[{"type":"conference","citation":{"ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Synchronizing the asynchronous,” presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ista":"Kragl B, Qadeer S, Henzinger TA. 2018. Synchronizing the asynchronous. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 118, 21.","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Synchronizing the Asynchronous,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.21</a>.","ama":"Kragl B, Qadeer S, Henzinger TA. Synchronizing the asynchronous. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">10.4230/LIPIcs.CONCUR.2018.21</a>","mla":"Kragl, Bernhard, et al. <i>Synchronizing the Asynchronous</i>. Vol. 118, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">10.4230/LIPIcs.CONCUR.2018.21</a>.","apa":"Kragl, B., Qadeer, S., &#38; Henzinger, T. A. (2018). Synchronizing the asynchronous (Vol. 118). Presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.21</a>"},"oa_version":"Published Version","date_created":"2018-12-11T11:44:48Z","pubrep_id":"1039","month":"08","quality_controlled":"1","date_published":"2018-08-13T00:00:00Z","doi":"10.4230/LIPIcs.CONCUR.2018.21","intvolume":"       118","article_number":"21","status":"public","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"6426"},{"status":"public","id":"8332","relation":"dissertation_contains"}]},"day":"13","oa":1,"volume":118,"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","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)"},"scopus_import":1,"year":"2018","language":[{"iso":"eng"}],"conference":{"location":"Beijing, China","name":"CONCUR: International Conference on Concurrency Theory","start_date":"2018-09-04","end_date":"2018-09-07"},"author":[{"orcid":"0000-0001-7745-9117","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","full_name":"Kragl, Bernhard","first_name":"Bernhard"},{"first_name":"Shaz","full_name":"Qadeer, Shaz","last_name":"Qadeer"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"publication_identifier":{"issn":["18688969"]},"date_updated":"2023-09-07T13:18:00Z","file":[{"file_size":745438,"date_created":"2018-12-12T10:18:46Z","file_id":"5368","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"system","checksum":"c90895f4c5fafc18ddc54d1c8848077e","file_name":"IST-2018-853-v2+2_concur2018.pdf","date_updated":"2020-07-14T12:44:44Z"}],"abstract":[{"text":"Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent computation threads. We present synchronization, a new proof rule that simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Modular verification is enabled via pending asynchronous calls in atomic summaries, and a complementary proof rule that eliminates pending asynchronous calls when components and their specifications are composed. We evaluate synchronization in the context of a multi-layer refinement verification methodology on a collection of benchmark programs.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publist_id":"7790","_id":"133","ddc":["000"],"publication_status":"published","file_date_updated":"2020-07-14T12:44:44Z","project":[{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S11402-N23"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"}],"title":"Synchronizing the asynchronous","alternative_title":["LIPIcs"],"department":[{"_id":"ToHe"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term &quot;leaky resistance.&quot; We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”."}],"file":[{"file_name":"2018_Plos_Chaudhry.pdf","date_updated":"2020-07-14T12:48:10Z","checksum":"527076f78265cd4ea192cd1569851587","file_size":4007095,"date_created":"2018-12-17T12:55:31Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_id":"5706","relation":"main_file"}],"date_updated":"2023-09-13T08:45:41Z","article_processing_charge":"Yes","author":[{"first_name":"Waqas","full_name":"Chaudhry, Waqas","last_name":"Chaudhry"},{"orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros","last_name":"Pleska","first_name":"Maros"},{"first_name":"Nilang","full_name":"Shah, Nilang","last_name":"Shah"},{"full_name":"Weiss, Howard","last_name":"Weiss","first_name":"Howard"},{"first_name":"Ingrid","full_name":"Mccall, Ingrid","last_name":"Mccall"},{"first_name":"Justin","last_name":"Meyer","full_name":"Meyer, Justin"},{"full_name":"Gupta, Animesh","last_name":"Gupta","first_name":"Animesh"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"last_name":"Levin","full_name":"Levin, Bruce","first_name":"Bruce"}],"language":[{"iso":"eng"}],"year":"2018","tmp":{"short":"CC BY (4.0)","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)"},"issue":"8","scopus_import":"1","has_accepted_license":"1","volume":16,"department":[{"_id":"CaGu"}],"title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","file_date_updated":"2020-07-14T12:48:10Z","publication_status":"published","ddc":["570"],"_id":"82","publist_id":"7972","publisher":"Public Library of Science","quality_controlled":"1","month":"08","date_created":"2018-12-11T11:44:32Z","citation":{"chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” <i>PLoS Biology</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pbio.2005971\">https://doi.org/10.1371/journal.pbio.2005971</a>.","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","ieee":"W. Chaudhry <i>et al.</i>, “Leaky resistance and the conditions for the existence of lytic bacteriophage,” <i>PLoS Biology</i>, vol. 16, no. 8. Public Library of Science, 2018.","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005971\">https://doi.org/10.1371/journal.pbio.2005971</a>","mla":"Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” <i>PLoS Biology</i>, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971\">10.1371/journal.pbio.2005971</a>.","ama":"Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. <i>PLoS Biology</i>. 2018;16(8). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971\">10.1371/journal.pbio.2005971</a>"},"oa_version":"Published Version","publication":"PLoS Biology","type":"journal_article","oa":1,"day":"16","external_id":{"isi":["000443383300024"]},"related_material":{"record":[{"id":"9810","relation":"research_data","status":"public"}]},"status":"public","article_number":"2005971","isi":1,"intvolume":"        16","date_published":"2018-08-16T00:00:00Z","doi":"10.1371/journal.pbio.2005971"},{"type":"dissertation","oa_version":"Published Version","citation":{"ama":"Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">10.15479/AT:ISTA:TH_1046</a>","mla":"Abusalah, Hamza M. <i>Proof Systems for Sustainable Decentralized Cryptocurrencies</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">10.15479/AT:ISTA:TH_1046</a>.","apa":"Abusalah, H. M. (2018). <i>Proof systems for sustainable decentralized cryptocurrencies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">https://doi.org/10.15479/AT:ISTA:TH_1046</a>","ieee":"H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018.","short":"H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018.","ista":"Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria.","chicago":"Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">https://doi.org/10.15479/AT:ISTA:TH_1046</a>."},"date_created":"2018-12-11T11:44:32Z","degree_awarded":"PhD","month":"09","pubrep_id":"1046","date_published":"2018-09-05T00:00:00Z","doi":"10.15479/AT:ISTA:TH_1046","related_material":{"record":[{"relation":"part_of_dissertation","id":"1229","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"1235"},{"id":"1236","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"559","relation":"part_of_dissertation"}]},"status":"public","oa":1,"day":"05","has_accepted_license":"1","year":"2018","publication_identifier":{"issn":["2663-337X"]},"author":[{"full_name":"Abusalah, Hamza M","last_name":"Abusalah","id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M"}],"language":[{"iso":"eng"}],"abstract":[{"text":"A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work.\r\nProofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","file":[{"checksum":"c4b5f7d111755d1396787f41886fc674","date_updated":"2020-07-14T12:48:11Z","file_name":"2018_Thesis_Abusalah.pdf","date_created":"2019-04-09T06:43:41Z","file_size":876241,"relation":"main_file","file_id":"6245","creator":"dernst","content_type":"application/pdf","access_level":"open_access"},{"checksum":"0f382ac56b471c48fd907d63eb87dafe","date_updated":"2020-07-14T12:48:11Z","file_name":"2018_Thesis_Abusalah_source.tar.gz","relation":"source_file","file_id":"6246","creator":"dernst","content_type":"application/x-gzip","access_level":"closed","date_created":"2019-04-09T06:43:41Z","file_size":2029190}],"date_updated":"2023-09-07T12:30:23Z","ec_funded":1,"_id":"83","publisher":"Institute of Science and Technology Austria","publist_id":"7971","ddc":["004"],"file_date_updated":"2020-07-14T12:48:11Z","publication_status":"published","title":"Proof systems for sustainable decentralized cryptocurrencies","page":"59","supervisor":[{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654"}],"project":[{"grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"alternative_title":["ISTA Thesis"],"department":[{"_id":"KrPi"}]},{"citation":{"short":"E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479.","ieee":"E. Gilad, T. A. Brown, M. Oskin, and Y. Etsion, “Snapshot based synchronization: A fast replacement for Hand-over-Hand locking,” presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy, 2018, vol. 11014, pp. 465–479.","chicago":"Gilad, Eran, Trevor A Brown, Mark Oskin, and Yoav Etsion. “Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking,” 11014:465–79. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">https://doi.org/10.1007/978-3-319-96983-1_33</a>.","ista":"Gilad E, Brown TA, Oskin M, Etsion Y. 2018. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11014, 465–479.","ama":"Gilad E, Brown TA, Oskin M, Etsion Y. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. In: Vol 11014. Springer; 2018:465-479. doi:<a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">10.1007/978-3-319-96983-1_33</a>","apa":"Gilad, E., Brown, T. A., Oskin, M., &#38; Etsion, Y. (2018). Snapshot based synchronization: A fast replacement for Hand-over-Hand locking (Vol. 11014, pp. 465–479). Presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">https://doi.org/10.1007/978-3-319-96983-1_33</a>","mla":"Gilad, Eran, et al. <i>Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking</i>. Vol. 11014, Springer, 2018, pp. 465–79, doi:<a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">10.1007/978-3-319-96983-1_33</a>."},"oa_version":"Preprint","date_created":"2018-12-11T11:44:33Z","type":"conference","quality_controlled":"1","acknowledgement":"Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14) and by a NSERC post-doctoral fellowship.","month":"08","status":"public","date_published":"2018-08-01T00:00:00Z","doi":"10.1007/978-3-319-96983-1_33","intvolume":"     11014","isi":1,"external_id":{"isi":["000851042300031"]},"day":"01","oa":1,"scopus_import":"1","year":"2018","volume":11014,"has_accepted_license":"1","article_processing_charge":"No","date_updated":"2023-09-18T09:32:36Z","file":[{"checksum":"13a3f250be8878405e791b53c19722ad","date_updated":"2020-07-14T12:48:14Z","file_name":"2018_Brown.pdf","relation":"main_file","file_id":"5954","creator":"dernst","content_type":"application/pdf","access_level":"open_access","date_created":"2019-02-12T07:40:40Z","file_size":665372}],"abstract":[{"text":"Concurrent accesses to shared data structures must be synchronized to avoid data races. Coarse-grained synchronization, which locks the entire data structure, is easy to implement but does not scale. Fine-grained synchronization can scale well, but can be hard to reason about. Hand-over-hand locking, in which operations are pipelined as they traverse the data structure, combines fine-grained synchronization with ease of use. However, the traditional implementation suffers from inherent overheads. This paper introduces snapshot-based synchronization (SBS), a novel hand-over-hand locking mechanism. SBS decouples the synchronization state from the data, significantly improving cache utilization. Further, it relies on guarantees provided by pipelining to minimize synchronization that requires cross-thread communication. Snapshot-based synchronization thus scales much better than traditional hand-over-hand locking, while maintaining the same ease of use.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"author":[{"first_name":"Eran","full_name":"Gilad, Eran","last_name":"Gilad"},{"first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A","last_name":"Brown"},{"first_name":"Mark","last_name":"Oskin","full_name":"Oskin, Mark"},{"last_name":"Etsion","full_name":"Etsion, Yoav","first_name":"Yoav"}],"conference":{"end_date":"2018-08-31","location":"Turin, Italy","start_date":"2018-08-27","name":"Euro-Par: European Conference on Parallel Processing"},"publication_identifier":{"issn":["03029743"]},"ddc":["000"],"publication_status":"published","file_date_updated":"2020-07-14T12:48:14Z","publisher":"Springer","publist_id":"7969","_id":"85","alternative_title":["LNCS"],"department":[{"_id":"DaAl"}],"project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"page":"465 - 479","title":"Snapshot based synchronization: A fast replacement for Hand-over-Hand locking"},{"type":"preprint","year":"2018","publication":"bioRxiv","date_created":"2020-09-21T12:01:50Z","oa_version":"Preprint","citation":{"mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/494088\">https://doi.org/10.1101/494088</a>","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/494088\">https://doi.org/10.1101/494088</a>.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, <a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>.","ieee":"A. Llorca <i>et al.</i>, “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.)."},"language":[{"iso":"eng"}],"month":"12","author":[{"last_name":"Llorca","full_name":"Llorca, Alfredo","first_name":"Alfredo"},{"last_name":"Ciceri","full_name":"Ciceri, Gabriele","first_name":"Gabriele"},{"first_name":"Robert J","last_name":"Beattie","full_name":"Beattie, Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753"},{"first_name":"Fong K.","last_name":"Wong","full_name":"Wong, Fong K."},{"first_name":"Giovanni","last_name":"Diana","full_name":"Diana, Giovanni"},{"first_name":"Eleni","full_name":"Serafeimidou, Eleni","last_name":"Serafeimidou"},{"first_name":"Marian","full_name":"Fernández-Otero, Marian","last_name":"Fernández-Otero"},{"first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","last_name":"Streicher"},{"last_name":"Arnold","full_name":"Arnold, Sebastian J.","first_name":"Sebastian J."},{"first_name":"Martin","full_name":"Meyer, Martin","last_name":"Meyer"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Miguel","full_name":"Maravall, Miguel","last_name":"Maravall"},{"last_name":"Marín","full_name":"Marín, Oscar","first_name":"Oscar"}],"date_updated":"2021-01-12T08:20:00Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex."}],"date_published":"2018-12-13T00:00:00Z","doi":"10.1101/494088","publisher":"Cold Spring Harbor Laboratory","_id":"8547","ec_funded":1,"status":"public","publication_status":"submitted","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780"},{"grant_number":"M02416","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/494088"}],"day":"13","oa":1,"title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","department":[{"_id":"SiHi"}]},{"type":"book_chapter","date_created":"2018-12-11T11:44:33Z","oa_version":"Submitted Version","citation":{"ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in <i>Principles of Modeling</i>, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In <i>Principles of Modeling</i>, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">https://doi.org/10.1007/978-3-319-95246-8_9</a>.","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. <i>Principles of Modeling</i>. Vol 10760. Springer; 2018:143-161. doi:<a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">10.1007/978-3-319-95246-8_9</a>","mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” <i>Principles of Modeling</i>, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:<a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">10.1007/978-3-319-95246-8_9</a>.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, &#38; M. Sirjani (Eds.), <i>Principles of Modeling</i> (Vol. 10760, pp. 143–161). Springer. <a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">https://doi.org/10.1007/978-3-319-95246-8_9</a>"},"publication":"Principles of Modeling","month":"07","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","quality_controlled":"1","intvolume":"     10760","doi":"10.1007/978-3-319-95246-8_9","date_published":"2018-07-20T00:00:00Z","status":"public","oa":1,"editor":[{"last_name":"Lohstroh","full_name":"Lohstroh, Marten","first_name":"Marten"},{"full_name":"Derler, Patricia","last_name":"Derler","first_name":"Patricia"},{"first_name":"Marjan","last_name":"Sirjani","full_name":"Sirjani, Marjan"}],"day":"20","has_accepted_license":"1","volume":10760,"year":"2018","scopus_import":1,"author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","first_name":"Jan"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms."}],"date_updated":"2021-01-12T08:20:14Z","file":[{"file_name":"2018_PrinciplesModeling_Chatterjee.pdf","date_updated":"2020-07-14T12:48:14Z","checksum":"9995c6ce6957333baf616fc4f20be597","file_size":516307,"date_created":"2019-11-19T08:22:18Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_id":"7053","relation":"main_file"}],"_id":"86","ec_funded":1,"publist_id":"7968","publisher":"Springer","file_date_updated":"2020-07-14T12:48:14Z","ddc":["000"],"publication_status":"published","page":"143 - 161","title":"Computing average response time","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"alternative_title":["LNCS"]},{"oa":1,"day":"09","external_id":{"pmid":["29426833"],"isi":["000424630400037"]},"keyword":["Multidisciplinary"],"article_number":"2724","isi":1,"intvolume":"         8","doi":"10.1038/s41598-018-19947-1","date_published":"2018-02-09T00:00:00Z","status":"public","month":"02","quality_controlled":"1","type":"journal_article","date_created":"2020-10-06T16:33:37Z","citation":{"apa":"Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., &#38; Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-018-19947-1\">https://doi.org/10.1038/s41598-018-19947-1</a>","mla":"Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” <i>Scientific Reports</i>, vol. 8, 2724, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-19947-1\">10.1038/s41598-018-19947-1</a>.","ama":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. 