[{"year":"2021","publication":"Nature","date_updated":"2023-08-14T08:01:21Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/boosting-the-cells-power-house/","description":"News on IST Webpage","relation":"press_release"}]},"page":"364-367","article_type":"original","department":[{"_id":"LeSa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-10-14T00:00:00Z","external_id":{"pmid":["34616041"],"isi":["000704581600001"]},"date_created":"2021-10-17T22:01:17Z","scopus_import":"1","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"publisher":"Springer Nature","intvolume":"       598","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","title":"Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV","author":[{"last_name":"Vercellino","full_name":"Vercellino, Irene","first_name":"Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5618-3449"},{"orcid":"0000-0002-0977-7989","last_name":"Sazanov","full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"_id":"10146","abstract":[{"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.","lang":"eng"}],"issue":"7880","doi":"10.1038/s41586-021-03927-z","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"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.","publication_status":"published","status":"public","ec_funded":1,"citation":{"chicago":"Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII<sub>2</sub>CIV.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-021-03927-z\">https://doi.org/10.1038/s41586-021-03927-z</a>.","mla":"Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII<sub>2</sub>CIV.” <i>Nature</i>, vol. 598, no. 7880, Springer Nature, 2021, pp. 364–67, doi:<a href=\"https://doi.org/10.1038/s41586-021-03927-z\">10.1038/s41586-021-03927-z</a>.","ieee":"I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV,” <i>Nature</i>, vol. 598, no. 7880. Springer Nature, pp. 364–367, 2021.","apa":"Vercellino, I., &#38; Sazanov, L. A. (2021). Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-021-03927-z\">https://doi.org/10.1038/s41586-021-03927-z</a>","ama":"Vercellino I, Sazanov LA. Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV. <i>Nature</i>. 2021;598(7880):364-367. doi:<a href=\"https://doi.org/10.1038/s41586-021-03927-z\">10.1038/s41586-021-03927-z</a>","short":"I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367.","ista":"Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV. Nature. 598(7880), 364–367."},"day":"14","month":"10","pmid":1,"oa_version":"None","article_processing_charge":"No","volume":598},{"_id":"10148","title":"Capturing tactile properties of real surfaces for haptic reproduction","author":[{"full_name":"Degraen, Donald","last_name":"Degraen","first_name":"Donald"},{"last_name":"Piovarci","full_name":"Piovarci, Michael","first_name":"Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"},{"full_name":"Kruger, Antonio","last_name":"Kruger","first_name":"Antonio"}],"doi":"10.1145/3472749.3474798","abstract":[{"lang":"eng","text":"Tactile feedback of an object’s surface enables us to discern its material properties and affordances. This understanding is used in digital fabrication processes by creating objects with high-resolution surface variations to influence a user’s tactile perception. As the design of such surface haptics commonly relies on knowledge from real-life experiences, it is unclear how to adapt this information for digital design methods. In this work, we investigate replicating the haptics of real materials. Using an existing process for capturing an object’s microgeometry, we digitize and reproduce the stable surface information of a set of 15 fabric samples. In a psychophysical experiment, we evaluate the tactile qualities of our set of original samples and their replicas. From our results, we see that direct reproduction of surface variations is able to influence different psychophysical dimensions of the tactile perception of surface textures. While the fabrication process did not preserve all properties, our approach underlines that replication of surface microgeometries benefits fabrication methods in terms of haptic perception by covering a large range of tactile variations. Moreover, by changing the surface structure of a single fabricated material, its material perception can be influenced. We conclude by proposing strategies for capturing and reproducing digitized textures to better resemble the perceived haptics of the originals."}],"project":[{"grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Distributed 3D Object Design"}],"publication_identifier":{"isbn":["978-1-4503-8635-7"]},"ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"Our gratitude goes out to Kamila Mushkina, Akhmajon Makhsadov, Jordan Espenshade, Bruno Fruchard, Roland Bennewitz, and Robert Drumm. This project has received funding from the EU’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO).","ddc":["000"],"file_date_updated":"2021-10-18T07:36:03Z","month":"10","citation":{"chicago":"Degraen, Donald, Michael Piovarci, Bernd Bickel, and Antonio Kruger. “Capturing Tactile Properties of Real Surfaces for Haptic Reproduction.” In <i>34th Annual ACM Symposium</i>, 954–71. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3472749.3474798\">https://doi.org/10.1145/3472749.3474798</a>.","mla":"Degraen, Donald, et al. “Capturing Tactile Properties of Real Surfaces for Haptic Reproduction.” <i>34th Annual ACM Symposium</i>, Association for Computing Machinery, 2021, pp. 954–71, doi:<a href=\"https://doi.org/10.1145/3472749.3474798\">10.1145/3472749.3474798</a>.","apa":"Degraen, D., Piovarci, M., Bickel, B., &#38; Kruger, A. (2021). Capturing tactile properties of real surfaces for haptic reproduction. In <i>34th Annual ACM Symposium</i> (pp. 954–971). Virtual: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3472749.3474798\">https://doi.org/10.1145/3472749.3474798</a>","ieee":"D. Degraen, M. Piovarci, B. Bickel, and A. Kruger, “Capturing tactile properties of real surfaces for haptic reproduction,” in <i>34th Annual ACM Symposium</i>, Virtual, 2021, pp. 954–971.","short":"D. Degraen, M. Piovarci, B. Bickel, A. Kruger, in:, 34th Annual ACM Symposium, Association for Computing Machinery, 2021, pp. 954–971.","ama":"Degraen D, Piovarci M, Bickel B, Kruger A. Capturing tactile properties of real surfaces for haptic reproduction. In: <i>34th Annual ACM Symposium</i>. Association for Computing Machinery; 2021:954-971. doi:<a href=\"https://doi.org/10.1145/3472749.3474798\">10.1145/3472749.3474798</a>","ista":"Degraen D, Piovarci M, Bickel B, Kruger A. 2021. Capturing tactile properties of real surfaces for haptic reproduction. 34th Annual ACM Symposium. UIST: User Interface Software and Technology, 954–971."},"day":"10","oa_version":"Preprint","conference":{"name":"UIST: User Interface Software and Technology","end_date":"2021-10-14","start_date":"2021-10-10","location":"Virtual"},"file":[{"date_updated":"2021-10-18T07:36:03Z","content_type":"application/pdf","checksum":"b0b26464df79b3a59e8ed82e4e19ab15","access_level":"open_access","relation":"main_file","file_size":29796364,"creator":"bbickel","file_name":"degraen-UIST2021_Texture_Appropriation_CR_preprint.pdf","date_created":"2021-10-18T07:36:03Z","file_id":"10149"}],"article_processing_charge":"No","has_accepted_license":"1","oa":1,"year":"2021","date_updated":"2021-10-19T19:29:06Z","publication":"34th Annual ACM Symposium","page":"954-971","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"BeBi"}],"date_created":"2021-10-18T07:36:11Z","date_published":"2021-10-10T00:00:00Z","publisher":"Association for Computing Machinery","language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1"},{"intvolume":"         5","publisher":"Association for Computing Machinery","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","department":[{"_id":"ToHe"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2021-10-15T00:00:00Z","date_created":"2021-10-19T12:48:44Z","publication":"Proceedings of the ACM on Programming Languages","date_updated":"2021-11-12T11:30:07Z","article_type":"original","article_number":"127","oa":1,"year":"2021","keyword":["gradual typing","gradual guarantee","nominal","structural","call tags"],"tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"file":[{"creator":"fmuehlbo","file_size":770269,"relation":"main_file","file_name":"monnom-oopsla21.pdf","date_updated":"2021-10-19T12:52:23Z","success":1,"content_type":"application/pdf","checksum":"71011efd2da771cafdec7f0d9693f8c1","access_level":"open_access","date_created":"2021-10-19T12:52:23Z","file_id":"10154"}],"has_accepted_license":"1","article_processing_charge":"No","volume":5,"day":"15","citation":{"chicago":"Mühlböck, Fabian, and Ross Tate. “Transitioning from Structural to Nominal Code with Efficient Gradual Typing.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3485504\">https://doi.org/10.1145/3485504</a>.","mla":"Mühlböck, Fabian, and Ross Tate. “Transitioning from Structural to Nominal Code with Efficient Gradual Typing.