toman. “The Reads-from Equivalence for the TSO and PSO Memory Models.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2021. https://doi.org/10.1145/3485541.","short":"T.L. Bui, K. Chatterjee, T. Gautam, A. Pavlogiannis, V. Toman, Proceedings of the ACM on Programming Languages 5 (2021).","mla":"Bui, Truc Lam, et al. “The Reads-from Equivalence for the TSO and PSO Memory Models.” Proceedings of the ACM on Programming Languages, vol. 5, no. OOPSLA, 164, Association for Computing Machinery, 2021, doi:10.1145/3485541."},"article_type":"original","file_date_updated":"2021-11-04T07:24:48Z","ec_funded":1,"article_number":"164","author":[{"first_name":"Truc Lam","last_name":"Bui","full_name":"Bui, Truc Lam"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Gautam, Tushar","first_name":"Tushar","last_name":"Gautam"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas"},{"full_name":"Toman, Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X","first_name":"Viktor","last_name":"Toman"}],"related_material":{"record":[{"id":"10199","status":"public","relation":"dissertation_contains"}]},"date_created":"2021-10-27T15:05:34Z","date_updated":"2023-09-07T13:30:27Z","volume":5,"acknowledgement":"The research was partially funded by the ERC CoG 863818 (ForM-SMArt) and the Vienna Science\r\nand Technology Fund (WWTF) through project ICT15-003.","year":"2021","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","month":"10","publication_identifier":{"eissn":["2475-1421"]},"doi":"10.1145/3485541","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":["2011.11763"]},"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"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}]},{"doi":"10.48550/arXiv.2108.01733","date_published":"2021-08-03T00:00:00Z","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2108.01733"}],"citation":{"ista":"Hensel S, Laux T. Weak-strong uniqueness for the mean curvature flow of double bubbles. arXiv, 2108.01733.","apa":"Hensel, S., & Laux, T. (n.d.). Weak-strong uniqueness for the mean curvature flow of double bubbles. arXiv. https://doi.org/10.48550/arXiv.2108.01733","ieee":"S. Hensel and T. Laux, “Weak-strong uniqueness for the mean curvature flow of double bubbles,” arXiv. .","ama":"Hensel S, Laux T. Weak-strong uniqueness for the mean curvature flow of double bubbles. arXiv. doi:10.48550/arXiv.2108.01733","chicago":"Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2108.01733.","mla":"Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” ArXiv, 2108.01733, doi:10.48550/arXiv.2108.01733.","short":"S. Hensel, T. Laux, ArXiv (n.d.)."},"oa":1,"external_id":{"arxiv":["2108.01733"]},"publication":"arXiv","project":[{"call_identifier":"H2020","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819"}],"article_processing_charge":"No","day":"03","month":"08","related_material":{"record":[{"status":"public","relation":"later_version","id":"13043"},{"id":"10007","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Hensel, Sebastian","orcid":"0000-0001-7252-8072","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","last_name":"Hensel","first_name":"Sebastian"},{"full_name":"Laux, Tim","first_name":"Tim","last_name":"Laux"}],"oa_version":"Preprint","date_created":"2021-09-13T12:17:11Z","date_updated":"2023-09-07T13:30:45Z","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 948819), and from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2047/1 – 390685813.","_id":"10013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","department":[{"_id":"JuFi"}],"status":"public","publication_status":"submitted","title":"Weak-strong uniqueness for the mean curvature flow of double bubbles","ec_funded":1,"abstract":[{"lang":"eng","text":"We derive a weak-strong uniqueness principle for BV solutions to multiphase mean curvature flow of triple line clusters in three dimensions. Our proof is based on the explicit construction of a gradient-flow calibration in the sense of the recent work of Fischer et al. [arXiv:2003.05478] for any such cluster. This extends the two-dimensional construction to the three-dimensional case of surfaces meeting along triple junctions."}],"type":"preprint","article_number":"2108.01733"},{"type":"journal_article","abstract":[{"text":"There are two elementary superconducting qubit types that derive directly from the quantum harmonic oscillator. In one, the inductor is replaced by a nonlinear Josephson junction to realize the widely used charge qubits with a compact phase variable and a discrete charge wave function. In the other, the junction is added in parallel, which gives rise to an extended phase variable, continuous wave functions, and a rich energy-level structure due to the loop topology. While the corresponding rf superconducting quantum interference device Hamiltonian was introduced as a quadratic quasi-one-dimensional potential approximation to describe the fluxonium qubit implemented with long Josephson-junction arrays, in this work we implement it directly using a linear superinductor formed by a single uninterrupted aluminum wire. We present a large variety of qubits, all stemming from the same circuit but with drastically different characteristic energy scales. This includes flux and fluxonium qubits but also the recently introduced quasicharge qubit with strongly enhanced zero-point phase fluctuations and a heavily suppressed flux dispersion. The use of a geometric inductor results in high reproducibility of the inductive energy as guaranteed by top-down lithography—a key ingredient for intrinsically protected superconducting qubits.","lang":"eng"}],"issue":"4","ddc":["530"],"status":"public","title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction","intvolume":" 2","_id":"9928","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"date_updated":"2022-01-18T11:29:33Z","date_created":"2022-01-18T11:29:33Z","checksum":"36eb41ea43d8ca22b0efab12419e4eb2","success":1,"relation":"main_file","file_id":"10641","content_type":"application/pdf","file_size":4247422,"creator":"cchlebak","file_name":"2021_PRXQuantum_Peruzzo.pdf","access_level":"open_access"}],"keyword":["quantum physics","mesoscale and nanoscale physics"],"scopus_import":"1","day":"24","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","page":"040341","publication":"PRX Quantum","citation":{"apa":"Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M., & Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. PRX Quantum. American Physical Society. https://doi.org/10.1103/PRXQuantum.2.040341","ieee":"M. Peruzzo et al., “Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction,” PRX Quantum, vol. 2, no. 4. American Physical Society, p. 040341, 2021.","ista":"Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM. 2021. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. PRX Quantum. 2(4), 040341.","ama":"Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. PRX Quantum. 2021;2(4):040341. doi:10.1103/PRXQuantum.2.040341","chicago":"Peruzzo, Matilda, Farid Hassani, Gregory Szep, Andrea Trioni, Elena Redchenko, Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” PRX Quantum. American Physical Society, 2021. https://doi.org/10.1103/PRXQuantum.2.040341.","short":"M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, PRX Quantum 2 (2021) 040341.","mla":"Peruzzo, Matilda, et al. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” PRX Quantum, vol. 2, no. 4, American Physical Society, 2021, p. 040341, doi:10.1103/PRXQuantum.2.040341."},"date_published":"2021-11-24T00:00:00Z","file_date_updated":"2022-01-18T11:29:33Z","ec_funded":1,"publication_status":"published","department":[{"_id":"JoFi"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"publisher":"American Physical Society","acknowledgement":"We thank W. Hughes for analytic and numerical modeling during the early stages of this work, J. Koch for discussions and support with the scqubits package, R. Sett, P. Zielinski, and L. Drmic for software development, and G. Katsaros for equipment support, as well as the MIBA workshop and the Institute of Science and Technology Austria nanofabrication facility. We thank I. Pop, S. Deleglise, and E. Flurin for discussions. This work was supported by a NOMIS Foundation research grant, the Austrian Science Fund (FWF) through BeyondC (F7105), and IST Austria. M.P. is the recipient of a Pöttinger scholarship at IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.","year":"2021","date_updated":"2023-09-07T13:31:22Z","date_created":"2021-08-17T08:14:18Z","volume":2,"author":[{"first_name":"Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda"},{"full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","first_name":"Farid","last_name":"Hassani"},{"first_name":"Gregory","last_name":"Szep","full_name":"Szep, Gregory"},{"full_name":"Trioni, Andrea","first_name":"Andrea","last_name":"Trioni","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Redchenko"},{"first_name":"Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M"}],"related_material":{"record":[{"id":"13057","relation":"research_data","status":"public"},{"id":"9920","status":"public","relation":"dissertation_contains"}]},"month":"11","publication_identifier":{"eissn":["2691-3399"]},"quality_controlled":"1","isi":1,"project":[{"name":"Integrating superconducting quantum circuits","call_identifier":"FWF","grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"_id":"2622978C-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"}],"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":["2106.05882"],"isi":["000723015100001"]},"oa":1,"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"doi":"10.1103/PRXQuantum.2.040341"},{"related_material":{"record":[{"id":"10022","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9792"},{"status":"public","relation":"part_of_dissertation","id":"7573"}]},"author":[{"id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","last_name":"Portinale","first_name":"Lorenzo","full_name":"Portinale, Lorenzo"}],"date_updated":"2023-09-07T13:31:06Z","date_created":"2021-09-21T09:14:15Z","year":"2021","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No W1245.","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","file_date_updated":"2022-03-10T12:14:42Z","doi":"10.15479/at:ista:10030","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"260788DE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"}],"publication_identifier":{"issn":["2663-337X"]},"month":"09","file":[{"content_type":"application/x-zip-compressed","file_size":3876668,"creator":"cchlebak","access_level":"closed","file_name":"tex_and_pictures.zip","checksum":"8cd60dcb8762e8f21867e21e8001e183","date_created":"2021-09-21T09:17:34Z","date_updated":"2022-03-10T12:14:42Z","relation":"source_file","file_id":"10032"},{"content_type":"application/pdf","file_size":2532673,"creator":"cchlebak","access_level":"open_access","file_name":"thesis_portinale_Final (1).pdf","checksum":"9789e9d967c853c1503ec7f307170279","date_created":"2021-09-27T11:14:31Z","date_updated":"2021-09-27T11:14:31Z","relation":"main_file","file_id":"10047"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10030","ddc":["515"],"status":"public","title":"Discrete-to-continuum limits of transport problems and gradient flows in the space of measures","abstract":[{"lang":"eng","text":"This PhD thesis is primarily focused on the study of discrete transport problems, introduced for the first time in the seminal works of Maas [Maa11] and Mielke [Mie11] on finite state Markov chains and reaction-diffusion equations, respectively. More in detail, my research focuses on the study of transport costs on graphs, in particular the convergence and the stability of such problems in the discrete-to-continuum limit. This thesis also includes some results concerning\r\nnon-commutative optimal transport. The first chapter of this thesis consists of a general introduction to the optimal transport problems, both in the discrete, the continuous, and the non-commutative setting. Chapters 2 and 3 present the content of two works, obtained in collaboration with Peter Gladbach, Eva Kopfer, and Jan Maas, where we have been able to show the convergence of discrete transport costs on periodic graphs to suitable continuous ones, which can be described by means of a homogenisation result. We first focus on the particular case of quadratic costs on the real line and then extending the result to more general costs in arbitrary dimension. Our results are the first complete characterisation of limits of transport costs on periodic graphs in arbitrary dimension which do not rely on any additional symmetry. In Chapter 4 we turn our attention to one of the intriguing connection between evolution equations and optimal transport, represented by the theory of gradient flows. We show that discrete gradient flow structures associated to a finite volume approximation of a certain class of diffusive equations (Fokker–Planck) is stable in the limit of vanishing meshes, reproving the convergence of the scheme via the method of evolutionary Γ-convergence and exploiting a more variational point of view on the problem. This is based on a collaboration with Dominik Forkert and Jan Maas. Chapter 5 represents a change of perspective, moving away from the discrete world and reaching the non-commutative one. As in the discrete case, we discuss how classical tools coming from the commutative optimal transport can be translated into the setting of density matrices. In particular, in this final chapter we present a non-commutative version of the Schrödinger problem (or entropic regularised optimal transport problem) and discuss existence and characterisation of minimisers, a duality result, and present a non-commutative version of the well-known Sinkhorn algorithm to compute the above mentioned optimisers. This is based on a joint work with Dario Feliciangeli and Augusto Gerolin. Finally, Appendix A and B contain some additional material and discussions, with particular attention to Harnack inequalities and the regularity of flows on discrete spaces."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2021-09-22T00:00:00Z","citation":{"ista":"Portinale L. 2021. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria.","apa":"Portinale, L. (2021). Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10030","ieee":"L. Portinale, “Discrete-to-continuum limits of transport problems and gradient flows in the space of measures,” Institute of Science and Technology Austria, 2021.","ama":"Portinale L. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. 2021. doi:10.15479/at:ista:10030","chicago":"Portinale, Lorenzo. “Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10030.","mla":"Portinale, Lorenzo. Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10030.","short":"L. Portinale, Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures, Institute of Science and Technology Austria, 2021."},"article_processing_charge":"No","has_accepted_license":"1","day":"22"},{"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-013-8"]},"month":"08","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"degree_awarded":"PhD","supervisor":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"}],"doi":"10.15479/at:ista:9920","oa":1,"file_date_updated":"2021-09-06T08:39:47Z","date_created":"2021-08-16T09:44:09Z","date_updated":"2023-09-07T13:31:22Z","related_material":{"record":[{"id":"9928","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8755"}]},"author":[{"full_name":"Peruzzo, Matilda","first_name":"Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"publication_status":"published","year":"2021","article_processing_charge":"No","has_accepted_license":"1","day":"19","keyword":["quantum computing","superinductor","quantum metrology"],"date_published":"2021-08-19T00:00:00Z","page":"149","citation":{"chicago":"Peruzzo, Matilda. “Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9920.","mla":"Peruzzo, Matilda. Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9920.","short":"M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics, Institute of Science and Technology Austria, 2021.","ista":"Peruzzo M. 2021. Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria.","ieee":"M. Peruzzo, “Geometric superinductors and their applications in circuit quantum electrodynamics,” Institute of Science and Technology Austria, 2021.","apa":"Peruzzo, M. (2021). Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9920","ama":"Peruzzo M. Geometric superinductors and their applications in circuit quantum electrodynamics. 2021. doi:10.15479/at:ista:9920"},"abstract":[{"lang":"eng","text":"This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"relation":"source_file","file_id":"9924","checksum":"3cd1986efde5121d7581f6fcf9090da8","date_updated":"2021-09-06T08:39:47Z","date_created":"2021-08-16T09:33:21Z","access_level":"closed","file_name":"GeometricSuperinductorsForCQED.zip","content_type":"application/x-zip-compressed","file_size":151387283,"creator":"mperuzzo"},{"date_created":"2021-08-18T14:20:06Z","date_updated":"2021-09-06T08:39:47Z","checksum":"50928c621cdf0775d7a5906b9dc8602c","relation":"main_file","file_id":"9939","content_type":"application/pdf","file_size":17596344,"creator":"mperuzzo","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf","access_level":"open_access"},{"access_level":"closed","description":"Extra copy of the thesis as PDF/A-2b","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf","creator":"mperuzzo","content_type":"application/pdf","file_size":17592425,"file_id":"9940","relation":"other","checksum":"37f486aa1b622fe44af00d627ec13f6c","date_updated":"2021-09-06T08:39:47Z","date_created":"2021-08-18T14:20:09Z"}],"oa_version":"Published Version","title":"Geometric superinductors and their applications in circuit quantum electrodynamics","ddc":["539"],"status":"public","_id":"9920","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_updated":"2023-09-07T13:31:39Z","date_created":"2021-12-09T09:21:35Z","volume":35,"author":[{"full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","first_name":"Giorgi","last_name":"Nadiradze"},{"full_name":"Markov, Ilia","last_name":"Markov","first_name":"Ilia","id":"D0CF4148-C985-11E9-8066-0BDEE5697425"},{"full_name":"Chatterjee, Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2742-4028","first_name":"Bapi","last_name":"Chatterjee"},{"last_name":"Kungurtsev","first_name":"Vyacheslav ","full_name":"Kungurtsev, Vyacheslav "},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"10429","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","department":[{"_id":"DaAl"}],"year":"2021","acknowledgement":"We would like to thank Christopher De Sa for his feedback on an earlier draft of this paper, as well as the anonymous AAAI reviewers for their useful comments. This project has received\r\nfunding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). Bapi\r\nChatterjee was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 754411 (ISTPlus).","ec_funded":1,"language":[{"iso":"eng"}],"conference":{"name":"AAAI: Association for the Advancement of Artificial Intelligence","end_date":"2021-02-09","start_date":"2021-02-02","location":"Virtual"},"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"main_file_link":[{"url":"https://ojs.aaai.org/index.php/AAAI/article/view/17092","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2001.05918"]},"month":"05","oa_version":"Published Version","title":"Elastic consistency: A practical consistency model for distributed stochastic gradient descent","status":"public","intvolume":" 35","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10432","abstract":[{"lang":"eng","text":"One key element behind the recent progress of machine learning has been the ability to train machine learning models in large-scale distributed shared-memory and message-passing environments. Most of these models are trained employing variants of stochastic gradient descent (SGD) based optimization, but most methods involve some type of consistency relaxation relative to sequential SGD, to mitigate its large communication or synchronization costs at scale. In this paper, we introduce a general consistency condition covering communication-reduced and asynchronous distributed SGD implementations. Our framework, called elastic consistency, decouples the system-specific aspects of the implementation from the SGD convergence requirements, giving a general way to obtain convergence bounds for a wide variety of distributed SGD methods used in practice. Elastic consistency can be used to re-derive or improve several previous convergence bounds in message-passing and shared-memory settings, but also to analyze new models and distribution schemes. As a direct application, we propose and analyze a new synchronization-avoiding scheduling scheme for distributed SGD, and show that it can be used to efficiently train deep convolutional models for image classification."}],"issue":"10","type":"conference","date_published":"2021-05-18T00:00:00Z","page":"9037-9045","publication":"Proceedings of the AAAI Conference on Artificial Intelligence","citation":{"ama":"Nadiradze G, Markov I, Chatterjee B, Kungurtsev V, Alistarh D-A. Elastic consistency: A practical consistency model for distributed stochastic gradient descent. In: Proceedings of the AAAI Conference on Artificial Intelligence. Vol 35. ; 2021:9037-9045.","ista":"Nadiradze G, Markov I, Chatterjee B, Kungurtsev V, Alistarh D-A. 2021. Elastic consistency: A practical consistency model for distributed stochastic gradient descent. Proceedings of the AAAI Conference on Artificial Intelligence. AAAI: Association for the Advancement of Artificial Intelligence vol. 35, 9037–9045.","apa":"Nadiradze, G., Markov, I., Chatterjee, B., Kungurtsev, V., & Alistarh, D.-A. (2021). Elastic consistency: A practical consistency model for distributed stochastic gradient descent. In Proceedings of the AAAI Conference on Artificial Intelligence (Vol. 35, pp. 9037–9045). Virtual.","ieee":"G. Nadiradze, I. Markov, B. Chatterjee, V. Kungurtsev, and D.-A. Alistarh, “Elastic consistency: A practical consistency model for distributed stochastic gradient descent,” in Proceedings of the AAAI Conference on Artificial Intelligence, Virtual, 2021, vol. 35, no. 10, pp. 9037–9045.","mla":"Nadiradze, Giorgi, et al. “Elastic Consistency: A Practical Consistency Model for Distributed Stochastic Gradient Descent.” Proceedings of the AAAI Conference on Artificial Intelligence, vol. 35, no. 10, 2021, pp. 9037–45.","short":"G. Nadiradze, I. Markov, B. Chatterjee, V. Kungurtsev, D.-A. Alistarh, in:, Proceedings of the AAAI Conference on Artificial Intelligence, 2021, pp. 9037–9045.","chicago":"Nadiradze, Giorgi, Ilia Markov, Bapi Chatterjee, Vyacheslav Kungurtsev, and Dan-Adrian Alistarh. “Elastic Consistency: A Practical Consistency Model for Distributed Stochastic Gradient Descent.” In Proceedings of the AAAI Conference on Artificial Intelligence, 35:9037–45, 2021."},"day":"18","article_processing_charge":"No"},{"article_processing_charge":"No","day":"11","date_published":"2021-08-11T00:00:00Z","page":"486-515","citation":{"short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, D. Wichs, in:, 41st Annual International Cryptology Conference, Part II , Springer Nature, Cham, 2021, pp. 486–515.","mla":"Kamath Hosdurg, Chethan, et al. “Limits on the Adaptive Security of Yao’s Garbling.” 41st Annual International Cryptology Conference, Part II , vol. 12826, Springer Nature, 2021, pp. 486–515, doi:10.1007/978-3-030-84245-1_17.","chicago":"Kamath Hosdurg, Chethan, Karen Klein, Krzysztof Z Pietrzak, and Daniel Wichs. “Limits on the Adaptive Security of Yao’s Garbling.” In 41st Annual International Cryptology Conference, Part II , 12826:486–515. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-84245-1_17.","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Wichs D. Limits on the Adaptive Security of Yao’s Garbling. In: 41st Annual International Cryptology Conference, Part II . Vol 12826. Cham: Springer Nature; 2021:486-515. doi:10.1007/978-3-030-84245-1_17","apa":"Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Wichs, D. (2021). Limits on the Adaptive Security of Yao’s Garbling. In 41st Annual International Cryptology Conference, Part II (Vol. 12826, pp. 486–515). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-84245-1_17","ieee":"C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and D. Wichs, “Limits on the Adaptive Security of Yao’s Garbling,” in 41st Annual International Cryptology Conference, Part II , Virtual, 2021, vol. 12826, pp. 486–515.","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Wichs D. 2021. Limits on the Adaptive Security of Yao’s Garbling. 41st Annual International Cryptology Conference, Part II . CRYPTO: Annual International Cryptology Conference, LCNS, vol. 12826, 486–515."},"publication":"41st Annual International Cryptology Conference, Part II ","abstract":[{"lang":"eng","text":"Yao’s garbling scheme is one of the most fundamental cryptographic constructions. Lindell and Pinkas (Journal of Cryptograhy 2009) gave a formal proof of security in the selective setting where the adversary chooses the challenge inputs before seeing the garbled circuit assuming secure symmetric-key encryption (and hence one-way functions). This was followed by results, both positive and negative, concerning its security in the, stronger, adaptive setting. Applebaum et al. (Crypto 2013) showed that it cannot satisfy adaptive security as is, due to a simple incompressibility argument. Jafargholi and Wichs (TCC 2017) considered a natural adaptation of Yao’s scheme (where the output mapping is sent in the online phase, together with the garbled input) that circumvents this negative result, and proved that it is adaptively secure, at least for shallow circuits. In particular, they showed that for the class of circuits of depth δ , the loss in security is at most exponential in δ . The above results all concern the simulation-based notion of security. In this work, we show that the upper bound of Jafargholi and Wichs is basically optimal in a strong sense. As our main result, we show that there exists a family of Boolean circuits, one for each depth δ∈N , such that any black-box reduction proving the adaptive indistinguishability of the natural adaptation of Yao’s scheme from any symmetric-key encryption has to lose a factor that is exponential in δ√ . Since indistinguishability is a weaker notion than simulation, our bound also applies to adaptive simulation. To establish our results, we build on the recent approach of Kamath et al. (Eprint 2021), which uses pebbling lower bounds in conjunction with oracle separations to prove fine-grained lower bounds on loss in cryptographic security."}],"alternative_title":["LCNS"],"type":"conference","oa_version":"Preprint","intvolume":" 12826","status":"public","title":"Limits on the Adaptive Security of Yao’s Garbling","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10041","publication_identifier":{"isbn":["978-3-030-84244-4"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["978-3-030-84245-1"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-84245-1_17","conference":{"name":"CRYPTO: Annual International Cryptology Conference","start_date":"2021-08-16","location":"Virtual","end_date":"2021-08-20"},"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/945"}],"oa":1,"ec_funded":1,"place":"Cham","volume":12826,"date_updated":"2023-09-07T13:32:11Z","date_created":"2021-09-23T14:06:15Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10035"}]},"author":[{"full_name":"Kamath Hosdurg, Chethan","first_name":"Chethan","last_name":"Kamath Hosdurg","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87"},{"id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","first_name":"Karen","full_name":"Klein, Karen"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Wichs, Daniel","last_name":"Wichs","first_name":"Daniel"}],"department":[{"_id":"KrPi"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","acknowledgement":"We would like to thank the anonymous reviewers of Crypto’21 whose detailed comments helped us considerably improve the presentation of the paper."},{"month":"08","doi":"10.1109/sp40001.2021.00035","conference":{"end_date":"2021-05-27","location":"San Francisco, CA, United States","start_date":"2021-05-24","name":"SP: Symposium on Security and Privacy"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1489"}],"oa":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","ec_funded":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10035"}]},"author":[{"id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Klein","full_name":"Klein, Karen"},{"full_name":"Pascual Perez, Guillermo","orcid":"0000-0001-8630-415X","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","last_name":"Pascual Perez","first_name":"Guillermo"},{"full_name":"Walter, Michael","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","last_name":"Walter","first_name":"Michael"},{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Capretto, Margarita","last_name":"Capretto","first_name":"Margarita"},{"first_name":"Miguel","last_name":"Cueto Noval","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","full_name":"Cueto Noval, Miguel"},{"full_name":"Markov, Ilia","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","last_name":"Markov","first_name":"Ilia"},{"last_name":"Yeo","first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X"},{"full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"}],"date_created":"2021-09-27T13:46:27Z","date_updated":"2023-09-07T13:32:11Z","acknowledgement":"The first three authors contributed equally to this work. Funded by the European Research Council (ERC) under the European Union’s Horizon2020 research and innovation programme (682815-TOCNeT). Funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No.665385.","year":"2021","department":[{"_id":"KrPi"},{"_id":"DaAl"}],"publisher":"IEEE","publication_status":"published","article_processing_charge":"No","day":"26","date_published":"2021-08-26T00:00:00Z","citation":{"short":"K. Klein, G. Pascual Perez, M. Walter, C. Kamath Hosdurg, M. Capretto, M. Cueto Noval, I. Markov, M.X. Yeo, J.F. Alwen, K.Z. Pietrzak, in:, 2021 IEEE Symposium on Security and Privacy , IEEE, 2021, pp. 268–284.","mla":"Klein, Karen, et al. “Keep the Dirt: Tainted TreeKEM, Adaptively and Actively Secure Continuous Group Key Agreement.” 2021 IEEE Symposium on Security and Privacy , IEEE, 2021, pp. 268–84, doi:10.1109/sp40001.2021.00035.","chicago":"Klein, Karen, Guillermo Pascual Perez, Michael Walter, Chethan Kamath Hosdurg, Margarita Capretto, Miguel Cueto Noval, Ilia Markov, Michelle X Yeo, Joel F Alwen, and Krzysztof Z Pietrzak. “Keep the Dirt: Tainted TreeKEM, Adaptively and Actively Secure Continuous Group Key Agreement.” In 2021 IEEE Symposium on Security and Privacy , 268–84. IEEE, 2021. https://doi.org/10.1109/sp40001.2021.00035.","ama":"Klein K, Pascual Perez G, Walter M, et al. Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement. In: 2021 IEEE Symposium on Security and Privacy . IEEE; 2021:268-284. doi:10.1109/sp40001.2021.00035","ieee":"K. Klein et al., “Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement,” in 2021 IEEE Symposium on Security and Privacy , San Francisco, CA, United States, 2021, pp. 268–284.","apa":"Klein, K., Pascual Perez, G., Walter, M., Kamath Hosdurg, C., Capretto, M., Cueto Noval, M., … Pietrzak, K. Z. (2021). Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement. In 2021 IEEE Symposium on Security and Privacy (pp. 268–284). San Francisco, CA, United States: IEEE. https://doi.org/10.1109/sp40001.2021.00035","ista":"Klein K, Pascual Perez G, Walter M, Kamath Hosdurg C, Capretto M, Cueto Noval M, Markov I, Yeo MX, Alwen JF, Pietrzak KZ. 2021. Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement. 2021 IEEE Symposium on Security and Privacy . SP: Symposium on Security and Privacy, 268–284."},"publication":"2021 IEEE Symposium on Security and Privacy ","page":"268-284","abstract":[{"text":"While messaging systems with strong security guarantees are widely used in practice, designing a protocol that scales efficiently to large groups and enjoys similar security guarantees remains largely open. The two existing proposals to date are ART (Cohn-Gordon et al., CCS18) and TreeKEM (IETF, The Messaging Layer Security Protocol, draft). TreeKEM is the currently considered candidate by the IETF MLS working group, but dynamic group operations (i.e. adding and removing users) can cause efficiency issues. In this paper we formalize and analyze a variant of TreeKEM which we term Tainted TreeKEM (TTKEM for short). The basic idea underlying TTKEM was suggested by Millican (MLS mailing list, February 2018). This version is more efficient than TreeKEM for some natural distributions of group operations, we quantify this through simulations.Our second contribution is two security proofs for TTKEM which establish post compromise and forward secrecy even against adaptive attackers. The security loss (to the underlying PKE) in the Random Oracle Model is a polynomial factor, and a quasipolynomial one in the Standard Model. Our proofs can be adapted to TreeKEM as well. Before our work no security proof for any TreeKEM-like protocol establishing tight security against an adversary who can adaptively choose the sequence of operations was known. We also are the first to prove (or even formalize) active security where the server can arbitrarily deviate from the protocol specification. Proving fully active security – where also the users can arbitrarily deviate – remains open.","lang":"eng"}],"type":"conference","oa_version":"Preprint","_id":"10049","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement","status":"public"},{"_id":"10044","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledgement":"We would like to thank Daniel Wichs for helpful discussions on the landscape of adaptive security of Yao’s garbling. ","year":"2021","publisher":"International Association for Cryptologic Research","department":[{"_id":"KrPi"}],"publication_status":"published","status":"public","title":"On treewidth, separators and Yao's garbling","related_material":{"record":[{"relation":"later_version","status":"public","id":"10409"},{"id":"10035","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Klein"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"}],"oa_version":"Preprint","date_created":"2021-09-24T12:01:34Z","date_updated":"2023-09-07T13:32:11Z","type":"conference","article_number":"2021/926","ec_funded":1,"abstract":[{"lang":"eng","text":"We show that Yao’s garbling scheme is adaptively indistinguishable for the class of Boolean circuits of size S and treewidth w with only a S^O(w) loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly O(d w log(S)), d being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity."}],"citation":{"ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ. On treewidth, separators and Yao’s garbling. In: 19th Theory of Cryptography Conference 2021. International Association for Cryptologic Research; 2021.","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ. 2021. On treewidth, separators and Yao’s garbling. 19th Theory of Cryptography Conference 2021. TCC: Theory of Cryptography Conference, 2021/926.","apa":"Kamath Hosdurg, C., Klein, K., & Pietrzak, K. Z. (2021). On treewidth, separators and Yao’s garbling. In 19th Theory of Cryptography Conference 2021. Raleigh, NC, United States: International Association for Cryptologic Research.","ieee":"C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “On treewidth, separators and Yao’s garbling,” in 19th Theory of Cryptography Conference 2021, Raleigh, NC, United States, 2021.","mla":"Kamath Hosdurg, Chethan, et al. “On Treewidth, Separators and Yao’s Garbling.” 19th Theory of Cryptography Conference 2021, 2021/926, International Association for Cryptologic Research, 2021.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, 19th Theory of Cryptography Conference 2021, International Association for Cryptologic Research, 2021.","chicago":"Kamath Hosdurg, Chethan, Karen Klein, and Krzysztof Z Pietrzak. “On Treewidth, Separators and Yao’s Garbling.” In 19th Theory of Cryptography Conference 2021. 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It seems that a numerical technique called automatic differentiation together with increasing supply of computational accelerators will soon shift many methods of the material design from the category ”unimaginable” to the category ”expensive but possible”. Approach we suggest is not an exception. Our overall goal is to have an efficient and generalizable approach allowing to solve inverse design problems. In this thesis we scratch its surface. We consider jammed systems of identical particles. And ask ourselves how the shape of those particles (or the parameters codifying it) may affect mechanical properties of the system. An indispensable part of reaching the answer is an appropriate particle parametrization. We come up with a simple, yet generalizable and purposeful scheme for it. Using our generalizable shape parameterization, we simulate the formation of a solid composed of pentagonal-like particles and measure anisotropy in the resulting elastic response. Through automatic differentiation techniques, we directly connect the shape parameters with the elastic response. Interestingly, for our system we find that less isotropic particles lead to a more isotropic elastic response. Together with other results known about our method it seems that it can be successfully generalized for different inverse design problems."