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Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.","mla":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing, vol. 69, Institute of Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:10.1109/TSP.2021.3087899.","chicago":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/TSP.2021.3087899."},"publication":"IEEE Transactions on Signal Processing","date_published":"2021-06-09T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Amplitude demodulation is a classical operation used in signal processing. For a long time, its effective applications in practice have been limited to narrowband signals. In this work, we generalize amplitude demodulation to wideband signals. We pose demodulation as a recovery problem of an oversampled corrupted signal and introduce special iterative schemes belonging to the family of alternating projection algorithms to solve it. Sensibly chosen structural assumptions on the demodulation outputs allow us to reveal the high inferential accuracy of the method over a rich set of relevant signals. This new approach surpasses current state-of-the-art demodulation techniques apt to wideband signals in computational efficiency by up to many orders of magnitude with no sacrifice in quality. Such performance opens the door for applications of the amplitude demodulation procedure in new contexts. In particular, the new method makes online and large-scale offline data processing feasible, including the calculation of modulator-carrier pairs in higher dimensions and poor sampling conditions, independent of the signal bandwidth. We illustrate the utility and specifics of applications of the new method in practice by using natural speech and synthetic signals."}],"intvolume":" 69","title":"Fast and accurate amplitude demodulation of wideband signals","status":"public","_id":"9828","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","publication_identifier":{"issn":["1053-587X"],"eissn":["1941-0476"]},"month":"06","quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["2102.04832"],"isi":["000682123900002"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.04832"}],"language":[{"iso":"eng"}],"doi":"10.1109/TSP.2021.3087899","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"GaTk"}],"publication_status":"published","year":"2021","acknowledgement":"The author thanks his colleagues K. Huszár and G. Tkačik for valuable discussions and comments on the manuscript.","volume":69,"date_updated":"2023-08-10T14:19:33Z","date_created":"2021-08-08T22:01:31Z","author":[{"first_name":"Mantas","last_name":"Gabrielaitis","id":"4D5B0CBC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7758-2016","full_name":"Gabrielaitis, Mantas"}]},{"doi":"10.15479/AT:ISTA:9327","date_published":"2021-05-01T00:00:00Z","citation":{"ama":"Sperl G, Narain R, Wojtan C. Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data). 2021. doi:10.15479/AT:ISTA:9327","ista":"Sperl G, Narain R, Wojtan C. 2021. Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data), IST Austria, 10.15479/AT:ISTA:9327.","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021.","apa":"Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data). IST Austria. https://doi.org/10.15479/AT:ISTA:9327","mla":"Sperl, Georg, et al. Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data). IST Austria, 2021, doi:10.15479/AT:ISTA:9327.","short":"G. Sperl, R. Narain, C. Wojtan, (2021).","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9327."},"tmp":{"name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT","short":"MIT"},"oa":1,"has_accepted_license":"1","month":"05","related_material":{"record":[{"status":"public","relation":"used_for_analysis_in","id":"9818"}]},"author":[{"full_name":"Sperl, Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Sperl"},{"full_name":"Narain, Rahul","first_name":"Rahul","last_name":"Narain"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan"}],"gitlab_url":"https://git.ist.ac.at/gsperl/MADYPG","file":[{"relation":"main_file","file_id":"9328","checksum":"0324cb519273371708743f3282e7c081","success":1,"date_updated":"2021-04-16T14:15:12Z","date_created":"2021-04-16T14:15:12Z","access_level":"open_access","file_name":"MADYPG_extra_data.zip","content_type":"application/zip","file_size":802586232,"creator":"gsperl"},{"file_name":"MADYPG.zip","access_level":"open_access","creator":"pub-gitlab-bot","file_size":64962865,"content_type":"application/gzip","file_id":"9353","relation":"main_file","date_updated":"2021-04-26T09:33:44Z","date_created":"2021-04-26T09:33:44Z","checksum":"4c224551adf852b136ec21a4e13f0c1b"}],"date_updated":"2023-08-10T14:24:36Z","date_created":"2021-04-16T14:26:19Z","_id":"9327","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2021","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"publisher":"IST Austria","ddc":["005"],"title":"Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data)","status":"public","abstract":[{"lang":"eng","text":"This archive contains the missing sweater mesh animations and displacement models for the code of \"Mechanics-Aware Deformation of Yarn Pattern Geometry\"\r\n\r\nCode Repository: https://git.ist.ac.at/gsperl/MADYPG"}],"file_date_updated":"2021-04-26T09:33:44Z","type":"software","gitlab_commit_id":"6a77e7e22769230ae5f5edaa090fb4b828e57573"},{"article_type":"original","citation":{"short":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan, Physical Review B 104 (2021).","mla":"Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” Physical Review B, vol. 104, no. 2, 024430, American Physical Society, 2021, doi:10.1103/physrevb.104.024430.","chicago":"Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko, and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/physrevb.104.024430.","ama":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 2021;104(2). doi:10.1103/physrevb.104.024430","apa":"Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., & Ghazaryan, A. (2021). Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.104.024430","ieee":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan, “Interplay between friction and spin-orbit coupling as a source of spin polarization,” Physical Review B, vol. 104, no. 2. American Physical Society, 2021.","ista":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 104(2), 024430."},"publication":"Physical Review B","date_published":"2021-07-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 104","title":"Interplay between friction and spin-orbit coupling as a source of spin polarization","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9770","oa_version":"Preprint","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We study an effective one-dimensional quantum model that includes friction and spin-orbit coupling (SOC), and show that the model exhibits spin polarization when both terms are finite. Most important, strong spin polarization can be observed even for moderate SOC, provided that the friction is strong. Our findings might help to explain the pronounced effect of chirality on spin distribution and transport in chiral molecules. In particular, our model implies static magnetic properties of a chiral molecule, which lead to Shiba-like states when a molecule is placed on a superconductor, in accordance with recent experimental data."}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2101.05173"}],"oa":1,"external_id":{"arxiv":["2101.05173"],"isi":["000678780800003"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.104.024430","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"07","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","acknowledgement":"We thank Rafael Barfknecht for useful discussions. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program. O.M. is thankful for support through the Harry de Jur Chair in Applied Science.","year":"2021","volume":104,"date_created":"2021-08-04T15:05:32Z","date_updated":"2023-08-10T14:27:07Z","author":[{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev","full_name":"Volosniev, Artem"},{"full_name":"Alpern, Hen","first_name":"Hen","last_name":"Alpern"},{"last_name":"Paltiel","first_name":"Yossi","full_name":"Paltiel, Yossi"},{"full_name":"Millo, Oded","first_name":"Oded","last_name":"Millo"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"},{"first_name":"Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg"}],"article_number":"024430","ec_funded":1},{"_id":"9827","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 886","status":"public","title":"Concurrent linearizable nearest neighbour search in LockFree-kD-tree","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"The Nearest neighbour search (NNS) is a fundamental problem in many application domains dealing with multidimensional data. In a concurrent setting, where dynamic modifications are allowed, a linearizable implementation of the NNS is highly desirable.This paper introduces the LockFree-kD-tree (LFkD-tree ): a lock-free concurrent kD-tree, which implements an abstract data type (ADT) that provides the operations Add, Remove, Contains, and NNS. Our implementation is linearizable. The operations in the LFkD-tree use single-word read and compare-and-swap (Image 1 ) atomic primitives, which are readily supported on available multi-core processors. We experimentally evaluate the LFkD-tree using several benchmarks comprising real-world and synthetic datasets. The experiments show that the presented design is scalable and achieves significant speed-up compared to the implementations of an existing sequential kD-tree and a recently proposed multidimensional indexing structure, PH-tree."}],"citation":{"ieee":"B. Chatterjee, I. Walulya, and P. Tsigas, “Concurrent linearizable nearest neighbour search in LockFree-kD-tree,” Theoretical Computer Science, vol. 886. Elsevier, pp. 27–48, 2021.","apa":"Chatterjee, B., Walulya, I., & Tsigas, P. (2021). Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2021.06.041","ista":"Chatterjee B, Walulya I, Tsigas P. 2021. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. 886, 27–48.","ama":"Chatterjee B, Walulya I, Tsigas P. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. 2021;886:27-48. doi:10.1016/j.tcs.2021.06.041","chicago":"Chatterjee, Bapi, Ivan Walulya, and Philippas Tsigas. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” Theoretical Computer Science. Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.06.041.","short":"B. Chatterjee, I. Walulya, P. Tsigas, Theoretical Computer Science 886 (2021) 27–48.","mla":"Chatterjee, Bapi, et al. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” Theoretical Computer Science, vol. 886, Elsevier, 2021, pp. 27–48, doi:10.1016/j.tcs.2021.06.041."},"publication":"Theoretical Computer Science","page":"27-48","article_type":"original","date_published":"2021-09-13T00:00:00Z","scopus_import":"1","keyword":["Concurrent data structure","kD-tree","Nearest neighbor search","Similarity search","Lock-free","Linearizability"],"article_processing_charge":"No","day":"13","year":"2021","publisher":"Elsevier","department":[{"_id":"DaAl"}],"publication_status":"published","author":[{"first_name":"Bapi","last_name":"Chatterjee","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2742-4028","full_name":"Chatterjee, Bapi"},{"last_name":"Walulya","first_name":"Ivan","full_name":"Walulya, Ivan"},{"first_name":"Philippas","last_name":"Tsigas","full_name":"Tsigas, Philippas"}],"volume":886,"date_updated":"2023-08-10T14:27:43Z","date_created":"2021-08-08T22:01:31Z","main_file_link":[{"url":"https://publications.lib.chalmers.se/records/fulltext/232185/232185.pdf","open_access":"1"}],"external_id":{"isi":["000694718900004"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1016/j.tcs.2021.06.041","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0304-3975"]},"month":"09"},{"abstract":[{"lang":"eng","text":"Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution."}],"issue":"29","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1898360,"creator":"asandaue","relation":"main_file","file_id":"9879","date_updated":"2021-08-11T09:31:41Z","date_created":"2021-08-11T09:31:41Z","checksum":"19e84ad8c03c60222744ee8e16cd6998","success":1}],"ddc":["580","570"],"status":"public","title":"Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting","intvolume":" 118","_id":"9877","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"16","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","date_published":"2021-07-16T00:00:00Z","article_type":"original","publication":"Proceedings of the National Academy of Sciences","citation":{"chicago":"Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118.","short":"J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 118 (2021).","mla":"Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” Proceedings of the National Academy of Sciences, vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:10.1073/pnas.2104445118.","ieee":"J. A. Rodrigues et al., “Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting,” Proceedings of the National Academy of Sciences, vol. 118, no. 29. National Academy of Sciences, 2021.","apa":"Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma, R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2104445118","ista":"Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. 118(29), e2104445118.","ama":"Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. 2021;118(29). doi:10.1073/pnas.2104445118"},"file_date_updated":"2021-08-11T09:31:41Z","article_number":"e2104445118","date_created":"2021-08-10T19:30:41Z","date_updated":"2023-08-11T10:28:10Z","volume":118,"author":[{"last_name":"Rodrigues","first_name":"Jessica A.","full_name":"Rodrigues, Jessica A."},{"first_name":"Ping-Hung","last_name":"Hsieh","full_name":"Hsieh, Ping-Hung"},{"first_name":"Deling","last_name":"Ruan","full_name":"Ruan, Deling"},{"full_name":"Nishimura, Toshiro","first_name":"Toshiro","last_name":"Nishimura"},{"full_name":"Sharma, Manoj K.","first_name":"Manoj K.","last_name":"Sharma"},{"first_name":"Rita","last_name":"Sharma","full_name":"Sharma, Rita"},{"last_name":"Ye","first_name":"XinYi","full_name":"Ye, XinYi"},{"full_name":"Nguyen, Nicholas D.","first_name":"Nicholas D.","last_name":"Nguyen"},{"full_name":"Nijjar, Sukhranjan","first_name":"Sukhranjan","last_name":"Nijjar"},{"last_name":"Ronald","first_name":"Pamela C.","full_name":"Ronald, Pamela C."},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"DaZi"}],"year":"2021","acknowledgement":"We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing team for generating the IR64 genome sequence and initial analysis; L. Bartley and E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University of California (UC), Berkeley Sanger sequencing team for technical advice and service. This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.","pmid":1,"month":"07","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2104445118","quality_controlled":"1","isi":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"},"oa":1,"external_id":{"pmid":["34272287"],"isi":["000685037700012"]}},{"article_processing_charge":"Yes","has_accepted_license":"1","day":"10","genbank":["GSE178867"],"scopus_import":"1","date_published":"2021-08-10T00:00:00Z","article_type":"original","citation":{"short":"A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen, L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas, C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H. van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).","mla":"Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications, vol. 12, 4808, Springer Nature, 2021, doi:10.1038/s41467-021-25211-4.","chicago":"Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-25211-4.","ama":"Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. 2021;12. doi:10.1038/s41467-021-25211-4","ieee":"A. Raso et al., “A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration,” Nature Communications, vol. 12. Springer Nature, 2021.","apa":"Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen, D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-25211-4","ista":"Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. 12, 4808."},"publication":"Nature Communications","abstract":[{"text":"Myocardial regeneration is restricted to early postnatal life, when mammalian cardiomyocytes still retain the ability to proliferate. The molecular cues that induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster is higher expressed in the early postnatal myocardium and decreases in expression towards adulthood, especially under conditions of overload, and orchestrates the transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse heart provokes cardiomyocyte proliferation by targeting a network of negative cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated remodeling to overload by derepression of the prohypertrophic transcription factors Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25 provokes nearly complete regeneration of the adult myocardium after ischemic injury. Our data demonstrate that exploitation of conserved molecular programs can enhance the regenerative capacity of the injured heart.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"9876","relation":"main_file","date_created":"2021-08-10T12:29:59Z","date_updated":"2021-08-10T12:29:59Z","success":1,"checksum":"48d8562e8229e4282f3f354b329722c5","file_name":"2021_NatureCommunications_Raso.pdf","access_level":"open_access","creator":"asandaue","file_size":4364333,"content_type":"application/pdf"}],"intvolume":" 12","ddc":["610","570"],"title":"A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9874","publication_identifier":{"eissn":["2041-1723"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1038/s41467-021-25211-4","isi":1,"quality_controlled":"1","external_id":{"pmid":["34376683"],"isi":["000683910200042"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2021-08-10T12:29:59Z","article_number":"4808","volume":12,"date_created":"2021-08-10T11:49:20Z","date_updated":"2023-08-11T10:27:03Z","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-32785-0","relation":"erratum"}]},"author":[{"last_name":"Raso","first_name":"Andrea","full_name":"Raso, Andrea"},{"last_name":"Dirkx","first_name":"Ellen","full_name":"Dirkx, Ellen"},{"last_name":"Sampaio-Pinto","first_name":"Vasco","full_name":"Sampaio-Pinto, Vasco"},{"first_name":"Hamid","last_name":"el Azzouzi","full_name":"el Azzouzi, Hamid"},{"orcid":"0000-0003-0002-1867","id":"850B2E12-9CD4-11E9-837F-E719E6697425","last_name":"Cubero","first_name":"Ryan J","full_name":"Cubero, Ryan J"},{"first_name":"Daniel W.","last_name":"Sorensen","full_name":"Sorensen, Daniel W."},{"full_name":"Ottaviani, Lara","first_name":"Lara","last_name":"Ottaviani"},{"full_name":"Olieslagers, Servé","last_name":"Olieslagers","first_name":"Servé"},{"first_name":"Manon M.","last_name":"Huibers","full_name":"Huibers, Manon M."},{"first_name":"Roel","last_name":"de Weger","full_name":"de Weger, Roel"},{"full_name":"Siddiqi, Sailay","first_name":"Sailay","last_name":"Siddiqi"},{"first_name":"Silvia","last_name":"Moimas","full_name":"Moimas, Silvia"},{"full_name":"Torrini, Consuelo","first_name":"Consuelo","last_name":"Torrini"},{"last_name":"Zentillin","first_name":"Lorena","full_name":"Zentillin, Lorena"},{"first_name":"Luca","last_name":"Braga","full_name":"Braga, Luca"},{"full_name":"Nascimento, Diana S.","first_name":"Diana S.","last_name":"Nascimento"},{"last_name":"da Costa Martins","first_name":"Paula A.","full_name":"da Costa Martins, Paula A."},{"full_name":"van Berlo, Jop H.","last_name":"van Berlo","first_name":"Jop H."},{"first_name":"Serena","last_name":"Zacchigna","full_name":"Zacchigna, Serena"},{"first_name":"Mauro","last_name":"Giacca","full_name":"Giacca, Mauro"},{"first_name":"Leon J.","last_name":"De Windt","full_name":"De Windt, Leon J."}],"department":[{"_id":"SaSi"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2021","acknowledgement":"E.D. is supported by a VENI award 916-150-16 from the Netherlands Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship (EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number 627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência, Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART)."},{"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"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":{"arxiv":["2101.10958"],"isi":["000680039500013"]},"language":[{"iso":"eng"}],"doi":"10.21468/scipostphys.11.1.008","publication_identifier":{"eissn":["2542-4653"]},"month":"07","department":[{"_id":"MiLe"}],"publisher":"SciPost","publication_status":"published","acknowledgement":"We thank Matthias Heinz and Volker Karle for helpful comments on the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing with us the data for the densities presented in Ref. [14]. This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G. V.) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in Many-Body Quantum Systems – From Atoms to Quarks\". This infrastructure is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824093. H.-W.H. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 279384907 - SFB 1245.","year":"2021","volume":11,"date_updated":"2023-08-11T10:25:44Z","date_created":"2021-08-04T15:00:55Z","author":[{"full_name":"Brauneis, Fabian","last_name":"Brauneis","first_name":"Fabian"},{"first_name":"Hans-Werner","last_name":"Hammer","full_name":"Hammer, Hans-Werner"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"},{"first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}],"article_number":"008","ec_funded":1,"file_date_updated":"2021-08-10T11:44:59Z","article_type":"original","citation":{"ama":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 2021;11(1). doi:10.21468/scipostphys.11.1.008","apa":"Brauneis, F., Hammer, H.-W., Lemeshko, M., & Volosniev, A. (2021). Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. SciPost. https://doi.org/10.21468/scipostphys.11.1.008","ieee":"F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in a one-dimensional Bose gas: The flow equation approach,” SciPost Physics, vol. 11, no. 1. SciPost, 2021.","ista":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.","short":"F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11 (2021).","mla":"Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost Physics, vol. 11, no. 1, 008, SciPost, 2021, doi:10.21468/scipostphys.11.1.008.","chicago":"Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.1.008."},"publication":"SciPost Physics","date_published":"2021-07-13T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"13","intvolume":" 11","status":"public","title":"Impurities in a one-dimensional Bose gas: The flow equation approach","ddc":["530"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9769","file":[{"file_id":"9875","relation":"main_file","date_updated":"2021-08-10T11:44:59Z","date_created":"2021-08-10T11:44:59Z","success":1,"checksum":"eaa847346b1a023d97bbb291779610ed","file_name":"2021_SciPostPhysics_Brauneis.pdf","access_level":"open_access","creator":"asandaue","content_type":"application/pdf","file_size":1085300}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"A few years ago, flow equations were introduced as a technique for calculating the ground-state energies of cold Bose gases with and without impurities. In this paper, we extend this approach to compute observables other than the energy. As an example, we calculate the densities, and phase fluctuations of one-dimensional Bose gases with one and two impurities. For a single mobile impurity, we use flow equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation. We show that the mean-field approximation is accurate for all values of the boson-impurity interaction strength as long as the phase coherence length is much larger than the healing length of the condensate. For two static impurities, we calculate impurity-impurity interactions induced by the Bose gas. We find that leading order perturbation theory fails when boson-impurity interactions are stronger than boson-boson interactions. The mean-field approximation reproduces the flow equation results for all values of the boson-impurity interaction strength as long as boson-boson interactions are weak."}]},{"quality_controlled":"1","isi":1,"external_id":{"isi":["000692027800001"],"pmid":["34318749"]},"main_file_link":[{"url":"https://doi.org/10.7554/eLife.68876","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/elife.68876","month":"07","publication_identifier":{"eissn":["2050-084X"]},"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"CaGu"}],"acknowledgement":"We would like to thank Leif Tueffers and João Botelho for discussions and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS, and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further supported by the German Science Foundation Research Infrastructure NGS_CC (project 407495230) as part of the Next Generation Sequencing Competence Network (project 423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis Kiel (CCGA Kiel).","year":"2021","pmid":1,"date_updated":"2023-08-11T10:26:29Z","date_created":"2021-07-28T13:36:57Z","volume":10,"author":[{"full_name":"Batra, Aditi","first_name":"Aditi","last_name":"Batra"},{"last_name":"Römhild","first_name":"Roderich","orcid":"0000-0001-9480-5261","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","full_name":"Römhild, Roderich"},{"full_name":"Rousseau, Emilie","first_name":"Emilie","last_name":"Rousseau"},{"full_name":"Franzenburg, Sören","first_name":"Sören","last_name":"Franzenburg"},{"last_name":"Niemann","first_name":"Stefan","full_name":"Niemann, Stefan"},{"last_name":"Schulenburg","first_name":"Hinrich","full_name":"Schulenburg, Hinrich"}],"article_number":"e68876","article_type":"original","publication":"eLife","citation":{"ista":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10, e68876.","apa":"Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., & Schulenburg, H. (2021). High potency of sequential therapy with only beta-lactam antibiotics. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68876","ieee":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg, “High potency of sequential therapy with only beta-lactam antibiotics,” eLife, vol. 10. eLife Sciences Publications, 2021.","ama":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 2021;10. doi:10.7554/elife.68876","chicago":"Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.68876.","mla":"Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” ELife, vol. 10, e68876, eLife Sciences Publications, 2021, doi:10.7554/elife.68876.","short":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg, ELife 10 (2021)."},"date_published":"2021-07-28T00:00:00Z","scopus_import":"1","day":"28","article_processing_charge":"No","status":"public","title":"High potency of sequential therapy with only beta-lactam antibiotics","intvolume":" 10","_id":"9746","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only β-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs."}]},{"publication_identifier":{"eissn":["1365-2818"],"issn":["0022-2720"]},"month":"08","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jmi.13041"}],"external_id":{"isi":["000683702700001"]},"language":[{"iso":"eng"}],"doi":"10.1111/jmi.13041","department":[{"_id":"Bio"}],"publisher":"Wiley","publication_status":"published","acknowledgement":"We thank https://www.somersault1824.com/somersault18:24 BV (Leuven, Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122, in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.","year":"2021","volume":284,"date_updated":"2023-08-11T10:30:40Z","date_created":"2021-08-15T22:01:29Z","author":[{"full_name":"Nelson, Glyn","last_name":"Nelson","first_name":"Glyn"},{"first_name":"Ulrike","last_name":"Boehm","full_name":"Boehm, Ulrike"},{"first_name":"Steve","last_name":"Bagley","full_name":"Bagley, Steve"},{"first_name":"Peter","last_name":"Bajcsy","full_name":"Bajcsy, Peter"},{"first_name":"Johanna","last_name":"Bischof","full_name":"Bischof, Johanna"},{"last_name":"Brown","first_name":"Claire M.","full_name":"Brown, Claire M."},{"first_name":"Aurélien","last_name":"Dauphin","full_name":"Dauphin, Aurélien"},{"full_name":"Dobbie, Ian M.","first_name":"Ian M.","last_name":"Dobbie"},{"first_name":"John E.","last_name":"Eriksson","full_name":"Eriksson, John E."},{"last_name":"Faklaris","first_name":"Orestis","full_name":"Faklaris, Orestis"},{"first_name":"Julia","last_name":"Fernandez-Rodriguez","full_name":"Fernandez-Rodriguez, Julia"},{"full_name":"Ferrand, Alexia","first_name":"Alexia","last_name":"Ferrand"},{"first_name":"Laurent","last_name":"Gelman","full_name":"Gelman, Laurent"},{"first_name":"Ali","last_name":"Gheisari","full_name":"Gheisari, Ali"},{"full_name":"Hartmann, Hella","last_name":"Hartmann","first_name":"Hella"},{"last_name":"Kukat","first_name":"Christian","full_name":"Kukat, Christian"},{"full_name":"Laude, Alex","last_name":"Laude","first_name":"Alex"},{"first_name":"Miso","last_name":"Mitkovski","full_name":"Mitkovski, Miso"},{"first_name":"Sebastian","last_name":"Munck","full_name":"Munck, Sebastian"},{"last_name":"North","first_name":"Alison J.","full_name":"North, Alison J."},{"first_name":"Tobias M.","last_name":"Rasse","full_name":"Rasse, Tobias M."},{"full_name":"Resch-Genger, Ute","last_name":"Resch-Genger","first_name":"Ute"},{"last_name":"Schuetz","first_name":"Lucas C.","full_name":"Schuetz, Lucas C."},{"last_name":"Seitz","first_name":"Arne","full_name":"Seitz, Arne"},{"last_name":"Strambio-De-Castillia","first_name":"Caterina","full_name":"Strambio-De-Castillia, Caterina"},{"full_name":"Swedlow, Jason R.","last_name":"Swedlow","first_name":"Jason R."},{"last_name":"Alexopoulos","first_name":"Ioannis","full_name":"Alexopoulos, Ioannis"},{"first_name":"Karin","last_name":"Aumayr","full_name":"Aumayr, Karin"},{"first_name":"Sergiy","last_name":"Avilov","full_name":"Avilov, Sergiy"},{"full_name":"Bakker, Gert Jan","last_name":"Bakker","first_name":"Gert Jan"},{"full_name":"Bammann, Rodrigo R.","first_name":"Rodrigo R.","last_name":"Bammann"},{"first_name":"Andrea","last_name":"Bassi","full_name":"Bassi, Andrea"},{"full_name":"Beckert, Hannes","last_name":"Beckert","first_name":"Hannes"},{"last_name":"Beer","first_name":"Sebastian","full_name":"Beer, Sebastian"},{"first_name":"Yury","last_name":"Belyaev","full_name":"Belyaev, Yury"},{"last_name":"Bierwagen","first_name":"Jakob","full_name":"Bierwagen, Jakob"},{"full_name":"Birngruber, Konstantin A.","first_name":"Konstantin A.","last_name":"Birngruber"},{"last_name":"Bosch","first_name":"Manel","full_name":"Bosch, Manel"},{"last_name":"Breitlow","first_name":"Juergen","full_name":"Breitlow, Juergen"},{"full_name":"Cameron, Lisa A.","last_name":"Cameron","first_name":"Lisa A."},{"first_name":"Joe","last_name":"Chalfoun","full_name":"Chalfoun, Joe"},{"full_name":"Chambers, James J.","last_name":"Chambers","first_name":"James J."},{"full_name":"Chen, Chieh Li","first_name":"Chieh Li","last_name":"Chen"},{"full_name":"Conde-Sousa, Eduardo","first_name":"Eduardo","last_name":"Conde-Sousa"},{"full_name":"Corbett, Alexander D.","first_name":"Alexander D.","last_name":"Corbett"},{"full_name":"Cordelieres, Fabrice P.","first_name":"Fabrice P.","last_name":"Cordelieres"},{"full_name":"Nery, Elaine Del","last_name":"Nery","first_name":"Elaine 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Elton","first_name":"Elton","last_name":"Rexhepaj"},{"first_name":"Arnaud","last_name":"Royon","full_name":"Royon, Arnaud"},{"full_name":"Saari, Markku A.","last_name":"Saari","first_name":"Markku A."},{"last_name":"Schapman","first_name":"Damien","full_name":"Schapman, Damien"},{"last_name":"Schoonderwoert","first_name":"Vincent","full_name":"Schoonderwoert, Vincent"},{"full_name":"Schroth-Diez, Britta","first_name":"Britta","last_name":"Schroth-Diez"},{"full_name":"Schwartz, Stanley","first_name":"Stanley","last_name":"Schwartz"},{"last_name":"Shaw","first_name":"Michael","full_name":"Shaw, Michael"},{"full_name":"Spitaler, Martin","last_name":"Spitaler","first_name":"Martin"},{"full_name":"Stoeckl, Martin T.","last_name":"Stoeckl","first_name":"Martin T."},{"first_name":"Damir","last_name":"Sudar","full_name":"Sudar, Damir"},{"first_name":"Jeremie","last_name":"Teillon","full_name":"Teillon, Jeremie"},{"full_name":"Terjung, Stefan","first_name":"Stefan","last_name":"Terjung"},{"full_name":"Thuenauer, Roland","first_name":"Roland","last_name":"Thuenauer"},{"first_name":"Christian D.","last_name":"Wilms","full_name":"Wilms, Christian D."},{"full_name":"Wright, Graham D.","first_name":"Graham D.","last_name":"Wright"},{"full_name":"Nitschke, Roland","first_name":"Roland","last_name":"Nitschke"}],"scopus_import":"1","article_processing_charge":"Yes","day":"11","page":"56-73","article_type":"original","citation":{"ista":"Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 284(1), 56–73.","apa":"Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M., … Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. Wiley. https://doi.org/10.1111/jmi.13041","ieee":"G. Nelson et al., “QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy,” Journal of Microscopy, vol. 284, no. 1. Wiley, pp. 56–73, 2021.","ama":"Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 2021;284(1):56-73. doi:10.1111/jmi.13041","chicago":"Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy. Wiley, 2021. https://doi.org/10.1111/jmi.13041.","mla":"Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy, vol. 284, no. 1, Wiley, 2021, pp. 56–73, doi:10.1111/jmi.13041.","short":"G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin, I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L. Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck, A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia, J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann, A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch, J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa, A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli, A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich, G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler, M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins, D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami, A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj, A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz, M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer, C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73."},"publication":"Journal of Microscopy","date_published":"2021-08-11T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics."}],"intvolume":" 284","title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9911","oa_version":"Published Version"},{"acknowledgement":"Open access funding provided by Medical University of Vienna. The authors would like to thank all the participants and health professionals involved in the present study. We want to thank our technical assistants Barbara Widmar and Matthias Witzmann-Stern for their diligent work and constant assistance. We would like to thank Simon Hippenmeyer for access to\r\nbioinformatic infrastructure and resources.","year":"2021","department":[{"_id":"SiHi"}],"publisher":"MDPI","publication_status":"published","author":[{"last_name":"Yotova","first_name":"Iveta","full_name":"Yotova, Iveta"},{"full_name":"Hudson, Quanah J.","first_name":"Quanah J.","last_name":"Hudson"},{"full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048"},{"full_name":"Proestling, Katharina","last_name":"Proestling","first_name":"Katharina"},{"last_name":"Haslinger","first_name":"Isabella","full_name":"Haslinger, Isabella"},{"full_name":"Kuessel, Lorenz","first_name":"Lorenz","last_name":"Kuessel"},{"full_name":"Perricos, Alexandra","first_name":"Alexandra","last_name":"Perricos"},{"first_name":"Heinrich","last_name":"Husslein","full_name":"Husslein, Heinrich"},{"full_name":"Wenzl, René","first_name":"René","last_name":"Wenzl"}],"volume":22,"date_updated":"2023-08-11T10:34:13Z","date_created":"2021-08-15T22:01:27Z","article_number":"8385","file_date_updated":"2021-08-16T09:29:17Z","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":["000689147400001"]},"isi":1,"quality_controlled":"1","doi":"10.3390/ijms22168385","language":[{"iso":"eng"}],"publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"month":"08","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9906","intvolume":" 22","title":"LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line","ddc":["570"],"status":"public","oa_version":"Published Version","file":[{"file_id":"9922","relation":"main_file","date_created":"2021-08-16T09:29:17Z","date_updated":"2021-08-16T09:29:17Z","success":1,"checksum":"be7f0042607ca60549cb27513c19c6af","file_name":"2021_InternationalJournalOfMolecularSciences_Yotova.pdf","access_level":"open_access","creator":"asandaue","content_type":"application/pdf","file_size":2646018}],"type":"journal_article","issue":"16","abstract":[{"lang":"eng","text":"Endometriosis is a common gynecological disorder characterized by ectopic growth of endometrium outside the uterus and is associated with chronic pain and infertility. We investigated the role of the long intergenic noncoding RNA 01133 (LINC01133) in endometriosis, an lncRNA that has been implicated in several types of cancer. We found that LINC01133 is upregulated in ectopic endometriotic lesions. As expression appeared higher in the epithelial endometrial layer, we performed a siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic assays indicated that LINC01133 may promote proliferation and suppress cellular migration, and affect the cytoskeleton and morphology of the cells. Gene ontology analysis of differentially expressed genes indicated that cell proliferation and migration pathways were affected in line with the observed phenotype. We validated upregulation of p21 and downregulation of Cyclin A at the protein level, which together with the quantification of the DNA content using fluorescence-activated cell sorting (FACS) analysis indicated that the observed effects on cellular proliferation may be due to changes in cell cycle. Further, we found testis-specific protein kinase 1 (TESK1) kinase upregulation corresponding with phosphorylation and inactivation of actin severing protein Cofilin, which could explain changes in the cytoskeleton and cellular migration. These results indicate that endometriosis is associated with LINC01133 upregulation, which may affect pathogenesis via the cellular proliferation and migration pathways."}],"citation":{"ama":"Yotova I, Hudson QJ, Pauler F, et al. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. 2021;22(16). doi:10.3390/ijms22168385","apa":"Yotova, I., Hudson, Q. J., Pauler, F., Proestling, K., Haslinger, I., Kuessel, L., … Wenzl, R. (2021). LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22168385","ieee":"I. Yotova et al., “LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line,” International Journal of Molecular Sciences, vol. 22, no. 16. MDPI, 2021.","ista":"Yotova I, Hudson QJ, Pauler F, Proestling K, Haslinger I, Kuessel L, Perricos A, Husslein H, Wenzl R. 2021. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. 22(16), 8385.","short":"I. Yotova, Q.J. Hudson, F. Pauler, K. Proestling, I. Haslinger, L. Kuessel, A. Perricos, H. Husslein, R. Wenzl, International Journal of Molecular Sciences 22 (2021).","mla":"Yotova, Iveta, et al. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” International Journal of Molecular Sciences, vol. 22, no. 16, 8385, MDPI, 2021, doi:10.3390/ijms22168385.","chicago":"Yotova, Iveta, Quanah J. Hudson, Florian Pauler, Katharina Proestling, Isabella Haslinger, Lorenz Kuessel, Alexandra Perricos, Heinrich Husslein, and René Wenzl. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22168385."},"publication":"International Journal of Molecular Sciences","article_type":"original","date_published":"2021-08-04T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"04"},{"abstract":[{"lang":"eng","text":"Adult height inspired the first biometrical and quantitative genetic studies and is a test-case trait for understanding heritability. The studies of height led to formulation of the classical polygenic model, that has a profound influence on the way we view and analyse complex traits. An essential part of the classical model is an assumption of additivity of effects and normality of the distribution of the residuals. However, it may be expected that the normal approximation will become insufficient in bigger studies. Here, we demonstrate that when the height of hundreds of thousands of individuals is analysed, the model complexity needs to be increased to include non-additive interactions between sex, environment and genes. Alternatively, the use of log-normal approximation allowed us to still use the additive effects model. These findings are important for future genetic and methodologic studies that make use of adult height as an exemplar trait."}],"issue":"7","type":"journal_article","file":[{"access_level":"open_access","file_name":"2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf","creator":"asandaue","content_type":"application/pdf","file_size":1079395,"file_id":"9921","relation":"main_file","success":1,"checksum":"a676d76f91b0dbe0504c63e469129c2a","date_created":"2021-08-16T09:14:36Z","date_updated":"2021-08-16T09:14:36Z"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9910","ddc":["576"],"title":"The limits of normal approximation for adult height","status":"public","intvolume":" 29","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","date_published":"2021-07-01T00:00:00Z","publication":"European Journal of Human Genetics","citation":{"ama":"Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation for adult height. European Journal of Human Genetics. 2021;29(7):1082-1091. doi:10.1038/s41431-021-00836-7","ista":"Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European Journal of Human Genetics. 29(7), 1082–1091.","apa":"Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich, T. I., Kondrashov, F., & Aulchenko, Y. S. (2021). The limits of normal approximation for adult height. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-021-00836-7","ieee":"S. A. Slavskii et al., “The limits of normal approximation for adult height,” European Journal of Human Genetics, vol. 29, no. 7. Springer Nature, pp. 1082–1091, 2021.","mla":"Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.” European Journal of Human Genetics, vol. 29, no. 7, Springer Nature, 2021, pp. 1082–91, doi:10.1038/s41431-021-00836-7.","short":"S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich, F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.","chicago":"Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A. Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The Limits of Normal Approximation for Adult Height.” European Journal of Human Genetics. Springer Nature, 2021. https://doi.org/10.1038/s41431-021-00836-7."},"article_type":"original","page":"1082-1091","file_date_updated":"2021-08-16T09:14:36Z","ec_funded":1,"author":[{"full_name":"Slavskii, Sergei A.","last_name":"Slavskii","first_name":"Sergei A."},{"full_name":"Kuznetsov, Ivan A.","last_name":"Kuznetsov","first_name":"Ivan A."},{"full_name":"Shashkova, Tatiana I.","last_name":"Shashkova","first_name":"Tatiana I."},{"first_name":"Georgii A.","last_name":"Bazykin","full_name":"Bazykin, Georgii A."},{"full_name":"Axenovich, Tatiana I.","last_name":"Axenovich","first_name":"Tatiana I."},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"first_name":"Yurii S.","last_name":"Aulchenko","full_name":"Aulchenko, Yurii S."}],"date_created":"2021-08-15T22:01:28Z","date_updated":"2023-08-11T10:33:42Z","volume":29,"year":"2021","acknowledgement":"We are grateful to Marianna Bevova and Pavel Borodin for fruitful discussion and help with conceptualising our findings and to Lennart C. Karssen for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects in control of complex human traits”). The work of SAS, IAK, and TIS were supported by Russian Ministry of Science and Education under the 5–100 Excellence Programme. The work of YSA and TIA was supported by the Ministry of Education and Science of the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4). FAK is supported by the ERC Consolidator Grant (ChrFL: 771209).","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"month":"07","publication_identifier":{"eissn":["14765438"],"issn":["10184813"]},"doi":"10.1038/s41431-021-00836-7","language":[{"iso":"eng"}],"external_id":{"isi":["000625853200001"],"pmid":["33664501"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209","call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales"}]},{"date_published":"2021-12-01T00:00:00Z","citation":{"short":"L. Erdös, T.H. Krüger, Y. Nemish, Annales Henri Poincaré 22 (2021) 4205–4269.","mla":"Erdös, László, et al. “Scattering in Quantum Dots via Noncommutative Rational Functions.” Annales Henri Poincaré , vol. 22, Springer Nature, 2021, pp. 4205–4269, doi:10.1007/s00023-021-01085-6.","chicago":"Erdös, László, Torben H Krüger, and Yuriy Nemish. “Scattering in Quantum Dots via Noncommutative Rational Functions.” Annales Henri Poincaré . Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01085-6.","ama":"Erdös L, Krüger TH, Nemish Y. Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . 2021;22:4205–4269. doi:10.1007/s00023-021-01085-6","ieee":"L. Erdös, T. H. Krüger, and Y. Nemish, “Scattering in quantum dots via noncommutative rational functions,” Annales Henri Poincaré , vol. 22. Springer Nature, pp. 4205–4269, 2021.","apa":"Erdös, L., Krüger, T. H., & Nemish, Y. (2021). Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . Springer Nature. https://doi.org/10.1007/s00023-021-01085-6","ista":"Erdös L, Krüger TH, Nemish Y. 2021. Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . 22, 4205–4269."},"publication":"Annales Henri Poincaré ","page":"4205–4269","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","scopus_import":"1","file":[{"relation":"main_file","file_id":"11365","checksum":"8d6bac0e2b0a28539608b0538a8e3b38","success":1,"date_updated":"2022-05-12T12:50:27Z","date_created":"2022-05-12T12:50:27Z","access_level":"open_access","file_name":"2021_AnnHenriPoincare_Erdoes.pdf","file_size":1162454,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9912","intvolume":" 22","title":"Scattering in quantum dots via noncommutative rational functions","status":"public","ddc":["510"],"abstract":[{"lang":"eng","text":"In the customary random matrix model for transport in quantum dots with M internal degrees of freedom coupled to a chaotic environment via 𝑁≪𝑀 channels, the density 𝜌 of transmission eigenvalues is computed from a specific invariant ensemble for which explicit formula for the joint probability density of all eigenvalues is available. We revisit this problem in the large N regime allowing for (i) arbitrary ratio 𝜙:=𝑁/𝑀≤1; and (ii) general distributions for the matrix elements of the Hamiltonian of the quantum dot. In the limit 𝜙→0, we recover the formula for the density 𝜌 that Beenakker (Rev Mod Phys 69:731–808, 1997) has derived for a special matrix ensemble. We also prove that the inverse square root singularity of the density at zero and full transmission in Beenakker’s formula persists for any 𝜙<1 but in the borderline case 𝜙=1 an anomalous 𝜆−2/3 singularity arises at zero. To access this level of generality, we develop the theory of global and local laws on the spectral density of a large class of noncommutative rational expressions in large random matrices with i.i.d. entries."}],"type":"journal_article","doi":"10.1007/s00023-021-01085-6","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":["000681531500001"],"arxiv":["1911.05112"]},"oa":1,"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["1424-0637"],"eissn":["1424-0661"]},"month":"12","author":[{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"full_name":"Krüger, Torben H","last_name":"Krüger","first_name":"Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nemish","first_name":"Yuriy","orcid":"0000-0002-7327-856X","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","full_name":"Nemish, Yuriy"}],"volume":22,"date_created":"2021-08-15T22:01:29Z","date_updated":"2023-08-11T10:31:48Z","acknowledgement":"The authors are very grateful to Yan Fyodorov for discussions on the physical background and for providing references, and to the anonymous referee for numerous valuable remarks.","year":"2021","publisher":"Springer Nature","department":[{"_id":"LaEr"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2022-05-12T12:50:27Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9891","intvolume":" 62","ddc":["530"],"status":"public","title":"Floating Wigner crystal and periodic jellium configurations","file":[{"file_name":"2021_JMathPhy_Lauritsen.pdf","access_level":"open_access","creator":"cziletti","content_type":"application/pdf","file_size":4352640,"file_id":"10188","relation":"main_file","date_created":"2021-10-27T12:57:06Z","date_updated":"2021-10-27T12:57:06Z","success":1,"checksum":"d035be2b894c4d50d90ac5ce252e27cd"}],"oa_version":"Published Version","type":"journal_article","issue":"8","abstract":[{"lang":"eng","text":"Extending on ideas of Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)], we present a modified “floating crystal” trial state for jellium (also known as the classical homogeneous electron gas) with density equal to a characteristic function. This allows us to show that three definitions of the jellium energy coincide in dimensions d ≥ 2, thus extending the result of Cotar and Petrache [“Equality of the Jellium and uniform electron gas next-order asymptotic terms for Coulomb and Riesz potentials,” arXiv: 1707.07664 (2019)] and Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)] that the three definitions coincide in dimension d ≥ 3. We show that the jellium energy is also equivalent to a “renormalized energy” studied in a series of papers by Serfaty and others, and thus, by the work of Bétermin and Sandier [Constr. Approximation 47, 39–74 (2018)], we relate the jellium energy to the order n term in the logarithmic energy of n points on the unit 2-sphere. We improve upon known lower bounds for this renormalized energy. Additionally, we derive formulas for the jellium energy of periodic configurations."