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 5, 127, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3485504\">10.1145/3485504</a>.","ieee":"F. Mühlböck and R. Tate, “Transitioning from structural to nominal code with efficient gradual typing,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 5. Association for Computing Machinery, 2021.","apa":"Mühlböck, F., &#38; Tate, R. (2021). Transitioning from structural to nominal code with efficient gradual typing. <i>Proceedings of the ACM on Programming Languages</i>. Chicago, IL, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3485504\">https://doi.org/10.1145/3485504</a>","short":"F. Mühlböck, R. Tate, Proceedings of the ACM on Programming Languages 5 (2021).","ama":"Mühlböck F, Tate R. Transitioning from structural to nominal code with efficient gradual typing. <i>Proceedings of the ACM on Programming Languages</i>. 2021;5. doi:<a href=\"https://doi.org/10.1145/3485504\">10.1145/3485504</a>","ista":"Mühlböck F, Tate R. 2021. Transitioning from structural to nominal code with efficient gradual typing. Proceedings of the ACM on Programming Languages. 5, 127."},"file_date_updated":"2021-10-19T12:52:23Z","ddc":["005"],"month":"10","license":"https://creativecommons.org/licenses/by-nd/4.0/","conference":{"name":"OOPSLA: Object-Oriented Programming, Systems, Languages, and Applications","start_date":"2021-10-17","location":"Chicago, IL, United States","end_date":"2021-10-23"},"oa_version":"Published Version","publication_identifier":{"eissn":["2475-1421"]},"project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"We thank the reviewers for their valuable suggestions towards improving the paper. We also \r\nthank Mae Milano and Adrian Sampson, as well as the members of the Programming Languages Discussion Group at Cornell University and of the Programming Research Laboratory at Northeastern University, for their helpful feedback on preliminary findings of this work.\r\n\r\nThis material is based upon work supported in part by the National Science Foundation (NSF) through grant CCF-1350182 and the Austrian Science Fund (FWF) through grant Z211-N23 (Wittgenstein~Award).\r\nAny opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the NSF or the FWF.","publication_status":"published","status":"public","author":[{"first_name":"Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck","full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177"},{"first_name":"Ross","full_name":"Tate, Ross","last_name":"Tate"}],"title":"Transitioning from structural to nominal code with efficient gradual typing","_id":"10153","abstract":[{"text":"Gradual typing is a principled means for mixing typed and untyped code. But typed and untyped code often exhibit different programming patterns. There is already substantial research investigating gradually giving types to code exhibiting typical untyped patterns, and some research investigating gradually removing types from code exhibiting typical typed patterns. This paper investigates how to extend these established gradual-typing concepts to give formal guarantees not only about how to change types as code evolves but also about how to change such programming patterns as well.\r\n\r\nIn particular, we explore mixing untyped \"structural\" code with typed \"nominal\" code in an object-oriented language. But whereas previous work only allowed \"nominal\" objects to be treated as \"structural\" objects, we also allow \"structural\" objects to dynamically acquire certain nominal types, namely interfaces. We present a calculus that supports such \"cross-paradigm\" code migration and interoperation in a manner satisfying both the static and dynamic gradual guarantees, and demonstrate that the calculus can be implemented efficiently.","lang":"eng"}],"doi":"10.1145/3485504"},{"license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","citation":{"ieee":"L.-M. Appel <i>et al.</i>, “PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26360-2\">https://doi.org/10.1038/s41467-021-26360-2</a>","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).","ama":"Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-26360-2\">10.1038/s41467-021-26360-2</a>","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.","mla":"Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” <i>Nature Communications</i>, vol. 12, no. 1, 6078, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26360-2\">10.1038/s41467-021-26360-2</a>.","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.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26360-2\">https://doi.org/10.1038/s41467-021-26360-2</a>."},"day":"19","month":"10","file_date_updated":"2021-10-21T13:51:49Z","ddc":["610"],"has_accepted_license":"1","volume":12,"article_processing_charge":"No","file":[{"date_created":"2021-10-21T13:51:49Z","file_id":"10169","creator":"cchlebak","file_size":5111706,"relation":"main_file","file_name":"2021_NatComm_Appel.pdf","date_updated":"2021-10-21T13:51:49Z","success":1,"checksum":"d99fcd51aebde19c21314e3de0148007","content_type":"application/pdf","access_level":"open_access"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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"}],"issue":"1","doi":"10.1038/s41467-021-26360-2","title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","author":[{"last_name":"Appel","full_name":"Appel, Lisa-Marie","first_name":"Lisa-Marie"},{"first_name":"Vedran","last_name":"Franke","full_name":"Franke, Vedran"},{"first_name":"Melania","last_name":"Bruno","full_name":"Bruno, Melania"},{"full_name":"Grishkovskaya, Irina","last_name":"Grishkovskaya","first_name":"Irina"},{"full_name":"Kasiliauskaite, Aiste","last_name":"Kasiliauskaite","first_name":"Aiste"},{"last_name":"Kaufmann","full_name":"Kaufmann, Tanja","first_name":"Tanja"},{"first_name":"Ursula E.","last_name":"Schoeberl","full_name":"Schoeberl, Ursula E."},{"first_name":"Martin G.","last_name":"Puchinger","full_name":"Puchinger, Martin G."},{"first_name":"Sebastian","last_name":"Kostrhon","full_name":"Kostrhon, Sebastian"},{"last_name":"Ebenwaldner","full_name":"Ebenwaldner, Carmen","first_name":"Carmen"},{"first_name":"Marek","full_name":"Sebesta, Marek","last_name":"Sebesta"},{"last_name":"Beltzung","full_name":"Beltzung, Etienne","first_name":"Etienne"},{"full_name":"Mechtler, Karl","last_name":"Mechtler","first_name":"Karl"},{"first_name":"Gen","full_name":"Lin, Gen","last_name":"Lin"},{"first_name":"Anna","last_name":"Vlasova","full_name":"Vlasova, Anna"},{"first_name":"Martin","full_name":"Leeb, Martin","last_name":"Leeb"},{"full_name":"Pavri, Rushad","last_name":"Pavri","first_name":"Rushad"},{"first_name":"Alexander","last_name":"Stark","full_name":"Stark, Alexander"},{"first_name":"Altuna","last_name":"Akalin","full_name":"Akalin, Altuna"},{"full_name":"Stefl, Richard","last_name":"Stefl","first_name":"Richard"},{"orcid":"0000-0003-0893-7036","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","full_name":"Bernecky, Carrie A"},{"first_name":"Kristina","last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina"},{"last_name":"Slade","full_name":"Slade, Dea","first_name":"Dea"}],"_id":"10163","publication_status":"published","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.","status":"public","publication_identifier":{"eissn":["2041-1723"]},"date_published":"2021-10-19T00:00:00Z","external_id":{"isi":["000709050300001"]},"date_created":"2021-10-20T14:40:32Z","department":[{"_id":"CaBe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Springer Nature","intvolume":"        12","year":"2021","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"oa":1,"related_material":{"link":[{"relation":"earlier_version","url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159","description":"Preprint "}]},"article_number":"6078","article_type":"original","publication":"Nature Communications","date_updated":"2023-08-14T08:02:31Z"},{"ec_funded":1,"acknowledgement":"We thank the Vicoso laboratory, Thomas Lenormand and Tanja Schwander for helpful discussions, the group of Gonzalo Gajardo, especially Cristian Gallardo-Escárate and Margarita Parraguez Donoso, for sequencing data and advice, and the IST Scientific Computing Group for their support. This work was supported by the European Research Council under the European Union's Horizon 2020 research and innovation program (grant agreement no. 715257).","publication_status":"published","status":"public","project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["1471-2954"],"issn":["0962-8452"]},"doi":"10.1098/rspb.2021.1720","abstract":[{"lang":"eng","text":"While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations."}],"issue":"1959","_id":"10166","title":"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp","author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","full_name":"Huylmans, Ann K","last_name":"Huylmans","orcid":"0000-0001-8871-4961"},{"last_name":"Macon","full_name":"Macon, Ariana","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hontoria, Francisco","last_name":"Hontoria","first_name":"Francisco"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"volume":288,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"76e7f253b7040bca2ad76f82bd7c45c0","success":1,"date_updated":"2021-10-22T11:48:02Z","file_name":"2021_ProRoSocBBioSci_Huylmans.pdf","file_size":995806,"creator":"cchlebak","relation":"main_file","file_id":"10172","date_created":"2021-10-22T11:48:02Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","month":"09","file_date_updated":"2021-10-22T11:48:02Z","ddc":["595"],"pmid":1,"citation":{"short":"A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 288 (2021).","ista":"Huylmans AK, Macon A, Hontoria F, Vicoso B. 2021. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. 