2018;8. doi:<a href=\"https://doi.org/10.1038/s41598-018-19947-1\">10.1038/s41598-018-19947-1</a>","ista":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.","chicago":"Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” <i>Scientific Reports</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41598-018-19947-1\">https://doi.org/10.1038/s41598-018-19947-1</a>.","ieee":"C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S. W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA,” <i>Scientific Reports</i>, vol. 8. Springer Nature, 2018.","short":"C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell, Scientific Reports 8 (2018)."},"oa_version":"Published Version","publication":"Scientific Reports","title":"Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA","department":[{"_id":"JoDa"}],"_id":"8618","article_type":"original","publisher":"Springer Nature","file_date_updated":"2020-10-06T16:35:16Z","ddc":["570"],"publication_status":"published","publication_identifier":{"issn":["2045-2322"]},"author":[{"last_name":"Gregor","full_name":"Gregor, Carola","first_name":"Carola"},{"last_name":"Sidenstein","full_name":"Sidenstein, Sven C.","first_name":"Sven C."},{"full_name":"Andresen, Martin","last_name":"Andresen","first_name":"Martin"},{"first_name":"Steffen J.","last_name":"Sahl","full_name":"Sahl, Steffen J."},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973"},{"first_name":"Stefan W.","last_name":"Hell","full_name":"Hell, Stefan W."}],"language":[{"iso":"eng"}],"pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT nanoscopy have been developed from fluorescent proteins of the GFP superfamily. These proteins are bright, but exhibit several drawbacks such as relatively large size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore, RSFPs from other origins with improved properties need to be explored. Here, we report the development of two RSFPs based on the LOV domain of the photoreceptor protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by association with the abundant cellular cofactor flavin mononucleotide (FMN). Under illumination with blue and ultraviolet light, they undergo a photocycle, making these proteins inherently photoswitchable. Our first improved variant, rsLOV1, can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy of living cells with a resolution of down to 50 nm. In addition to their smaller size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date. Therefore, LOV-domain-based RSFPs have potential for applications where the switching speed of GFP-based proteins is limiting."}],"file":[{"relation":"main_file","file_id":"8619","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2020-10-06T16:35:16Z","file_size":2818077,"success":1,"checksum":"e642080fcbde9584c63544f587c74f03","date_updated":"2020-10-06T16:35:16Z","file_name":"2018_ScientificReports_Gregor.pdf"}],"date_updated":"2023-09-19T15:04:49Z","article_processing_charge":"No","has_accepted_license":"1","volume":8,"year":"2018","tmp":{"short":"CC BY (4.0)","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)"}},{"oa":1,"day":"01","main_file_link":[{"url":"https://arxiv.org/abs/1705.02870","open_access":"1"}],"external_id":{"arxiv":["1705.02870"],"isi":["000442893500018"]},"isi":1,"intvolume":"        28","doi":"10.1214/18-AAP1389","date_published":"2018-10-01T00:00:00Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6287"}]},"status":"public","month":"10","arxiv":1,"quality_controlled":"1","type":"journal_article","date_created":"2018-12-11T11:44:33Z","citation":{"ista":"Edelsbrunner H, Nikitenko A. 2018. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 28(5), 3215–3238.","chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2018. <a href=\"https://doi.org/10.1214/18-AAP1389\">https://doi.org/10.1214/18-AAP1389</a>.","short":"H. Edelsbrunner, A. Nikitenko, Annals of Applied Probability 28 (2018) 3215–3238.","ieee":"H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics,” <i>Annals of Applied Probability</i>, vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018.","apa":"Edelsbrunner, H., &#38; Nikitenko, A. (2018). Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/18-AAP1389\">https://doi.org/10.1214/18-AAP1389</a>","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” <i>Annals of Applied Probability</i>, vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:<a href=\"https://doi.org/10.1214/18-AAP1389\">10.1214/18-AAP1389</a>.","ama":"Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. <i>Annals of Applied Probability</i>. 2018;28(5):3215-3238. doi:<a href=\"https://doi.org/10.1214/18-AAP1389\">10.1214/18-AAP1389</a>"},"oa_version":"Preprint","publication":"Annals of Applied Probability","page":"3215 - 3238","title":"Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics","project":[{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"department":[{"_id":"HeEd"}],"_id":"87","publist_id":"7967","article_type":"original","publisher":"Institute of Mathematical Statistics","publication_status":"published","author":[{"first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"orcid":"0000-0002-0659-3201","full_name":"Nikitenko, Anton","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","first_name":"Anton"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Using the geodesic distance on the n-dimensional sphere, we study the expected radius function of the Delaunay mosaic of a random set of points. Specifically, we consider the partition of the mosaic into intervals of the radius function and determine the expected number of intervals whose radii are less than or equal to a given threshold. We find that the expectations are essentially the same as for the Poisson–Delaunay mosaic in n-dimensional Euclidean space. Assuming the points are not contained in a hemisphere, the Delaunay mosaic is isomorphic to the boundary complex of the convex hull in Rn+1, so we also get the expected number of faces of a random inscribed polytope. As proved in Antonelli et al. [Adv. in Appl. Probab. 9–12 (1977–1980)], an orthant section of the n-sphere is isometric to the standard n-simplex equipped with the Fisher information metric. It follows that the latter space has similar stochastic properties as the n-dimensional Euclidean space. Our results are therefore relevant in information geometry and in population genetics."}],"date_updated":"2023-09-15T12:10:35Z","article_processing_charge":"No","volume":28,"year":"2018","scopus_import":"1","issue":"5"},{"status":"public","date_published":"2018-07-01T00:00:00Z","doi":"10.15479/AT:ISTA:th1064","oa":1,"day":"01","date_created":"2018-12-11T11:44:08Z","citation":{"chicago":"Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">https://doi.org/10.15479/AT:ISTA:th1064</a>.","ista":"Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria.","short":"V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo , Institute of Science and Technology Austria, 2018.","ieee":"V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ,” Institute of Science and Technology Austria, 2018.","apa":"Belyaeva, V. (2018). <i>Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">https://doi.org/10.15479/AT:ISTA:th1064</a>","mla":"Belyaeva, Vera. <i>Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo </i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">10.15479/AT:ISTA:th1064</a>.","ama":"Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">10.15479/AT:ISTA:th1064</a>"},"oa_version":"Published Version","degree_awarded":"PhD","type":"dissertation","pubrep_id":"1064","month":"07","file_date_updated":"2021-02-11T11:17:16Z","ddc":["570"],"publication_status":"published","_id":"9","publist_id":"8047","publisher":"Institute of Science and Technology Austria","department":[{"_id":"DaSi"}],"alternative_title":["ISTA Thesis"],"title":"Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ","page":"96","supervisor":[{"orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"}],"year":"2018","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Immune cells migrating to the sites of infection navigate through diverse tissue architectures and switch their migratory mechanisms upon demand. However, little is known about systemic regulators that could allow the acquisition of these mechanisms. We performed a genetic screen in Drosophila melanogaster to identify regulators of germband invasion by embryonic macrophages into the confined space between the ectoderm and mesoderm. We have found that bZIP circadian transcription factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are enriched in the macrophages during migration and genetically interact to control it. Kayak sets a less coordinated mode of migration of the macrophage group and increases the probability and length of Levy walks. Intriguingly, the motility of kayak mutant macrophages was also strongly affected during initial germband invasion but not along another less confined route. Inhibiting Rho1 signaling within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly suggesting that migrating macrophages have to overcome a barrier imposed by the stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance of the round cell shape and the rear edge translocation of the macrophages invading the germband. Complementary