}],"type":"dissertation","alternative_title":["ISTA Master's Thesis"],"author":[{"id":"865E3C26-AA8C-11E9-A409-C4C4E5697425","last_name":"Piankov","first_name":"Anton","full_name":"Piankov, Anton"}],"file":[{"file_name":"Thesis.zip","access_level":"closed","creator":"cchlebak","file_size":394018,"content_type":"application/x-zip-compressed","file_id":"10424","relation":"source_file","date_created":"2021-12-07T11:13:52Z","date_updated":"2022-03-10T12:10:25Z","checksum":"114e8f4b2c002c6c352416c12de2c695"},{"file_size":47638,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cchlebak","file_name":"Preliminary_pages_Piankov.docx","access_level":"closed","date_updated":"2022-03-10T12:10:25Z","date_created":"2021-12-07T11:14:01Z","checksum":"cd15ae991ced352a9959815f794e657c","relation":"source_file","file_id":"10425"},{"file_name":"2021_Piankov_combined.pdf","access_level":"open_access","content_type":"application/pdf","file_size":484965,"creator":"cchlebak","relation":"main_file","file_id":"10426","date_created":"2021-12-07T11:20:35Z","date_updated":"2021-12-07T11:20:35Z","checksum":"e6899c798b75ba42fab9822bce309050","success":1}],"oa_version":"Published Version","date_updated":"2023-09-07T13:34:12Z","date_created":"2021-12-07T10:48:06Z","year":"2021","_id":"10422","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"CaGo"}],"publication_status":"published","title":"Towards designer materials using customizable particle shape","status":"public","ddc":["530"],"article_processing_charge":"No","publication_identifier":{"issn":["2791-4585"]},"has_accepted_license":"1","month":"12","day":"07","date_published":"2021-12-07T00:00:00Z","doi":"10.15479/at:ista:10422","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"}],"degree_awarded":"MS","oa":1,"citation":{"ama":"Piankov A. Towards designer materials using customizable particle shape. 2021. doi:10.15479/at:ista:10422","apa":"Piankov, A. (2021). Towards designer materials using customizable particle shape. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10422","ieee":"A. Piankov, “Towards designer materials using customizable particle shape,” Institute of Science and Technology Austria, 2021.","ista":"Piankov A. 2021. Towards designer materials using customizable particle shape. Institute of Science and Technology Austria.","short":"A. Piankov, Towards Designer Materials Using Customizable Particle Shape, Institute of Science and Technology Austria, 2021.","mla":"Piankov, Anton. Towards Designer Materials Using Customizable Particle Shape. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10422.","chicago":"Piankov, Anton. “Towards Designer Materials Using Customizable Particle Shape.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10422."}},{"month":"06","day":"07","article_processing_charge":"No","publication":"arXiv","main_file_link":[{"url":"https://arxiv.org/abs/2102.05996","open_access":"1"}],"citation":{"chicago":"Konstantinov, Nikola H, and Christoph Lampert. “Fairness through Regularization for Learning to Rank.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2102.05996.","short":"N.H. Konstantinov, C. Lampert, ArXiv (n.d.).","mla":"Konstantinov, Nikola H., and Christoph Lampert. “Fairness through Regularization for Learning to Rank.” ArXiv, 2102.05996, doi:10.48550/arXiv.2102.05996.","ieee":"N. H. Konstantinov and C. Lampert, “Fairness through regularization for learning to rank,” arXiv. .","apa":"Konstantinov, N. H., & Lampert, C. (n.d.). Fairness through regularization for learning to rank. arXiv. https://doi.org/10.48550/arXiv.2102.05996","ista":"Konstantinov NH, Lampert C. Fairness through regularization for learning to rank. arXiv, 2102.05996.","ama":"Konstantinov NH, Lampert C. Fairness through regularization for learning to rank. arXiv. doi:10.48550/arXiv.2102.05996"},"oa":1,"external_id":{"arxiv":["2102.05996"]},"language":[{"iso":"eng"}],"date_published":"2021-06-07T00:00:00Z","doi":"10.48550/arXiv.2102.05996","article_number":"2102.05996","type":"preprint","abstract":[{"text":"Given the abundance of applications of ranking in recent years, addressing fairness concerns around automated ranking systems becomes necessary for increasing the trust among end-users. Previous work on fair ranking has mostly focused on application-specific fairness notions, often tailored to online advertising, and it rarely considers learning as part of the process. In this work, we show how to transfer numerous fairness notions from binary classification to a learning to rank setting. Our formalism allows us to design methods for incorporating fairness objectives with provable generalization guarantees. An extensive experimental evaluation shows that our method can improve ranking fairness substantially with no or only little loss of model quality.","lang":"eng"}],"publication_status":"submitted","title":"Fairness through regularization for learning to rank","status":"public","department":[{"_id":"ChLa"}],"year":"2021","_id":"10803","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-07T13:42:08Z","date_created":"2022-02-28T14:13:59Z","oa_version":"Preprint","author":[{"id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola H","last_name":"Konstantinov","full_name":"Konstantinov, Nikola H"},{"orcid":"0000-0002-4561-241X","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"}],"related_material":{"record":[{"id":"10799","relation":"dissertation_contains","status":"public"}]}},{"department":[{"_id":"MiLe"}],"status":"public","title":"Artificial neural network states for non-additive systems","publication_status":"submitted","_id":"10762","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We acknowledge fruitful discussions with Giacomo Bighin, Giammarco Fabiani, Areg Ghazaryan, Christoph\r\nLampert, and Artem Volosniev at various stages of this work. W.R. is a recipient of a DOC Fellowship of the\r\nAustrian Academy of Sciences and has received funding from the EU Horizon 2020 programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 665385. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). This work is part of the Shell-NWO/FOM-initiative “Computational sciences for energy research” of Shell and Chemical Sciences, Earth and Life Sciences, Physical Sciences, FOM and STW.","year":"2021","oa_version":"Preprint","date_created":"2022-02-17T11:18:57Z","date_updated":"2023-09-07T13:44:16Z","related_material":{"record":[{"id":"10759","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Rzadkowski, Wojciech","last_name":"Rzadkowski","first_name":"Wojciech","orcid":"0000-0002-1106-4419","id":"48C55298-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mentink, Johan H.","first_name":"Johan H.","last_name":"Mentink"}],"type":"preprint","ec_funded":1,"abstract":[{"lang":"eng","text":"Methods inspired from machine learning have recently attracted great interest in the computational study of quantum many-particle systems. So far, however, it has proven challenging to deal with microscopic models in which the total number of particles is not conserved. To address this issue, we propose a new variant of neural network states, which we term neural coherent states. Taking the Fröhlich impurity model as a case study, we show that neural coherent states can learn the ground state of non-additive systems very well. In particular, we observe substantial improvement over the standard coherent state estimates in the most challenging intermediate coupling regime. Our approach is generic and does not assume specific details of the system, suggesting wide applications."}],"page":"2105.15193","project":[{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2105.15193"}],"citation":{"apa":"Rzadkowski, W., Lemeshko, M., & Mentink, J. H. (n.d.). Artificial neural network states for non-additive systems. arXiv. https://doi.org/10.48550/arXiv.2105.15193","ieee":"W. Rzadkowski, M. Lemeshko, and J. H. Mentink, “Artificial neural network states for non-additive systems,” arXiv. .","ista":"Rzadkowski W, Lemeshko M, Mentink JH. Artificial neural network states for non-additive systems. arXiv, 10.48550/arXiv.2105.15193.","ama":"Rzadkowski W, Lemeshko M, Mentink JH. Artificial neural network states for non-additive systems. arXiv. doi:10.48550/arXiv.2105.15193","chicago":"Rzadkowski, Wojciech, Mikhail Lemeshko, and Johan H. Mentink. “Artificial Neural Network States for Non-Additive Systems.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2105.15193.","short":"W. Rzadkowski, M. Lemeshko, J.H. Mentink, ArXiv (n.d.).","mla":"Rzadkowski, Wojciech, et al. “Artificial Neural Network States for Non-Additive Systems.” ArXiv, doi:10.48550/arXiv.2105.15193."},"oa":1,"external_id":{"arxiv":["2105.15193"]},"publication":"arXiv","language":[{"iso":"eng"}],"doi":"10.48550/arXiv.2105.15193","date_published":"2021-05-31T00:00:00Z","article_processing_charge":"No","month":"05","day":"31"},{"article_processing_charge":"No","has_accepted_license":"1","day":"30","citation":{"chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418.","mla":"Phuong, Mary. Underspecification in Deep Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418.","short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021.","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","apa":"Phuong, M. (2021). Underspecification in deep learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9418","ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021.","ama":"Phuong M. Underspecification in deep learning. 2021. doi:10.15479/AT:ISTA:9418"},"page":"125","date_published":"2021-05-30T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models.","lang":"eng"}],"_id":"9418","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"title":"Underspecification in deep learning","status":"public","file":[{"file_name":"mph-thesis-v519-pdfimages.pdf","access_level":"open_access","file_size":2673905,"content_type":"application/pdf","creator":"bphuong","relation":"main_file","file_id":"9419","date_created":"2021-05-24T11:22:29Z","date_updated":"2021-05-24T11:22:29Z","checksum":"4f0abe64114cfed264f9d36e8d1197e3","success":1},{"creator":"bphuong","file_size":92995100,"content_type":"application/zip","file_name":"thesis.zip","access_level":"closed","date_updated":"2021-05-24T11:56:02Z","date_created":"2021-05-24T11:56:02Z","checksum":"f5699e876bc770a9b0df8345a77720a2","file_id":"9420","relation":"source_file"}],"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"month":"05","oa":1,"doi":"10.15479/AT:ISTA:9418","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"degree_awarded":"PhD","file_date_updated":"2021-05-24T11:56:02Z","year":"2021","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"7435","relation":"part_of_dissertation","status":"deleted"},{"id":"7481","relation":"part_of_dissertation","status":"public"},{"id":"9416","relation":"part_of_dissertation","status":"public"},{"id":"7479","relation":"part_of_dissertation","status":"public"}]},"author":[{"id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","last_name":"Bui Thi Mai","first_name":"Phuong","full_name":"Bui Thi Mai, Phuong"}],"date_updated":"2023-09-08T11:11:12Z","date_created":"2021-05-24T13:06:23Z"},{"extern":"1","year":"2021","publication_status":"published","publisher":"ML Research Press","department":[{"_id":"FrLo"}],"author":[{"full_name":"Träuble, Frederik","first_name":"Frederik","last_name":"Träuble"},{"full_name":"Creager, Elliot","first_name":"Elliot","last_name":"Creager"},{"full_name":"Kilbertus, Niki","last_name":"Kilbertus","first_name":"Niki"},{"last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco"},{"full_name":"Dittadi, Andrea","first_name":"Andrea","last_name":"Dittadi"},{"first_name":"Anirudh","last_name":"Goyal","full_name":"Goyal, Anirudh"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"full_name":"Bauer, Stefan","first_name":"Stefan","last_name":"Bauer"}],"date_updated":"2023-09-11T10:18:48Z","date_created":"2023-08-22T14:03:47Z","volume":139,"month":"08","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2006.07886"}],"oa":1,"external_id":{"arxiv":["2006.07886"]},"quality_controlled":"1","conference":{"start_date":"2021-07-18","location":"Virtual","end_date":"2021-07-24","name":"ICML: International Conference on Machine Learning"},"language":[{"iso":"eng"}],"type":"conference","alternative_title":["PMLR"],"abstract":[{"lang":"eng","text":"The focus of disentanglement approaches has been on identifying independent factors of variation in data. However, the causal variables underlying real-world observations are often not statistically independent. In this work, we bridge the gap to real-world scenarios by analyzing the behavior of the most prominent disentanglement approaches on correlated data in a large-scale empirical study (including 4260 models). We show and quantify that systematically induced correlations in the dataset are being learned and reflected in the latent representations, which has implications for downstream applications of disentanglement such as fairness. We also demonstrate how to resolve these latent correlations, either using weak supervision during\r\ntraining or by post-hoc correcting a pre-trained model with a small number of labels."}],"_id":"14177","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"On disentangled representations learned from correlated data","status":"public","intvolume":" 139","oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Proceedings of the 38th International Conference on Machine Learning","citation":{"ama":"Träuble F, Creager E, Kilbertus N, et al. On disentangled representations learned from correlated data. In: Proceedings of the 38th International Conference on Machine Learning. Vol 139. ML Research Press; 2021:10401-10412.","ieee":"F. Träuble et al., “On disentangled representations learned from correlated data,” in Proceedings of the 38th International Conference on Machine Learning, Virtual, 2021, vol. 139, pp. 10401–10412.","apa":"Träuble, F., Creager, E., Kilbertus, N., Locatello, F., Dittadi, A., Goyal, A., … Bauer, S. (2021). On disentangled representations learned from correlated data. In Proceedings of the 38th International Conference on Machine Learning (Vol. 139, pp. 10401–10412). Virtual: ML Research Press.","ista":"Träuble F, Creager E, Kilbertus N, Locatello F, Dittadi A, Goyal A, Schölkopf B, Bauer S. 2021. On disentangled representations learned from correlated data. Proceedings of the 38th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 139, 10401–10412.","short":"F. Träuble, E. Creager, N. Kilbertus, F. Locatello, A. Dittadi, A. Goyal, B. Schölkopf, S. Bauer, in:, Proceedings of the 38th International Conference on Machine Learning, ML Research Press, 2021, pp. 10401–10412.","mla":"Träuble, Frederik, et al. “On Disentangled Representations Learned from Correlated Data.” Proceedings of the 38th International Conference on Machine Learning, vol. 139, ML Research Press, 2021, pp. 10401–12.","chicago":"Träuble, Frederik, Elliot Creager, Niki Kilbertus, Francesco Locatello, Andrea Dittadi, Anirudh Goyal, Bernhard Schölkopf, and Stefan Bauer. “On Disentangled Representations Learned from Correlated Data.” In Proceedings of the 38th International Conference on Machine Learning, 139:10401–12. ML Research Press, 2021."},"page":"10401-10412","date_published":"2021-08-01T00:00:00Z"},{"language":[{"iso":"eng"}],"conference":{"start_date":"2021-07-18","location":"Virtual","end_date":"2021-07-24","name":"International Conference on Machine Learning"},"quality_controlled":"1","oa":1,"external_id":{"arxiv":["2106.05142"]},"main_file_link":[{"url":"https://arxiv.org/abs/2106.05142","open_access":"1"}],"month":"08","date_created":"2023-08-22T14:03:04Z","date_updated":"2023-09-11T10:16:55Z","volume":139,"author":[{"last_name":"Yèche","first_name":"Hugo","full_name":"Yèche, Hugo"},{"full_name":"Dresdner, Gideon","last_name":"Dresdner","first_name":"Gideon"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco"},{"last_name":"Hüser","first_name":"Matthias","full_name":"Hüser, Matthias"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"}],"publication_status":"published","publisher":"ML Research Press","department":[{"_id":"FrLo"}],"year":"2021","extern":"1","date_published":"2021-08-01T00:00:00Z","page":"11964-11974","publication":"Proceedings of 38th International Conference on Machine Learning","citation":{"chicago":"Yèche, Hugo, Gideon Dresdner, Francesco Locatello, Matthias Hüser, and Gunnar Rätsch. “Neighborhood Contrastive Learning Applied to Online Patient Monitoring.” In Proceedings of 38th International Conference on Machine Learning, 139:11964–74. ML Research Press, 2021.","short":"H. Yèche, G. Dresdner, F. Locatello, M. Hüser, G. Rätsch, in:, Proceedings of 38th International Conference on Machine Learning, ML Research Press, 2021, pp. 11964–11974.","mla":"Yèche, Hugo, et al. “Neighborhood Contrastive Learning Applied to Online Patient Monitoring.” Proceedings of 38th International Conference on Machine Learning, vol. 139, ML Research Press, 2021, pp. 11964–74.","ieee":"H. Yèche, G. Dresdner, F. Locatello, M. Hüser, and G. Rätsch, “Neighborhood contrastive learning applied to online patient monitoring,” in Proceedings of 38th International Conference on Machine Learning, Virtual, 2021, vol. 139, pp. 11964–11974.","apa":"Yèche, H., Dresdner, G., Locatello, F., Hüser, M., & Rätsch, G. (2021). Neighborhood contrastive learning applied to online patient monitoring. In Proceedings of 38th International Conference on Machine Learning (Vol. 139, pp. 11964–11974). Virtual: ML Research Press.","ista":"Yèche H, Dresdner G, Locatello F, Hüser M, Rätsch G. 2021. Neighborhood contrastive learning applied to online patient monitoring. Proceedings of 38th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 139, 11964–11974.","ama":"Yèche H, Dresdner G, Locatello F, Hüser M, Rätsch G. Neighborhood contrastive learning applied to online patient monitoring. In: Proceedings of 38th International Conference on Machine Learning. Vol 139. ML Research Press; 2021:11964-11974."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","status":"public","title":"Neighborhood contrastive learning applied to online patient monitoring","intvolume":" 139","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14176","abstract":[{"text":"Intensive care units (ICU) are increasingly looking towards machine learning for methods to provide online monitoring of critically ill patients. In machine learning, online monitoring is often formulated as a supervised learning problem. Recently, contrastive learning approaches have demonstrated promising improvements over competitive supervised benchmarks. These methods rely on well-understood data augmentation techniques developed for image data which do not apply to online monitoring. In this work, we overcome this limitation by\r\nsupplementing time-series data augmentation techniques with a novel contrastive\r\nlearning objective which we call neighborhood contrastive learning (NCL). Our objective explicitly groups together contiguous time segments from each patient while maintaining state-specific information. Our experiments demonstrate a marked improvement over existing work applying contrastive methods to medical time-series.","lang":"eng"}],"alternative_title":["PMLR"],"type":"conference"},{"publication":"35th Conference on Neural Information Processing Systems","external_id":{"arxiv":["2107.01057"]},"citation":{"ama":"Träuble F, Kügelgen J von, Kleindessner M, Locatello F, Schölkopf B, Gehler P. Backward-compatible prediction updates: A probabilistic approach. In: 35th Conference on Neural Information Processing Systems. Vol 34. ; 2021:116-128.","ista":"Träuble F, Kügelgen J von, Kleindessner M, Locatello F, Schölkopf B, Gehler P. 2021. Backward-compatible prediction updates: A probabilistic approach. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 34, 116–128.","apa":"Träuble, F., Kügelgen, J. von, Kleindessner, M., Locatello, F., Schölkopf, B., & Gehler, P. (2021). Backward-compatible prediction updates: A probabilistic approach. In 35th Conference on Neural Information Processing Systems (Vol. 34, pp. 116–128). Virtual.","ieee":"F. Träuble, J. von Kügelgen, M. Kleindessner, F. Locatello, B. Schölkopf, and P. Gehler, “Backward-compatible prediction updates: A probabilistic approach,” in 35th Conference on Neural Information Processing Systems, Virtual, 2021, vol. 34, pp. 116–128.","mla":"Träuble, Frederik, et al. “Backward-Compatible Prediction Updates: A Probabilistic Approach.” 35th Conference on Neural Information Processing Systems, vol. 34, 2021, pp. 116–28.","short":"F. Träuble, J. von Kügelgen, M. Kleindessner, F. Locatello, B. Schölkopf, P. Gehler, in:, 35th Conference on Neural Information Processing Systems, 2021, pp. 116–128.","chicago":"Träuble, Frederik, Julius von Kügelgen, Matthäus Kleindessner, Francesco Locatello, Bernhard Schölkopf, and Peter Gehler. “Backward-Compatible Prediction Updates: A Probabilistic Approach.” In 35th Conference on Neural Information Processing Systems, 34:116–28, 2021."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2107.01057"}],"oa":1,"quality_controlled":"1","page":"116-128","conference":{"end_date":"2021-12-10","start_date":"2021-12-07","location":"Virtual","name":"NeurIPS: Neural Information Processing Systems"},"date_published":"2021-07-02T00:00:00Z","language":[{"iso":"eng"}],"day":"02","month":"07","article_processing_charge":"No","publication_identifier":{"isbn":["9781713845393"]},"year":"2021","_id":"14182","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Backward-compatible prediction updates: A probabilistic approach","intvolume":" 34","department":[{"_id":"FrLo"}],"author":[{"full_name":"Träuble, Frederik","first_name":"Frederik","last_name":"Träuble"},{"full_name":"Kügelgen, Julius von","first_name":"Julius von","last_name":"Kügelgen"},{"full_name":"Kleindessner, Matthäus","first_name":"Matthäus","last_name":"Kleindessner"},{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"full_name":"Gehler, Peter","first_name":"Peter","last_name":"Gehler"}],"date_updated":"2023-09-11T11:31:59Z","date_created":"2023-08-22T14:05:41Z","oa_version":"Preprint","volume":34,"type":"conference","abstract":[{"lang":"eng","text":"When machine learning systems meet real world applications, accuracy is only\r\none of several requirements. In this paper, we assay a complementary\r\nperspective originating from the increasing availability of pre-trained and\r\nregularly improving state-of-the-art models. While new improved models develop\r\nat a fast pace, downstream tasks vary more slowly or stay constant. Assume that\r\nwe have a large unlabelled data set for which we want to maintain accurate\r\npredictions. Whenever a new and presumably better ML models becomes available,\r\nwe encounter two problems: (i) given a limited budget, which data points should\r\nbe re-evaluated using the new model?; and (ii) if the new predictions differ\r\nfrom the current ones, should we update? Problem (i) is about compute cost,\r\nwhich matters for very large data sets and models. Problem (ii) is about\r\nmaintaining consistency of the predictions, which can be highly relevant for\r\ndownstream applications; our demand is to avoid negative flips, i.e., changing\r\ncorrect to incorrect predictions. In this paper, we formalize the Prediction\r\nUpdate Problem and present an efficient probabilistic approach as answer to the\r\nabove questions. In extensive experiments on standard classification benchmark\r\ndata sets, we show that our method outperforms alternative strategies along key\r\nmetrics for backward-compatible prediction updates."}],"extern":"1"},{"month":"05","day":"19","publication_identifier":{"eisbn":["9780999241196"]},"article_processing_charge":"No","publication":"Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence","oa":1,"external_id":{"arxiv":["2105.09240"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2105.09240","open_access":"1"}],"citation":{"chicago":"Dresdner, Gideon, Saurav Shekhar, Fabian Pedregosa, Francesco Locatello, and Gunnar Rätsch. “Boosting Variational Inference with Locally Adaptive Step-Sizes.” In Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence, 2337–43. International Joint Conferences on Artificial Intelligence, 2021. https://doi.org/10.24963/ijcai.2021/322.","short":"G. Dresdner, S. Shekhar, F. Pedregosa, F. Locatello, G. Rätsch, in:, Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence, 2021, pp. 2337–2343.","mla":"Dresdner, Gideon, et al. “Boosting Variational Inference with Locally Adaptive Step-Sizes.” Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence, 2021, pp. 2337–43, doi:10.24963/ijcai.2021/322.","ieee":"G. Dresdner, S. Shekhar, F. Pedregosa, F. Locatello, and G. Rätsch, “Boosting variational inference with locally adaptive step-sizes,” in Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence, Montreal, Canada, 2021, pp. 2337–2343.","apa":"Dresdner, G., Shekhar, S., Pedregosa, F., Locatello, F., & Rätsch, G. (2021). Boosting variational inference with locally adaptive step-sizes. In Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence (pp. 2337–2343). Montreal, Canada: International Joint Conferences on Artificial Intelligence. https://doi.org/10.24963/ijcai.2021/322","ista":"Dresdner G, Shekhar S, Pedregosa F, Locatello F, Rätsch G. 2021. Boosting variational inference with locally adaptive step-sizes. Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence, 2337–2343.","ama":"Dresdner G, Shekhar S, Pedregosa F, Locatello F, Rätsch G. Boosting variational inference with locally adaptive step-sizes. In: Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence. International Joint Conferences on Artificial Intelligence; 2021:2337-2343. doi:10.24963/ijcai.2021/322"},"quality_controlled":"1","page":"2337-2343","conference":{"name":"IJCAI: International Joint Conference on Artificial Intelligence","end_date":"2021-08-27","start_date":"2021-08-19","location":"Montreal, Canada"},"date_published":"2021-05-19T00:00:00Z","doi":"10.24963/ijcai.2021/322","language":[{"iso":"eng"}],"type":"conference","abstract":[{"lang":"eng","text":"Variational Inference makes a trade-off between the capacity of the variational family and the tractability of finding an approximate posterior distribution. Instead, Boosting Variational Inference allows practitioners to obtain increasingly good posterior approximations by spending more compute. The main obstacle to widespread adoption of Boosting Variational Inference is the amount of resources necessary to improve over a strong Variational Inference baseline. In our work, we trace this limitation back to the global curvature of the KL-divergence. We characterize how the global curvature impacts time and memory consumption, address the problem with the notion of local curvature, and provide a novel approximate backtracking algorithm for estimating local curvature. We give new theoretical convergence rates for our algorithms and provide experimental validation on synthetic and real-world datasets."}],"extern":"1","year":"2021","_id":"14181","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Boosting variational inference with locally adaptive step-sizes","publication_status":"published","status":"public","publisher":"International Joint Conferences on Artificial Intelligence","department":[{"_id":"FrLo"}],"author":[{"last_name":"Dresdner","first_name":"Gideon","full_name":"Dresdner, Gideon"},{"last_name":"Shekhar","first_name":"Saurav","full_name":"Shekhar, Saurav"},{"full_name":"Pedregosa, Fabian","first_name":"Fabian","last_name":"Pedregosa"},{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"}],"date_created":"2023-08-22T14:05:14Z","date_updated":"2023-09-11T11:14:30Z","oa_version":"Published Version"},{"_id":"14179","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","title":"Self-supervised learning with data augmentations provably isolates content from style","publication_status":"published","status":"public","department":[{"_id":"FrLo"}],"intvolume":" 34","author":[{"full_name":"Kügelgen, Julius von","first_name":"Julius von","last_name":"Kügelgen"},{"full_name":"Sharma, Yash","last_name":"Sharma","first_name":"Yash"},{"full_name":"Gresele, Luigi","last_name":"Gresele","first_name":"Luigi"},{"full_name":"Brendel, Wieland","first_name":"Wieland","last_name":"Brendel"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"last_name":"Besserve","first_name":"Michel","full_name":"Besserve, Michel"},{"last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco"}],"date_created":"2023-08-22T14:04:36Z","date_updated":"2023-09-11T10:33:19Z","volume":34,"oa_version":"Preprint","type":"conference","abstract":[{"text":"Self-supervised representation learning has shown remarkable success in a number of domains. A common practice is to perform data augmentation via hand-crafted transformations intended to leave the semantics of the data invariant. We seek to understand the empirical success of this approach from a theoretical perspective. We formulate the augmentation process as a latent variable model by postulating a partition of the latent representation into a content component, which is assumed invariant to augmentation, and a style component, which is allowed to change. Unlike prior work on disentanglement and independent component analysis, we allow for both nontrivial statistical and causal dependencies in the latent space. We study the identifiability of the latent representation based on pairs of views of the observations and prove sufficient conditions that allow us to identify the invariant content partition up to an invertible mapping in both generative and discriminative settings. We find numerical simulations with dependent latent variables are consistent with our theory. Lastly, we introduce Causal3DIdent, a dataset of high-dimensional, visually complex images with rich causal dependencies, which we use to study the effect of data augmentations performed in practice.","lang":"eng"}],"extern":"1","publication":"Advances in Neural Information Processing Systems","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2106.04619"}],"external_id":{"arxiv":["2106.04619"]},"citation":{"ista":"Kügelgen J von, Sharma Y, Gresele L, Brendel W, Schölkopf B, Besserve M, Locatello F. 2021. Self-supervised learning with data augmentations provably isolates content from style. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 34, 16451–16467.","ieee":"J. von Kügelgen et al., “Self-supervised learning with data augmentations provably isolates content from style,” in Advances in Neural Information Processing Systems, Virtual, 2021, vol. 34, pp. 16451–16467.","apa":"Kügelgen, J. von, Sharma, Y., Gresele, L., Brendel, W., Schölkopf, B., Besserve, M., & Locatello, F. (2021). Self-supervised learning with data augmentations provably isolates content from style. In Advances in Neural Information Processing Systems (Vol. 34, pp. 16451–16467). Virtual.","ama":"Kügelgen J von, Sharma Y, Gresele L, et al. Self-supervised learning with data augmentations provably isolates content from style. In: Advances in Neural Information Processing Systems. Vol 34. ; 2021:16451-16467.","chicago":"Kügelgen, Julius von, Yash Sharma, Luigi Gresele, Wieland Brendel, Bernhard Schölkopf, Michel Besserve, and Francesco Locatello. “Self-Supervised Learning with Data Augmentations Provably Isolates Content from Style.” In Advances in Neural Information Processing Systems, 34:16451–67, 2021.","mla":"Kügelgen, Julius von, et al. “Self-Supervised Learning with Data Augmentations Provably Isolates Content from Style.” Advances in Neural Information Processing Systems, vol. 34, 2021, pp. 16451–67.","short":"J. von Kügelgen, Y. Sharma, L. Gresele, W. Brendel, B. Schölkopf, M. Besserve, F. Locatello, in:, Advances in Neural Information Processing Systems, 2021, pp. 16451–16467."},"quality_controlled":"1","page":"16451-16467","conference":{"end_date":"2021-12-10","location":"Virtual","start_date":"2021-12-07","name":"NeurIPS: Neural Information Processing Systems"},"date_published":"2021-06-08T00:00:00Z","language":[{"iso":"eng"}],"day":"08","month":"06","article_processing_charge":"No","publication_identifier":{"isbn":["9781713845393"]}},{"publication_identifier":{"isbn":["9781713845393"]},"article_processing_charge":"No","day":"12","month":"10","language":[{"iso":"eng"}],"date_published":"2021-10-12T00:00:00Z","conference":{"end_date":"2021-12-10","location":"Virtual","start_date":"2021-12-07","name":"NeurIPS: Neural Information Processing Systems"},"page":"10985-10998","quality_controlled":"1","external_id":{"arxiv":["2110.06399"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2110.06399","open_access":"1"}],"citation":{"mla":"Rahaman, Nasim, et al. “Dynamic Inference with Neural Interpreters.” Advances in Neural Information Processing Systems, vol. 34, 2021, pp. 10985–98.","short":"N. Rahaman, M.W. Gondal, S. Joshi, P. Gehler, Y. Bengio, F. Locatello, B. Schölkopf, in:, Advances in Neural Information Processing Systems, 2021, pp. 10985–10998.","chicago":"Rahaman, Nasim, Muhammad Waleed Gondal, Shruti Joshi, Peter Gehler, Yoshua Bengio, Francesco Locatello, and Bernhard Schölkopf. “Dynamic Inference with Neural Interpreters.” In Advances in Neural Information Processing Systems, 34:10985–98, 2021.","ama":"Rahaman N, Gondal MW, Joshi S, et al. Dynamic inference with neural interpreters. In: Advances in Neural Information Processing Systems. Vol 34. ; 2021:10985-10998.","ista":"Rahaman N, Gondal MW, Joshi S, Gehler P, Bengio Y, Locatello F, Schölkopf B. 2021. Dynamic inference with neural interpreters. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 34, 10985–10998.","apa":"Rahaman, N., Gondal, M. W., Joshi, S., Gehler, P., Bengio, Y., Locatello, F., & Schölkopf, B. (2021). Dynamic inference with neural interpreters. In Advances in Neural Information Processing Systems (Vol. 34, pp. 10985–10998). Virtual.","ieee":"N. Rahaman et al., “Dynamic inference with neural interpreters,” in Advances in Neural Information Processing Systems, Virtual, 2021, vol. 34, pp. 10985–10998."},"oa":1,"publication":"Advances in Neural Information Processing Systems","extern":"1","abstract":[{"lang":"eng","text":"Modern neural network architectures can leverage large amounts of data to generalize well within the training distribution. However, they are less capable of systematic generalization to data drawn from unseen but related distributions, a feat that is hypothesized to require compositional reasoning and reuse of knowledge. In this work, we present Neural Interpreters, an architecture that factorizes inference in a self-attention network as a system of modules, which we call \\emph{functions}. Inputs to the model are routed through a sequence of functions in a way that is end-to-end learned. The proposed architecture can flexibly compose computation along width and depth, and lends itself well to capacity extension after training. To demonstrate the versatility of Neural Interpreters, we evaluate it in two distinct settings: image classification and visual abstract reasoning on Raven Progressive Matrices. In the former, we show that Neural Interpreters perform on par with the vision transformer using fewer parameters, while being transferrable to a new task in a sample efficient manner. In the latter, we find that Neural Interpreters are competitive with respect to the state-of-the-art in terms of systematic generalization. "}],"type":"conference","volume":34,"oa_version":"Preprint","date_created":"2023-08-22T14:04:55Z","date_updated":"2023-09-11T11:33:46Z","author":[{"last_name":"Rahaman","first_name":"Nasim","full_name":"Rahaman, Nasim"},{"full_name":"Gondal, Muhammad Waleed","last_name":"Gondal","first_name":"Muhammad Waleed"},{"last_name":"Joshi","first_name":"Shruti","full_name":"Joshi, Shruti"},{"first_name":"Peter","last_name":"Gehler","full_name":"Gehler, Peter"},{"full_name":"Bengio, Yoshua","last_name":"Bengio","first_name":"Yoshua"},{"full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Schölkopf, Bernhard","first_name":"Bernhard","last_name":"Schölkopf"}],"department":[{"_id":"FrLo"}],"intvolume":" 34","status":"public","publication_status":"published","title":"Dynamic inference with neural interpreters","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14180","year":"2021"},{"year":"2021","department":[{"_id":"FrLo"}],"publisher":"Institute of Electrical and Electronics Engineers","publication_status":"published","author":[{"full_name":"Scholkopf, Bernhard","last_name":"Scholkopf","first_name":"Bernhard"},{"full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"full_name":"Bauer, Stefan","last_name":"Bauer","first_name":"Stefan"},{"first_name":"Nan Rosemary","last_name":"Ke","full_name":"Ke, Nan Rosemary"},{"full_name":"Kalchbrenner, Nal","first_name":"Nal","last_name":"Kalchbrenner"},{"last_name":"Goyal","first_name":"Anirudh","full_name":"Goyal, Anirudh"},{"full_name":"Bengio, Yoshua","last_name":"Bengio","first_name":"Yoshua"}],"volume":109,"date_updated":"2023-09-11T11:43:35Z","date_created":"2023-08-21T12:19:30Z","extern":"1","external_id":{"arxiv":["2102.11107"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1109/JPROC.2021.3058954"}],"oa":1,"quality_controlled":"1","doi":"10.1109/jproc.2021.3058954","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0018-9219"],"eissn":["1558-2256"]},"month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14117","intvolume":" 109","status":"public","title":"Toward causal representation learning","oa_version":"Published Version","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"The two fields of machine learning and graphical causality arose and are developed separately. However, there is, now, cross-pollination and increasing interest in both fields to benefit from the advances of the other. In this article, we review fundamental concepts of causal inference and relate them to crucial open problems of machine learning, including transfer and generalization, thereby assaying how causality can contribute to modern machine learning research. This also applies in the opposite direction: we note that most work in causality starts from the premise that the causal variables are given. A central problem for AI and causality is, thus, causal representation learning, that is, the discovery of high-level causal variables from low-level observations. Finally, we delineate some implications of causality for machine learning and propose key research areas at the intersection of both communities."}],"citation":{"chicago":"Scholkopf, Bernhard, Francesco Locatello, Stefan Bauer, Nan Rosemary Ke, Nal Kalchbrenner, Anirudh Goyal, and Yoshua Bengio. “Toward Causal Representation Learning.” Proceedings of the IEEE. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/jproc.2021.3058954.","short":"B. Scholkopf, F. Locatello, S. Bauer, N.R. Ke, N. Kalchbrenner, A. Goyal, Y. Bengio, Proceedings of the IEEE 109 (2021) 612–634.","mla":"Scholkopf, Bernhard, et al. “Toward Causal Representation Learning.” Proceedings of the IEEE, vol. 109, no. 5, Institute of Electrical and Electronics Engineers, 2021, pp. 612–34, doi:10.1109/jproc.2021.3058954.","apa":"Scholkopf, B., Locatello, F., Bauer, S., Ke, N. R., Kalchbrenner, N., Goyal, A., & Bengio, Y. (2021). Toward causal representation learning. Proceedings of the IEEE. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/jproc.2021.3058954","ieee":"B. Scholkopf et al., “Toward causal representation learning,” Proceedings of the IEEE, vol. 109, no. 5. Institute of Electrical and Electronics Engineers, pp. 612–634, 2021.","ista":"Scholkopf B, Locatello F, Bauer S, Ke NR, Kalchbrenner N, Goyal A, Bengio Y. 2021. Toward causal representation learning. Proceedings of the IEEE. 109(5), 612–634.","ama":"Scholkopf B, Locatello F, Bauer S, et al. Toward causal representation learning. Proceedings of the IEEE. 2021;109(5):612-634. doi:10.1109/jproc.2021.3058954"},"publication":"Proceedings of the IEEE","page":"612-634","article_type":"original","date_published":"2021-05-01T00:00:00Z","scopus_import":"1","keyword":["Electrical and Electronic Engineering"],"article_processing_charge":"No","day":"01"},{"abstract":[{"text":"Learning meaningful representations that disentangle the underlying structure of the data generating process is considered to be of key importance in machine learning. While disentangled representations were found to be useful for diverse tasks such as abstract reasoning and fair classification, their scalability and real-world impact remain questionable. We introduce a new high-resolution dataset with 1M simulated images and over 1,800 annotated real-world images of the same setup. In contrast to previous work, this new dataset exhibits correlations, a complex underlying structure, and allows to evaluate transfer to unseen simulated and real-world settings where the encoder i) remains in distribution or ii) is out of distribution. We propose new architectures in order to scale disentangled representation learning to realistic high-resolution settings and conduct a large-scale empirical study of disentangled representations on this dataset. We observe that disentanglement is a good predictor for out-of-distribution (OOD) task performance.","lang":"eng"}],"extern":"1","type":"conference","author":[{"full_name":"Dittadi, Andrea","last_name":"Dittadi","first_name":"Andrea"},{"last_name":"Träuble","first_name":"Frederik","full_name":"Träuble, Frederik"},{"full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"last_name":"Wüthrich","first_name":"Manuel","full_name":"Wüthrich, Manuel"},{"last_name":"Agrawal","first_name":"Vaibhav","full_name":"Agrawal, Vaibhav"},{"last_name":"Winther","first_name":"Ole","full_name":"Winther, Ole"},{"full_name":"Bauer, Stefan","first_name":"Stefan","last_name":"Bauer"},{"full_name":"Schölkopf, Bernhard","first_name":"Bernhard","last_name":"Schölkopf"}],"oa_version":"Preprint","date_created":"2023-08-22T14:04:16Z","date_updated":"2023-09-11T10:55:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14178","year":"2021","department":[{"_id":"FrLo"}],"title":"On the transfer of disentangled representations in realistic settings","publication_status":"published","status":"public","article_processing_charge":"No","month":"05","day":"04","date_published":"2021-05-04T00:00:00Z","conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2021-05-07","location":"Virtual","start_date":"2021-05-03"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2010.14407","open_access":"1"}],"citation":{"ama":"Dittadi A, Träuble F, Locatello F, et al. On the transfer of disentangled representations in realistic settings. In: The Ninth International Conference on Learning Representations. ; 2021.","ista":"Dittadi A, Träuble F, Locatello F, Wüthrich M, Agrawal V, Winther O, Bauer S, Schölkopf B. 2021. On the transfer of disentangled representations in realistic settings. The Ninth International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ieee":"A. Dittadi et al., “On the transfer of disentangled representations in realistic settings,” in The Ninth International Conference on Learning Representations, Virtual, 2021.","apa":"Dittadi, A., Träuble, F., Locatello, F., Wüthrich, M., Agrawal, V., Winther, O., … Schölkopf, B. (2021). On the transfer of disentangled representations in realistic settings. In The Ninth International Conference on Learning Representations. Virtual.","mla":"Dittadi, Andrea, et al. “On the Transfer of Disentangled Representations in Realistic Settings.” The Ninth International Conference on Learning Representations, 2021.","short":"A. Dittadi, F. Träuble, F. Locatello, M. Wüthrich, V. Agrawal, O. Winther, S. Bauer, B. Schölkopf, in:, The Ninth International Conference on Learning Representations, 2021.","chicago":"Dittadi, Andrea, Frederik Träuble, Francesco Locatello, Manuel Wüthrich, Vaibhav Agrawal, Ole Winther, Stefan Bauer, and Bernhard Schölkopf. “On the Transfer of Disentangled Representations in Realistic Settings.” In The Ninth International Conference on Learning Representations, 2021."},"oa":1,"external_id":{"arxiv":["2010.14407"]},"publication":"The Ninth International Conference on Learning Representations","quality_controlled":"1"},{"language":[{"iso":"eng"}],"date_published":"2021-11-26T00:00:00Z","doi":"10.48550/arXiv.2111.13693","external_id":{"arxiv":["2111.13693"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2111.13693"}],"oa":1,"citation":{"ama":"Locatello F. Enforcing and discovering structure in machine learning. arXiv. doi:10.48550/arXiv.2111.13693","apa":"Locatello, F. (n.d.). Enforcing and discovering structure in machine learning. arXiv. https://doi.org/10.48550/arXiv.2111.13693","ieee":"F. Locatello, “Enforcing and discovering structure in machine learning,” arXiv. .","ista":"Locatello F. Enforcing and discovering structure in machine learning. arXiv, 2111.13693.","short":"F. Locatello, ArXiv (n.d.).","mla":"Locatello, Francesco. “Enforcing and Discovering Structure in Machine Learning.” ArXiv, 2111.13693, doi:10.48550/arXiv.2111.13693.","chicago":"Locatello, Francesco. “Enforcing and Discovering Structure in Machine Learning.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2111.13693."},"publication":"arXiv","article_processing_charge":"No","month":"11","day":"26","oa_version":"Preprint","date_created":"2023-08-22T14:23:35Z","date_updated":"2023-09-12T07:04:44Z","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco"}],"department":[{"_id":"FrLo"}],"publication_status":"submitted","status":"public","title":"Enforcing and discovering structure in machine learning","year":"2021","_id":"14221","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","abstract":[{"lang":"eng","text":"The world is structured in countless ways. It may be prudent to enforce corresponding structural properties to a learning algorithm's solution, such as incorporating prior beliefs, natural constraints, or causal structures. Doing so may translate to faster, more accurate, and more flexible models, which may directly relate to real-world impact. In this dissertation, we consider two different research areas that concern structuring a learning algorithm's solution: when the structure is known and when it has to be discovered."}],"type":"preprint","article_number":"2111.13693"},{"abstract":[{"text":"The Birkhoff conjecture says that the boundary of a strictly convex integrable billiard table is necessarily an ellipse. In this article, we consider a stronger notion of integrability, namely, integrability close to the boundary, and prove a local version of this conjecture: a small perturbation of almost every ellipse that preserves integrability near the boundary, is itself an ellipse. We apply this result to study local spectral rigidity of ellipses using the connection between the wave trace of the Laplacian and the dynamics near the boundary and establish rigidity for almost all of them.","lang":"eng"}],"type":"preprint","article_number":"2111.12171","author":[{"full_name":"Koval, Illya","id":"2eed1f3b-896a-11ed-bdf8-93c7c4bf159e","last_name":"Koval","first_name":"Illya"}],"oa_version":"Preprint","date_updated":"2023-09-15T06:44:00Z","date_created":"2023-09-06T08:35:43Z","_id":"14278","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","department":[{"_id":"GradSch"}],"publication_status":"submitted","title":"Local strong Birkhoff conjecture and local spectral rigidity of almost every ellipse","status":"public","article_processing_charge":"No","month":"11","day":"23","doi":"10.48550/ARXIV.2111.12171","date_published":"2021-11-23T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"citation":{"mla":"Koval, Illya. “Local Strong Birkhoff Conjecture and Local Spectral Rigidity of Almost Every Ellipse.” ArXiv, 2111.12171, doi:10.48550/ARXIV.2111.12171.","short":"I. Koval, ArXiv (n.d.).","chicago":"Koval, Illya. “Local Strong Birkhoff Conjecture and Local Spectral Rigidity of Almost Every Ellipse.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2111.12171.","ama":"Koval I. Local strong Birkhoff conjecture and local spectral rigidity of almost every ellipse. arXiv. doi:10.48550/ARXIV.2111.12171","ista":"Koval I. Local strong Birkhoff conjecture and local spectral rigidity of almost every ellipse. arXiv, 2111.12171.","apa":"Koval, I. (n.d.). Local strong Birkhoff conjecture and local spectral rigidity of almost every ellipse. arXiv. https://doi.org/10.48550/ARXIV.2111.12171","ieee":"I. 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In particular, concurrent programs are notoriously difficult both to be written correctly and to be analyzed formally, as complex thread interaction has to be accounted for. The difficulties are further exacerbated when concurrent programs get executed on modern-day hardware, which contains various buffering and caching mechanisms for efficiency reasons. This causes further subtle non-determinism, which can often produce very unintuitive behavior of the concurrent programs. Model checking is at the forefront of tackling the verification problem, where the task is to decide, given as input a concurrent system and a desired property, whether the system satisfies the property. The inherent state-space explosion problem in model checking of concurrent systems causes naïve explicit methods not to scale, thus more inventive methods are required. One such method is stateless model checking (SMC), which explores in memory-efficient manner the program executions rather than the states of the program. State-of-the-art SMC is typically coupled with partial order reduction (POR) techniques, which argue that certain executions provably produce identical system behavior, thus limiting the amount of executions one needs to explore in order to cover all possible behaviors. Another method to tackle the state-space explosion is symbolic model checking, where the considered techniques operate on a succinct implicit representation of the input system rather than explicitly accessing the system. In this thesis we present new techniques for verification of concurrent systems. We present several novel POR methods for SMC of concurrent programs under various models of semantics, some of which account for write-buffering mechanisms. Additionally, we present novel algorithms for symbolic model checking of finite-state concurrent systems, where the desired property of the systems is to ensure a formally defined notion of fairness."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10199","status":"public","ddc":["000"],"title":"Improved verification techniques for concurrent systems","oa_version":"Published Version","file":[{"date_created":"2021-11-08T14:12:22Z","date_updated":"2021-11-08T14:12:22Z","checksum":"4f412a1ee60952221b499a4b1268df35","file_id":"10225","relation":"main_file","creator":"vtoman","content_type":"application/pdf","file_size":2915234,"file_name":"toman_th_final.pdf","access_level":"open_access"},{"checksum":"9584943f99127be2dd2963f6784c37d4","date_updated":"2021-11-09T09:00:50Z","date_created":"2021-11-08T14:12:46Z","relation":"source_file","file_id":"10226","file_size":8616056,"content_type":"application/zip","creator":"vtoman","access_level":"closed","file_name":"toman_thesis.zip"}],"keyword":["concurrency","verification","model checking"],"day":"31","has_accepted_license":"1","article_processing_charge":"No","citation":{"chicago":"Toman, Viktor. “Improved Verification Techniques for Concurrent Systems.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10199.","short":"V. Toman, Improved Verification Techniques for Concurrent Systems, Institute of Science and Technology Austria, 2021.","mla":"Toman, Viktor. Improved Verification Techniques for Concurrent Systems. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10199.","apa":"Toman, V. (2021). Improved verification techniques for concurrent systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10199","ieee":"V. Toman, “Improved verification techniques for concurrent systems,” Institute of Science and Technology Austria, 2021.","ista":"Toman V. 2021. Improved verification techniques for concurrent systems. Institute of Science and Technology Austria.","ama":"Toman V. Improved verification techniques for concurrent systems. 2021. doi:10.15479/at:ista:10199"},"page":"166","date_published":"2021-10-31T00:00:00Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8429","status":"public","title":"Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits","ddc":["610"],"intvolume":" 12","file":[{"date_created":"2021-12-06T07:47:11Z","date_updated":"2021-12-06T07:47:11Z","success":1,"checksum":"384681be17aff902c149a48f52d13d4f","file_id":"10419","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","file_size":6519771,"file_name":"2021_NatComm_Paxtot.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only ≤10% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32–44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having ≥95% probability of contributing ≥0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data.","lang":"eng"}],"issue":"1","publication":"Nature Communications","citation":{"chicago":"Patxot, Marion, Daniel Trejo Banos, Athanasios Kousathanas, Etienne J Orliac, Sven E Ojavee, Gerhard Moser, Julia Sidorenko, et al. “Probabilistic Inference of the Genetic Architecture Underlying Functional Enrichment of Complex Traits.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-27258-9.","mla":"Patxot, Marion, et al. “Probabilistic Inference of the Genetic Architecture Underlying Functional Enrichment of Complex Traits.” Nature Communications, vol. 12, no. 1, 6972, Springer Nature, 2021, doi:10.1038/s41467-021-27258-9.","short":"M. Patxot, D. Trejo Banos, A. Kousathanas, E.J. Orliac, S.E. Ojavee, G. Moser, J. Sidorenko, Z. Kutalik, R. Magi, P.M. Visscher, L. Ronnegard, M.R. Robinson, Nature Communications 12 (2021).","ista":"Patxot M, Trejo Banos D, Kousathanas A, Orliac EJ, Ojavee SE, Moser G, Sidorenko J, Kutalik Z, Magi R, Visscher PM, Ronnegard L, Robinson MR. 2021. Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. Nature Communications. 12(1), 6972.","apa":"Patxot, M., Trejo Banos, D., Kousathanas, A., Orliac, E. J., Ojavee, S. E., Moser, G., … Robinson, M. R. (2021). Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-27258-9","ieee":"M. Patxot et al., “Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ama":"Patxot M, Trejo Banos D, Kousathanas A, et al. Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-27258-9"},"article_type":"original","date_published":"2021-11-30T00:00:00Z","scopus_import":"1","day":"30","article_processing_charge":"No","has_accepted_license":"1","acknowledgement":"This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria. We would like to thank the participants of the cohort studies, and the Ecole Polytechnique Federal Lausanne (EPFL) SCITAS for their excellent compute resources, their generosity with their time and the kindness of their support. P.M.V. acknowledges funding from the Australian National Health and Medical Research Council (1113400) and the Australian Research Council (FL180100072). L.R. acknowledges funding from the Kjell & Märta Beijer Foundation (Stockholm, Sweden). We also would like to acknowledge Simone Rubinacci, Oliver Delanau, Alexander Terenin, Eleonora Porcu, and Mike Goddard for their useful comments and suggestions.","year":"2021","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"MaRo"}],"author":[{"full_name":"Patxot, Marion","first_name":"Marion","last_name":"Patxot"},{"first_name":"Daniel","last_name":"Trejo Banos","full_name":"Trejo Banos, Daniel"},{"last_name":"Kousathanas","first_name":"Athanasios","full_name":"Kousathanas, Athanasios"},{"full_name":"Orliac, Etienne J","last_name":"Orliac","first_name":"Etienne J"},{"full_name":"Ojavee, Sven E","last_name":"Ojavee","first_name":"Sven E"},{"first_name":"Gerhard","last_name":"Moser","full_name":"Moser, Gerhard"},{"full_name":"Sidorenko, Julia","last_name":"Sidorenko","first_name":"Julia"},{"full_name":"Kutalik, Zoltan","first_name":"Zoltan","last_name":"Kutalik"},{"full_name":"Magi, Reedik","first_name":"Reedik","last_name":"Magi"},{"first_name":"Peter M","last_name":"Visscher","full_name":"Visscher, Peter M"},{"full_name":"Ronnegard, Lars","first_name":"Lars","last_name":"Ronnegard"},{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson"}],"related_material":{"record":[{"id":"13063","status":"public","relation":"research_data"}]},"date_updated":"2023-09-26T10:36:14Z","date_created":"2020-09-17T10:52:38Z","volume":12,"article_number":"6972","file_date_updated":"2021-12-06T07:47:11Z","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":["000724450600023"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-021-27258-9","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"eissn":["2041-1723"]}},{"oa":1,"external_id":{"arxiv":["2005.07637"]},"main_file_link":[{"url":"https://arxiv.org/abs/2005.07637","open_access":"1"}],"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"},{"name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020","grant_number":"840605","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1145/3410220.3453923","conference":{"name":"SIGMETRICS: International Conference on Measurement and Modeling of Computer Systems","start_date":"2021-06-14","location":"Virtual, Online","end_date":"2021-06-18"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450380720"]},"month":"05","acknowledgement":"We thank Jukka Suomela for discussions. We also thank our shepherd Mohammad Hajiesmaili and the reviewers for their time and suggestions on how to improve the paper. 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 805223 ScaleML), from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska–Curie grant agreement No. 840605, from the Vienna Science and Technology Fund (WWTF) project WHATIF, ICT19-045, 2020-2024, and from the Austrian Science Fund (FWF) and netIDEE SCIENCE project P 33775-N.","year":"2021","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"publication_status":"published","related_material":{"record":[{"id":"10855","status":"public","relation":"extended_version"}]},"author":[{"full_name":"Foerster, Klaus-Tycho","first_name":"Klaus-Tycho","last_name":"Foerster"},{"full_name":"Korhonen, Janne","last_name":"Korhonen","first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425"},{"last_name":"Paz","first_name":"Ami","full_name":"Paz, Ami"},{"full_name":"Rybicki, Joel","last_name":"Rybicki","first_name":"Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"}],"date_updated":"2023-09-26T10:40:55Z","date_created":"2022-03-18T08:48:41Z","ec_funded":1,"citation":{"chicago":"Foerster, Klaus-Tycho, Janne Korhonen, Ami Paz, Joel Rybicki, and Stefan Schmid. “Input-Dynamic Distributed Algorithms for Communication Networks.” In Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems, 71–72. Association for Computing Machinery, 2021. https://doi.org/10.1145/3410220.3453923.","mla":"Foerster, Klaus-Tycho, et al. “Input-Dynamic Distributed Algorithms for Communication Networks.” Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems, Association for Computing Machinery, 2021, pp. 71–72, doi:10.1145/3410220.3453923.","short":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, S. Schmid, in:, Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems, Association for Computing Machinery, 2021, pp. 71–72.","ista":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. 2021. Input-dynamic distributed algorithms for communication networks. Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems. SIGMETRICS: International Conference on Measurement and Modeling of Computer Systems, 71–72.","apa":"Foerster, K.-T., Korhonen, J., Paz, A., Rybicki, J., & Schmid, S. (2021). Input-dynamic distributed algorithms for communication networks. In Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems (pp. 71–72). Virtual, Online: Association for Computing Machinery. https://doi.org/10.1145/3410220.3453923","ieee":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, and S. Schmid, “Input-dynamic distributed algorithms for communication networks,” in Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems, Virtual, Online, 2021, pp. 71–72.","ama":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. Input-dynamic distributed algorithms for communication networks. In: Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems. Association for Computing Machinery; 2021:71-72. doi:10.1145/3410220.3453923"},"publication":"Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems","page":"71-72","date_published":"2021-05-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10854","title":"Input-dynamic distributed algorithms for communication networks","status":"public","oa_version":"Preprint","type":"conference","abstract":[{"text":"Consider a distributed task where the communication network is fixed but the local inputs given to the nodes of the distributed system may change over time. In this work, we explore the following question: if some of the local inputs change, can an existing solution be updated efficiently, in a dynamic and distributed manner?\r\nTo address this question, we define the batch dynamic CONGEST model in which we are given a bandwidth-limited communication network and a dynamic edge labelling defines the problem input. The task is to maintain a solution to a graph problem on the labelled graph under batch changes. We investigate, when a batch of alpha edge label changes arrive, - how much time as a function of alpha we need to update an existing solution, and - how much information the nodes have to keep in local memory between batches in order to update the solution quickly.\r\nOur work lays the foundations for the theory of input-dynamic distributed network algorithms. We give a general picture of the complexity landscape in this model, design both universal algorithms and algorithms for concrete problems, and present a general framework for lower bounds. The diverse time complexity of our model spans from constant time, through time polynomial in alpha, and to alpha time, which we show to be enough for any task.","lang":"eng"}]},{"author":[{"full_name":"Foerster, Klaus-Tycho","first_name":"Klaus-Tycho","last_name":"Foerster"},{"last_name":"Korhonen","first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","full_name":"Korhonen, Janne"},{"full_name":"Paz, Ami","last_name":"Paz","first_name":"Ami"},{"orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","first_name":"Joel","full_name":"Rybicki, Joel"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"}],"related_material":{"record":[{"id":"10854","relation":"shorter_version","status":"public"}]},"date_created":"2022-03-18T09:10:27Z","date_updated":"2023-09-26T10:40:55Z","volume":5,"year":"2021","acknowledgement":"We thank Jukka Suomela for discussions. We also thank our shepherd Mohammad Hajiesmaili\r\nand the reviewers for their time and suggestions on how to improve the paper. This project\r\nhas received funding from the European Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation programme (grant agreement No 805223 ScaleML), from the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSk lodowska–Curie grant agreement No. 840605, from the Vienna Science and Technology Fund (WWTF) project WHATIF, ICT19-045, 2020-2024, and from the Austrian Science Fund (FWF) and netIDEE SCIENCE project P 33775-N.","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"ec_funded":1,"doi":"10.1145/3447384","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.07637"}],"external_id":{"arxiv":["2005.07637"]},"oa":1,"quality_controlled":"1","project":[{"name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","grant_number":"840605"},{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"month":"03","publication_identifier":{"issn":["2476-1249"]},"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10855","status":"public","title":"Input-dynamic distributed algorithms for communication networks","intvolume":" 5","abstract":[{"lang":"eng","text":"Consider a distributed task where the communication network is fixed but the local inputs given to the nodes of the distributed system may change over time. In this work, we explore the following question: if some of the local inputs change, can an existing solution be updated efficiently, in a dynamic and distributed manner? To address this question, we define the batch dynamic \\congest model in which we are given a bandwidth-limited communication network and a dynamic edge labelling defines the problem input. The task is to maintain a solution to a graph problem on the labeled graph under batch changes. We investigate, when a batch of α edge label changes arrive, \\beginitemize \\item how much time as a function of α we need to update an existing solution, and \\item how much information the nodes have to keep in local memory between batches in order to update the solution quickly. \\enditemize Our work lays the foundations for the theory of input-dynamic distributed network algorithms. We give a general picture of the complexity landscape in this model, design both universal algorithms and algorithms for concrete problems, and present a general framework for lower bounds. In particular, we derive non-trivial upper bounds for two selected, contrasting problems: maintaining a minimum spanning tree and detecting cliques."}],"issue":"1","type":"journal_article","date_published":"2021-03-01T00:00:00Z","publication":"Proceedings of the ACM on Measurement and Analysis of Computing Systems","citation":{"ama":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. Input-dynamic distributed algorithms for communication networks. Proceedings of the ACM on Measurement and Analysis of Computing Systems. 2021;5(1):1-33. doi:10.1145/3447384","apa":"Foerster, K.-T., Korhonen, J., Paz, A., Rybicki, J., & Schmid, S. (2021). Input-dynamic distributed algorithms for communication networks. Proceedings of the ACM on Measurement and Analysis of Computing Systems. Association for Computing Machinery. https://doi.org/10.1145/3447384","ieee":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, and S. Schmid, “Input-dynamic distributed algorithms for communication networks,” Proceedings of the ACM on Measurement and Analysis of Computing Systems, vol. 5, no. 1. Association for Computing Machinery, pp. 1–33, 2021.","ista":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. 2021. Input-dynamic distributed algorithms for communication networks. Proceedings of the ACM on Measurement and Analysis of Computing Systems. 5(1), 1–33.","short":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, S. Schmid, Proceedings of the ACM on Measurement and Analysis of Computing Systems 5 (2021) 1–33.","mla":"Foerster, Klaus-Tycho, et al. “Input-Dynamic Distributed Algorithms for Communication Networks.” Proceedings of the ACM on Measurement and Analysis of Computing Systems, vol. 5, no. 1, Association for Computing Machinery, 2021, pp. 1–33, doi:10.1145/3447384.","chicago":"Foerster, Klaus-Tycho, Janne Korhonen, Ami Paz, Joel Rybicki, and Stefan Schmid. “Input-Dynamic Distributed Algorithms for Communication Networks.” Proceedings of the ACM on Measurement and Analysis of Computing Systems. Association for Computing Machinery, 2021. https://doi.org/10.1145/3447384."},"article_type":"original","page":"1-33","day":"01","article_processing_charge":"No","scopus_import":"1","keyword":["Computer Networks and Communications","Hardware and Architecture","Safety","Risk","Reliability and Quality","Computer Science (miscellaneous)"]},{"title":"Algorithms and conditional lower bounds for planning problems","status":"public","intvolume":" 297","_id":"9293","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We consider planning problems for graphs, Markov Decision Processes (MDPs), and games on graphs in an explicit state space. While graphs represent the most basic planning model, MDPs represent interaction with nature and games on graphs represent interaction with an adversarial environment. We consider two planning problems with k different target sets: (a) the coverage problem asks whether there is a plan for each individual target set; and (b) the sequential target reachability problem asks whether the targets can be reached in a given sequence. For the coverage problem, we present a linear-time algorithm for graphs, and quadratic conditional lower bound for MDPs and games on graphs. For the sequential target problem, we present a linear-time algorithm for graphs, a sub-quadratic algorithm for MDPs, and a quadratic conditional lower bound for games on graphs. Our results with conditional lower bounds, based on the boolean matrix multiplication (BMM) conjecture and strong exponential time hypothesis (SETH), establish (i) model-separation results showing that for the coverage problem MDPs and games on graphs are harder than graphs, and for the sequential reachability problem games on graphs are harder than MDPs and graphs; and (ii) problem-separation results showing that for MDPs the coverage problem is harder than the sequential target problem.","lang":"eng"}],"issue":"8","article_type":"original","publication":"Artificial Intelligence","citation":{"ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Algorithms and conditional lower bounds for planning problems. Artificial Intelligence. 2021;297(8). doi:10.1016/j.artint.2021.103499","ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2021. Algorithms and conditional lower bounds for planning problems. Artificial Intelligence. 297(8), 103499.","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Algorithms and conditional lower bounds for planning problems,” Artificial Intelligence, vol. 297, no. 8. Elsevier, 2021.","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2021). Algorithms and conditional lower bounds for planning problems. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2021.103499","mla":"Chatterjee, Krishnendu, et al. “Algorithms and Conditional Lower Bounds for Planning Problems.” Artificial Intelligence, vol. 297, no. 8, 103499, Elsevier, 2021, doi:10.1016/j.artint.2021.103499.","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, Artificial Intelligence 297 (2021).","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Algorithms and Conditional Lower Bounds for Planning Problems.” Artificial Intelligence. Elsevier, 2021. https://doi.org/10.1016/j.artint.2021.103499."},"date_published":"2021-03-16T00:00:00Z","scopus_import":"1","day":"16","article_processing_charge":"No","publication_status":"published","publisher":"Elsevier","department":[{"_id":"KrCh"}],"year":"2021","date_created":"2021-03-28T22:01:40Z","date_updated":"2023-09-26T10:41:42Z","volume":297,"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Dvořák, Wolfgang","first_name":"Wolfgang","last_name":"Dvořák"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"last_name":"Svozil","first_name":"Alexander","full_name":"Svozil, Alexander"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"35"}]},"article_number":"103499","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.07031"}],"external_id":{"arxiv":["1804.07031"],"isi":["000657537500003"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.artint.2021.103499","month":"03","publication_identifier":{"issn":["0004-3702"]}},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only $\\leq$ 10\\% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32-44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having >95% probability of contributing >0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data."}],"status":"public","ddc":["570"],"title":"Probabilistic inference of the genetic architecture of functional enrichment of complex traits","publisher":"Dryad","department":[{"_id":"MaRo"}],"year":"2021","_id":"13063","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-26T10:36:15Z","date_created":"2023-05-23T16:20:16Z","oa_version":"Published Version","author":[{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson","full_name":"Robinson, Matthew Richard"}],"related_material":{"link":[{"url":"https://github.com/medical-genomics-group/gmrm","relation":"software"}],"record":[{"status":"public","relation":"used_in_publication","id":"8429"}]},"day":"04","month":"11","article_processing_charge":"No","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"chicago":"Robinson, Matthew Richard. “Probabilistic Inference of the Genetic Architecture of Functional Enrichment of Complex Traits.” Dryad, 2021. https://doi.org/10.5061/dryad.sqv9s4n51.","short":"M.R. Robinson, (2021).","mla":"Robinson, Matthew Richard. Probabilistic Inference of the Genetic Architecture of Functional Enrichment of Complex Traits. Dryad, 2021, doi:10.5061/dryad.sqv9s4n51.","ieee":"M. R. Robinson, “Probabilistic inference of the genetic architecture of functional enrichment of complex traits.” Dryad, 2021.","apa":"Robinson, M. R. (2021). Probabilistic inference of the genetic architecture of functional enrichment of complex traits. Dryad. https://doi.org/10.5061/dryad.sqv9s4n51","ista":"Robinson MR. 2021. Probabilistic inference of the genetic architecture of functional enrichment of complex traits, Dryad, 10.5061/dryad.sqv9s4n51.","ama":"Robinson MR. Probabilistic inference of the genetic architecture of functional enrichment of complex traits. 2021. doi:10.5061/dryad.sqv9s4n51"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.sqv9s4n51","open_access":"1"}],"date_published":"2021-11-04T00:00:00Z","doi":"10.5061/dryad.sqv9s4n51"},{"intvolume":" 418","status":"public","title":"Influence of copper telluride nanodomains on the transport properties of n-type bismuth telluride","_id":"9304","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"8","abstract":[{"lang":"eng","text":"The high processing cost, poor mechanical properties and moderate performance of Bi2Te3–based alloys used in thermoelectric devices limit the cost-effectiveness of this energy conversion technology. Towards solving these current challenges, in the present work, we detail a low temperature solution-based approach to produce Bi2Te3-Cu2-xTe nanocomposites with improved thermoelectric performance. Our approach consists in combining proper ratios of colloidal nanoparticles and to consolidate the resulting mixture into nanocomposites using a hot press. The transport properties of the nanocomposites are characterized and compared with those of pure Bi2Te3 nanomaterials obtained following the same procedure. In contrast with most previous works, the presence of Cu2-xTe nanodomains does not result in a significant reduction of the lattice thermal conductivity of the reference Bi2Te3 nanomaterial, which is already very low. However, the introduction of Cu2-xTe yields a nearly threefold increase of the power factor associated to a simultaneous increase of the Seebeck coefficient and electrical conductivity at temperatures above 400 K. Taking into account the band alignment of the two materials, we rationalize this increase by considering that Cu2-xTe nanostructures, with a relatively low electron affinity, are able to inject electrons into Bi2Te3, enhancing in this way its electrical conductivity. The simultaneous increase of the Seebeck coefficient is related to the energy filtering of charge carriers at energy barriers within Bi2Te3 domains associated with the accumulation of electrons in regions nearby a Cu2-xTe/Bi2Te3 heterojunction. Overall, with the incorporation of a proper amount of Cu2-xTe nanoparticles, we demonstrate a 250% improvement of the thermoelectric figure of merit of Bi2Te3."}],"article_type":"original","citation":{"ieee":"Y. Zhang et al., “Influence of copper telluride nanodomains on the transport properties of n-type bismuth telluride,” Chemical Engineering Journal, vol. 418, no. 8. Elsevier, 2021.","apa":"Zhang, Y., Xing, C., Liu, Y., Li, M., Xiao, K., Guardia, P., … Cabot, A. (2021). Influence of copper telluride nanodomains on the transport properties of n-type bismuth telluride. Chemical Engineering Journal. Elsevier. https://doi.org/10.1016/j.cej.2021.129374","ista":"Zhang Y, Xing C, Liu Y, Li M, Xiao K, Guardia P, Lee S, Han X, Moghaddam A, Roa JJ, Arbiol J, Ibáñez M, Pan K, Prato M, Xie Y, Cabot A. 2021. Influence of copper telluride nanodomains on the transport properties of n-type bismuth telluride. Chemical Engineering Journal. 418(8), 129374.","ama":"Zhang Y, Xing C, Liu Y, et al. Influence of copper telluride nanodomains on the transport properties of n-type bismuth telluride. Chemical Engineering Journal. 2021;418(8). doi:10.1016/j.cej.2021.129374","chicago":"Zhang, Yu, Congcong Xing, Yu Liu, Mengyao Li, Ke Xiao, Pablo Guardia, Seungho Lee, et al. “Influence of Copper Telluride Nanodomains on the Transport Properties of N-Type Bismuth Telluride.” Chemical Engineering Journal. Elsevier, 2021. https://doi.org/10.1016/j.cej.2021.129374.","short":"Y. Zhang, C. Xing, Y. Liu, M. Li, K. Xiao, P. Guardia, S. Lee, X. Han, A. Moghaddam, J.J. Roa, J. Arbiol, M. Ibáñez, K. Pan, M. Prato, Y. Xie, A. Cabot, Chemical Engineering Journal 418 (2021).","mla":"Zhang, Yu, et al. “Influence of Copper Telluride Nanodomains on the Transport Properties of N-Type Bismuth Telluride.” Chemical Engineering Journal, vol. 418, no. 8, 129374, Elsevier, 2021, doi:10.1016/j.cej.2021.129374."