[{"month":"11","quality_controlled":"1","date_updated":"2023-09-13T09:10:47Z","external_id":{"isi":["000450976700002"]},"acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19).","isi":1,"article_processing_charge":"No","date_published":"2018-11-03T00:00:00Z","title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","publist_id":"8035","volume":19,"status":"public","publication_identifier":{"issn":["1471-2164"]},"type":"journal_article","related_material":{"record":[{"status":"public","relation":"research_data","id":"9807"},{"status":"public","id":"9808","relation":"research_data"}]},"publisher":"BioMed Central","oa_version":"Published Version","citation":{"ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. <i>BMC Genomics</i>. 2018;19(1). doi:<a href=\"https://doi.org/10.1186/s12864-018-5173-0\">10.1186/s12864-018-5173-0</a>","ieee":"J. Higareda Almaraz <i>et al.</i>, “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” <i>BMC Genomics</i>, vol. 19, no. 1. BioMed Central, 2018.","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” <i>BMC Genomics</i>, vol. 19, no. 1, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s12864-018-5173-0\">10.1186/s12864-018-5173-0</a>.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1).","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., &#38; Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12864-018-5173-0\">https://doi.org/10.1186/s12864-018-5173-0</a>","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” <i>BMC Genomics</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s12864-018-5173-0\">https://doi.org/10.1186/s12864-018-5173-0</a>."},"scopus_import":"1","abstract":[{"text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.","lang":"eng"}],"intvolume":"        19","file":[{"file_size":4629784,"date_updated":"2020-07-14T12:45:23Z","relation":"main_file","content_type":"application/pdf","creator":"dernst","checksum":"a56516e734dab589dc7f3e1915973b4d","file_name":"2018_BMCGenomics_Higareda.pdf","access_level":"open_access","date_created":"2018-12-17T14:52:57Z","file_id":"5712"}],"doi":"10.1186/s12864-018-5173-0","publication_status":"published","oa":1,"author":[{"first_name":"Juan","last_name":"Higareda Almaraz","full_name":"Higareda Almaraz, Juan"},{"first_name":"Michael","last_name":"Karbiener","full_name":"Karbiener, Michael"},{"first_name":"Maude","last_name":"Giroud","full_name":"Giroud, Maude"},{"last_name":"Pauler","first_name":"Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian"},{"last_name":"Gerhalter","first_name":"Teresa","full_name":"Gerhalter, Teresa"},{"first_name":"Stephan","last_name":"Herzig","full_name":"Herzig, Stephan"},{"full_name":"Scheideler, Marcel","first_name":"Marcel","last_name":"Scheideler"}],"ddc":["570"],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:23Z","article_type":"original","date_created":"2018-12-11T11:44:12Z","year":"2018","publication":"BMC Genomics","day":"03","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"1","department":[{"_id":"SiHi"}],"_id":"20","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"page":"146","has_accepted_license":"1","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"department":[{"_id":"NiBa"}],"_id":"200","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","OA_place":"publisher","day":"21","date_created":"2018-12-11T11:45:10Z","alternative_title":["ISTA Thesis"],"year":"2018","doi":"10.15479/AT:ISTA:th_963","file":[{"date_updated":"2020-07-14T12:45:23Z","relation":"main_file","content_type":"application/pdf","file_size":5792935,"file_id":"5111","date_created":"2018-12-12T10:14:55Z","access_level":"open_access","file_name":"IST-2018-963-v1+1_thesis.pdf","checksum":"8cc534d2b528ae017acf80874cce48c9","creator":"system"},{"relation":"source_file","content_type":"application/zip","date_updated":"2020-07-14T12:45:23Z","file_size":113365,"access_level":"closed","file_name":"2018_thesis_ringbauer_source.zip","checksum":"6af18d7e5a7e2728ceda2f41ee24f628","creator":"dernst","file_id":"6224","date_created":"2019-04-05T09:30:12Z"}],"publication_status":"published","oa":1,"degree_awarded":"PhD","pubrep_id":"963","file_date_updated":"2020-07-14T12:45:23Z","author":[{"orcid":"0000-0002-4884-9682","first_name":"Harald","last_name":"Ringbauer","full_name":"Ringbauer, Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87"}],"ddc":["576"],"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","citation":{"chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">https://doi.org/10.15479/AT:ISTA:th_963</a>.","apa":"Ringbauer, H. (2018). <i>Inferring recent demography from spatial genetic structure</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">https://doi.org/10.15479/AT:ISTA:th_963</a>","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","mla":"Ringbauer, Harald. <i>Inferring Recent Demography from Spatial Genetic Structure</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">10.15479/AT:ISTA:th_963</a>.","ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">10.15479/AT:ISTA:th_963</a>"},"abstract":[{"lang":"eng","text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm."}],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","status":"public","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"563"},{"id":"1074","relation":"part_of_dissertation","status":"public"}]},"title":"Inferring recent demography from spatial genetic structure","date_published":"2018-02-21T00:00:00Z","article_processing_charge":"No","publist_id":"7713","month":"02","date_updated":"2026-04-08T14:06:37Z","license":"https://creativecommons.org/licenses/by-nc/4.0/"},{"publisher":"National Academy of Sciences","main_file_link":[{"open_access":"1","url":"http://eprints.nottingham.ac.uk/52388/"}],"scopus_import":"1","citation":{"ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. <i>PNAS</i>. 2018;115(26):6864-6869. doi:<a href=\"https://doi.org/10.1073/pnas.1806565115\">10.1073/pnas.1806565115</a>","ieee":"M. Abbas <i>et al.</i>, “Auxin methylation is required for differential growth in Arabidopsis,” <i>PNAS</i>, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018.","short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869.","ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.","mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” <i>PNAS</i>, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:<a href=\"https://doi.org/10.1073/pnas.1806565115\">10.1073/pnas.1806565115</a>.","chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1806565115\">https://doi.org/10.1073/pnas.1806565115</a>.","apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1806565115\">https://doi.org/10.1073/pnas.1806565115</a>"},"abstract":[{"lang":"eng","text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses."}],"oa_version":"Submitted Version","type":"journal_article","status":"public","OA_type":"green","title":"Auxin methylation is required for differential growth in Arabidopsis","article_processing_charge":"No","date_published":"2018-06-26T00:00:00Z","isi":1,"volume":115,"publist_id":"7710","month":"06","external_id":{"isi":["000436245000096"]},"quality_controlled":"1","date_updated":"2026-04-28T08:29:26Z","page":"6864-6869","_id":"203","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"26","department":[{"_id":"JiFr"}],"ec_funded":1,"OA_place":"repository","publication":"PNAS","day":"26","date_created":"2018-12-11T11:45:11Z","article_type":"original","year":"2018","publication_status":"published","oa":1,"doi":"10.1073/pnas.1806565115","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"intvolume":"       115","language":[{"iso":"eng"}],"author":[{"last_name":"Abbas","first_name":"Mohamad","full_name":"Abbas, Mohamad","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hernández","first_name":"García J","full_name":"Hernández, García J"},{"last_name":"Pollmann","first_name":"Stephan","full_name":"Pollmann, Stephan"},{"last_name":"Samodelov","first_name":"Sophia L","full_name":"Samodelov, Sophia L"},{"last_name":"Kolb","first_name":"Martina","full_name":"Kolb, Martina"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"first_name":"Ulrich Z","last_name":"Hammes","full_name":"Hammes, Ulrich Z"},{"last_name":"Zurbriggen","first_name":"Matias D","full_name":"Zurbriggen, Matias D"},{"full_name":"Blázquez, Miguel","first_name":"Miguel","last_name":"Blázquez"},{"full_name":"Alabadí, David","first_name":"David","last_name":"Alabadí"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"104","department":[{"_id":"GradSch"}],"issue":"10","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","page":"2277 - 2287","day":"01","publication":"Molecular Plant Pathology","year":"2018","date_created":"2018-12-11T11:44:39Z","ddc":["580"],"language":[{"iso":"eng"}],"author":[{"last_name":"Seitner","first_name":"Denise","full_name":"Seitner, Denise"},{"full_name":"Uhse, Simon","last_name":"Uhse","first_name":"Simon"},{"full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","last_name":"Gallei","first_name":"Michelle C"},{"full_name":"Djamei, Armin","last_name":"Djamei","first_name":"Armin"}],"file_date_updated":"2018-12-18T09:46:00Z","intvolume":"        19","publication_status":"published","oa":1,"doi":"10.1111/mpp.12698","file":[{"date_updated":"2018-12-18T09:46:00Z","relation":"main_file","content_type":"application/pdf","file_size":682335,"file_name":"2018_MolecPlantPath_Seitner.pdf","access_level":"open_access","creator":"dernst","success":1,"file_id":"5740","date_created":"2018-12-18T09:46:00Z"}],"citation":{"ama":"Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required for early infection of maize by Ustilago maydis. <i>Molecular Plant Pathology</i>. 