to this, the cortical actin cytoskeleton of Kayak- deficient macrophages was strongly affected. RNA sequencing revealed the filamin Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation and immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages for germband invasion, and expression of constitutively active Diaphanous in macrophages was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak, through its targets, increases actin polymerization and cortical tension in macrophages and thus allows extra force generation necessary for macrophage dissemination and migration through confined stiff tissues, while Vrille counterbalances it.","lang":"eng"}],"file":[{"file_size":102737483,"date_created":"2019-04-08T14:13:12Z","file_id":"6243","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","creator":"dernst","checksum":"d27b2465cb70d0c9678a0381b9b6ced1","file_name":"2018_Thesis_Belyaeva_source.docx","date_updated":"2020-07-14T12:48:14Z","embargo_to":"open_access"},{"file_size":88077843,"date_created":"2019-04-08T14:14:08Z","file_id":"6244","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","checksum":"a2939b61bde2de7b8ced77bbae0eaaed","file_name":"2018_Thesis_Belyaeva.pdf","date_updated":"2021-02-11T11:17:16Z","embargo":"2019-11-19"}],"date_updated":"2023-09-07T12:43:10Z","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"author":[{"first_name":"Vera","last_name":"Belyaeva","full_name":"Belyaeva, Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}]},{"external_id":{"isi":["000424842400019"]},"day":"29","oa":1,"date_published":"2018-01-29T00:00:00Z","doi":"10.1242/jcs.204198","intvolume":"       131","isi":1,"article_number":"jcs.204198","status":"public","pubrep_id":"988","month":"01","quality_controlled":"1","type":"journal_article","publication":"Journal of Cell Science","citation":{"ama":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. <i>Journal of Cell Science</i>. 2018;131(2). doi:<a href=\"https://doi.org/10.1242/jcs.204198\">10.1242/jcs.204198</a>","mla":"Tejos, Ricardo, et al. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>, vol. 131, no. 2, jcs. 204198, Company of Biologists, 2018, doi:<a href=\"https://doi.org/10.1242/jcs.204198\">10.1242/jcs.204198</a>.","apa":"Tejos, R., Rodríguez Furlán, C., Adamowski, M., Sauer, M., Norambuena, L., &#38; Friml, J. (2018). PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.204198\">https://doi.org/10.1242/jcs.204198</a>","ieee":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, and J. Friml, “PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana,” <i>Journal of Cell Science</i>, vol. 131, no. 2. Company of Biologists, 2018.","short":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, J. Friml, Journal of Cell Science 131 (2018).","ista":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. 2018. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. 131(2), jcs. 204198.","chicago":"Tejos, Ricardo, Cecilia Rodríguez Furlán, Maciek Adamowski, Michael Sauer, Lorena Norambuena, and Jiří Friml. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>. Company of Biologists, 2018. <a href=\"https://doi.org/10.1242/jcs.204198\">https://doi.org/10.1242/jcs.204198</a>."},"oa_version":"Published Version","date_created":"2018-12-11T11:49:10Z","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"title":"PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana","department":[{"_id":"JiFr"}],"publisher":"Company of Biologists","publist_id":"6530","ec_funded":1,"_id":"913","publication_status":"published","file_date_updated":"2020-07-14T12:48:15Z","ddc":["581"],"language":[{"iso":"eng"}],"author":[{"last_name":"Tejos","full_name":"Tejos, Ricardo","first_name":"Ricardo"},{"full_name":"Rodríguez Furlán, Cecilia","last_name":"Rodríguez Furlán","first_name":"Cecilia"},{"last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","first_name":"Maciek","orcid":"0000-0001-6463-5257"},{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"last_name":"Norambuena","full_name":"Norambuena, Lorena","first_name":"Lorena"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí"}],"publication_identifier":{"issn":["00219533"]},"article_processing_charge":"No","date_updated":"2025-05-07T11:12:29Z","file":[{"checksum":"bf156c20a4f117b4b932370d54cbac8c","file_name":"2017_adamowski_PATELLINS_are.pdf","date_updated":"2020-07-14T12:48:15Z","file_id":"6299","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_size":14925985,"date_created":"2019-04-12T08:46:32Z"}],"abstract":[{"text":"Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We performed a microarray-based approach to find regulators of the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs (PATL). Here, we show that PATLs are expressed in partially overlapping cells types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia, and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests PATLs redundantly play a crucial role in polarity and patterning in Arabidopsis.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":131,"has_accepted_license":"1","scopus_import":"1","issue":"2","year":"2018"},{"volume":4,"issue":"S1","scopus_import":"1","year":"2018","publication_identifier":{"issn":["2500-2287"],"eissn":["2500-2295"]},"author":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973"}],"language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","date_updated":"2021-12-03T07:31:05Z","_id":"9229","publisher":"Lobachevsky State University of Nizhny Novgorod","article_type":"letter_note","publication_status":"published","title":"Diffraction-unlimited optical imaging for synaptic physiology","page":"11","alternative_title":["Molecular and cellular neuroscience"],"department":[{"_id":"JoDa"}],"type":"journal_article","oa_version":"Published Version","citation":{"mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” <i>Opera Medica et Physiologica</i>, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:<a href=\"https://doi.org/10.20388/omp2018.00s1.001\">10.20388/omp2018.00s1.001</a>.","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. <i>Opera Medica et Physiologica</i>. Lobachevsky State University of Nizhny Novgorod. <a href=\"https://doi.org/10.20388/omp2018.00s1.001\">https://doi.org/10.20388/omp2018.00s1.001</a>","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. <i>Opera Medica et Physiologica</i>. 2018;4(S1):11. doi:<a href=\"https://doi.org/10.20388/omp2018.00s1.001\">10.20388/omp2018.00s1.001</a>","chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” <i>Opera Medica et Physiologica</i>. Lobachevsky State University of Nizhny Novgorod, 2018. <a href=\"https://doi.org/10.20388/omp2018.00s1.001\">https://doi.org/10.20388/omp2018.00s1.001</a>.","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11.","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” <i>Opera Medica et Physiologica</i>, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018."},"date_created":"2021-03-07T23:01:25Z","publication":"Opera Medica et Physiologica","month":"06","quality_controlled":"1","date_published":"2018-06-30T00:00:00Z","doi":"10.20388/omp2018.00s1.001","intvolume":"         4","status":"public","oa":1,"day":"30","main_file_link":[{"open_access":"1","url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience"}]},{"project":[{"_id":"254BA948-B435-11E9-9278-68D0E5697425","name":"Probing development and reversibility of autism spectrum disorders","grant_number":"401299"}],"title":"A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features","page":"48 - 54","department":[{"_id":"GaNo"}],"publist_id":"7016","article_type":"original","publisher":"BMJ Publishing Group","_id":"691","publication_status":"published","language":[{"iso":"eng"}],"pmid":1,"publication_identifier":{"issn":["0022-2593"]},"author":[{"full_name":"Marin Valencia, Isaac","last_name":"Marin Valencia","first_name":"Isaac"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia","first_name":"Gaia","orcid":"0000-0002-7673-7178"},{"first_name":"Anide","full_name":"Johansen, Anide","last_name":"Johansen"},{"full_name":"Rosti, Başak","last_name":"Rosti","first_name":"Başak"},{"first_name":"Mahmoud","full_name":"Issa, Mahmoud","last_name":"Issa"},{"first_name":"Damir","last_name":"Musaev","full_name":"Musaev, Damir"},{"full_name":"Bhat, Gifty","last_name":"Bhat","first_name":"Gifty"},{"full_name":"Scott, Eric","last_name":"Scott","first_name":"Eric"},{"last_name":"Silhavy","full_name":"Silhavy, Jennifer","first_name":"Jennifer"},{"last_name":"Stanley","full_name":"Stanley, Valentina","first_name":"Valentina"},{"first_name":"Rasim","last_name":"Rosti","full_name":"Rosti, Rasim"},{"last_name":"Gleeson","full_name":"Gleeson, Jeremy","first_name":"Jeremy"},{"last_name":"Imam","full_name":"Imam, Farhad","first_name":"Farhad"},{"first_name":"Maha","full_name":"Zaki, Maha","last_name":"Zaki"},{"full_name":"Gleeson, Joseph","last_name":"Gleeson","first_name":"Joseph"}],"date_updated":"2023-10-16T09:55:43Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Background: Transport protein particle (TRAPP) is a multisubunit complex that regulates membrane trafficking through the Golgi apparatus. The clinical phenotype associated with mutations in various TRAPP subunits has allowed elucidation of their functions in specific tissues. The role of some subunits in human disease, however, has not been fully established, and their functions remain uncertain.