288(1959), 20211720.","ama":"Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2021;288(1959). doi:<a href=\"https://doi.org/10.1098/rspb.2021.1720\">10.1098/rspb.2021.1720</a>","apa":"Huylmans, A. K., Macon, A., Hontoria, F., &#38; Vicoso, B. (2021). Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1720\">https://doi.org/10.1098/rspb.2021.1720</a>","ieee":"A. K. Huylmans, A. Macon, F. Hontoria, and B. Vicoso, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 288, no. 1959. The Royal Society, 2021.","chicago":"Huylmans, Ann K, Ariana Macon, Francisco Hontoria, and Beatriz Vicoso. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2021. <a href=\"https://doi.org/10.1098/rspb.2021.1720\">https://doi.org/10.1098/rspb.2021.1720</a>.","mla":"Huylmans, Ann K., et al. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 288, no. 1959, 20211720, The Royal Society, 2021, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1720\">10.1098/rspb.2021.1720</a>."},"day":"22","article_number":"20211720","article_type":"original","related_material":{"link":[{"relation":"supplementary_material","url":"https://doi.org/10.6084/m9.figshare.c.5615488.v1"}],"record":[{"relation":"research_data","status":"public","id":"9949"}]},"date_updated":"2024-02-21T12:40:29Z","publication":"Proceedings of the Royal Society B: Biological Sciences","keyword":["asexual reproduction","parthenogenesis","sex-biased genes","sexual conflict","automixis","crustaceans"],"year":"2021","oa":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"publisher":"The Royal Society","intvolume":"       288","date_created":"2021-10-21T07:46:06Z","acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","date_published":"2021-09-22T00:00:00Z","external_id":{"pmid":["34547909"],"isi":["000697643700001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BeVi"}]},{"article_type":"original","publication":"Molecular Biology and Evolution","date_updated":"2023-08-14T08:03:06Z","year":"2021","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"oa":1,"isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Oxford University Press ","date_published":"2021-06-19T00:00:00Z","external_id":{"pmid":["34146097"],"isi":["000741368600009"]},"date_created":"2021-10-21T07:49:12Z","scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"department":[{"_id":"BeVi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","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.","status":"public","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","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."}],"doi":"10.1093/molbev/msab178","title":"Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","author":[{"orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi"},{"orcid":"0000-0002-8876-6494","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","first_name":"Mikhail A.","full_name":"Moldovan, Mikhail A.","last_name":"Moldovan"},{"orcid":"0000-0002-8101-2518","last_name":"Picard","full_name":"Picard, Marion A L","first_name":"Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"_id":"10167","has_accepted_license":"1","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","relation":"main_file","file_size":1008594,"creator":"dernst","success":1,"date_updated":"2022-05-06T09:47:18Z","access_level":"open_access","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","content_type":"application/pdf","file_id":"11352","date_created":"2022-05-06T09:47:18Z"}],"oa_version":"Published Version","citation":{"mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, Oxford University Press , 2021, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>.","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.” <i>Molecular Biology and Evolution</i>. Oxford University Press , 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>.","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,” <i>Molecular Biology and Evolution</i>. Oxford University Press , 2021.","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press . <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution (2021).","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. <i>Molecular Biology and Evolution</i>. 2021. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>","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."},"day":"19","month":"06","file_date_updated":"2022-05-06T09:47:18Z","ddc":["610"],"pmid":1},{"year":"2021","abstract":[{"lang":"eng","text":"Quantitative stochastic homogenization of linear elliptic operators is by now well-understood. In this contribution we move forward to the nonlinear setting of monotone operators with p-growth. This first work is dedicated to a quantitative two-scale expansion result. Fluctuations will be addressed in companion articles. By treating the range of exponents 2≤p<∞ in dimensions d≤3, we are able to consider genuinely nonlinear elliptic equations and systems such as −∇⋅A(x)(1+|∇u|p−2)∇u=f (with A random, non-necessarily symmetric) for the first time. When going from p=2 to p>2, the main difficulty is to analyze the associated linearized operator, whose coefficients are degenerate, unbounded, and depend on the random input A via the solution of a nonlinear equation. One of our main achievements is the control of this intricate nonlinear dependence, leading to annealed Meyers' estimates for the linearized operator, which are key to the quantitative two-scale expansion result."}],"_id":"10174","author":[{"full_name":"Clozeau, Nicolas","last_name":"Clozeau","id":"fea1b376-906f-11eb-847d-b2c0cf46455b","first_name":"Nicolas"},{"first_name":"Antoine","full_name":"Gloria, Antoine","last_name":"Gloria"}],"title":"Quantitative nonlinear homogenization: control of oscillations","oa":1,"article_number":"2104.04263","publication_status":"submitted","acknowledgement":"The authors warmly thank Mitia Duerinckx for discussions on annealed estimates, and Mathias Schäffner for pointing out that the conditions of [14] apply to  ̄a in the setting of Theorem 2.2 and for discussions on regularity theory for operators with non-standard growth conditions. The authors received financial support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement n◦ 864066).","status":"public","date_updated":"2021-10-28T15:44:05Z","publication":"arXiv","date_created":"2021-10-23T10:50:55Z","oa_version":"Preprint","date_published":"2021-04-09T00:00:00Z","external_id":{"arxiv":["2104.04263"]},"month":"04","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","day":"09","department":[{"_id":"JuFi"}],"citation":{"mla":"Clozeau, Nicolas, and Antoine Gloria. “Quantitative Nonlinear Homogenization: Control of Oscillations.” <i>ArXiv</i>, 2104.04263.","chicago":"Clozeau, Nicolas, and Antoine Gloria. “Quantitative Nonlinear Homogenization: Control of Oscillations.” <i>ArXiv</i>, n.d.","ieee":"N. Clozeau and A. Gloria, “Quantitative nonlinear homogenization: control of oscillations,” <i>arXiv</i>. .","apa":"Clozeau, N., &#38; Gloria, A. (n.d.). Quantitative nonlinear homogenization: control of oscillations. <i>arXiv</i>.","short":"N. Clozeau, A. Gloria, ArXiv (n.d.).","ama":"Clozeau N, Gloria A. Quantitative nonlinear homogenization: control of oscillations. <i>arXiv</i>.","ista":"Clozeau N, Gloria A. Quantitative nonlinear homogenization: control of oscillations. arXiv, 2104.04263."},"type":"preprint","language":[{"iso":"eng"}],"article_processing_charge":"No","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.04263"}]},{"_id":"10176","title":"Topological field theory on r-spin surfaces and the Arf-invariant","author":[{"first_name":"Ingo","full_name":"Runkel, Ingo","last_name":"Runkel"},{"orcid":"0000-0003-2834-5054","last_name":"Szegedy","full_name":"Szegedy, Lorant","first_name":"Lorant","id":"7943226E-220E-11EA-94C7-D59F3DDC885E"}],"doi":"10.1063/5.0037826","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","publication_identifier":{"issn":["00222488"]},"publication_status":"published","status":"public","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.”","month":"10","citation":{"mla":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” <i>Journal of Mathematical Physics</i>, vol. 62, no. 10, 102302, AIP Publishing, 2021, doi:<a href=\"https://doi.org/10.1063/5.0037826\">10.1063/5.0037826</a>.","chicago":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2021. <a href=\"https://doi.org/10.1063/5.0037826\">https://doi.org/10.1063/5.0037826</a>.","ama":"Runkel I, Szegedy L. Topological field theory on r-spin surfaces and the Arf-invariant. <i>Journal of Mathematical Physics</i>. 2021;62(10). doi:<a href=\"https://doi.org/10.1063/5.0037826\">10.1063/5.0037826</a>","short":"I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021).","ista":"Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302.","apa":"Runkel, I., &#38; Szegedy, L. (2021). Topological field theory on r-spin surfaces and the Arf-invariant. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0037826\">https://doi.org/10.1063/5.0037826</a>","ieee":"I. Runkel and L. Szegedy, “Topological field theory on r-spin surfaces and the Arf-invariant,” <i>Journal of Mathematical Physics</i>, vol. 62, no. 10. AIP Publishing, 2021."