[{"_id":"81","status":"public","type":"conference","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","start_date":"2018-09-04","end_date":"2018-09-06","location":"Beijing, China"},"ddc":["000"],"date_updated":"2023-09-13T08:58:34Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-10-09T06:24:21Z","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We solve the offline monitoring problem for timed propositional temporal logic (TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider extends linear temporal logic (LTL) with clock variables and reset quantifiers, providing a mechanism to specify real-time constraints. We first describe a general monitoring algorithm based on an exhaustive computation of the set of satisfying clock assignments as a finite union of zones. We then propose a specialized monitoring algorithm for the one-variable case using a partition of the time domain based on the notion of region equivalence, whose complexity is linear in the length of the signal, thereby generalizing a known result regarding the monitoring of metric temporal logic (MTL). The region and zone representations of time constraints are known from timed automata verification and can also be used in the discrete-time case. Our prototype implementation appears to outperform previous discrete-time implementations of TPTL monitoring,"}],"month":"08","intvolume":" 11022","alternative_title":["LNCS"],"scopus_import":"1","file":[{"file_name":"2018_LNCS_Elgyuett.pdf","date_created":"2020-10-09T06:24:21Z","creator":"dernst","file_size":537219,"date_updated":"2020-10-09T06:24:21Z","success":1,"file_id":"8638","checksum":"e5d81c9b50a6bd9d8a2c16953aad7e23","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":11022,"project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.","ieee":"A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.","ama":"Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables. In: Vol 11022. Springer; 2018:53-70. doi:10.1007/978-3-030-00151-3_4","apa":"Elgyütt, A., Ferrere, T., & Henzinger, T. A. (2018). Monitoring temporal logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_4","mla":"Elgyütt, Adrian, et al. Monitoring Temporal Logic with Clock Variables. Vol. 11022, Springer, 2018, pp. 53–70, doi:10.1007/978-3-030-00151-3_4.","ista":"Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 53–70.","chicago":"Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal Logic with Clock Variables,” 11022:53–70. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_4."},"title":"Monitoring temporal logic with clock variables","author":[{"id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","first_name":"Adrian","full_name":"Elgyütt, Adrian","last_name":"Elgyütt"},{"orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","last_name":"Ferrere","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"publist_id":"7973","external_id":{"isi":["000884993200004"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"Springer","oa":1,"day":"26","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1007/978-3-030-00151-3_4","date_published":"2018-08-26T00:00:00Z","date_created":"2018-12-11T11:44:31Z","page":"53 - 70"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing.","chicago":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6.","ama":"Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads. Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6","apa":"Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6","short":"C. Lenzen, J. Rybicki, Distributed Computing (2018).","ieee":"C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing squads,” Distributed Computing. Springer, 2018.","mla":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6."},"title":"Near-optimal self-stabilising counting and firing squads","external_id":{"isi":["000475627800005"]},"article_processing_charge":"Yes (via OA deal)","publist_id":"7978","author":[{"first_name":"Christoph","full_name":"Lenzen, Christoph","last_name":"Lenzen"},{"first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646"}],"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publication":"Distributed Computing","day":"12","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:44:30Z","date_published":"2018-09-12T00:00:00Z","doi":"10.1007/s00446-018-0342-6","oa":1,"quality_controlled":"1","publisher":"Springer","ddc":["000"],"date_updated":"2023-09-13T09:01:06Z","department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:48:01Z","_id":"76","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-17T14:21:22Z","file_name":"2018_DistributedComputing_Lenzen.pdf","date_updated":"2020-07-14T12:48:01Z","file_size":799337,"creator":"dernst","checksum":"872db70bba9b401500abe3c6ae2f1a61","file_id":"5711","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","oa_version":"Published Version","abstract":[{"text":"Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C>1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions.","lang":"eng"}],"month":"09","scopus_import":"1"},{"intvolume":" 68","month":"03","scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software."}],"ec_funded":1,"volume":68,"language":[{"iso":"eng"}],"file":[{"file_id":"5953","checksum":"1c8d58cd489a66cd3e2064c1141c8c5e","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_Edelsbrunner.pdf","date_created":"2019-02-12T06:47:52Z","file_size":708357,"date_updated":"2020-07-14T12:46:38Z","creator":"dernst"}],"publication_status":"published","status":"public","type":"journal_article","_id":"530","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:46:38Z","ddc":["000"],"date_updated":"2023-09-13T08:59:00Z","oa":1,"publisher":"Elsevier","quality_controlled":"1","date_created":"2018-12-11T11:46:59Z","doi":"10.1016/j.comgeo.2017.06.014","date_published":"2018-03-01T00:00:00Z","page":"119 - 133","publication":"Computational Geometry: Theory and Applications","day":"01","year":"2018","has_accepted_license":"1","isi":1,"project":[{"name":"Topological Complex Systems","grant_number":"318493","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"title":"Multiple covers with balls I: Inclusion–exclusion","external_id":{"isi":["000415778300010"]},"article_processing_charge":"No","publist_id":"7289","author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel","full_name":"Iglesias Ham, Mabel","last_name":"Iglesias Ham"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications. Elsevier, 2018. https://doi.org/10.1016/j.comgeo.2017.06.014.","ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications, vol. 68, Elsevier, 2018, pp. 119–33, doi:10.1016/j.comgeo.2017.06.014.","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 2018;68:119-133. doi:10.1016/j.comgeo.2017.06.014","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2018). Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.014","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,” Computational Geometry: Theory and Applications, vol. 68. Elsevier, pp. 119–133, 2018.","short":"H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133."}},{"title":"Nanoscopy of pairs of atoms by fluorescence in a magnetic field","article_processing_charge":"No","external_id":{"arxiv":["1712.10127"],"isi":["000429454000015"]},"author":[{"last_name":"Redchenko","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"first_name":"Alexander","full_name":"Makarov, Alexander","last_name":"Makarov"},{"full_name":"Yudson, Vladimir","last_name":"Yudson","first_name":"Vladimir"}],"publist_id":"7572","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"E. Redchenko, A. Makarov, and V. Yudson, “Nanoscopy of pairs of atoms by fluorescence in a magnetic field,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018.","short":"E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","apa":"Redchenko, E., Makarov, A., & Yudson, V. (2018). Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043812","ama":"Redchenko E, Makarov A, Yudson V. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043812","mla":"Redchenko, Elena, et al. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, 043812, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043812.","ista":"Redchenko E, Makarov A, Yudson V. 2018. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4), 043812.","chicago":"Redchenko, Elena, Alexander Makarov, and Vladimir Yudson. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043812."},"article_number":" 043812 ","date_created":"2018-12-11T11:45:44Z","date_published":"2018-04-09T00:00:00Z","doi":"10.1103/PhysRevA.97.043812","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","day":"09","year":"2018","isi":1,"oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"The work was partially supported by Russian Foundation for Basic Research (Grant No. 15-02-05657a) and by the Basic research program of Higher School of Economics (HSE).","department":[{"_id":"JoFi"}],"date_updated":"2023-09-13T09:00:41Z","status":"public","type":"journal_article","article_type":"original","_id":"307","issue":"4","volume":97,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 97","month":"04","main_file_link":[{"url":"https://arxiv.org/abs/1712.10127","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Spontaneous emission spectra of two initially excited closely spaced identical atoms are very sensitive to the strength and the direction of the applied magnetic field. We consider the relevant schemes that ensure the determination of the mutual spatial orientation of the atoms and the distance between them by entirely optical means. A corresponding theoretical description is given accounting for the dipole-dipole interaction between the two atoms in the presence of a magnetic field and for polarizations of the quantum field interacting with magnetic sublevels of the two-atom system. "}]},{"external_id":{"isi":["000433986200001"]},"article_processing_charge":"No","publist_id":"7620","author":[{"last_name":"Zapata","full_name":"Zapata, Luis","first_name":"Luis"},{"last_name":"Pich","full_name":"Pich, Oriol","first_name":"Oriol"},{"last_name":"Serrano","full_name":"Serrano, Luis","first_name":"Luis"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"first_name":"Stephan","full_name":"Ossowski, Stephan","last_name":"Ossowski"},{"full_name":"Schaefer, Martin","last_name":"Schaefer","first_name":"Martin"}],"title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","citation":{"ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1434-0.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0","mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology, vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Systematic investigation of epistasis in molecular evolution","grant_number":"335980","_id":"26120F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"67","date_created":"2018-12-11T11:45:35Z","doi":"10.1186/s13059-018-1434-0","date_published":"2018-05-31T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"Genome Biology","day":"31","oa":1,"quality_controlled":"1","publisher":"BioMed Central","department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:45:47Z","date_updated":"2023-09-13T09:01:32Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"279","ec_funded":1,"volume":19,"related_material":{"record":[{"id":"9811","status":"public","relation":"research_data"},{"relation":"research_data","id":"9812","status":"public"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"2018_GenomeBiology_Zapata.pdf","date_created":"2018-12-17T14:05:01Z","file_size":1414722,"date_updated":"2020-07-14T12:45:47Z","creator":"dernst","file_id":"5708","checksum":"f3e4922486bd9bf1483271bdbed394a7","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"scopus_import":"1","intvolume":" 19","month":"05","abstract":[{"text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.","lang":"eng"}],"oa_version":"Published Version"},{"publication":"The EMBO Journal","day":"01","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:44:52Z","date_published":"2018-08-01T00:00:00Z","doi":"10.15252/embj.201798044","acknowledgement":"We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We thank Erwin Neher for help with the development of the mathematical model of the synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner for providing the illustrations of synaptic vesicle and protein dynamics. We thank Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is a recipient of long-term fellowships from the European Molecular Biology Organization (ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013). The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05, and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the German Federal Ministry of Education and Research (03F0626A).","oa":1,"quality_controlled":"1","publisher":"Wiley","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. Wiley. https://doi.org/10.15252/embj.201798044","ama":"Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 2018;37(15). doi:10.15252/embj.201798044","short":"S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).","ieee":"S. M. Truckenbrodt et al., “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” The EMBO Journal, vol. 37, no. 15. Wiley, 2018.","mla":"Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal, vol. 37, no. 15, e98044, Wiley, 2018, doi:10.15252/embj.201798044.","ista":"Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 37(15), e98044.","chicago":"Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal. Wiley, 2018. https://doi.org/10.15252/embj.201798044."},"title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","article_processing_charge":"No","external_id":{"pmid":["29950309"],"isi":["000440416900005"]},"author":[{"last_name":"Truckenbrodt","full_name":"Truckenbrodt, Sven M","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Viplav, Abhiyan","last_name":"Viplav","first_name":"Abhiyan"},{"full_name":"Jähne, Sebsatian","last_name":"Jähne","first_name":"Sebsatian"},{"last_name":"Vogts","full_name":"Vogts, Angela","first_name":"Angela"},{"first_name":"Annette","full_name":"Denker, Annette","last_name":"Denker"},{"last_name":"Wildhagen","full_name":"Wildhagen, Hanna","first_name":"Hanna"},{"full_name":"Fornasiero, Eugenio","last_name":"Fornasiero","first_name":"Eugenio"},{"last_name":"Rizzoli","full_name":"Rizzoli, Silvio","first_name":"Silvio"}],"publist_id":"7778","article_number":"e98044","language":[{"iso":"eng"}],"file":[{"file_id":"5710","checksum":"a540feb6c9af6aefc78de531461a8835","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-17T14:17:29Z","file_name":"2018_EMBO_Truckenbrodt.pdf","creator":"dernst","date_updated":"2020-07-14T12:44:56Z","file_size":2846470}],"publication_status":"published","publication_identifier":{"issn":["0261-4189"]},"issue":"15","volume":37,"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins."}],"intvolume":" 37","month":"08","scopus_import":"1","ddc":["570"],"date_updated":"2023-09-13T09:02:48Z","department":[{"_id":"JoDa"}],"file_date_updated":"2020-07-14T12:44:56Z","_id":"145","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original"},{"volume":41,"language":[{"iso":"eng"}],"file":[{"file_id":"7042","checksum":"6a20f843565f962cb20281cdf5e40914","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_PlantCellEnv_Fan.pdf","date_created":"2019-11-18T16:22:22Z","file_size":1937976,"date_updated":"2020-07-14T12:46:32Z","creator":"dernst"}],"publication_status":"published","intvolume":" 41","month":"05","scopus_import":"1","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. "}],"file_date_updated":"2020-07-14T12:46:32Z","department":[{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2023-09-13T09:03:18Z","status":"public","tmp":{"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)","short":"CC BY-NC (4.0)"},"article_type":"original","type":"journal_article","_id":"462","date_created":"2018-12-11T11:46:36Z","date_published":"2018-05-01T00:00:00Z","doi":"10.1111/pce.13153","page":"850 - 864","publication":"Plant, Cell and Environment","day":"01","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","acknowledgement":"This work was supported by the National Natural Science Foundation of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope assay. ","title":"NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development","article_processing_charge":"No","external_id":{"pmid":["29360148"],"isi":["000426870500012"]},"author":[{"full_name":"Fan, Ligang","last_name":"Fan","first_name":"Ligang"},{"first_name":"Lei","last_name":"Zhao","full_name":"Zhao, Lei"},{"last_name":"Hu","full_name":"Hu, Wei","first_name":"Wei"},{"first_name":"Weina","full_name":"Li, Weina","last_name":"Li"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"first_name":"Miroslav","full_name":"Strnad, Miroslav","last_name":"Strnad"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu","last_name":"Simon","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Jinbo","last_name":"Shen","full_name":"Shen, Jinbo"},{"last_name":"Jiang","full_name":"Jiang, Liwen","first_name":"Liwen"},{"first_name":"Quan","last_name":"Qiu","full_name":"Qiu, Quan"}],"publist_id":"7359","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:10.1111/pce.13153.","ama":"Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 2018;41:850-864. doi:10.1111/pce.13153","apa":"Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018). NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. Wiley-Blackwell. https://doi.org/10.1111/pce.13153","ieee":"L. Fan et al., “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” Plant, Cell and Environment, vol. 41. Wiley-Blackwell, pp. 850–864, 2018.","short":"L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J. Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864.","chicago":"Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad, Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment. Wiley-Blackwell, 2018. https://doi.org/10.1111/pce.13153.","ista":"Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 41, 850–864."