}],"citation":{"ieee":"A. B. Lauritsen, “Floating Wigner crystal and periodic jellium configurations,” Journal of Mathematical Physics, vol. 62, no. 8. AIP Publishing, 2021.","apa":"Lauritsen, A. B. (2021). Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0053494","ista":"Lauritsen AB. 2021. Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. 62(8), 083305.","ama":"Lauritsen AB. Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. 2021;62(8). doi:10.1063/5.0053494","chicago":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” Journal of Mathematical Physics. AIP Publishing, 2021. https://doi.org/10.1063/5.0053494.","short":"A.B. Lauritsen, Journal of Mathematical Physics 62 (2021).","mla":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” Journal of Mathematical Physics, vol. 62, no. 8, 083305, AIP Publishing, 2021, doi:10.1063/5.0053494."},"publication":"Journal of Mathematical Physics","article_type":"original","date_published":"2021-08-01T00:00:00Z","scopus_import":"1","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"article_processing_charge":"No","has_accepted_license":"1","day":"01","year":"2021","acknowledgement":"The author would like to thank Robert Seiringer for guidance and many helpful comments on this project. The author would also like to thank Mathieu Lewin for his comments on the manuscript and Lorenzo Portinale for providing his lecture notes for the course “Mathematics of quantum many-body systems” in spring 2020, taught by Robert Seiringer. The Proof of Theorem III.1 is inspired by these lecture notes.","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"publisher":"AIP Publishing","publication_status":"published","author":[{"full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard"}],"volume":62,"date_updated":"2023-08-11T10:29:48Z","date_created":"2021-08-12T07:08:36Z","article_number":"083305","file_date_updated":"2021-10-27T12:57:06Z","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":["000683960800003"],"arxiv":["2103.07975"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1063/5.0053494","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-2488"],"eissn":["1089-7658"]},"month":"08"},{"file_date_updated":"2021-08-16T09:02:40Z","article_number":"1141","date_created":"2021-08-15T22:01:28Z","date_updated":"2023-08-11T10:32:21Z","volume":12,"author":[{"first_name":"Yinwei","last_name":"Zeng","full_name":"Zeng, Yinwei"},{"full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","first_name":"Inge"},{"first_name":"Hoang Khai","last_name":"Trinh","full_name":"Trinh, Hoang Khai"},{"last_name":"Heugebaert","first_name":"Thomas","full_name":"Heugebaert, Thomas"},{"last_name":"Stevens","first_name":"Christian V.","full_name":"Stevens, Christian V."},{"full_name":"Garcia-Maquilon, Irene","first_name":"Irene","last_name":"Garcia-Maquilon"},{"full_name":"Rodriguez, Pedro L.","last_name":"Rodriguez","first_name":"Pedro L."},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"last_name":"Geelen","first_name":"Danny","full_name":"Geelen, Danny"}],"publication_status":"published","publisher":"MDPI","department":[{"_id":"JiFr"}],"year":"2021","acknowledgement":"We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis mutants and ABA signaling mutants.","month":"07","publication_identifier":{"eissn":["20734425"]},"language":[{"iso":"eng"}],"doi":"10.3390/genes12081141","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000690558000001"]},"abstract":[{"text":"Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at concentrations above 1 µM, suggesting that it was more selective in triggering a root inhibition response. Analysis of a series of phosphonamide and phosphonate pyrabactin analogs suggested that adventitious root formation and lateral root branching are differentially regulated by ABA signaling. ABA biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition.","lang":"eng"}],"issue":"8","type":"journal_article","file":[{"file_id":"9919","relation":"main_file","success":1,"checksum":"3d99535618cf9a5b14d264408fa52e97","date_updated":"2021-08-16T09:02:40Z","date_created":"2021-08-16T09:02:40Z","access_level":"open_access","file_name":"2021_Genes_Zeng.pdf","creator":"asandaue","content_type":"application/pdf","file_size":1340305}],"oa_version":"Published Version","title":"Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling","ddc":["580","570"],"status":"public","intvolume":" 12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9909","day":"27","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2021-07-27T00:00:00Z","article_type":"original","publication":"Genes","citation":{"ieee":"Y. Zeng et al., “Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling,” Genes, vol. 12, no. 8. MDPI, 2021.","apa":"Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon, I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. MDPI. https://doi.org/10.3390/genes12081141","ista":"Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 12(8), 1141.","ama":"Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 2021;12(8). doi:10.3390/genes12081141","chicago":"Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12081141.","short":"Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon, P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).","mla":"Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” Genes, vol. 12, no. 8, 1141, MDPI, 2021, doi:10.3390/genes12081141."}},{"article_processing_charge":"Yes","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2021-08-01T00:00:00Z","article_type":"original","citation":{"short":"N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International Journal of Molecular Sciences 22 (2021).","mla":"Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” International Journal of Molecular Sciences, vol. 22, no. 15, 8350, MDPI, 2021, doi:10.3390/ijms22158350.","chicago":"Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22158350.","ama":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. 2021;22(15). doi:10.3390/ijms22158350","ieee":"N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák, “Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva,” International Journal of Molecular Sciences, vol. 22, no. 15. MDPI, 2021.","apa":"Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., & Barák, I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22158350","ista":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. 22(15), 8350."},"publication":"International Journal of Molecular Sciences","issue":"15","abstract":[{"lang":"eng","text":"DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane. "}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"asandaue","content_type":"application/pdf","file_size":6132410,"file_name":"2021_InternationalJournalOfMolecularSciences_Labajová .pdf","access_level":"open_access","date_updated":"2021-08-16T09:35:56Z","date_created":"2021-08-16T09:35:56Z","success":1,"checksum":"a4bc06e9a2c803ceff5a91f10b174054","file_id":"9923","relation":"main_file"}],"intvolume":" 22","title":"Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva","status":"public","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9907","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"month":"08","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.3390/ijms22158350","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["34361115"],"isi":["000681815400001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"ec_funded":1,"file_date_updated":"2021-08-16T09:35:56Z","article_number":"8350","volume":22,"date_created":"2021-08-15T22:01:27Z","date_updated":"2023-08-11T10:34:44Z","author":[{"first_name":"Naďa","last_name":"Labajová","full_name":"Labajová, Naďa"},{"orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","first_name":"Natalia S.","full_name":"Baranova, Natalia S."},{"full_name":"Jurásek, Miroslav","first_name":"Miroslav","last_name":"Jurásek"},{"full_name":"Vácha, Robert","first_name":"Robert","last_name":"Vácha"},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose"},{"full_name":"Barák, Imrich","last_name":"Barák","first_name":"Imrich"}],"department":[{"_id":"MaLo"}],"publisher":"MDPI","publication_status":"published","pmid":1,"acknowledgement":"We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova and other members of Barák’s laboratory for useful discussions, suggestions and help. Special thanks also to Emília Chovancová for technical support. We are grateful to Juraj Labaj for drawing the model and for help with graphics. Many thanks to all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp Radler, and other members of the Loose’s laboratory for sharing their knowledge of SLB preparation and TIRF experiment chambers, for sharing coverslips and for help with the TIRF microscope and data analysis. We also thank the members of the Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J. Bauer for critically reading the manuscript.","year":"2021"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period."}],"issue":"1","_id":"9905","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains","ddc":["570","610"],"status":"public","intvolume":" 11","oa_version":"Published Version","file":[{"file_id":"9927","relation":"main_file","date_created":"2021-08-16T11:36:49Z","date_updated":"2021-08-16T11:36:49Z","success":1,"checksum":"ac86892ed17e6724c7251844da5cef5c","file_name":"2021_ScientificReports_Rella.pdf","access_level":"open_access","creator":"asandaue","content_type":"application/pdf","file_size":3432001}],"scopus_import":"1","day":"30","article_processing_charge":"Yes","has_accepted_license":"1","publication":"Scientific Reports","citation":{"chicago":"Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-95025-3.","short":"S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021).","mla":"Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3.","apa":"Rella, S., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-95025-3","ieee":"S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,” Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.","ista":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 11(1), 15729.","ama":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-95025-3"},"article_type":"original","date_published":"2021-07-30T00:00:00Z","article_number":"15729","file_date_updated":"2021-08-16T11:36:49Z","ec_funded":1,"year":"2021","acknowledgement":"We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta, Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España for useful comments. The opinions expressed in this document are exclusively of the authors and, therefore, do not necessarily coincide with those of the Banco de España or the Eurosystem. ETD is supported by the Swiss National Science and Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator Grant (771209-CharFL).","pmid":1,"publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","author":[{"id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","last_name":"Rella","first_name":"Simon","full_name":"Rella, Simon"},{"full_name":"Kulikova, Yuliya A.","last_name":"Kulikova","first_name":"Yuliya A."},{"full_name":"Dermitzakis, Emmanouil T.","first_name":"Emmanouil T.","last_name":"Dermitzakis"},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Website","url":"https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/"}]},"date_updated":"2023-08-11T10:42:58Z","date_created":"2021-08-15T22:01:26Z","volume":11,"month":"07","publication_identifier":{"eissn":["20452322"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["34330988"],"isi":["000683329100001"]},"quality_controlled":"1","isi":1,"project":[{"name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209"}],"doi":"10.1038/s41598-021-95025-3","language":[{"iso":"eng"}]},{"abstract":[{"text":"Eigenstate thermalization in quantum many-body systems implies that eigenstates at high energy are similar to random vectors. Identifying systems where at least some eigenstates are nonthermal is an outstanding question. In this Letter we show that interacting quantum models that have a nullspace—a degenerate subspace of eigenstates at zero energy (zero modes), which corresponds to infinite temperature, provide a route to nonthermal eigenstates. We analytically show the existence of a zero mode which can be represented as a matrix product state for a certain class of local Hamiltonians. In the more general case we use a subspace disentangling algorithm to generate an orthogonal basis of zero modes characterized by increasing entanglement entropy. We show evidence for an area-law entanglement scaling of the least-entangled zero mode in the broad parameter regime, leading to a conjecture that all local Hamiltonians with the nullspace feature zero modes with area-law entanglement scaling and, as such, break the strong thermalization hypothesis. Finally, we find zero modes in constrained models and propose a setup for observing their experimental signatures.","lang":"eng"}],"issue":"6","type":"journal_article","file":[{"creator":"mserbyn","file_size":5064231,"content_type":"application/pdf","access_level":"open_access","file_name":"PhysRevLett.127.060602_SOM.pdf","success":1,"checksum":"51218f302dcef99d90d1209809fcc874","date_created":"2021-08-13T09:28:08Z","date_updated":"2021-08-13T09:28:08Z","file_id":"9904","relation":"main_file"}],"oa_version":"Published Version","_id":"9903","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["539"],"title":"Area-law entangled eigenstates from nullspaces of local Hamiltonians","status":"public","intvolume":" 127","day":"06","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","date_published":"2021-08-06T00:00:00Z","publication":"Physical Review Letters","citation":{"ama":"Karle V, Serbyn M, Michailidis A. Area-law entangled eigenstates from nullspaces of local Hamiltonians. Physical Review Letters. 2021;127(6). doi:10.1103/physrevlett.127.060602","ista":"Karle V, Serbyn M, Michailidis A. 2021. Area-law entangled eigenstates from nullspaces of local Hamiltonians. Physical Review Letters. 127(6), 060602.","ieee":"V. Karle, M. Serbyn, and A. Michailidis, “Area-law entangled eigenstates from nullspaces of local Hamiltonians,” Physical Review Letters, vol. 127, no. 6. American Physical Society, 2021.","apa":"Karle, V., Serbyn, M., & Michailidis, A. (2021). Area-law entangled eigenstates from nullspaces of local Hamiltonians. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.127.060602","mla":"Karle, Volker, et al. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” Physical Review Letters, vol. 127, no. 6, 060602, American Physical Society, 2021, doi:10.1103/physrevlett.127.060602.","short":"V. Karle, M. Serbyn, A. Michailidis, Physical Review Letters 127 (2021).","chicago":"Karle, Volker, Maksym Serbyn, and Alexios Michailidis. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.060602."},"article_type":"letter_note","file_date_updated":"2021-08-13T09:28:08Z","ec_funded":1,"article_number":"060602","author":[{"orcid":"0000-0002-6963-0129","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","last_name":"Karle","first_name":"Volker","full_name":"Karle, Volker"},{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","first_name":"Alexios","full_name":"Michailidis, Alexios"}],"date_updated":"2023-08-11T10:43:27Z","date_created":"2021-08-13T09:27:39Z","volume":127,"acknowledgement":"We acknowledge useful discussions with V. Gritsev and A. Garkun and suggestions on implementation of the\r\nPPXPP model by D. Bluvstein. A. M. and M. S. were supported by the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899)","year":"2021","publication_status":"published","department":[{"_id":"MaSe"},{"_id":"GradSch"},{"_id":"MiLe"}],"publisher":"American Physical Society","month":"08","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"doi":"10.1103/physrevlett.127.060602","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":["000684276000002"],"arxiv":["2102.13633"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}]},{"article_number":"jcs255018","file_date_updated":"2021-08-23T07:32:20Z","year":"2021","acknowledgement":"We would like to thank the entire Paluch and Baum laboratories at the MRC-LMCB and the Chalut lab at the Cambridge SCI for discussions and feedback throughout the project, and the MRC-LMCB microscopy platform, in particular Andrew Vaughan, for technical support.","department":[{"_id":"EdHa"}],"publisher":"The Company of Biologists","publication_status":"published","author":[{"full_name":"Chaigne, Agathe","first_name":"Agathe","last_name":"Chaigne"},{"first_name":"Matthew B.","last_name":"Smith","full_name":"Smith, Matthew B."},{"full_name":"Cavestany, R. L.","last_name":"Cavestany","first_name":"R. L."},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"last_name":"Chalut","first_name":"Kevin J.","full_name":"Chalut, Kevin J."},{"full_name":"Paluch, Ewa K.","last_name":"Paluch","first_name":"Ewa K."}],"volume":134,"date_created":"2021-08-22T22:01:20Z","date_updated":"2023-08-11T10:55:36Z","publication_identifier":{"issn":["00219533"],"eissn":["14779137"]},"month":"07","external_id":{"isi":["000681395800008"]},"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,"isi":1,"quality_controlled":"1","doi":"10.1242/jcs.255018","language":[{"iso":"eng"}],"type":"journal_article","issue":"14","abstract":[{"text":"Proper control of division orientation and symmetry, largely determined by spindle positioning, is essential to development and homeostasis. Spindle positioning has been extensively studied in cells dividing in two-dimensional (2D) environments and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient division along the interphase long axis of the cell. However, little is known about how cells control spindle positioning in three-dimensional (3D) environments, such as early mammalian embryos and a variety of adult tissues. Here, we use mouse embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate division in 3D. We observe that, at the periphery of 3D colonies, ESCs display high spindle mobility and divide asymmetrically. Our data suggest that enhanced spindle movements are due to unequal distribution of the cell–cell junction protein E-cadherin between future daughter cells. Interestingly, when cells progress towards differentiation, division becomes more symmetric, with more elongated shapes in metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this study suggests that in 3D contexts, the geometry of the cell and its contacts with neighbors control division orientation and symmetry.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9952","intvolume":" 134","title":"Three-dimensional geometry controls division symmetry in stem cell colonies","status":"public","ddc":["570"],"file":[{"relation":"main_file","file_id":"9954","checksum":"f086f9d7cb63b2474c01921cb060c513","success":1,"date_created":"2021-08-23T07:32:20Z","date_updated":"2021-08-23T07:32:20Z","access_level":"open_access","file_name":"2021_JournalOfCellScience_Chaigne.pdf","content_type":"application/pdf","file_size":8651724,"creator":"asandaue"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","citation":{"ista":"Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. 2021. Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. 134(14), jcs255018.","ieee":"A. Chaigne, M. B. Smith, R. L. Cavestany, E. B. Hannezo, K. J. Chalut, and E. K. Paluch, “Three-dimensional geometry controls division symmetry in stem cell colonies,” Journal of Cell Science, vol. 134, no. 14. The Company of Biologists, 2021.","apa":"Chaigne, A., Smith, M. B., Cavestany, R. L., Hannezo, E. B., Chalut, K. J., & Paluch, E. K. (2021). Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.255018","ama":"Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. 2021;134(14). doi:10.1242/jcs.255018","chicago":"Chaigne, Agathe, Matthew B. Smith, R. L. Cavestany, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” Journal of Cell Science. The Company of Biologists, 2021. https://doi.org/10.1242/jcs.255018.","mla":"Chaigne, Agathe, et al. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” Journal of Cell Science, vol. 134, no. 14, jcs255018, The Company of Biologists, 2021, doi:10.1242/jcs.255018.","short":"A. Chaigne, M.B. Smith, R.L. Cavestany, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Journal of Cell Science 134 (2021)."},"publication":"Journal of Cell Science","article_type":"original","date_published":"2021-07-01T00:00:00Z"},{"_id":"9908","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 12","ddc":["570"],"title":"Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict","status":"public","oa_version":"Published Version","file":[{"creator":"asandaue","content_type":"application/pdf","file_size":2297655,"access_level":"open_access","file_name":"2021_Genes_Picard.pdf","success":1,"checksum":"744e60e56d290a96da3c91a9779f886f","date_created":"2021-08-16T09:49:35Z","date_updated":"2021-08-16T09:49:35Z","file_id":"9926","relation":"main_file"}],"type":"journal_article","issue":"8","abstract":[{"text":"About eight million animal species are estimated to live on Earth, and all except those belonging to one subphylum are invertebrates. Invertebrates are incredibly diverse in their morphologies, life histories, and in the range of the ecological niches that they occupy. A great variety of modes of reproduction and sex determination systems is also observed among them, and their mosaic-distribution across the phylogeny shows that transitions between them occur frequently and rapidly. Genetic conflict in its various forms is a long-standing theory to explain what drives those evolutionary transitions. Here, we review (1) the different modes of reproduction among invertebrate species, highlighting sexual reproduction as the probable ancestral state; (2) the paradoxical diversity of sex determination systems; (3) the different types of genetic conflicts that could drive the evolution of such different systems.","lang":"eng"}],"citation":{"ista":"Picard MAL, Vicoso B, Bertrand S, Escriva H. 2021. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. 12(8), 1136.","apa":"Picard, M. A. L., Vicoso, B., Bertrand, S., & Escriva, H. (2021). Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. MDPI. https://doi.org/10.3390/genes12081136","ieee":"M. A. L. Picard, B. Vicoso, S. Bertrand, and H. Escriva, “Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict,” Genes, vol. 12, no. 8. MDPI, 2021.","ama":"Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. 2021;12(8). doi:10.3390/genes12081136","chicago":"Picard, Marion A L, Beatriz Vicoso, Stéphanie Bertrand, and Hector Escriva. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12081136.","mla":"Picard, Marion A. L., et al. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” Genes, vol. 12, no. 8, 1136, MDPI, 2021, doi:10.3390/genes12081136.","short":"M.A.L. Picard, B. Vicoso, S. Bertrand, H. Escriva, Genes 12 (2021)."},"publication":"Genes","article_type":"review","date_published":"2021-08-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","year":"2021","department":[{"_id":"BeVi"}],"publisher":"MDPI","publication_status":"published","author":[{"full_name":"Picard, Marion A L","first_name":"Marion A L","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bertrand","first_name":"Stéphanie","full_name":"Bertrand, Stéphanie"},{"full_name":"Escriva, Hector","first_name":"Hector","last_name":"Escriva"}],"volume":12,"date_created":"2021-08-15T22:01:27Z","date_updated":"2023-08-11T10:42:32Z","article_number":"1136","ec_funded":1,"file_date_updated":"2021-08-16T09:49:35Z","external_id":{"isi":["000690475900001"]},"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":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.3390/genes12081136","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20734425"]},"month":"08"},{"abstract":[{"text":"In 2020, many in-person scientific events were canceled due to the COVID-19 pandemic, creating a vacuum in networking and knowledge exchange between scientists. To fill this void in scientific communication, a group of early career nanocrystal enthusiasts launched the virtual seminar series, News in Nanocrystals, in the summer of 2020. By the end of the year, the series had attracted over 850 participants from 46 countries. In this Nano Focus, we describe the process of organizing the News in Nanocrystals seminar series; discuss its growth, emphasizing what the organizers have learned in terms of diversity and accessibility; and provide an outlook for the next steps and future opportunities. This summary and analysis of experiences and learned lessons are intended to inform the broader scientific community, especially those who are looking for avenues to continue fostering discussion and scientific engagement virtually, both during the pandemic and after.","lang":"eng"}],"issue":"7","type":"journal_article","oa_version":"Published Version","title":"News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience","status":"public","intvolume":" 15","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9829","day":"06","article_processing_charge":"No","scopus_import":"1","date_published":"2021-07-06T00:00:00Z","article_type":"original","page":"10743–10747","publication":"ACS Nano","citation":{"apa":"Baranov, D., Šverko, T., Moot, T., Keller, H. R., Klein, M. D., Vishnu, E. K., … Shulenberger, K. E. (2021). News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.1c03276","ieee":"D. Baranov et al., “News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience,” ACS Nano, vol. 15, no. 7. American Chemical Society, pp. 10743–10747, 2021.","ista":"Baranov D, Šverko T, Moot T, Keller HR, Klein MD, Vishnu EK, Balazs D, Shulenberger KE. 2021. News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. ACS Nano. 15(7), 10743–10747.","ama":"Baranov D, Šverko T, Moot T, et al. News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. ACS Nano. 2021;15(7):10743–10747. doi:10.1021/acsnano.1c03276","chicago":"Baranov, Dmitry, Tara Šverko, Taylor Moot, Helena R. Keller, Megan D. Klein, E. K. Vishnu, Daniel Balazs, and Katherine E. Shulenberger. “News in Nanocrystals Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible Nanoscience.” ACS Nano. American Chemical Society, 2021. https://doi.org/10.1021/acsnano.1c03276.","short":"D. Baranov, T. Šverko, T. Moot, H.R. Keller, M.D. Klein, E.K. Vishnu, D. Balazs, K.E. Shulenberger, ACS Nano 15 (2021) 10743–10747.","mla":"Baranov, Dmitry, et al. “News in Nanocrystals Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible Nanoscience.” ACS Nano, vol. 15, no. 7, American Chemical Society, 2021, pp. 10743–10747, doi:10.1021/acsnano.1c03276."},"date_updated":"2023-08-11T10:55:08Z","date_created":"2021-08-08T22:01:31Z","volume":15,"author":[{"full_name":"Baranov, Dmitry","last_name":"Baranov","first_name":"Dmitry"},{"full_name":"Šverko, Tara","first_name":"Tara","last_name":"Šverko"},{"last_name":"Moot","first_name":"Taylor","full_name":"Moot, Taylor"},{"first_name":"Helena R.","last_name":"Keller","full_name":"Keller, Helena R."},{"full_name":"Klein, Megan D.","last_name":"Klein","first_name":"Megan D."},{"first_name":"E. K.","last_name":"Vishnu","full_name":"Vishnu, E. K."},{"full_name":"Balazs, Daniel","orcid":"0000-0001-7597-043X","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs","first_name":"Daniel"},{"full_name":"Shulenberger, Katherine E.","last_name":"Shulenberger","first_name":"Katherine E."}],"publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","acknowledgement":"K. E. Shulenberger, M. D. Klein, T. Šverko, and H. R. Keller would like to thank Professors Moungi Bawendi (MIT) and Gordana Dukovic (CU Boulder) for their feedback and support of the News in Nanocrystals initiative. The authors thank Madison Jilek (CU Boulder) and Dhananjeya Kumaar (ETH Zurich) for their help in the organization of the seminar, and Professors Brandi Cossairt (University of Washington) and Gordana Dukovic for their feedback on an earlier version of this manuscript. The authors thank all the seminar speakers and attendees for their interest and continuing participation in the seminar series.","year":"2021","pmid":1,"month":"07","publication_identifier":{"issn":["19360851"],"eissn":["1936086X"]},"language":[{"iso":"eng"}],"doi":"10.1021/acsnano.1c03276","quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acsnano.1c03276"}],"external_id":{"isi":["000679406500002"],"pmid":["34228432"]},"oa":1},{"status":"public","ddc":["530"],"title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction","publisher":"Zenodo","department":[{"_id":"JoFi"}],"_id":"13057","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-05-23T13:42:27Z","date_updated":"2023-08-11T10:44:21Z","oa_version":"Published Version","author":[{"full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","first_name":"Matilda","last_name":"Peruzzo"},{"full_name":"Hassani, Farid","first_name":"Farid","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773"},{"first_name":"Grisha","last_name":"Szep","full_name":"Szep, Grisha"},{"full_name":"Trioni, Andrea","last_name":"Trioni","first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena"},{"full_name":"Zemlicka, Martin","first_name":"Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"related_material":{"record":[{"id":"9928","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction\". Additional raw data are available from the corresponding author on reasonable request."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"chicago":"Peruzzo, Matilda, Farid Hassani, Grisha Szep, Andrea Trioni, Elena Redchenko, Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5592103.","short":"M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, (2021).","mla":"Peruzzo, Matilda, et al. Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction. Zenodo, 2021, doi:10.5281/ZENODO.5592103.","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. Zenodo. https://doi.org/10.5281/ZENODO.5592103","ieee":"M. Peruzzo et al., “Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction.” Zenodo, 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, Zenodo, 10.5281/ZENODO.5592103.","ama":"Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. 2021. doi:10.5281/ZENODO.5592103"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5592104","open_access":"1"}],"doi":"10.5281/ZENODO.5592103","date_published":"2021-10-22T00:00:00Z","month":"10","day":"22","article_processing_charge":"No"},{"file_date_updated":"2021-09-08T12:57:06Z","article_number":"5083","volume":12,"date_created":"2021-09-05T22:01:23Z","date_updated":"2023-08-11T11:07:51Z","author":[{"full_name":"Watson, Jake","last_name":"Watson","first_name":"Jake","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"last_name":"Pinggera","first_name":"Alexandra","full_name":"Pinggera, Alexandra"},{"full_name":"Ho, Hinze","last_name":"Ho","first_name":"Hinze"},{"full_name":"Greger, Ingo H.","last_name":"Greger","first_name":"Ingo H."}],"department":[{"_id":"PeJo"}],"publisher":"Nature Publishing Group","publication_status":"published","pmid":1,"acknowledgement":"The authors are very grateful to Andrew Penn for advice and discussions on surface receptor labelling in slice tissue, dissociated culture transfection, and for providing tdTomato and BirAER expression plasmids. This work would not have been possible without support from the Biological Services teams at both the Laboratory of Molecular Biology and Ares facilities. We are also very grateful to Nick Barry and Jerome Boulanger of the LMB Light Microscopy facility for support with confocal and STORM imaging and analysis, Junichi Takagi for providing scFv-Clasp expression constructs, Veronica Chang for assistance with scFv-Clasp protein production, and Nejc Kejzar for assistance with cluster analysis. We would like to thank Teru Nakagawa and Ole Paulsen for critical reading of the manuscript and constructive feedback. This work was supported by grants from the Medical Research Council (MC_U105174197) and BBSRC (BB/N002113/1).","year":"2021","publication_identifier":{"eissn":["2041-1723"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1038/s41467-021-25281-4","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":{"isi":["000687672000006"],"pmid":["34426577 "]},"issue":"1","abstract":[{"text":"AMPA receptor (AMPAR) abundance and positioning at excitatory synapses regulates the strength of transmission. Changes in AMPAR localisation can enact synaptic plasticity, allowing long-term information storage, and is therefore tightly controlled. Multiple mechanisms regulating AMPAR synaptic anchoring have been described, but with limited coherence or comparison between reports, our understanding of this process is unclear. Here, combining synaptic recordings from mouse hippocampal slices and super-resolution imaging in dissociated cultures, we compare the contributions of three AMPAR interaction domains controlling transmission at hippocampal CA1 synapses. We show that the AMPAR C-termini play only a modulatory role, whereas the extracellular N-terminal domain (NTD) and PDZ interactions of the auxiliary subunit TARP γ8 are both crucial, and each is sufficient to maintain transmission. Our data support a model in which γ8 accumulates AMPARs at the postsynaptic density, where the NTD further tunes their positioning. This interplay between cytosolic (TARP γ8) and synaptic cleft (NTD) interactions provides versatility to regulate synaptic transmission and plasticity.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2021_NatureCommunications_Watson.pdf","access_level":"open_access","creator":"cchlebak","file_size":18310502,"content_type":"application/pdf","file_id":"9991","relation":"main_file","date_created":"2021-09-08T12:57:06Z","date_updated":"2021-09-08T12:57:06Z","success":1,"checksum":"1bf4f6a561f96bc426d754de9cb57710"}],"oa_version":"Published Version","intvolume":" 12","title":"AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions","ddc":["612"],"status":"public","_id":"9985","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","has_accepted_license":"1","day":"23","scopus_import":"1","date_published":"2021-08-23T00:00:00Z","article_type":"original","citation":{"ista":"Watson J, Pinggera A, Ho H, Greger IH. 2021. AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications. 12(1), 5083.","apa":"Watson, J., Pinggera, A., Ho, H., & Greger, I. H. (2021). AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-021-25281-4","ieee":"J. Watson, A. Pinggera, H. Ho, and I. H. Greger, “AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions,” Nature Communications, vol. 12, no. 1. Nature Publishing Group, 2021.","ama":"Watson J, Pinggera A, Ho H, Greger IH. AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-25281-4","chicago":"Watson, Jake, Alexandra Pinggera, Hinze Ho, and Ingo H. Greger. “AMPA Receptor Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.” Nature Communications. Nature Publishing Group, 2021. https://doi.org/10.1038/s41467-021-25281-4.","mla":"Watson, Jake, et al. “AMPA Receptor Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.” Nature Communications, vol. 12, no. 1, 5083, Nature Publishing Group, 2021, doi:10.1038/s41467-021-25281-4.","short":"J. Watson, A. Pinggera, H. Ho, I.H. Greger, Nature Communications 12 (2021)."},"publication":"Nature Communications"},{"type":"journal_article","abstract":[{"lang":"eng","text":"The numerical simulation of dynamical phenomena in interacting quantum systems is a notoriously hard problem. Although a number of promising numerical methods exist, they often have limited applicability due to the growth of entanglement or the presence of the so-called sign problem. In this work, we develop an importance sampling scheme for the simulation of quantum spin dynamics, building on a recent approach mapping quantum spin systems to classical stochastic processes. The importance sampling scheme is based on identifying the classical trajectory that yields the largest contribution to a given quantum observable. An exact transformation is then carried out to preferentially sample trajectories that are close to the dominant one. We demonstrate that this approach is capable of reducing the temporal growth of fluctuations in the stochastic quantities, thus extending the range of accessible times and system sizes compared to direct sampling. We discuss advantages and limitations of the proposed approach, outlining directions\r\nfor further developments."}],"issue":"3","title":"Importance sampling scheme for the stochastic simulation of quantum spin dynamics","status":"public","ddc":["519"],"intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9981","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":373833,"creator":"cchlebak","access_level":"open_access","file_name":"2021_SciPostPhys_DeNicola.pdf","checksum":"e4ec69d893e31811efc6093cb6ea8eb7","success":1,"date_updated":"2021-09-02T14:05:43Z","date_created":"2021-09-02T14:05:43Z","relation":"main_file","file_id":"9984"}],"keyword":["General Physics and Astronomy"],"day":"02","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"SciPost Physics","citation":{"mla":"De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation of Quantum Spin Dynamics.” SciPost Physics, vol. 11, no. 3, 048, SciPost, 2021, doi:10.21468/scipostphys.11.3.048.","short":"S. De Nicola, SciPost Physics 11 (2021).","chicago":"De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation of Quantum Spin Dynamics.” SciPost Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.3.048.","ama":"De Nicola S. Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. 2021;11(3). doi:10.21468/scipostphys.11.3.048","ista":"De Nicola S. 2021. Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. 11(3), 048.","apa":"De Nicola, S. (2021). Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. SciPost. https://doi.org/10.21468/scipostphys.11.3.048","ieee":"S. De Nicola, “Importance sampling scheme for the stochastic simulation of quantum spin dynamics,” SciPost Physics, vol. 11, no. 3. SciPost, 2021."},"date_published":"2021-09-02T00:00:00Z","article_number":"048","file_date_updated":"2021-09-02T14:05:43Z","ec_funded":1,"publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"SciPost","year":"2021","date_updated":"2023-08-11T10:59:29Z","date_created":"2021-09-02T11:49:47Z","volume":11,"author":[{"orcid":"0000-0002-4842-6671","id":"42832B76-F248-11E8-B48F-1D18A9856A87","last_name":"De Nicola","first_name":"Stefano","full_name":"De Nicola, Stefano"}],"month":"09","publication_identifier":{"eissn":["2666-9366"],"issn":["2542-4653"]},"isi":1,"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"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":["2103.16468"],"isi":["000692534200001"]},"language":[{"iso":"eng"}],"doi":"10.21468/scipostphys.11.3.048"},{"date_updated":"2023-08-11T10:56:04Z","date_created":"2021-08-22T22:01:20Z","oa_version":"None","author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"id":"4B865388-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Töpfer","full_name":"Töpfer, Martin"},{"full_name":"Uznański, Przemysław","last_name":"Uznański","first_name":"Przemysław"}],"title":"Comparison dynamics in population protocols","status":"public","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"year":"2021","_id":"9951","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We would like to thank Rati Gelashvili for very useful discussions, and the PODC anonymous reviewers for their careful reading of our paper, and for their useful remarks. This work is partially supported by the Polish National Science Center (NCN) grant UMO2017/25/B/ST6/02010.","abstract":[{"text":"There has recently been a surge of interest in the computational and complexity properties of the population model, which assumes n anonymous, computationally-bounded nodes, interacting at random, with the goal of jointly computing global predicates. Significant work has gone towards investigating majority or consensus dynamics in this model: that is, assuming that every node is initially in one of two states X or Y, determine which state had higher initial count.\r\n\r\nIn this paper, we consider a natural generalization of majority/consensus, which we call comparison : in its simplest formulation, we are given two baseline states, X and Y, present in any initial configuration in fixed, but possibly small counts. One of these states has higher count than the other: we will assume |X_0| > C |Y_0| for some constant C > 1. The challenge is to design a protocol by which nodes can quickly and reliably decide on which of the baseline states X_0 and Y_0 has higher initial count. We begin by analyzing a simple and general dynamics solving the above comparison problem, which uses O( log n ) states per node, and converges in O(log n) (parallel) time, with high probability, to a state where the whole population votes on opinions X or Y at rates proportional to the initial concentrations of |X_0| vs. |Y_0|. We then describe how this procedure can be bootstrapped to solve comparison, i.e. have every node in the population reach the \"correct'' decision, with probability 1 - o(1), at the cost of O (log log n) additional states. Further, we prove that this dynamics is self-stabilizing, in the sense that it converges to the correct decision from arbitrary initial states, and leak-robust, in the sense that it can withstand spurious faulty reactions, which are known to occur in practical implementations of population protocols. Our analysis is based on a new martingale concentration result relating the discrete-time evolution of a population protocol to its expected (steady-state) analysis, which should be a useful tool when analyzing opinion dynamics and epidemic dissemination in the population model.","lang":"eng"}],"type":"conference","language":[{"iso":"eng"}],"conference":{"start_date":"2021-07-26","location":"Virtual, Italy","end_date":"2021-07-30","name":"PODC: Symposium on Principles of Distributed Computing"},"date_published":"2021-07-21T00:00:00Z","doi":"10.1145/3465084.3467915","quality_controlled":"1","isi":1,"page":"55-65","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","external_id":{"isi":["000744439800005"]},"citation":{"mla":"Alistarh, Dan-Adrian, et al. “Comparison Dynamics in Population Protocols.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 55–65, doi:10.1145/3465084.3467915.","short":"D.-A. Alistarh, M. Töpfer, P. Uznański, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 55–65.","chicago":"Alistarh, Dan-Adrian, Martin Töpfer, and Przemysław Uznański. “Comparison Dynamics in Population Protocols.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 55–65. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467915.","ama":"Alistarh D-A, Töpfer M, Uznański P. Comparison dynamics in population protocols. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:55-65. doi:10.1145/3465084.3467915","ista":"Alistarh D-A, Töpfer M, Uznański P. 2021. Comparison dynamics in population protocols. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 55–65.","ieee":"D.-A. Alistarh, M. Töpfer, and P. Uznański, “Comparison dynamics in population protocols,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 55–65.","apa":"Alistarh, D.-A., Töpfer, M., & Uznański, P. (2021). Comparison dynamics in population protocols. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 55–65). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467915"},"month":"07","day":"21","publication_identifier":{"isbn":["9781450385480"]},"article_processing_charge":"No","scopus_import":"1"},{"volume":127,"date_created":"2021-08-28T08:08:58Z","date_updated":"2023-08-11T10:57:51Z","author":[{"last_name":"Maskara","first_name":"N.","full_name":"Maskara, N."},{"last_name":"Michailidis","first_name":"Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios"},{"full_name":"Ho, W. W.","last_name":"Ho","first_name":"W. W."},{"full_name":"Bluvstein, D.","last_name":"Bluvstein","first_name":"D."},{"last_name":"Choi","first_name":"S.","full_name":"Choi, S."},{"full_name":"Lukin, M. D.","first_name":"M. D.","last_name":"Lukin"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"}],"publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","acknowledgement":"We thank Dmitry Abanin, Ehud Altman, Iris Cong, Sepehr Ebadi, Alex Keesling, Harry Levine, Ahmed Omran, Hannes Pichler, Rhine Samajdar, Guilia Semeghini, Tout Wang, Norman Yao, and Harry Zhou or stimulating discussions. We acknowledge support from the Center for Ultracold Atoms, the National Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of Energy, the Army Research Office MURI, and the DARPA ONISQ program (M. L., N. M, W. W. H., D. B.); the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme Grant Agreement No. 850899 (A. M. and M. S.); the Department of Energy Computational Science Graduate Fellowship under Awards No. DESC0021110 (N. M.); the Moore Foundation EPiQS initiative Grant No. GBMF4306, the National University of Singapore (NUS) Development Grant AY2019/2020 and the Stanford Institute for Theoretical Physics (W. W. H.); the NSF Graduate Research Fellowship Program (Grant No. DGE1745303) and The Fannie and John Hertz Foundation (D. B.); the Miller Institute for Basic Research in Science (S. C.); DOE Quantum Systems Accelerator – Contract No. 7568717; and DOE Programmable Quantum Simulators for Lattice Gauge Theories and Gauge-Gravity Correspondence – Grant No. DE-SC0021013.","year":"2021","ec_funded":1,"article_number":"090602","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.127.090602","project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000692200100002"],"arxiv":["2102.13160"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.13160"}],"oa":1,"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"month":"08","oa_version":"Submitted Version","intvolume":" 127","title":"Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving","status":"public","_id":"9960","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"9","abstract":[{"lang":"eng","text":"The control of many-body quantum dynamics in complex systems is a key challenge in the quest to reliably produce and manipulate large-scale quantum entangled states. Recently, quench experiments in Rydberg atom arrays [Bluvstein et al. Science 371, 1355 (2021)] demonstrated that coherent revivals associated with quantum many-body scars can be stabilized by periodic driving, generating stable subharmonic responses over a wide parameter regime. We analyze a simple, related model where these phenomena originate from spatiotemporal ordering in an effective Floquet unitary, corresponding to discrete time-crystalline behavior in a prethermal regime. Unlike conventional discrete time crystals, the subharmonic response exists only for Néel-like initial states, associated with quantum scars. We predict robustness to perturbations and identify emergent timescales that could be observed in future experiments. Our results suggest a route to controlling entanglement in interacting quantum systems by combining periodic driving with many-body scars."}],"type":"journal_article","date_published":"2021-08-27T00:00:00Z","article_type":"letter_note","citation":{"ista":"Maskara N, Michailidis A, Ho WW, Bluvstein D, Choi S, Lukin MD, Serbyn M. 2021. Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. Physical Review Letters. 127(9), 090602.","apa":"Maskara, N., Michailidis, A., Ho, W. W., Bluvstein, D., Choi, S., Lukin, M. D., & Serbyn, M. (2021). Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.127.090602","ieee":"N. Maskara et al., “Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving,” Physical Review Letters, vol. 127, no. 9. American Physical Society, 2021.","ama":"Maskara N, Michailidis A, Ho WW, et al. Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. Physical Review Letters. 2021;127(9). doi:10.1103/PhysRevLett.127.090602","chicago":"Maskara, N., Alexios Michailidis, W. W. Ho, D. Bluvstein, S. Choi, M. D. Lukin, and Maksym Serbyn. “Discrete Time-Crystalline Order Enabled by Quantum Many-Body Scars: Entanglement Steering via Periodic Driving.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.127.090602.","mla":"Maskara, N., et al. “Discrete Time-Crystalline Order Enabled by Quantum Many-Body Scars: Entanglement Steering via Periodic Driving.” Physical Review Letters, vol. 127, no. 9, 090602, American Physical Society, 2021, doi:10.1103/PhysRevLett.127.090602.","short":"N. Maskara, A. Michailidis, W.W. Ho, D. Bluvstein, S. Choi, M.D. Lukin, M. Serbyn, Physical Review Letters 127 (2021)."},"publication":"Physical Review Letters","article_processing_charge":"No","day":"27"},{"month":"08","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"external_id":{"isi":["000689734500009"],"arxiv":["2012.15676"]},"main_file_link":[{"url":"https://arxiv.org/abs/2012.15676","open_access":"1"}],"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"doi":"10.1103/PhysRevB.104.L081112","language":[{"iso":"eng"}],"article_number":"L081112","ec_funded":1,"acknowledgement":"We thank S. Garratt for useful comments on the manuscript. This work was supported by the Swiss National Science Foundation (M. Sonner and D.A.A.) and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (M. Serbyn, Grant Agreement No. 850899, and D.A.A., Grant Agreement No. 864597). Z.P. acknowledges support from EPSRC Grant No. EP/R020612/1 and from Leverhulme Trust Research Leadership Award No. RL-2019-015. The computations were performed on the Baobab cluster of the University\r\nof Geneva.","year":"2021","publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","author":[{"first_name":"Michael","last_name":"Sonner","full_name":"Sonner, Michael"},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"},{"last_name":"Papić","first_name":"Zlatko","full_name":"Papić, Zlatko"},{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"}],"date_created":"2021-08-28T16:44:55Z","date_updated":"2023-08-11T10:57:09Z","volume":104,"day":"15","article_processing_charge":"No","publication":"Physical Review B","citation":{"ama":"Sonner M, Serbyn M, Papić Z, Abanin DA. Thouless energy across the many-body localization transition in Floquet systems. Physical Review B. 2021;104(8). doi:10.1103/PhysRevB.104.L081112","ieee":"M. Sonner, M. Serbyn, Z. Papić, and D. A. Abanin, “Thouless energy across the many-body localization transition in Floquet systems,” Physical Review B, vol. 104, no. 8. American Physical Society, 2021.","apa":"Sonner, M., Serbyn, M., Papić, Z., & Abanin, D. A. (2021). Thouless energy across the many-body localization transition in Floquet systems. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.104.L081112","ista":"Sonner M, Serbyn M, Papić Z, Abanin DA. 2021. Thouless energy across the many-body localization transition in Floquet systems. Physical Review B. 104(8), L081112.","short":"M. Sonner, M. Serbyn, Z. Papić, D.A. Abanin, Physical Review B 104 (2021).","mla":"Sonner, Michael, et al. “Thouless Energy across the Many-Body Localization Transition in Floquet Systems.” Physical Review B, vol. 104, no. 8, L081112, American Physical Society, 2021, doi:10.1103/PhysRevB.104.L081112.","chicago":"Sonner, Michael, Maksym Serbyn, Zlatko Papić, and Dmitry A. Abanin. “Thouless Energy across the Many-Body Localization Transition in Floquet Systems.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/PhysRevB.104.L081112."},"article_type":"letter_note","date_published":"2021-08-15T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The notion of Thouless energy plays a central role in the theory of Anderson localization. We investigate and compare the scaling of Thouless energy across the many-body localization (MBL) transition in a Floquet model. We use a combination of methods that are reliable on the ergodic side of the transition (e.g., spectral form factor) and methods that work on the MBL side (e.g., typical matrix elements of local operators) to obtain a complete picture of the Thouless energy behavior across the transition. On the ergodic side, Thouless energy decreases slowly with the system size, while at the transition it becomes comparable to the level spacing. Different probes yield consistent estimates of Thouless energy in their overlapping regime of applicability, giving the location of the transition point nearly free of finite-size drift. This work establishes a connection between different definitions of Thouless energy in a many-body setting and yields insights into the MBL transition in Floquet systems."}],"issue":"8","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9961","status":"public","title":"Thouless energy across the many-body localization transition in Floquet systems","intvolume":" 104","oa_version":"Submitted Version"},{"type":"conference","abstract":[{"lang":"eng","text":"The reflectance field of a face describes the reflectance properties responsible for complex lighting effects including diffuse, specular, inter-reflection and self shadowing. Most existing methods for estimating the face reflectance from a monocular image assume faces to be diffuse with very few approaches adding a specular component. This still leaves out important perceptual aspects of reflectance as higher-order global illumination effects and self-shadowing are not modeled. We present a new neural representation for face reflectance where we can estimate all components of the reflectance responsible for the final appearance from a single monocular image. Instead of modeling each component of the reflectance separately using parametric models, our neural representation allows us to generate a basis set of faces in a geometric deformation-invariant space, parameterized by the input light direction, viewpoint and face geometry. We learn to reconstruct this reflectance field of a face just from a monocular image, which can be used to render the face from any viewpoint in any light condition. Our method is trained on a light-stage training dataset, which captures 300 people illuminated with 150 light conditions from 8 viewpoints. We show that our method outperforms existing monocular reflectance reconstruction methods, in terms of photorealism due to better capturing of physical premitives, such as sub-surface scattering, specularities, self-shadows and other higher-order effects."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9957","status":"public","title":"Monocular reconstruction of neural face reflectance fields","ddc":["000"],"oa_version":"Preprint","file":[{"file_id":"9958","relation":"main_file","date_updated":"2021-08-24T06:02:15Z","date_created":"2021-08-24T06:02:15Z","checksum":"961db0bde76dd87cf833930080bb9f38","file_name":"R_Monocular_Reconstruction_of_Neural_Face_Reflectance_Fields_CVPR_2021_paper[1].pdf","access_level":"open_access","creator":"bbickel","file_size":4746649,"content_type":"application/pdf"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"chicago":"B R, Mallikarjun, Ayush Tewari, Tae-Hyun Oh, Tim Weyrich, Bernd Bickel, Hans-Peter Seidel, Hanspeter Pfister, Wojciech Matusik, Mohamed Elgharib, and Christian Theobalt. “Monocular Reconstruction of Neural Face Reflectance Fields.” In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 4791–4800. IEEE, 2021. https://doi.org/10.1109/CVPR46437.2021.00476.","short":"M. B R, A. Tewari, T.-H. Oh, T. Weyrich, B. Bickel, H.-P. Seidel, H. Pfister, W. Matusik, M. Elgharib, C. Theobalt, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2021, pp. 4791–4800.","mla":"B R, Mallikarjun, et al. “Monocular Reconstruction of Neural Face Reflectance Fields.” Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2021, pp. 4791–800, doi:10.1109/CVPR46437.2021.00476.","apa":"B R, M., Tewari, A., Oh, T.-H., Weyrich, T., Bickel, B., Seidel, H.-P., … Theobalt, C. (2021). Monocular reconstruction of neural face reflectance fields. In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (pp. 4791–4800). Nashville, TN, United States; Virtual: IEEE. https://doi.org/10.1109/CVPR46437.2021.00476","ieee":"M. B R et al., “Monocular reconstruction of neural face reflectance fields,” in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Nashville, TN, United States; Virtual, 2021, pp. 4791–4800.","ista":"B R M, Tewari A, Oh T-H, Weyrich T, Bickel B, Seidel H-P, Pfister H, Matusik W, Elgharib M, Theobalt C. 2021. Monocular reconstruction of neural face reflectance fields. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 4791–4800.","ama":"B R M, Tewari A, Oh T-H, et al. Monocular reconstruction of neural face reflectance fields. In: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE; 2021:4791-4800. doi:10.1109/CVPR46437.2021.00476"},"publication":"Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition","page":"4791-4800","date_published":"2021-09-01T00:00:00Z","file_date_updated":"2021-08-24T06:02:15Z","acknowledgement":"We thank Tarun Yenamandra and Duarte David for helping us with the comparisons. This work was supported by the\r\nERC Consolidator Grant 4DReply (770784). We also acknowledge support from InterDigital.","year":"2021","publisher":"IEEE","department":[{"_id":"BeBi"}],"publication_status":"published","author":[{"full_name":"B R, Mallikarjun","first_name":"Mallikarjun","last_name":"B R"},{"first_name":"Ayush","last_name":"Tewari","full_name":"Tewari, Ayush"},{"last_name":"Oh","first_name":"Tae-Hyun","full_name":"Oh, Tae-Hyun"},{"last_name":"Weyrich","first_name":"Tim","full_name":"Weyrich, Tim"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"},{"last_name":"Seidel","first_name":"Hans-Peter","full_name":"Seidel, Hans-Peter"},{"full_name":"Pfister, Hanspeter","first_name":"Hanspeter","last_name":"Pfister"},{"last_name":"Matusik","first_name":"Wojciech","full_name":"Matusik, Wojciech"},{"full_name":"Elgharib, Mohamed","first_name":"Mohamed","last_name":"Elgharib"},{"first_name":"Christian","last_name":"Theobalt","full_name":"Theobalt, Christian"}],"date_created":"2021-08-24T06:03:00Z","date_updated":"2023-08-11T11:08:35Z","publication_identifier":{"isbn":["978-166544509-2"],"issn":["1063-6919"]},"month":"09","external_id":{"arxiv":["2008.10247"],"isi":["000739917304096"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1109/CVPR46437.2021.00476","conference":{"name":"CVPR: Conference on Computer Vision and Pattern Recognition","end_date":"2021-06-25","location":"Nashville, TN, United States; Virtual","start_date":"2021-06-20"},"language":[{"iso":"eng"}]},{"type":"journal_article","abstract":[{"text":"In this article we introduce a complete gradient estimate for symmetric quantum Markov semigroups on von Neumann algebras equipped with a normal faithful tracial state, which implies semi-convexity of the entropy with respect to the recently introduced noncommutative 2-Wasserstein distance. We show that this complete gradient estimate is stable under tensor products and free products and establish its validity for a number of examples. As an application we prove a complete modified logarithmic Sobolev inequality with optimal constant for Poisson-type semigroups on free group factors.","lang":"eng"}],"_id":"9973","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 387","status":"public","ddc":["621"],"title":"Complete gradient estimates of quantum Markov semigroups","file":[{"relation":"main_file","file_id":"9990","checksum":"8a602f916b1c2b0dc1159708b7cb204b","date_created":"2021-09-08T07:34:24Z","date_updated":"2021-09-08T09:46:34Z","access_level":"open_access","file_name":"2021_CommunMathPhys_Wirth.pdf","file_size":505971,"content_type":"application/pdf","creator":"cchlebak"}],"oa_version":"Published Version","scopus_import":"1","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"30","citation":{"short":"M. Wirth, H. Zhang, Communications in Mathematical Physics 387 (2021) 761–791.","mla":"Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum Markov Semigroups.” Communications in Mathematical Physics, vol. 387, Springer Nature, 2021, pp. 761–791, doi:10.1007/s00220-021-04199-4.","chicago":"Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum Markov Semigroups.” Communications in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s00220-021-04199-4.","ama":"Wirth M, Zhang H. Complete gradient estimates of quantum Markov semigroups. Communications in Mathematical Physics. 2021;387:761–791. doi:10.1007/s00220-021-04199-4","ieee":"M. Wirth and H. Zhang, “Complete gradient estimates of quantum Markov semigroups,” Communications in Mathematical Physics, vol. 387. Springer Nature, pp. 761–791, 2021.","apa":"Wirth, M., & Zhang, H. (2021). Complete gradient estimates of quantum Markov semigroups. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-021-04199-4","ista":"Wirth M, Zhang H. 2021. Complete gradient estimates of quantum Markov semigroups. Communications in Mathematical Physics. 387, 761–791."},"publication":"Communications in Mathematical Physics","page":"761–791","article_type":"original","date_published":"2021-08-30T00:00:00Z","ec_funded":1,"file_date_updated":"2021-09-08T09:46:34Z","acknowledgement":"Both authors would like to thank Jan Maas for fruitful discussions and helpful comments.","year":"2021","publisher":"Springer Nature","department":[{"_id":"JaMa"}],"publication_status":"published","author":[{"last_name":"Wirth","first_name":"Melchior","orcid":"0000-0002-0519-4241","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","full_name":"Wirth, Melchior"},{"id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","last_name":"Zhang","first_name":"Haonan","full_name":"Zhang, Haonan"}],"volume":387,"date_created":"2021-08-30T10:07:44Z","date_updated":"2023-08-11T11:09:07Z","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"month":"08","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":["000691214200001"],"arxiv":["2007.13506"]},"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"}],"quality_controlled":"1","isi":1,"doi":"10.1007/s00220-021-04199-4","language":[{"iso":"eng"}]},{"scopus_import":"1","day":"16","has_accepted_license":"1","article_processing_charge":"Yes","article_type":"original","publication":"Investigative Ophthalmology and Visual Science","citation":{"ieee":"H. M. Schmitt et al., “Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression,” Investigative Ophthalmology and Visual Science, vol. 62, no. 10. Association for Research in Vision and Ophthalmology, 2021.","apa":"Schmitt, H. M., Fehrman, R. L., Maes, M. E., Yang, H., Guo, L. W., Schlamp, C. L., … Nickells, R. W. (2021). Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology and Visual Science. Association for Research in Vision and Ophthalmology. https://doi.org/10.1167/IOVS.62.10.14","ista":"Schmitt HM, Fehrman RL, Maes ME, Yang H, Guo LW, Schlamp CL, Pelzel HR, Nickells RW. 2021. Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology and Visual Science. 62(10), 14.","ama":"Schmitt HM, Fehrman RL, Maes ME, et al. Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology and Visual Science. 2021;62(10). doi:10.1167/IOVS.62.10.14","chicago":"Schmitt, Heather M., Rachel L. Fehrman, Margaret E Maes, Huan Yang, Lian Wang Guo, Cassandra L. Schlamp, Heather R. Pelzel, and Robert W. Nickells. “Increased Susceptibility and Intrinsic Apoptotic Signaling in Neurons by Induced HDAC3 Expression.” Investigative Ophthalmology and Visual Science. Association for Research in Vision and Ophthalmology, 2021. https://doi.org/10.1167/IOVS.62.10.14.","short":"H.M. Schmitt, R.L. Fehrman, M.E. Maes, H. Yang, L.W. Guo, C.L. Schlamp, H.R. Pelzel, R.W. Nickells, Investigative Ophthalmology and Visual Science 62 (2021).","mla":"Schmitt, Heather M., et al. “Increased Susceptibility and Intrinsic Apoptotic Signaling in Neurons by Induced HDAC3 Expression.” Investigative Ophthalmology and Visual Science, vol. 62, no. 10, 14, Association for Research in Vision and Ophthalmology, 2021, doi:10.1167/IOVS.62.10.14."},"date_published":"2021-08-16T00:00:00Z","type":"journal_article","abstract":[{"text":"Inhibition or targeted deletion of histone deacetylase 3 (HDAC3) is neuroprotective in a variety neurodegenerative conditions, including retinal ganglion cells (RGCs) after acute optic nerve damage. Consistent with this, induced HDAC3 expression in cultured cells shows selective toxicity to neurons. Despite an established role for HDAC3 in neuronal pathology, little is known regarding the mechanism of this pathology.","lang":"eng"}],"issue":"10","ddc":["570"],"title":"Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression","status":"public","intvolume":" 62","_id":"10000","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"checksum":"c430967746f653aa1ae84ee617f62b73","date_updated":"2022-05-13T07:40:15Z","date_created":"2022-05-13T07:40:15Z","file_id":"11369","relation":"main_file","creator":"dernst","file_size":19707796,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_IOVS_Schmitt.pdf"}],"oa_version":"Published Version","month":"08","publication_identifier":{"issn":["0146-0404"],"eissn":["1552-5783"]},"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000695230000014"],"pmid":["34398198"]},"language":[{"iso":"eng"}],"doi":"10.1167/IOVS.62.10.14","article_number":"14","file_date_updated":"2022-05-13T07:40:15Z","publication_status":"published","publisher":"Association for Research in Vision and Ophthalmology","department":[{"_id":"SaSi"}],"acknowledgement":"The authors thank Joel Dietz for maintaining the mice used in this study, Satoshi Kinoshita and the Translational Research Initiative in Pathology Laboratory at the University of Wisconsin-Madison for cutting retinal sections analyzed in this study, and Mark Banghart for statistical review of the data analysis. Supported by National Eye Institute Grants R01 EY012223 (RWN), R01 EY030123 (RWN), R01 EY029809 (LWG), R01 EY029809 (LWG) and a Vision Research CORE grant P30 EY016665, NRSA grant T32 GM081061, by an unrestricted research grant from Research to Prevent Blindness, Inc., and by a University of Wisconsin-Madison Vilas Life Cycle award and the Frederick A. Davis Research Chair (RWN). ","year":"2021","pmid":1,"date_updated":"2023-08-14T06:35:17Z","date_created":"2021-09-12T22:01:23Z","volume":62,"author":[{"full_name":"Schmitt, Heather M.","last_name":"Schmitt","first_name":"Heather M."},{"full_name":"Fehrman, Rachel L.","first_name":"Rachel L.","last_name":"Fehrman"},{"full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","first_name":"Margaret E"},{"full_name":"Yang, Huan","last_name":"Yang","first_name":"Huan"},{"full_name":"Guo, Lian Wang","first_name":"Lian Wang","last_name":"Guo"},{"full_name":"Schlamp, Cassandra L.","first_name":"Cassandra L.","last_name":"Schlamp"},{"full_name":"Pelzel, Heather R.","last_name":"Pelzel","first_name":"Heather R."},{"first_name":"Robert W.","last_name":"Nickells","full_name":"Nickells, Robert W."}]},{"file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":584648,"file_name":"2021_SelectaMath_Koroteev.pdf","access_level":"open_access","date_created":"2021-09-13T11:31:34Z","date_updated":"2021-09-13T11:31:34Z","success":1,"checksum":"beadc5a722ffb48190e1e63ee2dbfee5","file_id":"10010","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9998","status":"public","title":"Quantum K-theory of quiver varieties and many-body systems","ddc":["530"],"intvolume":" 27","abstract":[{"lang":"eng","text":"We define quantum equivariant K-theory of Nakajima quiver varieties. We discuss type A in detail as well as its connections with quantum XXZ spin chains and trigonometric Ruijsenaars-Schneider models. Finally we study a limit which produces a K-theoretic version of results of Givental and Kim, connecting quantum geometry of flag varieties and Toda lattice."}],"issue":"5","type":"journal_article","date_published":"2021-08-30T00:00:00Z","publication":"Selecta Mathematica","citation":{"ama":"Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. 2021;27(5). doi:10.1007/s00029-021-00698-3","ista":"Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. 2021. Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. 27(5), 87.","ieee":"P. Koroteev, P. Pushkar, A. V. Smirnov, and A. M. Zeitlin, “Quantum K-theory of quiver varieties and many-body systems,” Selecta Mathematica, vol. 27, no. 5. Springer Nature, 2021.","apa":"Koroteev, P., Pushkar, P., Smirnov, A. V., & Zeitlin, A. M. (2021). Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. Springer Nature. https://doi.org/10.1007/s00029-021-00698-3","mla":"Koroteev, Peter, et al. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” Selecta Mathematica, vol. 27, no. 5, 87, Springer Nature, 2021, doi:10.1007/s00029-021-00698-3.","short":"P. Koroteev, P. Pushkar, A.V. Smirnov, A.M. Zeitlin, Selecta Mathematica 27 (2021).","chicago":"Koroteev, Peter, Petr Pushkar, Andrey V. Smirnov, and Anton M. Zeitlin. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” Selecta Mathematica. Springer Nature, 2021. https://doi.org/10.1007/s00029-021-00698-3."},"article_type":"original","day":"30","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","author":[{"full_name":"Koroteev, Peter","last_name":"Koroteev","first_name":"Peter"},{"full_name":"Pushkar, Petr","last_name":"Pushkar","first_name":"Petr","id":"151DCEB6-9EC3-11E9-8480-ABECE5697425"},{"first_name":"Andrey V.","last_name":"Smirnov","full_name":"Smirnov, Andrey V."},{"last_name":"Zeitlin","first_name":"Anton M.","full_name":"Zeitlin, Anton M."}],"date_updated":"2023-08-14T06:34:14Z","date_created":"2021-09-12T22:01:22Z","volume":27,"acknowledgement":"First of all we would like to thank Andrei Okounkov for invaluable discussions, advises and sharing with us his fantastic viewpoint on modern quantum geometry. We are also grateful to D. Korb and Z. Zhou for their interest and comments. The work of A. Smirnov was supported in part by RFBR Grants under Numbers 15-02-04175 and 15-01-04217 and in part by NSF Grant DMS–2054527. The work of P. Koroteev, A.M. Zeitlin and A. Smirnov is supported in part by AMS Simons travel Grant. A. M. Zeitlin is partially supported by Simons Collaboration Grant, Award ID: 578501. Open access funding provided by Institute of Science and Technology (IST Austria).","year":"2021","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"TaHa"}],"file_date_updated":"2021-09-13T11:31:34Z","article_number":"87","doi":"10.1007/s00029-021-00698-3","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000692795200001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"month":"08","publication_identifier":{"eissn":["1420-9020"],"issn":["1022-1824"]}},{"year":"2021","pmid":1,"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"CaHe"}],"author":[{"full_name":"Pulgar, Eduardo","first_name":"Eduardo","last_name":"Pulgar"},{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226","first_name":"Cornelia","last_name":"Schwayer","full_name":"Schwayer, Cornelia"},{"last_name":"Guerrero","first_name":"Néstor","full_name":"Guerrero, Néstor"},{"full_name":"López, Loreto","first_name":"Loreto","last_name":"López"},{"full_name":"Márquez, Susana","last_name":"Márquez","first_name":"Susana"},{"full_name":"Härtel, Steffen","first_name":"Steffen","last_name":"Härtel"},{"first_name":"Rodrigo","last_name":"Soto","full_name":"Soto, Rodrigo"},{"full_name":"Heisenberg, Carl Philipp","last_name":"Heisenberg","first_name":"Carl Philipp"},{"full_name":"Concha, Miguel L.","last_name":"Concha","first_name":"Miguel L."}],"date_created":"2021-09-12T22:01:23Z","date_updated":"2023-08-14T06:53:33Z","volume":10,"article_number":"e66483","file_date_updated":"2022-05-13T08:03:37Z","ec_funded":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":["34448451"],"isi":["000700428500001"]},"quality_controlled":"1","isi":1,"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"doi":"10.7554/eLife.66483","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"eissn":["2050-084X"]},"_id":"9999","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism","intvolume":" 10","oa_version":"Published Version","file":[{"date_created":"2022-05-13T08:03:37Z","date_updated":"2022-05-13T08:03:37Z","success":1,"checksum":"a3f82b0499cc822ac1eab48a01f3f57e","file_id":"11371","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":9010446,"file_name":"2021_eLife_Pulgar.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The developmental strategies used by progenitor cells to endure a safe journey from their induction place towards the site of terminal differentiation are still poorly understood. Here we uncovered a progenitor cell allocation mechanism that stems from an incomplete process of epithelial delamination that allows progenitors to coordinate their movement with adjacent extra-embryonic tissues. Progenitors of the zebrafish laterality organ originate from the surface epithelial enveloping layer by an apical constriction process of cell delamination. During this process, progenitors retain long-term apical contacts that enable the epithelial layer to pull a subset of progenitors along their way towards the vegetal pole. The remaining delaminated progenitors follow apically-attached progenitors’ movement by a co-attraction mechanism, avoiding sequestration by the adjacent endoderm, ensuring their fate and collective allocation at the differentiation site. Thus, we reveal that incomplete delamination serves as a cellular platform for coordinated tissue movements during development. Impact Statement: Incomplete delamination serves as a cellular platform for coordinated tissue movements during development, guiding newly formed progenitor cell groups to the differentiation site."}],"publication":"eLife","citation":{"chicago":"Pulgar, Eduardo, Cornelia Schwayer, Néstor Guerrero, Loreto López, Susana Márquez, Steffen Härtel, Rodrigo Soto, Carl Philipp Heisenberg, and Miguel L. Concha. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.66483.","short":"E. Pulgar, C. Schwayer, N. Guerrero, L. López, S. Márquez, S. Härtel, R. Soto, C.P. Heisenberg, M.L. Concha, ELife 10 (2021).","mla":"Pulgar, Eduardo, et al. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” ELife, vol. 10, e66483, eLife Sciences Publications, 2021, doi:10.7554/eLife.66483.","ieee":"E. Pulgar et al., “Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Pulgar, E., Schwayer, C., Guerrero, N., López, L., Márquez, S., Härtel, S., … Concha, M. L. (2021). Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.66483","ista":"Pulgar E, Schwayer C, Guerrero N, López L, Márquez S, Härtel S, Soto R, Heisenberg CP, Concha ML. 2021. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. eLife. 10, e66483.","ama":"Pulgar E, Schwayer C, Guerrero N, et al. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. eLife. 2021;10. doi:10.7554/eLife.66483"},"article_type":"original","date_published":"2021-08-27T00:00:00Z","scopus_import":"1","keyword":["cell delamination","apical constriction","dragging","mechanical forces","collective 18 locomotion","dorsal forerunner cells","zebrafish"],"day":"27","article_processing_charge":"Yes","has_accepted_license":"1"},{"ec_funded":1,"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Wolfgang","last_name":"Dvorak","full_name":"Dvorak, Wolfgang"},{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"last_name":"Svozil","first_name":"Alexander","full_name":"Svozil, Alexander"}],"date_created":"2021-09-12T22:01:24Z","date_updated":"2023-08-14T06:51:33Z","acknowledgement":"The authors are grateful to the anonymous referees for their valuable comments. A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15–003. K. C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and by the ERC CoG 863818 (ForM-SMArt). For M. H. the research leading to these results has received funding from the European Research Council under the European Unions Seventh Framework Programme (FP/2007–2013) / ERC Grant Agreement no. 340506.","year":"2021","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"KrCh"}],"publication_status":"published","publication_identifier":{"eisbn":["978-1-6654-4895-6"],"issn":["1043-6871"],"isbn":["978-1-6654-4896-3"]},"month":"07","doi":"10.1109/LICS52264.2021.9470739","conference":{"end_date":"2021-07-02","location":"Rome, Italy","start_date":"2021-06-29","name":"LICS: Symposium on Logic in Computer Science"},"language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2104.07466"],"isi":["000947350400089"]},"main_file_link":[{"url":"https://arxiv.org/abs/2104.07466","open_access":"1"}],"project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"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,"abstract":[{"text":"We present a faster symbolic algorithm for the following central problem in probabilistic verification: Compute the maximal end-component (MEC) decomposition of Markov decision processes (MDPs). This problem generalizes the SCC decomposition problem of graphs and closed recurrent sets of Markov chains. The model of symbolic algorithms is widely used in formal verification and model-checking, where access to the input model is restricted to only symbolic operations (e.g., basic set operations and computation of one-step neighborhood). For an input MDP with n vertices and m edges, the classical symbolic algorithm from the 1990s for the MEC decomposition requires O(n2) symbolic operations and O(1) symbolic space. The only other symbolic algorithm for the MEC decomposition requires O(nm−−√) symbolic operations and O(m−−√) symbolic space. A main open question is whether the worst-case O(n2) bound for symbolic operations can be beaten. We present a symbolic algorithm that requires O˜(n1.5) symbolic operations and O˜(n−−√) symbolic space. Moreover, the parametrization of our algorithm provides a trade-off between symbolic operations and symbolic space: for all 0<ϵ≤1/2 the symbolic algorithm requires O˜(n2−ϵ) symbolic operations and O˜(nϵ) symbolic space ( O˜ hides poly-logarithmic factors). Using our techniques we present faster algorithms for computing the almost-sure winning regions of ω -regular objectives for MDPs. We consider the canonical parity objectives for ω -regular objectives, and for parity objectives with d -priorities we present an algorithm that computes the almost-sure winning region with O˜(n2−ϵ) symbolic operations and O˜(nϵ) symbolic space, for all 0<ϵ≤1/2 .","lang":"eng"}],"type":"conference","oa_version":"Preprint","_id":"10002","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Symbolic time and space tradeoffs for probabilistic verification","article_processing_charge":"No","day":"07","scopus_import":"1","keyword":["Computer science","Computational modeling","Markov processes","Probabilistic logic","Formal verification","Game Theory"],"date_published":"2021-07-07T00:00:00Z","citation":{"chicago":"Chatterjee, Krishnendu, Wolfgang Dvorak, Monika H Henzinger, and Alexander Svozil. “Symbolic Time and Space Tradeoffs for Probabilistic Verification.” In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, 1–13. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470739.","short":"K. Chatterjee, W. Dvorak, M.H. Henzinger, A. Svozil, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13.","mla":"Chatterjee, Krishnendu, et al. “Symbolic Time and Space Tradeoffs for Probabilistic Verification.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13, doi:10.1109/LICS52264.2021.9470739.","ieee":"K. Chatterjee, W. Dvorak, M. H. Henzinger, and A. Svozil, “Symbolic time and space tradeoffs for probabilistic verification,” in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Rome, Italy, 2021, pp. 1–13.","apa":"Chatterjee, K., Dvorak, W., Henzinger, M. H., & Svozil, A. (2021). Symbolic time and space tradeoffs for probabilistic verification. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 1–13). Rome, Italy: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS52264.2021.9470739","ista":"Chatterjee K, Dvorak W, Henzinger MH, Svozil A. 2021. Symbolic time and space tradeoffs for probabilistic verification. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 1–13.","ama":"Chatterjee K, Dvorak W, Henzinger MH, Svozil A. Symbolic time and space tradeoffs for probabilistic verification. In: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers; 2021:1-13. doi:10.1109/LICS52264.2021.9470739"},"publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","page":"1-13"},{"type":"journal_article","abstract":[{"text":"In this paper, we introduce a random environment for the exclusion process in obtained by assigning a maximal occupancy to each site. This maximal occupancy is allowed to randomly vary among sites, and partial exclusion occurs. Under the assumption of ergodicity under translation and uniform ellipticity of the environment, we derive a quenched hydrodynamic limit in path space by strengthening the mild solution approach initiated in Nagy (2002) and Faggionato (2007). To this purpose, we prove, employing the technology developed for the random conductance model, a homogenization result in the form of an arbitrary starting point quenched invariance principle for a single particle in the same environment, which is a result of independent interest. The self-duality property of the partial exclusion process allows us to transfer this homogenization result to the particle system and, then, apply the tightness criterion in Redig et al. (2020).","lang":"eng"}],"_id":"10024","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["519"],"title":"Hydrodynamics for the partial exclusion process in random environment","status":"public","intvolume":" 142","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_StochasticProcessesAppl_Floreani.pdf","content_type":"application/pdf","file_size":2115791,"creator":"dernst","relation":"main_file","file_id":"11370","checksum":"56768c553d7218ee5714902ffec90ec4","success":1,"date_updated":"2022-05-13T07:55:50Z","date_created":"2022-05-13T07:55:50Z"}],"scopus_import":"1","keyword":["hydrodynamic limit","random environment","random conductance model","arbitrary starting point quenched invariance principle","duality","mild solution"],"day":"27","has_accepted_license":"1","article_processing_charge":"Yes","publication":"Stochastic Processes and their Applications","citation":{"short":"S. Floreani, F. Redig, F. Sau, Stochastic Processes and Their Applications 142 (2021) 124–158.","mla":"Floreani, Simone, et al. “Hydrodynamics for the Partial Exclusion Process in Random Environment.” Stochastic Processes and Their Applications, vol. 142, Elsevier, 2021, pp. 124–58, doi:10.1016/j.spa.2021.08.006.","chicago":"Floreani, Simone, Frank Redig, and Federico Sau. “Hydrodynamics for the Partial Exclusion Process in Random Environment.” Stochastic Processes and Their Applications. Elsevier, 2021. https://doi.org/10.1016/j.spa.2021.08.006.","ama":"Floreani S, Redig F, Sau F. Hydrodynamics for the partial exclusion process in random environment. Stochastic Processes and their Applications. 2021;142:124-158. doi:10.1016/j.spa.2021.08.006","ieee":"S. Floreani, F. Redig, and F. Sau, “Hydrodynamics for the partial exclusion process in random environment,” Stochastic Processes and their Applications, vol. 142. Elsevier, pp. 124–158, 2021.","apa":"Floreani, S., Redig, F., & Sau, F. (2021). Hydrodynamics for the partial exclusion process in random environment. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2021.08.006","ista":"Floreani S, Redig F, Sau F. 2021. Hydrodynamics for the partial exclusion process in random environment. Stochastic Processes and their Applications. 142, 124–158."},"article_type":"original","page":"124-158","date_published":"2021-08-27T00:00:00Z","file_date_updated":"2022-05-13T07:55:50Z","ec_funded":1,"acknowledgement":"The authors would like to thank Marek Biskup and Alberto Chiarini for useful suggestions and Cristian Giardina, Frank den Hollander and Shubhamoy Nandan for inspiring discussions. S.F. acknowledges Simona Villa for her help in creating the picture. Furthermore, the authors thank two anonymous referees for the careful reading of the manuscript. S.F. acknowledges financial support from NWO, The Netherlands via the grant TOP1.17.019. F.S. acknowledges financial support from NWO via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411.","year":"2021","publication_status":"published","publisher":"Elsevier","department":[{"_id":"JaMa"}],"author":[{"last_name":"Floreani","first_name":"Simone","full_name":"Floreani, Simone"},{"last_name":"Redig","first_name":"Frank","full_name":"Redig, Frank"},{"full_name":"Sau, Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425","last_name":"Sau","first_name":"Federico"}],"date_created":"2021-09-19T22:01:25Z","date_updated":"2023-08-14T06:52:43Z","volume":142,"month":"08","publication_identifier":{"issn":["0304-4149"]},"external_id":{"arxiv":["1911.12564"],"isi":["000697748500005"]},"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,"isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"doi":"10.1016/j.spa.2021.08.006","language":[{"iso":"eng"}]},{"type":"conference","abstract":[{"text":"Markov chains are the de facto finite-state model for stochastic dynamical systems, and Markov decision processes (MDPs) extend Markov chains by incorporating non-deterministic behaviors. Given an MDP and rewards on states, a classical optimization criterion is the maximal expected total reward where the MDP stops after T steps, which can be computed by a simple dynamic programming algorithm. We consider a natural generalization of the problem where the stopping times can be chosen according to a probability distribution, such that the expected stopping time is T, to optimize the expected total reward. Quite surprisingly we establish inter-reducibility of the expected stopping-time problem for Markov chains with the Positivity problem (which is related to the well-known Skolem problem), for which establishing either decidability or undecidability would be a major breakthrough. Given the hardness of the exact problem, we consider the approximate version of the problem: we show that it can be solved in exponential time for Markov chains and in exponential space for MDPs.","lang":"eng"}],"title":"Stochastic processes with expected stopping time","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10004","oa_version":"Preprint","keyword":["Computer science","Heuristic algorithms","Memory management","Automata","Markov processes","Probability distribution","Complexity theory"],"scopus_import":"1","article_processing_charge":"No","day":"07","page":"1-13","citation":{"ista":"Chatterjee K, Doyen L. 2021. Stochastic processes with expected stopping time. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 1–13.","ieee":"K. Chatterjee and L. Doyen, “Stochastic processes with expected stopping time,” in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Rome, Italy, 2021, pp. 1–13.","apa":"Chatterjee, K., & Doyen, L. (2021). Stochastic processes with expected stopping time. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 1–13). Rome, Italy: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS52264.2021.9470595","ama":"Chatterjee K, Doyen L. Stochastic processes with expected stopping time. In: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers; 2021:1-13. doi:10.1109/LICS52264.2021.9470595","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected Stopping Time.” In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, 1–13. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470595.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected Stopping Time.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13, doi:10.1109/LICS52264.2021.9470595.","short":"K. Chatterjee, L. Doyen, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13."},"publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","date_published":"2021-07-07T00:00:00Z","ec_funded":1,"publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2021","acknowledgement":"We are grateful to the anonymous reviewers of LICS 2021 and of a previous version of this paper for insightful comments that helped improving the presentation. This research was partially supported by the grant ERC CoG 863818 (ForM-SMArt).","date_updated":"2023-08-14T06:52:07Z","date_created":"2021-09-12T22:01:25Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"}],"publication_identifier":{"eisbn":["978-1-6654-4895-6"],"issn":["1043-6871"],"isbn":["978-1-6654-4896-3"]},"month":"07","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.07278"}],"external_id":{"isi":["000947350400036"],"arxiv":["2104.07278"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1109/LICS52264.2021.9470595","conference":{"name":"LICS: Symposium on Logic in Computer Science","end_date":"2021-07-02","start_date":"2021-06-29","location":"Rome, Italy"}},{"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000701502202078"],"arxiv":["2012.13378"]},"main_file_link":[{"url":"https://arxiv.org/abs/2012.13378","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1109/ISIT45174.2021.9518153","conference":{"name":"ISIT: International Symposium on Information Theory","end_date":"2021-07-20","start_date":"2021-07-12","location":"Melbourne, Australia"},"publication_identifier":{"issn":["2157-8095"],"eisbn":["978-1-5386-8209-8"],"isbn":["978-1-5386-8210-4"]},"month":"09","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"MaMo"}],"publication_status":"published","acknowledgement":"S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council\r\nof Canada (NSERC) and by Huawei. M. Mondelli is partially supported by the 2019 Lopez-Loreta Prize. A. Fazeli and A. Vardy were supported in part by the National Science Foundation under Grant CCF-1764104.","year":"2021","date_created":"2021-09-27T14:33:14Z","date_updated":"2023-08-14T06:55:58Z","related_material":{"record":[{"id":"10364","relation":"later_version","status":"public"}]},"author":[{"full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi","first_name":"Seyyed Ali"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli","full_name":"Mondelli, Marco"},{"last_name":"Fazeli","first_name":"Arman","full_name":"Fazeli, Arman"},{"first_name":"Alexander","last_name":"Vardy","full_name":"Vardy, Alexander"},{"first_name":"John","last_name":"Cioffi","full_name":"Cioffi, John"},{"full_name":"Goldsmith, Andrea","last_name":"Goldsmith","first_name":"Andrea"}],"page":"2369-2374","citation":{"ista":"Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. 2021. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. 2021 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 2369–2374.","apa":"Hashemi, S. A., Mondelli, M., Fazeli, A., Vardy, A., Cioffi, J., & Goldsmith, A. (2021). Parallelism versus latency in simplified successive-cancellation decoding of polar codes. In 2021 IEEE International Symposium on Information Theory (pp. 2369–2374). Melbourne, Australia: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/ISIT45174.2021.9518153","ieee":"S. A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, and A. Goldsmith, “Parallelism versus latency in simplified successive-cancellation decoding of polar codes,” in 2021 IEEE International Symposium on Information Theory, Melbourne, Australia, 2021, pp. 2369–2374.","ama":"Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. In: 2021 IEEE International Symposium on Information Theory. Institute of Electrical and Electronics Engineers; 2021:2369-2374. doi:10.1109/ISIT45174.2021.9518153","chicago":"Hashemi, Seyyed Ali, Marco Mondelli, Arman Fazeli, Alexander Vardy, John Cioffi, and Andrea Goldsmith. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” In 2021 IEEE International Symposium on Information Theory, 2369–74. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/ISIT45174.2021.9518153.","mla":"Hashemi, Seyyed Ali, et al. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” 2021 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2021, pp. 2369–74, doi:10.1109/ISIT45174.2021.9518153.","short":"S.A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, A. Goldsmith, in:, 2021 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2021, pp. 2369–2374."},"publication":"2021 IEEE International Symposium on Information Theory","date_published":"2021-09-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","title":"Parallelism versus latency in simplified successive-cancellation decoding of polar codes","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10053","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"This paper characterizes the latency of the simplified successive-cancellation (SSC) decoding scheme for polar codes under hardware resource constraints. In particular, when the number of processing elements P that can perform SSC decoding operations in parallel is limited, as is the case in practice, the latency of SSC decoding is O(N1−1 μ+NPlog2log2NP), where N is the block length of the code and μ is the scaling exponent of polar codes for the channel. Three direct consequences of this bound are presented. First, in a fully-parallel implementation where P=N2 , the latency of SSC decoding is O(N1−1/μ) , which is sublinear in the block length. This recovers a result from an earlier work. Second, in a fully-serial implementation where P=1 , the latency of SSC decoding scales as O(Nlog2log2N) . The multiplicative constant is also calculated: we show that the latency of SSC decoding when P=1 is given by (2+o(1))Nlog2log2N . Third, in a semi-parallel implementation, the smallest P that gives the same latency as that of the fully-parallel implementation is P=N1/μ . The tightness of our bound on SSC decoding latency and the applicability of the foregoing results is validated through extensive simulations."}]},{"project":[{"grant_number":"M02751","_id":"26B96266-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Algebro-Geometric Applications of Factorization Homology"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000707040300031"],"arxiv":["1610.00212"]},"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":"10.1016/j.aim.2021.107992","publication_identifier":{"issn":["0001-8708"],"eissn":["1090-2082"]},"month":"09","publisher":"Elsevier","department":[{"_id":"TaHa"}],"publication_status":"published","year":"2021","acknowledgement":"The author would like to express his gratitude to D. Gaitsgory, without whose tireless guidance and encouragement in pursuing this problem, this work would not have been possible. The author is grateful to his advisor B.C. Ngô for many years of patient guidance and support. This paper is revised while the author is a postdoc in Hausel group at IST Austria. We thank him and the group for providing a wonderful research environment. The author also gratefully acknowledges the support of the Lise Meitner fellowship “Algebro-Geometric Applications of Factorization Homology,” Austrian Science Fund (FWF): M 2751.","volume":392,"date_updated":"2023-08-14T06:54:35Z","date_created":"2021-09-21T15:58:59Z","author":[{"full_name":"Ho, Quoc P","first_name":"Quoc P","last_name":"Ho","id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6889-1418"}],"article_number":"107992","file_date_updated":"2021-09-21T15:58:52Z","article_type":"original","citation":{"mla":"Ho, Quoc P. “The Atiyah-Bott Formula and Connectivity in Chiral Koszul Duality.” Advances in Mathematics, vol. 392, 107992, Elsevier, 2021, doi:10.1016/j.aim.2021.107992.","short":"Q.P. Ho, Advances in Mathematics 392 (2021).","chicago":"Ho, Quoc P. “The Atiyah-Bott Formula and Connectivity in Chiral Koszul Duality.” Advances in Mathematics. Elsevier, 2021. https://doi.org/10.1016/j.aim.2021.107992.","ama":"Ho QP. The Atiyah-Bott formula and connectivity in chiral Koszul duality. Advances in Mathematics. 2021;392. doi:10.1016/j.aim.2021.107992","ista":"Ho QP. 2021. The Atiyah-Bott formula and connectivity in chiral Koszul duality. Advances in Mathematics. 392, 107992.","apa":"Ho, Q. P. (2021). The Atiyah-Bott formula and connectivity in chiral Koszul duality. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2021.107992","ieee":"Q. P. Ho, “The Atiyah-Bott formula and connectivity in chiral Koszul duality,” Advances in Mathematics, vol. 392. Elsevier, 2021."},"publication":"Advances in Mathematics","date_published":"2021-09-21T00:00:00Z","keyword":["Chiral algebras","Chiral homology","Factorization algebras","Koszul duality","Ran space"],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"21","intvolume":" 392","ddc":["514"],"title":"The Atiyah-Bott formula and connectivity in chiral Koszul duality","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10033","oa_version":"Published Version","file":[{"file_size":840635,"content_type":"application/pdf","creator":"qho","file_name":"1-s2.0-S000187082100431X-main.pdf","access_level":"open_access","date_updated":"2021-09-21T15:58:52Z","date_created":"2021-09-21T15:58:52Z","checksum":"f3c0086d41af11db31c00014efb38072","relation":"main_file","file_id":"10034"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The ⊗*-monoidal structure on the category of sheaves on the Ran space is not pro-nilpotent in the sense of [3]. However, under some connectivity assumptions, we prove that Koszul duality induces an equivalence of categories and that this equivalence behaves nicely with respect to Verdier duality on the Ran space and integrating along the Ran space, i.e. taking factorization homology. Based on ideas sketched in [4], we show that these results also offer a simpler alternative to one of the two main steps in the proof of the Atiyah-Bott formula given in [7] and [5]."}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"15","scopus_import":"1","date_published":"2021-09-15T00:00:00Z","page":"7742-7767","article_type":"original","citation":{"ista":"Butola T, Alvanos T, Hintze A, Koppensteiner P, Kleindienst D, Shigemoto R, Wichmann C, Moser T. 2021. RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse. Journal of Neuroscience. 41(37), 7742–7767.","ieee":"T. Butola et al., “RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse,” Journal of Neuroscience, vol. 41, no. 37. Society for Neuroscience, pp. 7742–7767, 2021.","apa":"Butola, T., Alvanos, T., Hintze, A., Koppensteiner, P., Kleindienst, D., Shigemoto, R., … Moser, T. (2021). RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0586-21.2021","ama":"Butola T, Alvanos T, Hintze A, et al. RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse. Journal of Neuroscience. 2021;41(37):7742-7767. doi:10.1523/JNEUROSCI.0586-21.2021","chicago":"Butola, Tanvi, Theocharis Alvanos, Anika Hintze, Peter Koppensteiner, David Kleindienst, Ryuichi Shigemoto, Carolin Wichmann, and Tobias Moser. “RIM-Binding Protein 2 Organizes Ca21 Channel Topography and Regulates Release Probability and Vesicle Replenishment at a Fast Central Synapse.” Journal of Neuroscience. Society for Neuroscience, 2021. https://doi.org/10.1523/JNEUROSCI.0586-21.2021.","mla":"Butola, Tanvi, et al. “RIM-Binding Protein 2 Organizes Ca21 Channel Topography and Regulates Release Probability and Vesicle Replenishment at a Fast Central Synapse.” Journal of Neuroscience, vol. 41, no. 37, Society for Neuroscience, 2021, pp. 7742–67, doi:10.1523/JNEUROSCI.0586-21.2021.","short":"T. Butola, T. Alvanos, A. Hintze, P. Koppensteiner, D. Kleindienst, R. Shigemoto, C. Wichmann, T. Moser, Journal of Neuroscience 41 (2021) 7742–7767."},"publication":"Journal of Neuroscience","issue":"37","abstract":[{"lang":"eng","text":"Rab-interacting molecule (RIM)-binding protein 2 (BP2) is a multidomain protein of the presynaptic active zone (AZ). By binding to RIM, bassoon (Bsn), and voltage-gated Ca2+ channels (CaV), it is considered to be a central organizer of the topography of CaV and release sites of synaptic vesicles (SVs) at the AZ. Here, we used RIM-BP2 knock-out (KO) mice and their wild-type (WT) littermates of either sex to investigate the role of RIM-BP2 at the endbulb of Held synapse of auditory nerve fibers (ANFs) with bushy cells (BCs) of the cochlear nucleus, a fast relay of the auditory pathway with high release probability. Disruption of RIM-BP2 lowered release probability altering short-term plasticity and reduced evoked EPSCs. Analysis of SV pool dynamics during high-frequency train stimulation indicated a reduction of SVs with high release probability but an overall normal size of the readily releasable SV pool (RRP). The Ca2+-dependent fast component of SV replenishment after RRP depletion was slowed. Ultrastructural analysis by superresolution light and electron microscopy revealed an impaired topography of presynaptic CaV and a reduction of docked and membrane-proximal SVs at the AZ. We conclude that RIM-BP2 organizes the topography of CaV, and promotes SV tethering and docking. This way RIM-BP2 is critical for establishing a high initial release probability as required to reliably signal sound onset information that we found to be degraded in BCs of RIM-BP2-deficient mice in vivo. SIGNIFICANCE STATEMENT: Rab-interacting molecule (RIM)-binding proteins (BPs) are key organizers of the active zone (AZ). Using a multidisciplinary approach to the calyceal endbulb of Held synapse that transmits auditory information at rates of up to hundreds of Hertz with submillisecond precision we demonstrate a requirement for RIM-BP2 for normal auditory signaling. Endbulb synapses lacking RIM-BP2 show a reduced release probability despite normal whole-terminal Ca2+ influx and abundance of the key priming protein Munc13-1, a reduced rate of SV replenishment, as well as an altered topography of voltage-gated (CaV)2.1 Ca2+ channels, and fewer docked and membrane proximal synaptic vesicles (SVs). This hampers transmission of sound onset information likely affecting downstream neural computations such as of sound localization."