},"day":"01","oa_version":"Preprint","arxiv":1,"volume":62,"article_processing_charge":"No","oa":1,"year":"2021","date_updated":"2023-08-14T08:04:12Z","publication":"Journal of Mathematical Physics","article_number":"102302","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MiLe"}],"date_created":"2021-10-24T22:01:32Z","scopus_import":"1","external_id":{"isi":["000755638500010"],"arxiv":["1802.09978"]},"date_published":"2021-10-01T00:00:00Z","publisher":"AIP Publishing","intvolume":"        62","main_file_link":[{"url":"https://arxiv.org/abs/1802.09978","open_access":"1"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1},{"year":"2021","oa":1,"article_number":"abj0127","article_type":"original","date_updated":"2023-08-14T08:04:42Z","publication":"Science Advances","date_created":"2021-10-24T22:01:33Z","scopus_import":"1","external_id":{"arxiv":["2103.10852"],"isi":["000704912700024"]},"date_published":"2021-10-08T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"NanoFab"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"publisher":"American Association for the Advancement of Science","intvolume":"         7","doi":"10.1126/sciadv.abj0127","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","_id":"10177","title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","author":[{"first_name":"Javier","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, Javier"},{"last_name":"Duan","full_name":"Duan, Jiahua","first_name":"Jiahua"},{"last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, Javier","first_name":"Javier"},{"full_name":"Álvarez-Pérez, Gonzalo","last_name":"Álvarez-Pérez","first_name":"Gonzalo"},{"first_name":"Kirill V.","full_name":"Voronin, Kirill V.","last_name":"Voronin"},{"full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan","orcid":"0000-0002-7370-5357"},{"last_name":"Ma","full_name":"Ma, Weiliang","first_name":"Weiliang"},{"first_name":"Qiaoliang","last_name":"Bao","full_name":"Bao, Qiaoliang"},{"last_name":"Volkov","full_name":"Volkov, Valentyn S.","first_name":"Valentyn S."},{"first_name":"Rainer","full_name":"Hillenbrand, Rainer","last_name":"Hillenbrand"},{"first_name":"Alexey Y.","last_name":"Nikitin","full_name":"Nikitin, Alexey Y."},{"first_name":"Pablo","full_name":"Alonso-González, Pablo","last_name":"Alonso-González"}],"publication_status":"published","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).","status":"public","publication_identifier":{"eissn":["23752548"]},"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc/4.0/","ddc":["530"],"month":"10","file_date_updated":"2021-10-27T14:16:06Z","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.” <i>Science Advances</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/sciadv.abj0127\">https://doi.org/10.1126/sciadv.abj0127</a>.","mla":"Martín-Sánchez, Javier, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” <i>Science Advances</i>, vol. 7, no. 41, abj0127, American Association for the Advancement of Science, 2021, doi:<a href=\"https://doi.org/10.1126/sciadv.abj0127\">10.1126/sciadv.abj0127</a>.","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. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.abj0127\">https://doi.org/10.1126/sciadv.abj0127</a>","ieee":"J. Martín-Sánchez <i>et al.</i>, “Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas,” <i>Science Advances</i>, vol. 7, no. 41. American Association for the Advancement of Science, 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.","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. <i>Science Advances</i>. 2021;7(41). doi:<a href=\"https://doi.org/10.1126/sciadv.abj0127\">10.1126/sciadv.abj0127</a>","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)."},"day":"08","article_processing_charge":"Yes","volume":7,"has_accepted_license":"1","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file":[{"checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-10-27T14:16:06Z","success":1,"relation":"main_file","creator":"cziletti","file_size":2441163,"file_name":"2021_ScienceAdv_Martin-Sanchez.pdf","date_created":"2021-10-27T14:16:06Z","file_id":"10189"}],"arxiv":1},{"year":"2021","oa":1,"article_type":"original","article_number":"093043","publication":"New Journal of Physics","date_updated":"2023-08-14T08:10:31Z","date_published":"2021-09-29T00:00:00Z","external_id":{"isi":["000702042400001"],"arxiv":["2102.05397"]},"scopus_import":"1","date_created":"2021-10-24T22:01:34Z","department":[{"_id":"EdHa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","intvolume":"        23","publisher":"IOP Publishing","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"}],"doi":"10.1088/1367-2630/ac23f1","author":[{"id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","first_name":"Preeti","full_name":"Sahu, Preeti","last_name":"Sahu"},{"full_name":"Schwarz, J. M.","last_name":"Schwarz","first_name":"J. M."},{"first_name":"M. Lisa","last_name":"Manning","full_name":"Manning, M. Lisa"}],"title":"Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue","_id":"10178","publication_status":"published","status":"public","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","publication_identifier":{"eissn":["13672630"]},"oa_version":"Published Version","day":"29","citation":{"chicago":"Sahu, Preeti, J. M. Schwarz, and M. Lisa Manning. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” <i>New Journal of Physics</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">https://doi.org/10.1088/1367-2630/ac23f1</a>.","mla":"Sahu, Preeti, et al. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” <i>New Journal of Physics</i>, vol. 23, no. 9, 093043, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">10.1088/1367-2630/ac23f1</a>.","apa":"Sahu, P., Schwarz, J. M., &#38; Manning, M. L. (2021). Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">https://doi.org/10.1088/1367-2630/ac23f1</a>","ieee":"P. Sahu, J. M. Schwarz, and M. L. Manning, “Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue,” <i>New Journal of Physics</i>, vol. 23, no. 9. IOP Publishing, 2021.","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.","short":"P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021).","ama":"Sahu P, Schwarz JM, Manning ML. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. <i>New Journal of Physics</i>. 2021;23(9). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">10.1088/1367-2630/ac23f1</a>"},"month":"09","file_date_updated":"2021-10-28T12:06:01Z","ddc":["570"],"has_accepted_license":"1","volume":23,"article_processing_charge":"Yes","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","file_size":2215016,"creator":"cziletti","file_name":"2021_NewJPhys_Sahu.pdf","date_updated":"2021-10-28T12:06:01Z","success":1,"content_type":"application/pdf","checksum":"ace603e8f0962b3ba55f23fa34f57764","access_level":"open_access","date_created":"2021-10-28T12:06:01Z","file_id":"10193"}],"arxiv":1},{"publisher":"Embo Press","intvolume":"        40","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"Bio"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000708012800001"],"pmid":["34661293"]},"date_published":"2021-10-18T00:00:00Z","date_created":"2021-10-24T22:01:34Z","scopus_import":"1","publication":"EMBO Journal","date_updated":"2023-08-14T08:05:23Z","article_number":"e108714","article_type":"original","oa":1,"year":"2021","file":[{"file_name":"2021_EMBO_Bajaj.pdf","file_size":7819881,"relation":"main_file","creator":"alisjak","access_level":"open_access","content_type":"application/pdf","checksum":"78d2d02e775322297e774f72810a41a4","success":1,"date_updated":"2021-12-13T14:54:14Z","file_id":"10541","date_created":"2021-12-13T14:54:14Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","volume":40,"citation":{"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.” <i>EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2021108714\">https://doi.org/10.15252/embj.2021108714</a>.","mla":"Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” <i>EMBO Journal</i>, vol. 40, no. 23, e108714, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2021108714\">10.15252/embj.2021108714</a>.","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. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2021108714\">https://doi.org/10.15252/embj.2021108714</a>","ieee":"S. Bajaj <i>et al.</i>, “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” <i>EMBO Journal</i>, vol. 40, no. 23. Embo Press, 2021.","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).","ama":"Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. <i>EMBO Journal</i>. 2021;40(23). doi:<a href=\"https://doi.org/10.15252/embj.2021108714\">10.15252/embj.2021108714</a>","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."},"day":"18","month":"10","pmid":1,"ddc":["610"],"file_date_updated":"2021-12-13T14:54:14Z","oa_version":"Published Version","publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"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).","status":"public","publication_status":"published","title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","author":[{"last_name":"Bajaj","full_name":"Bajaj, Sunanjay","first_name":"Sunanjay"},{"full_name":"Bagley, Joshua A.","last_name":"Bagley","first_name":"Joshua A."