}},{"title":"Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow","external_id":{"isi":["000425547700061"]},"article_processing_charge":"No","publist_id":"7297","author":[{"last_name":"Altmeyer","orcid":"0000-0001-5964-0203","full_name":"Altmeyer, Sebastian","first_name":"Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. Elsevier. https://doi.org/10.1016/j.jmmm.2017.12.073","ama":"Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 2018;452:427-441. doi:10.1016/j.jmmm.2017.12.073","short":"S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441.","ieee":"S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow,” Journal of Magnetism and Magnetic Materials, vol. 452. Elsevier, pp. 427–441, 2018.","mla":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials, vol. 452, Elsevier, 2018, pp. 427–41, doi:10.1016/j.jmmm.2017.12.073.","ista":"Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 452, 427–441.","chicago":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials. Elsevier, 2018. https://doi.org/10.1016/j.jmmm.2017.12.073."},"oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"S.Altmeyer is a Serra Húnter Fellow","date_created":"2018-12-11T11:46:56Z","date_published":"2018-04-15T00:00:00Z","doi":"10.1016/j.jmmm.2017.12.073","page":"427 - 441","publication":"Journal of Magnetism and Magnetic Materials","day":"15","year":"2018","isi":1,"has_accepted_license":"1","status":"public","type":"journal_article","article_type":"original","_id":"519","file_date_updated":"2020-07-14T12:46:37Z","department":[{"_id":"BjHo"}],"ddc":["530"],"date_updated":"2023-09-13T09:03:44Z","intvolume":" 452","month":"04","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion. ","lang":"eng"}],"volume":452,"language":[{"iso":"eng"}],"file":[{"file_id":"7838","checksum":"431f5cd4a628d7ca21161f82b14ccb4f","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-05-14T14:41:17Z","file_name":"2018_Magnetism_Altmeyer.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:37Z","file_size":17309535}],"publication_status":"published"},{"date_updated":"2023-09-13T09:02:22Z","department":[{"_id":"KrCh"}],"_id":"5679","status":"public","type":"conference","conference":{"end_date":"2018-12-06","location":"Wellington, New Zealand","start_date":"2018-12-02","name":"16th Asian Symposium on Programming Languages and Systems, APLAS"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["03029743"],"isbn":["9783030027674"]},"volume":11275,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study the almost-sure termination problem for probabilistic programs. First, we show that supermartingales with lower bounds on conditional absolute difference provide a sound approach for the almost-sure termination problem. Moreover, using this approach we can obtain explicit optimal bounds on tail probabilities of non-termination within a given number of steps. Second, we present a new approach based on Central Limit Theorem for the almost-sure termination problem, and show that this approach can establish almost-sure termination of programs which none of the existing approaches can handle. Finally, we discuss algorithmic approaches for the two above methods that lead to automated analysis techniques for almost-sure termination of probabilistic programs."}],"month":"12","intvolume":" 11275","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1806.06683"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201.","ieee":"M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination of probabilistic programs,” presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201.","ama":"Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:10.1007/978-3-030-02768-1_11","apa":"Huang, M., Fu, H., & Chatterjee, K. (2018). New approaches for almost-sure termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201). Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand: Springer. https://doi.org/10.1007/978-3-030-02768-1_11","mla":"Huang, Mingzhang, et al. New Approaches for Almost-Sure Termination of Probabilistic Programs. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201, doi:10.1007/978-3-030-02768-1_11.","ista":"Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems, APLAS, LNCS, vol. 11275, 181–201.","chicago":"Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu, 11275:181–201. Springer, 2018. https://doi.org/10.1007/978-3-030-02768-1_11."},"editor":[{"first_name":"Sukyoung","full_name":"Ryu, Sukyoung","last_name":"Ryu"}],"title":"New approaches for almost-sure termination of probabilistic programs","author":[{"first_name":"Mingzhang","last_name":"Huang","full_name":"Huang, Mingzhang"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"external_id":{"arxiv":["1806.06683"],"isi":["000916310900011"]},"article_processing_charge":"No","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"day":"01","isi":1,"year":"2018","doi":"10.1007/978-3-030-02768-1_11","date_published":"2018-12-01T00:00:00Z","date_created":"2018-12-16T22:59:20Z","page":"181-201","quality_controlled":"1","publisher":"Springer","oa":1},{"type":"research_data_reference","status":"public","_id":"9812","author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"last_name":"Pich","full_name":"Pich, Oriol","first_name":"Oriol"},{"first_name":"Luis","last_name":"Serrano","full_name":"Serrano, Luis"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Stephan","last_name":"Ossowski","full_name":"Ossowski, Stephan"},{"first_name":"Martin","full_name":"Schaefer, Martin","last_name":"Schaefer"}],"article_processing_charge":"No","title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","department":[{"_id":"FyKo"}],"date_updated":"2023-09-13T09:01:31Z","citation":{"ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401414.v1","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401414.v1","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","mla":"Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401414.v1."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Springer Nature","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.6401414.v1"}],"month":"05","abstract":[{"text":"This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)","lang":"eng"}],"oa_version":"Published Version","date_published":"2018-05-31T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"279","status":"public"}]},"doi":"10.6084/m9.figshare.6401414.v1","date_created":"2021-08-06T12:58:25Z","year":"2018","day":"31"},{"_id":"9811","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-13T09:01:31Z","citation":{"ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401390.v1","mla":"Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1."