}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"769ab627c7355a50ccfd445e43a5f351","success":1,"date_created":"2022-05-31T09:10:15Z","date_updated":"2022-05-31T09:10:15Z","relation":"main_file","file_id":"11423","content_type":"application/pdf","file_size":11571961,"creator":"dernst","access_level":"open_access","file_name":"2021_JourNeuroscience_Butola.pdf"}],"intvolume":" 41","status":"public","title":"RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse","ddc":["570"],"_id":"10051","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1529-2401"],"issn":["0270-6474"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.0586-21.2021","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":["34353898"],"isi":["000752287700005"]},"file_date_updated":"2022-05-31T09:10:15Z","volume":41,"date_updated":"2023-08-14T06:56:30Z","date_created":"2021-09-27T14:33:13Z","author":[{"full_name":"Butola, Tanvi","last_name":"Butola","first_name":"Tanvi"},{"last_name":"Alvanos","first_name":"Theocharis","full_name":"Alvanos, Theocharis"},{"first_name":"Anika","last_name":"Hintze","full_name":"Hintze, Anika"},{"orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter","full_name":"Koppensteiner, Peter"},{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Kleindienst"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"full_name":"Wichmann, Carolin","last_name":"Wichmann","first_name":"Carolin"},{"full_name":"Moser, Tobias","first_name":"Tobias","last_name":"Moser"}],"department":[{"_id":"RySh"}],"publisher":"Society for Neuroscience","publication_status":"published","pmid":1,"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the Collaborative Sensory Research Center 1286 [to C.W. (A4) and T.M. (B5)] and under Germany’s Excellence Strategy Grant EXC 2067/1-390729940. We thank S. Gerke, A.J. Goldak, and C. Senger-Freitag for expert technical assistance; G. Hoch for developing image analysis routines; and S. Chepurwar and N. Strenzke for technical support and discussion regarding in vivo experiments. We also thank Dr. Christian Rosenmund, Dr. Katharina Grauel, and Dr. Stephan Sigrist for providing RIM-BP2 KO mice and Dr. Masahiko Watanabe for providing the anti-neurexin-antibody, and Dr. Toshihisa Ohtsuka for the anti-ELKS-antibody. J. Neef for help with the STED imaging and image analysis; E. Neher and S. Rizzoli for discussion and comments on the manuscript; K. Eguchi for help with the statistical analysis; and C. H. Huang and J. Neef for constant support and scientific discussion.","year":"2021"},{"publication_identifier":{"isbn":["978-3-9597-7180-1"],"issn":["1868-8969"]},"month":"03","external_id":{"isi":["000635691700044"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"doi":"10.4230/LIPIcs.STACS.2021.44","conference":{"start_date":"2021-03-16","location":"Saarbrücken, Germany","end_date":"2021-03-19","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"language":[{"iso":"eng"}],"article_number":"44","ec_funded":1,"file_date_updated":"2021-10-01T09:55:00Z","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. I wish to thank Michaël Cadilhac, Emmanuel Filiot and Charles Paperman for their valuable insights concerning Green’s relations.","year":"2021","publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik","department":[{"_id":"KrCh"}],"publication_status":"published","author":[{"full_name":"Jecker, Ismael R","last_name":"Jecker","first_name":"Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425"}],"volume":187,"date_created":"2021-09-27T14:33:15Z","date_updated":"2023-08-14T07:03:23Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"10","citation":{"chicago":"Jecker, Ismael R. “A Ramsey Theorem for Finite Monoids.” In 38th International Symposium on Theoretical Aspects of Computer Science, Vol. 187. Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.STACS.2021.44.","short":"I.R. Jecker, in:, 38th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021.","mla":"Jecker, Ismael R. “A Ramsey Theorem for Finite Monoids.” 38th International Symposium on Theoretical Aspects of Computer Science, vol. 187, 44, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021, doi:10.4230/LIPIcs.STACS.2021.44.","apa":"Jecker, I. R. (2021). A Ramsey theorem for finite monoids. In 38th International Symposium on Theoretical Aspects of Computer Science (Vol. 187). Saarbrücken, Germany: Schloss Dagstuhl - Leibniz Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2021.44","ieee":"I. R. Jecker, “A Ramsey theorem for finite monoids,” in 38th International Symposium on Theoretical Aspects of Computer Science, Saarbrücken, Germany, 2021, vol. 187.","ista":"Jecker IR. 2021. A Ramsey theorem for finite monoids. 38th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 187, 44.","ama":"Jecker IR. A Ramsey theorem for finite monoids. In: 38th International Symposium on Theoretical Aspects of Computer Science. Vol 187. Schloss Dagstuhl - Leibniz Zentrum für Informatik; 2021. doi:10.4230/LIPIcs.STACS.2021.44"},"publication":"38th International Symposium on Theoretical Aspects of Computer Science","date_published":"2021-03-10T00:00:00Z","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"Repeated idempotent elements are commonly used to characterise iterable behaviours in abstract models of computation. Therefore, given a monoid M, it is natural to ask how long a sequence of elements of M needs to be to ensure the presence of consecutive idempotent factors. This question is formalised through the notion of the Ramsey function R_M associated to M, obtained by mapping every k ∈ ℕ to the minimal integer R_M(k) such that every word u ∈ M^* of length R_M(k) contains k consecutive non-empty factors that correspond to the same idempotent element of M. In this work, we study the behaviour of the Ramsey function R_M by investigating the regular 𝒟-length of M, defined as the largest size L(M) of a submonoid of M isomorphic to the set of natural numbers {1,2, …, L(M)} equipped with the max operation. We show that the regular 𝒟-length of M determines the degree of R_M, by proving that k^L(M) ≤ R_M(k) ≤ (k|M|⁴)^L(M). To allow applications of this result, we provide the value of the regular 𝒟-length of diverse monoids. In particular, we prove that the full monoid of n × n Boolean matrices, which is used to express transition monoids of non-deterministic automata, has a regular 𝒟-length of (n²+n+2)/2."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10055","intvolume":" 187","ddc":["000"],"status":"public","title":"A Ramsey theorem for finite monoids","file":[{"checksum":"17432a05733f408de300e17e390a90e4","success":1,"date_updated":"2021-10-01T09:55:00Z","date_created":"2021-10-01T09:55:00Z","relation":"main_file","file_id":"10063","content_type":"application/pdf","file_size":720250,"creator":"cchlebak","access_level":"open_access","file_name":"2021_LIPIcs_Jecker.pdf"}],"oa_version":"Published Version"},{"oa_version":"Published Version","file":[{"file_name":"2021_ScientificReports_Robinson.pdf","access_level":"open_access","creator":"cchlebak","file_size":6970368,"content_type":"application/pdf","file_id":"10091","relation":"main_file","date_created":"2021-10-05T14:56:48Z","date_updated":"2021-10-05T14:56:48Z","success":1,"checksum":"f002ec22f609f58e1263b79e7f79601e"}],"ddc":["618"],"title":"Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy","status":"public","intvolume":" 11","_id":"10069","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"The extent to which women differ in the course of blood cell counts throughout pregnancy, and the importance of these changes to pregnancy outcomes has not been well defined. Here, we develop a series of statistical analyses of repeated measures data to reveal the degree to which women differ in the course of pregnancy, predict the changes that occur, and determine the importance of these changes for post-partum hemorrhage (PPH) which is one of the leading causes of maternal mortality. We present a prospective cohort of 4082 births recorded at the University Hospital, Lausanne, Switzerland between 2009 and 2014 where full labour records could be obtained, along with complete blood count data taken at hospital admission. We find significant differences, at a [Formula: see text] level, among women in how blood count values change through pregnancy for mean corpuscular hemoglobin, mean corpuscular volume, mean platelet volume, platelet count and red cell distribution width. We find evidence that almost all complete blood count values show trimester-specific associations with PPH. For example, high platelet count (OR 1.20, 95% CI 1.01-1.53), high mean platelet volume (OR 1.58, 95% CI 1.04-2.08), and high erythrocyte levels (OR 1.36, 95% CI 1.01-1.57) in trimester 1 increased PPH, but high values in trimester 3 decreased PPH risk (OR 0.85, 0.79, 0.67 respectively). We show that differences among women in the course of blood cell counts throughout pregnancy have an important role in shaping pregnancy outcome and tracking blood count value changes through pregnancy improves identification of women at increased risk of postpartum hemorrhage. This study provides greater understanding of the complex changes in blood count values that occur through pregnancy and provides indicators to guide the stratification of patients into risk groups.","lang":"eng"}],"type":"journal_article","date_published":"2021-09-28T00:00:00Z","article_type":"original","publication":"Scientific Reports","citation":{"ista":"Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. 2021. Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. Scientific Reports. 11, 19238.","apa":"Robinson, M. R., Patxot, M., Stojanov, M., Blum, S., & Baud, D. (2021). Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-98411-z","ieee":"M. R. Robinson, M. Patxot, M. Stojanov, S. Blum, and D. Baud, “Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy,” Scientific Reports, vol. 11. Springer Nature, 2021.","ama":"Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. Scientific Reports. 2021;11. doi:10.1038/s41598-021-98411-z","chicago":"Robinson, Matthew Richard, Marion Patxot, Miloš Stojanov, Sabine Blum, and David Baud. “Postpartum Hemorrhage Risk Is Driven by Changes in Blood Composition through Pregnancy.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-98411-z.","mla":"Robinson, Matthew Richard, et al. “Postpartum Hemorrhage Risk Is Driven by Changes in Blood Composition through Pregnancy.” Scientific Reports, vol. 11, 19238, Springer Nature, 2021, doi:10.1038/s41598-021-98411-z.","short":"M.R. Robinson, M. Patxot, M. Stojanov, S. Blum, D. Baud, Scientific Reports 11 (2021)."},"day":"28","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_updated":"2023-08-14T07:05:15Z","date_created":"2021-10-03T22:01:21Z","volume":11,"author":[{"full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"},{"full_name":"Patxot, Marion","first_name":"Marion","last_name":"Patxot"},{"last_name":"Stojanov","first_name":"Miloš","full_name":"Stojanov, Miloš"},{"full_name":"Blum, Sabine","first_name":"Sabine","last_name":"Blum"},{"last_name":"Baud","first_name":"David","full_name":"Baud, David"}],"publication_status":"published","department":[{"_id":"MaRo"}],"publisher":"Springer Nature","year":"2021","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 study and all the midwives and doctors for the computerized obstetrical data.","pmid":1,"file_date_updated":"2021-10-05T14:56:48Z","article_number":"19238","language":[{"iso":"eng"}],"doi":"10.1038/s41598-021-98411-z","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["34584125"],"isi":["000701575500083"]},"month":"09","publication_identifier":{"eissn":["2045-2322"]}},{"external_id":{"isi":["000706977400002"],"arxiv":["2104.00653"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2104.00653","open_access":"1"}],"quality_controlled":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41586-021-03938-w","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"acknowledgement":"The authors acknowledge discussions with A. Macdonald, L. Fu, F. Wang and M. Zaletel. AFY acknowledges support of the National Science Foundation under DMR1654186, and the Gordon and Betty Moore Foundation under award GBMF9471. The authors acknowledge the use of the research facilities within the California NanoSystems Institute, supported by the University of California, Santa Barbara and the University of California, Office of the President.\r\nK.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, Grant Number JPMXP0112101001 and JSPS KAKENHI, Grant Number JP20H00354. EB and TH were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799). A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement\r\nNo. 754411.\r\n","year":"2021","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"MaSe"},{"_id":"MiLe"}],"author":[{"full_name":"Zhou, Haoxin","first_name":"Haoxin","last_name":"Zhou"},{"first_name":"Tian","last_name":"Xie","full_name":"Xie, Tian"},{"last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg"},{"last_name":"Holder","first_name":"Tobias","full_name":"Holder, Tobias"},{"last_name":"Ehrets","first_name":"James R.","full_name":"Ehrets, James R."},{"last_name":"Spanton","first_name":"Eric M.","full_name":"Spanton, Eric M."},{"full_name":"Taniguchi, Takashi","first_name":"Takashi","last_name":"Taniguchi"},{"last_name":"Watanabe","first_name":"Kenji","full_name":"Watanabe, Kenji"},{"full_name":"Berg, Erez","last_name":"Berg","first_name":"Erez"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"},{"last_name":"Young","first_name":"Andrea F.","full_name":"Young, Andrea F."}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-021-04181-z"}]},"date_updated":"2023-08-14T07:04:06Z","date_created":"2021-09-19T22:01:25Z","ec_funded":1,"publication":"Nature","citation":{"ista":"Zhou H, Xie T, Ghazaryan A, Holder T, Ehrets JR, Spanton EM, Taniguchi T, Watanabe K, Berg E, Serbyn M, Young AF. 2021. Half and quarter metals in rhombohedral trilayer graphene. Nature.","ieee":"H. Zhou et al., “Half and quarter metals in rhombohedral trilayer graphene,” Nature. Springer Nature, 2021.","apa":"Zhou, H., Xie, T., Ghazaryan, A., Holder, T., Ehrets, J. R., Spanton, E. M., … Young, A. F. (2021). Half and quarter metals in rhombohedral trilayer graphene. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03938-w","ama":"Zhou H, Xie T, Ghazaryan A, et al. Half and quarter metals in rhombohedral trilayer graphene. Nature. 2021. doi:10.1038/s41586-021-03938-w","chicago":"Zhou, Haoxin, Tian Xie, Areg Ghazaryan, Tobias Holder, James R. Ehrets, Eric M. Spanton, Takashi Taniguchi, et al. “Half and Quarter Metals in Rhombohedral Trilayer Graphene.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03938-w.","mla":"Zhou, Haoxin, et al. “Half and Quarter Metals in Rhombohedral Trilayer Graphene.” Nature, Springer Nature, 2021, doi:10.1038/s41586-021-03938-w.","short":"H. Zhou, T. Xie, A. Ghazaryan, T. Holder, J.R. Ehrets, E.M. Spanton, T. Taniguchi, K. Watanabe, E. Berg, M. Serbyn, A.F. Young, Nature (2021)."},"article_type":"original","date_published":"2021-09-01T00:00:00Z","scopus_import":"1","keyword":["condensed matter - mesoscale and nanoscale physics","condensed matter - strongly correlated electrons","multidisciplinary"],"day":"01","article_processing_charge":"No","_id":"10025","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Half and quarter metals in rhombohedral trilayer graphene","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Ferromagnetism is most common in transition metal compounds but may also arise in low-density two-dimensional electron systems, with signatures observed in silicon, III-V semiconductor systems, and graphene moiré heterostructures. Here we show that gate-tuned van Hove singularities in rhombohedral trilayer graphene drive the spontaneous ferromagnetic polarization of the electron system into one or more spin- and valley flavors. Using capacitance measurements on graphite-gated van der Waals heterostructures, we find a cascade of density- and electronic displacement field tuned phase transitions marked by negative electronic compressibility. The transitions define the boundaries between phases where quantum oscillations have either four-fold, two-fold, or one-fold degeneracy, associated with a spin and valley degenerate normal metal, spin-polarized `half-metal', and spin and valley polarized `quarter metal', respectively. For electron doping, the salient features are well captured by a phenomenological Stoner model with a valley-anisotropic Hund's coupling, likely arising from interactions at the lattice scale. For hole filling, we observe a richer phase diagram featuring a delicate interplay of broken symmetries and transitions in the Fermi surface topology. Finally, by rotational alignment of a hexagonal boron nitride substrate to induce a moiré superlattice, we find that the superlattice perturbs the preexisting isospin order only weakly, leaving the basic phase diagram intact while catalyzing the formation of topologically nontrivial gapped states whenever itinerant half- or quarter metal states occur at half- or quarter superlattice band filling. Our results show that rhombohedral trilayer graphene is an ideal platform for well-controlled tests of many-body theory and reveal magnetism in moiré materials to be fundamentally itinerant in nature."}]},{"abstract":[{"text":"We present a novel approach for blockchain asset owners to reclaim their funds in case of accidental private-key loss or transfer to a mistyped address. Our solution can be deployed upon failure or absence of proactively implemented backup mechanisms, such as secret sharing and cold storage. The main advantages against previous proposals is it does not require any prior action from users and works with both single-key and multi-sig accounts. We achieve this by a 3-phase Commit()→Reveal()→Claim()−or−Challenge() smart contract that enables accessing funds of addresses for which the spending key is not available. We provide an analysis of the threat and incentive models and formalize the concept of reactive KEy-Loss Protection (KELP).","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10076","title":"Reactive key-loss protection in blockchains","status":"public","day":"17","article_processing_charge":"No","scopus_import":"1","date_published":"2021-09-17T00:00:00Z","publication":"FC 2021 Workshops","citation":{"mla":"Blackshear, Sam, et al. “Reactive Key-Loss Protection in Blockchains.” FC 2021 Workshops, vol. 12676, Springer Nature, 2021, pp. 431–50, doi:10.1007/978-3-662-63958-0_34.","short":"S. Blackshear, K. Chalkias, P. Chatzigiannis, R. Faizullabhoy, I. Khaburzaniya, E. Kokoris Kogias, J. Lind, D. Wong, T. Zakian, in:, FC 2021 Workshops, Springer Nature, 2021, pp. 431–450.","chicago":"Blackshear, Sam, Konstantinos Chalkias, Panagiotis Chatzigiannis, Riyaz Faizullabhoy, Irakliy Khaburzaniya, Eleftherios Kokoris Kogias, Joshua Lind, David Wong, and Tim Zakian. “Reactive Key-Loss Protection in Blockchains.” In FC 2021 Workshops, 12676:431–50. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-63958-0_34.","ama":"Blackshear S, Chalkias K, Chatzigiannis P, et al. Reactive key-loss protection in blockchains. In: FC 2021 Workshops. Vol 12676. Springer Nature; 2021:431-450. doi:10.1007/978-3-662-63958-0_34","ista":"Blackshear S, Chalkias K, Chatzigiannis P, Faizullabhoy R, Khaburzaniya I, Kokoris Kogias E, Lind J, Wong D, Zakian T. 2021. Reactive key-loss protection in blockchains. FC 2021 Workshops. FC: International Conference on Financial Cryptography and Data Security, LNCS, vol. 12676, 431–450.","apa":"Blackshear, S., Chalkias, K., Chatzigiannis, P., Faizullabhoy, R., Khaburzaniya, I., Kokoris Kogias, E., … Zakian, T. (2021). Reactive key-loss protection in blockchains. In FC 2021 Workshops (Vol. 12676, pp. 431–450). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-63958-0_34","ieee":"S. Blackshear et al., “Reactive key-loss protection in blockchains,” in FC 2021 Workshops, Virtual, 2021, vol. 12676, pp. 431–450."},"page":"431-450","author":[{"full_name":"Blackshear, Sam","first_name":"Sam","last_name":"Blackshear"},{"last_name":"Chalkias","first_name":"Konstantinos","full_name":"Chalkias, Konstantinos"},{"full_name":"Chatzigiannis, Panagiotis","first_name":"Panagiotis","last_name":"Chatzigiannis"},{"first_name":"Riyaz","last_name":"Faizullabhoy","full_name":"Faizullabhoy, Riyaz"},{"last_name":"Khaburzaniya","first_name":"Irakliy","full_name":"Khaburzaniya, Irakliy"},{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"full_name":"Lind, Joshua","first_name":"Joshua","last_name":"Lind"},{"first_name":"David","last_name":"Wong","full_name":"Wong, David"},{"full_name":"Zakian, Tim","last_name":"Zakian","first_name":"Tim"}],"date_updated":"2023-08-14T07:06:16Z","date_created":"2021-10-03T22:01:24Z","volume":"12676 ","year":"2021","acknowledgement":"The authors would like to thank all anonymous reviewers of FC21 WTSC workshop for comments and suggestions that greatly improved the quality of this paper.","publication_status":"published","department":[{"_id":"ElKo"}],"publisher":"Springer Nature","month":"09","publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-662-63958-0"],"eissn":["1611-3349"],"isbn":["978-3-6626-3957-3"]},"conference":{"end_date":"2021-03-05","start_date":"2021-03-01","location":"Virtual","name":"FC: International Conference on Financial Cryptography and Data Security"},"doi":"10.1007/978-3-662-63958-0_34","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://research.fb.com/publications/reactive-key-loss-protection-in-blockchains/","open_access":"1"}],"oa":1,"external_id":{"isi":["000713005000034"]},"quality_controlled":"1","isi":1},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10070","title":"Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces","status":"public","intvolume":" 281","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We extensively discuss the Rademacher and Sobolev-to-Lipschitz properties for generalized intrinsic distances on strongly local Dirichlet spaces possibly without square field operator. We present many non-smooth and infinite-dimensional examples. As an application, we prove the integral Varadhan short-time asymptotic with respect to a given distance function for a large class of strongly local Dirichlet forms.","lang":"eng"}],"issue":"11","publication":"Journal of Functional Analysis","citation":{"ama":"Dello Schiavo L, Suzuki K. Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. 2021;281(11). doi:10.1016/j.jfa.2021.109234","ista":"Dello Schiavo L, Suzuki K. 2021. Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. 281(11), 109234.","apa":"Dello Schiavo, L., & Suzuki, K. (2021). Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109234","ieee":"L. Dello Schiavo and K. Suzuki, “Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces,” Journal of Functional Analysis, vol. 281, no. 11. Elsevier, 2021.","mla":"Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” Journal of Functional Analysis, vol. 281, no. 11, 109234, Elsevier, 2021, doi:10.1016/j.jfa.2021.109234.","short":"L. Dello Schiavo, K. Suzuki, Journal of Functional Analysis 281 (2021).","chicago":"Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” Journal of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109234."},"article_type":"original","date_published":"2021-09-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","year":"2021","acknowledgement":"The authors are grateful to Professor Kazuhiro Kuwae for kindly providing a copy of [49]. They are also grateful to Dr. Bang-Xian Han for helpful discussions on the Sobolev-to-Lipschitz property on metric measure spaces. They wish to express their deepest gratitude to an anonymous Reviewer, whose punctual remarks and comments greatly improved the accessibility and overall quality of the initial submission. This work was completed while L.D.S. was a member of the Institut für Angewandte Mathematik of the University of Bonn. He acknowledges funding of his position at that time by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the Sonderforschungsbereich (Sfb, Collaborative Research Center) 1060 - project number 211504053. He also acknowledges funding of his current position by the Austrian Science Fund (FWF) grant F65, and by the European Research Council (ERC, grant No. 716117, awarded to Prof. Dr. Jan Maas). K.S. gratefully acknowledges funding by: the JSPS Overseas Research Fellowships, Grant Nr. 290142; World Premier International Research Center Initiative (WPI), MEXT, Japan; and JSPS Grant-in-Aid for Scientific Research on Innovative Areas “Discrete Geometric Analysis for Materials Design”, Grant Number 17H06465.","publication_status":"published","department":[{"_id":"JaMa"}],"publisher":"Elsevier","author":[{"last_name":"Dello Schiavo","first_name":"Lorenzo","orcid":"0000-0002-9881-6870","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","full_name":"Dello Schiavo, Lorenzo"},{"full_name":"Suzuki, Kohei","first_name":"Kohei","last_name":"Suzuki"}],"date_updated":"2023-08-14T07:05:44Z","date_created":"2021-10-03T22:01:21Z","volume":281,"article_number":"109234","ec_funded":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2008.01492"}],"external_id":{"arxiv":["2008.01492"],"isi":["000703896600005"]},"quality_controlled":"1","isi":1,"project":[{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.jfa.2021.109234","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]}},{"pmid":1,"acknowledgement":"Y.L. and M.C. contributed equally to this work. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was 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. M.C. has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385. Y.Y. and O.C.-M. acknowledge the financial support from DFG within the project SFB 917: Nanoswitches. J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia program. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N.","year":"2021","department":[{"_id":"EM-Fac"},{"_id":"MaIb"}],"publisher":"Wiley","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12885"}]},"author":[{"full_name":"Liu, Yu","first_name":"Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740"},{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877","first_name":"Mariano","last_name":"Calcabrini","full_name":"Calcabrini, Mariano"},{"last_name":"Yu","first_name":"Yuan","full_name":"Yu, Yuan"},{"full_name":"Genç, Aziz","last_name":"Genç","first_name":"Aziz"},{"full_name":"Chang, Cheng","first_name":"Cheng","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277"},{"full_name":"Costanzo, Tommaso","first_name":"Tommaso","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815"},{"full_name":"Kleinhanns, Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","last_name":"Kleinhanns","first_name":"Tobias"},{"orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee","first_name":"Seungho","full_name":"Lee, Seungho"},{"last_name":"Llorca","first_name":"Jordi","full_name":"Llorca, Jordi"},{"full_name":"Cojocaru‐Mirédin, Oana","first_name":"Oana","last_name":"Cojocaru‐Mirédin"},{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"}],"volume":33,"date_created":"2021-10-11T20:07:24Z","date_updated":"2023-08-14T07:25:27Z","article_number":"2106858","ec_funded":1,"file_date_updated":"2022-02-03T13:16:14Z","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":["000709899300001"],"pmid":["34626034"]},"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"isi":1,"quality_controlled":"1","doi":"10.1002/adma.202106858","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"month":"12","_id":"10123","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 33","status":"public","title":"The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe","ddc":["620"],"file":[{"date_updated":"2022-02-03T13:16:14Z","date_created":"2022-02-03T13:16:14Z","checksum":"990bccc527c64d85cf1c97885110b5f4","success":1,"relation":"main_file","file_id":"10720","file_size":5595666,"content_type":"application/pdf","creator":"cchlebak","file_name":"2021_AdvancedMaterials_Liu.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"52","abstract":[{"lang":"eng","text":"Solution synthesis of particles emerged as an alternative to prepare thermoelectric materials with less demanding processing conditions than conventional solid-state synthetic methods. However, solution synthesis generally involves the presence of additional molecules or ions belonging to the precursors or added to enable solubility and/or regulate nucleation and growth. These molecules or ions can end up in the particles as surface adsorbates and interfere in the material properties. This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically adsorbed in SnSe particles synthesized in water and play a crucial role not only in directing the material nano/microstructure but also in determining the transport properties of the consolidated material. In dense pellets prepared by sintering SnSe particles, Na remains within the crystal lattice as dopant, in dislocations, precipitates, and forming grain boundary complexions. These results highlight the importance of considering all the possible unintentional impurities to establish proper structure-property relationships and control material properties in solution-processed thermoelectric materials."}],"citation":{"apa":"Liu, Y., Calcabrini, M., Yu, Y., Genç, A., Chang, C., Costanzo, T., … Ibáñez, M. (2021). The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202106858","ieee":"Y. Liu et al., “The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe,” Advanced Materials, vol. 33, no. 52. Wiley, 2021.","ista":"Liu Y, Calcabrini M, Yu Y, Genç A, Chang C, Costanzo T, Kleinhanns T, Lee S, Llorca J, Cojocaru‐Mirédin O, Ibáñez M. 2021. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 33(52), 2106858.","ama":"Liu Y, Calcabrini M, Yu Y, et al. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 2021;33(52). doi:10.1002/adma.202106858","chicago":"Liu, Yu, Mariano Calcabrini, Yuan Yu, Aziz Genç, Cheng Chang, Tommaso Costanzo, Tobias Kleinhanns, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” Advanced Materials. Wiley, 2021. https://doi.org/10.1002/adma.202106858.","short":"Y. Liu, M. Calcabrini, Y. Yu, A. Genç, C. Chang, T. Costanzo, T. Kleinhanns, S. Lee, J. Llorca, O. Cojocaru‐Mirédin, M. Ibáñez, Advanced Materials 33 (2021).","mla":"Liu, Yu, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” Advanced Materials, vol. 33, no. 52, 2106858, Wiley, 2021, doi:10.1002/adma.202106858."},"publication":"Advanced Materials","article_type":"original","date_published":"2021-12-29T00:00:00Z","scopus_import":"1","keyword":["mechanical engineering","mechanics of materials","general materials science"],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"29"},{"type":"journal_article","abstract":[{"text":"Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism.","lang":"eng"}],"issue":"3","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10117","status":"public","ddc":["612"],"title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling","intvolume":" 297","file":[{"date_updated":"2021-10-11T12:20:58Z","date_created":"2021-10-11T12:20:58Z","checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","success":1,"relation":"main_file","file_id":"10121","content_type":"application/pdf","file_size":1680010,"creator":"cchlebak","file_name":"2021_JBC_Artan.pdf","access_level":"open_access"}],"oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","publication":"Journal of Biological Chemistry","citation":{"chicago":"Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel, Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry. Elsevier, 2021. https://doi.org/10.1016/J.JBC.2021.101094.","short":"M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021).","mla":"Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry, vol. 297, no. 3, 101094, Elsevier, 2021, doi:10.1016/J.JBC.2021.101094.","ieee":"M. Artan et al., “Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling,” Journal of Biological Chemistry, vol. 297, no. 3. Elsevier, 2021.","apa":"Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., & de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. Elsevier. https://doi.org/10.1016/J.JBC.2021.101094","ista":"Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 297(3), 101094.","ama":"Artan M, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 2021;297(3). doi:10.1016/J.JBC.2021.101094"},"article_type":"original","date_published":"2021-09-01T00:00:00Z","article_number":"101094","file_date_updated":"2021-10-11T12:20:58Z","ec_funded":1,"acknowledgement":"We thank de Bono lab members for helpful comments on the manuscript, IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions and comments for the optimization of mass spec analyses of worm samples. The biotin auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg). Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University of Vienna).","year":"2021","publication_status":"published","department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"publisher":"Elsevier","author":[{"full_name":"Artan, Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992","first_name":"Murat","last_name":"Artan"},{"id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677","last_name":"Barratt","first_name":"Stephen","full_name":"Barratt, Stephen"},{"full_name":"Flynn, Sean M.","last_name":"Flynn","first_name":"Sean M."},{"full_name":"Begum, Farida","first_name":"Farida","last_name":"Begum"},{"first_name":"Mark","last_name":"Skehel","full_name":"Skehel, Mark"},{"first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"first_name":"Mario","last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"De Bono, Mario"}],"date_created":"2021-10-10T22:01:23Z","date_updated":"2023-08-14T07:24:09Z","volume":297,"month":"09","publication_identifier":{"issn":["0021-9258"],"eissn":["1083-351X"]},"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":["000706409200006"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/J.JBC.2021.101094","language":[{"iso":"eng"}]},{"author":[{"full_name":"Mühlböck, Fabian","first_name":"Fabian","last_name":"Mühlböck","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"related_material":{"record":[{"relation":"extended_version","status":"public","id":"9946"}]},"date_created":"2021-10-07T23:30:10Z","date_updated":"2023-08-14T07:20:30Z","volume":12974,"acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Mae Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","year":"2021","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","file_date_updated":"2021-10-07T23:32:18Z","place":"Cham","conference":{"name":"RV: Runtime Verification","end_date":"2021-10-14","start_date":"2021-10-11","location":"Virtual"},"doi":"10.1007/978-3-030-88494-9_12","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000719383800012"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"month":"10","publication_identifier":{"isbn":["978-3-030-88493-2"],"eissn":["1611-3349"],"eisbn":["978-3-030-88494-9"],"issn":["0302-9743"]},"oa_version":"Preprint","file":[{"checksum":"554c7fdb259eda703a8b6328a6dad55a","success":1,"date_created":"2021-10-07T23:32:18Z","date_updated":"2021-10-07T23:32:18Z","relation":"main_file","file_id":"10109","content_type":"application/pdf","file_size":350632,"creator":"fmuehlbo","access_level":"open_access","file_name":"differentialmonitoring-cameraready-openaccess.pdf"}],"_id":"10108","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Differential monitoring","ddc":["005"],"status":"public","intvolume":" 12974","abstract":[{"text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2021-10-06T00:00:00Z","publication":"International Conference on Runtime Verification","citation":{"chicago":"Mühlböck, Fabian, and Thomas A Henzinger. “Differential Monitoring.” In International Conference on Runtime Verification, 12974:231–43. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_12.","short":"F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 231–243.","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. “Differential Monitoring.” International Conference on Runtime Verification, vol. 12974, Springer Nature, 2021, pp. 231–43, doi:10.1007/978-3-030-88494-9_12.","apa":"Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. In International Conference on Runtime Verification (Vol. 12974, pp. 231–243). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-88494-9_12","ieee":"F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in International Conference on Runtime Verification, Virtual, 2021, vol. 12974, pp. 231–243.","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring. International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 231–243.","ama":"Mühlböck F, Henzinger TA. Differential monitoring. In: International Conference on Runtime Verification. Vol 12974. Cham: Springer Nature; 2021:231-243. doi:10.1007/978-3-030-88494-9_12"},"page":"231-243","day":"06","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","keyword":["run-time verification","software engineering","implicit specification"]},{"file":[{"success":1,"checksum":"b465e172d2b1f57aa26a2571a085d052","date_updated":"2021-10-11T14:15:07Z","date_created":"2021-10-11T14:15:07Z","file_id":"10122","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","file_size":1774624,"access_level":"open_access","file_name":"2021_eLife_VuongBrender.pdf"}],"oa_version":"Published Version","_id":"10116","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Neuronal calmodulin levels are controlled by CAMTA transcription factors","ddc":["610"],"status":"public","intvolume":" 10","abstract":[{"text":"The ubiquitous Ca2+ sensor calmodulin (CaM) binds and regulates many proteins, including ion channels, CaM kinases, and calcineurin, according to Ca2+-CaM levels. What regulates neuronal CaM levels, is, however, unclear. CaM-binding transcription activators (CAMTAs) are ancient proteins expressed broadly in nervous systems and whose loss confers pleiotropic behavioral defects in flies, mice, and humans. Using Caenorhabditis elegans and Drosophila, we show that CAMTAs control neuronal CaM levels. The behavioral and neuronal Ca2+ signaling defects in mutants lacking camt-1, the sole C. elegans CAMTA, can be rescued by supplementing neuronal CaM. CAMT-1 binds multiple sites in the CaM promoter and deleting these sites phenocopies camt-1. Our data suggest CAMTAs mediate a conserved and general mechanism that controls neuronal CaM levels, thereby regulating Ca2+ signaling, physiology, and behavior.","lang":"eng"}],"type":"journal_article","date_published":"2021-09-17T00:00:00Z","publication":"eLife","citation":{"ieee":"T. Vuong-Brender, S. Flynn, Y. Vallis, and M. de Bono, “Neuronal calmodulin levels are controlled by CAMTA transcription factors,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Vuong-Brender, T., Flynn, S., Vallis, Y., & de Bono, M. (2021). Neuronal calmodulin levels are controlled by CAMTA transcription factors. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.68238","ista":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. 2021. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife. 10, e68238.","ama":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife. 2021;10. doi:10.7554/eLife.68238","chicago":"Vuong-Brender, Thanh, Sean Flynn, Yvonne Vallis, and Mario de Bono. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.68238.","short":"T. Vuong-Brender, S. Flynn, Y. Vallis, M. de Bono, ELife 10 (2021).","mla":"Vuong-Brender, Thanh, et al. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” ELife, vol. 10, e68238, eLife Sciences Publications, 2021, doi:10.7554/eLife.68238."},"article_type":"original","day":"17","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Vuong-Brender, Thanh","last_name":"Vuong-Brender","first_name":"Thanh","id":"D389312E-10C4-11EA-ABF4-A4B43DDC885E"},{"first_name":"Sean","last_name":"Flynn","full_name":"Flynn, Sean"},{"full_name":"Vallis, Yvonne","last_name":"Vallis","first_name":"Yvonne","id":"05A2795C-31B5-11EA-83A7-7DA23DDC885E"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"De Bono","first_name":"Mario","full_name":"De Bono, Mario"}],"date_updated":"2023-08-14T07:23:39Z","date_created":"2021-10-10T22:01:22Z","volume":10,"acknowledgement":"The authors thank the MRC-LMB Flow Cytometry facility and Imaging Service for support, the Cancer Research UK Cambridge Institute Genomics Core for Next Generation Sequencing, Julie Ahringer and Alex Appert for advice and technical help for ChIP-seq experiments, Paula Freire-Pritchett, Tim Stevens, and Gurpreet Ghattaoraya for RNA-seq and ChIP-seq analyses, Nikos Chronis for the TN-XL plasmid, Hong-Sheng Li and Daisuke Yamamoto for generously sending the tes2 and cro mutants, Daria Siekhaus for hosting the fly work, Michaela Misova for technical assistance. The authors are very grateful to Salihah Ece Sönmez for teaching us how to dissect, mount and stain Drosophila retinae. This work was supported by an Advanced ERC grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB, and an IST Plus Fellowship to TV-B (Marie Sklodowska-Curie Agreement no 754411).","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"MaDe"}],"publisher":"eLife Sciences Publications","file_date_updated":"2021-10-11T14:15:07Z","ec_funded":1,"article_number":"e68238","doi":"10.7554/eLife.68238","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000695716100001"],"pmid":["34499028"]},"isi":1,"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"month":"09","publication_identifier":{"eissn":["2050-084X"]}},{"date_published":"2021-09-17T00:00:00Z","article_type":"original","citation":{"mla":"Obr, Martin, et al. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses, vol. 13, no. 9, 1853, MDPI, 2021, doi:10.3390/v13091853.","short":"M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021).","chicago":"Obr, Martin, Florian KM Schur, and Robert A. Dick. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses. MDPI, 2021. https://doi.org/10.3390/v13091853.","ama":"Obr M, Schur FK, Dick RA. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 2021;13(9). doi:10.3390/v13091853","ista":"Obr M, Schur FK, Dick RA. 2021. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 13(9), 1853.","ieee":"M. Obr, F. K. Schur, and R. A. Dick, “A structural perspective of the role of IP6 in immature and mature retroviral assembly,” Viruses, vol. 13, no. 9. MDPI, 2021.","apa":"Obr, M., Schur, F. K., & Dick, R. A. (2021). A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. MDPI. https://doi.org/10.3390/v13091853"},"publication":"Viruses","has_accepted_license":"1","article_processing_charge":"Yes","day":"17","keyword":["virology","infectious diseases"],"file":[{"date_created":"2021-10-08T10:38:15Z","date_updated":"2021-10-08T10:38:15Z","checksum":"bcfd72a12977d48e22df3d0cc55aacf1","success":1,"relation":"main_file","file_id":"10115","file_size":4146796,"content_type":"application/pdf","creator":"cchlebak","file_name":"2021_Viruses_Obr.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 13","title":"A structural perspective of the role of IP6 in immature and mature retroviral assembly","status":"public","ddc":["616"],"_id":"10103","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"9","abstract":[{"lang":"eng","text":"The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.3390/v13091853","project":[{"grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000699841100001"],"pmid":["34578434"]},"publication_identifier":{"issn":["1999-4915"]},"month":"09","volume":13,"date_updated":"2023-08-14T07:21:51Z","date_created":"2021-10-07T09:13:29Z","author":[{"first_name":"Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","full_name":"Obr, Martin"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM"},{"last_name":"Dick","first_name":"Robert A.","full_name":"Dick, Robert A."}],"publisher":"MDPI","department":[{"_id":"FlSc"}],"publication_status":"published","pmid":1,"year":"2021","acknowledgement":"We thank Volker M. Vogt for his critical comments in preparation of the review.","file_date_updated":"2021-10-08T10:38:15Z","article_number":"1853"},{"article_type":"original","citation":{"chicago":"Medina Ramos, Raimel A, Romain Vasseur, and Maksym Serbyn. “Entanglement Transitions from Restricted Boltzmann Machines.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/physrevb.104.104205.","short":"R.A. Medina Ramos, R. Vasseur, M. Serbyn, Physical Review B 104 (2021).","mla":"Medina Ramos, Raimel A., et al. “Entanglement Transitions from Restricted Boltzmann Machines.” Physical Review B, vol. 104, no. 10, 104205, American Physical Society, 2021, doi:10.1103/physrevb.104.104205.","ieee":"R. A. Medina Ramos, R. Vasseur, and M. Serbyn, “Entanglement transitions from restricted Boltzmann machines,” Physical Review B, vol. 104, no. 10. American Physical Society, 2021.","apa":"Medina Ramos, R. A., Vasseur, R., & Serbyn, M. (2021). Entanglement transitions from restricted Boltzmann machines. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.104.104205","ista":"Medina Ramos RA, Vasseur R, Serbyn M. 2021. Entanglement transitions from restricted Boltzmann machines. Physical Review B. 104(10), 104205.","ama":"Medina Ramos RA, Vasseur R, Serbyn M. Entanglement transitions from restricted Boltzmann machines. Physical Review B. 2021;104(10). doi:10.1103/physrevb.104.104205"},"publication":"Physical Review B","date_published":"2021-09-30T00:00:00Z","article_processing_charge":"No","day":"30","intvolume":" 104","status":"public","title":"Entanglement transitions from restricted Boltzmann machines","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10067","oa_version":"Preprint","type":"journal_article","issue":"10","abstract":[{"lang":"eng","text":"The search for novel entangled phases of matter has lead to the recent discovery of a new class of “entanglement transitions,” exemplified by random tensor networks and monitored quantum circuits. Most known examples can be understood as some classical ordering transitions in an underlying statistical mechanics model, where entanglement maps onto the free-energy cost of inserting a domain wall. In this paper we study the possibility of entanglement transitions driven by physics beyond such statistical mechanics mappings. Motivated by recent applications of neural-network-inspired variational Ansätze, we investigate under what conditions on the variational parameters these Ansätze can capture an entanglement transition. We study the entanglement scaling of short-range restricted Boltzmann machine (RBM) quantum states with random phases. For uncorrelated random phases, we analytically demonstrate the absence of an entanglement transition and reveal subtle finite-size effects in finite-size numerical simulations. Introducing phases with correlations decaying as 1/r^α in real space, we observe three regions with a different scaling of entanglement entropy depending on the exponent α. We study the nature of the transition between these regions, finding numerical evidence for critical behavior. Our work establishes the presence of long-range correlated phases in RBM-based wave functions as a required ingredient for entanglement transitions."}],"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","oa":1,"external_id":{"arxiv":["2107.05735"],"isi":["000704414400002"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2107.05735"}],"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.104.104205","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"09","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","acknowledgement":"We would like to thank S. De Nicola, P. Brighi, and V. Karle for fruitful discussions and valuable feedback on the manuscript. R.M. and M.S. acknowledge support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.V. acknowledges support from the US Department of Energy, Office of Science, Basic Energy Sciences, under Early Career Award No. DE-SC0019168, and the Alfred P. Sloan Foundation through a Sloan Research Fellowship.","year":"2021","volume":104,"date_updated":"2023-08-14T07:24:47Z","date_created":"2021-10-02T09:03:42Z","author":[{"last_name":"Medina Ramos","first_name":"Raimel A","orcid":"0000-0002-5383-2869","id":"CE680B90-D85A-11E9-B684-C920E6697425","full_name":"Medina Ramos, Raimel A"},{"full_name":"Vasseur, Romain","first_name":"Romain","last_name":"Vasseur"},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"}],"article_number":"104205","ec_funded":1},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","keyword":["run-time verification","software engineering","implicit specification"],"date_published":"2021-09-01T00:00:00Z","citation":{"ama":"Mühlböck F, Henzinger TA. Differential Monitoring. IST Austria; 2021. doi:10.15479/AT:ISTA:9946","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p.","ieee":"F. Mühlböck and T. A. Henzinger, Differential monitoring. IST Austria, 2021.","apa":"Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. IST Austria. https://doi.org/10.15479/AT:ISTA:9946","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. Differential Monitoring. IST Austria, 2021, doi:10.15479/AT:ISTA:9946.","short":"F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021.","chicago":"Mühlböck, Fabian, and Thomas A Henzinger. Differential Monitoring. IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9946."},"page":"17","abstract":[{"lang":"eng","text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs."}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"file":[{"file_id":"9948","relation":"main_file","checksum":"0f9aafd59444cb6bdca6925d163ab946","date_created":"2021-08-20T19:59:44Z","date_updated":"2021-09-03T12:34:28Z","access_level":"open_access","file_name":"differentialmonitoring-techreport.pdf","creator":"fmuehlbo","file_size":"320453","content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9946","status":"public","ddc":["005"],"title":"Differential monitoring","publication_identifier":{"issn":["2664-1690"]},"month":"09","doi":"10.15479/AT:ISTA:9946","language":[{"iso":"eng"}],"oa":1,"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"file_date_updated":"2021-09-03T12:34:28Z","related_material":{"record":[{"status":"public","relation":"other","id":"9281"},{"id":"10108","status":"public","relation":"shorter_version"}]},"author":[{"orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck","first_name":"Fabian","full_name":"Mühlböck, Fabian"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"date_created":"2021-08-20T20:00:37Z","date_updated":"2023-08-14T07:20:29Z","year":"2021","acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Matthew Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","publisher":"IST Austria","department":[{"_id":"ToHe"}],"publication_status":"published"},{"date_published":"2021-09-19T00:00:00Z","article_type":"original","publication":"Materials","citation":{"ista":"Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 14(18), 5416.","ieee":"C. Chang and M. Ibáñez, “Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites,” Materials, vol. 14, no. 18. MDPI, 2021.","apa":"Chang, C., & Ibáñez, M. (2021). Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. MDPI. https://doi.org/10.3390/ma14185416","ama":"Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 2021;14(18). doi:10.3390/ma14185416","chicago":"Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” Materials. MDPI, 2021. https://doi.org/10.3390/ma14185416.","mla":"Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” Materials, vol. 14, no. 18, 5416, MDPI, 2021, doi:10.3390/ma14185416.","short":"C. Chang, M. Ibáñez, Materials 14 (2021)."},"day":"19","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","file":[{"access_level":"open_access","file_name":"2021_Materials_Chang.pdf","file_size":4404141,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"10140","checksum":"4929dfc673a3ae77c010b6174279cc1d","success":1,"date_created":"2021-10-14T11:56:39Z","date_updated":"2021-10-14T11:56:39Z"}],"oa_version":"Published Version","ddc":["540"],"title":"Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites","status":"public","intvolume":" 14","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10073","abstract":[{"lang":"eng","text":"Thermoelectric materials enable the direct conversion between heat and electricity. SnTe is a promising candidate due to its high charge transport performance. Here, we prepared SnTe nanocomposites by employing an aqueous method to synthetize SnTe nanoparticles (NP), followed by a unique surface treatment prior NP consolidation. This synthetic approach allowed optimizing the charge and phonon transport synergistically. The novelty of this strategy was the use of a soluble PbS molecular complex prepared using a thiol-amine solvent mixture that upon blending is adsorbed on the SnTe NP surface. Upon consolidation with spark plasma sintering, SnTe-PbS nanocomposite is formed. The presence of PbS complexes significantly compensates for the Sn vacancy and increases the average grain size of the nanocomposite, thus improving the carrier mobility. Moreover, lattice thermal conductivity is also reduced by the Pb and S-induced mass and strain fluctuation. As a result, an enhanced ZT of ca. 0.8 is reached at 873 K. Our finding provides a novel strategy to conduct rational surface treatment on NP-based thermoelectrics."}],"issue":"18","type":"journal_article","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.3390/ma14185416","quality_controlled":"1","isi":1,"project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889"}],"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":["34576640"],"isi":["000700689400001"]},"month":"09","publication_identifier":{"eissn":["1996-1944"]},"date_updated":"2023-08-14T08:00:01Z","date_created":"2021-10-03T22:01:23Z","volume":14,"author":[{"full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","first_name":"Cheng","last_name":"Chang"},{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"}],"publication_status":"published","publisher":"MDPI","department":[{"_id":"MaIb"}],"year":"2021","acknowledgement":"The authors thank the EMF facility in IST Austria for providing SEM and EDX measurements.\r\n","pmid":1,"file_date_updated":"2021-10-14T11:56:39Z","article_number":"5416"},{"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"month":"06","external_id":{"isi":["000741368600009"],"pmid":["34146097"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"doi":"10.1093/molbev/msab178","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"file_date_updated":"2022-05-06T09:47:18Z","pmid":1,"year":"2021","acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","publisher":"Oxford University Press ","department":[{"_id":"BeVi"}],"publication_status":"published","author":[{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","first_name":"Marwan N"},{"id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","orcid":"0000-0002-8876-6494","first_name":"Mikhail A.","last_name":"Moldovan","full_name":"Moldovan, Mikhail A."},{"full_name":"Picard, Marion A L","orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","first_name":"Marion A L"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"date_updated":"2023-08-14T08:03:06Z","date_created":"2021-10-21T07:49:12Z","scopus_import":"1","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"has_accepted_license":"1","article_processing_charge":"No","day":"19","citation":{"short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution (2021).","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” Molecular Biology and Evolution, Oxford University Press , 2021, doi:10.1093/molbev/msab178.","chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” Molecular Biology and Evolution. Oxford University Press , 2021. https://doi.org/10.1093/molbev/msab178.","ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 2021. doi:10.1093/molbev/msab178","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” Molecular Biology and Evolution. Oxford University Press , 2021.","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., & Vicoso, B. (2021). Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. Oxford University Press . https://doi.org/10.1093/molbev/msab178","ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution."},"publication":"Molecular Biology and Evolution","article_type":"original","date_published":"2021-06-19T00:00:00Z","type":"journal_article","abstract":[{"text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10167","ddc":["610"],"status":"public","title":"Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","creator":"dernst","content_type":"application/pdf","file_size":1008594,"file_id":"11352","relation":"main_file","success":1,"checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","date_updated":"2022-05-06T09:47:18Z","date_created":"2022-05-06T09:47:18Z"}]},{"language":[{"iso":"eng"}],"doi":"10.1038/s41467-021-26360-2","isi":1,"quality_controlled":"1","external_id":{"isi":["000709050300001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["2041-1723"]},"month":"10","volume":12,"date_created":"2021-10-20T14:40:32Z","date_updated":"2023-08-14T08:02:31Z","related_material":{"link":[{"description":"Preprint ","relation":"earlier_version","url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159"}]},"author":[{"full_name":"Appel, Lisa-Marie","first_name":"Lisa-Marie","last_name":"Appel"},{"last_name":"Franke","first_name":"Vedran","full_name":"Franke, Vedran"},{"full_name":"Bruno, Melania","last_name":"Bruno","first_name":"Melania"},{"first_name":"Irina","last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina"},{"full_name":"Kasiliauskaite, Aiste","first_name":"Aiste","last_name":"Kasiliauskaite"},{"full_name":"Kaufmann, Tanja","last_name":"Kaufmann","first_name":"Tanja"},{"full_name":"Schoeberl, Ursula E.","first_name":"Ursula E.","last_name":"Schoeberl"},{"first_name":"Martin G.","last_name":"Puchinger","full_name":"Puchinger, Martin G."},{"full_name":"Kostrhon, Sebastian","last_name":"Kostrhon","first_name":"Sebastian"},{"first_name":"Carmen","last_name":"Ebenwaldner","full_name":"Ebenwaldner, Carmen"},{"full_name":"Sebesta, Marek","last_name":"Sebesta","first_name":"Marek"},{"full_name":"Beltzung, Etienne","first_name":"Etienne","last_name":"Beltzung"},{"full_name":"Mechtler, Karl","last_name":"Mechtler","first_name":"Karl"},{"last_name":"Lin","first_name":"Gen","full_name":"Lin, Gen"},{"last_name":"Vlasova","first_name":"Anna","full_name":"Vlasova, Anna"},{"first_name":"Martin","last_name":"Leeb","full_name":"Leeb, Martin"},{"full_name":"Pavri, Rushad","last_name":"Pavri","first_name":"Rushad"},{"full_name":"Stark, Alexander","first_name":"Alexander","last_name":"Stark"},{"full_name":"Akalin, Altuna","last_name":"Akalin","first_name":"Altuna"},{"first_name":"Richard","last_name":"Stefl","full_name":"Stefl, Richard"},{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","first_name":"Carrie A"},{"full_name":"Djinovic-Carugo, Kristina","first_name":"Kristina","last_name":"Djinovic-Carugo"},{"first_name":"Dea","last_name":"Slade","full_name":"Slade, Dea"}],"publisher":"Springer Nature","department":[{"_id":"CaBe"}],"publication_status":"published","year":"2021","acknowledgement":"D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase; Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for design of the arrest assay sequences; Petra van der Lelij for help with generating mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing; Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis; staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support; Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for critical comments on the manuscript; Life Science Editors for editing assistance. M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K. is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S. is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic (CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement no. 649030); this publication reflects only the author’s view and the Research Executive Agency is not responsible for any use that may be made of the information it contains. M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276, P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative ‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action BM1405 Non-globular proteins - from sequence to structure, function and application in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF LS17-008), and by the University of Vienna. This project was funded by the MFPL start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”) to D.S.","file_date_updated":"2021-10-21T13:51:49Z","article_number":"6078","date_published":"2021-10-19T00:00:00Z","article_type":"original","citation":{"chicago":"Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26360-2.","mla":"Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications, vol. 12, no. 1, 6078, Springer Nature, 2021, doi:10.1038/s41467-021-26360-2.","short":"L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T. Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta, E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A. Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications 12 (2021).","ista":"Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.","apa":"Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26360-2","ieee":"L.-M. Appel et al., “PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ama":"Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26360-2"},"publication":"Nature Communications","article_processing_charge":"No","has_accepted_license":"1","day":"19","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10169","date_created":"2021-10-21T13:51:49Z","date_updated":"2021-10-21T13:51:49Z","checksum":"d99fcd51aebde19c21314e3de0148007","success":1,"file_name":"2021_NatComm_Appel.pdf","access_level":"open_access","file_size":5111706,"content_type":"application/pdf","creator":"cchlebak"}],"intvolume":" 12","ddc":["610"],"title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","status":"public","_id":"10163","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"1","abstract":[{"text":"The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay.","lang":"eng"}],"type":"journal_article"},{"oa":1,"external_id":{"isi":["000657959600017"]},"project":[{"call_identifier":"H2020","name":"Distributed 3D Object Design","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"isi":1,"quality_controlled":"1","doi":"10.1111/cgf.142626","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"month":"05","acknowledgement":"We thank Sebastian Cucerca for processing and capturing the phys-cal printouts. This work was supported by the Charles University grant SVV-260588 and Czech Science Foundation grant 19-07626S. This project has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska Curie grant agreements No 642841 (DISTRO) and No765911 (RealVision), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE).","year":"2021","department":[{"_id":"BeBi"}],"publisher":"Wiley","publication_status":"published","author":[{"last_name":"Rittig","first_name":"Tobias","full_name":"Rittig, Tobias"},{"full_name":"Sumin, Denis","last_name":"Sumin","first_name":"Denis"},{"last_name":"Babaei","first_name":"Vahid","full_name":"Babaei, Vahid"},{"full_name":"Didyk, Piotr","first_name":"Piotr","last_name":"Didyk"},{"last_name":"Voloboy","first_name":"Alexey","full_name":"Voloboy, Alexey"},{"last_name":"Wilkie","first_name":"Alexander","full_name":"Wilkie, Alexander"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"},{"full_name":"Myszkowski, Karol","first_name":"Karol","last_name":"Myszkowski"},{"full_name":"Weyrich, Tim","last_name":"Weyrich","first_name":"Tim"},{"first_name":"Jaroslav","last_name":"Křivánek","full_name":"Křivánek, Jaroslav"}],"volume":40,"date_created":"2021-06-13T22:01:32Z","date_updated":"2023-08-14T08:01:50Z","ec_funded":1,"file_date_updated":"2021-10-11T12:06:50Z","citation":{"chicago":"Rittig, Tobias, Denis Sumin, Vahid Babaei, Piotr Didyk, Alexey Voloboy, Alexander Wilkie, Bernd Bickel, Karol Myszkowski, Tim Weyrich, and Jaroslav Křivánek. “Neural Acceleration of Scattering-Aware Color 3D Printing.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.142626.","short":"T. Rittig, D. Sumin, V. Babaei, P. Didyk, A. Voloboy, A. Wilkie, B. Bickel, K. Myszkowski, T. Weyrich, J. Křivánek, Computer Graphics Forum 40 (2021) 205–219.","mla":"Rittig, Tobias, et al. “Neural Acceleration of Scattering-Aware Color 3D Printing.” Computer Graphics Forum, vol. 40, no. 2, Wiley, 2021, pp. 205–19, doi:10.1111/cgf.142626.","ieee":"T. Rittig et al., “Neural acceleration of scattering-aware color 3D printing,” Computer Graphics Forum, vol. 40, no. 2. Wiley, pp. 205–219, 2021.","apa":"Rittig, T., Sumin, D., Babaei, V., Didyk, P., Voloboy, A., Wilkie, A., … Křivánek, J. (2021). Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.142626","ista":"Rittig T, Sumin D, Babaei V, Didyk P, Voloboy A, Wilkie A, Bickel B, Myszkowski K, Weyrich T, Křivánek J. 2021. Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. 40(2), 205–219.","ama":"Rittig T, Sumin D, Babaei V, et al. Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. 2021;40(2):205-219. doi:10.1111/cgf.142626"},"publication":"Computer Graphics Forum","page":"205-219","article_type":"original","date_published":"2021-05-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","_id":"9547","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 40","status":"public","ddc":["004"],"title":"Neural acceleration of scattering-aware color 3D printing","file":[{"file_id":"10120","relation":"main_file","date_created":"2021-10-11T12:06:50Z","date_updated":"2021-10-11T12:06:50Z","success":1,"checksum":"33271724215f54a75c39d2ed40f2c502","file_name":"ScatteringAwareColor3DPrinting_authorVersion.pdf","access_level":"open_access","creator":"bbickel","content_type":"application/pdf","file_size":26026501}],"oa_version":"Submitted Version","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"With the wider availability of full-color 3D printers, color-accurate 3D-print preparation has received increased attention. A key challenge lies in the inherent translucency of commonly used print materials that blurs out details of the color texture. Previous work tries to compensate for these scattering effects through strategic assignment of colored primary materials to printer voxels. To date, the highest-quality approach uses iterative optimization that relies on computationally expensive Monte Carlo light transport simulation to predict the surface appearance from subsurface scattering within a given print material distribution; that optimization, however, takes in the order of days on a single machine. In our work, we dramatically speed up the process by replacing the light transport simulation with a data-driven approach. Leveraging a deep neural network to predict the scattering within a highly heterogeneous medium, our method performs around two orders of magnitude faster than Monte Carlo rendering while yielding optimization results of similar quality level. The network is based on an established method from atmospheric cloud rendering, adapted to our domain and extended by a physically motivated weight sharing scheme that substantially reduces the network size. We analyze its performance in an end-to-end print preparation pipeline and compare quality and runtime to alternative approaches, and demonstrate its generalization to unseen geometry and material values. This for the first time enables full heterogenous material optimization for 3D-print preparation within time frames in the order of the actual printing time."}]},{"file_date_updated":"2021-10-27T14:16:06Z","article_number":"abj0127","date_created":"2021-10-24T22:01:33Z","date_updated":"2023-08-14T08:04:42Z","volume":7,"author":[{"full_name":"Martín-Sánchez, Javier","first_name":"Javier","last_name":"Martín-Sánchez"},{"full_name":"Duan, Jiahua","last_name":"Duan","first_name":"Jiahua"},{"last_name":"Taboada-Gutiérrez","first_name":"Javier","full_name":"Taboada-Gutiérrez, Javier"},{"full_name":"Álvarez-Pérez, Gonzalo","last_name":"Álvarez-Pérez","first_name":"Gonzalo"},{"first_name":"Kirill V.","last_name":"Voronin","full_name":"Voronin, Kirill V."},{"full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","first_name":"Ivan"},{"last_name":"Ma","first_name":"Weiliang","full_name":"Ma, Weiliang"},{"full_name":"Bao, Qiaoliang","last_name":"Bao","first_name":"Qiaoliang"},{"full_name":"Volkov, Valentyn S.","first_name":"Valentyn S.","last_name":"Volkov"},{"full_name":"Hillenbrand, Rainer","last_name":"Hillenbrand","first_name":"Rainer"},{"full_name":"Nikitin, Alexey Y.","last_name":"Nikitin","first_name":"Alexey Y."},{"full_name":"Alonso-González, Pablo","first_name":"Pablo","last_name":"Alonso-González"}],"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"NanoFab"}],"acknowledgement":"J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain and FSE (RYC2018-026196-I) and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA, and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00). J.T.-G. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-18-PF-BP17-126). G.A.-P. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-20-PF-BP19-053). K.V.V. and V.S.V. acknowledge the financial support from the Ministry of Science and Higher Education of the Russian Federation (agreement no. 075-15-2021-606). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation, and Universities (national projects MAT2017-88358-C3-3-R and PID2020-115221GB-C42) and the Basque Department of Education (PIBA-2020-1-0014). R.H. acknowledges financial support from the Spanish Ministry of Science, Innovation, and Universities (national project number RTI2018-094830-B-100 and project number MDM-2016-0618 of the Marie de Maeztu Units of Excellence Program) and the Basque Government (grant number IT1164-19).","year":"2021","month":"10","publication_identifier":{"eissn":["23752548"]},"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.abj0127","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000704912700024"],"arxiv":["2103.10852"]},"abstract":[{"lang":"eng","text":"Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane hyperbolic dispersion exhibit ray-like propagation with large wave vectors and enhanced density of optical states along certain directions on a surface. As such, they have raised a surge of interest, promising unprecedented manipulation of infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end, we developed metallic nanoantennas of convex geometries for both efficient launching and focusing of the polaritons. The foci obtained exhibit enhanced near-field confinement and absorption compared to foci produced by in-plane isotropic PhPs. Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces a first and most basic building block developing planar polariton optics using in-plane anisotropic van der Waals materials."}],"issue":"41","type":"journal_article","oa_version":"Published Version","file":[{"checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","success":1,"date_updated":"2021-10-27T14:16:06Z","date_created":"2021-10-27T14:16:06Z","relation":"main_file","file_id":"10189","file_size":2441163,"content_type":"application/pdf","creator":"cziletti","access_level":"open_access","file_name":"2021_ScienceAdv_Martin-Sanchez.pdf"}],"ddc":["530"],"status":"public","title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","intvolume":" 7","_id":"10177","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"08","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2021-10-08T00:00:00Z","article_type":"original","publication":"Science Advances","citation":{"chicago":"Martín-Sánchez, Javier, Jiahua Duan, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Kirill V. Voronin, Ivan Prieto Gonzalez, Weiliang Ma, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/sciadv.abj0127.","mla":"Martín-Sánchez, Javier, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances, vol. 7, no. 41, abj0127, American Association for the Advancement of Science, 2021, doi:10.1126/sciadv.abj0127.","short":"J. Martín-Sánchez, J. Duan, J. Taboada-Gutiérrez, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, W. Ma, Q. Bao, V.S. Volkov, R. Hillenbrand, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","ista":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Ma W, Bao Q, Volkov VS, Hillenbrand R, Nikitin AY, Alonso-González P. 2021. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 7(41), abj0127.","apa":"Martín-Sánchez, J., Duan, J., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., … Alonso-González, P. (2021). Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abj0127","ieee":"J. Martín-Sánchez et al., “Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas,” Science Advances, vol. 7, no. 41. American Association for the Advancement of Science, 2021.","ama":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, et al. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 2021;7(41). doi:10.1126/sciadv.abj0127"}},{"ec_funded":1,"publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Springer Nature","acknowledgement":"We thank the pre-clinical facility of the IST Austria and A. Venturino for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan Krios data collection, performed at the IST Austria. The data processing was performed at the IST high-performance computing cluster. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411.","year":"2021","pmid":1,"date_created":"2021-10-17T22:01:17Z","date_updated":"2023-08-14T08:01:21Z","volume":598,"author":[{"id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5618-3449","first_name":"Irene","last_name":"Vercellino","full_name":"Vercellino, Irene"},{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/boosting-the-cells-power-house/","description":"News on IST Webpage","relation":"press_release"}]},"month":"10","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"external_id":{"isi":["000704581600001"],"pmid":["34616041"]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41586-021-03927-z","type":"journal_article","abstract":[{"lang":"eng","text":"The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2 (refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in mammals, but in contrast to CICIII2 and the respirasome, to date the only known eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and plants13, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly intermediates, in different conformations. We describe the assembly of CIII2CIV from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while its C terminus is integrated into CIV. Our structures (which include CICIII2 and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2 is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII2, explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer in the electron transport chain."}],"issue":"7880","status":"public","title":"Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV","intvolume":" 598","_id":"10146","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","scopus_import":"1","day":"14","article_processing_charge":"No","article_type":"original","page":"364-367","publication":"Nature","citation":{"mla":"Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature, vol. 598, no. 7880, Springer Nature, 2021, pp. 364–67, doi:10.1038/s41586-021-03927-z.","short":"I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367.","chicago":"Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03927-z.","ama":"Vercellino I, Sazanov LA. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 2021;598(7880):364-367. doi:10.1038/s41586-021-03927-z","ista":"Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 598(7880), 364–367.","apa":"Vercellino, I., & Sazanov, L. A. (2021). Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03927-z","ieee":"I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV,” Nature, vol. 598, no. 7880. Springer Nature, pp. 364–367, 2021."},"date_published":"2021-10-14T00:00:00Z"},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2021-10-01T00:00:00Z","publication":"Journal of Mathematical Physics","citation":{"ista":"Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302.","ieee":"I. Runkel and L. Szegedy, “Topological field theory on r-spin surfaces and the Arf-invariant,” Journal of Mathematical Physics, vol. 62, no. 10. AIP Publishing, 2021.","apa":"Runkel, I., & Szegedy, L. (2021). Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0037826","ama":"Runkel I, Szegedy L. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 2021;62(10). doi:10.1063/5.0037826","chicago":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” Journal of Mathematical Physics. AIP Publishing, 2021. https://doi.org/10.1063/5.0037826.","mla":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” Journal of Mathematical Physics, vol. 62, no. 10, 102302, AIP Publishing, 2021, doi:10.1063/5.0037826.","short":"I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021)."},"article_type":"original","abstract":[{"lang":"eng","text":"We give a combinatorial model for r-spin surfaces with parameterized boundary based on Novak (“Lattice topological field theories in two dimensions,” Ph.D. thesis, Universität Hamburg, 2015). The r-spin structure is encoded in terms of ℤ𝑟-valued indices assigned to the edges of a polygonal decomposition. This combinatorial model is designed for our state-sum construction of two-dimensional topological field theories on r-spin surfaces. We show that an example of such a topological field theory computes the Arf-invariant of an r-spin surface as introduced by Randal-Williams [J. Topol. 7, 155 (2014)] and Geiges et al. [Osaka J. Math. 49, 449 (2012)]. This implies, in particular, that the r-spin Arf-invariant is constant on orbits of the mapping class group, providing an alternative proof of that fact."}],"issue":"10","type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10176","status":"public","title":"Topological field theory on r-spin surfaces and the Arf-invariant","intvolume":" 62","month":"10","publication_identifier":{"issn":["00222488"]},"doi":"10.1063/5.0037826","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1802.09978"],"isi":["000755638500010"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.09978"}],"isi":1,"quality_controlled":"1","article_number":"102302","author":[{"full_name":"Runkel, Ingo","first_name":"Ingo","last_name":"Runkel"},{"last_name":"Szegedy","first_name":"Lorant","orcid":"0000-0003-2834-5054","id":"7943226E-220E-11EA-94C7-D59F3DDC885E","full_name":"Szegedy, Lorant"}],"date_created":"2021-10-24T22:01:32Z","date_updated":"2023-08-14T08:04:12Z","volume":62,"acknowledgement":"We would like to thank Nils Carqueville, Tobias Dyckerhoff, Jan Hesse, Ehud Meir, Sebastian Novak, Louis-Hadrien Robert, Nick Salter, Walker Stern, and Lukas Woike for helpful discussions and comments. L.S. was supported by the DFG Research Training Group 1670 “Mathematics Inspired by String Theory and Quantum Field Theory.”","year":"2021","publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"MiLe"}]},{"_id":"10179","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["610"],"title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","status":"public","intvolume":" 40","file":[{"creator":"alisjak","content_type":"application/pdf","file_size":7819881,"access_level":"open_access","file_name":"2021_EMBO_Bajaj.pdf","success":1,"checksum":"78d2d02e775322297e774f72810a41a4","date_updated":"2021-12-13T14:54:14Z","date_created":"2021-12-13T14:54:14Z","file_id":"10541","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Inhibitory GABAergic interneurons migrate over long distances from their extracortical origin into the developing cortex. In humans, this process is uniquely slow and prolonged, and it is unclear whether guidance cues unique to humans govern the various phases of this complex developmental process. Here, we use fused cerebral organoids to identify key roles of neurotransmitter signaling pathways in guiding the migratory behavior of human cortical interneurons. We use scRNAseq to reveal expression of GABA, glutamate, glycine, and serotonin receptors along distinct maturation trajectories across interneuron migration. We develop an image analysis software package, TrackPal, to simultaneously assess 48 parameters for entire migration tracks of individual cells. By chemical screening, we show that different modes of interneuron migration depend on distinct neurotransmitter signaling pathways, linking transcriptional maturation of interneurons with their migratory behavior. Altogether, our study provides a comprehensive quantitative analysis of human interneuron migration and its functional modulation by neurotransmitter signaling.","lang":"eng"}],"issue":"23","publication":"EMBO Journal","citation":{"mla":"Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” EMBO Journal, vol. 40, no. 23, e108714, Embo Press, 2021, doi:10.15252/embj.2021108714.","short":"S. Bajaj, J.A. Bagley, C.M. Sommer, A. Vertesy, S. Nagumo Wong, V. Krenn, J. Lévi-Strauss, J.A. Knoblich, EMBO Journal 40 (2021).","chicago":"Bajaj, Sunanjay, Joshua A. Bagley, Christoph M Sommer, Abel Vertesy, Sakurako Nagumo Wong, Veronica Krenn, Julie Lévi-Strauss, and Juergen A. Knoblich. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2021108714.","ama":"Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 2021;40(23). doi:10.15252/embj.2021108714","ista":"Bajaj S, Bagley JA, Sommer CM, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss J, Knoblich JA. 2021. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 40(23), e108714.","ieee":"S. Bajaj et al., “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” EMBO Journal, vol. 40, no. 23. Embo Press, 2021.","apa":"Bajaj, S., Bagley, J. A., Sommer, C. M., Vertesy, A., Nagumo Wong, S., Krenn, V., … Knoblich, J. A. (2021). Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2021108714"},"article_type":"original","date_published":"2021-10-18T00:00:00Z","scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","acknowledgement":"We thank all Knoblich laboratory members for continued support and discussions. We thank the IMP/IMBA BioOptics facility, particularly Pawel Pasierbek, Alberto Moreno Cencerrado and Gerald Schmauss, the IMP/IMBA Molecular Biology Service, in particular Robert Heinen, the IMP Bioinformatics facility, in particular Thomas Burkard, the Vienna Biocenter Core Facilities (VBCF) Histopathology facility, in particular Tamara Engelmaier, and the VBCF Next Generation Sequencing Facility, notably Volodymyr Shubchynskyy and Carmen Czepe. We would also like to thank Simon Haendeler for advice on statistical analyses, Jose Guzman for discussions and assistance with slice culture setups, Oliver L. Eichmueller for discussions and assistance with microscopy, and E.H. Gustafson, S. Wolfinger, and D. Reumann for technical assistance regarding generation of cerebral organoids. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie fellowship agreement Nr.707109 awarded to J.A.B. Work in J.A.K.'s laboratory is supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, the City of Vienna, a Research Program of the Austrian Science Fund FWF (SFBF78 Stem Cell, F 7803-B) and a European Research Council (ERC) Advanced Grant under the European 20 Union’s Horizon 2020 program (grant agreement no. 695642).","year":"2021","pmid":1,"publication_status":"published","publisher":"Embo Press","department":[{"_id":"Bio"}],"author":[{"last_name":"Bajaj","first_name":"Sunanjay","full_name":"Bajaj, Sunanjay"},{"first_name":"Joshua A.","last_name":"Bagley","full_name":"Bagley, Joshua A."},{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","full_name":"Sommer, Christoph M"},{"last_name":"Vertesy","first_name":"Abel","full_name":"Vertesy, Abel"},{"full_name":"Nagumo Wong, Sakurako","first_name":"Sakurako","last_name":"Nagumo Wong"},{"full_name":"Krenn, Veronica","first_name":"Veronica","last_name":"Krenn"},{"first_name":"Julie","last_name":"Lévi-Strauss","full_name":"Lévi-Strauss, Julie"},{"full_name":"Knoblich, Juergen A.","first_name":"Juergen A.","last_name":"Knoblich"}],"date_created":"2021-10-24T22:01:34Z","date_updated":"2023-08-14T08:05:23Z","volume":40,"article_number":"e108714","file_date_updated":"2021-12-13T14:54:14Z","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":["34661293"],"isi":["000708012800001"]},"isi":1,"quality_controlled":"1","doi":"10.15252/embj.2021108714","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]}},{"article_number":"6063","file_date_updated":"2021-11-03T11:31:24Z","publisher":"Springer Nature","department":[{"_id":"BjHo"}],"publication_status":"published","acknowledgement":"L.S., P.G.Z., and A.I.T. thank the financial support of the European Graphene Flagship Project under grant agreements 881603 and EPSRC grant EP/S030751/1. L.S. and A.I.T. thank the European Union’s Horizon 2020 research and innovation programme under ITN Spin-NANO Marie Sklodowska-Curie grant agreement no. 676108. P.G.Z. and A.I.T. thank the European Union’s Horizon 2020 research and innovation programme under ITN 4PHOTON Marie Sklodowska-Curie grant agreement no. 721394. J.C., S.A.M., and R.S. acknowledge funding by EPSRC (EP/P033369 and EP/M013812). C.L.P., A.J.B., A.I.T., and A.M.F. acknowledge funding by EPSRC Programme Grant EP/N031776/1. S.A.M. acknowledges the Lee-Lucas Chair in Physics, the Solar Energies go Hybrid (SolTech) programme, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2089/1 - 390776260.","year":"2021","volume":12,"date_updated":"2023-08-14T08:12:12Z","date_created":"2021-10-31T23:01:30Z","author":[{"full_name":"Sortino, Luca","first_name":"Luca","last_name":"Sortino"},{"full_name":"Zotev, Panaiot G.","last_name":"Zotev","first_name":"Panaiot G."},{"full_name":"Phillips, Catherine L.","first_name":"Catherine L.","last_name":"Phillips"},{"full_name":"Brash, Alistair J.","first_name":"Alistair J.","last_name":"Brash"},{"full_name":"Cambiasso, Javier","first_name":"Javier","last_name":"Cambiasso"},{"full_name":"Marensi, Elena","last_name":"Marensi","first_name":"Elena","orcid":"0000-0001-7173-4923","id":"0BE7553A-1004-11EA-B805-18983DDC885E"},{"first_name":"A. Mark","last_name":"Fox","full_name":"Fox, A. Mark"},{"last_name":"Maier","first_name":"Stefan A.","full_name":"Maier, Stefan A."},{"last_name":"Sapienza","first_name":"Riccardo","full_name":"Sapienza, Riccardo"},{"full_name":"Tartakovskii, Alexander I.","first_name":"Alexander I.","last_name":"Tartakovskii"}],"publication_identifier":{"eissn":["2041-1723"]},"month":"10","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2103.16986"],"isi":["000708601800015"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-021-26262-3","type":"journal_article","abstract":[{"lang":"eng","text":"Single photon emitters in atomically-thin semiconductors can be deterministically positioned using strain induced by underlying nano-structures. Here, we couple monolayer WSe2 to high-refractive-index gallium phosphide dielectric nano-antennas providing both optical enhancement and monolayer deformation. For single photon emitters formed on such nano-antennas, we find very low (femto-Joule) saturation pulse energies and up to 104 times brighter photoluminescence than in WSe2 placed on low-refractive-index SiO2 pillars. We show that the key to these observations is the increase on average by a factor of 5 of the quantum efficiency of the emitters coupled to the nano-antennas. This further allows us to gain new insights into their photoluminescence dynamics, revealing the roles of the dark exciton reservoir and Auger processes. We also find that the coherence time of such emitters is limited by intrinsic dephasing processes. Our work establishes dielectric nano-antennas as a platform for high-efficiency quantum light generation in monolayer semiconductors."}],"intvolume":" 12","ddc":["530"],"title":"Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10203","file":[{"date_updated":"2021-11-03T11:31:24Z","date_created":"2021-11-03T11:31:24Z","checksum":"8580d128389860f732028c521cd5949e","success":1,"relation":"main_file","file_id":"10212","content_type":"application/pdf","file_size":1434201,"creator":"cchlebak","file_name":"2021_NatComm_Sortino.pdf","access_level":"open_access"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"18","article_type":"original","citation":{"short":"L. Sortino, P.G. Zotev, C.L. Phillips, A.J. Brash, J. Cambiasso, E. Marensi, A.M. Fox, S.A. Maier, R. Sapienza, A.I. Tartakovskii, Nature Communications 12 (2021).","mla":"Sortino, Luca, et al. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” Nature Communications, vol. 12, 6063, Springer Nature, 2021, doi:10.1038/s41467-021-26262-3.","chicago":"Sortino, Luca, Panaiot G. Zotev, Catherine L. Phillips, Alistair J. Brash, Javier Cambiasso, Elena Marensi, A. Mark Fox, Stefan A. Maier, Riccardo Sapienza, and Alexander I. Tartakovskii. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26262-3.","ama":"Sortino L, Zotev PG, Phillips CL, et al. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. 2021;12. doi:10.1038/s41467-021-26262-3","ieee":"L. Sortino et al., “Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas,” Nature Communications, vol. 12. Springer Nature, 2021.","apa":"Sortino, L., Zotev, P. G., Phillips, C. L., Brash, A. J., Cambiasso, J., Marensi, E., … Tartakovskii, A. I. (2021). Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26262-3","ista":"Sortino L, Zotev PG, Phillips CL, Brash AJ, Cambiasso J, Marensi E, Fox AM, Maier SA, Sapienza R, Tartakovskii AI. 2021. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. 12, 6063."},"publication":"Nature Communications","date_published":"2021-10-18T00:00:00Z"},{"citation":{"ista":"Sahu P, Schwarz JM, Manning ML. 2021. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 23(9), 093043.","ieee":"P. Sahu, J. M. Schwarz, and M. L. Manning, “Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue,” New Journal of Physics, vol. 23, no. 9. IOP Publishing, 2021.","apa":"Sahu, P., Schwarz, J. M., & Manning, M. L. (2021). Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac23f1","ama":"Sahu P, Schwarz JM, Manning ML. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 2021;23(9). doi:10.1088/1367-2630/ac23f1","chicago":"Sahu, Preeti, J. M. Schwarz, and M. Lisa Manning. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac23f1.","mla":"Sahu, Preeti, et al. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” New Journal of Physics, vol. 23, no. 9, 093043, IOP Publishing, 2021, doi:10.1088/1367-2630/ac23f1.","short":"P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021)."},"publication":"New Journal of Physics","article_type":"original","date_published":"2021-09-29T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"29","_id":"10178","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 23","ddc":["570"],"status":"public","title":"Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue","oa_version":"Published Version","file":[{"date_created":"2021-10-28T12:06:01Z","date_updated":"2021-10-28T12:06:01Z","success":1,"checksum":"ace603e8f0962b3ba55f23fa34f57764","file_id":"10193","relation":"main_file","creator":"cziletti","content_type":"application/pdf","file_size":2215016,"file_name":"2021_NewJPhys_Sahu.pdf","access_level":"open_access"}],"type":"journal_article","issue":"9","abstract":[{"text":"In dense biological tissues, cell types performing different roles remain segregated by maintaining sharp interfaces. To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic tension at the interface between two distinct cell types in a fully 3D Voronoi model for confluent tissues. We find that cells rapidly sort and self-organize to generate a tissue-scale interface between cell types, and cells adjacent to this interface exhibit signature geometric features including nematic-like ordering, bimodal facet areas, and registration, or alignment, of cell centers on either side of the two-tissue interface. The magnitude of these features scales directly with the magnitude of the imposed tension, suggesting that biologists can estimate the magnitude of tissue surface tension between two tissue types simply by segmenting a 3D tissue. To uncover the underlying physical mechanisms driving these geometric features, we develop two minimal, ordered models using two different underlying lattices that identify an energetic competition between bulk cell shapes and tissue interface area. When the interface area dominates, changes to neighbor topology are costly and occur less frequently, which generates the observed geometric features.","lang":"eng"}],"external_id":{"arxiv":["2102.05397"],"isi":["000702042400001"]},"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,"doi":"10.1088/1367-2630/ac23f1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["13672630"]},"month":"09","acknowledgement":"We thank Paula Sanematsu, Matthias Merkel, Daniel Sussman, Cristina Marchetti and Edouard Hannezo for helpful discussions, and M Merkel for developing and sharing the original version of the 3D Voronoi code. This work was primarily funded by NSF-PHY-1607416, NSF-PHY-2014192 , and are in the division of physics at the National Science Foundation. PS and MLM acknowledge additional support from Simons Grant No. 454947.\r\n","year":"2021","publisher":"IOP Publishing","department":[{"_id":"EdHa"}],"publication_status":"published","author":[{"full_name":"Sahu, Preeti","first_name":"Preeti","last_name":"Sahu","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E"},{"full_name":"Schwarz, J. M.","first_name":"J. M.","last_name":"Schwarz"},{"last_name":"Manning","first_name":"M. Lisa","full_name":"Manning, M. Lisa"}],"volume":23,"date_created":"2021-10-24T22:01:34Z","date_updated":"2023-08-14T08:10:31Z","article_number":"093043","file_date_updated":"2021-10-28T12:06:01Z"},{"publisher":"Springer Nature","department":[{"_id":"UlWa"}],"publication_status":"published","acknowledgement":"Theorem 2 was obtained at Steklov Mathematical Institute RAS and supported by Russian Science Foundation, grant N 19-11-00087.","year":"2021","date_created":"2021-10-24T22:01:35Z","date_updated":"2023-08-14T08:11:38Z","author":[{"last_name":"Ivanov","first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","full_name":"Ivanov, Grigory"},{"last_name":"Lopushanski","first_name":"Mariana S.","full_name":"Lopushanski, Mariana S."}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000705774800001"],"arxiv":["2012.10691"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.10691"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s11228-021-00612-1","publication_identifier":{"issn":["0927-6947"],"eissn":["1877-0541"]},"month":"10","title":"Rectifiable curves in proximally smooth sets","status":"public","_id":"10181","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"In this article we study some geometric properties of proximally smooth sets. First, we introduce a modification of the metric projection and prove its existence. Then we provide an algorithm for constructing a rectifiable curve between two sufficiently close points of a proximally smooth set in a uniformly convex and uniformly smooth Banach space, with the moduli of smoothness and convexity of power type. Our algorithm returns a reasonably short curve between two sufficiently close points of a proximally smooth set, is iterative and uses our modification of the metric projection. We estimate the length of the constructed curve and its deviation from the segment with the same endpoints. These estimates coincide up to a constant factor with those for the geodesics in a proximally smooth set in a Hilbert space.","lang":"eng"}],"article_type":"original","citation":{"ista":"Ivanov G, Lopushanski MS. 2021. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis.","apa":"Ivanov, G., & Lopushanski, M. S. (2021). Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. Springer Nature. https://doi.org/10.1007/s11228-021-00612-1","ieee":"G. Ivanov and M. S. Lopushanski, “Rectifiable curves in proximally smooth sets,” Set-Valued and Variational Analysis. Springer Nature, 2021.","ama":"Ivanov G, Lopushanski MS. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. 2021. doi:10.1007/s11228-021-00612-1","chicago":"Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” Set-Valued and Variational Analysis. Springer Nature, 2021. https://doi.org/10.1007/s11228-021-00612-1.","mla":"Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” Set-Valued and Variational Analysis, Springer Nature, 2021, doi:10.1007/s11228-021-00612-1.","short":"G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis (2021)."},"publication":"Set-Valued and Variational Analysis","date_published":"2021-10-09T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"09"},{"doi":"10.1038/s41467-021-26234-7","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000709050300016"],"pmid":["34667153"]},"isi":1,"quality_controlled":"1","month":"10","publication_identifier":{"eissn":["20411723"]},"author":[{"last_name":"Pradhan","first_name":"Saurabh J.","full_name":"Pradhan, Saurabh J."},{"first_name":"Puli Chandramouli","last_name":"Reddy","full_name":"Reddy, Puli Chandramouli"},{"full_name":"Smutny, Michael","orcid":"0000-0002-5920-9090","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","last_name":"Smutny","first_name":"Michael"},{"full_name":"Sharma, Ankita","first_name":"Ankita","last_name":"Sharma"},{"full_name":"Sako, Keisuke","orcid":"0000-0002-6453-8075","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","last_name":"Sako","first_name":"Keisuke"},{"last_name":"Oak","first_name":"Meghana S.","full_name":"Oak, Meghana S."},{"last_name":"Shah","first_name":"Rini","full_name":"Shah, Rini"},{"full_name":"Pal, Mrinmoy","last_name":"Pal","first_name":"Mrinmoy"},{"first_name":"Ojas","last_name":"Deshpande","full_name":"Deshpande, Ojas"},{"full_name":"Dsilva, Greg","last_name":"Dsilva","first_name":"Greg"},{"full_name":"Tang, Yin","last_name":"Tang","first_name":"Yin"},{"first_name":"Rakesh","last_name":"Mishra","full_name":"Mishra, Rakesh"},{"first_name":"Girish","last_name":"Deshpande","full_name":"Deshpande, Girish"},{"first_name":"Antonio J.","last_name":"Giraldez","full_name":"Giraldez, Antonio J."},{"full_name":"Sonawane, Mahendra","last_name":"Sonawane","first_name":"Mahendra"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"first_name":"Sanjeev","last_name":"Galande","full_name":"Galande, Sanjeev"}],"related_material":{"link":[{"url":"https://doi.org/10.1101/2020.11.23.394171 ","relation":"earlier_version","description":"Preprint"}]},"date_updated":"2023-08-14T10:32:48Z","date_created":"2021-10-31T23:01:29Z","volume":12,"acknowledgement":"We are grateful to the members of C.-P.H. and SG lab for discussions. Authors thank Shubha Tole for providing embryonic mouse tissues. Authors are grateful to Alessandro Mongera and Chetana Sachidanandan for generous help with Tg: Sox10: GFP line. Authors would like to thank Satyajeet Khare, Vanessa Barone, Jyothish S., Shalini Mishra, Yoshita Bhide, and Keshav Jha for assistance in experiments. We would also like to thank Chaitanya Dingare for valuable suggestions. We thank Diana Pinhiero and Alexandra Schauer for critical reading of early versions of the manuscript. This work was supported by the Centre of Excellence in Epigenetics program of the Department of Biotechnology, Government of India Phase I (BT/01/COE/09/07) to S.G. and R.K.M., and Phase II (BT/COE/34/SP17426/2016) to S.G. and JC Bose Fellowship (JCB/2019/000013) from Science and Engineering Research Board, Government of India to S.G., DST-BMWF Indo-Austrian bilateral program grant to S.G. and C.-P.H. The work using animal models was partly supported by the infrastructure support grants from the Department of Biotechnology (National Facility for Laboratory Model Organisms: BT/INF/22/SP17358/2016 and Establishment of a Pune Biotech Cluster, Model Organism to Human Disease: B-2 Whole Animal Imaging & Tissue Processing FacilityBT/Pune-Biocluster/01/2015). S.J.P. was supported by Fellowship from the Council of Scientific and Industrial Research, India and travel fellowship from the Company of Biologists, UK. P.C.R. was supported by the Early Career Fellowship of the Wellcome Trust-DBT India Alliance (IA/E/16/1/503057). A.S. was supported by UGC and R.S. was supported by CSIR India. M.S. was supported by core funding from the Tata Institute of Fundamental Research (TIFR 12P-121).","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Springer Nature","file_date_updated":"2021-11-09T13:59:26Z","article_number":"6094","date_published":"2021-10-19T00:00:00Z","publication":"Nature Communications","citation":{"ista":"Pradhan SJ, Reddy PC, Smutny M, Sharma A, Sako K, Oak MS, Shah R, Pal M, Deshpande O, Dsilva G, Tang Y, Mishra R, Deshpande G, Giraldez AJ, Sonawane M, Heisenberg C-PJ, Galande S. 2021. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 12(1), 6094.","ieee":"S. J. Pradhan et al., “Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","apa":"Pradhan, S. J., Reddy, P. C., Smutny, M., Sharma, A., Sako, K., Oak, M. S., … Galande, S. (2021). Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26234-7","ama":"Pradhan SJ, Reddy PC, Smutny M, et al. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26234-7","chicago":"Pradhan, Saurabh J., Puli Chandramouli Reddy, Michael Smutny, Ankita Sharma, Keisuke Sako, Meghana S. Oak, Rini Shah, et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26234-7.","mla":"Pradhan, Saurabh J., et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications, vol. 12, no. 1, 6094, Springer Nature, 2021, doi:10.1038/s41467-021-26234-7.","short":"S.J. Pradhan, P.C. Reddy, M. Smutny, A. Sharma, K. Sako, M.S. Oak, R. Shah, M. Pal, O. Deshpande, G. Dsilva, Y. Tang, R. Mishra, G. Deshpande, A.J. Giraldez, M. Sonawane, C.-P.J. Heisenberg, S. Galande, Nature Communications 12 (2021)."},"article_type":"original","day":"19","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":7144437,"creator":"cziletti","access_level":"open_access","file_name":"2021_NatureComm_Pradhan.pdf","checksum":"c40a69ae94435ecd3a30c9874a11ef2b","success":1,"date_created":"2021-11-09T13:59:26Z","date_updated":"2021-11-09T13:59:26Z","relation":"main_file","file_id":"10262"}],"_id":"10202","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis","ddc":["570"],"intvolume":" 12","abstract":[{"text":"Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant.","lang":"eng"}],"issue":"1","type":"journal_article"},{"_id":"10271","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 12","ddc":["610"],"title":"Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli","status":"public","file":[{"relation":"main_file","file_id":"10272","checksum":"d41321748e9588dd3cf03e9a7222127f","success":1,"date_updated":"2021-11-11T10:54:40Z","date_created":"2021-11-11T10:54:40Z","access_level":"open_access","file_name":"2021_FrontiersMicrob_Qi.pdf","file_size":2397203,"content_type":"application/pdf","creator":"cchlebak"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Understanding interactions between antibiotics used in combination is an important theme in microbiology. Using the interactions between the antifolate drug trimethoprim and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model, we applied a transcriptomic approach for dissecting interactions between two antibiotics with different modes of action. When trimethoprim and erythromycin were combined, the transcriptional response of genes from the sulfate reduction pathway deviated from the dominant effect of trimethoprim on the transcriptome. We successfully altered the drug interaction from additivity to suppression by increasing the sulfate level in the growth environment and identified sulfate reduction as an important metabolic determinant that shapes the interaction between the two drugs. Our work highlights the potential of using prioritization of gene expression patterns as a tool for identifying key metabolic determinants that shape drug-drug interactions. We further demonstrated that the sigma factor-binding protein gene crl shapes the interactions between the two antibiotics, which provides a rare example of how naturally occurring variations between strains of the same bacterial species can sometimes generate very different drug interactions.","lang":"eng"}],"citation":{"apa":"Qi, Q., Angermayr, S. A., & Bollenbach, M. T. (2021). Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2021.760017","ieee":"Q. Qi, S. A. Angermayr, and M. T. Bollenbach, “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli,” Frontiers in Microbiology, vol. 12. Frontiers, 2021.","ista":"Qi Q, Angermayr SA, Bollenbach MT. 2021. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. 12, 760017.","ama":"Qi Q, Angermayr SA, Bollenbach MT. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. 2021;12. doi:10.3389/fmicb.2021.760017","chicago":"Qi, Qin, S. Andreas Angermayr, and Mark Tobias Bollenbach. “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia Coli.” Frontiers in Microbiology. Frontiers, 2021. https://doi.org/10.3389/fmicb.2021.760017.","short":"Q. Qi, S.A. Angermayr, M.T. Bollenbach, Frontiers in Microbiology 12 (2021).","mla":"Qi, Qin, et al. “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia Coli.” Frontiers in Microbiology, vol. 12, 760017, Frontiers, 2021, doi:10.3389/fmicb.2021.760017."},"publication":"Frontiers in Microbiology","article_type":"original","date_published":"2021-10-20T00:00:00Z","scopus_import":"1","keyword":["microbiology"],"has_accepted_license":"1","article_processing_charge":"No","day":"20","pmid":1,"acknowledgement":"High-throughput sequencing data were generated by the Vienna BioCenter Core Facilities. The authors would like to thank Karin Mitosch, Bor Kavcic, and Nadine Kraupner for their constructive feedback. The authors would also like to thank Gertraud Stift, Julia Flor, Renate Srsek, Agnieszka Wiktor, and Booshini Fernando for technical support.","year":"2021","publisher":"Frontiers","publication_status":"published","author":[{"full_name":"Qi, Qin","first_name":"Qin","last_name":"Qi","id":"3B22D412-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6148-2416"},{"full_name":"Angermayr, S. Andreas","last_name":"Angermayr","first_name":"S. Andreas"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","last_name":"Bollenbach"}],"volume":12,"date_updated":"2023-08-14T11:43:23Z","date_created":"2021-11-11T10:39:37Z","article_number":"760017","ec_funded":1,"file_date_updated":"2021-11-11T10:54:40Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["34745067"],"isi":["000715997300001"]},"project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.3389/fmicb.2021.760017","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1664-302X"]},"month":"10"},{"issue":"2","abstract":[{"text":"We prove that any deterministic matrix is approximately the identity in the eigenbasis of a large random Wigner matrix with very high probability and with an optimal error inversely proportional to the square root of the dimension. Our theorem thus rigorously verifies the Eigenstate Thermalisation Hypothesis by Deutsch (Phys Rev A 43:2046–2049, 1991) for the simplest chaotic quantum system, the Wigner ensemble. In mathematical terms, we prove the strong form of Quantum Unique Ergodicity (QUE) with an optimal convergence rate for all eigenvectors simultaneously, generalizing previous probabilistic QUE results in Bourgade and Yau (Commun Math Phys 350:231–278, 2017) and Bourgade et al. (Commun Pure Appl Math 73:1526–1596, 2020).","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2022-02-02T10:19:55Z","date_created":"2022-02-02T10:19:55Z","success":1,"checksum":"a2c7b6f5d23b5453cd70d1261272283b","file_id":"10715","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","file_size":841426,"file_name":"2021_CommunMathPhys_Cipolloni.pdf","access_level":"open_access"}],"intvolume":" 388","ddc":["510"],"status":"public","title":"Eigenstate thermalization hypothesis for Wigner matrices","_id":"10221","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"29","scopus_import":"1","date_published":"2021-10-29T00:00:00Z","page":"1005–1048","article_type":"original","citation":{"ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Eigenstate thermalization hypothesis for Wigner matrices,” Communications in Mathematical Physics, vol. 388, no. 2. Springer Nature, pp. 1005–1048, 2021.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-021-04239-z","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. 388(2), 1005–1048.","ama":"Cipolloni G, Erdös L, Schröder DJ. Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. 2021;388(2):1005–1048. doi:10.1007/s00220-021-04239-z","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” Communications in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s00220-021-04239-z.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics 388 (2021) 1005–1048.","mla":"Cipolloni, Giorgio, et al. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” Communications in Mathematical Physics, vol. 388, no. 2, Springer Nature, 2021, pp. 1005–1048, doi:10.1007/s00220-021-04239-z."},"publication":"Communications in Mathematical Physics","file_date_updated":"2022-02-02T10:19:55Z","volume":388,"date_updated":"2023-08-14T10:29:49Z","date_created":"2021-11-07T23:01:25Z","author":[{"last_name":"Cipolloni","first_name":"Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio"},{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"Erdös, László"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","first_name":"Dominik J","last_name":"Schröder","full_name":"Schröder, Dominik J"}],"publisher":"Springer Nature","department":[{"_id":"LaEr"}],"publication_status":"published","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","year":"2021","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1007/s00220-021-04239-z","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":["000712232700001"],"arxiv":["2012.13215"]},"oa":1},{"publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1007/s00205-021-01715-7","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"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":["2101.12566"],"isi":["000710850600001"]},"ec_funded":1,"file_date_updated":"2021-12-14T08:35:42Z","volume":242,"date_created":"2021-11-07T23:01:26Z","date_updated":"2023-08-14T10:32:19Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9787"}]},"author":[{"full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","last_name":"Feliciangeli","first_name":"Dario"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"publisher":"Springer Nature","department":[{"_id":"RoSe"}],"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 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. 4.7.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"25","scopus_import":"1","date_published":"2021-10-25T00:00:00Z","page":"1835–1906","article_type":"original","citation":{"ista":"Feliciangeli D, Seiringer R. 2021. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. 242(3), 1835–1906.","apa":"Feliciangeli, D., & Seiringer, R. (2021). The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01715-7","ieee":"D. Feliciangeli and R. Seiringer, “The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics,” Archive for Rational Mechanics and Analysis, vol. 242, no. 3. Springer Nature, pp. 1835–1906, 2021.","ama":"Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. 2021;242(3):1835–1906. doi:10.1007/s00205-021-01715-7","chicago":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01715-7.","mla":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational Mechanics and Analysis, vol. 242, no. 3, Springer Nature, 2021, pp. 1835–1906, doi:10.1007/s00205-021-01715-7.","short":"D. Feliciangeli, R. Seiringer, Archive for Rational Mechanics and Analysis 242 (2021) 1835–1906."},"publication":"Archive for Rational Mechanics and Analysis","issue":"3","abstract":[{"lang":"eng","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."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2021_Springer_Feliciangeli.pdf","file_size":990529,"content_type":"application/pdf","creator":"alisjak","relation":"main_file","file_id":"10544","checksum":"672e9c21b20f1a50854b7c821edbb92f","success":1,"date_created":"2021-12-14T08:35:42Z","date_updated":"2021-12-14T08:35:42Z"}],"oa_version":"Published Version","intvolume":" 242","ddc":["530"],"title":"The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10224"},{"issue":"11","abstract":[{"text":"Mutations affecting mTOR or RAS signaling underlie defined syndromes (the so-called mTORopathies and RASopathies) with high risk for Autism Spectrum Disorder (ASD). These syndromes show a broad variety of somatic phenotypes including cancers, skin abnormalities, heart disease and facial dysmorphisms. Less well studied are the neuropsychiatric symptoms such as ASD. Here, we assess the relevance of these signalopathies in ASD reviewing genetic, human cell model, rodent studies and clinical trials. We conclude that signalopathies have an increased liability for ASD and that, in particular, ASD individuals with dysmorphic features and intellectual disability (ID) have a higher chance for disruptive mutations in RAS- and mTOR-related genes. Studies on rodent and human cell models confirm aberrant neuronal development as the underlying pathology. Human studies further suggest that multiple hits are necessary to induce the respective phenotypes. Recent clinical trials do only report improvements for comorbid conditions such as epilepsy or cancer but not for behavioral aspects. Animal models show that treatment during early development can rescue behavioral phenotypes. Taken together, we suggest investigating the differential roles of mTOR and RAS signaling in both human and rodent models, and to test drug treatment both during and after neuronal development in the available model systems","lang":"eng"}],"alternative_title":["Special Issue \"From Genes to Therapy in Autism Spectrum Disorder\""],"type":"journal_article","file":[{"file_id":"11380","relation":"main_file","date_updated":"2022-05-16T07:02:27Z","date_created":"2022-05-16T07:02:27Z","success":1,"checksum":"256cb832a9c3051c7dc741f6423b8cbd","file_name":"2021_Genes_Vasic.pdf","access_level":"open_access","creator":"dernst","file_size":1335308,"content_type":"application/pdf"}],"oa_version":"Published Version","intvolume":" 12","title":"Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment","ddc":["570"],"status":"public","_id":"10281","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","article_processing_charge":"No","day":"30","scopus_import":"1","date_published":"2021-10-30T00:00:00Z","article_type":"original","citation":{"chicago":"Vasic, Verica, Mattson S.O. Jones, Denise Haslinger, Lisa Knaus, Michael J. Schmeisser, Gaia Novarino, and Andreas G. Chiocchetti. “Translating the Role of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12111746.","short":"V. Vasic, M.S.O. Jones, D. Haslinger, L. Knaus, M.J. Schmeisser, G. Novarino, A.G. Chiocchetti, Genes 12 (2021).","mla":"Vasic, Verica, et al. “Translating the Role of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” Genes, vol. 12, no. 11, 1746, MDPI, 2021, doi:10.3390/genes12111746.","apa":"Vasic, V., Jones, M. S. O., Haslinger, D., Knaus, L., Schmeisser, M. J., Novarino, G., & Chiocchetti, A. G. (2021). Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. MDPI. https://doi.org/10.3390/genes12111746","ieee":"V. Vasic et al., “Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment,” Genes, vol. 12, no. 11. MDPI, 2021.","ista":"Vasic V, Jones MSO, Haslinger D, Knaus L, Schmeisser MJ, Novarino G, Chiocchetti AG. 2021. Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. 12(11), 1746.","ama":"Vasic V, Jones MSO, Haslinger D, et al. Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. 2021;12(11). doi:10.3390/genes12111746"},"publication":"Genes","ec_funded":1,"file_date_updated":"2022-05-16T07:02:27Z","article_number":"1746","volume":12,"date_updated":"2023-08-14T11:46:12Z","date_created":"2021-11-14T23:01:24Z","author":[{"full_name":"Vasic, Verica","first_name":"Verica","last_name":"Vasic"},{"last_name":"Jones","first_name":"Mattson S.O.","full_name":"Jones, Mattson S.O."},{"full_name":"Haslinger, Denise","last_name":"Haslinger","first_name":"Denise","id":"76922BDA-3D3B-11EA-90BD-A44F3DDC885E"},{"last_name":"Knaus","first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa"},{"first_name":"Michael J.","last_name":"Schmeisser","full_name":"Schmeisser, Michael J."},{"last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"},{"first_name":"Andreas G.","last_name":"Chiocchetti","full_name":"Chiocchetti, Andreas G."}],"publisher":"MDPI","department":[{"_id":"GaNo"}],"publication_status":"published","acknowledgement":"This review was funded by the IMI2 Initiative under the grant AIMS-2-TRIALS No 777394, by the Hessian Ministry for Science and Arts; State of Hesse Ministry for Science and Arts: LOEWE-Grant to the CePTER-Consortium (www.uni-frankfurt.de/67689811); Research (BMBF) under the grant RAISE-genic No 779282 all to AGC. This work was also supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM) and by the Austrian Science Fund (FWF) (DK W1232-B24) both to G.N. and both BMBF GeNeRARe 01GM1519A and CRC 1080, project B10, of the German Research Foundation (DFG) to M.J.S, respectively. We want to thank R. Waltes for her support in preparing this manuscript.","year":"2021","publication_identifier":{"eissn":["2073-4425"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.3390/genes12111746","project":[{"call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508"},{"grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000834044200002"]}},{"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Wiley","year":"2021","acknowledgement":"We thank Claus Schwechheimer for the pin34 and pin347 seeds, Yuliia Mironova for technical assistance, Ksenia Timofeyenko and Dmitry Konovalov for help with the evolutional analysis, Konstantin Kutashev and Siarhei Dabravolski for assistance with FRET-FLIM, Huibin Han for advice with hypocotyl imaging, Karel Müller for the initial qRT-PCR on the tobacco cell lines, Stano Pekár for suggestions regarding the statistical analysis of the morphodynamic measurements, and Jozef Mravec, Dolf Weijers and Lindy Abas for their comments on the manuscript. This work was supported by the Czech Science Foundation (projects 16-26428S and 19-23773S to IK, MH and KRůžička, 19-18917S to JHumpolíčková and 18-26981S to JF), and the Ministry of Education, Youth and Sports of the Czech Republic (MEYS, CZ.02.1.01/0.0/0.0/16_019/0000738) to KRůžička and JHejátko. The imaging facilities of the Institute of Experimental Botany and CEITEC are supported by MEYS (LM2018129 – Czech BioImaging and CZ.02.1.01/0.0/0.0/16_013/0001775). The authors declare no competing interests.","pmid":1,"date_updated":"2023-08-14T11:46:43Z","date_created":"2021-11-14T23:01:24Z","volume":233,"author":[{"first_name":"Ivan","last_name":"Kashkan","full_name":"Kashkan, Ivan"},{"first_name":"Mónika","last_name":"Hrtyan","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","full_name":"Hrtyan, Mónika"},{"full_name":"Retzer, Katarzyna","last_name":"Retzer","first_name":"Katarzyna"},{"first_name":"Jana","last_name":"Humpolíčková","full_name":"Humpolíčková, Jana"},{"last_name":"Jayasree","first_name":"Aswathy","full_name":"Jayasree, Aswathy"},{"full_name":"Filepová, Roberta","last_name":"Filepová","first_name":"Roberta"},{"last_name":"Vondráková","first_name":"Zuzana","full_name":"Vondráková, Zuzana"},{"last_name":"Simon","first_name":"Sibu","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu"},{"last_name":"Rombaut","first_name":"Debbie","full_name":"Rombaut, Debbie"},{"first_name":"Thomas B.","last_name":"Jacobs","full_name":"Jacobs, Thomas B."},{"full_name":"Frilander, Mikko J.","first_name":"Mikko J.","last_name":"Frilander"},{"last_name":"Hejátko","first_name":"Jan","full_name":"Hejátko, Jan"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"last_name":"Růžička","first_name":"Kamil","full_name":"Růžička, Kamil"}],"month":"11","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2"}],"external_id":{"isi":["000714678100001"],"pmid":["34637542"]},"language":[{"iso":"eng"}],"doi":"10.1111/nph.17792","type":"journal_article","abstract":[{"text":"Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development.","lang":"eng"}],"status":"public","title":"Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana","intvolume":" 233","_id":"10282","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","scopus_import":"1","day":"05","article_processing_charge":"No","article_type":"original","page":"329-343","publication":"New Phytologist","citation":{"chicago":"Kashkan, Ivan, Mónika Hrtyan, Katarzyna Retzer, Jana Humpolíčková, Aswathy Jayasree, Roberta Filepová, Zuzana Vondráková, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17792.","short":"I. Kashkan, M. Hrtyan, K. Retzer, J. Humpolíčková, A. Jayasree, R. Filepová, Z. Vondráková, S. Simon, D. Rombaut, T.B. Jacobs, M.J. Frilander, J. Hejátko, J. Friml, J. Petrášek, K. Růžička, New Phytologist 233 (2021) 329–343.","mla":"Kashkan, Ivan, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist, vol. 233, Wiley, 2021, pp. 329–43, doi:10.1111/nph.17792.","ieee":"I. Kashkan et al., “Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana,” New Phytologist, vol. 233. Wiley, pp. 329–343, 2021.","apa":"Kashkan, I., Hrtyan, M., Retzer, K., Humpolíčková, J., Jayasree, A., Filepová, R., … Růžička, K. (2021). Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. Wiley. https://doi.org/10.1111/nph.17792","ista":"Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J, Růžička K. 2021. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 233, 329–343.","ama":"Kashkan I, Hrtyan M, Retzer K, et al. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 2021;233:329-343. doi:10.1111/nph.17792"},"date_published":"2021-11-05T00:00:00Z"},{"quality_controlled":"1","isi":1,"project":[{"_id":"26611F5C-B435-11E9-9278-68D0E5697425","grant_number":"P31312","name":"Algorithms for Embeddings and Homotopy Theory","call_identifier":"FWF"}],"external_id":{"arxiv":["1511.03501"],"isi":["000712942100013"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1511.03501","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/s11856-021-2216-z","month":"10","publication_identifier":{"eissn":["1565-8511"],"issn":["0021-2172"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"acknowledgement":"Research supported by the Swiss National Science Foundation (Project SNSF-PP00P2-138948), by the Austrian Science Fund (FWF Project P31312-N35), by the Russian Foundation for Basic Research (Grants No. 15-01-06302 and 19-01-00169), by a Simons-IUM Fellowship, and by the D. Zimin Dynasty Foundation Grant. We would like to thank E. Alkin, A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful comments and discussions.","year":"2021","date_updated":"2023-08-14T11:43:55Z","date_created":"2021-11-07T23:01:24Z","volume":245,"author":[{"full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey","last_name":"Avvakumov"},{"first_name":"Isaac","last_name":"Mabillard","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac"},{"first_name":"Arkadiy B.","last_name":"Skopenkov","full_name":"Skopenkov, Arkadiy B."},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli"}],"related_material":{"record":[{"id":"8183","status":"public","relation":"earlier_version"},{"id":"9308","relation":"earlier_version","status":"public"}]},"article_type":"original","page":"501–534 ","publication":"Israel Journal of Mathematics","citation":{"ama":"Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 2021;245:501–534. doi:10.1007/s11856-021-2216-z","ista":"Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. 2021. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 245, 501–534.","ieee":"S. Avvakumov, I. Mabillard, A. B. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections. III. Codimension 2,” Israel Journal of Mathematics, vol. 245. Springer Nature, pp. 501–534, 2021.","apa":"Avvakumov, S., Mabillard, I., Skopenkov, A. B., & Wagner, U. (2021). Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-021-2216-z","mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel Journal of Mathematics, vol. 245, Springer Nature, 2021, pp. 501–534, doi:10.1007/s11856-021-2216-z.","short":"S. Avvakumov, I. Mabillard, A.B. Skopenkov, U. Wagner, Israel Journal of Mathematics 245 (2021) 501–534.","chicago":"Avvakumov, Sergey, Isaac Mabillard, Arkadiy B. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel Journal of Mathematics. Springer Nature, 2021. https://doi.org/10.1007/s11856-021-2216-z."},"date_published":"2021-10-30T00:00:00Z","scopus_import":"1","day":"30","article_processing_charge":"No","status":"public","title":"Eliminating higher-multiplicity intersections. III. Codimension 2","intvolume":" 245","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10220","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We study conditions under which a finite simplicial complex K can be mapped to ℝd without higher-multiplicity intersections. An almost r-embedding is a map f: K → ℝd such that the images of any r pairwise disjoint simplices of K do not have a common point. We show that if r is not a prime power and d ≥ 2r + 1, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost r-embedding of the (d +1)(r − 1)-simplex in ℝd. This improves on previous constructions of counterexamples (for d ≥ 3r) based on a series of papers by M. Özaydin, M. Gromov, P. Blagojević, F. Frick, G. Ziegler, and the second and fourth present authors.\r\n\r\nThe counterexamples are obtained by proving the following algebraic criterion in codimension 2: If r ≥ 3 and if K is a finite 2(r − 1)-complex, then there exists an almost r-embedding K → ℝ2r if and only if there exists a general position PL map f: K → ℝ2r such that the algebraic intersection number of the f-images of any r pairwise disjoint simplices of K is zero. This result can be restated in terms of a cohomological obstruction and extends an analogous codimension 3 criterion by the second and fourth authors. As another application, we classify ornaments f: S3 ⊔ S3 ⊔ S3 → ℝ5 up to ornament concordance.\r\n\r\nIt follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for r = 2 is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample.","lang":"eng"}]},{"date_published":"2021-10-29T00:00:00Z","doi":"10.5061/DRYAD.7PVMCVDTJ","oa":1,"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":"Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger, Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” Dryad, 2021. https://doi.org/10.5061/DRYAD.7PVMCVDTJ.","mla":"Casillas Perez, Barbara E., et al. Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies. Dryad, 2021, doi:10.5061/DRYAD.7PVMCVDTJ.","short":"B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, (2021).","ista":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2021. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies, Dryad, 10.5061/DRYAD.7PVMCVDTJ.","ieee":"B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S. Cremer, “Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies.” Dryad, 2021.","apa":"Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., & Cremer, S. (2021). Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. Dryad. https://doi.org/10.5061/DRYAD.7PVMCVDTJ","ama":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. 2021. doi:10.5061/DRYAD.7PVMCVDTJ"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.7pvmcvdtj"}],"project":[{"name":"Epidemics in ant societies on a chip","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402"}],"article_processing_charge":"No","day":"29","month":"10","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"10284"}]},"author":[{"first_name":"Barbara E","last_name":"Casillas Perez","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E"},{"full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","first_name":"Christopher"},{"full_name":"Naiser, Filip","last_name":"Naiser","first_name":"Filip"},{"full_name":"Naderlinger, Elisabeth","first_name":"Elisabeth","last_name":"Naderlinger"},{"first_name":"Jiri","last_name":"Matas","full_name":"Matas, Jiri"},{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"oa_version":"Published Version","date_updated":"2023-08-14T11:45:28Z","date_created":"2023-05-23T16:14:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13061","year":"2021","department":[{"_id":"SyCr"}],"publisher":"Dryad","title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","ddc":["570"],"status":"public","ec_funded":1,"abstract":[{"text":"Infections early in life can have enduring effects on an organism’s development and immunity. In this study, we show that this equally applies to developing “superorganisms” – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen’s immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen’s pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism.","lang":"eng"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"research_data_reference"},{"file_date_updated":"2021-11-18T07:02:02Z","article_number":"e71575","author":[{"first_name":"María J","last_name":"Conde-Dusman","full_name":"Conde-Dusman, María J"},{"full_name":"Dey, Partha N","first_name":"Partha N","last_name":"Dey"},{"last_name":"Elía-Zudaire","first_name":"Óscar","full_name":"Elía-Zudaire, Óscar"},{"full_name":"Garcia Rabaneda, Luis E","first_name":"Luis E","last_name":"Garcia Rabaneda","id":"33D1B084-F248-11E8-B48F-1D18A9856A87"},{"last_name":"García-Lira","first_name":"Carmen","full_name":"García-Lira, Carmen"},{"full_name":"Grand, Teddy","last_name":"Grand","first_name":"Teddy"},{"first_name":"Victor","last_name":"Briz","full_name":"Briz, Victor"},{"first_name":"Eric R","last_name":"Velasco","full_name":"Velasco, Eric R"},{"first_name":"Raül","last_name":"Andero Galí","full_name":"Andero Galí, Raül"},{"last_name":"Niñerola","first_name":"Sergio","full_name":"Niñerola, Sergio"},{"first_name":"Angel","last_name":"Barco","full_name":"Barco, Angel"},{"first_name":"Pierre","last_name":"Paoletti","full_name":"Paoletti, Pierre"},{"full_name":"Wesseling, John F","first_name":"John F","last_name":"Wesseling"},{"full_name":"Gardoni, Fabrizio","last_name":"Gardoni","first_name":"Fabrizio"},{"last_name":"Tavalin","first_name":"Steven J","full_name":"Tavalin, Steven J"},{"first_name":"Isabel","last_name":"Perez-Otaño","full_name":"Perez-Otaño, Isabel"}],"date_created":"2021-11-18T06:59:45Z","date_updated":"2023-08-14T11:50:50Z","volume":10,"acknowledgement":"We thank Stuart Lipton and Nobuki Nakanishi for providing the Grin3a knockout mice, Beverly Davidson for the AAV-caRheb, Jose Esteban for help with behavioral and biochemical experiments, and Noelia Campillo, Rebeca Martínez-Turrillas, and Ana Navarro for expert technical help. Work was funded by the UTE project CIMA; fellowships from the Fundación Tatiana Pérez de Guzmán el Bueno, FEBS, and IBRO (to M.J.C.D.), Generalitat Valenciana (to O.E.-Z.), Juan de la Cierva (to L.G.R.), FPI-MINECO (to E.R.V., to S.N.) and Intertalentum postdoctoral program (to V.B.); ANR (GluBrain3A) and ERC Advanced Grants (#693021) (to P.P.); Ramón y Cajal program RYC2014-15784, RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077 FEDER funds (to R.A.); RETOS-MINECO SAF2017-87928-R (to A.B.); an NIH grant (NS76637) and UTHSC College of Medicine funds (to S.J.T.); and NARSAD Independent Investigator Award and grants from the MINECO (CSD2008-00005, SAF2013-48983R, SAF2016-80895-R), Generalitat Valenciana (PROMETEO 2019/020)(to I.P.O.) and Severo-Ochoa Excellence Awards (SEV-2013-0317, SEV-2017-0723).","year":"2021","publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"GaNo"}],"month":"11","publication_identifier":{"issn":["2050-084X"]},"doi":"10.7554/elife.71575","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000720945900001"]},"quality_controlled":"1","isi":1,"abstract":[{"lang":"eng","text":"De novo protein synthesis is required for synapse modifications underlying stable memory encoding. Yet neurons are highly compartmentalized cells and how protein synthesis can be regulated at the synapse level is unknown. Here, we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR activation and restricts the mTOR-dependent translation of specific activity-regulated mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent protein synthesis, and facilitates the consolidation of associative and spatial memories in mice. The memory enhancement becomes evident with light or spaced training, can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood, and does not compromise other aspects of cognition such as memory flexibility or extinction. Our findings provide mechanistic insight into synaptic translational control and reveal a potentially selective target for cognitive enhancement."}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"lgarciar","file_size":2477302,"content_type":"application/pdf","file_name":"elife-71575-v1.pdf","access_level":"open_access","date_updated":"2021-11-18T07:02:02Z","date_created":"2021-11-18T07:02:02Z","success":1,"checksum":"59318e9e41507cec83c2f4070e6ad540","file_id":"10302","relation":"main_file"}],"_id":"10301","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","ddc":["570"],"intvolume":" 10","day":"17","has_accepted_license":"1","article_processing_charge":"No","keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"date_published":"2021-11-17T00:00:00Z","publication":"eLife","citation":{"chicago":"Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.71575.","mla":"Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife, vol. 10, e71575, eLife Sciences Publications, 2021, doi:10.7554/elife.71575.","short":"M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira, T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti, J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021).","ista":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Garcia Rabaneda LE, García-Lira C, Grand T, Briz V, Velasco ER, Andero Galí R, Niñerola S, Barco A, Paoletti P, Wesseling JF, Gardoni F, Tavalin SJ, Perez-Otaño I. 2021. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 10, e71575.","ieee":"M. J. Conde-Dusman et al., “Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E., García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.71575","ama":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 2021;10. doi:10.7554/elife.71575"},"article_type":"original"},{"doi":"10.15252/embr.202153824","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000714350000001"]},"oa":1,"quality_controlled":"1","isi":1,"month":"11","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"author":[{"full_name":"Restivo, Leonardo","last_name":"Restivo","first_name":"Leonardo"},{"last_name":"Gerlach","first_name":"Björn","full_name":"Gerlach, Björn"},{"full_name":"Tsoory, Michael","last_name":"Tsoory","first_name":"Michael"},{"first_name":"Lior","last_name":"Bikovski","full_name":"Bikovski, Lior"},{"full_name":"Badurek, Sylvia","first_name":"Sylvia","last_name":"Badurek"},{"full_name":"Pitzer, Claudia","first_name":"Claudia","last_name":"Pitzer"},{"last_name":"Kos-Braun","first_name":"Isabelle C.","full_name":"Kos-Braun, Isabelle C."},{"last_name":"Mausset-Bonnefont","first_name":"Anne Laure Mj","full_name":"Mausset-Bonnefont, Anne Laure Mj"},{"last_name":"Ward","first_name":"Jonathan","full_name":"Ward, Jonathan"},{"full_name":"Schunn, Michael","first_name":"Michael","last_name":"Schunn","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4326-5300"},{"last_name":"Noldus","first_name":"Lucas P.J.J.","full_name":"Noldus, Lucas P.J.J."},{"full_name":"Bespalov, Anton","first_name":"Anton","last_name":"Bespalov"},{"full_name":"Voikar, Vootele","last_name":"Voikar","first_name":"Vootele"}],"date_updated":"2023-08-14T11:47:35Z","date_created":"2021-11-14T23:01:24Z","volume":22,"year":"2021","acknowledgement":"This EQIPD project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement no. 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and EFPIA. LR was supported by the Faculty of Biology and Medicine, University of Lausanne. VV was supported by Biocenter Finland and the Jane and Aatos Erkko Foundation. CP and IKB received funding from the Federal Ministry of Education and Research (BMBF, grant 01PW18001). SB from the Vienna BioCenter Core Facilities (VBCF) Preclinical Phenotyping Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna. MT is an incumbent of the Carolito Stiftung Research Fellow Chair in Neurodegenerative Diseases. We thank Dr. Katja Kivinen (Helsinki Institute of Life Science) for discussions and feedback.","publication_status":"published","publisher":"EMBO Press","department":[{"_id":"PreCl"}],"file_date_updated":"2022-05-16T07:07:41Z","article_number":"e53824","date_published":"2021-11-04T00:00:00Z","publication":"EMBO Reports","citation":{"ama":"Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research: Role of academic core facilities. EMBO Reports. 2021;22. doi:10.15252/embr.202153824","ieee":"L. Restivo et al., “Towards best practices in research: Role of academic core facilities,” EMBO Reports, vol. 22. EMBO Press, 2021.","apa":"Restivo, L., Gerlach, B., Tsoory, M., Bikovski, L., Badurek, S., Pitzer, C., … Voikar, V. (2021). Towards best practices in research: Role of academic core facilities. EMBO Reports. EMBO Press. https://doi.org/10.15252/embr.202153824","ista":"Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LPJJ, Bespalov A, Voikar V. 2021. Towards best practices in research: Role of academic core facilities. EMBO Reports. 22, e53824.","short":"L. Restivo, B. Gerlach, M. Tsoory, L. Bikovski, S. Badurek, C. Pitzer, I.C. Kos-Braun, A.L.M. Mausset-Bonnefont, J. Ward, M. Schunn, L.P.J.J. Noldus, A. Bespalov, V. Voikar, EMBO Reports 22 (2021).","mla":"Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports, vol. 22, e53824, EMBO Press, 2021, doi:10.15252/embr.202153824.","chicago":"Restivo, Leonardo, Björn Gerlach, Michael Tsoory, Lior Bikovski, Sylvia Badurek, Claudia Pitzer, Isabelle C. Kos-Braun, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports. EMBO Press, 2021. https://doi.org/10.15252/embr.202153824."},"article_type":"original","day":"04","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","file":[{"success":1,"checksum":"74743baa6ef431ef60c3de3bc4da045a","date_created":"2022-05-16T07:07:41Z","date_updated":"2022-05-16T07:07:41Z","file_id":"11381","relation":"main_file","creator":"dernst","file_size":488583,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_EmboReports_Restivo.pdf"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10283","ddc":["570"],"status":"public","title":"Towards best practices in research: Role of academic core facilities","intvolume":" 22","abstract":[{"lang":"eng","text":"During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research."}],"type":"journal_article"},{"article_type":"original","publication":"Communications Biology","citation":{"ama":"Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 2021;4(1). doi:10.1038/s42003-021-01808-9","apa":"Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T., … Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. Springer . https://doi.org/10.1038/s42003-021-01808-9","ieee":"M. O. Çoruh et al., “Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” Communications Biology, vol. 4, no. 1. Springer , 2021.","ista":"Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 4(1), 304.","short":"M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K. Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021).","mla":"Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology, vol. 4, no. 1, 304, Springer , 2021, doi:10.1038/s42003-021-01808-9.","chicago":"Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk, and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology. Springer , 2021. https://doi.org/10.1038/s42003-021-01808-9."},"date_published":"2021-03-08T00:00:00Z","keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"],"scopus_import":"1","day":"08","article_processing_charge":"No","has_accepted_license":"1","ddc":["570"],"status":"public","title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","intvolume":" 4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10310","file":[{"relation":"main_file","file_id":"10318","checksum":"8ffd39f2bba7152a2441802ff313bf0b","success":1,"date_updated":"2021-11-19T15:09:18Z","date_created":"2021-11-19T15:09:18Z","access_level":"open_access","file_name":"2021_CommBio_Çoruh.pdf","content_type":"application/pdf","file_size":6030261,"creator":"cchlebak"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700."}],"issue":"1","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000627440700001"],"pmid":["33686186"]},"language":[{"iso":"eng"}],"doi":"10.1038/s42003-021-01808-9","month":"03","publication_identifier":{"issn":["2399-3642"]},"publication_status":"published","publisher":"Springer ","department":[{"_id":"LeSa"}],"acknowledgement":"We are grateful for additional support and valuable scientific input for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata, Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias Rögner. Parts of this research were funded by the German Research Council (DFG) within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the Platform Project for Supporting Drug Discovery and Life Science Research [Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.), 17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED to K.N. and G.K.","year":"2021","pmid":1,"date_updated":"2023-08-14T11:51:19Z","date_created":"2021-11-19T11:37:29Z","volume":4,"author":[{"full_name":"Çoruh, Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","orcid":"0000-0002-3219-2022","first_name":"Mehmet Orkun","last_name":"Çoruh"},{"last_name":"Frank","first_name":"Anna","full_name":"Frank, Anna"},{"first_name":"Hideaki","last_name":"Tanaka","full_name":"Tanaka, Hideaki"},{"full_name":"Kawamoto, Akihiro","last_name":"Kawamoto","first_name":"Akihiro"},{"full_name":"El-Mohsnawy, Eithar","first_name":"Eithar","last_name":"El-Mohsnawy"},{"last_name":"Kato","first_name":"Takayuki","full_name":"Kato, Takayuki"},{"last_name":"Namba","first_name":"Keiichi","full_name":"Namba, Keiichi"},{"last_name":"Gerle","first_name":"Christoph","full_name":"Gerle, Christoph"},{"full_name":"Nowaczyk, Marc M.","last_name":"Nowaczyk","first_name":"Marc M."},{"last_name":"Kurisu","first_name":"Genji","full_name":"Kurisu, Genji"}],"article_number":"304","file_date_updated":"2021-11-19T15:09:18Z"},{"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":["34723798"],"isi":["000734671200001"]},"quality_controlled":"1","isi":1,"doi":"10.7554/elife.72132","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["2050-084X"]},"year":"2021","acknowledgement":"e are grateful Richard Smith, Anne-Lise Routier, Crisanto Gutierrez and Juergen Kleine-Vehn for providing critical comments on the manuscript. Funding: This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016–0672 (2017–2021) to KW via the CBGP). In the frame of SEV-2016–0672 funding MM is supported with a postdoctoral contract. KW was supported by Programa Estatal de Generacion del Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I 2019 (PGC2018-093387-A-I00) from MICIU (to KW). MG is recipient of an IST Interdisciplinary Project (IC1022IPC03).","pmid":1,"publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"eLife Sciences Publications","author":[{"full_name":"Marconi, Marco","last_name":"Marconi","first_name":"Marco"},{"last_name":"Gallemi","first_name":"Marçal","orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi, Marçal"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"full_name":"Wabnik, Krzysztof","last_name":"Wabnik","first_name":"Krzysztof"}],"date_updated":"2023-08-14T11:49:23Z","date_created":"2021-11-11T10:05:18Z","volume":10,"article_number":"72132","file_date_updated":"2022-05-13T09:00:29Z","publication":"eLife","citation":{"ama":"Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 2021;10. doi:10.7554/elife.72132","ieee":"M. Marconi, M. Gallemi, E. Benková, and K. Wabnik, “A coupled mechano-biochemical model for cell polarity guided anisotropic root growth,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Marconi, M., Gallemi, M., Benková, E., & Wabnik, K. (2021). A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.72132","ista":"Marconi M, Gallemi M, Benková E, Wabnik K. 2021. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 10, 72132.","short":"M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021).","mla":"Marconi, Marco, et al. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife, vol. 10, 72132, eLife Sciences Publications, 2021, doi:10.7554/elife.72132.","chicago":"Marconi, Marco, Marçal Gallemi, Eva Benková, and Krzysztof Wabnik. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72132."},"article_type":"original","date_published":"2021-11-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10270","ddc":["570"],"status":"public","title":"A coupled mechano-biochemical model for cell polarity guided anisotropic root growth","intvolume":" 10","file":[{"file_id":"11372","relation":"main_file","success":1,"checksum":"fad13c509b53bb7a2bef9c946a7ca60a","date_updated":"2022-05-13T09:00:29Z","date_created":"2022-05-13T09:00:29Z","access_level":"open_access","file_name":"2021_eLife_Marconi.pdf","creator":"dernst","file_size":14137503,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development."}]},{"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10299","status":"public","title":"Experimental observation of the origin and structure of elastoinertial turbulence","intvolume":" 118","abstract":[{"text":"Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number.","lang":"eng"}],"issue":"45","type":"journal_article","date_published":"2021-11-03T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","citation":{"ama":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 2021;118(45). doi:10.1073/pnas.2102350118","ista":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 118(45), e2102350118.","ieee":"G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental observation of the origin and structure of elastoinertial turbulence,” Proceedings of the National Academy of Sciences, vol. 118, no. 45. National Academy of Sciences, 2021.","apa":"Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., & Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2102350118","mla":"Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:10.1073/pnas.2102350118.","short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences 118 (2021).","chicago":"Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar, and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2102350118."},"article_type":"original","day":"03","article_processing_charge":"No","scopus_import":"1","keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"author":[{"id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","last_name":"Choueiri","first_name":"George H","full_name":"Choueiri, George H"},{"last_name":"Lopez Alonso","first_name":"Jose M","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Alonso, Jose M"},{"full_name":"Varshney, Atul","last_name":"Varshney","first_name":"Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sarath","last_name":"Sankar","full_name":"Sankar, Sarath"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"date_updated":"2023-08-14T11:50:10Z","date_created":"2021-11-17T13:24:24Z","volume":118,"acknowledgement":"We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg, and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft research unit FOR 2688.","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"National Academy of Sciences","article_number":"e2102350118","doi":"10.1073/pnas.2102350118","language":[{"iso":"eng"}],"external_id":{"pmid":[" 34732570"],"isi":["000720926900019"],"arxiv":["2103.00023"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.00023"}],"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"I04188","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","call_identifier":"FWF"}],"month":"11","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]}},{"date_created":"2021-11-14T23:01:23Z","date_updated":"2023-08-14T11:48:37Z","volume":12,"author":[{"last_name":"Aubret","first_name":"Antoine","full_name":"Aubret, Antoine"},{"full_name":"Martinet, Quentin","last_name":"Martinet","first_name":"Quentin","orcid":"0000-0002-2916-6632","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab"},{"last_name":"Palacci","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A"}],"publication_status":"published","department":[{"_id":"JePa"}],"publisher":"Springer Nature","acknowledgement":"The authors thank R. Jazzar for useful advice regarding the synthesis of heterodimers. We thank S. Sacanna for critical reading. This material is based upon work supported by the National Science Foundation under Grant No. DMR-1554724 and Department of Army Research under grant W911NF-20-1-0112.","year":"2021","pmid":1,"file_date_updated":"2021-11-15T13:25:52Z","article_number":"6398","language":[{"iso":"eng"}],"doi":"10.1038/s41467-021-26699-6","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":["000714754400010"],"pmid":["34737315"]},"month":"11","publication_identifier":{"eissn":["2041-1723"]},"oa_version":"Published Version","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":6282703,"access_level":"open_access","file_name":"2021_NatComm_Aubret.pdf","success":1,"checksum":"1c392b12b9b7b615d422d9fabe19cdb9","date_updated":"2021-11-15T13:25:52Z","date_created":"2021-11-15T13:25:52Z","file_id":"10292","relation":"main_file"}],"status":"public","ddc":["530"],"title":"Metamachines of pluripotent colloids","intvolume":" 12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10280","abstract":[{"text":"Machines enabled the Industrial Revolution and are central to modern technological progress: A machine’s parts transmit forces, motion, and energy to one another in a predetermined manner. Today’s engineering frontier, building artificial micromachines that emulate the biological machinery of living organisms, requires faithful assembly and energy consumption at the microscale. Here, we demonstrate the programmable assembly of active particles into autonomous metamachines using optical templates. Metamachines, or machines made of machines, are stable, mobile and autonomous architectures, whose dynamics stems from the geometry. We use the interplay between anisotropic force generation of the active colloids with the control of their orientation by local geometry. This allows autonomous reprogramming of active particles of the metamachines to achieve multiple functions. It permits the modular assembly of metamachines by fusion, reconfiguration of metamachines and, we anticipate, a shift in focus of self-assembly towards active matter and reprogrammable materials.","lang":"eng"}],"issue":"1","type":"journal_article","date_published":"2021-11-04T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"ista":"Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids. Nature Communications. 