},"publication":"Chemical Engineering Journal","date_published":"2021-08-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"15","department":[{"_id":"MaIb"}],"publisher":"Elsevier","publication_status":"published","year":"2021","acknowledgement":"This work was supported by the European Regional Development Funds and by the Generalitat de Catalunya through the project 2017SGR1246. Y.Z, C.X, M.L, K.X and X.H thank the China Scholarship Council for the scholarship support. MI acknowledges financial support from IST Austria. YL acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. ICN2\r\nacknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project ENE2017-85087-C3. ICN2 is supported by the Severo Ochoa program from the Spanish MINECO (grant no. SEV-2017-0706) and is funded by the CERCA Program/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD program.","volume":418,"date_updated":"2023-09-27T07:36:29Z","date_created":"2021-04-04T22:01:20Z","author":[{"full_name":"Zhang, Yu","first_name":"Yu","last_name":"Zhang"},{"first_name":"Congcong","last_name":"Xing","full_name":"Xing, Congcong"},{"full_name":"Liu, Yu","first_name":"Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740"},{"last_name":"Li","first_name":"Mengyao","full_name":"Li, Mengyao"},{"last_name":"Xiao","first_name":"Ke","full_name":"Xiao, Ke"},{"first_name":"Pablo","last_name":"Guardia","full_name":"Guardia, Pablo"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","first_name":"Seungho","last_name":"Lee","full_name":"Lee, Seungho"},{"first_name":"Xu","last_name":"Han","full_name":"Han, Xu"},{"first_name":"Ahmad","last_name":"Moghaddam","full_name":"Moghaddam, Ahmad"},{"last_name":"Roa","first_name":"Joan J","full_name":"Roa, Joan J"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"full_name":"Pan, Kai","first_name":"Kai","last_name":"Pan"},{"last_name":"Prato","first_name":"Mirko","full_name":"Prato, Mirko"},{"last_name":"Xie","first_name":"Ying","full_name":"Xie, Ying"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"article_number":"129374","ec_funded":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000655672000005"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://ddd.uab.cat/record/271949"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.cej.2021.129374","publication_identifier":{"issn":["1385-8947"]},"month":"08"},{"ec_funded":1,"author":[{"last_name":"Baldwin","first_name":"Katherine T.","full_name":"Baldwin, Katherine T."},{"first_name":"Christabel X.","last_name":"Tan","full_name":"Tan, Christabel X."},{"full_name":"Strader, Samuel T.","last_name":"Strader","first_name":"Samuel T."},{"first_name":"Changyu","last_name":"Jiang","full_name":"Jiang, Changyu"},{"full_name":"Savage, Justin T.","last_name":"Savage","first_name":"Justin T."},{"first_name":"Xabier","last_name":"Elorza-Vidal","full_name":"Elorza-Vidal, Xabier"},{"full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Estévez","first_name":"Raúl","full_name":"Estévez, Raúl"},{"full_name":"Ji, Ru-Rong","first_name":"Ru-Rong","last_name":"Ji"},{"first_name":"Cagla","last_name":"Eroglu","full_name":"Eroglu, Cagla"}],"date_created":"2021-08-06T09:08:25Z","date_updated":"2023-09-27T07:46:09Z","volume":109,"acknowledgement":"This work was supported by the National Institutes of Health (R01 DA047258 and R01 NS102237 to C.E., F32 NS100392 to K.T.B.) and the Holland-Trice Brain Research Award (to C.E.). K.T.B. was supported by postdoctoral fellowships from the Foerster-Bernstein Family and The Hartwell Foundation. The Hippenmeyer lab was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovations program (725780 LinPro) to S.H. R.E. was supported by Ministerio de Ciencia y Tecnología (RTI2018-093493-B-I00). We thank the Duke Light Microscopy Core Facility, the Duke Transgenic Mouse Facility, Dr. U. Schulte for assistance with proteomic experiments, and Dr. D. Silver for critical review of the manuscript. Cartoon elements of figure panels were created using BioRender.com.","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Elsevier","month":"08","publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"doi":"10.1016/j.neuron.2021.05.025","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2021.05.025"}],"external_id":{"isi":["000692851900010"],"pmid":["34171291"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"Astrocytes extensively infiltrate the neuropil to regulate critical aspects of synaptic development and function. This process is regulated by transcellular interactions between astrocytes and neurons via cell adhesion molecules. How astrocytes coordinate developmental processes among one another to parse out the synaptic neuropil and form non-overlapping territories is unknown. Here we identify a molecular mechanism regulating astrocyte-astrocyte interactions during development to coordinate astrocyte morphogenesis and gap junction coupling. We show that hepaCAM, a disease-linked, astrocyte-enriched cell adhesion molecule, regulates astrocyte competition for territory and morphological complexity in the developing mouse cortex. Furthermore, conditional deletion of Hepacam from developing astrocytes significantly impairs gap junction coupling between astrocytes and disrupts the balance between synaptic excitation and inhibition. Mutations in HEPACAM cause megalencephalic leukoencephalopathy with subcortical cysts in humans. Therefore, our findings suggest that disruption of astrocyte self-organization mechanisms could be an underlying cause of neural pathology."}],"issue":"15","type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9793","title":"HepaCAM controls astrocyte self-organization and coupling","status":"public","intvolume":" 109","day":"04","article_processing_charge":"No","scopus_import":"1","date_published":"2021-08-04T00:00:00Z","publication":"Neuron","citation":{"chicago":"Baldwin, Katherine T., Christabel X. Tan, Samuel T. Strader, Changyu Jiang, Justin T. Savage, Xabier Elorza-Vidal, Ximena Contreras, et al. “HepaCAM Controls Astrocyte Self-Organization and Coupling.” Neuron. Elsevier, 2021. https://doi.org/10.1016/j.neuron.2021.05.025.","mla":"Baldwin, Katherine T., et al. “HepaCAM Controls Astrocyte Self-Organization and Coupling.” Neuron, vol. 109, no. 15, Elsevier, 2021, p. 2427–2442.e10, doi:10.1016/j.neuron.2021.05.025.","short":"K.T. Baldwin, C.X. Tan, S.T. Strader, C. Jiang, J.T. Savage, X. Elorza-Vidal, X. Contreras, T. Rülicke, S. Hippenmeyer, R. Estévez, R.-R. Ji, C. Eroglu, Neuron 109 (2021) 2427–2442.e10.","ista":"Baldwin KT, Tan CX, Strader ST, Jiang C, Savage JT, Elorza-Vidal X, Contreras X, Rülicke T, Hippenmeyer S, Estévez R, Ji R-R, Eroglu C. 2021. HepaCAM controls astrocyte self-organization and coupling. Neuron. 109(15), 2427–2442.e10.","ieee":"K. T. Baldwin et al., “HepaCAM controls astrocyte self-organization and coupling,” Neuron, vol. 109, no. 15. Elsevier, p. 2427–2442.e10, 2021.","apa":"Baldwin, K. T., Tan, C. X., Strader, S. T., Jiang, C., Savage, J. T., Elorza-Vidal, X., … Eroglu, C. (2021). HepaCAM controls astrocyte self-organization and coupling. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2021.05.025","ama":"Baldwin KT, Tan CX, Strader ST, et al. HepaCAM controls astrocyte self-organization and coupling. Neuron. 2021;109(15):2427-2442.e10. doi:10.1016/j.neuron.2021.05.025"},"article_type":"original","page":"2427-2442.e10"},{"date_published":"2021-07-01T00:00:00Z","article_type":"original","publication":"Nano Energy","citation":{"chicago":"Zhang, Yu, Congcong Xing, Yu Liu, Maria Chiara Spadaro, Xiang Wang, Mengyao Li, Ke Xiao, et al. “Doping-Mediated Stabilization of Copper Vacancies to Promote Thermoelectric Properties of Cu2-XS.” Nano Energy. Elsevier, 2021. https://doi.org/10.1016/j.nanoen.2021.105991.","mla":"Zhang, Yu, et al. “Doping-Mediated Stabilization of Copper Vacancies to Promote Thermoelectric Properties of Cu2-XS.” Nano Energy, vol. 85, no. 7, 105991, Elsevier, 2021, doi:10.1016/j.nanoen.2021.105991.","short":"Y. Zhang, C. Xing, Y. Liu, M.C. Spadaro, X. Wang, M. Li, K. Xiao, T. Zhang, P. Guardia, K.H. Lim, A.O. Moghaddam, J. Llorca, J. Arbiol, M. Ibáñez, A. Cabot, Nano Energy 85 (2021).","ista":"Zhang Y, Xing C, Liu Y, Spadaro MC, Wang X, Li M, Xiao K, Zhang T, Guardia P, Lim KH, Moghaddam AO, Llorca J, Arbiol J, Ibáñez M, Cabot A. 2021. Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS. Nano Energy. 85(7), 105991.","ieee":"Y. Zhang et al., “Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS,” Nano Energy, vol. 85, no. 7. Elsevier, 2021.","apa":"Zhang, Y., Xing, C., Liu, Y., Spadaro, M. C., Wang, X., Li, M., … Cabot, A. (2021). Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS. Nano Energy. Elsevier. https://doi.org/10.1016/j.nanoen.2021.105991","ama":"Zhang Y, Xing C, Liu Y, et al. Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS. Nano Energy. 2021;85(7). doi:10.1016/j.nanoen.2021.105991"},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","status":"public","title":"Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS","intvolume":" 85","_id":"9305","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Copper chalcogenides are outstanding thermoelectric materials for applications in the medium-high temperature range. Among different chalcogenides, while Cu2−xSe is characterized by higher thermoelectric figures of merit, Cu2−xS provides advantages in terms of low cost and element abundance. In the present work, we investigate the effect of different dopants to enhance the Cu2−xS performance and also its thermal stability. Among the tested options, Pb-doped Cu2−xS shows the highest improvement in stability against sulfur volatilization. Additionally, Pb incorporation allows tuning charge carrier concentration, which enables a significant improvement of the power factor. We demonstrate here that the introduction of an optimal additive amount of just 0.3% results in a threefold increase of the power factor in the middle-temperature range (500–800 K) and a record dimensionless thermoelectric figure of merit above 2 at 880 K."}],"issue":"7","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.nanoen.2021.105991","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"oa":1,"external_id":{"isi":["000663442200004"]},"main_file_link":[{"url":"https://ddd.uab.cat/record/271947","open_access":"1"}],"month":"07","publication_identifier":{"issn":["2211-2855"]},"date_created":"2021-04-04T22:01:21Z","date_updated":"2023-09-27T07:41:00Z","volume":85,"author":[{"last_name":"Zhang","first_name":"Yu","full_name":"Zhang, Yu"},{"first_name":"Congcong","last_name":"Xing","full_name":"Xing, Congcong"},{"first_name":"Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu"},{"first_name":"Maria Chiara","last_name":"Spadaro","full_name":"Spadaro, Maria Chiara"},{"full_name":"Wang, Xiang","last_name":"Wang","first_name":"Xiang"},{"full_name":"Li, Mengyao","first_name":"Mengyao","last_name":"Li"},{"full_name":"Xiao, Ke","last_name":"Xiao","first_name":"Ke"},{"full_name":"Zhang, Ting","last_name":"Zhang","first_name":"Ting"},{"last_name":"Guardia","first_name":"Pablo","full_name":"Guardia, Pablo"},{"full_name":"Lim, Khak Ho","first_name":"Khak Ho","last_name":"Lim"},{"first_name":"Ahmad Ostovari","last_name":"Moghaddam","full_name":"Moghaddam, Ahmad Ostovari"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"MaIb"}],"year":"2021","acknowledgement":"This work was supported by the European Regional Development Fund and by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP (ENE2016-77798-C4-3-R). MI acknowledges financial support from IST Austria. YL acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. YZ, CX, XW, KX and TZ thank the China Scholarship Council for the scholarship support. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project ENE2017-85087-C3. ICN2 is supported by the Severo Ochoa program from the Spanish MINECO (grant no. SEV-2017-0706) and is funded by the CERCA program/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science Ph.D. program. M.C.S. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754510 (PROBIST) and the Severo Ochoa programme. P.G. acknowledges financial support from the Spanish government (MICIU) through the RTI2018-102006-J-I00 project and the Catalan Agency of Competitiveness (ACCIO) through the TecnioSpring+ Marie Sklodowska-Curie action TECSPR16-1-0082. YZ and CX contributed equally to this work.","ec_funded":1,"article_number":"105991"},{"volume":13,"date_updated":"2023-09-27T06:44:06Z","date_created":"2021-03-01T10:08:32Z","author":[{"full_name":"Cavallari, Nicola","first_name":"Nicola","last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Artner, Christina","last_name":"Artner","first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}],"publisher":"Cold Spring Harbor Laboratory Press","department":[{"_id":"EvBe"}],"publication_status":"published","pmid":1,"acknowledgement":"We apologize to all the authors whose scientific work could not be cited and discussed because of space restrictions. We thank Dr. Inge Verstraeten (ISTAustria) and Dr. Juan Carlos Montesinos-Lopez (ETH Zürich) for helpful suggestions. This work was supported by the DOC Fellowship Programme of the Austrian Academy of Sciences (25008) to C.A.","year":"2021","article_number":"a039941","language":[{"iso":"eng"}],"doi":"10.1101/cshperspect.a039941","project":[{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"}],"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a039941"}],"external_id":{"pmid":["33558367"],"isi":["000692069100001"]},"oa":1,"publication_identifier":{"issn":["1943-0264"]},"month":"07","oa_version":"Published Version","intvolume":" 13","title":"Auxin-regulated lateral root organogenesis","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9212","issue":"7","abstract":[{"lang":"eng","text":"Plant fitness is largely dependent on the root, the underground organ, which, besides its anchoring function, supplies the plant body with water and all nutrients necessary for growth and development. To exploit the soil effectively, roots must constantly integrate environmental signals and react through adjustment of growth and development. Important components of the root management strategy involve a rapid modulation of the root growth kinetics and growth direction, as well as an increase of the root system radius through formation of lateral roots (LRs). At the molecular level, such a fascinating growth and developmental flexibility of root organ requires regulatory networks that guarantee stability of the developmental program but also allows integration of various environmental inputs. The plant hormone auxin is one of the principal endogenous regulators of root system architecture by controlling primary root growth and formation of LR. In this review, we discuss recent progress in understanding molecular networks where auxin is one of the main players shaping the root system and acting as mediator between endogenous cues and environmental factors."}],"type":"journal_article","date_published":"2021-07-01T00:00:00Z","article_type":"original","citation":{"ama":"Cavallari N, Artner C, Benková E. Auxin-regulated lateral root organogenesis. Cold Spring Harbor Perspectives in Biology. 2021;13(7). doi:10.1101/cshperspect.a039941","ieee":"N. Cavallari, C. Artner, and E. Benková, “Auxin-regulated lateral root organogenesis,” Cold Spring Harbor Perspectives in Biology, vol. 13, no. 7. Cold Spring Harbor Laboratory Press, 2021.","apa":"Cavallari, N., Artner, C., & Benková, E. (2021). Auxin-regulated lateral root organogenesis. Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/cshperspect.a039941","ista":"Cavallari N, Artner C, Benková E. 2021. Auxin-regulated lateral root organogenesis. Cold Spring Harbor Perspectives in Biology. 13(7), a039941.","short":"N. Cavallari, C. Artner, E. Benková, Cold Spring Harbor Perspectives in Biology 13 (2021).","mla":"Cavallari, Nicola, et al. “Auxin-Regulated Lateral Root Organogenesis.” Cold Spring Harbor Perspectives in Biology, vol. 13, no. 7, a039941, Cold Spring Harbor Laboratory Press, 2021, doi:10.1101/cshperspect.a039941.","chicago":"Cavallari, Nicola, Christina Artner, and Eva Benková. “Auxin-Regulated Lateral Root Organogenesis.” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory Press, 2021. https://doi.org/10.1101/cshperspect.a039941."},"publication":"Cold Spring Harbor Perspectives in Biology","article_processing_charge":"No","day":"01","scopus_import":"1"},{"date_published":"2021-10-01T00:00:00Z","publication":"Brain, Behavior, and Immunity","citation":{"mla":"Picard, Katherine, et al. “Microglial-Glucocorticoid Receptor Depletion Alters the Response of Hippocampal Microglia and Neurons in a Chronic Unpredictable Mild Stress Paradigm in Female Mice.” Brain, Behavior, and Immunity, vol. 97, Elsevier, 2021, pp. 423–39, doi:10.1016/j.bbi.2021.07.022.","short":"K. Picard, K. Bisht, S. Poggini, S. Garofalo, M.T. Golia, B. Basilico, F. Abdallah, N. Ciano Albanese, I. Amrein, N. Vernoux, K. Sharma, C.W. Hui, J. C. Savage, C. Limatola, D. Ragozzino, L. Maggi, I. Branchi, M.È. Tremblay, Brain, Behavior, and Immunity 97 (2021) 423–439.","chicago":"Picard, Katherine, Kanchan Bisht, Silvia Poggini, Stefano Garofalo, Maria Teresa Golia, Bernadette Basilico, Fatima Abdallah, et al. “Microglial-Glucocorticoid Receptor Depletion Alters the Response of Hippocampal Microglia and Neurons in a Chronic Unpredictable Mild Stress Paradigm in Female Mice.” Brain, Behavior, and Immunity. Elsevier, 2021. https://doi.org/10.1016/j.bbi.2021.07.022.","ama":"Picard K, Bisht K, Poggini S, et al. Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. Brain, Behavior, and Immunity. 2021;97:423-439. doi:10.1016/j.bbi.2021.07.022","ista":"Picard K, Bisht K, Poggini S, Garofalo S, Golia MT, Basilico B, Abdallah F, Ciano Albanese N, Amrein I, Vernoux N, Sharma K, Hui CW, C. Savage J, Limatola C, Ragozzino D, Maggi L, Branchi I, Tremblay MÈ. 2021. Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. Brain, Behavior, and Immunity. 97, 423–439.","apa":"Picard, K., Bisht, K., Poggini, S., Garofalo, S., Golia, M. T., Basilico, B., … Tremblay, M. È. (2021). Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. Brain, Behavior, and Immunity. Elsevier. https://doi.org/10.1016/j.bbi.2021.07.022","ieee":"K. Picard et al., “Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice,” Brain, Behavior, and Immunity, vol. 97. Elsevier, pp. 423–439, 2021."},"article_type":"original","page":"423-439","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9953","title":"Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice","status":"public","intvolume":" 97","abstract":[{"text":"Chronic psychological stress is one of the most important triggers and environmental risk factors for neuropsychiatric disorders. Chronic stress can influence all organs via the secretion of stress hormones, including glucocorticoids by the adrenal glands, which coordinate the stress response across the body. In the brain, glucocorticoid receptors (GR) are expressed by various cell types including microglia, which are its resident immune cells regulating stress-induced inflammatory processes. To study the roles of microglial GR under normal homeostatic conditions and following chronic stress, we generated a mouse model in which the GR gene is depleted in microglia specifically at adulthood to prevent developmental confounds. We first confirmed that microglia were depleted in GR in our model in males and females among the cingulate cortex and the hippocampus, both stress-sensitive brain regions. Then, cohorts of microglial-GR depleted and wild-type (WT) adult female mice were housed for 3 weeks in a standard or stressful condition, using a chronic unpredictable mild stress (CUMS) paradigm. CUMS induced stress-related behavior in both microglial-GR depleted and WT animals as demonstrated by a decrease of both saccharine preference and progressive ratio breakpoint. Nevertheless, the hippocampal microglial and neural mechanisms underlying the adaptation to stress occurred differently between the two genotypes. Upon CUMS exposure, microglial morphology was altered in the WT controls, without any apparent effect in microglial-GR depleted mice. Furthermore, in the standard environment condition, GR depleted-microglia showed increased expression of pro-inflammatory genes, and genes involved in microglial homeostatic functions (such as Trem2, Cx3cr1 and Mertk). On the contrary, in CUMS condition, GR depleted-microglia showed reduced expression levels of pro-inflammatory genes and increased neuroprotective as well as anti-inflammatory genes compared to WT-microglia. Moreover, in microglial-GR depleted mice, but not in WT mice, CUMS led to a significant reduction of CA1 long-term potentiation and paired-pulse ratio. Lastly, differences in adult hippocampal neurogenesis were observed between the genotypes during normal homeostatic conditions, with microglial-GR deficiency increasing the formation of newborn neurons in the dentate gyrus subgranular zone independently from stress exposure. Together, these findings indicate that, although the deletion of microglial GR did not prevent the animal’s ability to respond to stress, it contributed to modulating hippocampal functions in both standard and stressful conditions, notably by shaping the microglial response to chronic stress.","lang":"eng"}],"type":"journal_article","doi":"10.1016/j.bbi.2021.07.022","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.zora.uzh.ch/id/eprint/208855/1/ZORA208855.pdf","open_access":"1"}],"oa":1,"external_id":{"isi":["000702878400007"],"pmid":["34343616"]},"isi":1,"quality_controlled":"1","month":"10","publication_identifier":{"issn":["0889-1591"]},"author":[{"full_name":"Picard, Katherine","first_name":"Katherine","last_name":"Picard"},{"full_name":"Bisht, Kanchan","first_name":"Kanchan","last_name":"Bisht"},{"full_name":"Poggini, Silvia","first_name":"Silvia","last_name":"Poggini"},{"first_name":"Stefano","last_name":"Garofalo","full_name":"Garofalo, Stefano"},{"first_name":"Maria Teresa","last_name":"Golia","full_name":"Golia, Maria Teresa"},{"first_name":"Bernadette","last_name":"Basilico","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173","full_name":"Basilico, Bernadette"},{"full_name":"Abdallah, Fatima","first_name":"Fatima","last_name":"Abdallah"},{"first_name":"Naomi","last_name":"Ciano Albanese","full_name":"Ciano Albanese, Naomi"},{"full_name":"Amrein, Irmgard","first_name":"Irmgard","last_name":"Amrein"},{"last_name":"Vernoux","first_name":"Nathalie","full_name":"Vernoux, Nathalie"},{"first_name":"Kaushik","last_name":"Sharma","full_name":"Sharma, Kaushik"},{"full_name":"Hui, Chin Wai","last_name":"Hui","first_name":"Chin Wai"},{"first_name":"Julie","last_name":"C. Savage","full_name":"C. Savage, Julie"},{"full_name":"Limatola, Cristina","first_name":"Cristina","last_name":"Limatola"},{"full_name":"Ragozzino, Davide","first_name":"Davide","last_name":"Ragozzino"},{"full_name":"Maggi, Laura","last_name":"Maggi","first_name":"Laura"},{"full_name":"Branchi, Igor","last_name":"Branchi","first_name":"Igor"},{"first_name":"Marie Ève","last_name":"Tremblay","full_name":"Tremblay, Marie Ève"}],"date_updated":"2023-10-03T09:49:18Z","date_created":"2021-08-22T22:01:21Z","volume":97,"acknowledgement":"We acknowledge that Université Laval stands on the traditional and unceded land of the Huron-Wendat peoples; and that the University of Victoria exists on the territory of the Lekwungen peoples and that the Songhees, Esquimalt and WSÁNEÆ peoples have relationships to this land. We thank Emmanuel Planel for the access to the epifluorescence microscope and Julie-Christine Lévesque at the Bioimaging Platform of CRCHU de Québec-Université Laval for technical assistance. We also thank the Centre for Advanced Materials and Related Technology for the access to the confocal microscope with Airyscan. K.P. was supported by a doctoral scholarship from Fonds de Recherche du Québec – Santé (FRQS), an excellence award from Fondation du CHU de Québec, as well as from Centre Thématique de Recherche en Neurosciences and from Fondation Famille-Choquette. K.B. was supported by excellence scholarships from Université Laval and Fondation du CHU de Québec. S.G. is supported by FIRC-AIRC fellowship for Italy 22329/2018 and by Pilot ARISLA NKINALS 2019. C.W.H. and J.C.S. were supported by postdoctoral fellowships from FRQS. This study was funded by a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery grant (RGPIN-2014-05308) awarded to M.E.T., by ERANET neuron 2017 MicroSynDep to M.E.T. and I.B., and by the Italian Ministry of Health, grant RF-2018-12367249 to I.B, by PRIN 2017, AIRC 2019 and Ministero della Salute RF2018 to C.L. M.E.T. is a Tier II Canada Research Chair in Neurobiology of Aging and Cognition.","year":"2021","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"GaNo"}]},{"oa_version":"Submitted Version","title":"PbS–Pb–CuxS composites for thermoelectric application","status":"public","intvolume":" 13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10327","abstract":[{"lang":"eng","text":"Composite materials offer numerous advantages in a wide range of applications, including thermoelectrics. Here, semiconductor–metal composites are produced by just blending nanoparticles of a sulfide semiconductor obtained in aqueous solution and at room temperature with a metallic Cu powder. The obtained blend is annealed in a reducing atmosphere and afterward consolidated into dense polycrystalline pellets through spark plasma sintering (SPS). We observe that, during the annealing process, the presence of metallic copper activates a partial reduction of the PbS, resulting in the formation of PbS–Pb–CuxS composites. The presence of metallic lead during the SPS process habilitates the liquid-phase sintering of the composite. Besides, by comparing the transport properties of PbS, the PbS–Pb–CuxS composites, and PbS–CuxS composites obtained by blending PbS and CuxS nanoparticles, we demonstrate that the presence of metallic lead decisively contributes to a strong increase of the charge carrier concentration through spillover of charge carriers enabled by the low work function of lead. The increase in charge carrier concentration translates into much higher electrical conductivities and moderately lower Seebeck coefficients. These properties translate into power factors up to 2.1 mW m–1 K–2 at ambient temperature, well above those of PbS and PbS + CuxS. Additionally, the presence of multiple phases in the final composite results in a notable decrease in the lattice thermal conductivity. Overall, the introduction of metallic copper in the initial blend results in a significant improvement of the thermoelectric performance of PbS, reaching a dimensionless thermoelectric figure of merit ZT = 1.1 at 750 K, which represents about a 400% increase over bare PbS. Besides, an average ZTave = 0.72 in the temperature range 320–773 K is demonstrated."}],"issue":"43","type":"journal_article","date_published":"2021-10-19T00:00:00Z","article_type":"original","page":"51373–51382","publication":"ACS Applied Materials and Interfaces","citation":{"short":"M. Li, Y. Liu, Y. Zhang, X. Han, K. Xiao, M. Nabahat, J. Arbiol, J. Llorca, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 13 (2021) 51373–51382.","mla":"Li, Mengyao, et al. “PbS–Pb–CuxS Composites for Thermoelectric Application.” ACS Applied Materials and Interfaces, vol. 13, no. 43, American Chemical Society , 2021, pp. 51373–51382, doi:10.1021/acsami.1c15609.","chicago":"Li, Mengyao, Yu Liu, Yu Zhang, Xu Han, Ke Xiao, Mehran Nabahat, Jordi Arbiol, Jordi Llorca, Maria Ibáñez, and Andreu Cabot. “PbS–Pb–CuxS Composites for Thermoelectric Application.” ACS Applied Materials and Interfaces. American Chemical Society , 2021. https://doi.org/10.1021/acsami.1c15609.","ama":"Li M, Liu Y, Zhang Y, et al. PbS–Pb–CuxS composites for thermoelectric application. ACS Applied Materials and Interfaces. 2021;13(43):51373–51382. doi:10.1021/acsami.1c15609","apa":"Li, M., Liu, Y., Zhang, Y., Han, X., Xiao, K., Nabahat, M., … Cabot, A. (2021). PbS–Pb–CuxS composites for thermoelectric application. ACS Applied Materials and Interfaces. American Chemical Society . https://doi.org/10.1021/acsami.1c15609","ieee":"M. Li et al., “PbS–Pb–CuxS composites for thermoelectric application,” ACS Applied Materials and Interfaces, vol. 13, no. 43. American Chemical Society , pp. 51373–51382, 2021.","ista":"Li M, Liu Y, Zhang Y, Han X, Xiao K, Nabahat M, Arbiol J, Llorca J, Ibáñez M, Cabot A. 2021. PbS–Pb–CuxS composites for thermoelectric application. ACS Applied Materials and Interfaces. 13(43), 51373–51382."},"day":"19","article_processing_charge":"No","keyword":["CuxS","PbS","energy conversion","nanocomposite","nanoparticle","solution synthesis","thermoelectric"],"scopus_import":"1","date_updated":"2023-10-03T09:55:33Z","date_created":"2021-11-21T23:01:30Z","volume":13,"author":[{"full_name":"Li, Mengyao","last_name":"Li","first_name":"Mengyao"},{"full_name":"Liu, Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740","first_name":"Yu","last_name":"Liu"},{"last_name":"Zhang","first_name":"Yu","full_name":"Zhang, Yu"},{"last_name":"Han","first_name":"Xu","full_name":"Han, Xu"},{"full_name":"Xiao, Ke","last_name":"Xiao","first_name":"Ke"},{"last_name":"Nabahat","first_name":"Mehran","full_name":"Nabahat, Mehran"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society ","acknowledgement":"This work was supported by the European Regional Development Funds. M.L., Y.Z., X.H., and K.X. thank the China Scholarship Council for scholarship support. M. I. has been financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. J.L. is a Serra Húnter fellow and is grateful to ICREA Academia program and projects MICINN/FEDER RTI2018-093996-B-C31 and GC 2017 SGR 128. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project NANOGEN (PID2020-116093RB-C43). ICN2 was supported by the Severo Ochoa program from Spanish MINECO (grant no. SEV-2017-0706) and was funded by the CERCA Programme/Generalitat de Catalunya. X.H. thanks China Scholarship Council for scholarship support (201804910551). Part of the present work was performed in the framework of Universitat Autònoma de Barcelona Materials Science Ph.D. program.","year":"2021","pmid":1,"ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1021/acsami.1c15609","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"oa":1,"external_id":{"pmid":["34665616"],"isi":["000715852100070"]},"main_file_link":[{"open_access":"1","url":"https://upcommons.upc.edu/bitstream/2117/363528/1/Pb%20mengyao.pdf"}],"month":"10","publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9235","intvolume":" 15","status":"public","title":"Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide","oa_version":"Submitted Version","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Cu2–xS has become one of the most promising thermoelectric materials for application in the middle-high temperature range. Its advantages include the abundance, low cost, and safety of its elements and a high performance at relatively elevated temperatures. However, stability issues limit its operation current and temperature, thus calling for the optimization of the material performance in the middle temperature range. Here, we present a synthetic protocol for large scale production of covellite CuS nanoparticles at ambient temperature and atmosphere, and using water as a solvent. The crystal phase and stoichiometry of the particles are afterward tuned through an annealing process at a moderate temperature under inert or reducing atmosphere. While annealing under argon results in Cu1.8S nanopowder with a rhombohedral crystal phase, annealing in an atmosphere containing hydrogen leads to tetragonal Cu1.96S. High temperature X-ray diffraction analysis shows the material annealed in argon to transform to the cubic phase at ca. 400 K, while the material annealed in the presence of hydrogen undergoes two phase transitions, first to hexagonal and then to the cubic structure. The annealing atmosphere, temperature, and time allow adjustment of the density of copper vacancies and thus tuning of the charge carrier concentration and material transport properties. In this direction, the material annealed under Ar is characterized by higher electrical conductivities but lower Seebeck coefficients than the material annealed in the presence of hydrogen. By optimizing the charge carrier concentration through the annealing time, Cu2–xS with record figures of merit in the middle temperature range, up to 1.41 at 710 K, is obtained. We finally demonstrate that this strategy, based on a low-cost and scalable solution synthesis process, is also suitable for the production of high performance Cu2–xS layers using high throughput and cost-effective printing technologies."}],"citation":{"ama":"Li M, Liu Y, Zhang Y, et al. Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide. ACS Nano. 2021;15(3):4967–4978. doi:10.1021/acsnano.0c09866","ieee":"M. Li et al., “Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide,” ACS Nano, vol. 15, no. 3. American Chemical Society , pp. 4967–4978, 2021.","apa":"Li, M., Liu, Y., Zhang, Y., Han, X., Zhang, T., Zuo, Y., … Cabot, A. (2021). Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide. ACS Nano. American Chemical Society . https://doi.org/10.1021/acsnano.0c09866","ista":"Li M, Liu Y, Zhang Y, Han X, Zhang T, Zuo Y, Xie C, Xiao K, Arbiol J, Llorca J, Ibáñez M, Liu J, Cabot A. 2021. Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide. ACS Nano. 15(3), 4967–4978.","short":"M. Li, Y. Liu, Y. Zhang, X. Han, T. Zhang, Y. Zuo, C. Xie, K. Xiao, J. Arbiol, J. Llorca, M. Ibáñez, J. Liu, A. Cabot, ACS Nano 15 (2021) 4967–4978.","mla":"Li, Mengyao, et al. “Effect of the Annealing Atmosphere on Crystal Phase and Thermoelectric Properties of Copper Sulfide.” ACS Nano, vol. 15, no. 3, American Chemical Society , 2021, pp. 4967–4978, doi:10.1021/acsnano.0c09866.","chicago":"Li, Mengyao, Yu Liu, Yu Zhang, Xu Han, Ting Zhang, Yong Zuo, Chenyang Xie, et al. “Effect of the Annealing Atmosphere on Crystal Phase and Thermoelectric Properties of Copper Sulfide.” ACS Nano. American Chemical Society , 2021. https://doi.org/10.1021/acsnano.0c09866."},"publication":"ACS Nano","page":"4967–4978","article_type":"original","date_published":"2021-03-01T00:00:00Z","scopus_import":"1","keyword":["General Engineering","General Physics and Astronomy","General Materials Science"],"article_processing_charge":"No","day":"01","pmid":1,"year":"2021","acknowledgement":"This work was supported by the European Regional Development Funds. M.Y.L., X.H., T.Z., and K.X. thank the China Scholarship Council for scholarship support. M.I. acknowledges financial support from IST Austria. J.L. acknowledges support from the National Natural Science Foundation of China (No. 22008091), the funding for scientific research startup of Jiangsu University (No. 19JDG044), and Jiangsu Provincial Program for High-Level Innovative and Entrepreneurial Talents Introduction. J.L. is a Serra Húnter fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER RTI2018-093996-B-C31 and GC 2017 SGR 128. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO ENE2017-85087-C3. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD program. T.Z. has received funding from the CSC-UAB PhD scholarship program.","publisher":"American Chemical Society ","department":[{"_id":"MaIb"}],"publication_status":"published","author":[{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","first_name":"Yu","full_name":"Liu, Yu"},{"first_name":"Yu","last_name":"Zhang","full_name":"Zhang, Yu"},{"full_name":"Han, Xu","first_name":"Xu","last_name":"Han"},{"full_name":"Zhang, Ting","first_name":"Ting","last_name":"Zhang"},{"last_name":"Zuo","first_name":"Yong","full_name":"Zuo, Yong"},{"last_name":"Xie","first_name":"Chenyang","full_name":"Xie, Chenyang"},{"full_name":"Xiao, Ke","first_name":"Ke","last_name":"Xiao"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"last_name":"Llorca","first_name":"Jordi","full_name":"Llorca, Jordi"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"},{"full_name":"Liu, Junfeng","first_name":"Junfeng","last_name":"Liu"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"volume":15,"date_updated":"2023-10-03T09:59:55Z","date_created":"2021-03-10T20:12:45Z","main_file_link":[{"url":"https://upcommons.upc.edu/bitstream/handle/2117/363528/Pb%20mengyao.pdf?sequence=1&isAllowed=y","open_access":"1"}],"oa":1,"external_id":{"isi":["000634569100106"],"pmid":["33645986"]},"quality_controlled":"1","isi":1,"doi":"10.1021/acsnano.0c09866","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"month":"03"},{"type":"journal_article","issue":"40","abstract":[{"text":"Two common representations of close packings of identical spheres consisting of hexagonal layers, called Barlow stackings, appear abundantly in minerals and metals. These motifs, however, occupy an identical portion of space and bear identical first-order topological signatures as measured by persistent homology. Here we present a novel method based on k-fold covers that unambiguously distinguishes between these patterns. Moreover, our approach provides topological evidence that the FCC motif is the more stable of the two in the context of evolving experimental sphere packings during the transition from disordered to an ordered state. We conclude that our approach can be generalised to distinguish between various Barlow stackings manifested in minerals and metals.","lang":"eng"}],"intvolume":" 17","ddc":["540"],"title":"Topological signatures and stability of hexagonal close packing and Barlow stackings","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10204","file":[{"content_type":"application/pdf","file_size":4678788,"creator":"dernst","access_level":"open_access","file_name":"2021_SoftMatter_acceptedversion_Osang.pdf","checksum":"b4da0c420530295e61b153960f6cb350","success":1,"date_created":"2023-10-03T09:21:42Z","date_updated":"2023-10-03T09:21:42Z","relation":"main_file","file_id":"14385"}],"oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"20","page":"9107-9115","article_type":"original","citation":{"chicago":"Osang, Georg F, Herbert Edelsbrunner, and Mohammad Saadatfar. “Topological Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” Soft Matter. Royal Society of Chemistry , 2021. https://doi.org/10.1039/d1sm00774b.","mla":"Osang, Georg F., et al. “Topological Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” Soft Matter, vol. 17, no. 40, Royal Society of Chemistry , 2021, pp. 9107–15, doi:10.1039/d1sm00774b.","short":"G.F. Osang, H. Edelsbrunner, M. Saadatfar, Soft Matter 17 (2021) 9107–9115.","ista":"Osang GF, Edelsbrunner H, Saadatfar M. 2021. Topological signatures and stability of hexagonal close packing and Barlow stackings. Soft Matter. 