},"title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","department":[{"_id":"FyKo"}],"article_processing_charge":"No","author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"first_name":"Oriol","full_name":"Pich, Oriol","last_name":"Pich"},{"full_name":"Serrano, Luis","last_name":"Serrano","first_name":"Luis"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Stephan","last_name":"Ossowski","full_name":"Ossowski, Stephan"},{"first_name":"Martin","last_name":"Schaefer","full_name":"Schaefer, Martin"}],"oa_version":"Preprint","abstract":[{"text":"This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)","lang":"eng"}],"month":"05","oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401390.v1","open_access":"1"}],"publisher":"Springer Nature","day":"31","year":"2018","date_created":"2021-08-06T12:53:49Z","related_material":{"record":[{"relation":"used_in_publication","id":"279","status":"public"}]},"date_published":"2018-05-31T00:00:00Z","doi":"10.6084/m9.figshare.6401390.v1"},{"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"20","file_date_updated":"2020-07-14T12:45:23Z","department":[{"_id":"SiHi"}],"date_updated":"2023-09-13T09:10:47Z","ddc":["570"],"scopus_import":"1","month":"11","intvolume":" 19","abstract":[{"text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.","lang":"eng"}],"oa_version":"Published Version","issue":"1","volume":19,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9807"},{"status":"public","id":"9808","relation":"research_data"}]},"publication_identifier":{"issn":["1471-2164"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"a56516e734dab589dc7f3e1915973b4d","file_id":"5712","creator":"dernst","date_updated":"2020-07-14T12:45:23Z","file_size":4629784,"date_created":"2018-12-17T14:52:57Z","file_name":"2018_BMCGenomics_Higareda.pdf"}],"language":[{"iso":"eng"}],"publist_id":"8035","author":[{"last_name":"Higareda Almaraz","full_name":"Higareda Almaraz, Juan","first_name":"Juan"},{"first_name":"Michael","full_name":"Karbiener, Michael","last_name":"Karbiener"},{"full_name":"Giroud, Maude","last_name":"Giroud","first_name":"Maude"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler"},{"first_name":"Teresa","full_name":"Gerhalter, Teresa","last_name":"Gerhalter"},{"last_name":"Herzig","full_name":"Herzig, Stephan","first_name":"Stephan"},{"last_name":"Scheideler","full_name":"Scheideler, Marcel","first_name":"Marcel"}],"article_processing_charge":"No","external_id":{"isi":["000450976700002"]},"title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","citation":{"chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1).","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics, vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-018-5173-0","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","ieee":"J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” BMC Genomics, vol. 19, no. 1. BioMed Central, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"BioMed Central","quality_controlled":"1","oa":1,"acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19).","date_published":"2018-11-03T00:00:00Z","doi":"10.1186/s12864-018-5173-0","date_created":"2018-12-11T11:44:12Z","isi":1,"has_accepted_license":"1","year":"2018","day":"03","publication":"BMC Genomics"},{"citation":{"ista":"Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of the ACM. 65(4), 20.","chicago":"Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432.","short":"S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).","ieee":"S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal of the ACM, vol. 65, no. 4. ACM, 2018.","apa":"Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes. Journal of the ACM. ACM. https://doi.org/10.1145/3178432","ama":"Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the ACM. 2018;65(4). doi:10.1145/3178432","mla":"Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM, vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7947","author":[{"first_name":"Stefan","last_name":"Dziembowski","full_name":"Dziembowski, Stefan"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"full_name":"Wichs, Daniel","last_name":"Wichs","first_name":"Daniel"}],"external_id":{"isi":["000442938200004"]},"article_processing_charge":"No","title":"Non-malleable codes","article_number":"20","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"},{"name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"isi":1,"year":"2018","day":"01","publication":"Journal of the ACM","doi":"10.1145/3178432","date_published":"2018-08-01T00:00:00Z","date_created":"2018-12-11T11:44:40Z","publisher":"ACM","quality_controlled":"1","oa":1,"date_updated":"2023-09-13T09:05:17Z","department":[{"_id":"KrPi"}],"_id":"107","article_type":"original","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":65,"ec_funded":1,"abstract":[{"lang":"eng","text":"We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2009/608"}],"month":"08","intvolume":" 65"},{"department":[{"_id":"CaHe"}],"date_updated":"2023-09-13T09:11:17Z","type":"journal_article","status":"public","_id":"5676","ec_funded":1,"volume":217,"issue":"12","publication_status":"published","publication_identifier":{"issn":["00219525"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30228162","open_access":"1"}],"scopus_import":"1","intvolume":" 217","month":"12","abstract":[{"text":"In epithelial tissues, cells tightly connect to each other through cell–cell junctions, but they also present the remarkable capacity of reorganizing themselves without compromising tissue integrity. Upon injury, simple epithelia efficiently resolve small lesions through the action of actin cytoskeleton contractile structures at the wound edge and cellular rearrangements. However, the underlying mechanisms and how they cooperate are still poorly understood. In this study, we combine live imaging and theoretical modeling to reveal a novel and indispensable role for occluding junctions (OJs) in this process. We demonstrate that OJ loss of function leads to defects in wound-closure dynamics: instead of contracting, wounds dramatically increase their area. OJ mutants exhibit phenotypes in cell shape, cellular rearrangements, and mechanical properties as well as in actin cytoskeleton dynamics at the wound edge. We propose that OJs are essential for wound closure by impacting on epithelial mechanics at the tissue level, which in turn is crucial for correct regulation of the cellular events occurring at the wound edge.