\r\n\r\nObjective: We aimed to expand the range of neurodevelopmental disorders associated with mutations in TRAPP subunits by exome sequencing of consanguineous families.\r\n\r\nMethods: Linkage and homozygosity mapping and candidate gene analysis were used to identify homozygous mutations in families. Patient fibroblasts were used to study splicing defect and zebrafish to model the disease.\r\n\r\nResults: We identified six individuals from three unrelated families with a founder homozygous splice mutation in TRAPPC6B, encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features, and showed splicing defect. Zebrafish trappc6b morphants replicated the human phenotype, displaying decreased head size and neuronal hyperexcitability, leading to a lower seizure threshold.\r\n\r\nConclusion: This study provides clinical and functional evidence of the role of TRAPPC6B in brain development and function.","lang":"eng"}],"volume":55,"year":"2018","issue":"1","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056005/","open_access":"1"}],"day":"01","external_id":{"isi":["000418199800007"],"pmid":["28626029"]},"oa":1,"intvolume":"        55","doi":"10.1136/jmedgenet-2017-104627","date_published":"2018-01-01T00:00:00Z","isi":1,"status":"public","month":"01","quality_controlled":"1","type":"journal_article","publication":"Journal of Medical Genetics","date_created":"2018-12-11T11:47:57Z","citation":{"ista":"Marin Valencia I, Novarino G, Johansen A, Rosti B, Issa M, Musaev D, Bhat G, Scott E, Silhavy J, Stanley V, Rosti R, Gleeson J, Imam F, Zaki M, Gleeson J. 2018. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. Journal of Medical Genetics. 55(1), 48–54.","chicago":"Marin Valencia, Isaac, Gaia Novarino, Anide Johansen, Başak Rosti, Mahmoud Issa, Damir Musaev, Gifty Bhat, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and Autistic Features.” <i>Journal of Medical Genetics</i>. BMJ Publishing Group, 2018. <a href=\"https://doi.org/10.1136/jmedgenet-2017-104627\">https://doi.org/10.1136/jmedgenet-2017-104627</a>.","ieee":"I. Marin Valencia <i>et al.</i>, “A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features,” <i>Journal of Medical Genetics</i>, vol. 55, no. 1. BMJ Publishing Group, pp. 48–54, 2018.","short":"I. Marin Valencia, G. Novarino, A. Johansen, B. Rosti, M. Issa, D. Musaev, G. Bhat, E. Scott, J. Silhavy, V. Stanley, R. Rosti, J. Gleeson, F. Imam, M. Zaki, J. Gleeson, Journal of Medical Genetics 55 (2018) 48–54.","mla":"Marin Valencia, Isaac, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and Autistic Features.” <i>Journal of Medical Genetics</i>, vol. 55, no. 1, BMJ Publishing Group, 2018, pp. 48–54, doi:<a href=\"https://doi.org/10.1136/jmedgenet-2017-104627\">10.1136/jmedgenet-2017-104627</a>.","apa":"Marin Valencia, I., Novarino, G., Johansen, A., Rosti, B., Issa, M., Musaev, D., … Gleeson, J. (2018). A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. <i>Journal of Medical Genetics</i>. BMJ Publishing Group. <a href=\"https://doi.org/10.1136/jmedgenet-2017-104627\">https://doi.org/10.1136/jmedgenet-2017-104627</a>","ama":"Marin Valencia I, Novarino G, Johansen A, et al. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. <i>Journal of Medical Genetics</i>. 2018;55(1):48-54. doi:<a href=\"https://doi.org/10.1136/jmedgenet-2017-104627\">10.1136/jmedgenet-2017-104627</a>"},"oa_version":"Submitted Version"},{"has_accepted_license":"1","volume":194,"year":"2018","tmp":{"short":"CC BY (4.0)","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)"},"issue":"1","scopus_import":"1","author":[{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","full_name":"Akopyan, Arseniy","first_name":"Arseniy"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"We consider families of confocal conics and two pencils of Apollonian circles having the same foci. We will show that these families of curves generate trivial 3-webs and find the exact formulas describing them.","lang":"eng"}],"date_updated":"2023-09-08T11:40:29Z","file":[{"file_id":"7222","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"kschuh","file_size":1140860,"date_created":"2020-01-03T11:35:08Z","checksum":"1febcfc1266486053a069e3425ea3713","file_name":"2018_Springer_Akopyan.pdf","date_updated":"2020-07-14T12:47:44Z"}],"article_processing_charge":"Yes (via OA deal)","_id":"692","ec_funded":1,"publist_id":"7014","article_type":"original","publisher":"Springer","publication_status":"published","ddc":["510"],"file_date_updated":"2020-07-14T12:47:44Z","page":"55 - 64","title":"3-Webs generated by confocal conics and circles","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"department":[{"_id":"HeEd"}],"type":"journal_article","date_created":"2018-12-11T11:47:57Z","oa_version":"Published Version","citation":{"ama":"Akopyan A. 3-Webs generated by confocal conics and circles. <i>Geometriae Dedicata</i>. 2018;194(1):55-64. doi:<a href=\"https://doi.org/10.1007/s10711-017-0265-6\">10.1007/s10711-017-0265-6</a>","apa":"Akopyan, A. (2018). 3-Webs generated by confocal conics and circles. <i>Geometriae Dedicata</i>. Springer. <a href=\"https://doi.org/10.1007/s10711-017-0265-6\">https://doi.org/10.1007/s10711-017-0265-6</a>","mla":"Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” <i>Geometriae Dedicata</i>, vol. 194, no. 1, Springer, 2018, pp. 55–64, doi:<a href=\"https://doi.org/10.1007/s10711-017-0265-6\">10.1007/s10711-017-0265-6</a>.","short":"A. Akopyan, Geometriae Dedicata 194 (2018) 55–64.","ieee":"A. Akopyan, “3-Webs generated by confocal conics and circles,” <i>Geometriae Dedicata</i>, vol. 194, no. 1. Springer, pp. 55–64, 2018.","chicago":"Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” <i>Geometriae Dedicata</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s10711-017-0265-6\">https://doi.org/10.1007/s10711-017-0265-6</a>.","ista":"Akopyan A. 2018. 3-Webs generated by confocal conics and circles. Geometriae Dedicata. 194(1), 55–64."},"publication":"Geometriae Dedicata","month":"06","quality_controlled":"1","isi":1,"intvolume":"       194","doi":"10.1007/s10711-017-0265-6","date_published":"2018-06-01T00:00:00Z","status":"public","oa":1,"day":"01","external_id":{"isi":["000431418800004"]}},{"page":"480-499","title":"SpaceMint: A cryptocurrency based on proofs of space","project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"alternative_title":["LNCS"],"department":[{"_id":"KrPi"}],"ec_funded":1,"_id":"6941","publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Park, Sunoo","last_name":"Park","first_name":"Sunoo"},{"full_name":"Kwon, Albert","last_name":"Kwon","first_name":"Albert"},{"first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer"},{"first_name":"Peter","full_name":"Gazi, Peter","last_name":"Gazi","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F"},{"orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"conference":{"name":"FC: Financial Cryptography and Data Security","start_date":"2018-02-26","location":"Nieuwpoort, Curacao","end_date":"2018-03-02"},"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783662583869","9783662583876"]},"language":[{"iso":"eng"}],"abstract":[{"text":"Bitcoin has become the most successful cryptocurrency ever deployed, and its most distinctive feature is that it is decentralized. Its underlying protocol (Nakamoto consensus) achieves this by using proof of work, which has the drawback that it causes the consumption of vast amounts of energy to maintain the ledger. Moreover, Bitcoin mining dynamics have become less distributed over time.\r\n\r\nTowards addressing these issues, we propose SpaceMint, a cryptocurrency based on proofs of space instead of proofs of work. Miners in SpaceMint dedicate disk space rather than computation. We argue that SpaceMint’s design solves or alleviates several of Bitcoin’s issues: most notably, its large energy consumption. SpaceMint also rewards smaller miners fairly according to their contribution to the network, thus incentivizing more distributed participation.\r\n\r\nThis paper adapts proof of space to enable its use in cryptocurrency, studies the attacks that can arise against a Bitcoin-like blockchain that uses proof of space, and proposes a new blockchain format and transaction types to address these attacks. Our prototype shows that initializing 1 TB for mining takes about a day (a one-off setup cost), and miners spend on average just a fraction of a second per block mined. Finally, we provide a game-theoretic analysis modeling SpaceMint as an extensive game (the canonical game-theoretic notion for games that take place over time) and show that this stylized game satisfies a strong equilibrium notion, thereby arguing for SpaceMint ’s stability and consensus.