12(1), 6398.","ieee":"A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","apa":"Aubret, A., Martinet, Q., & Palacci, J. A. (2021). Metamachines of pluripotent colloids. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26699-6","ama":"Aubret A, Martinet Q, Palacci JA. Metamachines of pluripotent colloids. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26699-6","chicago":"Aubret, Antoine, Quentin Martinet, and Jérémie A Palacci. “Metamachines of Pluripotent Colloids.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26699-6.","mla":"Aubret, Antoine, et al. “Metamachines of Pluripotent Colloids.” Nature Communications, vol. 12, no. 1, 6398, Springer Nature, 2021, doi:10.1038/s41467-021-26699-6.","short":"A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021)."},"day":"04","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1"},{"related_material":{"record":[{"id":"13069","relation":"research_data","status":"public"}]},"author":[{"first_name":"Laetitia","last_name":"Chauve","full_name":"Chauve, Laetitia"},{"full_name":"Hodge, Francesca","last_name":"Hodge","first_name":"Francesca"},{"first_name":"Sharlene","last_name":"Murdoch","full_name":"Murdoch, Sharlene"},{"full_name":"Masoudzadeh, Fatemah","last_name":"Masoudzadeh","first_name":"Fatemah"},{"last_name":"Mann","first_name":"Harry Jack","full_name":"Mann, Harry Jack"},{"full_name":"Lopez-Clavijo, Andrea","first_name":"Andrea","last_name":"Lopez-Clavijo"},{"last_name":"Okkenhaug","first_name":"Hanneke","full_name":"Okkenhaug, Hanneke"},{"first_name":"Greg","last_name":"West","full_name":"West, Greg"},{"full_name":"Sousa, Bebiana C.","last_name":"Sousa","first_name":"Bebiana C."},{"full_name":"Segonds-Pichon, Anne","first_name":"Anne","last_name":"Segonds-Pichon"},{"first_name":"Cheryl","last_name":"Li","full_name":"Li, Cheryl"},{"first_name":"Steven","last_name":"Wingett","full_name":"Wingett, Steven"},{"last_name":"Kienberger","first_name":"Hermine","full_name":"Kienberger, Hermine"},{"full_name":"Kleigrewe, Karin","first_name":"Karin","last_name":"Kleigrewe"},{"full_name":"De Bono, Mario","last_name":"De Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wakelam, Michael","last_name":"Wakelam","first_name":"Michael"},{"last_name":"Casanueva","first_name":"Olivia","full_name":"Casanueva, Olivia"}],"volume":19,"date_created":"2021-11-21T23:01:28Z","date_updated":"2023-08-14T11:53:27Z","pmid":1,"year":"2021","acknowledgement":"We dedicate this work to the memory of Michael J.O. Wakelam. We would like to acknowledge Michael Fasseas (Invermis, Magnitude Biosciences) for plasmid injections and Sunny Biotech for transgenics; Catalina Vallejos and John Marioni for statistical advice at the beginning of the work; Simon Walker, Imaging, Bioinformatics and Lipidomics Facilities at Babraham Institute for technical support; and Cindy Voisine, Michael Witting, Jon Houseley, Len Stephens, Carmen Nussbaum Krammer, Rebeca Aldunate, Patricija van Oosten-Hawle, Jean-Louis Bessereau, and Jane Alfred for feedback on the manuscript. We thank Andy Dillin, Atsushi Kuhara, Amy Walker, Andrew Leifer, Yun Zhang, and Michalis Barkoulas for reagents and Julie Ahringer, Anne Ferguson-Smith, and Anne Corcoran for support and helpful discussions. We also acknowledge Babraham Institute Facilities.","publisher":"Public Library of Science","department":[{"_id":"MaDe"}],"publication_status":"published","file_date_updated":"2021-11-22T09:34:03Z","article_number":"e3001431","doi":"10.1371/journal.pbio.3001431","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":["000715818400001"],"pmid":["34723964"]},"oa":1,"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"month":"11","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10330","date_updated":"2021-11-22T09:34:03Z","date_created":"2021-11-22T09:34:03Z","checksum":"0c61b667f814fd9435b3ac42036fc36d","success":1,"file_name":"2021_PLoSBio_Chauve.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4069215,"creator":"cchlebak"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10322","intvolume":" 19","title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","ddc":["570"],"status":"public","issue":"11","abstract":[{"lang":"eng","text":"To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell autonomous. We have discovered that, in Caenorhabditis elegans, neuronal heat shock factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR), causes extensive fat remodeling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodeling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone morphogenetic protein (BMP) are required for signaling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodeling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell nonautonomously coordinate membrane saturation and composition across tissues in a multicellular animal."}],"type":"journal_article","date_published":"2021-11-01T00:00:00Z","citation":{"short":"L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, PLoS Biology 19 (2021).","mla":"Chauve, Laetitia, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” PLoS Biology, vol. 19, no. 11, e3001431, Public Library of Science, 2021, doi:10.1371/journal.pbio.3001431.","chicago":"Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” PLoS Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pbio.3001431.","ama":"Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. 2021;19(11). doi:10.1371/journal.pbio.3001431","ieee":"L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans,” PLoS Biology, vol. 19, no. 11. Public Library of Science, 2021.","apa":"Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H. J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3001431","ista":"Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann HJ, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. 19(11), e3001431."},"publication":"PLoS Biology","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1"},{"date_published":"2021-10-25T00:00:00Z","page":"1-15","article_type":"original","citation":{"short":"A. Akopyan, H. Edelsbrunner, A. Nikitenko, Experimental Mathematics (2021) 1–15.","mla":"Akopyan, Arseniy, et al. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics, Taylor and Francis, 2021, pp. 1–15, doi:10.1080/10586458.2021.1980459.","chicago":"Akopyan, Arseniy, Herbert Edelsbrunner, and Anton Nikitenko. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics. Taylor and Francis, 2021. https://doi.org/10.1080/10586458.2021.1980459.","ama":"Akopyan A, Edelsbrunner H, Nikitenko A. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics. 2021:1-15. doi:10.1080/10586458.2021.1980459","ieee":"A. Akopyan, H. Edelsbrunner, and A. Nikitenko, “The beauty of random polytopes inscribed in the 2-sphere,” Experimental Mathematics. Taylor and Francis, pp. 1–15, 2021.","apa":"Akopyan, A., Edelsbrunner, H., & Nikitenko, A. (2021). The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics. Taylor and Francis. https://doi.org/10.1080/10586458.2021.1980459","ista":"Akopyan A, Edelsbrunner H, Nikitenko A. 2021. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics., 1–15."},"publication":"Experimental Mathematics","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"25","scopus_import":"1","file":[{"date_updated":"2023-08-14T11:55:10Z","date_created":"2023-08-14T11:55:10Z","success":1,"checksum":"3514382e3a1eb87fa6c61ad622874415","file_id":"14053","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1966019,"file_name":"2023_ExperimentalMath_Akopyan.pdf","access_level":"open_access"}],"oa_version":"Published Version","ddc":["510"],"title":"The beauty of random polytopes inscribed in the 2-sphere","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10222","abstract":[{"lang":"eng","text":"Consider a random set of points on the unit sphere in ℝd, which can be either uniformly sampled or a Poisson point process. Its convex hull is a random inscribed polytope, whose boundary approximates the sphere. We focus on the case d = 3, for which there are elementary proofs and fascinating formulas for metric properties. In particular, we study the fraction of acute facets, the expected intrinsic volumes, the total edge length, and the distance to a fixed point. Finally we generalize the results to the ellipsoid with homeoid density."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1080/10586458.2021.1980459","project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"},{"name":"Discretization in Geometry and Dynamics","grant_number":"I4887","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["2007.07783"],"isi":["000710893500001"]},"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":["1058-6458"],"eissn":["1944-950X"]},"month":"10","date_updated":"2023-08-14T11:57:07Z","date_created":"2021-11-07T23:01:25Z","author":[{"first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"last_name":"Nikitenko","first_name":"Anton","orcid":"0000-0002-0659-3201","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","full_name":"Nikitenko, Anton"}],"department":[{"_id":"HeEd"}],"publisher":"Taylor and Francis","publication_status":"published","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.\r\nWe are grateful to Dmitry Zaporozhets and Christoph Thäle for valuable comments and for directing us to relevant references. We also thank to Anton Mellit for a useful discussion on Bessel functions.","year":"2021","ec_funded":1,"file_date_updated":"2023-08-14T11:55:10Z"},{"month":"10","publication_identifier":{"eissn":["2296-889X"]},"language":[{"iso":"eng"}],"doi":"10.3389/fmolb.2021.762005","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":{"pmid":["34760928"],"isi":["000717241700001"]},"file_date_updated":"2021-11-23T15:06:58Z","article_number":"762005","date_updated":"2023-08-14T11:55:04Z","date_created":"2021-11-21T23:01:29Z","volume":8,"author":[{"first_name":"Iva","last_name":"Sučec","full_name":"Sučec, Iva"},{"full_name":"Bersch, Beate","first_name":"Beate","last_name":"Bersch"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul"}],"publication_status":"published","department":[{"_id":"PaSc"}],"publisher":"Frontiers","year":"2021","acknowledgement":"We thank Juan C. Fontecilla-Camps for insightful discussions related to ATP-driven machineries, and Elif Karagöz for providing the structural model of the Hsp90-Tau complex. This study was supported by the European Research Council (StG-2012-311318-ProtDyn2Function) and the Agence Nationale de la Recherche (ANR-18-CE92-0032-MitoMemProtImp).","pmid":1,"day":"25","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2021-10-25T00:00:00Z","article_type":"original","publication":"Frontiers in Molecular Biosciences","citation":{"ista":"Sučec I, Bersch B, Schanda P. 2021. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 8, 762005.","apa":"Sučec, I., Bersch, B., & Schanda, P. (2021). How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. Frontiers. https://doi.org/10.3389/fmolb.2021.762005","ieee":"I. Sučec, B. Bersch, and P. Schanda, “How do chaperones bind (partly) unfolded client proteins?,” Frontiers in Molecular Biosciences, vol. 8. Frontiers, 2021.","ama":"Sučec I, Bersch B, Schanda P. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 2021;8. doi:10.3389/fmolb.2021.762005","chicago":"Sučec, Iva, Beate Bersch, and Paul Schanda. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences. Frontiers, 2021. https://doi.org/10.3389/fmolb.2021.762005.","mla":"Sučec, Iva, et al. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences, vol. 8, 762005, Frontiers, 2021, doi:10.3389/fmolb.2021.762005.","short":"I. Sučec, B. Bersch, P. Schanda, Frontiers in Molecular Biosciences 8 (2021)."},"abstract":[{"text":"Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10333","date_created":"2021-11-23T15:06:58Z","date_updated":"2021-11-23T15:06:58Z","checksum":"a5c9dbf80dc2c5aaa737f456c941d964","success":1,"file_name":"2021_FrontiersMolBioSc_Sučec.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4700798,"creator":"cchlebak"}],"ddc":["547"],"status":"public","title":"How do chaperones bind (partly) unfolded client proteins?","intvolume":" 8","_id":"10323","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"author":[{"first_name":"Enjun","last_name":"Xu","full_name":"Xu, Enjun"},{"full_name":"Chai, Liang","last_name":"Chai","first_name":"Liang"},{"full_name":"Zhang, Shiqi","last_name":"Zhang","first_name":"Shiqi"},{"full_name":"Yu, Ruixue","last_name":"Yu","first_name":"Ruixue"},{"last_name":"Zhang","first_name":"Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","full_name":"Zhang, Xixi"},{"full_name":"Xu, Chongyi","first_name":"Chongyi","last_name":"Xu"},{"last_name":"Hu","first_name":"Yuxin","full_name":"Hu, Yuxin"}],"date_created":"2021-11-21T23:01:30Z","date_updated":"2023-08-14T11:54:02Z","volume":7,"acknowledgement":"We thank J. Li (Institute of Genetics and Developmental Biology, China) for providing the at14-1, atmax2-1, atmax3-9, atmax4-1, atmax1-1, kai2-2 (Col-0 background) mutants and B. Xu for providing the complementary DNA of P. patens. We are grateful to L. Wang for assistance with MST, B. Han for assistance with UPLC–MS, J. Li for assistance with confocal microscopy and B. Mikael and J. Zhang for their comments on the manuscript. This work was supported by grants from Strategic Priority Research Program of Chinese Academy of Sciences (Y.H., XDB27030102) and the National Natural Science Foundation of China (E.X., 31700253; Y.H., 31830055).","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","month":"11","publication_identifier":{"eissn":["2055-0278"]},"doi":"10.1038/s41477-021-01011-y","language":[{"iso":"eng"}],"external_id":{"isi":["000717408000002"],"pmid":["34764442"]},"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot branching and communications between host plants and symbiotic fungi or root parasitic plants. Extensive studies have identified the key components participating in SL biosynthesis and signalling, whereas the catabolism or deactivation of endogenous SLs in planta remains largely unknown. Here, we report that the Arabidopsis carboxylesterase 15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently hydrolyse SLs both in vitro and in planta. We also provide evidence that AtCXE15 is capable of catalysing hydrolysis of diverse SL analogues and that such CXE15-dependent catabolism of SLs is evolutionarily conserved in seed plants. These results disclose a catalytic mechanism underlying homoeostatic regulation of SLs in plants, which also provides a rational approach to spatial-temporally manipulate the endogenous SLs and thus architecture of crops and ornamental plants."}],"type":"journal_article","oa_version":"None","_id":"10326","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Catabolism of strigolactones by a carboxylesterase","status":"public","intvolume":" 7","day":"11","article_processing_charge":"No","scopus_import":"1","date_published":"2021-11-11T00:00:00Z","publication":"Nature Plants","citation":{"ama":"Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 2021;7:1495–1504. doi:10.1038/s41477-021-01011-y","ieee":"E. Xu et al., “Catabolism of strigolactones by a carboxylesterase,” Nature Plants, vol. 7. Springer Nature, pp. 1495–1504, 2021.","apa":"Xu, E., Chai, L., Zhang, S., Yu, R., Zhang, X., Xu, C., & Hu, Y. (2021). Catabolism of strigolactones by a carboxylesterase. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-021-01011-y","ista":"Xu E, Chai L, Zhang S, Yu R, Zhang X, Xu C, Hu Y. 2021. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 7, 1495–1504.","short":"E. Xu, L. Chai, S. Zhang, R. Yu, X. Zhang, C. Xu, Y. Hu, Nature Plants 7 (2021) 1495–1504.","mla":"Xu, Enjun, et al. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants, vol. 7, Springer Nature, 2021, pp. 1495–1504, doi:10.1038/s41477-021-01011-y.","chicago":"Xu, Enjun, Liang Chai, Shiqi Zhang, Ruixue Yu, Xixi Zhang, Chongyi Xu, and Yuxin Hu. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants. Springer Nature, 2021. https://doi.org/10.1038/s41477-021-01011-y."},"article_type":"original","page":"1495–1504 "},{"abstract":[{"lang":"eng","text":"To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal."}],"type":"research_data_reference","date_created":"2023-05-23T16:40:56Z","date_updated":"2023-08-14T11:53:26Z","oa_version":"Published Version","author":[{"full_name":"Chauve, Laetitia","first_name":"Laetitia","last_name":"Chauve"},{"last_name":"Hodge","first_name":"Francesca","full_name":"Hodge, Francesca"},{"first_name":"Sharlene","last_name":"Murdoch","full_name":"Murdoch, Sharlene"},{"full_name":"Masoudzadeh, Fatemah","first_name":"Fatemah","last_name":"Masoudzadeh"},{"first_name":"Harry-Jack","last_name":"Mann","full_name":"Mann, Harry-Jack"},{"full_name":"Lopez-Clavijo, Andrea","first_name":"Andrea","last_name":"Lopez-Clavijo"},{"full_name":"Okkenhaug, Hanneke","first_name":"Hanneke","last_name":"Okkenhaug"},{"last_name":"West","first_name":"Greg","full_name":"West, Greg"},{"full_name":"Sousa, Bebiana C.","first_name":"Bebiana C.","last_name":"Sousa"},{"full_name":"Segonds-Pichon, Anne","last_name":"Segonds-Pichon","first_name":"Anne"},{"last_name":"Li","first_name":"Cheryl","full_name":"Li, Cheryl"},{"first_name":"Steven","last_name":"Wingett","full_name":"Wingett, Steven"},{"full_name":"Kienberger, Hermine","first_name":"Hermine","last_name":"Kienberger"},{"last_name":"Kleigrewe","first_name":"Karin","full_name":"Kleigrewe, Karin"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario","full_name":"de Bono, Mario"},{"last_name":"Wakelam","first_name":"Michael","full_name":"Wakelam, Michael"},{"first_name":"Olivia","last_name":"Casanueva","full_name":"Casanueva, Olivia"}],"related_material":{"record":[{"id":"10322","relation":"used_in_publication","status":"public"}]},"ddc":["570"],"status":"public","title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","publisher":"Zenodo","department":[{"_id":"MaDe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13069","year":"2021","day":"25","month":"12","article_processing_charge":"No","doi":"10.5281/ZENODO.5519410","date_published":"2021-12-25T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5547464","open_access":"1"}],"citation":{"chicago":"Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry-Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5519410.","short":"L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.-J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, (2021).","mla":"Chauve, Laetitia, et al. Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans. Zenodo, 2021, doi:10.5281/ZENODO.5519410.","ieee":"L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans.” Zenodo, 2021.","apa":"Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H.-J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. Zenodo. https://doi.org/10.5281/ZENODO.5519410","ista":"Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann H-J, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans, Zenodo, 10.5281/ZENODO.5519410.","ama":"Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. 2021. doi:10.5281/ZENODO.5519410"},"oa":1},{"date_published":"2021-10-23T00:00:00Z","publication":"25th International Conference on Financial Cryptography and Data Security","citation":{"ama":"Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. In: 25th International Conference on Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:3-36. doi:10.1007/978-3-662-64331-0_1","ista":"Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias A, Knottenbelt WJ. 2021. SoK: Communication across distributed ledgers. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 3–36.","ieee":"A. Zamyatin et al., “SoK: Communication across distributed ledgers,” in 25th International Conference on Financial Cryptography and Data Security, Virtual, 2021, vol. 12675, pp. 3–36.","apa":"Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., & Knottenbelt, W. J. (2021). SoK: Communication across distributed ledgers. In 25th International Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 3–36). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_1","mla":"Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” 25th International Conference on Financial Cryptography and Data Security, vol. 12675, Springer Nature, 2021, pp. 3–36, doi:10.1007/978-3-662-64331-0_1.","short":"A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 3–36.","chicago":"Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK: Communication across Distributed Ledgers.” In 25th International Conference on Financial Cryptography and Data Security, 12675:3–36. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_1."},"page":"3-36","day":"23","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","_id":"10325","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"SoK: Communication across distributed ledgers","abstract":[{"text":"Since the inception of Bitcoin, a plethora of distributed ledgers differing in design and purpose has been created. While by design, blockchains provide no means to securely communicate with external systems, numerous attempts towards trustless cross-chain communication have been proposed over the years. Today, cross-chain communication (CCC) plays a fundamental role in cryptocurrency exchanges, scalability efforts via sharding, extension of existing systems through sidechains, and bootstrapping of new blockchains. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence in their correctness and composability. We provide the first systematic exposition of cross-chain communication protocols. We formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. With this result in mind, we develop a framework to design new and evaluate existing CCC protocols, focusing on the inherent trust assumptions thereof, and derive a classification covering the field of cross-chain communication to date. We conclude by discussing open challenges for CCC research and the implications of interoperability on the security and privacy of blockchains.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"conference":{"name":"FC: Financial Cryptography","location":"Virtual","start_date":"2021-03-01","end_date":"2021-03-05"},"doi":"10.1007/978-3-662-64331-0_1","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://eprint.iacr.org/2019/1128","open_access":"1"}],"external_id":{"isi":["000712016200001"]},"oa":1,"quality_controlled":"1","isi":1,"month":"10","publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-662-64331-0"],"isbn":["9-783-6626-4330-3"],"eissn":["1611-3349"]},"author":[{"full_name":"Zamyatin, Alexei","last_name":"Zamyatin","first_name":"Alexei"},{"full_name":"Al-Bassam, Mustafa","last_name":"Al-Bassam","first_name":"Mustafa"},{"full_name":"Zindros, Dionysis","first_name":"Dionysis","last_name":"Zindros"},{"last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Moreno-Sanchez, Pedro","last_name":"Moreno-Sanchez","first_name":"Pedro"},{"first_name":"Aggelos","last_name":"Kiayias","full_name":"Kiayias, Aggelos"},{"first_name":"William J.","last_name":"Knottenbelt","full_name":"Knottenbelt, William J."}],"date_updated":"2023-08-14T12:59:26Z","date_created":"2021-11-21T23:01:29Z","volume":"12675 ","acknowledgement":"We would like express our gratitude to Georgia Avarikioti, Daniel Perez and Dominik Harz for helpful comments and feedback on earlier versions of this manuscript. We also thank Nicholas Stifter, Aljosha Judmayer, Philipp Schindler, Edgar Weippl, and Alistair Stewart for insightful discussions during the early stages of this research. We also wish to thank the anonymous reviewers for their valuable comments that helped improve the presentation of our results. This research was funded by Bridge 1 858561 SESC; Bridge 1 864738 PR4DLT (all FFG); the Christian Doppler Laboratory for Security and Quality Improvement in the Production System Lifecycle (CDL-SQI); the competence center SBA-K1 funded by COMET; Chaincode Labs through the project SLN: Scalability for the Lightning Network; and by the Austrian Science Fund (FWF) through the Meitner program (project M-2608). Mustafa Al-Bassam is funded by a scholarship from the Alan Turing Institute. Alexei Zamyatin conducted the early stages of this work during his time at SBA Research, and was supported by a Binance Research Fellowship.","year":"2021","publication_status":"published","department":[{"_id":"ElKo"}],"publisher":"Springer Nature"},{"article_processing_charge":"No","day":"23","scopus_import":"1","date_published":"2021-10-23T00:00:00Z","page":"209-230","citation":{"ama":"Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous incentive-compatible payment channels. In: 25th International Conference on Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:209-230. doi:10.1007/978-3-662-64331-0_11","ista":"Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. 2021. Brick: Asynchronous incentive-compatible payment channels. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 209–230.","ieee":"Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous incentive-compatible payment channels,” in 25th International Conference on Financial Cryptography and Data Security, Virtual, 2021, vol. 12675, pp. 209–230.","apa":"Avarikioti, Z., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (2021). Brick: Asynchronous incentive-compatible payment channels. In 25th International Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 209–230). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_11","mla":"Avarikioti, Zeta, et al. “Brick: Asynchronous Incentive-Compatible Payment Channels.” 25th International Conference on Financial Cryptography and Data Security, vol. 12675, Springer Nature, 2021, pp. 209–30, doi:10.1007/978-3-662-64331-0_11.","short":"Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 209–230.","chicago":"Avarikioti, Zeta, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Incentive-Compatible Payment Channels.” In 25th International Conference on Financial Cryptography and Data Security, 12675:209–30. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_11."},"publication":"25th International Conference on Financial Cryptography and Data Security","abstract":[{"lang":"eng","text":"Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee’s approval for the last valid state. Additionally, Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead, Brick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. We formally define and prove for Brick the properties a payment channel construction should fulfill. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","status":"public","title":"Brick: Asynchronous incentive-compatible payment channels","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10324","publication_identifier":{"eissn":["1611-3349"],"isbn":["9-783-6626-4330-3"],"issn":["0302-9743"],"eisbn":["978-3-662-64331-0"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-64331-0_11","conference":{"name":"FC: Financial Cryptography","start_date":"2021-03-01","location":"Virtual","end_date":"2021-03-05"},"isi":1,"quality_controlled":"1","external_id":{"isi":["000712016200011"],"arxiv":["1905.11360"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.11360"}],"volume":"12675 ","date_created":"2021-11-21T23:01:29Z","date_updated":"2023-08-14T12:59:58Z","author":[{"full_name":"Avarikioti, Zeta","first_name":"Zeta","last_name":"Avarikioti"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"first_name":"Roger","last_name":"Wattenhofer","full_name":"Wattenhofer, Roger"},{"first_name":"Dionysis","last_name":"Zindros","full_name":"Zindros, Dionysis"}],"publisher":"Springer Nature","department":[{"_id":"ElKo"}],"publication_status":"published","acknowledgement":"We would like to thank Kaoutar Elkhiyaoui for her valuable feedback as well as Jakub Sliwinski for his impactful contribution to this work.","year":"2021"},{"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","publication":"Protein Engineering, Design and Selection","citation":{"ama":"Lee J, Vernet A, Gruber N, et al. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 2021;34. doi:10.1093/protein/gzab025","ieee":"J. Lee et al., “Rational engineering of an erythropoietin fusion protein to treat hypoxia,” Protein Engineering, Design and Selection, vol. 34. Oxford University Press, 2021.","apa":"Lee, J., Vernet, A., Gruber, N., Kready, K. M., Burrill, D. R., Way, J. C., & Silver, P. A. (2021). Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. Oxford University Press. https://doi.org/10.1093/protein/gzab025","ista":"Lee J, Vernet A, Gruber N, Kready KM, Burrill DR, Way JC, Silver PA. 2021. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 34, gzab025.","short":"J. Lee, A. Vernet, N. Gruber, K.M. Kready, D.R. Burrill, J.C. Way, P.A. Silver, Protein Engineering, Design and Selection 34 (2021).","mla":"Lee, Jungmin, et al. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection, vol. 34, gzab025, Oxford University Press, 2021, doi:10.1093/protein/gzab025.","chicago":"Lee, Jungmin, Andyna Vernet, Nathalie Gruber, Kasia M. Kready, Devin R. Burrill, Jeffrey C. Way, and Pamela A. Silver. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection. Oxford University Press, 2021. https://doi.org/10.1093/protein/gzab025."},"date_published":"2021-11-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death, but its pro-thrombotic activity is problematic for use of erythropoietin in treating hypoxia. We constructed a fusion protein that stimulates red blood cell production and neuroprotection without triggering platelet production, a marker for thrombosis. The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant (L108A). The mutation reduces activation of erythropoietin receptor homodimers that induce erythropoiesis and thrombosis, but maintains the tissue-protective signaling. The binding of the nanobody element to glycophorin A rescues homodimeric erythropoietin receptor activation on red blood cell precursors. In a cell proliferation assay, the fusion protein is active at 10−14 M, allowing an estimate of the number of receptor–ligand complexes needed for signaling. This fusion protein stimulates erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity in vitro. Our erythropoietin fusion protein presents a novel molecule for treating hypoxia."}],"title":"Rational engineering of an erythropoietin fusion protein to treat hypoxia","status":"public","intvolume":" 34","_id":"10363","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","month":"11","publication_identifier":{"eissn":["1741-0134"],"issn":["1741-0126"]},"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/protein/gzab025"}],"external_id":{"isi":["000746596900001"],"pmid":["34725710"]},"language":[{"iso":"eng"}],"doi":"10.1093/protein/gzab025","article_number":"gzab025","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"CaGu"}],"acknowledgement":"This work was supported by funds from the Wyss Institute for Biologically Inspired Engineering and the Boston Biomedical Innovation Center (Pilot Award 112475; Drive Award U54HL119145). J.L., K.M.K., D.R.B., J.C.W. and P.A.S. were supported by the Harvard Medical School Department of Systems Biology. J.C.W. was further supported by the Harvard Medical School Laboratory of Systems Pharmacology. A.V., D.R.B. and P.A.S. were further supported by the Wyss Institute for Biologically Inspired Engineering. N.G.G. was sponsored by the Army Research Office under Grant Number W911NF-17-2-0092. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein. We sincerely thank Amanda Graveline and the Wyss Institute at Harvard for their scientific support.","year":"2021","pmid":1,"date_created":"2021-11-28T23:01:28Z","date_updated":"2023-08-14T13:01:38Z","volume":34,"author":[{"last_name":"Lee","first_name":"Jungmin","full_name":"Lee, Jungmin"},{"full_name":"Vernet, Andyna","last_name":"Vernet","first_name":"Andyna"},{"last_name":"Gruber","first_name":"Nathalie","id":"2C9C8316-AA17-11E9-B5C2-8BC2E5697425","full_name":"Gruber, Nathalie"},{"full_name":"Kready, Kasia M.","first_name":"Kasia M.","last_name":"Kready"},{"full_name":"Burrill, Devin R.","first_name":"Devin R.","last_name":"Burrill"},{"first_name":"Jeffrey C.","last_name":"Way","full_name":"Way, Jeffrey C."},{"full_name":"Silver, Pamela A.","first_name":"Pamela A.","last_name":"Silver"}]},{"volume":168,"date_created":"2021-11-28T23:01:30Z","date_updated":"2023-08-14T13:02:40Z","author":[{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Lennon, Ana Maria","last_name":"Lennon","first_name":"Ana Maria"},{"full_name":"Mayor, Roberto","last_name":"Mayor","first_name":"Roberto"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"}],"department":[{"_id":"CaHe"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2021","article_number":"203758","language":[{"iso":"eng"}],"doi":"10.1016/j.cdev.2021.203758","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000974771600028"],"pmid":["34800748"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.cdev.2021.203758","open_access":"1"}],"publication_identifier":{"issn":["2667-2901"]},"month":"11","oa_version":"Published Version","intvolume":" 168","status":"public","title":"Special rebranding issue: “Quantitative cell and developmental biology”","_id":"10366","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"12","type":"journal_article","date_published":"2021-11-17T00:00:00Z","article_type":"letter_note","citation":{"apa":"Heisenberg, C.-P. J., Lennon, A. M., Mayor, R., & Salbreux, G. (2021). Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. Elsevier. https://doi.org/10.1016/j.cdev.2021.203758","ieee":"C.-P. J. Heisenberg, A. M. Lennon, R. Mayor, and G. Salbreux, “Special rebranding issue: ‘Quantitative cell and developmental biology,’” Cells and Development, vol. 168, no. 12. Elsevier, 2021.","ista":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. 2021. Special rebranding issue: “Quantitative cell and developmental biology”. Cells and Development. 168(12), 203758.","ama":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. 2021;168(12). doi:10.1016/j.cdev.2021.203758","chicago":"Heisenberg, Carl-Philipp J, Ana Maria Lennon, Roberto Mayor, and Guillaume Salbreux. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development. Elsevier, 2021. https://doi.org/10.1016/j.cdev.2021.203758.","short":"C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development 168 (2021).","mla":"Heisenberg, Carl-Philipp J., et al. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development, vol. 168, no. 12, 203758, Elsevier, 2021, doi:10.1016/j.cdev.2021.203758."},"publication":"Cells and Development","article_processing_charge":"No","day":"17","scopus_import":"1"},{"ec_funded":1,"file_date_updated":"2021-12-10T08:54:09Z","article_number":"6830","related_material":{"record":[{"id":"13058","relation":"research_data","status":"public"}]},"author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","first_name":"Mehmet C","last_name":"Ucar","full_name":"Ucar, Mehmet C"},{"last_name":"Kamenev","first_name":"Dmitrii","full_name":"Kamenev, Dmitrii"},{"first_name":"Kazunori","last_name":"Sunadome","full_name":"Sunadome, Kazunori"},{"full_name":"Fachet, Dominik C","first_name":"Dominik C","last_name":"Fachet","id":"14FDD550-AA41-11E9-A0E5-1ACCE5697425"},{"full_name":"Lallemend, Francois","first_name":"Francois","last_name":"Lallemend"},{"first_name":"Igor","last_name":"Adameyko","full_name":"Adameyko, Igor"},{"first_name":"Saida","last_name":"Hadjab","full_name":"Hadjab, Saida"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"volume":12,"date_created":"2021-12-05T23:01:40Z","date_updated":"2023-08-14T13:18:46Z","pmid":1,"acknowledgement":"We thank all members of our respective groups for helpful discussion on the paper. The authors are also grateful to Prof. Abdel El. Manira for support and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core from the Karolinska Institutet for technical support. This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.); Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L. and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.); Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.).","year":"2021","department":[{"_id":"EdHa"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"month":"11","doi":"10.1038/s41467-021-27135-5","language":[{"iso":"eng"}],"external_id":{"isi":["000722322900020"],"pmid":["34819507"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Branching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"10529","relation":"main_file","success":1,"checksum":"63c56ec75314a71e63e7dd2920b3c5b5","date_created":"2021-12-10T08:54:09Z","date_updated":"2021-12-10T08:54:09Z","access_level":"open_access","file_name":"2021_NatComm_Ucar.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":2303405}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10402","intvolume":" 12","status":"public","ddc":["573"],"title":"Theory of branching morphogenesis by local interactions and global guidance","has_accepted_license":"1","article_processing_charge":"No","day":"24","scopus_import":"1","date_published":"2021-11-24T00:00:00Z","citation":{"mla":"Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications, vol. 12, 6830, Springer Nature, 2021, doi:10.1038/s41467-021-27135-5.","short":"M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021).","chicago":"Ucar, Mehmet C, Dmitrii Kamenev, Kazunori Sunadome, Dominik C Fachet, Francois Lallemend, Igor Adameyko, Saida Hadjab, and Edouard B Hannezo. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-27135-5.","ama":"Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 2021;12. doi:10.1038/s41467-021-27135-5","ista":"Ucar MC, Kamenev D, Sunadome K, Fachet DC, Lallemend F, Adameyko I, Hadjab S, Hannezo EB. 2021. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 12, 6830.","ieee":"M. C. Ucar et al., “Theory of branching morphogenesis by local interactions and global guidance,” Nature Communications, vol. 12. Springer Nature, 2021.","apa":"Ucar, M. C., Kamenev, D., Sunadome, K., Fachet, D. C., Lallemend, F., Adameyko, I., … Hannezo, E. B. (2021). Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-27135-5"},"publication":"Nature Communications","article_type":"original"},{"publication_identifier":{"isbn":["9-783-0309-0452-4"],"eissn":["1611-3349"],"issn":["0302-9743"]},"month":"11","doi":"10.1007/978-3-030-90453-1_14","conference":{"name":"TCC: Theory of Cryptography Conference","location":"Raleigh, NC, United States","start_date":"2021-11-08","end_date":"2021-11-11"},"language":[{"iso":"eng"}],"external_id":{"isi":["000728364000014"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1224"}],"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"ec_funded":1,"author":[{"id":"B9CD0494-D033-11E9-B219-A439E6697425","last_name":"Chakraborty","first_name":"Suvradip","full_name":"Chakraborty, Suvradip"},{"last_name":"Dziembowski","first_name":"Stefan","full_name":"Dziembowski, Stefan"},{"first_name":"Małgorzata","last_name":"Gałązka","full_name":"Gałązka, Małgorzata"},{"full_name":"Lizurej, Tomasz","first_name":"Tomasz","last_name":"Lizurej"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"first_name":"Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X"}],"volume":13043,"date_created":"2021-12-05T23:01:42Z","date_updated":"2023-08-14T13:07:46Z","year":"2021","department":[{"_id":"KrPi"}],"publisher":"Springer Nature","publication_status":"published","article_processing_charge":"No","day":"04","scopus_import":"1","date_published":"2021-11-04T00:00:00Z","citation":{"ama":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. Trojan-resilience without cryptography. In: Vol 13043. Springer Nature; 2021:397-428. doi:10.1007/978-3-030-90453-1_14","apa":"Chakraborty, S., Dziembowski, S., Gałązka, M., Lizurej, T., Pietrzak, K. Z., & Yeo, M. X. (2021). Trojan-resilience without cryptography (Vol. 13043, pp. 397–428). Presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_14","ieee":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K. Z. Pietrzak, and M. X. Yeo, “Trojan-resilience without cryptography,” presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 397–428.","ista":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. 2021. Trojan-resilience without cryptography. TCC: Theory of Cryptography Conference, LNCS, vol. 13043, 397–428.","short":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K.Z. Pietrzak, M.X. Yeo, in:, Springer Nature, 2021, pp. 397–428.","mla":"Chakraborty, Suvradip, et al. Trojan-Resilience without Cryptography. Vol. 13043, Springer Nature, 2021, pp. 397–428, doi:10.1007/978-3-030-90453-1_14.","chicago":"Chakraborty, Suvradip, Stefan Dziembowski, Małgorzata Gałązka, Tomasz Lizurej, Krzysztof Z Pietrzak, and Michelle X Yeo. “Trojan-Resilience without Cryptography,” 13043:397–428. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_14."},"page":"397-428","abstract":[{"lang":"eng","text":"Digital hardware Trojans are integrated circuits whose implementation differ from the specification in an arbitrary and malicious way. For example, the circuit can differ from its specified input/output behavior after some fixed number of queries (known as “time bombs”) or on some particular input (known as “cheat codes”). To detect such Trojans, countermeasures using multiparty computation (MPC) or verifiable computation (VC) have been proposed. On a high level, to realize a circuit with specification F one has more sophisticated circuits F⋄ manufactured (where F⋄ specifies a MPC or VC of F ), and then embeds these F⋄ ’s into a master circuit which must be trusted but is relatively simple compared to F . Those solutions impose a significant overhead as F⋄ is much more complex than F , also the master circuits are not exactly trivial. In this work, we show that in restricted settings, where F has no evolving state and is queried on independent inputs, we can achieve a relaxed security notion using very simple constructions. In particular, we do not change the specification of the circuit at all (i.e., F=F⋄ ). Moreover the master circuit basically just queries a subset of its manufactured circuits and checks if they’re all the same. The security we achieve guarantees that, if the manufactured circuits are initially tested on up to T inputs, the master circuit will catch Trojans that try to deviate on significantly more than a 1/T fraction of the inputs. This bound is optimal for the type of construction considered, and we provably achieve it using a construction where 12 instantiations of F need to be embedded into the master. We also discuss an extremely simple construction with just 2 instantiations for which we conjecture that it already achieves the optimal bound."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10407","intvolume":" 13043","title":"Trojan-resilience without cryptography","status":"public"},{"oa_version":"Published Version","file":[{"file_size":13131322,"content_type":"application/pdf","creator":"cchlebak","file_name":"2021_eLife_Biane.pdf","access_level":"open_access","date_created":"2021-12-10T08:31:41Z","date_updated":"2021-12-10T08:31:41Z","checksum":"c7c33c3319428d56e332e22349c50ed3","success":1,"relation":"main_file","file_id":"10528"}],"ddc":["570"],"status":"public","title":"Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons","intvolume":" 10","_id":"10403","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Synaptic transmission, connectivity, and dendritic morphology mature in parallel during brain development and are often disrupted in neurodevelopmental disorders. Yet how these changes influence the neuronal computations necessary for normal brain function are not well understood. To identify cellular mechanisms underlying the maturation of synaptic integration in interneurons, we combined patch-clamp recordings of excitatory inputs in mouse cerebellar stellate cells (SCs), three-dimensional reconstruction of SC morphology with excitatory synapse location, and biophysical modeling. We found that postnatal maturation of postsynaptic strength was homogeneously reduced along the somatodendritic axis, but dendritic integration was always sublinear. However, dendritic branching increased without changes in synapse density, leading to a substantial gain in distal inputs. Thus, changes in synapse distribution, rather than dendrite cable properties, are the dominant mechanism underlying the maturation of neuronal computation. These mechanisms favor the emergence of a spatially compartmentalized two-stage integration model promoting location-dependent integration within dendritic subunits.","lang":"eng"}],"type":"journal_article","date_published":"2021-11-03T00:00:00Z","article_type":"original","publication":"eLife","citation":{"short":"C. Biane, F. Rückerl, T. Abrahamsson, C. Saint-Cloment, J. Mariani, R. Shigemoto, D.A. Digregorio, R.M. Sherrard, L. Cathala, ELife 10 (2021).","mla":"Biane, Celia, et al. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife, vol. 10, e65954, eLife Sciences Publications, 2021, doi:10.7554/eLife.65954.","chicago":"Biane, Celia, Florian Rückerl, Therese Abrahamsson, Cécile Saint-Cloment, Jean Mariani, Ryuichi Shigemoto, David A. Digregorio, Rachel M. Sherrard, and Laurence Cathala. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.65954.","ama":"Biane C, Rückerl F, Abrahamsson T, et al. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 2021;10. doi:10.7554/eLife.65954","apa":"Biane, C., Rückerl, F., Abrahamsson, T., Saint-Cloment, C., Mariani, J., Shigemoto, R., … Cathala, L. (2021). Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.65954","ieee":"C. Biane et al., “Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons,” eLife, vol. 10. eLife Sciences Publications, 2021.","ista":"Biane C, Rückerl F, Abrahamsson T, Saint-Cloment C, Mariani J, Shigemoto R, Digregorio DA, Sherrard RM, Cathala L. 2021. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 10, e65954."},"day":"03","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_updated":"2023-08-14T13:12:07Z","date_created":"2021-12-05T23:01:40Z","volume":10,"author":[{"full_name":"Biane, Celia","last_name":"Biane","first_name":"Celia"},{"full_name":"Rückerl, Florian","last_name":"Rückerl","first_name":"Florian"},{"first_name":"Therese","last_name":"Abrahamsson","full_name":"Abrahamsson, Therese"},{"last_name":"Saint-Cloment","first_name":"Cécile","full_name":"Saint-Cloment, Cécile"},{"full_name":"Mariani, Jean","last_name":"Mariani","first_name":"Jean"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Digregorio, David A.","last_name":"Digregorio","first_name":"David A."},{"first_name":"Rachel M.","last_name":"Sherrard","full_name":"Sherrard, Rachel M."},{"full_name":"Cathala, Laurence","last_name":"Cathala","first_name":"Laurence"}],"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"RySh"}],"acknowledgement":"This study was supported by the Centre National de la Recherche Scientifique and the Agence Nationale de la Recherche (ANR-13-BSV4-00166, to LC and DAD). TA was supported by fellowships from the Fondation pour la Recherche Medicale and the Swedish Research Council. We thank Dmitry Ershov from the Image Analysis Hub of the Institut Pasteur, Elodie Le Monnier, Elena Hollergschwandtner, Vanessa Zheden, and Corinne Nantet for technical support and Haining Zhong for providing the Venus-tagged PSD95 mouse line. We would like to thank Alberto Bacci, Ann Lohof, and Nelson Rebola for comments on the manuscript.","year":"2021","file_date_updated":"2021-12-10T08:31:41Z","article_number":"e65954","language":[{"iso":"eng"}],"doi":"10.7554/eLife.65954","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":{"isi":["000715789500001"]},"month":"11","publication_identifier":{"eissn":["2050-084X"]}},{"scopus_import":"1","day":"26","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Communications Physics","citation":{"mla":"Barfknecht, Rafael E., et al. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics, vol. 4, no. 1, 252, Springer Nature, 2021, doi:10.1038/s42005-021-00753-7.","short":"R.E. Barfknecht, A. Foerster, N.T. Zinner, A. Volosniev, Communications Physics 4 (2021).","chicago":"Barfknecht, Rafael E., Angela Foerster, Nikolaj T. Zinner, and Artem Volosniev. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics. Springer Nature, 2021. https://doi.org/10.1038/s42005-021-00753-7.","ama":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 2021;4(1). doi:10.1038/s42005-021-00753-7","ista":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. 2021. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 4(1), 252.","ieee":"R. E. Barfknecht, A. Foerster, N. T. Zinner, and A. Volosniev, “Generation of spin currents by a temperature gradient in a two-terminal device,” Communications Physics, vol. 4, no. 1. Springer Nature, 2021.","apa":"Barfknecht, R. E., Foerster, A., Zinner, N. T., & Volosniev, A. (2021). Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-021-00753-7"},"date_published":"2021-11-26T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Theoretical and experimental studies of the interaction between spins and temperature are vital for the development of spin caloritronics, as they dictate the design of future devices. In this work, we propose a two-terminal cold-atom simulator to study that interaction. The proposed quantum simulator consists of strongly interacting atoms that occupy two temperature reservoirs connected by a one-dimensional link. First, we argue that the dynamics in the link can be described using an inhomogeneous Heisenberg spin chain whose couplings are defined by the local temperature. Second, we show the existence of a spin current in a system with a temperature difference by studying the dynamics that follows the spin-flip of an atom in the link. A temperature gradient accelerates the impurity in one direction more than in the other, leading to an overall spin current similar to the spin Seebeck effect."