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"article_processing_charge":"No","external_id":{"pmid":["30228162 "],"isi":["000451960800018"]},"author":[{"first_name":"Lara","full_name":"Carvalho, Lara","last_name":"Carvalho"},{"first_name":"Pedro","last_name":"Patricio","full_name":"Patricio, Pedro"},{"full_name":"Ponte, Susana","last_name":"Ponte","first_name":"Susana"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"},{"full_name":"Almeida, Luis","last_name":"Almeida","first_name":"Luis"},{"last_name":"Nunes","full_name":"Nunes, André S.","first_name":"André S."},{"full_name":"Araújo, Nuno A.M.","last_name":"Araújo","first_name":"Nuno A.M."},{"full_name":"Jacinto, Antonio","last_name":"Jacinto","first_name":"Antonio"}],"title":"Occluding junctions as novel regulators of tissue mechanics during wound repair","citation":{"chicago":"Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg, Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201804048.","ista":"Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 217(12), 4267–4283.","mla":"Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology, vol. 217, no. 12, Rockefeller University Press, 2018, pp. 4267–83, doi:10.1083/jcb.201804048.","ieee":"L. Carvalho et al., “Occluding junctions as novel regulators of tissue mechanics during wound repair,” Journal of Cell Biology, vol. 217, no. 12. Rockefeller University Press, pp. 4267–4283, 2018.","short":"L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S. Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283.","ama":"Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 2018;217(12):4267-4283. doi:10.1083/jcb.201804048","apa":"Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes, A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201804048"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"page":"4267-4283","date_created":"2018-12-16T22:59:19Z","date_published":"2018-12-01T00:00:00Z","doi":"10.1083/jcb.201804048","year":"2018","isi":1,"publication":"Journal of Cell Biology","day":"01","oa":1,"quality_controlled":"1","publisher":"Rockefeller University Press"},{"_id":"9807","type":"research_data_reference","status":"public","date_updated":"2023-09-13T09:10:47Z","citation":{"mla":"Higareda Almaraz, Juan, et al. Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1.","ieee":"J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295339.v1","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295339.v1","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295339.v1.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295339.v1."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Juan","last_name":"Higareda Almaraz","full_name":"Higareda Almaraz, Juan"},{"first_name":"Michael","full_name":"Karbiener, Michael","last_name":"Karbiener"},{"full_name":"Giroud, Maude","last_name":"Giroud","first_name":"Maude"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048"},{"full_name":"Gerhalter, Teresa","last_name":"Gerhalter","first_name":"Teresa"},{"last_name":"Herzig","full_name":"Herzig, Stephan","first_name":"Stephan"},{"first_name":"Marcel","last_name":"Scheideler","full_name":"Scheideler, Marcel"}],"article_processing_charge":"No","department":[{"_id":"SiHi"}],"title":"Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","abstract":[{"lang":"eng","text":"Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb)."}],"oa_version":"Published Version","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7295339.v1","open_access":"1"}],"oa":1,"month":"11","year":"2018","day":"03","date_published":"2018-11-03T00:00:00Z","doi":"10.6084/m9.figshare.7295339.v1","related_material":{"record":[{"relation":"used_in_publication","id":"20","status":"public"}]},"date_created":"2021-08-06T12:26:53Z"},{"publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7295369.v1"}],"oa":1,"month":"11","abstract":[{"text":"Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).","lang":"eng"}],"oa_version":"Published Version","date_published":"2018-11-03T00:00:00Z","related_material":{"record":[{"status":"public","id":"20","relation":"used_in_publication"}]},"doi":"10.6084/m9.figshare.7295369.v1","date_created":"2021-08-06T12:31:57Z","year":"2018","day":"03","type":"research_data_reference","status":"public","_id":"9808","author":[{"first_name":"Juan","last_name":"Higareda Almaraz","full_name":"Higareda Almaraz, Juan"},{"last_name":"Karbiener","full_name":"Karbiener, Michael","first_name":"Michael"},{"full_name":"Giroud, Maude","last_name":"Giroud","first_name":"Maude"},{"orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","last_name":"Pauler","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gerhalter","full_name":"Gerhalter, Teresa","first_name":"Teresa"},{"first_name":"Stephan","last_name":"Herzig","full_name":"Herzig, Stephan"},{"full_name":"Scheideler, Marcel","last_name":"Scheideler","first_name":"Marcel"}],"article_processing_charge":"No","title":"Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","department":[{"_id":"SiHi"}],"citation":{"mla":"Higareda Almaraz, Juan, et al. Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295369.v1","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295369.v1","ieee":"J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295369.v1.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295369.v1."