2018;19(10):2277-2287. doi:<a href=\"https://doi.org/10.1111/mpp.12698\">10.1111/mpp.12698</a>","ieee":"D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1 is required for early infection of maize by Ustilago maydis,” <i>Molecular Plant Pathology</i>, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018.","mla":"Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” <i>Molecular Plant Pathology</i>, vol. 19, no. 10, Wiley, 2018, pp. 2277–87, doi:<a href=\"https://doi.org/10.1111/mpp.12698\">10.1111/mpp.12698</a>.","ista":"Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10), 2277–2287.","short":"D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19 (2018) 2277–2287.","apa":"Seitner, D., Uhse, S., Gallei, M. C., &#38; Djamei, A. (2018). The core effector Cce1 is required for early infection of maize by Ustilago maydis. <i>Molecular Plant Pathology</i>. Wiley. <a href=\"https://doi.org/10.1111/mpp.12698\">https://doi.org/10.1111/mpp.12698</a>","chicago":"Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” <i>Molecular Plant Pathology</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/mpp.12698\">https://doi.org/10.1111/mpp.12698</a>."},"abstract":[{"lang":"eng","text":"The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host."}],"scopus_import":"1","oa_version":"Published Version","publisher":"Wiley","status":"public","type":"journal_article","publist_id":"7950","volume":19,"article_processing_charge":"No","date_published":"2018-10-01T00:00:00Z","acknowledgement":"the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22], and the Austrian Academy of Science (OEAW).","isi":1,"title":"The core effector Cce1 is required for early infection of maize by Ustilago maydis","quality_controlled":"1","date_updated":"2023-09-19T10:06:42Z","external_id":{"isi":["000445624100006"]},"month":"10"},{"date_updated":"2025-05-20T09:45:10Z","quality_controlled":"1","external_id":{"arxiv":["1610.01188"]},"month":"01","volume":2,"article_processing_charge":"No","arxiv":1,"date_published":"2018-01-01T00:00:00Z","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061.","title":"Data-centric dynamic partial order reduction","related_material":{"record":[{"status":"public","id":"5448","relation":"earlier_version"},{"status":"public","relation":"earlier_version","id":"5456"}]},"OA_type":"hybrid","status":"public","type":"journal_article","publication_identifier":{"eissn":["2475-1421"]},"citation":{"chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2018. <a href=\"https://doi.org/10.1145/3158119\">https://doi.org/10.1145/3158119</a>.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., &#38; Vaidya, K. (2018). Data-centric dynamic partial order reduction. <i>Proceedings of the ACM on Programming Languages</i>. Los Angeles, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3158119\">https://doi.org/10.1145/3158119</a>","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2018).","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2018. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31.","mla":"Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL, 31, Association for Computing Machinery, 2018, doi:<a href=\"https://doi.org/10.1145/3158119\">10.1145/3158119</a>.","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL. Association for Computing Machinery, 2018.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. <i>Proceedings of the ACM on Programming Languages</i>. 2018;2(POPL). doi:<a href=\"https://doi.org/10.1145/3158119\">10.1145/3158119</a>"},"scopus_import":"1","abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence."}],"article_number":"31","oa_version":"Published Version","publisher":"Association for Computing Machinery","ddc":["000"],"language":[{"iso":"eng"}],"author":[{"first_name":"Marek","last_name":"Chalupa","full_name":"Chalupa, Marek"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722"},{"first_name":"Nishant","last_name":"Sinha","full_name":"Sinha, Nishant"},{"first_name":"Kapil","last_name":"Vaidya","full_name":"Vaidya, Kapil"}],"file_date_updated":"2025-05-20T09:44:47Z","intvolume":"         2","oa":1,"publication_status":"published","file":[{"date_created":"2025-05-20T09:44:47Z","file_id":"19716","success":1,"creator":"dernst","checksum":"b27ab1745f6dba2387deb785798a657c","access_level":"open_access","file_name":"2018_ACM_Chalupa.pdf","file_size":388891,"date_updated":"2025-05-20T09:44:47Z","content_type":"application/pdf","relation":"main_file"}],"doi":"10.1145/3158119","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"year":"2018","article_type":"original","date_created":"2021-12-05T23:01:49Z","day":"01","publication":"Proceedings of the ACM on Programming Languages","OA_place":"publisher","_id":"10417","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"POPL","department":[{"_id":"KrCh"}],"conference":{"start_date":"2018-01-07","name":"POPL: Programming Languages","end_date":"2018-01-13","location":"Los Angeles, CA, United States"},"ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1"},{"quality_controlled":"1","date_updated":"2023-09-13T08:49:16Z","external_id":{"isi":["000444141200005"],"arxiv":["1702.05172"]},"month":"09","publist_id":"7948","volume":40,"arxiv":1,"date_published":"2018-09-01T00:00:00Z","article_processing_charge":"No","isi":1,"title":"Long geodesics on convex surfaces","status":"public","type":"journal_article","citation":{"ieee":"A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” <i>Mathematical Intelligencer</i>, vol. 40, no. 3. Springer, pp. 26–31, 2018.","ama":"Akopyan A, Petrunin A. Long geodesics on convex surfaces. <i>Mathematical Intelligencer</i>. 2018;40(3):26-31. doi:<a href=\"https://doi.org/10.1007/s00283-018-9795-5\">10.1007/s00283-018-9795-5</a>","chicago":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” <i>Mathematical Intelligencer</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00283-018-9795-5\">https://doi.org/10.1007/s00283-018-9795-5</a>.","apa":"Akopyan, A., &#38; Petrunin, A. (2018). Long geodesics on convex surfaces. <i>Mathematical Intelligencer</i>. Springer. <a href=\"https://doi.org/10.1007/s00283-018-9795-5\">https://doi.org/10.1007/s00283-018-9795-5</a>","ista":"Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31.","short":"A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.","mla":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” <i>Mathematical Intelligencer</i>, vol. 40, no. 3, Springer, 2018, pp. 26–31, doi:<a href=\"https://doi.org/10.1007/s00283-018-9795-5\">10.1007/s00283-018-9795-5</a>."},"abstract":[{"text":"The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below.","lang":"eng"}],"scopus_import":"1","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1702.05172","open_access":"1"}],"publisher":"Springer","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-2548-617X","last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anton","last_name":"Petrunin","full_name":"Petrunin, Anton"}],"intvolume":"        40","publication_status":"published","oa":1,"doi":"10.1007/s00283-018-9795-5","year":"2018","date_created":"2018-12-11T11:44:40Z","day":"01","publication":"Mathematical Intelligencer","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"106","department":[{"_id":"HeEd"}],"issue":"3","page":"26 - 31"},{"publisher":"Springer","abstract":[{"lang":"eng","text":"In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot be separated into two subfamilies by a straight line disjoint from the disks. In this note we show that essentially the same idea may work for different analogues and generalizations of their result. In particular, we prove the following: Given a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane disjoint from the homothets."}],"scopus_import":"1","citation":{"ama":"Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W. Goodman and R.E. Goodman. <i>Discrete &#38; Computational Geometry</i>. 2018;59(4):1001-1009. doi:<a href=\"https://doi.org/10.1007/s00454-017-9883-x\">10.1007/s00454-017-9883-x</a>","ieee":"A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem by A.W. Goodman and R.E. Goodman,” <i>Discrete &#38; Computational Geometry</i>, vol. 59, no. 4. Springer, pp. 1001–1009, 2018.","mla":"Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” <i>Discrete &#38; Computational Geometry</i>, vol. 59, no. 4, Springer, 2018, pp. 1001–09, doi:<a href=\"https://doi.org/10.1007/s00454-017-9883-x\">10.1007/s00454-017-9883-x</a>.","ista":"Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete &#38; Computational Geometry. 