}],"issue":"1","ddc":["530"],"title":"Generation of spin currents by a temperature gradient in a two-terminal device","status":"public","intvolume":" 4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10401","file":[{"file_size":1068984,"content_type":"application/pdf","creator":"alisjak","file_name":"2021_NatComm_Barfknecht.pdf","access_level":"open_access","date_created":"2021-12-06T14:53:41Z","date_updated":"2021-12-06T14:53:41Z","checksum":"9097319952cb9a3d96e7fd3aa9813a03","success":1,"relation":"main_file","file_id":"10420"}],"oa_version":"Published Version","month":"11","publication_identifier":{"eissn":["23993650"]},"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"external_id":{"isi":["10.1038/s42005-021-00753-7"],"arxiv":["2101.02020"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s42005-021-00753-7","article_number":"252","file_date_updated":"2021-12-06T14:53:41Z","ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"MiLe"}],"acknowledgement":"The authors acknowledge support from the European QuantERA ERA-NET Cofund in Quantum Technologies (Project QTFLAG Grant Agreement No. 731473) (R.E.B), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) Brazil (A.F.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V.), the Independent Research Fund Denmark, the Carlsberg Foundation, and Aarhus University Research Foundation under the Jens Christian Skou fellowship program (N.T.Z).","year":"2021","date_created":"2021-12-05T23:01:39Z","date_updated":"2023-08-14T13:04:34Z","volume":4,"author":[{"last_name":"Barfknecht","first_name":"Rafael E.","full_name":"Barfknecht, Rafael E."},{"full_name":"Foerster, Angela","first_name":"Angela","last_name":"Foerster"},{"full_name":"Zinner, Nikolaj T.","last_name":"Zinner","first_name":"Nikolaj T."},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"}]},{"doi":"10.1111/cgf.14418","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2110.07667"}],"external_id":{"arxiv":["2110.07667"],"isi":["000722952000024"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"month":"11","publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"author":[{"first_name":"Stefan","last_name":"Sietzen","full_name":"Sietzen, Stefan"},{"first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias"},{"first_name":"Judy","last_name":"Borowski","full_name":"Borowski, Judy"},{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"full_name":"Waldner, Manuela","first_name":"Manuela","last_name":"Waldner"}],"date_created":"2021-12-05T23:01:40Z","date_updated":"2023-08-14T13:11:42Z","volume":40,"year":"2021","acknowledgement":"We thank Robert Geirhos and Roland Zimmermann for their participation in the case study and valuable feedback, Chris Olah and Nick Cammarata for valuable discussions in the early phase of the project, as well as the Distill Slack workspace as a platform for discussions. M.L. is supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). J.B. is supported by the German Federal Ministry of Education and Research\r\n(BMBF) through the Competence Center for Machine Learning (TUE.AI, FKZ 01IS18039A) and the International Max Planck Research School for Intelligent Systems (IMPRS-IS). R.H. is partially supported by Boeing and Horizon-2020 ECSEL (grant 783163, iDev40).\r\n","publication_status":"published","publisher":"Wiley","department":[{"_id":"ToHe"}],"date_published":"2021-11-27T00:00:00Z","publication":"Computer Graphics Forum","citation":{"ista":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis of CNN robustness. Computer Graphics Forum. 40(7), 253–264.","apa":"Sietzen, S., Lechner, M., Borowski, J., Hasani, R., & Waldner, M. (2021). Interactive analysis of CNN robustness. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.14418","ieee":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, and M. Waldner, “Interactive analysis of CNN robustness,” Computer Graphics Forum, vol. 40, no. 7. Wiley, pp. 253–264, 2021.","ama":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis of CNN robustness. Computer Graphics Forum. 2021;40(7):253-264. doi:10.1111/cgf.14418","chicago":"Sietzen, Stefan, Mathias Lechner, Judy Borowski, Ramin Hasani, and Manuela Waldner. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.14418.","mla":"Sietzen, Stefan, et al. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum, vol. 40, no. 7, Wiley, 2021, pp. 253–64, doi:10.1111/cgf.14418.","short":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics Forum 40 (2021) 253–264."},"article_type":"original","page":"253-264","day":"27","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10404","status":"public","title":"Interactive analysis of CNN robustness","intvolume":" 40","abstract":[{"text":"While convolutional neural networks (CNNs) have found wide adoption as state-of-the-art models for image-related tasks, their predictions are often highly sensitive to small input perturbations, which the human vision is robust against. This paper presents Perturber, a web-based application that allows users to instantaneously explore how CNN activations and predictions evolve when a 3D input scene is interactively perturbed. Perturber offers a large variety of scene modifications, such as camera controls, lighting and shading effects, background modifications, object morphing, as well as adversarial attacks, to facilitate the discovery of potential vulnerabilities. Fine-tuned model versions can be directly compared for qualitative evaluation of their robustness. Case studies with machine learning experts have shown that Perturber helps users to quickly generate hypotheses about model vulnerabilities and to qualitatively compare model behavior. Using quantitative analyses, we could replicate users’ insights with other CNN architectures and input images, yielding new insights about the vulnerability of adversarially trained models.","lang":"eng"}],"issue":"7","type":"journal_article"},{"month":"08","publication_identifier":{"eissn":["1545-2948"],"issn":["0066-4197"]},"external_id":{"pmid":["34460295"],"isi":["000747220900010"]},"quality_controlled":"1","isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"doi":"10.1146/annurev-genet-071819-103748","language":[{"iso":"eng"}],"ec_funded":1,"year":"2021","acknowledgement":"The authors would like to thank Feyza Nur Arslan, Suyash Naik, Diana Pinheiro, Alexandra Schauer, and Shayan Shamipour for their comments on the draft. N.M. is supported by an ISTplus postdoctoral fellowship (H2020 Marie-Sklodowska-Curie COFUND Action).","pmid":1,"publication_status":"published","publisher":"Annual Reviews","department":[{"_id":"CaHe"}],"author":[{"first_name":"Nikhil","last_name":"Mishra","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","orcid":"0000-0002-6425-5788","full_name":"Mishra, Nikhil"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"date_updated":"2023-08-14T13:05:13Z","date_created":"2021-12-05T23:01:41Z","volume":55,"scopus_import":"1","keyword":["morphogenesis","forward genetics","high-resolution microscopy","biophysics","biochemistry","patterning"],"day":"30","article_processing_charge":"No","publication":"Annual Review of Genetics","citation":{"mla":"Mishra, Nikhil, and Carl-Philipp J. Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics, vol. 55, Annual Reviews, 2021, pp. 209–33, doi:10.1146/annurev-genet-071819-103748.","short":"N. Mishra, C.-P.J. Heisenberg, Annual Review of Genetics 55 (2021) 209–233.","chicago":"Mishra, Nikhil, and Carl-Philipp J Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics. Annual Reviews, 2021. https://doi.org/10.1146/annurev-genet-071819-103748.","ama":"Mishra N, Heisenberg C-PJ. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 2021;55:209-233. doi:10.1146/annurev-genet-071819-103748","ista":"Mishra N, Heisenberg C-PJ. 2021. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 55, 209–233.","ieee":"N. Mishra and C.-P. J. Heisenberg, “Dissecting organismal morphogenesis by bridging genetics and biophysics,” Annual Review of Genetics, vol. 55. Annual Reviews, pp. 209–233, 2021.","apa":"Mishra, N., & Heisenberg, C.-P. J. (2021). Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genet-071819-103748"},"article_type":"original","page":"209-233","date_published":"2021-08-30T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10406","status":"public","title":"Dissecting organismal morphogenesis by bridging genetics and biophysics","intvolume":" 55","oa_version":"None"},{"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5257161","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"mla":"Ucar, Mehmet C. Source Data for the Manuscript “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Zenodo, 2021, doi:10.5281/ZENODO.5257160.","short":"M.C. Ucar, (2021).","chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘Theory of Branching Morphogenesis by Local Interactions and Global Guidance.’” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5257160.","ama":"Ucar MC. Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” 2021. doi:10.5281/ZENODO.5257160","ista":"Ucar MC. 2021. Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance’, Zenodo, 10.5281/ZENODO.5257160.","ieee":"M. C. Ucar, “Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance.’” Zenodo, 2021.","apa":"Ucar, M. C. (2021). Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” Zenodo. https://doi.org/10.5281/ZENODO.5257160"},"oa":1,"doi":"10.5281/ZENODO.5257160","date_published":"2021-08-25T00:00:00Z","month":"08","day":"25","article_processing_charge":"No","status":"public","title":"Source data for the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\"","ddc":["570"],"publisher":"Zenodo","department":[{"_id":"EdHa"}],"_id":"13058","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","date_created":"2023-05-23T13:46:34Z","date_updated":"2023-08-14T13:18:46Z","oa_version":"Published Version","author":[{"last_name":"Ucar","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10402"}]},"type":"research_data_reference","abstract":[{"text":"The zip file includes source data used in the main text of the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\", as well as a representative Jupyter notebook to reproduce the main figures. A sample script for the simulations of branching and annihilating random walks is also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary branched networks under external guidance. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt.","lang":"eng"}]},{"isi":1,"quality_controlled":"1","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"external_id":{"isi":["000728363700008"]},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1158"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"TCC: Theory of Cryptography","start_date":"2021-11-08","location":"Raleigh, NC, United States","end_date":"2021-11-11"},"doi":"10.1007/978-3-030-90456-2_8","month":"11","publication_identifier":{"isbn":["9-783-0309-0455-5"],"eissn":["1611-3349"],"eisbn":["978-3-030-90456-2"],"issn":["0302-9743"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"acknowledgement":"B. Auerbach, M.A. Baig and K. Pietrzak—received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Karen Klein was supported in part by ERC CoG grant 724307 and conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Guillermo Pascual-Perez was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385; Michael Walter conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","year":"2021","date_updated":"2023-08-14T13:19:39Z","date_created":"2021-12-05T23:01:42Z","volume":13044,"author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","first_name":"Joel F","full_name":"Alwen, Joel F"},{"full_name":"Auerbach, Benedikt","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","orcid":"0000-0002-7553-6606","first_name":"Benedikt","last_name":"Auerbach"},{"last_name":"Baig","first_name":"Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","full_name":"Baig, Mirza Ahad"},{"full_name":"Cueto Noval, Miguel","last_name":"Cueto Noval","first_name":"Miguel","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc"},{"full_name":"Klein, Karen","last_name":"Klein","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"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":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z"},{"full_name":"Walter, Michael","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","last_name":"Walter","first_name":"Michael"}],"ec_funded":1,"page":"222-253","publication":"19th International Conference","citation":{"ieee":"J. F. Alwen et al., “Grafting key trees: Efficient key management for overlapping groups,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13044, pp. 222–253.","apa":"Alwen, J. F., Auerbach, B., Baig, M. A., Cueto Noval, M., Klein, K., Pascual Perez, G., … Walter, M. (2021). Grafting key trees: Efficient key management for overlapping groups. In 19th International Conference (Vol. 13044, pp. 222–253). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90456-2_8","ista":"Alwen JF, Auerbach B, Baig MA, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ, Walter M. 2021. Grafting key trees: Efficient key management for overlapping groups. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13044, 222–253.","ama":"Alwen JF, Auerbach B, Baig MA, et al. Grafting key trees: Efficient key management for overlapping groups. In: 19th International Conference. Vol 13044. Springer Nature; 2021:222-253. doi:10.1007/978-3-030-90456-2_8","chicago":"Alwen, Joel F, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” In 19th International Conference, 13044:222–53. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90456-2_8.","short":"J.F. Alwen, B. Auerbach, M.A. Baig, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 222–253.","mla":"Alwen, Joel F., et al. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” 19th International Conference, vol. 13044, Springer Nature, 2021, pp. 222–53, doi:10.1007/978-3-030-90456-2_8."},"date_published":"2021-11-04T00:00:00Z","scopus_import":"1","day":"04","article_processing_charge":"No","title":"Grafting key trees: Efficient key management for overlapping groups","status":"public","intvolume":" 13044","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10408","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Key trees are often the best solution in terms of transmission cost and storage requirements for managing keys in a setting where a group needs to share a secret key, while being able to efficiently rotate the key material of users (in order to recover from a potential compromise, or to add or remove users). Applications include multicast encryption protocols like LKH (Logical Key Hierarchies) or group messaging like the current IETF proposal TreeKEM. A key tree is a (typically balanced) binary tree, where each node is identified with a key: leaf nodes hold users’ secret keys while the root is the shared group key. For a group of size N, each user just holds log(N) keys (the keys on the path from its leaf to the root) and its entire key material can be rotated by broadcasting 2log(N) ciphertexts (encrypting each fresh key on the path under the keys of its parents). In this work we consider the natural setting where we have many groups with partially overlapping sets of users, and ask if we can find solutions where the cost of rotating a key is better than in the trivial one where we have a separate key tree for each group. We show that in an asymptotic setting (where the number m of groups is fixed while the number N of users grows) there exist more general key graphs whose cost converges to the cost of a single group, thus saving a factor linear in the number of groups over the trivial solution. As our asymptotic “solution” converges very slowly and performs poorly on concrete examples, we propose an algorithm that uses a natural heuristic to compute a key graph for any given group structure. Our algorithm combines two greedy algorithms, and is thus very efficient: it first converts the group structure into a “lattice graph”, which is then turned into a key graph by repeatedly applying the algorithm for constructing a Huffman code. To better understand how far our proposal is from an optimal solution, we prove lower bounds on the update cost of continuous group-key agreement and multicast encryption in a symbolic model admitting (asymmetric) encryption, pseudorandom generators, and secret sharing as building blocks."}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10527","intvolume":" 127","status":"public","title":"Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene","oa_version":"Preprint","type":"journal_article","issue":"24","abstract":[{"text":"We show that in a two-dimensional electron gas with an annular Fermi surface, long-range Coulomb interactions can lead to unconventional superconductivity by the Kohn-Luttinger mechanism. Superconductivity is strongly enhanced when the inner and outer Fermi surfaces are close to each other. The most prevalent state has chiral p-wave symmetry, but d-wave and extended s-wave pairing are also possible. We discuss these results in the context of rhombohedral trilayer graphene, where superconductivity was recently discovered in regimes where the normal state has an annular Fermi surface. Using realistic parameters, our mechanism can account for the order of magnitude of Tc, as well as its trends as a function of electron density and perpendicular displacement field. Moreover, it naturally explains some of the outstanding puzzles in this material, that include the weak temperature dependence of the resistivity above Tc, and the proximity of spin singlet superconductivity to the ferromagnetic phase.","lang":"eng"}],"citation":{"ama":"Ghazaryan A, Holder T, Serbyn M, Berg E. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 2021;127(24). doi:10.1103/physrevlett.127.247001","ista":"Ghazaryan A, Holder T, Serbyn M, Berg E. 2021. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 127(24), 247001.","ieee":"A. Ghazaryan, T. Holder, M. Serbyn, and E. Berg, “Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene,” Physical Review Letters, vol. 127, no. 24. American Physical Society, 2021.","apa":"Ghazaryan, A., Holder, T., Serbyn, M., & Berg, E. (2021). Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.127.247001","mla":"Ghazaryan, Areg, et al. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical Review Letters, vol. 127, no. 24, 247001, American Physical Society, 2021, doi:10.1103/physrevlett.127.247001.","short":"A. Ghazaryan, T. Holder, M. Serbyn, E. Berg, Physical Review Letters 127 (2021).","chicago":"Ghazaryan, Areg, Tobias Holder, Maksym Serbyn, and Erez Berg. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.247001."},"publication":"Physical Review Letters","article_type":"original","date_published":"2021-12-09T00:00:00Z","scopus_import":"1","keyword":["general physics and astronomy"],"article_processing_charge":"No","day":"09","year":"2021","acknowledgement":"We thank Yang-Zhi Chou, Andrey Chubukov, Johannes Hofmann, Steve Kivelson, Sri Raghu, and Sankar das Sarma, Jay Sau, Fengcheng Wu, and Andrea Young for many stimulating discussions and for their comments on the manuscript. E.B. thanks S. Chatterjee, T. Wang, and M. Zaletel for a collaboration on a related topic. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","related_material":{"link":[{"relation":"press_release","description":"News on IST Webpage","url":"https://ist.ac.at/en/news/resolving-the-puzzles-of-graphene-superconductivity/"}]},"author":[{"full_name":"Ghazaryan, Areg","first_name":"Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543"},{"full_name":"Holder, Tobias","first_name":"Tobias","last_name":"Holder"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"},{"full_name":"Berg, Erez","first_name":"Erez","last_name":"Berg"}],"volume":127,"date_updated":"2023-08-14T13:19:13Z","date_created":"2021-12-10T07:51:33Z","article_number":"247001","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2109.00011"}],"external_id":{"arxiv":["2109.00011"],"isi":["000923819400004"]},"oa":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1103/physrevlett.127.247001","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"12"},{"issue":"45","abstract":[{"text":"For many years, fullerene derivatives have been the main n-type material of organic electronics and optoelectronics. Recently, fullerene derivatives functionalized with ethylene glycol (EG) side chains have been showing important properties such as enhanced dielectric constants, facile doping and enhanced self-assembly capabilities. Here, we have prepared field-effect transistors using a series of these fullerene derivatives equipped with EG side chains of different lengths. Transport data show the beneficial effect of increasing the EG side chain. In order to understand the material properties, full structural determination of these fullerene derivatives has been achieved by coupling the X-ray data with molecular dynamics (MD) simulations. The increase in transport properties is paired with the formation of extended layered structures, efficient molecular packing and an increase in the crystallite alignment. The layer-like structure is composed of conducting layers, containing of closely packed C60 balls approaching the inter-distance of 1 nm, that are separated by well-defined EG layers, where the EG chains are rather splayed with the chain direction almost perpendicular to the layer normal. Such a layered structure appears highly ordered and highly aligned with the C60 planes oriented parallel to the substrate in the thin film configuration. The order inside the thin film increases with the EG chain length, allowing the systems to achieve mobilities as high as 0.053 cm2 V−1 s−1. Our work elucidates the structure of these interesting semiconducting organic molecules and shows that the synergistic use of X-ray structural analysis and MD simulations is a powerful tool to identify the structure of thin organic films for optoelectronic applications.","lang":"eng"}],"type":"journal_article","file":[{"content_type":"application/pdf","file_size":4979390,"creator":"cchlebak","access_level":"open_access","file_name":"2021_JMaterChemC_Dong.pdf","checksum":"6b73c214ce54a6894a5854b4364413d7","success":1,"date_created":"2021-12-13T09:24:42Z","date_updated":"2021-12-13T09:24:42Z","relation":"main_file","file_id":"10538"}],"oa_version":"Published Version","intvolume":" 9","status":"public","ddc":["540"],"title":"Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10534","article_processing_charge":"No","has_accepted_license":"1","day":"07","scopus_import":"1","date_published":"2021-12-07T00:00:00Z","page":"16217-16225","article_type":"original","citation":{"ama":"Dong J, Sami S, Balazs D, et al. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. 2021;9(45):16217-16225. doi:10.1039/d1tc02753k","ista":"Dong J, Sami S, Balazs D, Alessandri R, Jahani F, Qiu L, Marrink SJ, Havenith RWA, Hummelen JC, Loi MA, Portale G. 2021. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. 9(45), 16217–16225.","ieee":"J. Dong et al., “Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties,” Journal of Materials Chemistry C, vol. 9, no. 45. Royal Society of Chemistry, pp. 16217–16225, 2021.","apa":"Dong, J., Sami, S., Balazs, D., Alessandri, R., Jahani, F., Qiu, L., … Portale, G. (2021). Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. Royal Society of Chemistry. https://doi.org/10.1039/d1tc02753k","mla":"Dong, Jingjin, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” Journal of Materials Chemistry C, vol. 9, no. 45, Royal Society of Chemistry, 2021, pp. 16217–25, doi:10.1039/d1tc02753k.","short":"J. Dong, S. Sami, D. Balazs, R. Alessandri, F. Jahani, L. Qiu, S.J. Marrink, R.W.A. Havenith, J.C. Hummelen, M.A. Loi, G. Portale, Journal of Materials Chemistry C 9 (2021) 16217–16225.","chicago":"Dong, Jingjin, Selim Sami, Daniel Balazs, Riccardo Alessandri, Fatimeh Jahani, Li Qiu, Siewert J. Marrink, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” Journal of Materials Chemistry C. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1tc02753k."},"publication":"Journal of Materials Chemistry C","file_date_updated":"2021-12-13T09:24:42Z","volume":9,"date_created":"2021-12-12T23:01:27Z","date_updated":"2023-08-17T06:18:44Z","author":[{"last_name":"Dong","first_name":"Jingjin","full_name":"Dong, Jingjin"},{"full_name":"Sami, Selim","first_name":"Selim","last_name":"Sami"},{"full_name":"Balazs, Daniel","first_name":"Daniel","last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X"},{"full_name":"Alessandri, Riccardo","last_name":"Alessandri","first_name":"Riccardo"},{"first_name":"Fatimeh","last_name":"Jahani","full_name":"Jahani, Fatimeh"},{"full_name":"Qiu, Li","last_name":"Qiu","first_name":"Li"},{"first_name":"Siewert J.","last_name":"Marrink","full_name":"Marrink, Siewert J."},{"first_name":"Remco W.A.","last_name":"Havenith","full_name":"Havenith, Remco W.A."},{"full_name":"Hummelen, Jan C.","last_name":"Hummelen","first_name":"Jan C."},{"first_name":"Maria A.","last_name":"Loi","full_name":"Loi, Maria A."},{"first_name":"Giuseppe","last_name":"Portale","full_name":"Portale, Giuseppe"}],"publisher":"Royal Society of Chemistry","department":[{"_id":"MaIb"}],"publication_status":"published","acknowledgement":"J. D. gratefully acknowledges the China Scholarship Council (CSC No. 201606340158) for supporting his PhD studies. S. S. thanks J. Antoja-Lleonart for insightful discussions on simulating the X-ray diffraction patterns. Part of the work was sponsored by NWO Exact and Natural Sciences for the use of supercomputer facilities (Contract no. 17197 7095). Regarding S. S., R. A., R. W. A. H., J. C. H., and M. A. L., this is a publication by the FOM Focus Group “Next Generation Organic Photovoltaics”, participating in the Dutch Institute for Fundamental Energy Research (DIFFER). The ESRF is acknowledged for providing the beamtime. J. D. and G. P. are grateful to the BM26B staff for their great support during the beamtime. M. A. L., D. M. B. are grateful for the financial support of the European Research Council via a Starting Grant (HySPOD, No. 306983).","year":"2021","publication_identifier":{"eissn":["2050-7526"],"issn":["2050-7534"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1039/d1tc02753k","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000688135700001"]}},{"oa_version":"Published Version","file":[{"file_id":"11384","relation":"main_file","date_created":"2022-05-16T10:42:22Z","date_updated":"2022-05-16T10:42:22Z","success":1,"checksum":"22ed4c55fb550f6da02ae55c359be651","file_name":"2021_eLife_Choi.pdf","access_level":"open_access","creator":"dernst","file_size":2715200,"content_type":"application/pdf"}],"_id":"10533","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin","ddc":["570"],"status":"public","intvolume":" 10","abstract":[{"lang":"eng","text":"Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin."}],"type":"journal_article","date_published":"2021-12-01T00:00:00Z","publication":"eLife","citation":{"short":"J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).","mla":"Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” ELife, vol. 10, e72676, eLife Sciences Publications, 2021, doi:10.7554/elife.72676.","chicago":"Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72676.","ama":"Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 2021;10. doi:10.7554/elife.72676","ieee":"J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Choi, J., Lyons, D. B., & Zilberman, D. (2021). Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.72676","ista":"Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676."},"article_type":"original","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","keyword":["genetics and molecular biology"],"author":[{"first_name":"Jaemyung","last_name":"Choi","full_name":"Choi, Jaemyung"},{"full_name":"Lyons, David B","first_name":"David B","last_name":"Lyons"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel"}],"date_updated":"2023-08-17T06:21:08Z","date_created":"2021-12-10T13:12:08Z","volume":10,"year":"2021","acknowledgement":"We thank X Feng for helpful comments on the manuscript. This work was supported by a European Research Council grant MaintainMeth (725746) to DZ.","pmid":1,"publication_status":"published","department":[{"_id":"DaZi"}],"publisher":"eLife Sciences Publications","file_date_updated":"2022-05-16T10:42:22Z","ec_funded":1,"article_number":"e72676","doi":"10.7554/elife.72676","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":{"pmid":["34850679"],"isi":["000754832000001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Quantitative analysis of DNA methylation maintenance with chromatin","_id":"62935a00-2b32-11ec-9570-eff30fa39068","grant_number":"725746"}],"month":"12","publication_identifier":{"issn":["2050-084X"]}},{"department":[{"_id":"DaSi"}],"publisher":"Frontiers","publication_status":"published","pmid":1,"acknowledgement":"The authors acknowledge the assistance of the Laboratory Animal Services Center (LASC) – UZH, Center for Microscopy and Image Analysis, and the Flow Cytometry Center of the University of Zurich.","year":"2021","volume":11,"date_created":"2021-12-12T23:01:27Z","date_updated":"2023-08-17T06:20:32Z","author":[{"full_name":"Stefanescu, Cristina","last_name":"Stefanescu","first_name":"Cristina"},{"first_name":"Merel","last_name":"Van Gogh","full_name":"Van Gogh, Merel"},{"full_name":"Roblek, Marko","first_name":"Marko","last_name":"Roblek","id":"3047D808-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9588-1389"},{"last_name":"Heikenwalder","first_name":"Mathias","full_name":"Heikenwalder, Mathias"},{"first_name":"Lubor","last_name":"Borsig","full_name":"Borsig, Lubor"}],"article_number":"765151","file_date_updated":"2021-12-13T13:32:37Z","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000726603400001"],"pmid":["34868988"]},"language":[{"iso":"eng"}],"doi":"10.3389/fonc.2021.765151","publication_identifier":{"eissn":["2234-943X"]},"month":"11","intvolume":" 11","status":"public","ddc":["610"],"title":"TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms","_id":"10536","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"checksum":"56cbac80e6891ce750511a30161b7792","success":1,"date_updated":"2021-12-13T13:32:37Z","date_created":"2021-12-13T13:32:37Z","relation":"main_file","file_id":"10539","content_type":"application/pdf","file_size":9245199,"creator":"alisjak","access_level":"open_access","file_name":"2021_Frontiers_Stefanescu.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"TGFβ overexpression is commonly detected in cancer patients and correlates with poor prognosis and metastasis. Cancer progression is often associated with an enhanced recruitment of myeloid-derived cells to the tumor microenvironment. Here we show that functional TGFβ-signaling in myeloid cells is required for metastasis to the lungs and the liver. Myeloid-specific deletion of Tgfbr2 resulted in reduced spontaneous lung metastasis, which was associated with a reduction of proinflammatory cytokines in the metastatic microenvironment. Notably, CD8+ T cell depletion in myeloid-specific Tgfbr2-deficient mice rescued lung metastasis. Myeloid-specific Tgfbr2-deficiency resulted in reduced liver metastasis with an almost complete absence of myeloid cells within metastatic foci. On contrary, an accumulation of Tgfβ-responsive myeloid cells was associated with an increased recruitment of monocytes and granulocytes and higher proinflammatory cytokine levels in control mice. Monocytic cells isolated from metastatic livers of Tgfbr2-deficient mice showed increased polarization towards the M1 phenotype, Tnfα and Il-1β expression, reduced levels of M2 markers and reduced production of chemokines responsible for myeloid-cell recruitment. No significant differences in Tgfβ levels were observed at metastatic sites of any model. These data demonstrate that Tgfβ signaling in monocytic myeloid cells suppresses CD8+ T cell activity during lung metastasis, while these cells actively contribute to tumor growth during liver metastasis. Thus, myeloid cells modulate metastasis through different mechanisms in a tissue-specific manner."}],"article_type":"original","citation":{"ama":"Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 2021;11. doi:10.3389/fonc.2021.765151","ista":"Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. 2021. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 11, 765151.","apa":"Stefanescu, C., Van Gogh, M., Roblek, M., Heikenwalder, M., & Borsig, L. (2021). TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. Frontiers. https://doi.org/10.3389/fonc.2021.765151","ieee":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, and L. Borsig, “TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms,” Frontiers in Oncology, vol. 11. Frontiers, 2021.","mla":"Stefanescu, Cristina, et al. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” Frontiers in Oncology, vol. 11, 765151, Frontiers, 2021, doi:10.3389/fonc.2021.765151.","short":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, L. Borsig, Frontiers in Oncology 11 (2021).","chicago":"Stefanescu, Cristina, Merel Van Gogh, Marko Roblek, Mathias Heikenwalder, and Lubor Borsig. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” Frontiers in Oncology. Frontiers, 2021. https://doi.org/10.3389/fonc.2021.765151."},"publication":"Frontiers in Oncology","date_published":"2021-11-18T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"18"},{"language":[{"iso":"eng"}],"doi":"10.1007/s00023-021-01136-y","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000725405700001"],"arxiv":["2103.08224"]},"main_file_link":[{"url":"https://arxiv.org/abs/2103.08224","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["1424-0637"]},"month":"12","date_updated":"2023-08-17T06:19:14Z","date_created":"2021-12-12T23:01:28Z","author":[{"orcid":"0000-0002-1071-6091","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","last_name":"Benedikter","first_name":"Niels P","full_name":"Benedikter, Niels P"},{"last_name":"Nam","first_name":"Phan Thành","full_name":"Nam, Phan Thành"},{"full_name":"Porta, Marcello","last_name":"Porta","first_name":"Marcello"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"publisher":"Springer Nature","department":[{"_id":"RoSe"}],"publication_status":"published","acknowledgement":"NB was supported by Gruppo Nazionale per la Fisica Matematica (GNFM). RS was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 694227). PTN was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC-2111-390814868). MP was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC StG MaMBoQ, Grant Agreement No. 802901). BS was supported by the NCCR SwissMAP, the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates,” and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program through the ERC-AdG CLaQS (Grant Agreement No. 834782).","year":"2021","ec_funded":1,"date_published":"2021-12-02T00:00:00Z","article_type":"original","citation":{"chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Bosonization of Fermionic Many-Body Dynamics.” Annales Henri Poincaré. Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01136-y.","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Annales Henri Poincaré (2021).","mla":"Benedikter, Niels P., et al. “Bosonization of Fermionic Many-Body Dynamics.” Annales Henri Poincaré, Springer Nature, 2021, doi:10.1007/s00023-021-01136-y.","ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Bosonization of fermionic many-body dynamics,” Annales Henri Poincaré. Springer Nature, 2021.","apa":"Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., & Seiringer, R. (2021). Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. Springer Nature. https://doi.org/10.1007/s00023-021-01136-y","ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2021. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré.","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. 2021. doi:10.1007/s00023-021-01136-y"},"publication":"Annales Henri Poincaré","article_processing_charge":"No","day":"02","scopus_import":"1","oa_version":"Preprint","title":"Bosonization of fermionic many-body dynamics","status":"public","_id":"10537","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"We consider the quantum many-body evolution of a homogeneous Fermi gas in three dimensions in the coupled semiclassical and mean-field scaling regime. We study a class of initial data describing collective particle–hole pair excitations on the Fermi ball. Using a rigorous version of approximate bosonization, we prove that the many-body evolution can be approximated in Fock space norm by a quasi-free bosonic evolution of the collective particle–hole excitations.","lang":"eng"}],"type":"journal_article"},{"doi":"10.1007/s00205-021-01686-9","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000668431200001"],"arxiv":["1908.02273"]},"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"month":"06","author":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L","full_name":"Fischer, Julian L"},{"last_name":"Neukamm","first_name":"Stefan","full_name":"Neukamm, Stefan"}],"volume":242,"date_updated":"2023-08-17T06:23:21Z","date_created":"2021-12-16T12:12:33Z","year":"2021","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). SN acknowledges partial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project number 405009441.","department":[{"_id":"JuFi"}],"publisher":"Springer Nature","publication_status":"published","file_date_updated":"2021-12-16T14:58:08Z","date_published":"2021-06-30T00:00:00Z","citation":{"ama":"Fischer JL, Neukamm S. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. 2021;242(1):343-452. doi:10.1007/s00205-021-01686-9","ieee":"J. L. Fischer and S. Neukamm, “Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems,” Archive for Rational Mechanics and Analysis, vol. 242, no. 1. Springer Nature, pp. 343–452, 2021.","apa":"Fischer, J. L., & Neukamm, S. (2021). Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01686-9","ista":"Fischer JL, Neukamm S. 2021. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. 242(1), 343–452.","short":"J.L. Fischer, S. Neukamm, Archive for Rational Mechanics and Analysis 242 (2021) 343–452.","mla":"Fischer, Julian L., and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” Archive for Rational Mechanics and Analysis, vol. 242, no. 1, Springer Nature, 2021, pp. 343–452, doi:10.1007/s00205-021-01686-9.","chicago":"Fischer, Julian L, and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01686-9."},"publication":"Archive for Rational Mechanics and Analysis","page":"343-452","article_type":"original","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"30","scopus_import":"1","keyword":["Mechanical Engineering","Mathematics (miscellaneous)","Analysis"],"oa_version":"Published Version","file":[{"date_updated":"2021-12-16T14:58:08Z","date_created":"2021-12-16T14:58:08Z","checksum":"cc830b739aed83ca2e32c4e0ce266a4c","success":1,"relation":"main_file","file_id":"10558","content_type":"application/pdf","file_size":1640121,"creator":"cchlebak","file_name":"2021_ArchRatMechAnalysis_Fischer.pdf","access_level":"open_access"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10549","intvolume":" 242","title":"Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems","ddc":["530"],"status":"public","issue":"1","abstract":[{"text":"We derive optimal-order homogenization rates for random nonlinear elliptic PDEs with monotone nonlinearity in the uniformly elliptic case. More precisely, for a random monotone operator on \\mathbb {R}^d with stationary law (that is spatially homogeneous statistics) and fast decay of correlations on scales larger than the microscale \\varepsilon >0, we establish homogenization error estimates of the order \\varepsilon in case d\\geqq 3, and of the order \\varepsilon |\\log \\varepsilon |^{1/2} in case d=2. Previous results in nonlinear stochastic homogenization have been limited to a small algebraic rate of convergence \\varepsilon ^\\delta . We also establish error estimates for the approximation of the homogenized operator by the method of representative volumes of the order (L/\\varepsilon )^{-d/2} for a representative volume of size L. Our results also hold in the case of systems for which a (small-scale) C^{1,\\alpha } regularity theory is available.","lang":"eng"}],"type":"journal_article"},{"date_published":"2021-11-04T00:00:00Z","citation":{"short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, 19th International Conference, Springer Nature, 2021, pp. 486–517.","mla":"Kamath Hosdurg, Chethan, et al. “On Treewidth, Separators and Yao’s Garbling.” 19th International Conference, vol. 13043, Springer Nature, 2021, pp. 486–517, doi:10.1007/978-3-030-90453-1_17.","chicago":"Kamath Hosdurg, Chethan, Karen Klein, and Krzysztof Z Pietrzak. “On Treewidth, Separators and Yao’s Garbling.” In 19th International Conference, 13043:486–517. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_17.","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ. On treewidth, separators and Yao’s garbling. In: 19th International Conference. Vol 13043. Springer Nature; 2021:486-517. doi:10.1007/978-3-030-90453-1_17","ieee":"C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “On treewidth, separators and Yao’s garbling,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 486–517.","apa":"Kamath Hosdurg, C., Klein, K., & Pietrzak, K. Z. (2021). On treewidth, separators and Yao’s garbling. In 19th International Conference (Vol. 13043, pp. 486–517). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_17","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ. 2021. On treewidth, separators and Yao’s garbling. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13043, 486–517."},"publication":"19th International Conference","page":"486-517","article_processing_charge":"No","day":"04","scopus_import":"1","oa_version":"Preprint","_id":"10409","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"On treewidth, separators and Yao’s garbling","abstract":[{"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 SO(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(δwlog(S)) , δ being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity. with only a SO(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(δwlog(S)) , δ being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"doi":"10.1007/978-3-030-90453-1_17","conference":{"end_date":"2021-11-11","start_date":"2021-11-08","location":"Raleigh, NC, United States","name":"TCC: Theory of Cryptography"},"language":[{"iso":"eng"}],"external_id":{"isi":["000728364000017"]},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/926"}],"oa":1,"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0302-9743"],"isbn":["9-783-0309-0452-4"],"eissn":["1611-3349"]},"month":"11","related_material":{"record":[{"id":"10044","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg"},{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","first_name":"Karen"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"volume":"13043 ","date_created":"2021-12-05T23:01:43Z","date_updated":"2023-08-17T06:21:38Z","year":"2021","acknowledgement":"We are grateful to Daniel Wichs for helpful discussions on the landscape of adaptive security of Yao’s garbling. We would also like to thank Crypto 2021 and TCC 2021 reviewers for their detailed review and suggestions, which helped improve presentation considerably.","department":[{"_id":"KrPi"}],"publisher":"Springer Nature","publication_status":"published","ec_funded":1},{"article_processing_charge":"No","day":"14","date_published":"2021-12-14T00:00:00Z","article_type":"original","citation":{"ama":"Medina Ramos RA, Serbyn M. Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. 2021;104(6). doi:10.1103/physreva.104.062423","ista":"Medina Ramos RA, Serbyn M. 2021. Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. 104(6), 062423.","ieee":"R. A. Medina Ramos and M. Serbyn, “Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT),” Physical Review A, vol. 104, no. 6. American Physical Society, 2021.","apa":"Medina Ramos, R. A., & Serbyn, M. (2021). Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.104.062423","mla":"Medina Ramos, Raimel A., and Maksym Serbyn. “Duality Approach to Quantum Annealing of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” Physical Review A, vol. 104, no. 6, 062423, American Physical Society, 2021, doi:10.1103/physreva.104.062423.","short":"R.A. Medina Ramos, M. Serbyn, Physical Review A 104 (2021).","chicago":"Medina Ramos, Raimel A, and Maksym Serbyn. “Duality Approach to Quantum Annealing of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/physreva.104.062423."},"publication":"Physical Review A","issue":"6","abstract":[{"lang":"eng","text":"Classical models with complex energy landscapes represent a perspective avenue for the near-term application of quantum simulators. Until now, many theoretical works studied the performance of quantum algorithms for models with a unique ground state. However, when the classical problem is in a so-called clustering phase, the ground state manifold is highly degenerate. As an example, we consider a 3-XORSAT model defined on simple hypergraphs. The degeneracy of classical ground state manifold translates into the emergence of an extensive number of Z2 symmetries, which remain intact even in the presence of a quantum transverse magnetic field. We establish a general duality approach that restricts the quantum problem to a given sector of conserved Z2 charges and use it to study how the outcome of the quantum adiabatic algorithm depends on the hypergraph geometry. We show that the tree hypergraph which corresponds to a classically solvable instance of the 3-XORSAT problem features a constant gap, whereas the closed hypergraph encounters a second-order phase transition with a gap vanishing as a power-law in the problem size. The duality developed in this work provides a practical tool for studies of quantum models with classically degenerate energy manifold and reveals potential connections between glasses and gauge theories."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 104","status":"public","title":"Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT)","_id":"10545","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1103/physreva.104.062423","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["2106.06344"],"isi":["000753659200004"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2106.06344"}],"ec_funded":1,"article_number":"062423","volume":104,"date_created":"2021-12-14T20:46:07Z","date_updated":"2023-08-17T06:22:49Z","author":[{"first_name":"Raimel A","last_name":"Medina Ramos","id":"CE680B90-D85A-11E9-B684-C920E6697425","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A"},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"}],"publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","year":"2021","acknowledgement":"We would like to thank S. De Nicola, A. Michaidilis, T. Gulden, Y. Nez-Fernndez, P. Brighi, and S. Sack for fruitful discussions and valuable feedback on the manuscript. M.S. acknowledges useful discussions with E. Altman, L. Cugliandolo, and C. Laumann. We acknowledge support from the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreement No. 850899."},{"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2102.08325","open_access":"1"}],"external_id":{"arxiv":["2102.08325"],"isi":["000744439800016"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"PODC: Principles of Distributed Computing","start_date":"2021-07-26","location":"Virtual, Italy","end_date":"2021-07-30"},"doi":"10.1145/3465084.3467905","month":"07","publication_identifier":{"isbn":["978-1-4503-8548-0"]},"publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"ElKo"}],"acknowledgement":"Oded Naor is grateful to the Technion Hiroshi Fujiwara Cyber-Security Research Center for providing a research grant. Part of Oded’s work was done while at Novi Research. This work was funded by the Novi team at Facebook. We also wish to thank the Novi Research team for valuable feedback, and in particular George Danezis, Alberto Sonnino, and Dahlia Malkhi.\r\n","year":"2021","date_updated":"2023-08-17T06:24:44Z","date_created":"2021-12-16T13:21:13Z","author":[{"first_name":"Idit","last_name":"Keidar","full_name":"Keidar, Idit"},{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"full_name":"Naor, Oded","first_name":"Oded","last_name":"Naor"},{"full_name":"Spiegelman, Alexander","last_name":"Spiegelman","first_name":"Alexander"}],"page":"165-175","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","citation":{"short":"I. Keidar, E. Kokoris Kogias, O. Naor, A. Spiegelman, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 165–175.","mla":"Keidar, Idit, et al. “All You Need Is DAG.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 165–75, doi:10.1145/3465084.3467905.","chicago":"Keidar, Idit, Eleftherios Kokoris Kogias, Oded Naor, and Alexander Spiegelman. “All You Need Is DAG.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 165–75. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467905.","ama":"Keidar I, Kokoris Kogias E, Naor O, Spiegelman A. All You Need is DAG. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:165-175. doi:10.1145/3465084.3467905","apa":"Keidar, I., Kokoris Kogias, E., Naor, O., & Spiegelman, A. (2021). All You Need is DAG. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 165–175). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467905","ieee":"I. Keidar, E. Kokoris Kogias, O. Naor, and A. Spiegelman, “All You Need is DAG,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 165–175.","ista":"Keidar I, Kokoris Kogias E, Naor O, Spiegelman A. 2021. All You Need is DAG. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 165–175."},"date_published":"2021-07-21T00:00:00Z","scopus_import":"1","day":"21","article_processing_charge":"No","title":"All You Need is DAG","status":"public","_id":"10554","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"We present DAG-Rider, the first asynchronous Byzantine Atomic Broadcast protocol that achieves optimal resilience, optimal amortized communication complexity, and optimal time complexity. DAG-Rider is post-quantum safe and ensures that all values proposed by correct processes eventually get delivered. We construct DAG-Rider in two layers: In the first layer, processes reliably broadcast their proposals and build a structured Directed Acyclic Graph (DAG) of the communication among them. In the second layer, processes locally observe their DAGs and totally order all proposals with no extra communication."}]}]