},"date_updated":"2023-09-13T09:10:47Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"page":"51 - 65","doi":"10.1145/3196494.3196534","date_published":"2018-06-01T00:00:00Z","date_created":"2018-12-11T11:45:07Z","isi":1,"year":"2018","day":"01","publication":"Proceedings of the 2018 on Asia Conference on Computer and Communication Security","quality_controlled":"1","publisher":"ACM","oa":1,"acknowledgement":"Leonid Reyzin was supported in part by IST Austria and by US NSF grants 1012910, 1012798, and 1422965; this research was performed while he was visiting IST Austria.","author":[{"last_name":"Alwen","full_name":"Alwen, Joel F","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","last_name":"Gazi","full_name":"Gazi, Peter"},{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan"},{"last_name":"Klein","full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"},{"last_name":"Osang","full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lenoid","full_name":"Reyzin, Lenoid","last_name":"Reyzin"},{"last_name":"Rolinek","full_name":"Rolinek, Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"},{"first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","full_name":"Rybar, Michal","last_name":"Rybar"}],"publist_id":"7723","external_id":{"isi":["000516620100005"]},"article_processing_charge":"No","title":"On the memory hardness of data independent password hashing functions","citation":{"mla":"Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password Hashing Functions.” Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65, doi:10.1145/3196494.3196534.","short":"J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak, L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65.","ieee":"J. F. Alwen et al., “On the memory hardness of data independent password hashing functions,” in Proceedings of the 2018 on Asia Conference on Computer and Communication Security, Incheon, Republic of Korea, 2018, pp. 51–65.","ama":"Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data independent password hashing functions. In: Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ACM; 2018:51-65. doi:10.1145/3196494.3196534","apa":"Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak, K. Z., … Rybar, M. (2018). On the memory hardness of data independent password hashing functions. In Proceedings of the 2018 on Asia Conference on Computer and Communication Security (pp. 51–65). Incheon, Republic of Korea: ACM. https://doi.org/10.1145/3196494.3196534","chicago":"Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar. “On the Memory Hardness of Data Independent Password Hashing Functions.” In Proceedings of the 2018 on Asia Conference on Computer and Communication Security, 51–65. ACM, 2018. https://doi.org/10.1145/3196494.3196534.","ista":"Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password hashing functions. Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ASIACCS: Asia Conference on Computer and Communications Security , 51–65."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/783"}],"month":"06","abstract":[{"lang":"eng","text":"We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki'16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block'16] for analyzing the hardware costs of an iMHF."}],"oa_version":"Submitted Version","department":[{"_id":"KrPi"},{"_id":"HeEd"},{"_id":"VlKo"}],"date_updated":"2023-09-13T09:13:12Z","type":"conference","conference":{"name":"ASIACCS: Asia Conference on Computer and Communications Security ","start_date":"2018-06-04","end_date":"2018-06-08","location":"Incheon, Republic of Korea"},"status":"public","_id":"193"},{"project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"On the bit security of cryptographic primitives","article_processing_charge":"No","external_id":{"isi":["000517097500001"]},"author":[{"first_name":"Daniele","last_name":"Micciancio","full_name":"Micciancio, Daniele"},{"first_name":"Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","full_name":"Walter, Michael","last_name":"Walter"}],"publist_id":"7581","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Micciancio D, Walter M. 2018. On the bit security of cryptographic primitives. Eurocrypt: Advances in Cryptology, LNCS, vol. 10820, 3–28.","chicago":"Micciancio, Daniele, and Michael Walter. “On the Bit Security of Cryptographic Primitives,” 10820:3–28. Springer, 2018. https://doi.org/10.1007/978-3-319-78381-9_1.","ama":"Micciancio D, Walter M. On the bit security of cryptographic primitives. In: Vol 10820. Springer; 2018:3-28. doi:10.1007/978-3-319-78381-9_1","apa":"Micciancio, D., & Walter, M. (2018). On the bit security of cryptographic primitives (Vol. 10820, pp. 3–28). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78381-9_1","ieee":"D. Micciancio and M. Walter, “On the bit security of cryptographic primitives,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10820, pp. 3–28.","short":"D. Micciancio, M. Walter, in:, Springer, 2018, pp. 3–28.","mla":"Micciancio, Daniele, and Michael Walter. On the Bit Security of Cryptographic Primitives. Vol. 10820, Springer, 2018, pp. 3–28, doi:10.1007/978-3-319-78381-9_1."},"oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"Research supported in part by the Defense Advanced Research Projects Agency (DARPA) and the U.S. Army Research Office under the SafeWare program. Opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views, position or policy of the Government. The second author was also supported by the European Research Council, ERC consolidator grant (682815 - TOCNeT).","date_created":"2018-12-11T11:45:42Z","date_published":"2018-03-31T00:00:00Z","doi":"10.1007/978-3-319-78381-9_1","page":"3 - 28","day":"31","year":"2018","isi":1,"status":"public","conference":{"location":"Tel Aviv, Israel","end_date":"2018-05-03","start_date":"2018-04-29","name":"Eurocrypt: Advances in Cryptology"},"type":"conference","_id":"300","department":[{"_id":"KrPi"}],"date_updated":"2023-09-13T09:12:04Z","intvolume":" 10820","month":"03","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/077"}],"alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We introduce a formal quantitative notion of “bit security” for a general type of cryptographic games (capturing both decision and search problems), aimed at capturing the intuition that a