},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"full_name":"Vertesy, Abel","last_name":"Vertesy","first_name":"Abel"},{"first_name":"Sakurako","last_name":"Nagumo Wong","full_name":"Nagumo Wong, Sakurako"},{"first_name":"Veronica","last_name":"Krenn","full_name":"Krenn, Veronica"},{"first_name":"Julie","last_name":"Lévi-Strauss","full_name":"Lévi-Strauss, Julie"},{"first_name":"Juergen A.","full_name":"Knoblich, Juergen A.","last_name":"Knoblich"}],"_id":"10179","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","doi":"10.15252/embj.2021108714"},{"publication":"Journal of Machine Learning Research","date_updated":"2022-05-13T09:36:08Z","page":"1-124","article_type":"original","oa":1,"year":"2021","publisher":"Journal of Machine Learning Research","intvolume":"        22","main_file_link":[{"open_access":"1","url":"https://www.jmlr.org/papers/v22/21-0366.html"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","department":[{"_id":"DaAl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2102.00554"]},"date_published":"2021-09-01T00:00:00Z","date_created":"2021-10-24T22:01:34Z","scopus_import":"1","publication_identifier":{"eissn":["1533-7928"],"issn":["1532-4435"]},"status":"public","publication_status":"published","acknowledgement":"We thank Doug Burger, Steve Scott, Marco Heddes, and the respective teams at Microsoft for inspiring discussions on the topic. We thank Angelika Steger for uplifting debates about the connections to biological brains, Sidak Pal Singh for his support regarding experimental results, and Utku Evci as well as Xin Wang for comments on previous versions of this\r\nwork. Special thanks go to Bernhard Schölkopf, our JMLR editor Samy Bengio, and the three anonymous reviewers who provided excellent comprehensive, pointed, and deep review comments that improved the quality of our manuscript significantly.","title":"Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks","author":[{"full_name":"Hoefler, Torsten","last_name":"Hoefler","first_name":"Torsten"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"Tal","last_name":"Ben-Nun","full_name":"Ben-Nun, Tal"},{"first_name":"Nikoli","full_name":"Dryden, Nikoli","last_name":"Dryden"},{"first_name":"Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","last_name":"Peste","full_name":"Peste, Elena-Alexandra"}],"_id":"10180","abstract":[{"lang":"eng","text":"The growing energy and performance costs of deep learning have driven the community to reduce the size of neural networks by selectively pruning components. Similarly to their biological counterparts, sparse networks generalize just as well, sometimes even better than, the original dense networks. Sparsity promises to reduce the memory footprint of regular networks to fit mobile devices, as well as shorten training time for ever growing networks. In this paper, we survey prior work on sparsity in deep learning and provide an extensive tutorial of sparsification for both inference and training. We describe approaches to remove and add elements of neural networks, different training strategies to achieve model sparsity, and mechanisms to exploit sparsity in practice. Our work distills ideas from more than 300 research papers and provides guidance to practitioners who wish to utilize sparsity today, as well as to researchers whose goal is to push the frontier forward. We include the necessary background on mathematical methods in sparsification, describe phenomena such as early structure adaptation, the intricate relations between sparsity and the training process, and show techniques for achieving acceleration on real hardware. We also define a metric of pruned parameter efficiency that could serve as a baseline for comparison of different sparse networks. We close by speculating on how sparsity can improve future workloads and outline major open problems in the field."}],"issue":"241","arxiv":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2021_JMachLearnRes_Hoefler.pdf","creator":"cziletti","relation":"main_file","file_size":3527521,"success":1,"date_updated":"2021-10-27T15:34:18Z","access_level":"open_access","checksum":"3389d9d01fc58f8fb4c1a53e14a8abbf","content_type":"application/pdf","file_id":"10192","date_created":"2021-10-27T15:34:18Z"}],"has_accepted_license":"1","article_processing_charge":"No","volume":22,"citation":{"mla":"Hoefler, Torsten, et al. “Sparsity in Deep Learning: Pruning and Growth for Efficient Inference and Training in Neural Networks.” <i>Journal of Machine Learning Research</i>, vol. 22, no. 241, Journal of Machine Learning Research, 2021, pp. 1–124.","chicago":"Hoefler, Torsten, Dan-Adrian Alistarh, Tal Ben-Nun, Nikoli Dryden, and Elena-Alexandra Peste. “Sparsity in Deep Learning: Pruning and Growth for Efficient Inference and Training in Neural Networks.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2021.","ama":"Hoefler T, Alistarh D-A, Ben-Nun T, Dryden N, Peste E-A. Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks. <i>Journal of Machine Learning Research</i>. 2021;22(241):1-124.","ista":"Hoefler T, Alistarh D-A, Ben-Nun T, Dryden N, Peste E-A. 2021. Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks. Journal of Machine Learning Research. 22(241), 1–124.","short":"T. Hoefler, D.-A. Alistarh, T. Ben-Nun, N. Dryden, E.-A. Peste, Journal of Machine Learning Research 22 (2021) 1–124.","ieee":"T. Hoefler, D.-A. Alistarh, T. Ben-Nun, N. Dryden, and E.-A. Peste, “Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks,” <i>Journal of Machine Learning Research</i>, vol. 22, no. 241. Journal of Machine Learning Research, pp. 1–124, 2021.","apa":"Hoefler, T., Alistarh, D.-A., Ben-Nun, T., Dryden, N., &#38; Peste, E.-A. (2021). Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research."},"day":"01","ddc":["000"],"file_date_updated":"2021-10-27T15:34:18Z","month":"09","oa_version":"Published Version"},{"oa_version":"Published Version","citation":{"mla":"Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” <i>Set-Valued and Variational Analysis</i>, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s11228-021-00612-1\">10.1007/s11228-021-00612-1</a>.","chicago":"Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” <i>Set-Valued and Variational Analysis</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11228-021-00612-1\">https://doi.org/10.1007/s11228-021-00612-1</a>.","apa":"Ivanov, G., &#38; Lopushanski, M. S. (2021). Rectifiable curves in proximally smooth sets. <i>Set-Valued and Variational Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11228-021-00612-1\">https://doi.org/10.1007/s11228-021-00612-1</a>","ieee":"G. Ivanov and M. S. Lopushanski, “Rectifiable curves in proximally smooth sets,” <i>Set-Valued and Variational Analysis</i>. Springer Nature, 2021.","short":"G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis (2021).","ama":"Ivanov G, Lopushanski MS. Rectifiable curves in proximally smooth sets. <i>Set-Valued and Variational Analysis</i>. 2021. doi:<a href=\"https://doi.org/10.1007/s11228-021-00612-1\">10.1007/s11228-021-00612-1</a>","ista":"Ivanov G, Lopushanski MS. 2021. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis."},"day":"09","month":"10","article_processing_charge":"No","arxiv":1,"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"}],"doi":"10.1007/s11228-021-00612-1","title":"Rectifiable curves in proximally smooth sets","author":[{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory","full_name":"Ivanov, Grigory","last_name":"Ivanov"},{"full_name":"Lopushanski, Mariana S.","last_name":"Lopushanski","first_name":"Mariana S."}],"_id":"10181","status":"public","publication_status":"published","acknowledgement":"Theorem 2 was obtained at Steklov Mathematical Institute RAS and supported by Russian Science Foundation, grant N 19-11-00087.","publication_identifier":{"issn":["0927-6947"],"eissn":["1877-0541"]},"external_id":{"isi":["000705774800001"],"arxiv":["2012.10691"]},"date_published":"2021-10-09T00:00:00Z","date_created":"2021-10-24T22:01:35Z","scopus_import":"1","department":[{"_id":"UlWa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"Springer Nature","main_file_link":[{"url":"https://arxiv.org/abs/2012.10691","open_access":"1"}],"year":"2021","oa":1,"article_type":"original","publication":"Set-Valued and Variational Analysis","date_updated":"2023-08-14T08:11:38Z"},{"oa":1,"year":"2021","date_updated":"2024-02-28T12:52:48Z","publication":"ACM Transactions on Graphics","article_number":"272","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeBi"}],"date_created":"2021-10-27T07:08:19Z","external_id":{"isi":["000729846700077"]},"date_published":"2021-12-01T00:00:00Z","publisher":"Association for Computing Machinery","intvolume":"        40","main_file_link":[{"open_access":"1","url":"http://vcg.isti.cnr.it/Publications/2021/AMBCP21"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"_id":"10184","title":"Volume decomposition for two-piece rigid casting","author":[{"first_name":"Thomas","full_name":"Alderighi, Thomas","last_name":"Alderighi"},{"last_name":"Malomo","full_name":"Malomo, Luigi","first_name":"Luigi"},{"last_name":"Bickel","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"first_name":"Paolo","last_name":"Cignoni","full_name":"Cignoni, Paolo"},{"full_name":"Pietroni, Nico","last_name":"Pietroni","first_name":"Nico"}],"doi":"10.1145/3478513.3480555","abstract":[{"text":"We introduce a novel technique to automatically decompose an input object’s volume into a set of parts that can be represented by two opposite height fields. Such decomposition enables the manufacturing of individual parts using two-piece reusable rigid molds. Our decomposition strategy relies on a new energy formulation that utilizes a pre-computed signal on the mesh volume representing the accessibility for a predefined set of extraction directions. Thanks to this novel formulation, our method allows for efficient optimization of a fabrication-aware partitioning of volumes in a completely\r\nautomatic way. We demonstrate the efficacy of our approach by generating valid volume partitionings for a wide range of complex objects and physically reproducing several of them.","lang":"eng"}],"issue":"6","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368 "]},"ec_funded":1,"acknowledgement":"The authors thank Marco Callieri for all his precious help with the resin casts. The models used in the paper are courtesy of the Stanford 3D Scanning Repository, the AIM@SHAPE Shape Repository, and Thingi10K Repository. The research was partially funded by the European Research Council (ERC) MATERIALIZABLE: Intelligent fabrication-oriented computational design and modeling (grant no. 715767).","status":"public","publication_status":"published","month":"12","ddc":["000"],"file_date_updated":"2021-10-27T07:08:07Z","citation":{"ieee":"T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, and N. Pietroni, “Volume decomposition for two-piece rigid casting,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 6. Association for Computing Machinery, 2021.","apa":"Alderighi, T., Malomo, L., Bickel, B., Cignoni, P., &#38; Pietroni, N. (2021). Volume decomposition for two-piece rigid casting. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3478513.3480555\">https://doi.org/10.1145/3478513.3480555</a>","short":"T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions on Graphics 40 (2021).","ama":"Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. Volume decomposition for two-piece rigid casting. <i>ACM Transactions on Graphics</i>. 2021;40(6). doi:<a href=\"https://doi.org/10.1145/3478513.3480555\">10.1145/3478513.3480555</a>","ista":"Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. 2021. Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics. 40(6), 272.","chicago":"Alderighi, Thomas, Luigi Malomo, Bernd Bickel, Paolo Cignoni, and Nico Pietroni. “Volume Decomposition for Two-Piece Rigid Casting.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3478513.3480555\">https://doi.org/10.1145/3478513.3480555</a>.","mla":"Alderighi, Thomas, et al. “Volume Decomposition for Two-Piece Rigid Casting.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 6, 272, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3478513.3480555\">10.1145/3478513.3480555</a>."},"day":"01","oa_version":"Submitted Version","file":[{"access_level":"open_access","checksum":"384ece7a9ad1026787ba9560b04336d5","content_type":"application/pdf","date_updated":"2021-10-27T07:08:07Z","file_name":"rigidmolds-authorversion.pdf","file_size":107708317,"creator":"bbickel","relation":"main_file","file_id":"10185","date_created":"2021-10-27T07:08:07Z"}],"article_processing_charge":"No","volume":40,"has_accepted_license":"1"},{"issue":"OOPSLA","abstract":[{"lang":"eng","text":"In this work we solve the algorithmic problem of consistency verification for the TSO and PSO memory models given a reads-from map, denoted VTSO-rf and VPSO-rf, respectively. For an execution of n events over k threads and d variables, we establish novel bounds that scale as nk+1 for TSO and as nk+1· min(nk2, 2k· d) for PSO. Moreover, based on our solution to these problems, we develop an SMC algorithm under TSO and PSO that uses the RF equivalence. The algorithm is exploration-optimal, in the sense that it is guaranteed to explore each class of the RF partitioning exactly once, and spends polynomial time per class when k is bounded. Finally, we implement all our algorithms in the SMC tool Nidhugg, and perform a large number of experiments over benchmarks from existing literature. Our experimental results show that our algorithms for VTSO-rf and VPSO-rf provide significant scalability improvements over standard alternatives. Moreover, when used for SMC, the RF partitioning is often much coarser than the standard Shasha-Snir partitioning for TSO/PSO, which yields a significant speedup in the model checking task.\r\n\r\n"}],"doi":"10.1145/3485541","author":[{"last_name":"Bui","full_name":"Bui, Truc Lam","first_name":"Truc Lam"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Tushar","full_name":"Gautam, Tushar","last_name":"Gautam"},{"last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"},{"orcid":"0000-0001-9036-063X","first_name":"Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","last_name":"Toman","full_name":"Toman, Viktor"}],"title":"The reads-from equivalence for the TSO and PSO memory models","_id":"10191","status":"public","publication_status":"published","acknowledgement":"The research was partially funded by the ERC CoG 863818 (ForM-SMArt) and the Vienna Science\r\nand Technology Fund (WWTF) through project ICT15-003.","ec_funded":1,"publication_identifier":{"eissn":["2475-1421"]},"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"oa_version":"Published Version","day":"15","citation":{"mla":"Bui, Truc Lam, et al. “The Reads-from Equivalence for the TSO and PSO Memory Models.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 5, no. OOPSLA, 164, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3485541\">10.1145/3485541</a>.","chicago":"Bui, Truc Lam, Krishnendu Chatterjee, Tushar Gautam, Andreas Pavlogiannis, and Viktor Toman. “The Reads-from Equivalence for the TSO and PSO Memory Models.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3485541\">https://doi.org/10.1145/3485541</a>.","ama":"Bui TL, Chatterjee K, Gautam T, Pavlogiannis A, Toman V. The reads-from equivalence for the TSO and PSO memory models. <i>Proceedings of the ACM on Programming Languages</i>. 2021;5(OOPSLA). doi:<a href=\"https://doi.org/10.1145/3485541\">10.1145/3485541</a>","ista":"Bui TL, Chatterjee K, Gautam T, Pavlogiannis A, Toman V. 2021. The reads-from equivalence for the TSO and PSO memory models. Proceedings of the ACM on Programming Languages. 5(OOPSLA), 164.","short":"T.L. Bui, K. Chatterjee, T. Gautam, A. Pavlogiannis, V. Toman, Proceedings of the ACM on Programming Languages 5 (2021).","ieee":"T. L. Bui, K. Chatterjee, T. Gautam, A. Pavlogiannis, and V. Toman, “The reads-from equivalence for the TSO and PSO memory models,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 5, no. OOPSLA. Association for Computing Machinery, 2021.","apa":"Bui, T. L., Chatterjee, K., Gautam, T., Pavlogiannis, A., &#38; Toman, V. (2021). The reads-from equivalence for the TSO and PSO memory models. <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3485541\">https://doi.org/10.1145/3485541</a>"},"file_date_updated":"2021-11-04T07:24:48Z","ddc":["000"],"month":"10","has_accepted_license":"1","volume":5,"article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"file":[{"content_type":"application/pdf","checksum":"9d6dce7b611853c529bb7b1915ac579e","access_level":"open_access","date_updated":"2021-11-04T07:24:48Z","success":1,"file_size":2903485,"relation":"main_file","creator":"cchlebak","file_name":"2021_ProcACMPL_Bui.pdf","date_created":"2021-11-04T07:24:48Z","file_id":"10215"}],"year":"2021","keyword":["safety","risk","reliability and quality","software"],"oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10199"}]},"article_type":"original","article_number":"164","publication":"Proceedings of the ACM on Programming Languages","date_updated":"2025-07-14T09:10:16Z","external_id":{"arxiv":["2011.11763"]},"date_published":"2021-10-15T00:00:00Z","scopus_import":"1","date_created":"2021-10-27T15:05:34Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"         5","publisher":"Association for Computing Machinery"},{"date_updated":"2025-07-14T09:10:16Z","page":"166","related_material":{"record":[{"id":"10190","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"9987"},{"id":"141","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10191"}]},"oa":1,"keyword":["concurrency","verification","model checking"],"alternative_title":["ISTA Thesis"],"year":"2021","publisher":"Institute of Science and Technology Austria","type":"dissertation","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"date_created":"2021-10-29T20:09:01Z","acknowledged_ssus":[{"_id":"SSU"}],"date_published":"2021-10-31T00:00:00Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"status":"public","publication_status":"published","_id":"10199","supervisor":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"}],"title":"Improved verification techniques for concurrent systems","author":[{"first_name":"Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","last_name":"Toman","full_name":"Toman, Viktor","orcid":"0000-0001-9036-063X"}],"doi":"10.15479/at:ista:10199","abstract":[{"lang":"eng","text":"The design and verification of concurrent systems remains an open challenge due to the non-determinism that arises from the inter-process communication. In particular, concurrent programs are notoriously difficult both to be written correctly and to be analyzed formally, as complex thread interaction has to be accounted for. The difficulties are further exacerbated when concurrent programs get executed on modern-day hardware, which contains various buffering and caching mechanisms for efficiency reasons. This causes further subtle non-determinism, which can often produce very unintuitive behavior of the concurrent programs. Model checking