59(4), 1001–1009.","short":"A. Akopyan, A. Balitskiy, M. Grigorev, Discrete &#38; Computational Geometry 59 (2018) 1001–1009.","apa":"Akopyan, A., Balitskiy, A., &#38; Grigorev, M. (2018). On the circle covering theorem by A.W. Goodman and R.E. Goodman. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-017-9883-x\">https://doi.org/10.1007/s00454-017-9883-x</a>","chicago":"Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00454-017-9883-x\">https://doi.org/10.1007/s00454-017-9883-x</a>."},"oa_version":"Published Version","type":"journal_article","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"status":"public","title":"On the circle covering theorem by A.W. Goodman and R.E. Goodman","date_published":"2018-06-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","isi":1,"volume":59,"publist_id":"6324","month":"06","external_id":{"isi":["000432205500011"]},"date_updated":"2026-05-20T10:19:33Z","quality_controlled":"1","page":"1001-1009","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1064","issue":"4","ec_funded":1,"department":[{"_id":"HeEd"}],"corr_author":"1","publication":"Discrete & Computational Geometry","day":"01","date_created":"2018-12-11T11:49:57Z","article_type":"original","year":"2018","publication_status":"published","oa":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"file":[{"date_updated":"2019-01-18T09:27:36Z","content_type":"application/pdf","relation":"main_file","file_size":482518,"success":1,"file_id":"5844","date_created":"2019-01-18T09:27:36Z","file_name":"2018_DiscreteComp_Akopyan.pdf","access_level":"open_access","creator":"dernst"}],"doi":"10.1007/s00454-017-9883-x","intvolume":"        59","file_date_updated":"2019-01-18T09:27:36Z","language":[{"iso":"eng"}],"ddc":["516","000"],"author":[{"first_name":"Arseniy","last_name":"Akopyan","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy"},{"last_name":"Balitskiy","first_name":"Alexey","full_name":"Balitskiy, Alexey"},{"first_name":"Mikhail","last_name":"Grigorev","full_name":"Grigorev, Mikhail"}]},{"oa_version":"Preprint","scopus_import":"1","article_number":"20","abstract":[{"text":"We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory.","lang":"eng"}],"citation":{"ama":"Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. <i>Journal of the ACM</i>. 2018;65(4). doi:<a href=\"https://doi.org/10.1145/3178432\">10.1145/3178432</a>","ieee":"S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” <i>Journal of the ACM</i>, vol. 65, no. 4. ACM, 2018.","short":"S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).","ista":"Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of the ACM. 65(4), 20.","mla":"Dziembowski, Stefan, et al. “Non-Malleable Codes.” <i>Journal of the ACM</i>, vol. 65, no. 4, 20, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3178432\">10.1145/3178432</a>.","chicago":"Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable Codes.” <i>Journal of the ACM</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3178432\">https://doi.org/10.1145/3178432</a>.","apa":"Dziembowski, S., Pietrzak, K. Z., &#38; Wichs, D. (2018). Non-malleable codes. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3178432\">https://doi.org/10.1145/3178432</a>"},"main_file_link":[{"url":"https://eprint.iacr.org/2009/608","open_access":"1"}],"publisher":"ACM","status":"public","type":"journal_article","publist_id":"7947","volume":65,"isi":1,"date_published":"2018-08-01T00:00:00Z","article_processing_charge":"No","title":"Non-malleable codes","quality_controlled":"1","date_updated":"2025-04-14T07:22:06Z","external_id":{"isi":["000442938200004"]},"month":"08","department":[{"_id":"KrPi"}],"ec_funded":1,"issue":"4","_id":"107","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","publication":"Journal of the ACM","year":"2018","article_type":"original","date_created":"2018-12-11T11:44:40Z","author":[{"last_name":"Dziembowski","first_name":"Stefan","full_name":"Dziembowski, Stefan"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"},{"last_name":"Wichs","first_name":"Daniel","full_name":"Wichs, Daniel"}],"language":[{"iso":"eng"}],"intvolume":"        65","project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"},{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"doi":"10.1145/3178432","oa":1,"publication_status":"published"},{"language":[{"iso":"eng"}],"author":[{"first_name":"Marciej","last_name":"Obremski","full_name":"Obremski, Marciej"},{"last_name":"Skorski","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skorski, Maciej"}],"intvolume":"      