cryptographic primitive with k-bit security is as hard to break as an ideal cryptographic function requiring a brute force attack on a k-bit key space. Our new definition matches the notion of bit security commonly used by cryptographers and cryptanalysts when studying search (e.g., key recovery) problems, where the use of the traditional definition is well established. However, it produces a quantitatively different metric in the case of decision (indistinguishability) problems, where the use of (a straightforward generalization of) the traditional definition is more problematic and leads to a number of paradoxical situations or mismatches between theoretical/provable security and practical/common sense intuition. Key to our new definition is to consider adversaries that may explicitly declare failure of the attack. We support and justify the new definition by proving a number of technical results, including tight reductions between several standard cryptographic problems, a new hybrid theorem that preserves bit security, and an application to the security analysis of indistinguishability primitives making use of (approximate) floating point numbers. This is the first result showing that (standard precision) 53-bit floating point numbers can be used to achieve 100-bit security in the context of cryptographic primitives with general indistinguishability-based security definitions. Previous results of this type applied only to search problems, or special types of decision problems."}],"ec_funded":1,"volume":10820,"language":[{"iso":"eng"}],"publication_status":"published"},{"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Motivated by biological questions, we study configurations of equal spheres that neither pack nor cover. Placing their centers on a lattice, we define the soft density of the configuration by penalizing multiple overlaps. Considering the 1-parameter family of diagonally distorted 3-dimensional integer lattices, we show that the soft density is maximized at the FCC lattice."}],"month":"03","intvolume":" 32","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://pdfs.semanticscholar.org/d2d5/6da00fbc674e6a8b1bb9d857167e54200dc6.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["08954801"]},"publication_status":"published","issue":"1","volume":32,"_id":"312","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-09-13T09:34:38Z","department":[{"_id":"HeEd"}],"acknowledgement":"This work was partially supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics,” through grant I02979-N35 of the Austrian Science Fund (FWF).","publisher":"Society for Industrial and Applied Mathematics ","quality_controlled":"1","oa":1,"day":"29","publication":"SIAM J Discrete Math","isi":1,"year":"2018","date_published":"2018-03-29T00:00:00Z","doi":"10.1137/16M1097201","date_created":"2018-12-11T11:45:46Z","page":"750 - 782","project":[{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Edelsbrunner H, Iglesias Ham M. 2018. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 32(1), 750–782.","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1097201.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “On the optimality of the FCC lattice for soft sphere packing,” SIAM J Discrete Math, vol. 32, no. 1. Society for Industrial and Applied Mathematics , pp. 750–782, 2018.","short":"H. Edelsbrunner, M. Iglesias Ham, SIAM J Discrete Math 32 (2018) 750–782.","ama":"Edelsbrunner H, Iglesias Ham M. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 2018;32(1):750-782. doi:10.1137/16M1097201","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2018). On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1097201","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math, vol. 32, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 750–82, doi:10.1137/16M1097201."},"title":"On the optimality of the FCC lattice for soft sphere packing","publist_id":"7553","author":[{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel","last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel"}],"article_processing_charge":"No","external_id":{"isi":["000428958900038"]}},{"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1805.01652","open_access":"1"}],"month":"04","intvolume":" 356","abstract":[{"lang":"eng","text":"We give a simple proof of T. Stehling's result [4], whereby in any normal tiling of the plane with convex polygons with number of sides not less than six, all tiles except a finite number are hexagons."}],"oa_version":"Preprint","issue":"4","volume":356,"publication_identifier":{"issn":["1631073X"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"409","department":[{"_id":"HeEd"}],"date_updated":"2023-09-13T09:34:12Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"page":"412-414","doi":"10.1016/j.crma.2018.03.005","date_published":"2018-04-01T00:00:00Z","date_created":"2018-12-11T11:46:19Z","isi":1,"year":"2018","day":"01","publication":"Comptes Rendus Mathematique","author":[{"orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"}],"publist_id":"7420","article_processing_charge":"No","external_id":{"arxiv":["1805.01652"],"isi":["000430402700009"]},"title":"On the number of non-hexagons in a planar tiling","citation":{"chicago":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique. Elsevier, 2018. https://doi.org/10.1016/j.crma.2018.03.005.","ista":"Akopyan A. 2018. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 356(4), 412–414.","mla":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique, vol. 356, no. 4, Elsevier, 2018, pp. 412–14, doi:10.1016/j.crma.2018.03.005.","apa":"Akopyan, A. (2018). On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. Elsevier. https://doi.org/10.1016/j.crma.2018.03.005","ama":"Akopyan A. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 2018;356(4):412-414. doi:10.1016/j.crma.2018.03.005","short":"A. Akopyan, Comptes Rendus Mathematique 356 (2018) 412–414.","ieee":"A. Akopyan, “On the number of non-hexagons in a planar tiling,” Comptes Rendus Mathematique, vol. 356, no. 4. Elsevier, pp. 412–414, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"}]