is at the forefront of tackling the verification problem, where the task is to decide, given as input a concurrent system and a desired property, whether the system satisfies the property. The inherent state-space explosion problem in model checking of concurrent systems causes naïve explicit methods not to scale, thus more inventive methods are required. One such method is stateless model checking (SMC), which explores in memory-efficient manner the program executions rather than the states of the program. State-of-the-art SMC is typically coupled with partial order reduction (POR) techniques, which argue that certain executions provably produce identical system behavior, thus limiting the amount of executions one needs to explore in order to cover all possible behaviors. Another method to tackle the state-space explosion is symbolic model checking, where the considered techniques operate on a succinct implicit representation of the input system rather than explicitly accessing the system. In this thesis we present new techniques for verification of concurrent systems. We present several novel POR methods for SMC of concurrent programs under various models of semantics, some of which account for write-buffering mechanisms. Additionally, we present novel algorithms for symbolic model checking of finite-state concurrent systems, where the desired property of the systems is to ensure a formally defined notion of fairness."}],"file":[{"file_name":"toman_th_final.pdf","file_size":2915234,"relation":"main_file","creator":"vtoman","access_level":"open_access","checksum":"4f412a1ee60952221b499a4b1268df35","content_type":"application/pdf","date_updated":"2021-11-08T14:12:22Z","file_id":"10225","date_created":"2021-11-08T14:12:22Z"},{"access_level":"closed","checksum":"9584943f99127be2dd2963f6784c37d4","content_type":"application/zip","date_updated":"2021-11-09T09:00:50Z","file_name":"toman_thesis.zip","creator":"vtoman","file_size":8616056,"relation":"source_file","file_id":"10226","date_created":"2021-11-08T14:12:46Z"}],"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","ddc":["000"],"file_date_updated":"2021-11-09T09:00:50Z","month":"10","citation":{"ieee":"V. Toman, “Improved verification techniques for concurrent systems,” Institute of Science and Technology Austria, 2021.","apa":"Toman, V. (2021). <i>Improved verification techniques for concurrent systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10199\">https://doi.org/10.15479/at:ista:10199</a>","ama":"Toman V. Improved verification techniques for concurrent systems. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10199\">10.15479/at:ista:10199</a>","ista":"Toman V. 2021. Improved verification techniques for concurrent systems. Institute of Science and Technology Austria.","short":"V. Toman, Improved Verification Techniques for Concurrent Systems, Institute of Science and Technology Austria, 2021.","chicago":"Toman, Viktor. “Improved Verification Techniques for Concurrent Systems.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10199\">https://doi.org/10.15479/at:ista:10199</a>.","mla":"Toman, Viktor. <i>Improved Verification Techniques for Concurrent Systems</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10199\">10.15479/at:ista:10199</a>."},"day":"31","oa_version":"Published Version"},{"year":"2021","oa":1,"related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2020.11.23.394171 ","description":"Preprint"}]},"article_type":"original","article_number":"6094","publication":"Nature Communications","date_updated":"2023-08-14T10:32:48Z","date_published":"2021-10-19T00:00:00Z","external_id":{"pmid":["34667153"],"isi":["000709050300016"]},"scopus_import":"1","date_created":"2021-10-31T23:01:29Z","department":[{"_id":"CaHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"        12","publisher":"Springer Nature","issue":"1","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"}],"doi":"10.1038/s41467-021-26234-7","author":[{"last_name":"Pradhan","full_name":"Pradhan, Saurabh J.","first_name":"Saurabh J."},{"first_name":"Puli Chandramouli","last_name":"Reddy","full_name":"Reddy, Puli Chandramouli"},{"orcid":"0000-0002-5920-9090","first_name":"Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","last_name":"Smutny","full_name":"Smutny, Michael"},{"first_name":"Ankita","last_name":"Sharma","full_name":"Sharma, Ankita"},{"orcid":"0000-0002-6453-8075","full_name":"Sako, Keisuke","last_name":"Sako","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke"},{"full_name":"Oak, Meghana S.","last_name":"Oak","first_name":"Meghana S."},{"full_name":"Shah, Rini","last_name":"Shah","first_name":"Rini"},{"last_name":"Pal","full_name":"Pal, Mrinmoy","first_name":"Mrinmoy"},{"first_name":"Ojas","full_name":"Deshpande, Ojas","last_name":"Deshpande"},{"last_name":"Dsilva","full_name":"Dsilva, Greg","first_name":"Greg"},{"last_name":"Tang","full_name":"Tang, Yin","first_name":"Yin"},{"last_name":"Mishra","full_name":"Mishra, Rakesh","first_name":"Rakesh"},{"last_name":"Deshpande","full_name":"Deshpande, Girish","first_name":"Girish"},{"last_name":"Giraldez","full_name":"Giraldez, Antonio J.","first_name":"Antonio J."},{"first_name":"Mahendra","full_name":"Sonawane, Mahendra","last_name":"Sonawane"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"first_name":"Sanjeev","full_name":"Galande, Sanjeev","last_name":"Galande"}],"title":"Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis","_id":"10202","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).","status":"public","publication_status":"published","publication_identifier":{"eissn":["20411723"]},"oa_version":"Published Version","day":"19","citation":{"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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26234-7\">https://doi.org/10.1038/s41467-021-26234-7</a>","ieee":"S. J. Pradhan <i>et al.</i>, “Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","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.","ama":"Pradhan SJ, Reddy PC, Smutny M, et al. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-26234-7\">10.1038/s41467-021-26234-7</a>","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).","mla":"Pradhan, Saurabh J., et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” <i>Nature Communications</i>, vol. 12, no. 1, 6094, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26234-7\">10.1038/s41467-021-26234-7</a>.","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.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26234-7\">https://doi.org/10.1038/s41467-021-26234-7</a>."},"month":"10","pmid":1,"file_date_updated":"2021-11-09T13:59:26Z","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"Yes","volume":12,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","creator":"cziletti","file_size":7144437,"file_name":"2021_NatureComm_Pradhan.pdf","date_updated":"2021-11-09T13:59:26Z","success":1,"checksum":"c40a69ae94435ecd3a30c9874a11ef2b","content_type":"application/pdf","access_level":"open_access","date_created":"2021-11-09T13:59:26Z","file_id":"10262"}]},{"abstract":[{"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.","lang":"eng"}],"doi":"10.1038/s41467-021-26262-3","title":"Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas","author":[{"full_name":"Sortino, Luca","last_name":"Sortino","first_name":"Luca"},{"full_name":"Zotev, Panaiot G.","last_name":"Zotev","first_name":"Panaiot G."},{"first_name":"Catherine L.","full_name":"Phillips, Catherine L.","last_name":"Phillips"},{"first_name":"Alistair J.","last_name":"Brash","full_name":"Brash, Alistair J."},{"last_name":"Cambiasso","full_name":"Cambiasso, Javier","first_name":"Javier"},{"full_name":"Marensi, Elena","last_name":"Marensi","id":"0BE7553A-1004-11EA-B805-18983DDC885E","first_name":"Elena","orcid":"0000-0001-7173-4923"},{"full_name":"Fox, A. Mark","last_name":"Fox","first_name":"A. Mark"},{"full_name":"Maier, Stefan A.","last_name":"Maier","first_name":"Stefan A."},{"first_name":"Riccardo","last_name":"Sapienza","full_name":"Sapienza, Riccardo"},{"last_name":"Tartakovskii","full_name":"Tartakovskii, Alexander I.","first_name":"Alexander I."}],"_id":"10203","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.","publication_status":"published","status":"public","publication_identifier":{"eissn":["2041-1723"]},"oa_version":"Published Version","citation":{"mla":"Sortino, Luca, et al. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” <i>Nature Communications</i>, vol. 12, 6063, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26262-3\">10.1038/s41467-021-26262-3</a>.","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.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26262-3\">https://doi.org/10.1038/s41467-021-26262-3</a>.","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.","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).","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. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-26262-3\">10.1038/s41467-021-26262-3</a>","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26262-3\">https://doi.org/10.1038/s41467-021-26262-3</a>","ieee":"L. Sortino <i>et al.</i>, “Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021."