2018","oa":1,"publication_status":"published","doi":"10.1109/ISIT.2018.8437654","year":"2018","alternative_title":["ISIT Proceedings"],"date_created":"2018-12-11T11:44:40Z","day":"16","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"108","conference":{"start_date":"2018-06-17 ","name":"ISIT: International Symposium on Information Theory","end_date":"2018-06-22","location":"Vail, CO, USA"},"department":[{"_id":"KrPi"}],"date_updated":"2023-09-13T08:23:18Z","quality_controlled":"1","external_id":{"isi":["000448139300368"]},"month":"08","publist_id":"7946","volume":2018,"date_published":"2018-08-16T00:00:00Z","article_processing_charge":"No","isi":1,"title":"Inverted leftover hash lemma","status":"public","type":"conference","scopus_import":"1","abstract":[{"lang":"eng","text":"Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \\'collision graph\\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes."}],"citation":{"ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:<a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">10.1109/ISIT.2018.8437654</a>","ieee":"M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.","mla":"Obremski, Marciej, and Maciej Skórski. <i>Inverted Leftover Hash Lemma</i>. Vol. 2018, IEEE, 2018, doi:<a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">10.1109/ISIT.2018.8437654</a>.","short":"M. Obremski, M. Skórski, in:, IEEE, 2018.","ista":"Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018.","apa":"Obremski, M., &#38; Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. <a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">https://doi.org/10.1109/ISIT.2018.8437654</a>","chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. <a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">https://doi.org/10.1109/ISIT.2018.8437654</a>."},"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/507"}],"publisher":"IEEE"},{"citation":{"ista":"Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing.","short":"C. Lenzen, J. Rybicki, Distributed Computing (2018).","mla":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” <i>Distributed Computing</i>, Springer, 2018, doi:<a href=\"https://doi.org/10.1007/s00446-018-0342-6\">10.1007/s00446-018-0342-6</a>.","chicago":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” <i>Distributed Computing</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00446-018-0342-6\">https://doi.org/10.1007/s00446-018-0342-6</a>.","apa":"Lenzen, C., &#38; Rybicki, J. (2018). Near-optimal self-stabilising counting and firing squads. <i>Distributed Computing</i>. Springer. <a href=\"https://doi.org/10.1007/s00446-018-0342-6\">https://doi.org/10.1007/s00446-018-0342-6</a>","ama":"Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads. <i>Distributed Computing</i>. 2018. doi:<a href=\"https://doi.org/10.1007/s00446-018-0342-6\">10.1007/s00446-018-0342-6</a>","ieee":"C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing squads,” <i>Distributed Computing</i>. Springer, 2018."},"abstract":[{"lang":"eng","text":"Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C&gt;1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f&lt;n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions."}],"scopus_import":"1","oa_version":"Published Version","publisher":"Springer","type":"journal_article","status":"public","publist_id":"7978","title":"Near-optimal self-stabilising counting and firing squads","date_published":"2018-09-12T00:00:00Z","article_processing_charge":"Yes (via OA deal)","isi":1,"external_id":{"isi":["000475627800005"]},"date_updated":"2025-04-15T06:53:15Z","quality_controlled":"1","month":"09","_id":"76","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"DaAl"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","day":"12","corr_author":"1","publication":"Distributed Computing","year":"2018","date_created":"2018-12-11T11:44:30Z","file_date_updated":"2020-07-14T12:48:01Z","language":[{"iso":"eng"}],"ddc":["000"],"author":[{"last_name":"Lenzen","first_name":"Christoph","full_name":"Lenzen, Christoph"},{"orcid":"0000-0002-6432-6646","first_name":"Joel","last_name":"Rybicki","full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","oa":1,"file":[{"file_name":"2018_DistributedComputing_Lenzen.pdf","access_level":"open_access","checksum":"872db70bba9b401500abe3c6ae2f1a61","creator":"dernst","file_id":"5711","date_created":"2018-12-17T14:21:22Z","date_updated":"2020-07-14T12:48:01Z","relation":"main_file","content_type":"application/pdf","file_size":799337}],"doi":"10.1007/s00446-018-0342-6","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}]},{"intvolume":"         