17(40), 9107–9115.","ieee":"G. F. Osang, H. Edelsbrunner, and M. Saadatfar, “Topological signatures and stability of hexagonal close packing and Barlow stackings,” Soft Matter, vol. 17, no. 40. Royal Society of Chemistry , pp. 9107–9115, 2021.","apa":"Osang, G. F., Edelsbrunner, H., & Saadatfar, M. (2021). Topological signatures and stability of hexagonal close packing and Barlow stackings. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/d1sm00774b","ama":"Osang GF, Edelsbrunner H, Saadatfar M. Topological signatures and stability of hexagonal close packing and Barlow stackings. Soft Matter. 2021;17(40):9107-9115. doi:10.1039/d1sm00774b"},"publication":"Soft Matter","date_published":"2021-10-20T00:00:00Z","ec_funded":1,"file_date_updated":"2023-10-03T09:21:42Z","department":[{"_id":"HeEd"}],"publisher":"Royal Society of Chemistry ","publication_status":"published","pmid":1,"acknowledgement":"MS acknowledges the support by Australian Research Council funding through the ARC Training Centre for M3D Innovation (IC180100008). MS thanks M. Hanifpour and N. Francois for their input and valuable discussions. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme, grant no. 788183 and from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.","year":"2021","volume":17,"date_updated":"2023-10-03T09:24:27Z","date_created":"2021-10-31T23:01:30Z","author":[{"full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","first_name":"Georg F"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"first_name":"Mohammad","last_name":"Saadatfar","full_name":"Saadatfar, Mohammad"}],"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"month":"10","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["34569592"],"isi":["000700090000001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1039/d1sm00774b"},{"abstract":[{"lang":"eng","text":"Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness. "}],"type":"conference","alternative_title":["LIPIcs"],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_LIPIcs_Corbet.pdf","creator":"cziletti","content_type":"application/pdf","file_size":"1367983","file_id":"9610","relation":"main_file","success":1,"checksum":"0de217501e7ba8b267d58deed0d51761","date_created":"2021-06-28T12:40:47Z","date_updated":"2021-06-28T12:40:47Z"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"9605","intvolume":" 189","ddc":["516"],"status":"public","title":"Computing the multicover bifiltration","has_accepted_license":"1","article_processing_charge":"No","day":"02","scopus_import":"1","date_published":"2021-06-02T00:00:00Z","citation":{"chicago":"Corbet, René, Michael Kerber, Michael Lesnick, and Georg F Osang. “Computing the Multicover Bifiltration.” In Leibniz International Proceedings in Informatics, Vol. 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.SoCG.2021.27.","mla":"Corbet, René, et al. “Computing the Multicover Bifiltration.” Leibniz International Proceedings in Informatics, vol. 189, 27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:10.4230/LIPIcs.SoCG.2021.27.","short":"R. Corbet, M. Kerber, M. Lesnick, G.F. Osang, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","ista":"Corbet R, Kerber M, Lesnick M, Osang GF. 2021. Computing the multicover bifiltration. Leibniz International Proceedings in Informatics. SoCG: International Symposium on Computational Geometry, LIPIcs, vol. 189, 27.","ieee":"R. Corbet, M. Kerber, M. Lesnick, and G. F. Osang, “Computing the multicover bifiltration,” in Leibniz International Proceedings in Informatics, Online, 2021, vol. 189.","apa":"Corbet, R., Kerber, M., Lesnick, M., & Osang, G. F. (2021). Computing the multicover bifiltration. In Leibniz International Proceedings in Informatics (Vol. 189). Online: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2021.27","ama":"Corbet R, Kerber M, Lesnick M, Osang GF. Computing the multicover bifiltration. In: Leibniz International Proceedings in Informatics. Vol 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:10.4230/LIPIcs.SoCG.2021.27"},"publication":"Leibniz International Proceedings in Informatics","file_date_updated":"2021-06-28T12:40:47Z","article_number":"27","related_material":{"link":[{"url":"https://arxiv.org/abs/2103.07823","relation":"extended_version"}],"record":[{"relation":"later_version","status":"public","id":"12709"}]},"author":[{"last_name":"Corbet","first_name":"René","full_name":"Corbet, René"},{"full_name":"Kerber, Michael","last_name":"Kerber","first_name":"Michael"},{"full_name":"Lesnick, Michael","first_name":"Michael","last_name":"Lesnick"},{"orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","first_name":"Georg F","full_name":"Osang, Georg F"}],"volume":189,"date_updated":"2023-10-04T12:03:39Z","date_created":"2021-06-27T22:01:49Z","year":"2021","acknowledgement":"The authors want to thank the reviewers for many helpful comments and suggestions.","department":[{"_id":"HeEd"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","publication_identifier":{"issn":["18688969"],"isbn":["9783959771849"]},"month":"06","doi":"10.4230/LIPIcs.SoCG.2021.27","conference":{"name":"SoCG: International Symposium on Computational Geometry","end_date":"2021-06-11","location":"Online","start_date":"2021-06-07"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2103.07823"]},"quality_controlled":"1"},{"place":"Dagstuhl, Germany","ec_funded":1,"file_date_updated":"2021-06-02T10:22:33Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"HeEd"}],"publication_status":"published","acknowledgement":"We thank Dominique Attali, Guilherme de Fonseca, Arijit Ghosh, Vincent Pilaud and Aurélien Alvarez for their comments and suggestions. We also acknowledge the reviewers.","year":"2021","volume":189,"date_updated":"2023-10-10T07:34:34Z","date_created":"2021-06-02T10:10:55Z","related_material":{"record":[{"id":"12960","relation":"later_version","status":"public"}]},"author":[{"first_name":"Jean-Daniel","last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel"},{"last_name":"Kachanovich","first_name":"Siargey","full_name":"Kachanovich, Siargey"},{"full_name":"Wintraecken, Mathijs","first_name":"Mathijs","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-184-9"]},"month":"06","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"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,"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2021.17","conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2021-06-11","start_date":"2021-06-07","location":"Virtual"},"alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of ℝ^d defined as the zero set of some multivariate multivalued smooth function f: ℝ^d → ℝ^{d-n}, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M is to consider its Piecewise-Linear (PL) approximation M̂ based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ = 1/D (and unavoidably exponential in n). Since it is known that for δ = Ω (d^{2.5}), M̂ is O(D²)-close and isotopic to M, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M̂ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art. ","lang":"eng"}],"intvolume":" 189","title":"Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations","status":"public","ddc":["005","516","514"],"_id":"9441","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","file":[{"relation":"main_file","file_id":"9442","checksum":"c322aa48d5d35a35877896cc565705b6","success":1,"date_updated":"2021-06-02T10:22:33Z","date_created":"2021-06-02T10:22:33Z","access_level":"open_access","file_name":"LIPIcs-SoCG-2021-17.pdf","file_size":1972902,"content_type":"application/pdf","creator":"mwintrae"}],"oa_version":"Published Version","series_title":"Leibniz International Proceedings in Informatics (LIPIcs)","has_accepted_license":"1","article_processing_charge":"No","day":"02","page":"17:1-17:16","citation":{"ieee":"J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations,” in 37th International Symposium on Computational Geometry (SoCG 2021), Virtual, 2021, vol. 189, p. 17:1-17:16.","apa":"Boissonnat, J.-D., Kachanovich, S., & Wintraecken, M. (2021). Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. In 37th International Symposium on Computational Geometry (SoCG 2021) (Vol. 189, p. 17:1-17:16). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2021.17","ista":"Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. 37th International Symposium on Computational Geometry (SoCG 2021). SoCG: Symposium on Computational GeometryLeibniz International Proceedings in Informatics (LIPIcs), LIPIcs, vol. 189, 17:1-17:16.","ama":"Boissonnat J-D, Kachanovich S, Wintraecken M. Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. In: 37th International Symposium on Computational Geometry (SoCG 2021). Vol 189. Leibniz International Proceedings in Informatics (LIPIcs). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021:17:1-17:16. doi:10.4230/LIPIcs.SoCG.2021.17","chicago":"Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter-Freudenthal-Kuhn Triangulations.” In 37th International Symposium on Computational Geometry (SoCG 2021), 189:17:1-17:16. Leibniz International Proceedings in Informatics (LIPIcs). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.SoCG.2021.17.","short":"J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, in:, 37th International Symposium on Computational Geometry (SoCG 2021), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Dagstuhl, Germany, 2021, p. 17:1-17:16.","mla":"Boissonnat, Jean-Daniel, et al. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter-Freudenthal-Kuhn Triangulations.” 37th International Symposium on Computational Geometry (SoCG 2021), vol. 189, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, p. 17:1-17:16, doi:10.4230/LIPIcs.SoCG.2021.17."},"publication":"37th International Symposium on Computational Geometry (SoCG 2021)","date_published":"2021-06-02T00:00:00Z"},{"publication_identifier":{"issn":["0925-9856"],"eissn":["1572-8102"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1007/s10703-021-00373-5","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000645490300001"],"arxiv":["1504.07384"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1504.07384","open_access":"1"}],"ec_funded":1,"volume":57,"date_created":"2021-05-16T22:01:47Z","date_updated":"2023-10-10T11:13:20Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389"},{"first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"}],"publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2021","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start Grant (279307: Graph Games), and Microsoft faculty fellows award.","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2021-09-01T00:00:00Z","page":"401-428","article_type":"original","citation":{"ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2021. Faster algorithms for quantitative verification in bounded treewidth graphs. Formal Methods in System Design. 57, 401–428.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for quantitative verification in bounded treewidth graphs,” Formal Methods in System Design, vol. 57. Springer, pp. 401–428, 2021.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2021). Faster algorithms for quantitative verification in bounded treewidth graphs. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-021-00373-5","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative verification in bounded treewidth graphs. Formal Methods in System Design. 2021;57:401-428. doi:10.1007/s10703-021-00373-5","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Verification in Bounded Treewidth Graphs.” Formal Methods in System Design. Springer, 2021. https://doi.org/10.1007/s10703-021-00373-5.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Quantitative Verification in Bounded Treewidth Graphs.” Formal Methods in System Design, vol. 57, Springer, 2021, pp. 401–28, doi:10.1007/s10703-021-00373-5.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Formal Methods in System Design 57 (2021) 401–428."},"publication":"Formal Methods in System Design","abstract":[{"lang":"eng","text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff, the ratio, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with bounded treewidth—a class that contains the control flow graphs of most programs. Let n denote the number of nodes of a graph, m the number of edges (for bounded treewidth 𝑚=𝑂(𝑛)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for the minimum initial credit problem we show that (1) for general graphs the problem can be solved in 𝑂(𝑛2⋅𝑚) time and the associated decision problem in 𝑂(𝑛⋅𝑚) time, improving the previous known 𝑂(𝑛3⋅𝑚⋅log(𝑛⋅𝑊)) and 𝑂(𝑛2⋅𝑚) bounds, respectively; and (2) for bounded treewidth graphs we present an algorithm that requires 𝑂(𝑛⋅log𝑛) time. Second, for bounded treewidth graphs we present an algorithm that approximates the mean-payoff value within a factor of 1+𝜖 in time 𝑂(𝑛⋅log(𝑛/𝜖)) as compared to the classical exact algorithms on general graphs that require quadratic time. Third, for the ratio property we present an algorithm that for bounded treewidth graphs works in time 𝑂(𝑛⋅log(|𝑎⋅𝑏|))=𝑂(𝑛⋅log(𝑛⋅𝑊)), when the output is 𝑎𝑏, as compared to the previously best known algorithm on general graphs with running time 𝑂(𝑛2⋅log(𝑛⋅𝑊)). We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 57","title":"Faster algorithms for quantitative verification in bounded treewidth graphs","status":"public","_id":"9393","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"intvolume":" 17","ddc":["530"],"status":"public","title":"Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation","_id":"10365","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"channezo","content_type":"application/pdf","file_size":40285498,"file_name":"50145_4_merged_1630498627.pdf","access_level":"open_access","date_created":"2023-10-11T09:31:43Z","date_updated":"2023-10-11T09:31:43Z","success":1,"checksum":"5d6d76750a71d7cb632bb15417c38ef7","file_id":"14420","relation":"main_file"}],"oa_version":"Submitted Version","type":"journal_article","issue":"12","abstract":[{"text":"The early development of many organisms involves the folding of cell monolayers, but this behaviour is difficult to reproduce in vitro; therefore, both mechanistic causes and effects of local curvature remain unclear. Here we study epithelial cell monolayers on corrugated hydrogels engineered into wavy patterns, examining how concave and convex curvatures affect cellular and nuclear shape. We find that substrate curvature affects monolayer thickness, which is larger in valleys than crests. We show that this feature generically arises in a vertex model, leading to the hypothesis that cells may sense curvature by modifying the thickness of the tissue. We find that local curvature also affects nuclear morphology and positioning, which we explain by extending the vertex model to take into account membrane–nucleus interactions, encoding thickness modulation in changes to nuclear deformation and position. We propose that curvature governs the spatial distribution of yes-associated proteins via nuclear shape and density changes. We show that curvature also induces significant variations in lamins, chromatin condensation and cell proliferation rate in folded epithelial tissues. Together, this work identifies active cell mechanics and nuclear mechanoadaptation as the key players of the mechanistic regulation of epithelia to substrate curvature.","lang":"eng"}],"page":"1382–1390","article_type":"original","citation":{"chicago":"Luciano, Marine, Shi-lei Xue, Winnok H. De Vos, Lorena Redondo-Morata, Mathieu Surin, Frank Lafont, Edouard B Hannezo, and Sylvain Gabriele. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” Nature Physics. Springer Nature, 2021. https://doi.org/10.1038/s41567-021-01374-1.","mla":"Luciano, Marine, et al. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” Nature Physics, vol. 17, no. 12, Springer Nature, 2021, pp. 1382–1390, doi:10.1038/s41567-021-01374-1.","short":"M. Luciano, S. Xue, W.H. De Vos, L. Redondo-Morata, M. Surin, F. Lafont, E.B. Hannezo, S. Gabriele, Nature Physics 17 (2021) 1382–1390.","ista":"Luciano M, Xue S, De Vos WH, Redondo-Morata L, Surin M, Lafont F, Hannezo EB, Gabriele S. 2021. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. 17(12), 1382–1390.","ieee":"M. Luciano et al., “Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation,” Nature Physics, vol. 17, no. 12. Springer Nature, pp. 1382–1390, 2021.","apa":"Luciano, M., Xue, S., De Vos, W. H., Redondo-Morata, L., Surin, M., Lafont, F., … Gabriele, S. (2021). Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-021-01374-1","ama":"Luciano M, Xue S, De Vos WH, et al. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. 2021;17(12):1382–1390. doi:10.1038/s41567-021-01374-1"},"publication":"Nature Physics","date_published":"2021-11-18T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"18","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"publication_status":"published","acknowledgement":"S.G. acknowledges funding from FEDER Prostem Research Project no. 1510614 (Wallonia DG06), F.R.S.-FNRS Epiforce Research Project no. T.0092.21 and Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen (Fonds Européen de Développement Régional, FEDER-ERDF). This project was supported by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme grant agreement 851288 (to E.H.), and by the Austrian Science Fund (FWF) (P 31639; to E.H.). L.R.M. acknowledges funding from the Agence National de la Recherche (ANR), as part of the ‘Investments d’Avenir’ Programme (I-SITE ULNE/ANR-16-IDEX-0004 ULNE). This work benefited from ANR-10-EQPX-04-01 and FEDER 12001407 grants to F.L. W.D.V. is supported by the Research Foundation Flanders (FWO 1516619N, FWO GOO5819N, FWO I003420N, FWO IRI I000321N) and is member of the Research Excellence Consortium µNEURO at the University of Antwerp. M.L. is financially supported by FRIA (F.R.S.-FNRS). M.S. is a Senior Research Associate of the Fund for Scientific Research (F.R.S.-FNRS) and acknowledges EOS grant no. 30650939 (PRECISION). Sketches in Figs. 1a and 5e and Extended Data Fig. 9 were drawn by C. Levicek.","year":"2021","volume":17,"date_created":"2021-11-28T23:01:29Z","date_updated":"2023-10-16T06:31:54Z","related_material":{"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/how-cells-feel-curvature/"}]},"author":[{"last_name":"Luciano","first_name":"Marine","full_name":"Luciano, Marine"},{"full_name":"Xue, Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","last_name":"Xue","first_name":"Shi-lei"},{"full_name":"De Vos, Winnok H.","last_name":"De Vos","first_name":"Winnok H."},{"full_name":"Redondo-Morata, Lorena","last_name":"Redondo-Morata","first_name":"Lorena"},{"full_name":"Surin, Mathieu","last_name":"Surin","first_name":"Mathieu"},{"full_name":"Lafont, Frank","first_name":"Frank","last_name":"Lafont"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"full_name":"Gabriele, Sylvain","last_name":"Gabriele","first_name":"Sylvain"}],"ec_funded":1,"file_date_updated":"2023-10-11T09:31:43Z","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis"},{"call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000720204300004"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41567-021-01374-1","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"month":"11"},{"date_created":"2021-03-28T22:01:44Z","date_updated":"2023-10-16T09:43:56Z","volume":17,"author":[{"first_name":"Daniel J.","last_name":"Klionsky","full_name":"Klionsky, Daniel J."},{"last_name":"Abdel-Aziz","first_name":"Amal Kamal","full_name":"Abdel-Aziz, Amal Kamal"},{"last_name":"Abdelfatah","first_name":"Sara","full_name":"Abdelfatah, Sara"},{"full_name":"Abdellatif, Mahmoud","last_name":"Abdellatif","first_name":"Mahmoud"},{"first_name":"Asghar","last_name":"Abdoli","full_name":"Abdoli, Asghar"},{"last_name":"Abel","first_name":"Steffen","full_name":"Abel, Steffen"},{"full_name":"Abeliovich, Hagai","last_name":"Abeliovich","first_name":"Hagai"},{"first_name":"Marie H.","last_name":"Abildgaard","full_name":"Abildgaard, Marie H."},{"full_name":"Abudu, Yakubu Princely","last_name":"Abudu","first_name":"Yakubu Princely"},{"first_name":"Abraham","last_name":"Acevedo-Arozena","full_name":"Acevedo-Arozena, Abraham"},{"last_name":"Adamopoulos","first_name":"Iannis E.","full_name":"Adamopoulos, Iannis E."},{"last_name":"Adeli","first_name":"Khosrow","full_name":"Adeli, Khosrow"},{"last_name":"Adolph","first_name":"Timon E.","full_name":"Adolph, Timon E."},{"last_name":"Adornetto","first_name":"Annagrazia","full_name":"Adornetto, Annagrazia"},{"full_name":"Aflaki, Elma","last_name":"Aflaki","first_name":"Elma"},{"last_name":"Agam","first_name":"Galila","full_name":"Agam, Galila"},{"first_name":"Anupam","last_name":"Agarwal","full_name":"Agarwal, Anupam"},{"last_name":"Aggarwal","first_name":"Bharat B.","full_name":"Aggarwal, Bharat B."},{"full_name":"Agnello, Maria","last_name":"Agnello","first_name":"Maria"},{"full_name":"Agostinis, Patrizia","last_name":"Agostinis","first_name":"Patrizia"},{"full_name":"Agrewala, Javed N.","last_name":"Agrewala","first_name":"Javed N."},{"full_name":"Agrotis, Alexander","first_name":"Alexander","last_name":"Agrotis"},{"full_name":"Aguilar, Patricia V.","first_name":"Patricia V.","last_name":"Aguilar"},{"full_name":"Ahmad, S. 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Yu"},{"first_name":"Zhou","last_name":"Zhou","full_name":"Zhou, Zhou"},{"first_name":"Binglin","last_name":"Zhu","full_name":"Zhu, Binglin"},{"full_name":"Zhu, Changlian","last_name":"Zhu","first_name":"Changlian"},{"first_name":"Guo Qing","last_name":"Zhu","full_name":"Zhu, Guo Qing"},{"full_name":"Zhu, Haining","first_name":"Haining","last_name":"Zhu"},{"first_name":"Hongxin","last_name":"Zhu","full_name":"Zhu, Hongxin"},{"full_name":"Zhu, Hua","first_name":"Hua","last_name":"Zhu"},{"full_name":"Zhu, Wei Guo","first_name":"Wei Guo","last_name":"Zhu"},{"last_name":"Zhu","first_name":"Yanping","full_name":"Zhu, Yanping"},{"last_name":"Zhu","first_name":"Yushan","full_name":"Zhu, Yushan"},{"full_name":"Zhuang, Haixia","last_name":"Zhuang","first_name":"Haixia"},{"full_name":"Zhuang, Xiaohong","last_name":"Zhuang","first_name":"Xiaohong"},{"full_name":"Zientara-Rytter, Katarzyna","first_name":"Katarzyna","last_name":"Zientara-Rytter"},{"full_name":"Zimmermann, Christine M.","first_name":"Christine M.","last_name":"Zimmermann"},{"full_name":"Ziviani, Elena","last_name":"Ziviani","first_name":"Elena"},{"first_name":"Teresa","last_name":"Zoladek","full_name":"Zoladek, Teresa"},{"first_name":"Wei Xing","last_name":"Zong","full_name":"Zong, Wei Xing"},{"last_name":"Zorov","first_name":"Dmitry B.","full_name":"Zorov, Dmitry B."},{"full_name":"Zorzano, Antonio","last_name":"Zorzano","first_name":"Antonio"},{"first_name":"Weiping","last_name":"Zou","full_name":"Zou, Weiping"},{"last_name":"Zou","first_name":"Zhen","full_name":"Zou, Zhen"},{"first_name":"Zhengzhi","last_name":"Zou","full_name":"Zou, Zhengzhi"},{"last_name":"Zuryn","first_name":"Steven","full_name":"Zuryn, Steven"},{"full_name":"Zwerschke, Werner","last_name":"Zwerschke","first_name":"Werner"},{"full_name":"Brand-Saberi, Beate","first_name":"Beate","last_name":"Brand-Saberi"},{"full_name":"Dong, X. Charlie","first_name":"X. Charlie","last_name":"Dong"},{"first_name":"Chandra Shekar","last_name":"Kenchappa","full_name":"Kenchappa, Chandra Shekar"},{"last_name":"Li","first_name":"Zuguo","full_name":"Li, Zuguo"},{"full_name":"Lin, Yong","last_name":"Lin","first_name":"Yong"},{"last_name":"Oshima","first_name":"Shigeru","full_name":"Oshima, Shigeru"},{"full_name":"Rong, Yueguang","last_name":"Rong","first_name":"Yueguang"},{"last_name":"Sluimer","first_name":"Judith C.","full_name":"Sluimer, Judith C."},{"full_name":"Stallings, Christina L.","first_name":"Christina L.","last_name":"Stallings"},{"last_name":"Tong","first_name":"Chun Kit","full_name":"Tong, Chun Kit"}],"publication_status":"published","publisher":"Taylor & Francis","department":[{"_id":"JiFr"},{"_id":"CaHe"}],"year":"2021","acknowledgement":"This work was supported by the National Institute of General Medical Sciences [GM131919]. Due to space and other limitations, it is not possible to include all other sources of financial support.","pmid":1,"month":"02","publication_identifier":{"eissn":["1554-8635"],"issn":["1554-8627"]},"language":[{"iso":"eng"}],"doi":"10.1080/15548627.2020.1797280","quality_controlled":"1","isi":1,"external_id":{"pmid":["33634751"],"isi":["000636121800001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1080/15548627.2020.1797280"}],"oa":1,"abstract":[{"text":"In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field. ","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Published Version","title":"Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)","status":"public","intvolume":" 17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9298","day":"08","article_processing_charge":"No","scopus_import":"1","date_published":"2021-02-08T00:00:00Z","article_type":"review","page":"1-382","publication":"Autophagy","citation":{"ista":"Klionsky DJ et al. 2021. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 17(1), 1–382.","apa":"Klionsky, D. J., Abdel-Aziz, A. K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., … Tong, C. K. (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. Taylor & Francis. https://doi.org/10.1080/15548627.2020.1797280","ieee":"D. J. Klionsky et al., “Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition),” Autophagy, vol. 17, no. 1. Taylor & Francis, pp. 1–382, 2021.","ama":"Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 2021;17(1):1-382. doi:10.1080/15548627.2020.1797280","chicago":"Klionsky, Daniel J., Amal Kamal Abdel-Aziz, Sara Abdelfatah, Mahmoud Abdellatif, Asghar Abdoli, Steffen Abel, Hagai Abeliovich, et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” Autophagy. Taylor & Francis, 2021. https://doi.org/10.1080/15548627.2020.1797280.","mla":"Klionsky, Daniel J., et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” Autophagy, vol. 17, no. 1, Taylor & Francis, 2021, pp. 1–382, doi:10.1080/15548627.2020.1797280.","short":"D.J. Klionsky, A.K. Abdel-Aziz, S. Abdelfatah, M. Abdellatif, A. Abdoli, S. Abel, H. Abeliovich, M.H. Abildgaard, Y.P. Abudu, A. Acevedo-Arozena, I.E. Adamopoulos, K. Adeli, T.E. Adolph, A. Adornetto, E. Aflaki, G. Agam, A. Agarwal, B.B. Aggarwal, M. Agnello, P. Agostinis, J.N. Agrewala, A. Agrotis, P.V. Aguilar, S.T. Ahmad, Z.M. Ahmed, U. Ahumada-Castro, S. Aits, S. Aizawa, Y. Akkoc, T. Akoumianaki, H.A. Akpinar, A.M. Al-Abd, L. Al-Akra, A. Al-Gharaibeh, M.A. Alaoui-Jamali, S. Alberti, E. Alcocer-Gómez, C. Alessandri, M. Ali, M.A. Alim Al-Bari, S. Aliwaini, J. Alizadeh, E. Almacellas, A. Almasan, A. Alonso, G.D. Alonso, N. Altan-Bonnet, D.C. Altieri, É.M.C. Álvarez, S. Alves, C. Alves Da Costa, M.M. Alzaharna, M. Amadio, C. Amantini, C. Amaral, S. Ambrosio, A.O. Amer, V. Ammanathan, Z. An, S.U. Andersen, S.A. Andrabi, M. Andrade-Silva, A.M. Andres, S. Angelini, D. Ann, U.C. Anozie, M.Y. Ansari, P. Antas, A. Antebi, Z. Antón, T. Anwar, L. Apetoh, N. Apostolova, T. Araki, Y. Araki, K. Arasaki, W.L. Araújo, J. Araya, C. Arden, M.A. Arévalo, S. Arguelles, E. Arias, J. Arikkath, H. Arimoto, A.R. Ariosa, D. Armstrong-James, L. Arnauné-Pelloquin, A. Aroca, D.S. Arroyo, I. Arsov, R. Artero, D.M.L. Asaro, M. Aschner, M. Ashrafizadeh, O. Ashur-Fabian, A.G. Atanasov, A.K. Au, P. Auberger, H.W. Auner, L. Aurelian, R. Autelli, L. Avagliano, Y. Ávalos, S. Aveic, C.A. Aveleira, T. Avin-Wittenberg, Y. Aydin, S. Ayton, S. Ayyadevara, M. Azzopardi, M. Baba, J.M. Backer, S.K. Backues, D.H. Bae, O.N. Bae, S.H. Bae, E.H. Baehrecke, A. Baek, S.H. Baek, S.H. Baek, G. Bagetta, A. Bagniewska-Zadworna, H. Bai, J. Bai, X. Bai, Y. Bai, N. Bairagi, S. Baksi, T. Balbi, C.T. Baldari, W. Balduini, A. Ballabio, M. Ballester, S. Balazadeh, R. Balzan, R. Bandopadhyay, S. Banerjee, S. Banerjee, Á. Bánréti, Y. Bao, M.S. Baptista, A. Baracca, C. Barbati, A. Bargiela, D. Barilà, P.G. Barlow, S.J. Barmada, E. Barreiro, G.E. Barreto, J. Bartek, B. Bartel, A. Bartolome, G.R. Barve, S.H. Basagoudanavar, D.C. Bassham, R.C. Bast, A. Basu, H. Batoko, I. Batten, E.E. Baulieu, B.L. Baumgarner, J. Bayry, R. Beale, I. Beau, F. Beaumatin, L.R.G. Bechara, G.R. Beck, M.F. Beers, J. Begun, C. Behrends, G.M.N. Behrens, R. Bei, E. Bejarano, S. Bel, C. Behl, A. Belaid, N. Belgareh-Touzé, C. Bellarosa, F. Belleudi, M. Belló Pérez, R. Bello-Morales, J.S.D.O. Beltran, S. Beltran, D.M. Benbrook, M. Bendorius, B.A. Benitez, I. Benito-Cuesta, J. Bensalem, M.W. Berchtold, S. Berezowska, D. Bergamaschi, M. Bergami, A. Bergmann, L. Berliocchi, C. Berlioz-Torrent, A. Bernard, L. Berthoux, C.G. Besirli, S. Besteiro, V.M. Betin, R. Beyaert, J.S. Bezbradica, K. Bhaskar, I. Bhatia-Kissova, R. Bhattacharya, S. Bhattacharya, S. Bhattacharyya, M.S. Bhuiyan, S.K. Bhutia, L. Bi, X. Bi, T.J. Biden, K. Bijian, V.A. Billes, N. Binart, C. Bincoletto, A.B. Birgisdottir, G. Bjorkoy, G. Blanco, A. Blas-Garcia, J. Blasiak, R. Blomgran, K. Blomgren, J.S. Blum, E. Boada-Romero, M. Boban, K. Boesze-Battaglia, P. Boeuf, B. Boland, P. Bomont, P. Bonaldo, S.R. Bonam, L. Bonfili, J.S. Bonifacino, B.A. Boone, M.D. Bootman, M. Bordi, C. Borner, B.C. Bornhauser, G. Borthakur, J. Bosch, S. Bose, L.M. Botana, J. Botas, C.M. Boulanger, M.E. Boulton, M. Bourdenx, B. Bourgeois, N.M. Bourke, G. Bousquet, P. Boya, P.V. Bozhkov, L.H.M. Bozi, T.O. Bozkurt, D.E. Brackney, C.H. Brandts, R.J. Braun, G.H. Braus, R. Bravo-Sagua, J.M. Bravo-San Pedro, P. Brest, M.A. Bringer, A. Briones-Herrera, V.C. Broaddus, P. Brodersen, J.L. Brodsky, S.L. Brody, P.G. Bronson, J.M. Bronstein, C.N. Brown, R.E. Brown, P.C. Brum, J.H. Brumell, N. Brunetti-Pierri, D. Bruno, R.J. Bryson-Richardson, C. Bucci, C. Buchrieser, M. Bueno, L.E. Buitrago-Molina, S. Buraschi, S. Buch, J.R. Buchan, E.M. Buckingham, H. Budak, M. Budini, G. Bultynck, F. Burada, J.R. Burgoyne, M.I. Burón, V. Bustos, S. Büttner, E. Butturini, A. Byrd, I. Cabas, S. Cabrera-Benitez, K. Cadwell, J. Cai, L. Cai, Q. Cai, M. Cairó, J.A. Calbet, G.A. Caldwell, K.A. Caldwell, J.A. Call, R. Calvani, A.C. Calvo, M. Calvo-Rubio Barrera, N.O.S. Camara, J.H. Camonis, N. Camougrand, M. Campanella, E.M. Campbell, F.X. Campbell-Valois, S. Campello, I. Campesi, J.C. Campos, O. Camuzard, J. Cancino, D. Candido De Almeida, L. Canesi, I. Caniggia, B. Canonico, C. Cantí, B. Cao, M. Caraglia, B. Caramés, E.H. Carchman, E. Cardenal-Muñoz, C. Cardenas, L. Cardenas, S.M. Cardoso, J.S. Carew, G.F. Carle, G. Carleton, S. Carloni, D. Carmona-Gutierrez, L.A. Carneiro, O. Carnevali, J.M. Carosi, S. Carra, A. Carrier, L. Carrier, B. Carroll, A.B. Carter, A.N. Carvalho, M. Casanova, C. Casas, J. Casas, C. Cassioli, E.F. Castillo, K. Castillo, S. Castillo-Lluva, F. Castoldi, M. Castori, A.F. Castro, M. Castro-Caldas, J. Castro-Hernandez, S. Castro-Obregon, S.D. Catz, C. Cavadas, F. Cavaliere, G. Cavallini, M. Cavinato, M.L. Cayuela, P. Cebollada Rica, V. Cecarini, F. Cecconi, M. Cechowska-Pasko, S. Cenci, V. Ceperuelo-Mallafré, J.J. Cerqueira, J.M. Cerutti, D. Cervia, V.B. Cetintas, S. Cetrullo, H.J. Chae, A.S. 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Zhan, B. Zhang, D.D. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H.L. Zhang, J. Zhang, J. Zhang, J.P. Zhang, K.Y.B. Zhang, L.W. Zhang, L. Zhang, L. Zhang, L. Zhang, L. Zhang, M. Zhang, P. Zhang, S. Zhang, W. Zhang, X. Zhang, X.W. Zhang, X. Zhang, X. Zhang, X. Zhang, X. Zhang, X.D. Zhang, Y. Zhang, Y. Zhang, Y. Zhang, Y.D. Zhang, Y. Zhang, Y.Y. Zhang, Y. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, H. Zhao, L. Zhao, S. Zhao, T. Zhao, X.F. Zhao, Y. Zhao, Y. Zhao, Y. Zhao, Y. Zhao, G. Zheng, K. Zheng, L. Zheng, S. Zheng, X.L. Zheng, Y. Zheng, Z.G. Zheng, B. Zhivotovsky, Q. Zhong, A. Zhou, B. Zhou, C. Zhou, G. Zhou, H. Zhou, H. Zhou, H. Zhou, J. Zhou, J. Zhou, J. Zhou, J. Zhou, K. Zhou, R. Zhou, X.J. Zhou, Y. Zhou, Y. Zhou, Y. Zhou, Z.Y. Zhou, Z. Zhou, B. Zhu, C. Zhu, G.Q. Zhu, H. Zhu, H. Zhu, H. Zhu, W.G. Zhu, Y. Zhu, Y. Zhu, H. Zhuang, X. Zhuang, K. Zientara-Rytter, C.M. Zimmermann, E. Ziviani, T. Zoladek, W.X. Zong, D.B. Zorov, A. Zorzano, W. Zou, Z. Zou, Z. Zou, S. Zuryn, W. Zwerschke, B. Brand-Saberi, X.C. Dong, C.S. Kenchappa, Z. Li, Y. Lin, S. Oshima, Y. Rong, J.C. Sluimer, C.L. Stallings, C.K. Tong, Autophagy 17 (2021) 1–382."}},{"publisher":"De Gruyter","department":[{"_id":"TiBr"}],"publication_status":"published","year":"2021","volume":33,"date_created":"2020-11-08T23:01:25Z","date_updated":"2023-10-17T07:39:01Z","author":[{"full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning"},{"full_name":"Heath-Brown, Roger","first_name":"Roger","last_name":"Heath-Brown"}],"publication_identifier":{"eissn":["1435-5337"],"issn":["0933-7741"]},"month":"01","project":[{"grant_number":"P32428","_id":"26AEDAB2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"New frontiers of the Manin conjecture"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000604750900008"],"arxiv":["2003.09593"]},"main_file_link":[{"url":"https://arxiv.org/abs/2003.09593","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1515/forum-2020-0074","type":"journal_article","issue":"1","abstract":[{"text":"We develop a version of Ekedahl’s geometric sieve for integral quadratic forms of rank at least five. As one ranges over the zeros of such quadratic forms, we use the sieve to compute the density of coprime values of polynomials, and furthermore, to address a question about local solubility in families of varieties parameterised by the zeros.","lang":"eng"}],"intvolume":" 33","title":"The geometric sieve for quadrics","status":"public","_id":"8742","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","page":"147-165","article_type":"original","citation":{"ista":"Browning TD, Heath-Brown R. 2021. The geometric sieve for quadrics. Forum Mathematicum. 33(1), 147–165.","apa":"Browning, T. D., & Heath-Brown, R. (2021). The geometric sieve for quadrics. Forum Mathematicum. De Gruyter. https://doi.org/10.1515/forum-2020-0074","ieee":"T. D. Browning and R. Heath-Brown, “The geometric sieve for quadrics,” Forum Mathematicum, vol. 33, no. 1. De Gruyter, pp. 147–165, 2021.","ama":"Browning TD, Heath-Brown R. The geometric sieve for quadrics. Forum Mathematicum. 2021;33(1):147-165. doi:10.1515/forum-2020-0074","chicago":"Browning, Timothy D, and Roger Heath-Brown. “The Geometric Sieve for Quadrics.” Forum Mathematicum. De Gruyter, 2021. https://doi.org/10.1515/forum-2020-0074.","mla":"Browning, Timothy D., and Roger Heath-Brown. “The Geometric Sieve for Quadrics.” Forum Mathematicum, vol. 33, no. 1, De Gruyter, 2021, pp. 147–65, doi:10.1515/forum-2020-0074.","short":"T.D. Browning, R. Heath-Brown, Forum Mathematicum 33 (2021) 147–165."},"publication":"Forum Mathematicum","date_published":"2021-01-01T00:00:00Z"},{"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/at:ista:10035","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"09","date_created":"2021-09-23T07:31:44Z","date_updated":"2023-10-17T09:24:07Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10044"},{"id":"10049","relation":"part_of_dissertation","status":"public"},{"id":"637","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10041"},{"id":"6430","status":"public","relation":"part_of_dissertation"},{"id":"10048","relation":"part_of_dissertation","status":"public"}]},"author":[{"first_name":"Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"publication_status":"published","acknowledgement":"I want to acknowledge the funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).\r\n","year":"2021","ec_funded":1,"file_date_updated":"2022-03-10T12:15:18Z","date_published":"2021-09-23T00:00:00Z","page":"276","citation":{"ista":"Klein K. 2021. On the adaptive security of graph-based games. Institute of Science and Technology Austria.","ieee":"K. Klein, “On the adaptive security of graph-based games,” Institute of Science and Technology Austria, 2021.","apa":"Klein, K. (2021). On the adaptive security of graph-based games. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10035","ama":"Klein K. On the adaptive security of graph-based games. 2021. doi:10.15479/at:ista:10035","chicago":"Klein, Karen. “On the Adaptive Security of Graph-Based Games.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10035.","mla":"Klein, Karen. On the Adaptive Security of Graph-Based Games. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10035.","short":"K. Klein, On the Adaptive Security of Graph-Based Games, Institute of Science and Technology Austria, 2021."},"article_processing_charge":"No","has_accepted_license":"1","day":"23","file":[{"relation":"main_file","file_id":"10082","checksum":"73a44345c683e81f3e765efbf86fdcc5","success":1,"date_created":"2021-10-04T12:22:33Z","date_updated":"2021-10-04T12:22:33Z","access_level":"open_access","file_name":"thesis_pdfa.pdf","content_type":"application/pdf","file_size":2104726,"creator":"cchlebak"},{"file_size":9538359,"content_type":"application/x-zip-compressed","creator":"cchlebak","access_level":"closed","file_name":"thesis_final (1).zip","checksum":"7b80df30a0e686c3ef6a56d4e1c59e29","date_updated":"2022-03-10T12:15:18Z","date_created":"2021-10-05T07:04:37Z","relation":"source_file","file_id":"10085"}],"oa_version":"Published Version","ddc":["519"],"status":"public","title":"On the adaptive security of graph-based games","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10035","abstract":[{"lang":"eng","text":"Many security definitions come in two flavors: a stronger “adaptive” flavor, where the adversary can arbitrarily make various choices during the course of the attack, and a weaker “selective” flavor where the adversary must commit to some or all of their choices a-priori. For example, in the context of identity-based encryption, selective security requires the adversary to decide on the identity of the attacked party at the very beginning of the game whereas adaptive security allows the attacker to first see the master public key and some secret keys before making this choice. Often, it appears to be much easier to achieve selective security than it is to achieve adaptive security. A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption [Pan07][FJP15], constrained PRFs [FKPR14], and Yao’s garbled circuits [JW16]. Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework (published at Crypto ’17 [JKK+17a]) that connects all of these works and allows us to present them in a unified and simplified fashion. Having the framework in place, we show how to achieve adaptive security for proxy re-encryption schemes (published at PKC ’19 [FKKP19]) and provide the first adaptive security proofs for continuous group key agreement protocols (published at S&P ’21 [KPW+21]). Questioning optimality of our framework, we then show that currently used proof techniques cannot lead to significantly better security guarantees for \"graph-building\" games (published at TCC ’21 [KKPW21a]). These games cover generalized selective decryption, as well as the security of prominent constructions for constrained PRFs, continuous group key agreement, and proxy re-encryption. Finally, we revisit the adaptive security of Yao’s garbled circuits and extend the analysis of Jafargholi and Wichs in two directions: While they prove adaptive security only for a modified construction with increased online complexity, we provide the first positive results for the original construction by Yao (published at TCC ’21 [KKP21a]). On the negative side, we prove that the results of Jafargholi and Wichs are essentially optimal by showing that no black-box reduction can provide a significantly better security bound (published at Crypto ’21 [KKPW21c])."}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"external_id":{"isi":["000728364000019"]},"main_file_link":[{"open_access":"1","url":"https://ia.cr/2021/059"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"conference":{"end_date":"2021-11-11","location":"Raleigh, NC, United States","start_date":"2021-11-08","name":"TCC: Theory of Cryptography"},"doi":"10.1007/978-3-030-90453-1_19","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"isbn":["9-783-0309-0452-4"],"eissn":["1611-3349"],"issn":["0302-9743"]},"acknowledgement":"C. Kamath—Supported by Azrieli International Postdoctoral Fellowship. Most of the work was done while the author was at Northeastern University and Charles University, funded by the IARPA grant IARPA/2019-19-020700009 and project PRIMUS/17/SCI/9, respectively. K. Klein—Supported in part by ERC CoG grant 724307. Most of the work was done while the author was at IST Austria funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT). K. Pietrzak—Funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","year":"2021","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"author":[{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","first_name":"Chethan"},{"first_name":"Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen"},{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","last_name":"Walter","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","full_name":"Walter, Michael"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10048"}]},"date_created":"2021-12-05T23:01:43Z","date_updated":"2023-10-17T09:24:07Z","volume":13043,"ec_funded":1,"publication":"19th International Conference","citation":{"ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2021. The cost of adaptivity in security games on graphs. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13043, 550–581.","apa":"Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Walter, M. (2021). The cost of adaptivity in security games on graphs. In 19th International Conference (Vol. 13043, pp. 550–581). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_19","ieee":"C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “The cost of adaptivity in security games on graphs,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 550–581.","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. The cost of adaptivity in security games on graphs. In: 19th International Conference. Vol 13043. Springer Nature; 2021:550-581. doi:10.1007/978-3-030-90453-1_19","chicago":"Kamath Hosdurg, Chethan, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “The Cost of Adaptivity in Security Games on Graphs.” In 19th International Conference, 13043:550–81. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_19.","mla":"Kamath Hosdurg, Chethan, et al. “The Cost of Adaptivity in Security Games on Graphs.” 19th International Conference, vol. 13043, Springer Nature, 2021, pp. 550–81, doi:10.1007/978-3-030-90453-1_19.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 550–581."},"page":"550-581","date_published":"2021-11-04T00:00:00Z","scopus_import":"1","day":"04","article_processing_charge":"No","_id":"10410","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"The cost of adaptivity in security games on graphs","status":"public","intvolume":" 13043","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"The security of cryptographic primitives and protocols against adversaries that are allowed to make adaptive choices (e.g., which parties to corrupt or which queries to make) is notoriously difficult to establish. A broad theoretical framework was introduced by Jafargholi et al. [Crypto’17] for this purpose. In this paper we initiate the study of lower bounds on loss in adaptive security for certain cryptographic protocols considered in the framework. We prove lower bounds that almost match the upper bounds (proven using the framework) for proxy re-encryption, prefix-constrained PRFs and generalized selective decryption, a security game that captures the security of certain group messaging and broadcast encryption schemes. Those primitives have in common that their security game involves an underlying graph that can be adaptively built by the adversary. Some of our lower bounds only apply to a restricted class of black-box reductions which we term “oblivious” (the existing upper bounds are of this restricted type), some apply to the broader but still restricted class of non-rewinding reductions, while our lower bound for proxy re-encryption applies to all black-box reductions. The fact that some of our lower bounds seem to crucially rely on obliviousness or at least a non-rewinding reduction hints to the exciting possibility that the existing upper bounds can be improved by using more sophisticated reductions. Our main conceptual contribution is a two-player multi-stage game called the Builder-Pebbler Game. We can translate bounds on the winning probabilities for various instantiations of this game into cryptographic lower bounds for the above-mentioned primitives using oracle separation techniques."}]},{"title":"The cost of adaptivity in security games on graphs","publication_status":"published","status":"public","publisher":"International Association for Cryptologic Research","department":[{"_id":"KrPi"}],"_id":"10048","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-09-27T12:52:05Z","date_updated":"2023-10-17T09:24:08Z","oa_version":"Preprint","author":[{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","first_name":"Karen"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"full_name":"Walter, Michael","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","last_name":"Walter","first_name":"Michael"}],"related_material":{"record":[{"id":"10410","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"10035"}]},"type":"conference","abstract":[{"text":"The security of cryptographic primitives and protocols against adversaries that are allowed to make adaptive choices (e.g., which parties to corrupt or which queries to make) is notoriously difficult to establish. A broad theoretical\r\nframework was introduced by Jafargholi et al. [Crypto’17] for this purpose. In this paper we initiate the study of lower bounds on loss in adaptive security for certain cryptographic protocols considered in the framework. We prove lower\r\nbounds that almost match the upper bounds (proven using the framework) for proxy re-encryption, prefix-constrained PRFs and generalized selective decryption, a security game that captures the security of certain group messaging and\r\nbroadcast encryption schemes. Those primitives have in common that their security game involves an underlying graph that can be adaptively built by the adversary. Some of our lower bounds only apply to a restricted class of black-box reductions which we term “oblivious” (the existing upper bounds are of this restricted type), some apply to the broader but still restricted class of non-rewinding reductions, while our lower bound for proxy re-encryption applies to all black-box reductions. The fact that some of our lower bounds seem to crucially rely on obliviousness or at least a non-rewinding reduction hints to the exciting possibility that the existing upper bounds can be improved by using more sophisticated reductions. Our main conceptual contribution is a two-player multi-stage game called the Builder-Pebbler Game. We can translate bounds on the winning probabilities for various instantiations of this game into cryptographic lower bounds for the above-mentioned primitives using oracle separation techniques.\r\n","lang":"eng"}],"quality_controlled":"1","publication":"19th Theory of Cryptography Conference 2021","main_file_link":[{"url":"https://ia.cr/2021/059","open_access":"1"}],"citation":{"ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. The cost of adaptivity in security games on graphs. In: 19th Theory of Cryptography Conference 2021. International Association for Cryptologic Research; 2021.","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2021. The cost of adaptivity in security games on graphs. 19th Theory of Cryptography Conference 2021. TCC: Theory of Cryptography Conference.","apa":"Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Walter, M. (2021). The cost of adaptivity in security games on graphs. In 19th Theory of Cryptography Conference 2021. Raleigh, NC, United States: International Association for Cryptologic Research.","ieee":"C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “The cost of adaptivity in security games on graphs,” in 19th Theory of Cryptography Conference 2021, Raleigh, NC, United States, 2021.","mla":"Kamath Hosdurg, Chethan, et al. “The Cost of Adaptivity in Security Games on Graphs.” 19th Theory of Cryptography Conference 2021, International Association for Cryptologic Research, 2021.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, 19th Theory of Cryptography Conference 2021, International Association for Cryptologic Research, 2021.","chicago":"Kamath Hosdurg, Chethan, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “The Cost of Adaptivity in Security Games on Graphs.” In 19th Theory of Cryptography Conference 2021. International Association for Cryptologic Research, 2021."},"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2021-11-11","start_date":"2021-11-08","location":"Raleigh, NC, United States","name":"TCC: Theory of Cryptography Conference"},"date_published":"2021-07-08T00:00:00Z","day":"08","month":"07","article_processing_charge":"No"},{"ec_funded":1,"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Mathematical Sciences Publishers","year":"2021","acknowledgement":"N. L. and R. S. gratefully acknowledge financial support by the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (grant\r\nagreement No 694227). B. S. acknowledges support from the Swiss National Science Foundation (grant 200020_172623) and from the NCCR SwissMAP. N. L. would like to thank\r\nAndreas Deuchert and David Mitrouskas for interesting discussions. B. S. and R. S. would\r\nlike to thank Rupert Frank for stimulating discussions about the time-evolution of a polaron.\r\n","date_updated":"2023-10-17T11:26:45Z","date_created":"2022-02-06T23:01:33Z","volume":14,"author":[{"full_name":"Leopold, Nikolai K","last_name":"Leopold","first_name":"Nikolai K","orcid":"0000-0002-0495-6822","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"id":"856966FE-A408-11E9-977E-802DE6697425","orcid":"0000-0001-5059-4466","first_name":"Simone Anna Elvira","last_name":"Rademacher","full_name":"Rademacher, Simone Anna Elvira"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"month":"11","publication_identifier":{"issn":["2157-5045"],"eissn":["1948-206X"]},"quality_controlled":"1","isi":1,"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000733976600004"],"arxiv":["1904.12532"]},"main_file_link":[{"url":"https://arxiv.org/abs/1904.12532","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.2140/APDE.2021.14.2079","type":"journal_article","abstract":[{"text":"We prove an adiabatic theorem for the Landau–Pekar equations. This allows us to derive new results on the accuracy of their use as effective equations for the time evolution generated by the Fröhlich Hamiltonian with large coupling constant α. In particular, we show that the time evolution of Pekar product states with coherent phonon field and the electron being trapped by the phonons is well approximated by the Landau–Pekar equations until times short compared to α2.","lang":"eng"}],"issue":"7","status":"public","title":" The Landau–Pekar equations: Adiabatic theorem and accuracy","intvolume":" 14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10738","oa_version":"Preprint","scopus_import":"1","day":"10","article_processing_charge":"No","article_type":"original","page":"2079-2100","publication":"Analysis and PDE","citation":{"mla":"Leopold, Nikolai K., et al. “ The Landau–Pekar Equations: Adiabatic Theorem and Accuracy.” Analysis and PDE, vol. 14, no. 7, Mathematical Sciences Publishers, 2021, pp. 2079–100, doi:10.2140/APDE.2021.14.2079.","short":"N.K. Leopold, S.A.E. Rademacher, B. Schlein, R. Seiringer, Analysis and PDE 14 (2021) 2079–2100.","chicago":"Leopold, Nikolai K, Simone Anna Elvira Rademacher, Benjamin Schlein, and Robert Seiringer. “ The Landau–Pekar Equations: Adiabatic Theorem and Accuracy.” Analysis and PDE. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/APDE.2021.14.2079.","ama":"Leopold NK, Rademacher SAE, Schlein B, Seiringer R. The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. 2021;14(7):2079-2100. doi:10.2140/APDE.2021.14.2079","ista":"Leopold NK, Rademacher SAE, Schlein B, Seiringer R. 2021. The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. 14(7), 2079–2100.","apa":"Leopold, N. K., Rademacher, S. A. E., Schlein, B., & Seiringer, R. (2021). The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. Mathematical Sciences Publishers. https://doi.org/10.2140/APDE.2021.14.2079","ieee":"N. K. Leopold, S. A. E. Rademacher, B. Schlein, and R. Seiringer, “ The Landau–Pekar equations: Adiabatic theorem and accuracy,” Analysis and PDE, vol. 14, no. 7. Mathematical Sciences Publishers, pp. 2079–2100, 2021."},"date_published":"2021-11-10T00:00:00Z"},{"doi":"10.15479/at:ista:10429","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"degree_awarded":"PhD","oa":1,"project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"publication_identifier":{"issn":["2663-337X"]},"month":"12","related_material":{"record":[{"id":"10432","status":"public","relation":"part_of_dissertation"},{"id":"6673","status":"public","relation":"part_of_dissertation"},{"id":"5965","relation":"part_of_dissertation","status":"public"},{"id":"10435","status":"public","relation":"part_of_dissertation"}]},"author":[{"first_name":"Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi"}],"date_updated":"2023-10-17T11:48:55Z","date_created":"2021-12-08T21:52:28Z","year":"2021","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","ec_funded":1,"file_date_updated":"2022-03-28T12:55:12Z","date_published":"2021-12-09T00:00:00Z","citation":{"short":"G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021.","mla":"Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429.","chicago":"Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429.","ama":"Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429","ieee":"G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021.","apa":"Nadiradze, G. (2021). On achieving scalability through relaxation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429","ista":"Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria."},"page":"132","article_processing_charge":"No","has_accepted_license":"1","day":"09","oa_version":"Published Version","file":[{"creator":"gnadirad","content_type":"application/pdf","file_size":2370859,"access_level":"open_access","file_name":"Thesis_Final_09_12_2021.pdf","success":1,"checksum":"6bf14e9a523387328f016c0689f5e10e","date_created":"2021-12-09T17:47:49Z","date_updated":"2021-12-09T17:47:49Z","file_id":"10436","relation":"main_file"},{"checksum":"914d6c5ca86bd0add471971a8f4c4341","date_created":"2021-12-09T17:47:49Z","date_updated":"2022-03-28T12:55:12Z","file_id":"10437","relation":"source_file","creator":"gnadirad","content_type":"application/zip","file_size":2596924,"access_level":"closed","file_name":"Thesis_Final_09_12_2021.zip"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10429","ddc":["000"],"status":"public","title":"On achieving scalability through relaxation","abstract":[{"text":"The scalability of concurrent data structures and distributed algorithms strongly depends on\r\nreducing the contention for shared resources and the costs of synchronization and communication. We show how such cost reductions can be attained by relaxing the strict consistency conditions required by sequential implementations. In the first part of the thesis, we consider relaxation in the context of concurrent data structures. Specifically, in data structures \r\nsuch as priority queues, imposing strong semantics renders scalability impossible, since a correct implementation of the remove operation should return only the element with highest priority. Intuitively, attempting to invoke remove operations concurrently creates a race condition. This bottleneck can be circumvented by relaxing semantics of the affected data structure, thus allowing removal of the elements which are no longer required to have the highest priority. We prove that the randomized implementations of relaxed data structures provide provable guarantees on the priority of the removed elements even under concurrency. Additionally, we show that in some cases the relaxed data structures can be used to scale the classical algorithms which are usually implemented with the exact ones. In the second part, we study parallel variants of the stochastic gradient descent (SGD) algorithm, which distribute computation among the multiple processors, thus reducing the running time. Unfortunately, in order for standard parallel SGD to succeed, each processor has to maintain a local copy of the necessary model parameter, which is identical to the local copies of other processors; the overheads from this perfect consistency in terms of communication and synchronization can negate the speedup gained by distributing the computation. We show that the consistency conditions required by SGD can be relaxed, allowing the algorithm to be more flexible in terms of tolerating quantized communication, asynchrony, or even crash faults, while its convergence remains asymptotically the same.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"]},{"conference":{"end_date":"2021-12-14","start_date":"2021-12-06","location":"Sydney, Australia","name":"NeurIPS: Neural Information Processing Systems"},"date_published":"2021-12-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"35th Conference on Neural Information Processing Systems","external_id":{"arxiv":["1910.12308"]},"citation":{"short":"G. Nadiradze, A. Sabour, P. Davies, S. Li, D.-A. Alistarh, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","mla":"Nadiradze, Giorgi, et al. “Asynchronous Decentralized SGD with Quantized and Local Updates.” 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","chicago":"Nadiradze, Giorgi, Amirmojtaba Sabour, Peter Davies, Shigang Li, and Dan-Adrian Alistarh. “Asynchronous Decentralized SGD with Quantized and Local Updates.” In 35th Conference on Neural Information Processing Systems. Neural Information Processing Systems Foundation, 2021.","ama":"Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. Asynchronous decentralized SGD with quantized and local updates. In: 35th Conference on Neural Information Processing Systems. Neural Information Processing Systems Foundation; 2021.","apa":"Nadiradze, G., Sabour, A., Davies, P., Li, S., & Alistarh, D.-A. (2021). Asynchronous decentralized SGD with quantized and local updates. In 35th Conference on Neural Information Processing Systems. Sydney, Australia: Neural Information Processing Systems Foundation.","ieee":"G. Nadiradze, A. Sabour, P. Davies, S. Li, and D.-A. Alistarh, “Asynchronous decentralized SGD with quantized and local updates,” in 35th Conference on Neural Information Processing Systems, Sydney, Australia, 2021.","ista":"Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. 2021. Asynchronous decentralized SGD with quantized and local updates. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems."},"oa":1,"main_file_link":[{"url":"https://papers.nips.cc/paper/2021/hash/362c99307cdc3f2d8b410652386a9dd1-Abstract.html","open_access":"1"}],"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"month":"12","day":"01","article_processing_charge":"No","author":[{"full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","first_name":"Giorgi","last_name":"Nadiradze"},{"full_name":"Sabour, Amirmojtaba","first_name":"Amirmojtaba","last_name":"Sabour","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67"},{"full_name":"Davies, Peter","orcid":"0000-0002-5646-9524","id":"11396234-BB50-11E9-B24C-90FCE5697425","last_name":"Davies","first_name":"Peter"},{"full_name":"Li, Shigang","last_name":"Li","first_name":"Shigang"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10429"}]},"date_updated":"2023-10-17T11:48:56Z","date_created":"2021-12-09T10:59:12Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10435","year":"2021","acknowledgement":"We gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). PD partly conducted this work while at IST Austria and was supported by the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No. 754411. SL was funded in part by European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement DAPP, No. 678880, and EPiGRAM-HS, No. 801039).\r\n","publication_status":"published","title":"Asynchronous decentralized SGD with quantized and local updates","status":"public","department":[{"_id":"DaAl"}],"publisher":"Neural Information Processing Systems Foundation","abstract":[{"text":"Decentralized optimization is emerging as a viable alternative for scalable distributed machine learning, but also introduces new challenges in terms of synchronization costs. To this end, several communication-reduction techniques, such as non-blocking communication, quantization, and local steps, have been explored in the decentralized setting. Due to the complexity of analyzing optimization in such a relaxed setting, this line of work often assumes \\emph{global} communication rounds, which require additional synchronization. In this paper, we consider decentralized optimization in the simpler, but harder to analyze, \\emph{asynchronous gossip} model, in which communication occurs in discrete, randomly chosen pairings among nodes. Perhaps surprisingly, we show that a variant of SGD called \\emph{SwarmSGD} still converges in this setting, even if \\emph{non-blocking communication}, \\emph{quantization}, and \\emph{local steps} are all applied \\emph{in conjunction}, and even if the node data distributions and underlying graph topology are both \\emph{heterogenous}. Our analysis is based on a new connection with multi-dimensional load-balancing processes. We implement this algorithm and deploy it in a super-computing environment, showing that it can outperform previous decentralized methods in terms of end-to-end training time, and that it can even rival carefully-tuned large-batch SGD for certain tasks.","lang":"eng"}],"ec_funded":1,"type":"conference"},{"scopus_import":"1","day":"01","article_processing_charge":"No","page":"29616-29629","publication":"35th Conference on Neural Information Processing Systems","citation":{"mla":"Mondelli, Marco, and Ramji Venkataramanan. “PCA Initialization for Approximate Message Passing in Rotationally Invariant Models.” 35th Conference on Neural Information Processing Systems, vol. 35, Neural Information Processing Systems Foundation, 2021, pp. 29616–29.","short":"M. Mondelli, R. Venkataramanan, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 29616–29629.","chicago":"Mondelli, Marco, and Ramji Venkataramanan. “PCA Initialization for Approximate Message Passing in Rotationally Invariant Models.” In 35th Conference on Neural Information Processing Systems, 35:29616–29. Neural Information Processing Systems Foundation, 2021.","ama":"Mondelli M, Venkataramanan R. PCA initialization for approximate message passing in rotationally invariant models. In: 35th Conference on Neural Information Processing Systems. Vol 35. Neural Information Processing Systems Foundation; 2021:29616-29629.","ista":"Mondelli M, Venkataramanan R. 2021. PCA initialization for approximate message passing in rotationally invariant models. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 35, 29616–29629.","ieee":"M. Mondelli and R. Venkataramanan, “PCA initialization for approximate message passing in rotationally invariant models,” in 35th Conference on Neural Information Processing Systems, Virtual, 2021, vol. 35, pp. 29616–29629.","apa":"Mondelli, M., & Venkataramanan, R. (2021). PCA initialization for approximate message passing in rotationally invariant models. In 35th Conference on Neural Information Processing Systems (Vol. 35, pp. 29616–29629). Virtual: Neural Information Processing Systems Foundation."},"date_published":"2021-12-01T00:00:00Z","type":"conference","abstract":[{"text":"We study the problem of estimating a rank-$1$ signal in the presence of rotationally invariant noise-a class of perturbations more general than Gaussian noise. Principal Component Analysis (PCA) provides a natural estimator, and sharp results on its performance have been obtained in the high-dimensional regime. Recently, an Approximate Message Passing (AMP) algorithm has been proposed as an alternative estimator with the potential to improve the accuracy of PCA. However, the existing analysis of AMP requires an initialization that is both correlated with the signal and independent of the noise, which is often unrealistic in practice. In this work, we combine the two methods, and propose to initialize AMP with PCA. Our main result is a rigorous asymptotic characterization of the performance of this estimator. Both the AMP algorithm and its analysis differ from those previously derived in the Gaussian setting: at every iteration, our AMP algorithm requires a specific term to account for PCA initialization, while in the Gaussian case, PCA initialization affects only the first iteration of AMP. The proof is based on a two-phase artificial AMP that first approximates the PCA estimator and then mimics the true AMP. Our numerical simulations show an excellent agreement between AMP results and theoretical predictions, and suggest an interesting open direction on achieving Bayes-optimal performance.","lang":"eng"}],"title":"PCA initialization for approximate message passing in rotationally invariant models","status":"public","intvolume":" 35","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10593","oa_version":"Preprint","month":"12","publication_identifier":{"isbn":["9781713845393"],"issn":["1049-5258"]},"quality_controlled":"1","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"main_file_link":[{"url":"https://arxiv.org/abs/2106.02356","open_access":"1"}],"external_id":{"arxiv":["2106.02356"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2021-12-06","location":"Virtual","end_date":"2021-12-14"},"publication_status":"published","department":[{"_id":"MaMo"}],"publisher":"Neural Information Processing Systems Foundation","acknowledgement":"M. Mondelli would like to thank László Erdős for helpful discussions. M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize. R. Venkataramanan was partially supported by the Alan Turing Institute under the EPSRC grant EP/N510129/1.\r\n","year":"2021","date_updated":"2023-10-17T11:48:23Z","date_created":"2022-01-03T10:50:02Z","volume":35,"author":[{"last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"},{"last_name":"Venkataramanan","first_name":"Ramji","full_name":"Venkataramanan, Ramji"}]},{"month":"12","publication_identifier":{"isbn":["9781713845393"],"issn":["1049-5258"]},"language":[{"iso":"eng"}],"conference":{"location":"Virtual","start_date":"2021-12-06","end_date":"2021-12-14","name":"35th Conference on Neural Information Processing Systems"},"quality_controlled":"1","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"external_id":{"arxiv":["2102.09671"]},"main_file_link":[{"url":"https://arxiv.org/abs/2102.09671","open_access":"1"}],"oa":1,"date_updated":"2023-10-17T11:48:40Z","date_created":"2022-01-03T10:56:20Z","volume":35,"author":[{"full_name":"Nguyen, Quynh","last_name":"Nguyen","first_name":"Quynh"},{"first_name":"Pierre","last_name":"Bréchet","full_name":"Bréchet, Pierre"},{"full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"publication_status":"published","publisher":"Neural Information Processing Systems Foundation","department":[{"_id":"MaMo"}],"year":"2021","acknowledgement":"MM was partially supported by the 2019 Lopez-Loreta Prize. QN and PB acknowledge support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 757983).","day":"01","article_processing_charge":"No","date_published":"2021-12-01T00:00:00Z","publication":"35th Conference on Neural Information Processing Systems","citation":{"apa":"Nguyen, Q., Bréchet, P., & Mondelli, M. (2021). When are solutions connected in deep networks? In 35th Conference on Neural Information Processing Systems (Vol. 35). Virtual: Neural Information Processing Systems Foundation.","ieee":"Q. Nguyen, P. Bréchet, and M. Mondelli, “When are solutions connected in deep networks?,” in 35th Conference on Neural Information Processing Systems, Virtual, 2021, vol. 35.","ista":"Nguyen Q, Bréchet P, Mondelli M. 2021. When are solutions connected in deep networks? 35th Conference on Neural Information Processing Systems. 35th Conference on Neural Information Processing Systems vol. 35.","ama":"Nguyen Q, Bréchet P, Mondelli M. When are solutions connected in deep networks? In: 35th Conference on Neural Information Processing Systems. Vol 35. Neural Information Processing Systems Foundation; 2021.","chicago":"Nguyen, Quynh, Pierre Bréchet, and Marco Mondelli. “When Are Solutions Connected in Deep Networks?” In 35th Conference on Neural Information Processing Systems, Vol. 35. Neural Information Processing Systems Foundation, 2021.","short":"Q. Nguyen, P. Bréchet, M. Mondelli, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","mla":"Nguyen, Quynh, et al. “When Are Solutions Connected in Deep Networks?” 35th Conference on Neural Information Processing Systems, vol. 35, Neural Information Processing Systems Foundation, 2021."},"abstract":[{"lang":"eng","text":"The question of how and why the phenomenon of mode connectivity occurs in training deep neural networks has gained remarkable attention in the research community. From a theoretical perspective, two possible explanations have been proposed: (i) the loss function has connected sublevel sets, and (ii) the solutions found by stochastic gradient descent are dropout stable. While these explanations provide insights into the phenomenon, their assumptions are not always satisfied in practice. In particular, the first approach requires the network to have one layer with order of N neurons (N being the number of training samples), while the second one requires the loss to be almost invariant after removing half of the neurons at each layer (up to some rescaling of the remaining ones). In this work, we improve both conditions by exploiting the quality of the features at every intermediate layer together with a milder over-parameterization condition. More specifically, we show that: (i) under generic assumptions on the features of intermediate layers, it suffices that the last two hidden layers have order of N−−√ neurons, and (ii) if subsets of features at each layer are linearly separable, then no over-parameterization is needed to show the connectivity. Our experiments confirm that the proposed condition ensures the connectivity of solutions found by stochastic gradient descent, even in settings where the previous requirements do not hold."}],"type":"conference","oa_version":"Preprint","title":"When are solutions connected in deep networks?","status":"public","intvolume":" 35","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10594"},{"language":[{"iso":"eng"}],"doi":"10.1088/2058-9565/ac0f36","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":{"arxiv":["2008.08764"],"isi":["000673081500001"]},"publication_identifier":{"eissn":["2058-9565"]},"month":"07","volume":6,"date_updated":"2023-10-17T12:54:54Z","date_created":"2021-08-08T22:01:25Z","author":[{"full_name":"Mobassem, Sonia","last_name":"Mobassem","first_name":"Sonia"},{"full_name":"Lambert, Nicholas J.","last_name":"Lambert","first_name":"Nicholas J."},{"full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez","first_name":"Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"last_name":"Schwefel","first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L."}],"publisher":"IOP Publishing","department":[{"_id":"JoFi"}],"publication_status":"published","year":"2021","acknowledgement":"NJL is supported by the MBIE Endeavour Fund (UOOX1805) and GL is by the Julius von Haast Fellowship of New Zealand. SM acknowledges stimulating discussions with T M Jensen.","file_date_updated":"2021-08-09T12:23:13Z","article_number":"045005","date_published":"2021-07-15T00:00:00Z","article_type":"original","citation":{"ieee":"S. Mobassem, N. J. Lambert, A. R. Rueda Sanchez, J. M. Fink, G. Leuchs, and H. G. L. Schwefel, “Thermal noise in electro-optic devices at cryogenic temperatures,” Quantum Science and Technology, vol. 6, no. 4. IOP Publishing, 2021.","apa":"Mobassem, S., Lambert, N. J., Rueda Sanchez, A. R., Fink, J. M., Leuchs, G., & Schwefel, H. G. L. (2021). Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. IOP Publishing. https://doi.org/10.1088/2058-9565/ac0f36","ista":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. 2021. Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. 6(4), 045005.","ama":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. 2021;6(4). doi:10.1088/2058-9565/ac0f36","chicago":"Mobassem, Sonia, Nicholas J. Lambert, Alfredo R Rueda Sanchez, Johannes M Fink, Gerd Leuchs, and Harald G.L. Schwefel. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” Quantum Science and Technology. IOP Publishing, 2021. https://doi.org/10.1088/2058-9565/ac0f36.","short":"S. Mobassem, N.J. Lambert, A.R. Rueda Sanchez, J.M. Fink, G. Leuchs, H.G.L. Schwefel, Quantum Science and Technology 6 (2021).","mla":"Mobassem, Sonia, et al. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” Quantum Science and Technology, vol. 6, no. 4, 045005, IOP Publishing, 2021, doi:10.1088/2058-9565/ac0f36."},"publication":"Quantum Science and Technology","article_processing_charge":"Yes","has_accepted_license":"1","day":"15","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":2366118,"creator":"cchlebak","access_level":"open_access","file_name":"2021_QuantumScienceTechnology_Mobassem.pdf","checksum":"b15c2c228487a75002c3b52d56f23d5c","date_updated":"2021-08-09T12:23:13Z","date_created":"2021-08-09T12:23:13Z","relation":"main_file","file_id":"9836"}],"oa_version":"Published Version","intvolume":" 6","ddc":["530"],"status":"public","title":"Thermal noise in electro-optic devices at cryogenic temperatures","_id":"9815","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","abstract":[{"text":"The quantum bits (qubits) on which superconducting quantum computers are based have energy scales corresponding to photons with GHz frequencies. The energy of photons in the gigahertz domain is too low to allow transmission through the noisy room-temperature environment, where the signal would be lost in thermal noise. Optical photons, on the other hand, have much higher energies, and signals can be detected using highly efficient single-photon detectors. Transduction from microwave to optical frequencies is therefore a potential enabling technology for quantum devices. However, in such a device the optical pump can be a source of thermal noise and thus degrade the fidelity; the similarity of input microwave state to the output optical state. In order to investigate the magnitude of this effect we model the sub-Kelvin thermal behavior of an electro-optic transducer based on a lithium niobate whispering gallery mode resonator. We find that there is an optimum power level for a continuous pump, whilst pulsed operation of the pump increases the fidelity of the conversion.","lang":"eng"}],"type":"journal_article"},{"_id":"9978","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Sharp kinetic acceleration potentials during mediated redox catalysis of insulators","ddc":["541"],"status":"public","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":1019662,"access_level":"open_access","file_name":"2021_ResearchSquare_Cao.pdf","success":1,"checksum":"1878e91c29d5769ed5a827b0b7addf00","date_created":"2021-08-31T14:02:19Z","date_updated":"2021-08-31T14:02:19Z","file_id":"9979","relation":"main_file"}],"oa_version":"Preprint","type":"preprint","abstract":[{"lang":"eng","text":"Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li-S and Li-O 2 batteries by shuttling electrons/holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics yet the lowest possible overpotential. Here, we found that when the redox potentials of mediators are tuned via, e.g., Li + concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediators and electrolyte. The acceleration originates from the overpotentials required to activate fast Li + /e – extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids requires therefore carefully considering the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents."}],"citation":{"ama":"Cao D, Shen X, Wang A, et al. Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square. doi:10.21203/rs.3.rs-750965/v1","ista":"Cao D, Shen X, Wang A, Yu F, Wu Y, Shi S, Freunberger SA, Chen Y. Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square, 10.21203/rs.3.rs-750965/v1.","ieee":"D. Cao et al., “Sharp kinetic acceleration potentials during mediated redox catalysis of insulators,” Research Square. Research Square.","apa":"Cao, D., Shen, X., Wang, A., Yu, F., Wu, Y., Shi, S., … Chen, Y. (n.d.). Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square. Research Square. https://doi.org/10.21203/rs.3.rs-750965/v1","mla":"Cao, Deqing, et al. “Sharp Kinetic Acceleration Potentials during Mediated Redox Catalysis of Insulators.” Research Square, Research Square, doi:10.21203/rs.3.rs-750965/v1.","short":"D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen, Research Square (n.d.).","chicago":"Cao, Deqing, Xiaoxiao Shen, Aiping Wang, Fengjiao Yu, Yuping Wu, Siqi Shi, Stefan Alexander Freunberger, and Yuhui Chen. “Sharp Kinetic Acceleration Potentials during Mediated Redox Catalysis of Insulators.” Research Square. Research Square, n.d. https://doi.org/10.21203/rs.3.rs-750965/v1."},"publication":"Research Square","page":"21","date_published":"2021-08-18T00:00:00Z","keyword":["Catalysis","Energy engineering","Materials theory and modeling"],"article_processing_charge":"No","has_accepted_license":"1","day":"18","year":"2021","acknowledgement":"This work was financially supported by the National Natural Science Foundation of China (51773092, 21975124, 11874254, 51802187, U2030206). S.A.F. is indebted to IST Austria for support. ","publisher":"Research Square","department":[{"_id":"StFr"}],"publication_status":"submitted","related_material":{"record":[{"status":"public","relation":"later_version","id":"10813"}]},"author":[{"full_name":"Cao, Deqing","first_name":"Deqing","last_name":"Cao"},{"full_name":"Shen, Xiaoxiao","last_name":"Shen","first_name":"Xiaoxiao"},{"full_name":"Wang, Aiping","last_name":"Wang","first_name":"Aiping"},{"full_name":"Yu, Fengjiao","first_name":"Fengjiao","last_name":"Yu"},{"full_name":"Wu, Yuping","last_name":"Wu","first_name":"Yuping"},{"full_name":"Shi, Siqi","first_name":"Siqi","last_name":"Shi"},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"},{"last_name":"Chen","first_name":"Yuhui","full_name":"Chen, Yuhui"}],"date_updated":"2023-10-17T13:06:29Z","date_created":"2021-08-31T12:54:16Z","file_date_updated":"2021-08-31T14:02:19Z","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,"doi":"10.21203/rs.3.rs-750965/v1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2693-5015"]},"month":"08"},{"oa_version":"Published Version","intvolume":" 41","status":"public","title":"Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8730","issue":"7","abstract":[{"text":"P-glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) restrict at the blood–brain barrier (BBB) the brain distribution of the majority of currently known molecularly targeted anticancer drugs. To improve brain delivery of dual ABCB1/ABCG2 substrates, both ABCB1 and ABCG2 need to be inhibited simultaneously at the BBB. We examined the feasibility of simultaneous ABCB1/ABCG2 inhibition with i.v. co-infusion of erlotinib and tariquidar by studying brain distribution of the model ABCB1/ABCG2 substrate [11C]erlotinib in mice and rhesus macaques with PET. Tolerability of the erlotinib/tariquidar combination was assessed in human embryonic stem cell-derived cerebral organoids. In mice and macaques, baseline brain distribution of [11C]erlotinib was low (brain distribution volume, VT,brain < 0.3 mL/cm3). Co-infusion of erlotinib and tariquidar increased VT,brain in mice by 3.0-fold and in macaques by 3.4- to 5.0-fold, while infusion of erlotinib alone or tariquidar alone led to less pronounced VT,brain increases in both species. Treatment of cerebral organoids with erlotinib/tariquidar led to an induction of Caspase-3-dependent apoptosis. Co-infusion of erlotinib/tariquidar may potentially allow for complete ABCB1/ABCG2 inhibition at the BBB, while simultaneously achieving brain-targeted EGFR inhibition. Our protocol may be applicable to enhance brain delivery of molecularly targeted anticancer drugs for a more effective treatment of brain tumors.","lang":"eng"}],"type":"journal_article","date_published":"2021-07-01T00:00:00Z","page":"1634-1646","article_type":"original","citation":{"ista":"Tournier N, Goutal S, Mairinger S, Lozano I, Filip T, Sauberer M, Caillé F, Breuil L, Stanek J, Freeman A, Novarino G, Truillet C, Wanek T, Langer O. 2021. Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal of Cerebral Blood Flow and Metabolism. 41(7), 1634–1646.","apa":"Tournier, N., Goutal, S., Mairinger, S., Lozano, I., Filip, T., Sauberer, M., … Langer, O. (2021). Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal of Cerebral Blood Flow and Metabolism. SAGE Publications. https://doi.org/10.1177/0271678X20965500","ieee":"N. Tournier et al., “Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib,” Journal of Cerebral Blood Flow and Metabolism, vol. 41, no. 7. SAGE Publications, pp. 1634–1646, 2021.","ama":"Tournier N, Goutal S, Mairinger S, et al. Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal of Cerebral Blood Flow and Metabolism. 2021;41(7):1634-1646. doi:10.1177/0271678X20965500","chicago":"Tournier, N, S Goutal, S Mairinger, IH Lozano, T Filip, M Sauberer, F Caillé, et al. “Complete Inhibition of ABCB1 and ABCG2 at the Blood-Brain Barrier by Co-Infusion of Erlotinib and Tariquidar to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Journal of Cerebral Blood Flow and Metabolism. SAGE Publications, 2021. https://doi.org/10.1177/0271678X20965500.","mla":"Tournier, N., et al. “Complete Inhibition of ABCB1 and ABCG2 at the Blood-Brain Barrier by Co-Infusion of Erlotinib and Tariquidar to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Journal of Cerebral Blood Flow and Metabolism, vol. 41, no. 7, SAGE Publications, 2021, pp. 1634–46, doi:10.1177/0271678X20965500.","short":"N. Tournier, S. Goutal, S. Mairinger, I. Lozano, T. Filip, M. Sauberer, F. Caillé, L. Breuil, J. Stanek, A. Freeman, G. Novarino, C. Truillet, T. Wanek, O. Langer, Journal of Cerebral Blood Flow and Metabolism 41 (2021) 1634–1646."},"publication":"Journal of Cerebral Blood Flow and Metabolism","article_processing_charge":"No","day":"01","scopus_import":"1","volume":41,"date_updated":"2023-10-18T06:45:30Z","date_created":"2020-11-06T08:39:01Z","author":[{"full_name":"Tournier, N","first_name":"N","last_name":"Tournier"},{"first_name":"S","last_name":"Goutal","full_name":"Goutal, S"},{"last_name":"Mairinger","first_name":"S","full_name":"Mairinger, S"},{"last_name":"Lozano","first_name":"IH","full_name":"Lozano, IH"},{"full_name":"Filip, T","last_name":"Filip","first_name":"T"},{"full_name":"Sauberer, M","first_name":"M","last_name":"Sauberer"},{"first_name":"F","last_name":"Caillé","full_name":"Caillé, F"},{"full_name":"Breuil, L","last_name":"Breuil","first_name":"L"},{"full_name":"Stanek, J","first_name":"J","last_name":"Stanek"},{"last_name":"Freeman","first_name":"AF","full_name":"Freeman, AF"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"},{"first_name":"C","last_name":"Truillet","full_name":"Truillet, C"},{"full_name":"Wanek, T","last_name":"Wanek","first_name":"T"},{"last_name":"Langer","first_name":"O","full_name":"Langer, O"}],"department":[{"_id":"GaNo"}],"publisher":"SAGE Publications","publication_status":"published","pmid":1,"year":"2021","language":[{"iso":"eng"}],"doi":"10.1177/0271678X20965500","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8221757/"}],"oa":1,"external_id":{"pmid":["33081568"],"isi":["000664214100012"]},"publication_identifier":{"issn":["0271-678x"],"eissn":["1559-7016"]},"month":"07"},{"language":[{"iso":"eng"}],"doi":"10.1111/evo.14215","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000647226400001"]},"oa":1,"month":"03","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"date_updated":"2023-10-18T08:16:01Z","date_created":"2021-05-09T22:01:39Z","volume":75,"author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","acknowledgement":"We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson, and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara, J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE (Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed the simulations and analyses presented in Box 3. We would also like to extend our thanks to everyone who took part in the speciation survey, which received ethical approval through the University of Sheffield Ethics Review Procedure (Application 029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout the writing of the manuscript and for feedback on an earlier draft.","year":"2021","file_date_updated":"2022-03-25T12:02:04Z","date_published":"2021-03-22T00:00:00Z","article_type":"original","page":"1256-1273","publication":"Evolution","citation":{"ama":"Stankowski S, Ravinet M. Defining the speciation continuum. Evolution. 2021;75(6):1256-1273. doi:10.1111/evo.14215","apa":"Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum. Evolution. Oxford University Press. https://doi.org/10.1111/evo.14215","ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” Evolution, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.","ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273.","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.","mla":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:10.1111/evo.14215.","chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215."},"day":"22","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2021_Evolution_Stankowski.pdf","access_level":"open_access","content_type":"application/pdf","file_size":719991,"creator":"kschuh","relation":"main_file","file_id":"10921","date_created":"2022-03-25T12:02:04Z","date_updated":"2022-03-25T12:02:04Z","checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6","success":1}],"status":"public","title":"Defining the speciation continuum","ddc":["570"],"intvolume":" 75","_id":"9383","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.","lang":"eng"}],"issue":"6","type":"journal_article"},{"ec_funded":1,"author":[{"last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"},{"full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","first_name":"Inge"},{"last_name":"Roosjen","first_name":"Mark","full_name":"Roosjen, Mark"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"first_name":"Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia"},{"full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chen, Jian","first_name":"Jian","last_name":"Chen"},{"first_name":"Lana","last_name":"Shabala","full_name":"Shabala, Lana"},{"full_name":"Smet, Wouter","first_name":"Wouter","last_name":"Smet"},{"last_name":"Ren","first_name":"Hong","full_name":"Ren, Hong"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Shabala, Sergey","first_name":"Sergey","last_name":"Shabala"},{"full_name":"De Rybel, Bert","last_name":"De Rybel","first_name":"Bert"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"full_name":"Kinoshita, Toshinori","first_name":"Toshinori","last_name":"Kinoshita"},{"last_name":"Gray","first_name":"William M.","full_name":"Gray, William M."},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10095"}],"link":[{"relation":"press_release","description":"News on IST Webpage","url":"https://ist.ac.at/en/news/stop-and-grow/"}]},"date_created":"2021-11-07T23:01:25Z","date_updated":"2023-10-18T08:30:53Z","volume":599,"year":"2021","acknowledgement":"We thank N. Gnyliukh and L. Hörmayer for technical assistance and N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R. and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship Council to J.C.","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"publisher":"Springer Nature","month":"11","publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"doi":"10.1038/s41586-021-04037-6","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000713338100006"],"pmid":["34707283"]},"main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3"}],"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"abstract":[{"text":"Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments.","lang":"eng"}],"issue":"7884","type":"journal_article","oa_version":"Preprint","_id":"10223","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Cell surface and intracellular auxin signalling for H+ fluxes in root growth","status":"public","intvolume":" 599","day":"11","article_processing_charge":"No","scopus_import":"1","keyword":["Multidisciplinary"],"date_published":"2021-11-11T00:00:00Z","publication":"Nature","citation":{"ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. 2021;599(7884):273-277. doi:10.1038/s41586-021-04037-6","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. 599(7884), 273–277.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-04037-6","ieee":"L. Li et al., “Cell surface and intracellular auxin signalling for H+ fluxes in root growth,” Nature, vol. 599, no. 7884. Springer Nature, pp. 273–277, 2021.","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+ Fluxes in Root Growth.” Nature, vol. 599, no. 7884, Springer Nature, 2021, pp. 273–77, doi:10.1038/s41586-021-04037-6.","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277.","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+ Fluxes in Root Growth.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-04037-6."},"article_type":"original","page":"273-277"},{"publication_identifier":{"eissn":["2296-634X"]},"month":"04","doi":"10.3389/fcell.2021.649433","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["33928084"],"isi":["000644419500001"]},"isi":1,"quality_controlled":"1","file_date_updated":"2021-05-11T15:09:23Z","article_number":"649433","author":[{"last_name":"Bolger-Munro","first_name":"Madison","orcid":"0000-0002-8176-4824","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","full_name":"Bolger-Munro, Madison"},{"first_name":"Kate","last_name":"Choi","full_name":"Choi, Kate"},{"first_name":"Faith","last_name":"Cheung","full_name":"Cheung, Faith"},{"full_name":"Liu, Yi Tian","last_name":"Liu","first_name":"Yi Tian"},{"full_name":"Dang-Lawson, May","last_name":"Dang-Lawson","first_name":"May"},{"full_name":"Deretic, Nikola","last_name":"Deretic","first_name":"Nikola"},{"full_name":"Keane, Connor","last_name":"Keane","first_name":"Connor"},{"last_name":"Gold","first_name":"Michael R.","full_name":"Gold, Michael R."}],"volume":9,"date_updated":"2023-10-18T08:19:49Z","date_created":"2021-05-09T22:01:37Z","pmid":1,"acknowledgement":"We thank the UBC Life Sciences Institute Imaging Facility andthe UBC Flow Cytometry Facility.","year":"2021","publisher":"Frontiers Media","department":[{"_id":"CaHe"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"13","scopus_import":"1","keyword":["B cell","actin","immune synapse","cell spreading","cofilin","WDR1 (AIP1)","LIM domain kinase","B cell receptor (BCR)"],"date_published":"2021-04-13T00:00:00Z","citation":{"ama":"Bolger-Munro M, Choi K, Cheung F, et al. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 2021;9. doi:10.3389/fcell.2021.649433","ieee":"M. Bolger-Munro et al., “The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse,” Frontiers in Cell and Developmental Biology, vol. 9. Frontiers Media, 2021.","apa":"Bolger-Munro, M., Choi, K., Cheung, F., Liu, Y. T., Dang-Lawson, M., Deretic, N., … Gold, M. R. (2021). The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. Frontiers Media. https://doi.org/10.3389/fcell.2021.649433","ista":"Bolger-Munro M, Choi K, Cheung F, Liu YT, Dang-Lawson M, Deretic N, Keane C, Gold MR. 2021. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 9, 649433.","short":"M. Bolger-Munro, K. Choi, F. Cheung, Y.T. Liu, M. Dang-Lawson, N. Deretic, C. Keane, M.R. Gold, Frontiers in Cell and Developmental Biology 9 (2021).","mla":"Bolger-Munro, Madison, et al. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” Frontiers in Cell and Developmental Biology, vol. 9, 649433, Frontiers Media, 2021, doi:10.3389/fcell.2021.649433.","chicago":"Bolger-Munro, Madison, Kate Choi, Faith Cheung, Yi Tian Liu, May Dang-Lawson, Nikola Deretic, Connor Keane, and Michael R. Gold. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” Frontiers in Cell and Developmental Biology. Frontiers Media, 2021. https://doi.org/10.3389/fcell.2021.649433."},"publication":"Frontiers in Cell and Developmental Biology","article_type":"original","abstract":[{"lang":"eng","text":"When B cells encounter membrane-bound antigens, the formation and coalescence of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability of B cells to probe the surface of antigen-presenting cells (APCs) and respond to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization, which drives B cell spreading as well as the centripetal movement and coalescence of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization depends on concomitant actin filament depolymerization, which enables the recycling of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments is a rate-limiting step in the morphological changes that occur during immune synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin and LIMK phosphorylates cofilin and prevents it from binding to actin filaments. We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of the peripheral actin structures that drive B cell spreading, and that cofilin, Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus, the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for B cell responses to APC-bound antigens."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"9386","date_updated":"2021-05-11T15:09:23Z","date_created":"2021-05-11T15:09:23Z","checksum":"8c8a03575d2f7583f88dc3b658b0976b","success":1,"file_name":"2021_Frontiers_Cell_Bolger-Munro.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4076024,"creator":"kschuh"}],"oa_version":"Published Version","_id":"9379","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 9","title":"The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse","ddc":["570"],"status":"public"},{"pmid":1,"acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","year":"2021","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published","author":[{"full_name":"Chalk, Matthew J","last_name":"Chalk","first_name":"Matthew J","orcid":"0000-0001-7782-4436","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"}],"volume":16,"date_updated":"2023-10-18T08:17:42Z","date_created":"2021-05-02T22:01:28Z","article_number":"e0248940","file_date_updated":"2021-05-04T13:22:19Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["33857170"],"isi":["000641474900072"]},"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pone.0248940","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["19326203"]},"month":"04","_id":"9362","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 16","ddc":["570"],"title":"Inferring the function performed by a recurrent neural network","status":"public","file":[{"file_id":"9371","relation":"main_file","success":1,"checksum":"c52da133850307d2031f552d998f00e8","date_updated":"2021-05-04T13:22:19Z","date_created":"2021-05-04T13:22:19Z","access_level":"open_access","file_name":"2021_pone_Chalk.pdf","creator":"kschuh","content_type":"application/pdf","file_size":2768282}],"oa_version":"Published Version","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics."}],"citation":{"ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940.","ieee":"M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” PLoS ONE, vol. 16, no. 4. Public Library of Science, 2021.","apa":"Chalk, M. J., Tkačik, G., & Marre, O. (2021). Inferring the function performed by a recurrent neural network. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0248940","ama":"Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. PLoS ONE. 2021;16(4). doi:10.1371/journal.pone.0248940","chicago":"Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0248940.","mla":"Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:10.1371/journal.pone.0248940.","short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021)."},"publication":"PLoS ONE","article_type":"original","date_published":"2021-04-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"15"},{"date_published":"2021-08-26T00:00:00Z","publication":"International Journal of Molecular Sciences","citation":{"short":"S.M. Velasquez, X. Guo, M. Gallemi, B. Aryal, P. Venhuizen, E. Barbez, K.A. Dünser, M. Darino, A. Pӗnčík, O. Novák, M. Kalyna, G. Mouille, E. Benková, R.P. Bhalerao, J. Mravec, J. Kleine-Vehn, International Journal of Molecular Sciences 22 (2021).","mla":"Velasquez, Silvia Melina, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” International Journal of Molecular Sciences, vol. 22, no. 17, 9222, MDPI, 2021, doi:10.3390/ijms22179222.","chicago":"Velasquez, Silvia Melina, Xiaoyuan Guo, Marçal Gallemi, Bibek Aryal, Peter Venhuizen, Elke Barbez, Kai Alexander Dünser, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22179222.","ama":"Velasquez SM, Guo X, Gallemi M, et al. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 2021;22(17). doi:10.3390/ijms22179222","ieee":"S. M. Velasquez et al., “Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants,” International Journal of Molecular Sciences, vol. 22, no. 17. MDPI, 2021.","apa":"Velasquez, S. M., Guo, X., Gallemi, M., Aryal, B., Venhuizen, P., Barbez, E., … Kleine-Vehn, J. (2021). Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22179222","ista":"Velasquez SM, Guo X, Gallemi M, Aryal B, Venhuizen P, Barbez E, Dünser KA, Darino M, Pӗnčík A, Novák O, Kalyna M, Mouille G, Benková E, Bhalerao RP, Mravec J, Kleine-Vehn J. 2021. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 22(17), 9222."},"article_type":"original","day":"26","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","keyword":["auxin","growth","cell wall","xyloglucans","hypocotyls","gravitropism"],"file":[{"file_name":"2021_IntJMolecularSciences_Velasquez.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2162247,"creator":"cchlebak","relation":"main_file","file_id":"9988","date_created":"2021-09-06T12:50:19Z","date_updated":"2021-09-07T09:04:53Z","checksum":"6b7055cf89f1b7ed8594c3fdf56f000b"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9986","status":"public","title":"Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants","ddc":["575"],"intvolume":" 22","abstract":[{"text":"Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan’s molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth.","lang":"eng"}],"issue":"17","type":"journal_article","doi":"10.3390/ijms22179222","language":[{"iso":"eng"}],"external_id":{"isi":["000694347100001"],"pmid":["34502129"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"month":"08","publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"author":[{"first_name":"Silvia Melina","last_name":"Velasquez","full_name":"Velasquez, Silvia Melina"},{"first_name":"Xiaoyuan","last_name":"Guo","full_name":"Guo, Xiaoyuan"},{"id":"460C6802-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4675-6893","first_name":"Marçal","last_name":"Gallemi","full_name":"Gallemi, Marçal"},{"first_name":"Bibek","last_name":"Aryal","full_name":"Aryal, Bibek"},{"last_name":"Venhuizen","first_name":"Peter","full_name":"Venhuizen, Peter"},{"last_name":"Barbez","first_name":"Elke","full_name":"Barbez, Elke"},{"last_name":"Dünser","first_name":"Kai Alexander","full_name":"Dünser, Kai Alexander"},{"first_name":"Martin","last_name":"Darino","full_name":"Darino, Martin"},{"full_name":"Pӗnčík, Aleš","first_name":"Aleš","last_name":"Pӗnčík"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"last_name":"Kalyna","first_name":"Maria","full_name":"Kalyna, Maria"},{"full_name":"Mouille, Gregory","last_name":"Mouille","first_name":"Gregory"},{"full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"full_name":"Bhalerao, Rishikesh P.","first_name":"Rishikesh P.","last_name":"Bhalerao"},{"full_name":"Mravec, Jozef","first_name":"Jozef","last_name":"Mravec"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine-Vehn","first_name":"Jürgen"}],"date_created":"2021-09-05T22:01:24Z","date_updated":"2023-10-31T19:29:38Z","volume":22,"year":"2021","acknowledgement":"We are grateful to Paul Knox, Markus Pauly, Malcom O’Neill, and Ignacio Zarra for providing published material; the BOKU-VIBT Imaging Center for access and M. Debreczeny for expertise; J.I. Thaker and Georg Seifert for critical reading.\r\n","pmid":1,"publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"MDPI","file_date_updated":"2021-09-07T09:04:53Z","article_number":"9222"},{"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2021-06-01T00:00:00Z","article_type":"original","page":"1846-1857","publication":"Plant, Cell & Environment","citation":{"short":"Y. Zhao, L. Wu, Q. Fu, D. Wang, J. Li, B. Yao, S. Yu, L. Jiang, J. Qian, X. Zhou, L. Han, S. Zhao, C. Ma, Y. Zhang, C. Luo, Q. Dong, S. Li, L. Zhang, X. Jiang, Y. Li, H. Luo, K. Li, J. Yang, Q. Luo, L. Li, S. Peng, H. Huang, Z. Zuo, C. Liu, L. Wang, C. Li, X. He, J. Friml, Y. Du, Plant, Cell & Environment 44 (2021) 1846–1857.","mla":"Zhao, Y., et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant, Cell & Environment, vol. 44, no. 6, Wiley, 2021, pp. 1846–57, doi:10.1111/pce.14029.","chicago":"Zhao, Y, L Wu, Q Fu, D Wang, J Li, B Yao, S Yu, et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant, Cell & Environment. Wiley, 2021. https://doi.org/10.1111/pce.14029.","ama":"Zhao Y, Wu L, Fu Q, et al. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. 2021;44(6):1846-1857. doi:10.1111/pce.14029","apa":"Zhao, Y., Wu, L., Fu, Q., Wang, D., Li, J., Yao, B., … Du, Y. (2021). INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. Wiley. https://doi.org/10.1111/pce.14029","ieee":"Y. Zhao et al., “INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance,” Plant, Cell & Environment, vol. 44, no. 6. Wiley, pp. 1846–1857, 2021.","ista":"Zhao Y, Wu L, Fu Q, Wang D, Li J, Yao B, Yu S, Jiang L, Qian J, Zhou X, Han L, Zhao S, Ma C, Zhang Y, Luo C, Dong Q, Li S, Zhang L, Jiang X, Li Y, Luo H, Li K, Yang J, Luo Q, Li L, Peng S, Huang H, Zuo Z, Liu C, Wang L, Li C, He X, Friml J, Du Y. 2021. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. 44(6), 1846–1857."},"abstract":[{"lang":"eng","text":"Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin‐responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin‐responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses."}],"issue":"6","type":"journal_article","file":[{"checksum":"a812418fede076741c9c4dc07f317068","success":1,"date_updated":"2023-11-02T17:02:11Z","date_created":"2023-11-02T17:02:11Z","relation":"main_file","file_id":"14481","file_size":8437528,"content_type":"application/pdf","creator":"amally","access_level":"open_access","file_name":"Zhao PlantCellEnv 2021_accepted.pdf"}],"oa_version":"Submitted Version","ddc":["580"],"status":"public","title":"INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance","intvolume":" 44","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9189","month":"06","publication_identifier":{"eissn":["1365-3040"],"issn":["0140-7791"]},"language":[{"iso":"eng"}],"doi":"10.1111/pce.14029","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000625398600001"],"pmid":["33576018"]},"file_date_updated":"2023-11-02T17:02:11Z","date_updated":"2023-11-07T08:18:36Z","date_created":"2021-02-24T10:07:21Z","volume":44,"author":[{"full_name":"Zhao, Y","last_name":"Zhao","first_name":"Y"},{"first_name":"L","last_name":"Wu","full_name":"Wu, L"},{"full_name":"Fu, Q","first_name":"Q","last_name":"Fu"},{"last_name":"Wang","first_name":"D","full_name":"Wang, D"},{"last_name":"Li","first_name":"J","full_name":"Li, J"},{"last_name":"Yao","first_name":"B","full_name":"Yao, B"},{"last_name":"Yu","first_name":"S","full_name":"Yu, S"},{"full_name":"Jiang, L","last_name":"Jiang","first_name":"L"},{"full_name":"Qian, J","last_name":"Qian","first_name":"J"},{"first_name":"X","last_name":"Zhou","full_name":"Zhou, X"},{"first_name":"L","last_name":"Han","full_name":"Han, L"},{"full_name":"Zhao, S","last_name":"Zhao","first_name":"S"},{"full_name":"Ma, C","first_name":"C","last_name":"Ma"},{"first_name":"Y","last_name":"Zhang","full_name":"Zhang, Y"},{"first_name":"C","last_name":"Luo","full_name":"Luo, C"},{"full_name":"Dong, Q","last_name":"Dong","first_name":"Q"},{"first_name":"S","last_name":"Li","full_name":"Li, S"},{"full_name":"Zhang, L","last_name":"Zhang","first_name":"L"},{"full_name":"Jiang, X","first_name":"X","last_name":"Jiang"},{"full_name":"Li, Y","last_name":"Li","first_name":"Y"},{"full_name":"Luo, H","last_name":"Luo","first_name":"H"},{"full_name":"Li, K","first_name":"K","last_name":"Li"},{"full_name":"Yang, J","first_name":"J","last_name":"Yang"},{"full_name":"Luo, Q","last_name":"Luo","first_name":"Q"},{"first_name":"L","last_name":"Li","full_name":"Li, L"},{"full_name":"Peng, S","first_name":"S","last_name":"Peng"},{"first_name":"H","last_name":"Huang","full_name":"Huang, H"},{"last_name":"Zuo","first_name":"Z","full_name":"Zuo, Z"},{"first_name":"C","last_name":"Liu","full_name":"Liu, C"},{"first_name":"L","last_name":"Wang","full_name":"Wang, L"},{"first_name":"C","last_name":"Li","full_name":"Li, C"},{"first_name":"X","last_name":"He","full_name":"He, X"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Du, Y","last_name":"Du","first_name":"Y"}],"publication_status":"published","publisher":"Wiley","department":[{"_id":"JiFr"}],"year":"2021","pmid":1},{"article_processing_charge":"No","has_accepted_license":"1","day":"21","citation":{"mla":"Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” ArXiv, 2106.11217, doi:10.48550/arXiv.2106.11217.","short":"D. Feliciangeli, A. Gerolin, L. Portinale, ArXiv (n.d.).","chicago":"Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2106.11217.","ama":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv. doi:10.48550/arXiv.2106.11217","ista":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv, 2106.11217.","ieee":"D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” arXiv. .","apa":"Feliciangeli, D., Gerolin, A., & Portinale, L. (n.d.). A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv. https://doi.org/10.48550/arXiv.2106.11217"},"publication":"arXiv","date_published":"2021-07-21T00:00:00Z","type":"preprint","abstract":[{"lang":"eng","text":"This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on careful a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem."}],"title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","status":"public","ddc":["510"],"_id":"9792","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"07","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"external_id":{"arxiv":["2106.11217"]},"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/10.48550/arXiv.2106.11217","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.48550/arXiv.2106.11217","article_number":"2106.11217","ec_funded":1,"department":[{"_id":"RoSe"},{"_id":"JaMa"}],"publication_status":"submitted","acknowledgement":"This work started when A.G. was visiting the Erwin Schrödinger Institute and then continued when D.F. and L.P visited the Theoretical Chemistry Department of the Vrije Universiteit Amsterdam. The authors thanks the hospitality of both places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature suggestions in the early state of the project. Finally, the authors also thanks J. Maas and R. Seiringer for their feedback and useful comments to a first draft of the article. L.P. acknowledges support by the Austrian Science Fund (FWF), grants No W1245 and NoF65. D.F acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 716117 and No 694227). A.G. acknowledges funding by the European Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942].","year":"2021","date_created":"2021-08-06T09:07:12Z","date_updated":"2023-11-14T13:21:01Z","related_material":{"record":[{"id":"9733","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"10030"},{"id":"12911","status":"public","relation":"later_version"}]},"author":[{"last_name":"Feliciangeli","first_name":"Dario","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","full_name":"Feliciangeli, Dario"},{"full_name":"Gerolin, Augusto","last_name":"Gerolin","first_name":"Augusto"},{"first_name":"Lorenzo","last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo"}]},{"volume":23,"date_created":"2022-01-23T23:01:28Z","date_updated":"2023-11-16T13:12:03Z","author":[{"full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085","first_name":"Margaret E","last_name":"Maes"},{"first_name":"Gabriele M.","last_name":"Wögenstein","full_name":"Wögenstein, Gabriele M."},{"full_name":"Colombo, Gloria","last_name":"Colombo","first_name":"Gloria","orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Casado Polanco, Raquel","id":"15240fc1-dbcd-11ea-9d1d-ac5a786425fd","orcid":"0000-0001-8293-4568","first_name":"Raquel","last_name":"Casado Polanco"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","first_name":"Sandra","last_name":"Siegert","full_name":"Siegert, Sandra"}],"publisher":"Elsevier","department":[{"_id":"SaSi"},{"_id":"SiHi"}],"publication_status":"published","year":"2021","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. 715571). The research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility, the Life Science Facility, and the Pre-Clinical Facility, namely Sonja Haslinger and Michael Schunn for their animal colony management and support. We would also like to thank Chakrabarty Lab for sharing the plasmids for AAV2/6 production. Finally, we would like to thank the Siegert team members for discussion about the manuscript.","ec_funded":1,"file_date_updated":"2022-01-24T07:43:09Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"doi":"10.1016/j.omtm.2021.09.006","project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000748748500019"]},"oa":1,"publication_identifier":{"eissn":["2329-0501"]},"month":"12","file":[{"relation":"main_file","file_id":"10657","checksum":"77dc540e8011c5475031bdf6ccef20a6","success":1,"date_created":"2022-01-24T07:43:09Z","date_updated":"2022-01-24T07:43:09Z","access_level":"open_access","file_name":"2021_MolTherMethodsClinDev_Maes.pdf","content_type":"application/pdf","file_size":4794147,"creator":"cchlebak"}],"oa_version":"Published Version","intvolume":" 23","ddc":["570"],"title":"Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment","status":"public","_id":"10655","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Adeno-associated viruses (AAVs) are widely used to deliver genetic material in vivo to distinct cell types such as neurons or glial cells, allowing for targeted manipulation. Transduction of microglia is mostly excluded from this strategy, likely due to the cells’ heterogeneous state upon environmental changes, which makes AAV design challenging. Here, we established the retina as a model system for microglial AAV validation and optimization. First, we show that AAV2/6 transduced microglia in both synaptic layers, where layer preference corresponds to the intravitreal or subretinal delivery method. Surprisingly, we observed significantly enhanced microglial transduction during photoreceptor degeneration. Thus, we modified the AAV6 capsid to reduce heparin binding by introducing four point mutations (K531E, R576Q, K493S, and K459S), resulting in increased microglial transduction in the outer plexiform layer. Finally, to improve microglial-specific transduction, we validated a Cre-dependent transgene delivery cassette for use in combination with the Cx3cr1CreERT2 mouse line. Together, our results provide a foundation for future studies optimizing AAV-mediated microglia transduction and highlight that environmental conditions influence microglial transduction efficiency.\r\n"}],"type":"journal_article","date_published":"2021-12-10T00:00:00Z","page":"210-224","article_type":"original","citation":{"ista":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. 2021. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 23, 210–224.","ieee":"M. E. Maes, G. M. Wögenstein, G. Colombo, R. Casado Polanco, and S. Siegert, “Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment,” Molecular Therapy - Methods and Clinical Development, vol. 23. Elsevier, pp. 210–224, 2021.","apa":"Maes, M. E., Wögenstein, G. M., Colombo, G., Casado Polanco, R., & Siegert, S. (2021). Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. Elsevier. https://doi.org/10.1016/j.omtm.2021.09.006","ama":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 2021;23:210-224. doi:10.1016/j.omtm.2021.09.006","chicago":"Maes, Margaret E, Gabriele M. Wögenstein, Gloria Colombo, Raquel Casado Polanco, and Sandra Siegert. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular Therapy - Methods and Clinical Development. Elsevier, 2021. https://doi.org/10.1016/j.omtm.2021.09.006.","mla":"Maes, Margaret E., et al. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular Therapy - Methods and Clinical Development, vol. 23, Elsevier, 2021, pp. 210–24, doi:10.1016/j.omtm.2021.09.006.","short":"M.E. Maes, G.M. Wögenstein, G. Colombo, R. Casado Polanco, S. Siegert, Molecular Therapy - Methods and Clinical Development 23 (2021) 210–224."