},"day":"18","ddc":["530"],"month":"10","file_date_updated":"2021-11-03T11:31:24Z","has_accepted_license":"1","volume":12,"article_processing_charge":"No","file":[{"file_id":"10212","date_created":"2021-11-03T11:31:24Z","access_level":"open_access","content_type":"application/pdf","checksum":"8580d128389860f732028c521cd5949e","success":1,"date_updated":"2021-11-03T11:31:24Z","file_name":"2021_NatComm_Sortino.pdf","relation":"main_file","creator":"cchlebak","file_size":1434201}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"year":"2021","oa":1,"article_number":"6063","article_type":"original","publication":"Nature Communications","date_updated":"2023-08-14T08:12:12Z","date_published":"2021-10-18T00:00:00Z","external_id":{"arxiv":["2103.16986"],"isi":["000708601800015"]},"date_created":"2021-10-31T23:01:30Z","scopus_import":"1","department":[{"_id":"BjHo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"Springer Nature","intvolume":"        12"},{"article_type":"original","page":"9107-9115","date_updated":"2023-10-03T09:24:27Z","publication":"Soft Matter","year":"2021","oa":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"intvolume":"        17","publisher":"Royal Society of Chemistry ","scopus_import":"1","date_created":"2021-10-31T23:01:30Z","external_id":{"pmid":["34569592"],"isi":["000700090000001"]},"date_published":"2021-10-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"ec_funded":1,"status":"public","acknowledgement":"MS acknowledges the support by Australian Research Council funding through the ARC Training Centre for M3D Innovation (IC180100008). MS thanks M. Hanifpour and N. Francois for their input and valuable discussions. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme, grant no. 788183 and from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.","publication_status":"published","project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"doi":"10.1039/d1sm00774b","issue":"40","abstract":[{"text":"Two common representations of close packings of identical spheres consisting of hexagonal layers, called Barlow stackings, appear abundantly in minerals and metals. These motifs, however, occupy an identical portion of space and bear identical first-order topological signatures as measured by persistent homology. Here we present a novel method based on k-fold covers that unambiguously distinguishes between these patterns. Moreover, our approach provides topological evidence that the FCC motif is the more stable of the two in the context of evolving experimental sphere packings during the transition from disordered to an ordered state. We conclude that our approach can be generalised to distinguish between various Barlow stackings manifested in minerals and metals.","lang":"eng"}],"_id":"10204","author":[{"orcid":"0000-0002-8882-5116","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","full_name":"Osang, Georg F"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"first_name":"Mohammad","full_name":"Saadatfar, Mohammad","last_name":"Saadatfar"}],"title":"Topological signatures and stability of hexagonal close packing and Barlow stackings","article_processing_charge":"No","volume":17,"has_accepted_license":"1","file":[{"file_id":"14385","date_created":"2023-10-03T09:21:42Z","file_name":"2021_SoftMatter_acceptedversion_Osang.pdf","creator":"dernst","relation":"main_file","file_size":4678788,"success":1,"date_updated":"2023-10-03T09:21:42Z","access_level":"open_access","checksum":"b4da0c420530295e61b153960f6cb350","content_type":"application/pdf"}],"oa_version":"Submitted Version","month":"10","pmid":1,"ddc":["540"],"file_date_updated":"2023-10-03T09:21:42Z","day":"20","citation":{"chicago":"Osang, Georg F, Herbert Edelsbrunner, and Mohammad Saadatfar. “Topological Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” <i>Soft Matter</i>. Royal Society of Chemistry , 2021. <a href=\"https://doi.org/10.1039/d1sm00774b\">https://doi.org/10.1039/d1sm00774b</a>.","mla":"Osang, Georg F., et al. “Topological Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” <i>Soft Matter</i>, vol. 17, no. 40, Royal Society of Chemistry , 2021, pp. 9107–15, doi:<a href=\"https://doi.org/10.1039/d1sm00774b\">10.1039/d1sm00774b</a>.","apa":"Osang, G. F., Edelsbrunner, H., &#38; Saadatfar, M. (2021). Topological signatures and stability of hexagonal close packing and Barlow stackings. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/d1sm00774b\">https://doi.org/10.1039/d1sm00774b</a>","ieee":"G. F. Osang, H. Edelsbrunner, and M. Saadatfar, “Topological signatures and stability of hexagonal close packing and Barlow stackings,” <i>Soft Matter</i>, vol. 17, no. 40. Royal Society of Chemistry , pp. 9107–9115, 2021.","ista":"Osang GF, Edelsbrunner H, Saadatfar M. 2021. Topological signatures and stability of hexagonal close packing and Barlow stackings. Soft Matter. 17(40), 9107–9115.","ama":"Osang GF, Edelsbrunner H, Saadatfar M. Topological signatures and stability of hexagonal close packing and Barlow stackings. <i>Soft Matter</i>. 2021;17(40):9107-9115. doi:<a href=\"https://doi.org/10.1039/d1sm00774b\">10.1039/d1sm00774b</a>","short":"G.F. Osang, H. Edelsbrunner, M. Saadatfar, Soft Matter 17 (2021) 9107–9115."}},{"abstract":[{"text":"Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. The typical approach is to detect inputs from novel classes and retrain the classifier on an augmented dataset. However, not only the classifier but also the detection mechanism needs to adapt in order to distinguish between newly learned and yet unknown input classes. To address this challenge, we introduce an algorithmic framework for active monitoring of a neural network. A monitor wrapped in our framework operates in parallel with the neural network and interacts with a human user via a series of interpretable labeling queries for incremental adaptation. In addition, we propose an adaptive quantitative monitor to improve precision. An experimental evaluation on a diverse set of benchmarks with varying numbers of classes confirms the benefits of our active monitoring framework in dynamic scenarios.","lang":"eng"}],"doi":"10.1007/978-3-030-88494-9_3","author":[{"first_name":"Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","last_name":"Lukina","full_name":"Lukina, Anna"},{"last_name":"Schilling","full_name":"Schilling, Christian","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724"}],"title":"Into the unknown: active monitoring of neural networks","_id":"10206","publication_status":"published","acknowledgement":"We thank Christoph Lampert and Alex Greengold for fruitful discussions. This research was supported in part by the Simons Institute for the Theory of Computing, the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","status":"public","ec_funded":1,"place":"Cham","publication_identifier":{"eisbn":["978-3-030-88494-9"],"issn":["0302-9743"],"isbn":["9-783-0308-8493-2"],"eissn":["1611-3349"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"conference":{"name":"RV: Runtime Verification","start_date":"2021-10-11","location":"Virtual","end_date":"2021-10-14"},"oa_version":"Preprint","day":"06","citation":{"mla":"Lukina, Anna, et al. “Into the Unknown: Active Monitoring of Neural Networks.” <i>21st International Conference on Runtime Verification</i>, vol. 12974, Springer Nature, 2021, pp. 42–61, doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">10.1007/978-3-030-88494-9_3</a>.","chicago":"Lukina, Anna, Christian Schilling, and Thomas A Henzinger. “Into the Unknown: Active Monitoring of Neural Networks.” In <i>21st International Conference on Runtime Verification</i>, 12974:42–61. Cham: Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">https://doi.org/10.1007/978-3-030-88494-9_3</a>.","ista":"Lukina A, Schilling C, Henzinger TA. 2021. Into the unknown: active monitoring of neural networks. 21st International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 42–61.","ama":"Lukina A, Schilling C, Henzinger TA. Into the unknown: active monitoring of neural networks. In: <i>21st International Conference on Runtime Verification</i>. Vol 12974. Cham: Springer Nature; 2021:42-61. doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">10.1007/978-3-030-88494-9_3</a>","short":"A. Lukina, C. Schilling, T.A. Henzinger, in:, 21st International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 42–61.","apa":"Lukina, A., Schilling, C., &#38; Henzinger, T. A. (2021). Into the unknown: active monitoring of neural networks. In <i>21st International Conference on Runtime Verification</i> (Vol. 12974, pp. 42–61). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">https://doi.org/10.1007/978-3-030-88494-9_3</a>","ieee":"A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: active monitoring of neural networks,” in <i>21st International Conference on Runtime Verification</i>, Virtual, 2021, vol. 12974, pp. 42–61."},"month":"10","article_processing_charge":"No","volume":"12974 ","arxiv":1,"alternative_title":["LNCS"],"year":"2021","keyword":["monitoring","neural networks","novelty detection"],"oa":1,"related_material":{"record":[{"id":"13234","relation":"extended_version","status":"public"}]},"page":"42-61","publication":"21st International Conference on Runtime Verification","date_updated":"2024-01-30T12:06:56Z","external_id":{"arxiv":["2009.06429"],"isi":["000719383800003"]},"date_published":"2021-10-06T00:00:00Z","scopus_import":"1","date_created":"2021-10-31T23:01:31Z","department":[{"_id":"ToHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.06429"}],"publisher":"Springer Nature"}]