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","date_updated":"2023-09-19T15:02:13Z","volume":10957,"scopus_import":"1","year":"2018","oa":1,"external_id":{"isi":["000540656400026"]},"main_file_link":[{"url":"https://eprint.iacr.org/2015/528","open_access":"1"}],"day":"07","isi":1,"date_published":"2018-12-07T00:00:00Z","doi":"10.1007/978-3-662-58387-6_26","intvolume":"     10957","status":"public","month":"12","quality_controlled":"1","type":"conference","oa_version":"Submitted Version","citation":{"ieee":"S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J. F. Alwen, and K. Z. Pietrzak, “SpaceMint: A cryptocurrency based on proofs of space,” in <i>22nd International Conference on Financial Cryptography and Data Security</i>, Nieuwpoort, Curacao, 2018, vol. 10957, pp. 480–499.","short":"S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J.F. Alwen, K.Z. Pietrzak, in:, 22nd International Conference on Financial Cryptography and Data Security, Springer Nature, 2018, pp. 480–499.","chicago":"Park, Sunoo, Albert Kwon, Georg Fuchsbauer, Peter Gazi, Joel F Alwen, and Krzysztof Z Pietrzak. “SpaceMint: A Cryptocurrency Based on Proofs of Space.” In <i>22nd International Conference on Financial Cryptography and Data Security</i>, 10957:480–99. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-3-662-58387-6_26\">https://doi.org/10.1007/978-3-662-58387-6_26</a>.","ista":"Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. 2018. SpaceMint: A cryptocurrency based on proofs of space. 22nd International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 10957, 480–499.","ama":"Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. SpaceMint: A cryptocurrency based on proofs of space. In: <i>22nd International Conference on Financial Cryptography and Data Security</i>. Vol 10957. Springer Nature; 2018:480-499. doi:<a href=\"https://doi.org/10.1007/978-3-662-58387-6_26\">10.1007/978-3-662-58387-6_26</a>","mla":"Park, Sunoo, et al. “SpaceMint: A Cryptocurrency Based on Proofs of Space.” <i>22nd International Conference on Financial Cryptography and Data Security</i>, vol. 10957, Springer Nature, 2018, pp. 480–99, doi:<a href=\"https://doi.org/10.1007/978-3-662-58387-6_26\">10.1007/978-3-662-58387-6_26</a>.","apa":"Park, S., Kwon, A., Fuchsbauer, G., Gazi, P., Alwen, J. F., &#38; Pietrzak, K. Z. (2018). SpaceMint: A cryptocurrency based on proofs of space. In <i>22nd International Conference on Financial Cryptography and Data Security</i> (Vol. 10957, pp. 480–499). Nieuwpoort, Curacao: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-58387-6_26\">https://doi.org/10.1007/978-3-662-58387-6_26</a>"},"date_created":"2019-10-14T06:35:38Z","publication":"22nd International Conference on Financial Cryptography and Data Security"},{"type":"journal_article","date_created":"2018-12-11T11:44:07Z","oa_version":"Published Version","citation":{"ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. <i>Science</i>. 2018;362(6417):941-945. doi:<a href=\"https://doi.org/10.1126/science.aat4793\">10.1126/science.aat4793</a>","apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., &#38; Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.aat4793\">https://doi.org/10.1126/science.aat4793</a>","mla":"Stroeymeyt, Nathalie, et al. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” <i>Science</i>, vol. 362, no. 6417, AAAS, 2018, pp. 941–45, doi:<a href=\"https://doi.org/10.1126/science.aat4793\">10.1126/science.aat4793</a>.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, Science 362 (2018) 941–945.","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect,” <i>Science</i>, vol. 362, no. 6417. AAAS, pp. 941–945, 2018.","chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” <i>Science</i>. AAAS, 2018. <a href=\"https://doi.org/10.1126/science.aat4793\">https://doi.org/10.1126/science.aat4793</a>.","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect. Science. 362(6417), 941–945."},"publication":"Science","month":"11","acknowledgement":"This project was funded by two European Research Council Advanced Grants (Social Life, 249375, and resiliANT, 741491) and two Swiss National Science Foundation grants (CR32I3_141063 and 310030_156732) to L.K. and a European Research Council Starting Grant (SocialVaccines, 243071) to S.C.","quality_controlled":"1","isi":1,"intvolume":"       362","date_published":"2018-11-23T00:00:00Z","doi":"10.1126/science.aat4793","related_material":{"link":[{"url":"https://ist.ac.at/en/news/for-ants-unity-is-strength-and-health/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"status":"public","id":"13055","relation":"research_data"}]},"status":"public","oa":1,"main_file_link":[{"open_access":"1","url":"https://serval.unil.ch/resource/serval:BIB_E9228C205467.P001/REF.pdf"}],"day":"23","external_id":{"isi":["000451124500041"]},"volume":362,"year":"2018","issue":"6417","scopus_import":"1","publication_identifier":{"issn":["1095-9203"]},"author":[{"full_name":"Stroeymeyt, Nathalie","last_name":"Stroeymeyt","first_name":"Nathalie"},{"last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","first_name":"Anna V"},{"full_name":"Crespi, Alessandro","last_name":"Crespi","first_name":"Alessandro"},{"first_name":"Danielle","last_name":"Mersch","full_name":"Mersch, Danielle"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868"},{"first_name":"Laurent","full_name":"Keller, Laurent","last_name":"Keller"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Animal social networks are shaped by multiple selection pressures, including the need to ensure efficient communication and functioning while simultaneously limiting disease transmission. Social animals could potentially further reduce epidemic risk by altering their social networks in the presence of pathogens, yet there is currently no evidence for such pathogen-triggered responses. We tested this hypothesis experimentally in the ant Lasius niger using a combination of automated tracking, controlled pathogen exposure, transmission quantification, and temporally explicit simulations. Pathogen exposure induced behavioral changes in both exposed ants and their nestmates, which helped contain the disease by reinforcing key transmission-inhibitory properties of the colony's contact network. This suggests that social network plasticity in response to pathogens is an effective strategy for mitigating the effects of disease in social groups."}],"date_updated":"2023-10-17T11:50:05Z","article_processing_charge":"No","_id":"7","ec_funded":1,"article_type":"original","publist_id":"8049","publisher":"AAAS","publication_status":"published","title":"Social network plasticity decreases disease transmission in a eusocial insect","page":"941 - 945","project":[{"grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"SyCr"}]},{"quality_controlled":"1","month":"10","arxiv":1,"citation":{"apa":"Nejjar, P. (2018). Transition to shocks in TASEP and decoupling of last passage times. <i>Latin American Journal of Probability and Mathematical Statistics</i>. Instituto Nacional de Matematica Pura e Aplicada. <a href=\"https://doi.org/10.30757/ALEA.v15-49\">https://doi.org/10.30757/ALEA.v15-49</a>","mla":"Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage Times.” <i>Latin American Journal of Probability and Mathematical Statistics</i>, vol. 15, no. 2, Instituto Nacional de Matematica Pura e Aplicada, 2018, pp. 1311–34, doi:<a href=\"https://doi.org/10.30757/ALEA.v15-49\">10.30757/ALEA.v15-49</a>.","ama":"Nejjar P. Transition to shocks in TASEP and decoupling of last passage times. <i>Latin American Journal of Probability and Mathematical Statistics</i>. 2018;15(2):1311-1334. doi:<a href=\"https://doi.org/10.30757/ALEA.v15-49\">10.30757/ALEA.v15-49</a>","ista":"Nejjar P. 2018. Transition to shocks in TASEP and decoupling of last passage times. Latin American Journal of Probability and Mathematical Statistics. 15(2), 1311–1334.","chicago":"Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage Times.” <i>Latin American Journal of Probability and Mathematical Statistics</i>. Instituto Nacional de Matematica Pura e Aplicada, 2018. <a href=\"https://doi.org/10.30757/ALEA.v15-49\">https://doi.org/10.30757/ALEA.v15-49</a>.","short":"P. Nejjar, Latin American Journal of Probability and Mathematical Statistics 15 (2018) 1311–1334.","ieee":"P. Nejjar, “Transition to shocks in TASEP and decoupling of last passage times,” <i>Latin American Journal of Probability and Mathematical Statistics</i>, vol. 15, no. 2. Instituto Nacional de Matematica Pura e Aplicada, pp. 1311–1334, 2018."},"oa_version":"Published Version","date_created":"2018-12-11T11:44:28Z","publication":"Latin American Journal of Probability and Mathematical Statistics","type":"journal_article","oa":1,"external_id":{"isi":["000460475800022"],"arxiv":["1705.08836"]},"day":"01","status":"public","isi":1,"date_published":"2018-10-01T00:00:00Z","doi":"10.30757/ALEA.v15-49","intvolume":"        15","abstract":[{"lang":"eng","text":"We consider the totally asymmetric simple exclusion process in a critical scaling parametrized by a≥0, which creates a shock in the particle density of order aT−1/3, T the observation time. When starting from step initial data, we provide bounds on the limiting law which in particular imply that in the double limit lima→∞limT→∞ one recovers the product limit law and the degeneration of the correlation length observed at shocks of order 1. This result is shown to apply to a general last-passage percolation model. We also obtain bounds on the two-point functions of several airy processes."