},"publication":"Molecular Therapy - Methods and Clinical Development","article_processing_charge":"Yes","has_accepted_license":"1","day":"10","scopus_import":"1"},{"publication_status":"published","department":[{"_id":"SaSi"}],"publisher":"Elsevier ; Cell Press","year":"2021","acknowledgement":"This research was supported by the European Research Council (grant 715571 to S.S.). We thank Rouven Schulz, Michael Schunn, Claudia Gold, Gabriel Krens, Sarah Gorkiewicz, Margaret Maes, Jürgen Siegert, Marco Benevento, and Sara Oakeley for comments on the manuscript and the IST Austria Bioimaging Facility for the technical support.","date_updated":"2023-11-16T13:11:04Z","date_created":"2021-12-19T23:01:32Z","volume":2,"author":[{"last_name":"Venturino","first_name":"Alessandro","orcid":"0000-0003-2356-9403","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro"},{"last_name":"Siegert","first_name":"Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra"}],"article_number":"101012","file_date_updated":"2021-12-20T08:58:40Z","ec_funded":1,"quality_controlled":"1","project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"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"},"acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.xpro.2021.101012","month":"12","publication_identifier":{"eissn":["2666-1667"]},"status":"public","ddc":["573"],"title":"Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain","intvolume":" 2","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"10565","file":[{"access_level":"open_access","file_name":"2021_STARProt_Venturino.pdf","file_size":6207060,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"10570","checksum":"9ea2501056c5df99e84726b845e9b976","success":1,"date_updated":"2021-12-20T08:58:40Z","date_created":"2021-12-20T08:58:40Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Enzymatic digestion of the extracellular matrix with chondroitinase-ABC reinstates juvenile-like plasticity in the adult cortex as it also disassembles the perineuronal nets (PNNs). The disadvantage of the enzyme is that it must be applied intracerebrally and it degrades the ECM for several weeks. Here, we provide two minimally invasive and transient protocols for microglia-enabled PNN disassembly in mouse cortex: repeated treatment with ketamine-xylazine-acepromazine (KXA) anesthesia and 60-Hz light entrainment. We also discuss how to analyze PNNs within microglial endosomes-lysosomes. For complete details on the use and execution of this protocol, please refer to Venturino et al. (2021)."}],"issue":"4","article_type":"original","publication":"STAR Protocols","citation":{"ama":"Venturino A, Siegert S. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2021;2(4). doi:10.1016/j.xpro.2021.101012","ieee":"A. Venturino and S. Siegert, “Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain,” STAR Protocols, vol. 2, no. 4. Elsevier ; Cell Press, 2021.","apa":"Venturino, A., & Siegert, S. (2021). Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. Elsevier ; Cell Press. https://doi.org/10.1016/j.xpro.2021.101012","ista":"Venturino A, Siegert S. 2021. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2(4), 101012.","short":"A. Venturino, S. Siegert, STAR Protocols 2 (2021).","mla":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” STAR Protocols, vol. 2, no. 4, 101012, Elsevier ; Cell Press, 2021, doi:10.1016/j.xpro.2021.101012.","chicago":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” STAR Protocols. Elsevier ; Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.101012."},"date_published":"2021-12-17T00:00:00Z","scopus_import":"1","day":"17","article_processing_charge":"Yes","has_accepted_license":"1"},{"volume":2,"date_created":"2021-11-21T23:01:28Z","date_updated":"2023-11-16T13:08:03Z","author":[{"full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon"}],"publisher":"Cell Press","department":[{"_id":"SiHi"}],"publication_status":"published","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). We particularly thank Mohammad Goudarzi for assistance with photography of mouse perfusion and dissection. N.A. received support from FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria 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 agreement no. 725780 LinPro) to S.H.","year":"2021","ec_funded":1,"file_date_updated":"2021-11-22T08:23:58Z","article_number":"100939","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"doi":"10.1016/j.xpro.2021.100939","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF"},{"name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805","_id":"059F6AB4-7A3F-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"},"publication_identifier":{"eissn":["2666-1667"]},"month":"11","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":7309464,"creator":"cchlebak","file_name":"2021_STARProtocols_Amberg.pdf","access_level":"open_access","date_updated":"2021-11-22T08:23:58Z","date_created":"2021-11-22T08:23:58Z","checksum":"9e3f6d06bf583e7a8b6a9e9a60500a28","success":1,"relation":"main_file","file_id":"10329"}],"intvolume":" 2","title":"Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers","status":"public","ddc":["573"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"10321","issue":"4","abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice. MADM enables concomitant fluorescent cell labeling and introduction of a mutation of a gene of interest with single-cell resolution. This protocol highlights major steps for the generation of genetic mosaic tissue and the isolation and processing of respective tissues for downstream histological analysis. For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).","lang":"eng"}],"type":"journal_article","date_published":"2021-11-10T00:00:00Z","article_type":"original","citation":{"ieee":"N. Amberg and S. Hippenmeyer, “Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers,” STAR Protocols, vol. 2, no. 4. Cell Press, 2021.","apa":"Amberg, N., & Hippenmeyer, S. (2021). Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. Cell Press. https://doi.org/10.1016/j.xpro.2021.100939","ista":"Amberg N, Hippenmeyer S. 2021. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2(4), 100939.","ama":"Amberg N, Hippenmeyer S. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2021;2(4). doi:10.1016/j.xpro.2021.100939","chicago":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols. Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.100939.","short":"N. Amberg, S. Hippenmeyer, STAR Protocols 2 (2021).","mla":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols, vol. 2, no. 4, 100939, Cell Press, 2021, doi:10.1016/j.xpro.2021.100939."},"publication":"STAR Protocols","has_accepted_license":"1","article_processing_charge":"Yes","day":"10","scopus_import":"1"},{"publication_identifier":{"issn":["1047-8477"]},"month":"11","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":["000720259500002"]},"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"},{"_id":"2674F658-B435-11E9-9278-68D0E5697425","grant_number":"M02495","name":"Protein structure and function in filopodia across scales","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.jsb.2021.107808","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"article_number":"107808","file_date_updated":"2021-11-15T13:11:27Z","year":"2021","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data acquisition. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.","publisher":"Elsevier ","department":[{"_id":"FlSc"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"software","id":"14502"}]},"author":[{"full_name":"Dimchev, Georgi A","last_name":"Dimchev","first_name":"Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Amiri, Behnam","last_name":"Amiri","first_name":"Behnam"},{"full_name":"Fäßler, Florian","last_name":"Fäßler","first_name":"Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Falcke","first_name":"Martin","full_name":"Falcke, Martin"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM"}],"volume":213,"date_created":"2021-11-15T12:21:42Z","date_updated":"2023-11-21T08:36:02Z","scopus_import":"1","keyword":["Structural Biology"],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"03","citation":{"ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 2021;213(4). doi:10.1016/j.jsb.2021.107808","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. Elsevier . https://doi.org/10.1016/j.jsb.2021.107808","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” Journal of Structural Biology, vol. 213, no. 4. Elsevier , 2021.","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021).","mla":"Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology, vol. 213, no. 4, 107808, Elsevier , 2021, doi:10.1016/j.jsb.2021.107808.","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology. Elsevier , 2021. https://doi.org/10.1016/j.jsb.2021.107808."},"publication":"Journal of Structural Biology","article_type":"original","date_published":"2021-11-03T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10290","intvolume":" 213","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","ddc":["572"],"status":"public","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":16818304,"creator":"cchlebak","file_name":"2021_JournalStructBiol_Dimchev.pdf","access_level":"open_access","date_updated":"2021-11-15T13:11:27Z","date_created":"2021-11-15T13:11:27Z","checksum":"6b209e4d44775d4e02b50f78982c15fa","success":1,"relation":"main_file","file_id":"10291"}]},{"author":[{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Salem, Iosif","last_name":"Salem","first_name":"Iosif"},{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"},{"full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X","last_name":"Yeo"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14506"}]},"date_updated":"2023-11-30T10:54:50Z","date_created":"2021-08-29T22:01:16Z","year":"2021","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"IEEE","ec_funded":1,"conference":{"name":"2021 IFIP Networking Conference (IFIP Networking)","end_date":"2021-06-24","location":"Espoo and Helsinki, Finland","start_date":"2021-06-21"},"doi":"10.23919/IFIPNetworking52078.2021.9472205","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2104.04293","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2104.04293"],"isi":["000853016800008"]},"isi":1,"quality_controlled":"1","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"month":"06","publication_identifier":{"isbn":["978-1-6654-4501-6"],"eissn":["1861-2288"],"eisbn":["978-3-9031-7639-3"]},"oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9969","title":"LightPIR: Privacy-preserving route discovery for payment channel networks","status":"public","abstract":[{"lang":"eng","text":"Payment channel networks are a promising approach to improve the scalability of cryptocurrencies: they allow to perform transactions in a peer-to-peer fashion, along multihop routes in the network, without requiring consensus on the blockchain. However, during the discovery of cost-efficient routes for the transaction, critical information may be revealed about the transacting entities. This paper initiates the study of privacy-preserving route discovery mechanisms for payment channel networks. In particular, we present LightPIR, an approach which allows a client to learn the shortest (or cheapest in terms of fees) path between two nodes without revealing any information about the endpoints of the transaction to the servers. The two main observations which allow for an efficient solution in LightPIR are that: (1) surprisingly, hub labelling algorithms – which were developed to preprocess “street network like” graphs so one can later efficiently compute shortest paths – also perform well for the graphs underlying payment channel networks, and that (2) hub labelling algorithms can be conveniently combined with private information retrieval. LightPIR relies on a simple hub labeling heuristic on top of existing hub labeling algorithms which leverages the specific topological features of cryptocurrency networks to further minimize storage and bandwidth overheads. In a case study considering the Lightning network, we show that our approach is an order of magnitude more efficient compared to a privacy-preserving baseline based on using private information retrieval on a database that stores all pairs shortest paths."}],"type":"conference","date_published":"2021-06-21T00:00:00Z","citation":{"chicago":"Pietrzak, Krzysztof Z, Iosif Salem, Stefan Schmid, and Michelle X Yeo. “LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks.” IEEE, 2021. https://doi.org/10.23919/IFIPNetworking52078.2021.9472205.","mla":"Pietrzak, Krzysztof Z., et al. LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks. IEEE, 2021, doi:10.23919/IFIPNetworking52078.2021.9472205.","short":"K.Z. Pietrzak, I. Salem, S. Schmid, M.X. Yeo, in:, IEEE, 2021.","ista":"Pietrzak KZ, Salem I, Schmid S, Yeo MX. 2021. LightPIR: Privacy-preserving route discovery for payment channel networks. 2021 IFIP Networking Conference (IFIP Networking).","apa":"Pietrzak, K. Z., Salem, I., Schmid, S., & Yeo, M. X. (2021). LightPIR: Privacy-preserving route discovery for payment channel networks. Presented at the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland: IEEE. https://doi.org/10.23919/IFIPNetworking52078.2021.9472205","ieee":"K. Z. Pietrzak, I. Salem, S. Schmid, and M. X. Yeo, “LightPIR: Privacy-preserving route discovery for payment channel networks,” presented at the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland, 2021.","ama":"Pietrzak KZ, Salem I, Schmid S, Yeo MX. LightPIR: Privacy-preserving route discovery for payment channel networks. In: IEEE; 2021. doi:10.23919/IFIPNetworking52078.2021.9472205"},"day":"21","article_processing_charge":"No","scopus_import":"1"},{"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This research was partially supported by the ERCCoG 863818 (ForM-SMArt) and the Czech Science Foundation grant No. GJ19-15134Y.","year":"2021","date_updated":"2023-11-30T10:55:37Z","date_created":"2021-07-11T22:01:17Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Goharshady","first_name":"Ehsan Kafshdar","full_name":"Goharshady, Ehsan Kafshdar"},{"full_name":"Novotný, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotný"},{"first_name":"Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde"}],"related_material":{"record":[{"id":"14539","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"external_id":{"isi":["000723661700067"],"arxiv":["2104.01189"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.01189"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"Online","start_date":"2021-06-20","end_date":"2021-06-26","name":"PLDI: Programming Language Design and Implementation"},"doi":"10.1145/3453483.3454093","month":"06","publication_identifier":{"isbn":["9781450383912"]},"status":"public","title":"Proving non-termination by program reversal","_id":"9644","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"conference","abstract":[{"text":"We present a new approach to proving non-termination of non-deterministic integer programs. Our technique is rather simple but efficient. It relies on a purely syntactic reversal of the program's transition system followed by a constraint-based invariant synthesis with constraints coming from both the original and the reversed transition system. The latter task is performed by a simple call to an off-the-shelf SMT-solver, which allows us to leverage the latest advances in SMT-solving. Moreover, our method offers a combination of features not present (as a whole) in previous approaches: it handles programs with non-determinism, provides relative completeness guarantees and supports programs with polynomial arithmetic. The experiments performed with our prototype tool RevTerm show that our approach, despite its simplicity and stronger theoretical guarantees, is at least on par with the state-of-the-art tools, often achieving a non-trivial improvement under a proper configuration of its parameters.","lang":"eng"}],"page":"1033-1048","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","citation":{"chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, and Dorde Zikelic. “Proving Non-Termination by Program Reversal.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 1033–48. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454093.","short":"K. Chatterjee, E.K. Goharshady, P. Novotný, D. Zikelic, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1033–1048.","mla":"Chatterjee, Krishnendu, et al. “Proving Non-Termination by Program Reversal.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1033–48, doi:10.1145/3453483.3454093.","apa":"Chatterjee, K., Goharshady, E. K., Novotný, P., & Zikelic, D. (2021). Proving non-termination by program reversal. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 1033–1048). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454093","ieee":"K. Chatterjee, E. K. Goharshady, P. Novotný, and D. Zikelic, “Proving non-termination by program reversal,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 1033–1048.","ista":"Chatterjee K, Goharshady EK, Novotný P, Zikelic D. 2021. Proving non-termination by program reversal. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1033–1048.","ama":"Chatterjee K, Goharshady EK, Novotný P, Zikelic D. Proving non-termination by program reversal. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:1033-1048. doi:10.1145/3453483.3454093"},"date_published":"2021-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"publication_status":"published","acknowledgement":"We would like to thank D. Abanin and R. Medina for fruitful discussions and A. Smith and I. Kim for valuable feedback on the manuscript. We acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","year":"2021","volume":5,"date_created":"2021-08-01T22:01:21Z","date_updated":"2023-12-13T14:47:25Z","related_material":{"record":[{"id":"14622","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508","first_name":"Stefan","last_name":"Sack"},{"full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"article_number":"491","ec_funded":1,"file_date_updated":"2021-08-06T06:44:31Z","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2101.05742"],"isi":["000669830600001"]},"language":[{"iso":"eng"}],"doi":"10.22331/Q-2021-07-01-491","publication_identifier":{"eissn":["2521-327X"]},"month":"07","intvolume":" 5","ddc":["530"],"status":"public","title":"Quantum annealing initialization of the quantum approximate optimization algorithm","_id":"9760","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9774","date_updated":"2021-08-06T06:44:31Z","date_created":"2021-08-06T06:44:31Z","checksum":"9706c2bb8e748e9b5b138381995a7f6f","file_name":"2021_Quantum_Sack.pdf","access_level":"open_access","file_size":2312482,"content_type":"application/pdf","creator":"cchlebak"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) is a prospective near-term quantum algorithm due to its modest circuit depth and promising benchmarks. However, an external parameter optimization required in the QAOA could become a performance bottleneck. This motivates studies of the optimization landscape and search for heuristic ways of parameter initialization. In this work we visualize the optimization landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating that random initialization of the QAOA is prone to converging to local minima with suboptimal performance. We introduce the initialization of QAOA parameters based on the Trotterized quantum annealing (TQA) protocol, parameterized by the Trotter time step. We find that the TQA initialization allows to circumvent\r\nthe issue of false minima for a broad range of time steps, yielding the same performance as the best result out of an exponentially scaling number of random initializations. Moreover, we demonstrate that the optimal value of the time step coincides with the point of proliferation of Trotter errors in quantum annealing. Our results suggest practical ways of initializing QAOA protocols on near-term quantum devices and reveal new connections between QAOA and quantum annealing."}],"article_type":"original","citation":{"mla":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” Quantum, vol. 5, 491, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021, doi:10.22331/Q-2021-07-01-491.","short":"S. Sack, M. Serbyn, Quantum 5 (2021).","chicago":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021. https://doi.org/10.22331/Q-2021-07-01-491.","ama":"Sack S, Serbyn M. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 2021;5. doi:10.22331/Q-2021-07-01-491","ista":"Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 5, 491.","apa":"Sack, S., & Serbyn, M. (2021). Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. https://doi.org/10.22331/Q-2021-07-01-491","ieee":"S. Sack and M. Serbyn, “Quantum annealing initialization of the quantum approximate optimization algorithm,” Quantum, vol. 5. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021."},"publication":"Quantum","date_published":"2021-07-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"01"},{"ec_funded":1,"related_material":{"record":[{"id":"14539","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"later_version","id":"14778"}]},"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Goharshady","first_name":"Ehsan Kafshdar","full_name":"Goharshady, Ehsan Kafshdar"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotný","full_name":"Novotný, Petr"},{"full_name":"Zárevúcky, Jiří","last_name":"Zárevúcky","first_name":"Jiří"},{"full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde"}],"volume":13047,"date_updated":"2024-01-17T08:19:41Z","date_created":"2021-12-05T23:01:45Z","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the Czech Science Foundation grant No. GJ19-15134Y, and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","year":"2021","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["9-783-0309-0869-0"],"eisbn":["978-3-030-90870-6"],"issn":["0302-9743"]},"month":"11","doi":"10.1007/978-3-030-90870-6_33","conference":{"location":"Virtual","start_date":"2021-11-20","end_date":"2021-11-26","name":"FM: Formal Methods"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2108.02188"}],"external_id":{"arxiv":["2108.02188"],"isi":["000758218600033"]},"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"abstract":[{"text":"We consider the almost-sure (a.s.) termination problem for probabilistic programs, which are a stochastic extension of classical imperative programs. Lexicographic ranking functions provide a sound and practical approach for termination of non-probabilistic programs, and their extension to probabilistic programs is achieved via lexicographic ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous work have a limitation that impedes their automation: all of their components have to be non-negative in all reachable states. This might result in LexRSM not existing even for simple terminating programs. Our contributions are twofold: First, we introduce a generalization of LexRSMs which allows for some components to be negative. This standard feature of non-probabilistic termination proofs was hitherto not known to be sound in the probabilistic setting, as the soundness proof requires a careful analysis of the underlying stochastic process. Second, we present polynomial-time algorithms using our generalized LexRSMs for proving a.s. termination in broad classes of linear-arithmetic programs.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"10414","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13047","title":"On lexicographic proof rules for probabilistic termination","status":"public","article_processing_charge":"No","day":"10","scopus_import":"1","date_published":"2021-11-10T00:00:00Z","citation":{"ama":"Chatterjee K, Goharshady EK, Novotný P, Zárevúcky J, Zikelic D. On lexicographic proof rules for probabilistic termination. In: 24th International Symposium on Formal Methods. Vol 13047. Springer Nature; 2021:619-639. doi:10.1007/978-3-030-90870-6_33","ieee":"K. Chatterjee, E. K. Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic, “On lexicographic proof rules for probabilistic termination,” in 24th International Symposium on Formal Methods, Virtual, 2021, vol. 13047, pp. 619–639.","apa":"Chatterjee, K., Goharshady, E. K., Novotný, P., Zárevúcky, J., & Zikelic, D. (2021). On lexicographic proof rules for probabilistic termination. In 24th International Symposium on Formal Methods (Vol. 13047, pp. 619–639). Virtual: Springer Nature. https://doi.org/10.1007/978-3-030-90870-6_33","ista":"Chatterjee K, Goharshady EK, Novotný P, Zárevúcky J, Zikelic D. 2021. On lexicographic proof rules for probabilistic termination. 24th International Symposium on Formal Methods. FM: Formal Methods, LNCS, vol. 13047, 619–639.","short":"K. Chatterjee, E.K. Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, in:, 24th International Symposium on Formal Methods, Springer Nature, 2021, pp. 619–639.","mla":"Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic Termination.” 24th International Symposium on Formal Methods, vol. 13047, Springer Nature, 2021, pp. 619–39, doi:10.1007/978-3-030-90870-6_33.","chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, Jiří Zárevúcky, and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.” In 24th International Symposium on Formal Methods, 13047:619–39. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90870-6_33."},"publication":"24th International Symposium on Formal Methods","page":"619-639"},{"year":"2021","department":[{"_id":"MaIb"}],"publisher":"Peking University","publication_status":"published","author":[{"full_name":"Chang, Cheng","last_name":"Chang","first_name":"Cheng","orcid":"0000-0002-9515-4277","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"full_name":"Chen, Wei","last_name":"Chen","first_name":"Wei"},{"last_name":"Chen","first_name":"Ye","full_name":"Chen, Ye"},{"first_name":"Yonghua","last_name":"Chen","full_name":"Chen, Yonghua"},{"first_name":"Yu","last_name":"Chen","full_name":"Chen, Yu"},{"first_name":"Feng","last_name":"Ding","full_name":"Ding, Feng"},{"last_name":"Fan","first_name":"Chunhai","full_name":"Fan, Chunhai"},{"full_name":"Fan, Hong Jin","first_name":"Hong Jin","last_name":"Fan"},{"full_name":"Fan, Zhanxi","first_name":"Zhanxi","last_name":"Fan"},{"full_name":"Gong, Cheng","last_name":"Gong","first_name":"Cheng"},{"first_name":"Yongji","last_name":"Gong","full_name":"Gong, Yongji"},{"first_name":"Qiyuan","last_name":"He","full_name":"He, Qiyuan"},{"full_name":"Hong, Xun","first_name":"Xun","last_name":"Hong"},{"full_name":"Hu, Sheng","first_name":"Sheng","last_name":"Hu"},{"first_name":"Weida","last_name":"Hu","full_name":"Hu, Weida"},{"first_name":"Wei","last_name":"Huang","full_name":"Huang, Wei"},{"full_name":"Huang, Yuan","last_name":"Huang","first_name":"Yuan"},{"last_name":"Ji","first_name":"Wei","full_name":"Ji, Wei"},{"full_name":"Li, Dehui","first_name":"Dehui","last_name":"Li"},{"full_name":"Li, Lain Jong","first_name":"Lain Jong","last_name":"Li"},{"full_name":"Li, Qiang","first_name":"Qiang","last_name":"Li"},{"last_name":"Lin","first_name":"Li","full_name":"Lin, Li"},{"first_name":"Chongyi","last_name":"Ling","full_name":"Ling, Chongyi"},{"full_name":"Liu, Minghua","first_name":"Minghua","last_name":"Liu"},{"last_name":"Liu","first_name":"Nan","full_name":"Liu, Nan"},{"full_name":"Liu, Zhuang","last_name":"Liu","first_name":"Zhuang"},{"full_name":"Loh, Kian Ping","last_name":"Loh","first_name":"Kian Ping"},{"last_name":"Ma","first_name":"Jianmin","full_name":"Ma, Jianmin"},{"last_name":"Miao","first_name":"Feng","full_name":"Miao, Feng"},{"first_name":"Hailin","last_name":"Peng","full_name":"Peng, Hailin"},{"full_name":"Shao, Mingfei","last_name":"Shao","first_name":"Mingfei"},{"full_name":"Song, Li","last_name":"Song","first_name":"Li"},{"first_name":"Shao","last_name":"Su","full_name":"Su, Shao"},{"first_name":"Shuo","last_name":"Sun","full_name":"Sun, Shuo"},{"full_name":"Tan, Chaoliang","last_name":"Tan","first_name":"Chaoliang"},{"last_name":"Tang","first_name":"Zhiyong","full_name":"Tang, Zhiyong"},{"full_name":"Wang, Dingsheng","first_name":"Dingsheng","last_name":"Wang"},{"full_name":"Wang, Huan","last_name":"Wang","first_name":"Huan"},{"last_name":"Wang","first_name":"Jinlan","full_name":"Wang, Jinlan"},{"last_name":"Wang","first_name":"Xin","full_name":"Wang, Xin"},{"full_name":"Wang, Xinran","last_name":"Wang","first_name":"Xinran"},{"full_name":"Wee, Andrew T.S.","first_name":"Andrew T.S.","last_name":"Wee"},{"last_name":"Wei","first_name":"Zhongming","full_name":"Wei, Zhongming"},{"last_name":"Wu","first_name":"Yuen","full_name":"Wu, Yuen"},{"full_name":"Wu, Zhong Shuai","first_name":"Zhong Shuai","last_name":"Wu"},{"full_name":"Xiong, Jie","last_name":"Xiong","first_name":"Jie"},{"full_name":"Xiong, Qihua","last_name":"Xiong","first_name":"Qihua"},{"last_name":"Xu","first_name":"Weigao","full_name":"Xu, Weigao"},{"last_name":"Yin","first_name":"Peng","full_name":"Yin, Peng"},{"first_name":"Haibo","last_name":"Zeng","full_name":"Zeng, Haibo"},{"full_name":"Zeng, Zhiyuan","last_name":"Zeng","first_name":"Zhiyuan"},{"first_name":"Tianyou","last_name":"Zhai","full_name":"Zhai, Tianyou"},{"last_name":"Zhang","first_name":"Han","full_name":"Zhang, Han"},{"first_name":"Hui","last_name":"Zhang","full_name":"Zhang, Hui"},{"full_name":"Zhang, Qichun","first_name":"Qichun","last_name":"Zhang"},{"full_name":"Zhang, Tierui","first_name":"Tierui","last_name":"Zhang"},{"first_name":"Xiang","last_name":"Zhang","full_name":"Zhang, Xiang"},{"first_name":"Li Dong","last_name":"Zhao","full_name":"Zhao, Li Dong"},{"full_name":"Zhao, Meiting","first_name":"Meiting","last_name":"Zhao"},{"full_name":"Zhao, Weijie","last_name":"Zhao","first_name":"Weijie"},{"full_name":"Zhao, Yunxuan","first_name":"Yunxuan","last_name":"Zhao"},{"first_name":"Kai Ge","last_name":"Zhou","full_name":"Zhou, Kai Ge"},{"full_name":"Zhou, Xing","first_name":"Xing","last_name":"Zhou"},{"last_name":"Zhou","first_name":"Yu","full_name":"Zhou, Yu"},{"full_name":"Zhu, Hongwei","last_name":"Zhu","first_name":"Hongwei"},{"full_name":"Zhang, Hua","first_name":"Hua","last_name":"Zhang"},{"full_name":"Liu, Zhongfan","first_name":"Zhongfan","last_name":"Liu"}],"volume":37,"date_updated":"2024-01-17T11:29:33Z","date_created":"2024-01-14T23:00:58Z","article_number":"2108017","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3866/PKU.WHXB202108017"}],"oa":1,"quality_controlled":"1","doi":"10.3866/PKU.WHXB202108017","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1001-4861"]},"month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14800","intvolume":" 37","status":"public","title":"Recent progress on two-dimensional materials","oa_version":"Submitted Version","type":"journal_article","issue":"12","abstract":[{"lang":"eng","text":"Research on two-dimensional (2D) materials has been explosively increasing in last seventeen years in varying subjects including condensed matter physics, electronic engineering, materials science, and chemistry since the mechanical exfoliation of graphene in 2004. Starting from graphene, 2D materials now have become a big family with numerous members and diverse categories. The unique structural features and physicochemical properties of 2D materials make them one class of the most appealing candidates for a wide range of potential applications. In particular, we have seen some major breakthroughs made in the field of 2D materials in last five years not only in developing novel synthetic methods and exploring new structures/properties but also in identifying innovative applications and pushing forward commercialisation. In this review, we provide a critical summary on the recent progress made in the field of 2D materials with a particular focus on last five years. After a brief background introduction, we first discuss the major synthetic methods for 2D materials, including the mechanical exfoliation, liquid exfoliation, vapor phase deposition, and wet-chemical synthesis as well as phase engineering of 2D materials belonging to the field of phase engineering of nanomaterials (PEN). We then introduce the superconducting/optical/magnetic properties and chirality of 2D materials along with newly emerging magic angle 2D superlattices. Following that, the promising applications of 2D materials in electronics, optoelectronics, catalysis, energy storage, solar cells, biomedicine, sensors, environments, etc. are described sequentially. Thereafter, we present the theoretic calculations and simulations of 2D materials. Finally, after concluding the current progress, we provide some personal discussions on the existing challenges and future outlooks in this rapidly developing field. "}],"citation":{"ama":"Chang C, Chen W, Chen Y, et al. Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. 2021;37(12). doi:10.3866/PKU.WHXB202108017","ieee":"C. Chang et al., “Recent progress on two-dimensional materials,” Acta Physico-Chimica Sinica, vol. 37, no. 12. Peking University, 2021.","apa":"Chang, C., Chen, W., Chen, Y., Chen, Y., Chen, Y., Ding, F., … Liu, Z. (2021). Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. Peking University. https://doi.org/10.3866/PKU.WHXB202108017","ista":"Chang C, Chen W, Chen Y, Chen Y, Chen Y, Ding F, Fan C, Fan HJ, Fan Z, Gong C, Gong Y, He Q, Hong X, Hu S, Hu W, Huang W, Huang Y, Ji W, Li D, Li LJ, Li Q, Lin L, Ling C, Liu M, Liu N, Liu Z, Loh KP, Ma J, Miao F, Peng H, Shao M, Song L, Su S, Sun S, Tan C, Tang Z, Wang D, Wang H, Wang J, Wang X, Wang X, Wee ATS, Wei Z, Wu Y, Wu ZS, Xiong J, Xiong Q, Xu W, Yin P, Zeng H, Zeng Z, Zhai T, Zhang H, Zhang H, Zhang Q, Zhang T, Zhang X, Zhao LD, Zhao M, Zhao W, Zhao Y, Zhou KG, Zhou X, Zhou Y, Zhu H, Zhang H, Liu Z. 2021. Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. 37(12), 2108017.","short":"C. Chang, W. Chen, Y. Chen, Y. Chen, Y. Chen, F. Ding, C. Fan, H.J. Fan, Z. Fan, C. Gong, Y. Gong, Q. He, X. Hong, S. Hu, W. Hu, W. Huang, Y. Huang, W. Ji, D. Li, L.J. Li, Q. Li, L. Lin, C. Ling, M. Liu, N. Liu, Z. Liu, K.P. Loh, J. Ma, F. Miao, H. Peng, M. Shao, L. Song, S. Su, S. Sun, C. Tan, Z. Tang, D. Wang, H. Wang, J. Wang, X. Wang, X. Wang, A.T.S. Wee, Z. Wei, Y. Wu, Z.S. Wu, J. Xiong, Q. Xiong, W. Xu, P. Yin, H. Zeng, Z. Zeng, T. Zhai, H. Zhang, H. Zhang, Q. Zhang, T. Zhang, X. Zhang, L.D. Zhao, M. Zhao, W. Zhao, Y. Zhao, K.G. Zhou, X. Zhou, Y. Zhou, H. Zhu, H. Zhang, Z. Liu, Acta Physico-Chimica Sinica 37 (2021).","mla":"Chang, Cheng, et al. “Recent Progress on Two-Dimensional Materials.” Acta Physico-Chimica Sinica, vol. 37, no. 12, 2108017, Peking University, 2021, doi:10.3866/PKU.WHXB202108017.","chicago":"Chang, Cheng, Wei Chen, Ye Chen, Yonghua Chen, Yu Chen, Feng Ding, Chunhai Fan, et al. “Recent Progress on Two-Dimensional Materials.” Acta Physico-Chimica Sinica. Peking University, 2021. https://doi.org/10.3866/PKU.WHXB202108017."},"publication":"Acta Physico-Chimica Sinica","article_type":"review","date_published":"2021-10-13T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"13"},{"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","year":"2021","acknowledgement":"We thank Christoph Lampert and Alex Greengold for fruitful discussions. This research was supported in part by the Simons Institute for the Theory of Computing, the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","date_created":"2021-10-31T23:01:31Z","date_updated":"2024-01-30T12:06:56Z","volume":"12974 ","author":[{"full_name":"Lukina, Anna","last_name":"Lukina","first_name":"Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425"},{"full_name":"Schilling, Christian","first_name":"Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"related_material":{"record":[{"relation":"extended_version","status":"public","id":"13234"}]},"place":"Cham","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"external_id":{"arxiv":["2009.06429"],"isi":["000719383800003"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2009.06429","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2021-10-14","start_date":"2021-10-11","location":"Virtual","name":"RV: Runtime Verification"},"doi":"10.1007/978-3-030-88494-9_3","month":"10","publication_identifier":{"isbn":["9-783-0308-8493-2"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["978-3-030-88494-9"]},"status":"public","title":"Into the unknown: active monitoring of neural networks","_id":"10206","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. The typical approach is to detect inputs from novel classes and retrain the classifier on an augmented dataset. However, not only the classifier but also the detection mechanism needs to adapt in order to distinguish between newly learned and yet unknown input classes. To address this challenge, we introduce an algorithmic framework for active monitoring of a neural network. A monitor wrapped in our framework operates in parallel with the neural network and interacts with a human user via a series of interpretable labeling queries for incremental adaptation. In addition, we propose an adaptive quantitative monitor to improve precision. An experimental evaluation on a diverse set of benchmarks with varying numbers of classes confirms the benefits of our active monitoring framework in dynamic scenarios.","lang":"eng"}],"page":"42-61","publication":"21st International Conference on Runtime Verification","citation":{"chicago":"Lukina, Anna, Christian Schilling, and Thomas A Henzinger. “Into the Unknown: Active Monitoring of Neural Networks.” In 21st International Conference on Runtime Verification, 12974:42–61. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_3.","short":"A. Lukina, C. Schilling, T.A. Henzinger, in:, 21st International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 42–61.","mla":"Lukina, Anna, et al. “Into the Unknown: Active Monitoring of Neural Networks.” 21st International Conference on Runtime Verification, vol. 12974, Springer Nature, 2021, pp. 42–61, doi:10.1007/978-3-030-88494-9_3.","apa":"Lukina, A., Schilling, C., & Henzinger, T. A. (2021). Into the unknown: active monitoring of neural networks. In 21st International Conference on Runtime Verification (Vol. 12974, pp. 42–61). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-88494-9_3","ieee":"A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: active monitoring of neural networks,” in 21st International Conference on Runtime Verification, Virtual, 2021, vol. 12974, pp. 42–61.","ista":"Lukina A, Schilling C, Henzinger TA. 2021. Into the unknown: active monitoring of neural networks. 21st International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 42–61.","ama":"Lukina A, Schilling C, Henzinger TA. Into the unknown: active monitoring of neural networks. In: 21st International Conference on Runtime Verification. Vol 12974. Cham: Springer Nature; 2021:42-61. doi:10.1007/978-3-030-88494-9_3"},"date_published":"2021-10-06T00:00:00Z","keyword":["monitoring","neural networks","novelty detection"],"scopus_import":"1","day":"06","article_processing_charge":"No"}]