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","file":[{"checksum":"2ded46aa284a836a8cbb34133a64f1cb","file_name":"2018_ALEA_Nejjar.pdf","date_updated":"2020-07-14T12:47:46Z","file_id":"5981","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"kschuh","file_size":394851,"date_created":"2019-02-14T09:44:10Z"}],"date_updated":"2023-10-10T13:11:29Z","publication_identifier":{"issn":["1980-0436"]},"author":[{"last_name":"Nejjar","full_name":"Nejjar, Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"}],"language":[{"iso":"eng"}],"scopus_import":"1","issue":"2","year":"2018","has_accepted_license":"1","volume":15,"department":[{"_id":"LaEr"},{"_id":"JaMa"}],"page":"1311-1334","title":"Transition to shocks in TASEP and decoupling of last passage times","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"}],"ddc":["510"],"publication_status":"published","file_date_updated":"2020-07-14T12:47:46Z","ec_funded":1,"_id":"70","publisher":"Instituto Nacional de Matematica Pura e Aplicada","article_type":"original"},{"author":[{"full_name":"Shekhovtsov, Alexander","last_name":"Shekhovtsov","first_name":"Alexander"},{"full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","first_name":"Paul"},{"first_name":"Bogdan","full_name":"Savchynskyy, Bogdan","last_name":"Savchynskyy"}],"publication_identifier":{"issn":["01628828"]},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We consider the NP-hard problem of MAP-inference for undirected discrete graphical models. We propose a polynomial time and practically efficient algorithm for finding a part of its optimal solution. Specifically, our algorithm marks some labels of the considered graphical model either as (i) optimal, meaning that they belong to all optimal solutions of the inference problem; (ii) non-optimal if they provably do not belong to any solution. With access to an exact solver of a linear programming relaxation to the MAP-inference problem, our algorithm marks the maximal possible (in a specified sense) number of labels. We also present a version of the algorithm, which has access to a suboptimal dual solver only and still can ensure the (non-)optimality for the marked labels, although the overall number of the marked labels may decrease. We propose an efficient implementation, which runs in time comparable to a single run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art results on computational benchmarks from machine learning and computer vision."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:11:32Z","volume":40,"scopus_import":1,"issue":"7","year":"2018","page":"1668-1682","title":"Maximum persistency via iterative relaxed inference with graphical models","department":[{"_id":"VlKo"}],"_id":"703","publisher":"IEEE","publist_id":"6992","publication_status":"published","month":"07","arxiv":1,"quality_controlled":"1","type":"journal_article","oa_version":"Preprint","citation":{"chicago":"Shekhovtsov, Alexander, Paul Swoboda, and Bogdan Savchynskyy. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2018. <a href=\"https://doi.org/10.1109/TPAMI.2017.2730884\">https://doi.org/10.1109/TPAMI.2017.2730884</a>.","ista":"Shekhovtsov A, Swoboda P, Savchynskyy B. 2018. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(7), 1668–1682.","short":"A. Shekhovtsov, P. Swoboda, B. Savchynskyy, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1668–1682.","ieee":"A. Shekhovtsov, P. Swoboda, and B. Savchynskyy, “Maximum persistency via iterative relaxed inference with graphical models,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 40, no. 7. IEEE, pp. 1668–1682, 2018.","apa":"Shekhovtsov, A., Swoboda, P., &#38; Savchynskyy, B. (2018). Maximum persistency via iterative relaxed inference with graphical models. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/TPAMI.2017.2730884\">https://doi.org/10.1109/TPAMI.2017.2730884</a>","mla":"Shekhovtsov, Alexander, et al. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 40, no. 7, IEEE, 2018, pp. 1668–82, doi:<a href=\"https://doi.org/10.1109/TPAMI.2017.2730884\">10.1109/TPAMI.2017.2730884</a>.","ama":"Shekhovtsov A, Swoboda P, Savchynskyy B. Maximum persistency via iterative relaxed inference with graphical models. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2018;40(7):1668-1682. doi:<a href=\"https://doi.org/10.1109/TPAMI.2017.2730884\">10.1109/TPAMI.2017.2730884</a>"},"date_created":"2018-12-11T11:48:01Z","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","oa":1,"external_id":{"arxiv":["1508.07902"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.07902"}],"day":"01","date_published":"2018-07-01T00:00:00Z","doi":"10.1109/TPAMI.2017.2730884","intvolume":"        40","status":"public"},{"status":"public","isi":1,"date_published":"2018-06-01T00:00:00Z","doi":"10.1007/s12035-017-0688-y","intvolume":"        55","external_id":{"isi":["000431991500025"]},"day":"01","citation":{"ama":"Miklosi A, Del Favero G, Bulat T, et al. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. <i>Molecular Neurobiology</i>. 2018;55(6):4857 – 4869. doi:<a href=\"https://doi.org/10.1007/s12035-017-0688-y\">10.1007/s12035-017-0688-y</a>","mla":"Miklosi, Andras, et al. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” <i>Molecular Neurobiology</i>, vol. 55, no. 6, Springer, 2018, pp. 4857 – 4869, doi:<a href=\"https://doi.org/10.1007/s12035-017-0688-y\">10.1007/s12035-017-0688-y</a>.","apa":"Miklosi, A., Del Favero, G., Bulat, T., Höger, H., Shigemoto, R., Marko, D., &#38; Lubec, G. (2018). Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. <i>Molecular Neurobiology</i>. Springer. <a href=\"https://doi.org/10.1007/s12035-017-0688-y\">https://doi.org/10.1007/s12035-017-0688-y</a>","ieee":"A. Miklosi <i>et al.</i>, “Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes,” <i>Molecular Neurobiology</i>, vol. 55, no. 6. Springer, pp. 4857 – 4869, 2018.","short":"A. Miklosi, G. Del Favero, T. Bulat, H. Höger, R. Shigemoto, D. Marko, G. Lubec, Molecular Neurobiology 55 (2018) 4857 – 4869.","ista":"Miklosi A, Del Favero G, Bulat T, Höger H, Shigemoto R, Marko D, Lubec G. 2018. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 55(6), 4857 – 4869.","chicago":"Miklosi, Andras, Giorgia Del Favero, Tanja Bulat, Harald Höger, Ryuichi Shigemoto, Doris Marko, and Gert Lubec. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” <i>Molecular Neurobiology</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s12035-017-0688-y\">https://doi.org/10.1007/s12035-017-0688-y</a>."},"oa_version":"None","date_created":"2018-12-11T11:48:02Z","publication":"Molecular Neurobiology","type":"journal_article","quality_controlled":"1","month":"06","publication_status":"published","_id":"705","publisher":"Springer","publist_id":"6991","department":[{"_id":"RySh"}],"page":"4857 – 4869","title":"Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes","scopus_import":"1","issue":"6","year":"2018","volume":55,"abstract":[{"lang":"eng","text":"Although dopamine receptors D1 and D2 play key roles in hippocampal function, their synaptic localization within the hippocampus has not been fully elucidated. In order to understand precise functions of pre- or postsynaptic dopamine receptors (DRs), the development of protocols to differentiate pre- and postsynaptic DRs is essential. So far, most studies on determination and quantification of DRs did not discriminate between subsynaptic localization. Therefore, the aim of the study was to generate a robust workflow for the localization of DRs. This work provides the basis for future work on hippocampal DRs, in light that DRs may have different functions at pre- or postsynaptic sites. Synaptosomes from rat hippocampi isolated by a sucrose gradient protocol were prepared for super-resolution direct stochastic optical reconstruction microscopy (dSTORM) using Bassoon as a presynaptic zone and Homer1 as postsynaptic density marker. Direct labeling of primary validated antibodies against dopamine receptors D1 (D1R) and D2 (D2R) with Alexa Fluor 594 enabled unequivocal assignment of D1R and D2R to both, pre- and postsynaptic sites. D1R immunoreactivity clusters were observed within the presynaptic active zone as well as at perisynaptic sites at the edge of the presynaptic active zone. The results may be useful for the interpretation of previous studies and the design of future work on DRs in the hippocampus. Moreover, the reduction of the complexity of brain tissue by the use of synaptosomal preparations and dSTORM technology may represent a useful tool for synaptic localization of brain proteins."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","date_updated":"2023-09-19T09:58:11Z","author":[{"first_name":"Andras","last_name":"Miklosi","full_name":"Miklosi, Andras"},{"last_name":"Del Favero","full_name":"Del Favero, Giorgia","first_name":"Giorgia"},{"full_name":"Bulat, Tanja","last_name":"Bulat","first_name":"Tanja"},{"first_name":"Harald","full_name":"Höger, Harald","last_name":"Höger"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"},{"full_name":"Marko, Doris","last_name":"Marko","first_name":"Doris"},{"full_name":"Lubec, Gert","last_name":"Lubec","first_name":"Gert"}],"language":[{"iso":"eng"}]},{"date_published":"2018-03-26T00:00:00Z","doi":"10.5441/002/EDBT.2018.14","status":"public","day":"26","oa":1,"type":"conference","publication":"Proceedings of the 21st International Conference on Extending Database Technology","citation":{"ieee":"D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study,” in <i>Proceedings of the 21st International Conference on Extending Database Technology</i>, Vienna, Austria, 2018, pp. 145–156.","short":"D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–156.","ista":"Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. Proceedings of the 21st International Conference on Extending Database Technology. EDBT: Conference on Extending Database Technology, 145–156.","chicago":"Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” In <i>Proceedings of the 21st International Conference on Extending Database Technology</i>, 145–56. OpenProceedings, 2018. <a href=\"https://doi.org/10.5441/002/EDBT.2018.14\">https://doi.org/10.5441/002/EDBT.2018.14</a>.","ama":"Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In: <i>Proceedings of the 21st International Conference on Extending Database Technology</i>. OpenProceedings; 2018:145-156. doi:<a href=\"https://doi.org/10.5441/002/EDBT.2018.14\">10.5441/002/EDBT.2018.14</a>","mla":"Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” <i>Proceedings of the 21st International Conference on Extending Database Technology</i>, OpenProceedings, 2018, pp. 145–56, doi:<a href=\"https://doi.org/10.5441/002/EDBT.2018.14\">10.5441/002/EDBT.2018.14</a>.","apa":"Grubic, D., Tam, L., Alistarh, D.-A., &#38; Zhang, C. (2018). Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In <i>Proceedings of the 21st International Conference on Extending Database Technology</i> (pp. 145–156). Vienna, Austria: OpenProceedings. <a href=\"https://doi.org/10.5441/002/EDBT.2018.14\">https://doi.org/10.5441/002/EDBT.2018.14</a>"},"oa_version":"Published Version","date_created":"2019-11-26T14:19:11Z","month":"03","quality_controlled":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publisher":"OpenProceedings","_id":"7116","publication_status":"published","file_date_updated":"2020-07-14T12:47:49Z","ddc":["000"],"title":"Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study","page":"145-156","department":[{"_id":"DaAl"}],"has_accepted_license":"1","scopus_import":1,"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"year":"2018","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783893180783"],"issn":["2367-2005"]},"conference":{"end_date":"2018-03-29","location":"Vienna, Austria","name":"EDBT: Conference on Extending Database Technology","start_date":"2018-03-26"},"author":[{"full_name":"Grubic, Demjan","last_name":"Grubic","first_name":"Demjan"},{"full_name":"Tam, Leo","last_name":"Tam","first_name":"Leo"},{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"last_name":"Zhang","full_name":"Zhang, Ce","first_name":"Ce"}],"article_processing_charge":"No","date_updated":"2023-02-23T12:59:17Z","file":[{"date_created":"2019-11-26T14:23:04Z","file_size":1603204,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"7118","date_updated":"2020-07-14T12:47:49Z","file_name":"2018_OpenProceedings_Grubic.pdf","checksum":"ec979b56abc71016d6e6adfdadbb4afe"}],"abstract":[{"lang":"eng","text":"Training deep learning models has received tremendous research interest recently. In particular, there has been intensive research on reducing the communication cost of training when using multiple computational devices, through reducing the precision of the underlying data representation. Naturally, such methods induce system trade-offs—lowering communication precision could de-crease communication overheads and improve scalability; but, on the other hand, it can also reduce the accuracy of training. In this paper, we study this trade-off space, and ask:Can low-precision communication consistently improve the end-to-end performance of training modern neural networks, with no accuracy loss?From the performance point of view, the answer to this question may appear deceptively easy: compressing communication through low precision should help when the ratio between communication and computation is high. However, this answer is less straightforward when we try to generalize this principle across various neural network architectures (e.g., AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g., EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL), and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is not clear how a realistic realization of all these factors maps to the speed up provided by low-precision communication. In this paper, we conduct an empirical study to answer this question and report the insights."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"30","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.04947"}],"external_id":{"arxiv":["1704.04947"],"isi":["000483921200145"]},"oa":1,"status":"public","date_published":"2018-01-30T00:00:00Z","doi":"10.1137/1.9781611975031.144","isi":1,"quality_controlled":"1","arxiv":1,"month":"01","publication":"Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms","date_created":"2019-11-26T15:10:55Z","citation":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, and Rati Gelashvili. “Space-Optimal Majority in Population Protocols.” In <i>Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 2221–39. ACM, 2018. <a href=\"https://doi.org/10.1137/1.9781611975031.144\">https://doi.org/10.1137/1.9781611975031.144</a>.","ista":"Alistarh D-A, Aspnes J, Gelashvili R. 2018. Space-optimal majority in population protocols. Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 2221–2239.","short":"D.-A. Alistarh, J. Aspnes, R. Gelashvili, in:, Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms, ACM, 2018, pp. 2221–2239.","ieee":"D.-A. Alistarh, J. Aspnes, and R. Gelashvili, “Space-optimal majority in population protocols,” in <i>Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, New Orleans, LA, United States, 2018, pp. 2221–2239.","apa":"Alistarh, D.-A., Aspnes, J., &#38; Gelashvili, R. (2018). Space-optimal majority in population protocols. In <i>Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 2221–2239). New Orleans, LA, United States: ACM. <a href=\"https://doi.org/10.1137/1.9781611975031.144\">https://doi.org/10.1137/1.9781611975031.144</a>","mla":"Alistarh, Dan-Adrian, et al. “Space-Optimal Majority in Population Protocols.” <i>Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, ACM, 2018, pp. 2221–39, doi:<a href=\"https://doi.org/10.1137/1.9781611975031.144\">10.1137/1.9781611975031.144</a>.","ama":"Alistarh D-A, Aspnes J, Gelashvili R. Space-optimal majority in population protocols. In: <i>Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms</i>. ACM; 2018:2221-2239. doi:<a href=\"https://doi.org/10.1137/1.9781611975031.144\">10.1137/1.9781611975031.144</a>"},"oa_version":"Preprint","type":"conference","department":[{"_id":"DaAl"}],"title":"Space-optimal majority in population protocols","page":"2221-2239","publication_status":"published","publisher":"ACM","_id":"7123","date_updated":"2023-09-19T15:03:16Z","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Population protocols are a popular model of distributed computing, in which n agents with limited local state interact randomly, and cooperate to collectively compute global predicates. Inspired by recent developments in DNA programming, an extensive series of papers, across different communities, has examined the computability and complexity characteristics of this model. Majority, or consensus, is a central task in this model, in which agents need to collectively reach a decision as to which one of two states A or B had a higher initial count. Two metrics are important: the time that a protocol requires to stabilize to an output decision, and the state space size that each agent requires to do so. It is known that majority requires Ω(log log n) states per agent to allow for fast (poly-logarithmic time) stabilization, and that O(log2 n) states are sufficient. Thus, there is an exponential gap between the space upper and lower bounds for this problem. This paper addresses this question.\r\n\r\nOn the negative side, we provide a new lower bound of Ω(log n) states for any protocol which stabilizes in O(n1–c) expected time, for any constant c > 0. This result is conditional on monotonicity and output assumptions, satisfied by all known protocols. Technically, it represents a departure from previous lower bounds, in that it does not rely on the existence of dense configurations. Instead, we introduce a new generalized surgery technique to prove the existence of incorrect executions for any algorithm which would contradict the lower bound. Subsequently, our lower bound also applies to general initial configurations, including ones with a leader. On the positive side, we give a new algorithm for majority which uses O(log n) states, and stabilizes in O(log2 n) expected time. Central to the algorithm is a new leaderless phase clock technique, which allows agents to synchronize in phases of Θ(n log n) consecutive interactions using O(log n) states per agent, exploiting a new connection between population protocols and power-of-two-choices load balancing mechanisms. We also employ our phase clock to build a leader election algorithm with a state space of size O(log n), which stabilizes in O(log2 n) expected time.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781611975031"]},"conference":{"location":"New Orleans, LA, United States","name":"SODA: Symposium on Discrete Algorithms","start_date":"2018-01-07","end_date":"2018-01-10"},"author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian"},{"last_name":"Aspnes","full_name":"Aspnes, James","first_name":"James"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"}],"year":"2018"}]