9","file":[{"file_id":"5687","date_created":"2018-12-17T10:28:30Z","access_level":"open_access","file_name":"2018_NatureComm_Watzinger.pdf","creator":"dernst","checksum":"e7148c10a64497e279c4de570b6cc544","content_type":"application/pdf","date_updated":"2020-07-14T12:48:02Z","relation":"main_file","file_size":1063469}],"project":[{"call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires","grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","_id":"2552F888-B435-11E9-9278-68D0E5697425","grant_number":"Y00715"}],"doi":"10.1038/s41467-018-06418-4","publication_status":"published","oa":1,"author":[{"first_name":"Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes"},{"first_name":"Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip"},{"full_name":"Vukusic, Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636","first_name":"Lada","last_name":"Vukusic"},{"last_name":"Gao","first_name":"Fei","full_name":"Gao, Fei"},{"full_name":"Wang, Ting","last_name":"Wang","first_name":"Ting"},{"full_name":"Schäffler, Friedrich","last_name":"Schäffler","first_name":"Friedrich"},{"full_name":"Zhang, Jian","last_name":"Zhang","first_name":"Jian"},{"orcid":"0000-0001-8342-202X","last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"ddc":["530"],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:02Z","article_type":"original","date_created":"2018-12-11T11:44:30Z","year":"2018","publication":"Nature Communications","day":"25","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"3902 ","department":[{"_id":"GeKa"}],"ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"77","month":"09","date_updated":"2026-04-08T07:27:13Z","quality_controlled":"1","external_id":{"isi":["000445560800010"]},"isi":1,"article_processing_charge":"Yes","date_published":"2018-09-25T00:00:00Z","title":"A germanium hole spin qubit","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"volume":9,"status":"public","type":"journal_article","related_material":{"record":[{"id":"7977","relation":"popular_science"},{"status":"public","relation":"dissertation_contains","id":"7996"}]},"publisher":"Nature Publishing Group","oa_version":"Published Version","citation":{"mla":"Watzinger, Hannes, et al. “A Germanium Hole Spin Qubit.” <i>Nature Communications</i>, vol. 9, no. 3902, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-06418-4\">10.1038/s41467-018-06418-4</a>.","short":"H. Watzinger, J. Kukucka, L. Vukušić, F. Gao, T. Wang, F. Schäffler, J. Zhang, G. Katsaros, Nature Communications 9 (2018).","ista":"Watzinger H, Kukucka J, Vukušić L, Gao F, Wang T, Schäffler F, Zhang J, Katsaros G. 2018. A germanium hole spin qubit. Nature Communications. 9(3902).","apa":"Watzinger, H., Kukucka, J., Vukušić, L., Gao, F., Wang, T., Schäffler, F., … Katsaros, G. (2018). A germanium hole spin qubit. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-018-06418-4\">https://doi.org/10.1038/s41467-018-06418-4</a>","chicago":"Watzinger, Hannes, Josip Kukucka, Lada Vukušić, Fei Gao, Ting Wang, Friedrich Schäffler, Jian Zhang, and Georgios Katsaros. “A Germanium Hole Spin Qubit.” <i>Nature Communications</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41467-018-06418-4\">https://doi.org/10.1038/s41467-018-06418-4</a>.","ama":"Watzinger H, Kukucka J, Vukušić L, et al. A germanium hole spin qubit. <i>Nature Communications</i>. 2018;9(3902). doi:<a href=\"https://doi.org/10.1038/s41467-018-06418-4\">10.1038/s41467-018-06418-4</a>","ieee":"H. Watzinger <i>et al.</i>, “A germanium hole spin qubit,” <i>Nature Communications</i>, vol. 9, no. 3902. Nature Publishing Group, 2018."},"scopus_import":"1","abstract":[{"text":"Holes confined in quantum dots have gained considerable interest in the past few years due to their potential as spin qubits. Here we demonstrate two-axis control of a spin 3/2 qubit in natural Ge. The qubit is formed in a hut wire double quantum dot device. The Pauli spin blockade principle allowed us to demonstrate electric dipole spin resonance by applying a radio frequency electric field to one of the electrodes defining the double quantum dot. Coherent hole spin oscillations with Rabi frequencies reaching 140 MHz are demonstrated and dephasing times of 130 ns are measured. The reported results emphasize the potential of Ge as a platform for fast and electrically tunable hole spin qubit devices.","lang":"eng"}]},{"page":"215 - 232","has_accepted_license":"1","conference":{"start_date":"2018-09-04","end_date":"2018-09-06","name":"FORMATS: Formal Modeling and Analysis of Timed Systems","location":"Bejing, China"},"department":[{"_id":"ToHe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"78","day":"26","date_created":"2018-12-11T11:44:31Z","alternative_title":["LNCS"],"year":"2018","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"file":[{"file_size":374851,"content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-14T11:34:34Z","file_id":"7831","creator":"dernst","checksum":"436b7574934324cfa7d1d3986fddc65b","file_name":"2018_LNCS_Bakhirkin.pdf","access_level":"open_access"}],"doi":"10.1007/978-3-030-00151-3_13","oa":1,"publication_status":"published","intvolume":"     11022","file_date_updated":"2020-07-14T12:48:03Z","author":[{"full_name":"Bakhirkin, Alexey","first_name":"Alexey","last_name":"Bakhirkin"},{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas","first_name":"Thomas","last_name":"Ferrere","orcid":"0000-0001-5199-3143"},{"last_name":"Nickovic","first_name":"Dejan","full_name":"Nickovic, Dejan"},{"full_name":"Maler, Oded","first_name":"Oded","last_name":"Maler"},{"full_name":"Asarin, Eugene","first_name":"Eugene","last_name":"Asarin"}],"ddc":["000"],"language":[{"iso":"eng"}],"publisher":"Springer","oa_version":"Submitted Version","abstract":[{"text":"We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated.","lang":"eng"}],"citation":{"mla":"Bakhirkin, Alexey, et al. <i>Online Timed Pattern Matching Using Automata</i>. Vol. 11022, Springer, 2018, pp. 215–32, doi:<a href=\"https://doi.org/10.1007/978-3-030-00151-3_13\">10.1007/978-3-030-00151-3_13</a>.","short":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer, 2018, pp. 215–232.","ista":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 215–232.","apa":"Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., &#38; Asarin, E. (2018). Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-030-00151-3_13\">https://doi.org/10.1007/978-3-030-00151-3_13</a>","chicago":"Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-00151-3_13\">https://doi.org/10.1007/978-3-030-00151-3_13</a>.","ama":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:<a href=\"https://doi.org/10.1007/978-3-030-00151-3_13\">10.1007/978-3-030-00151-3_13</a>","ieee":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed pattern matching using automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232."},"scopus_import":"1","publication_identifier":{"isbn":["978-3-030-00150-6"]},"type":"conference","status":"public","title":"Online timed pattern matching using automata","isi":1,"date_published":"2018-08-26T00:00:00Z","article_processing_charge":"No","volume":11022,"publist_id":"7976","month":"08","external_id":{"isi":["000884993200013"]},"quality_controlled":"1","date_updated":"2025-04-15T06:26:03Z"},{"status":"public","type":"conference","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method,  differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model.  We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices."}],"scopus_import":"1","citation":{"ieee":"A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in <i>6th International Conference on Learning Representations</i>, Vancouver, Canada, 2018.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: <i>6th International Conference on Learning Representations</i>. ; 2018.","apa":"Polino, A., Pascanu, R., &#38; Alistarh, D.-A. (2018). Model compression via distillation and quantization. In <i>6th International Conference on Learning Representations</i>. Vancouver, Canada.","chicago":"Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In <i>6th International Conference on Learning Representations</i>, 2018.","mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” <i>6th International Conference on Learning Representations</i>, 2018.","ista":"Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018."},"date_updated":"2025-06-30T10:04:44Z","quality_controlled":"1","external_id":{"arxiv":["1802.05668"]},"month":"05","acknowledgement":"We would like to thank Ce Zhang (ETH Zurich), Hantian Zhang (ETH Zurich) and Martin Jaggi ´\r\n(EPFL) for their support with experiments and valuable feedback.\r\n","arxiv":1,"date_published":"2018-05-01T00:00:00Z","article_processing_charge":"No","title":"Model compression via distillation and quantization","day":"01","publication":"6th International Conference on Learning Representations","conference":{"start_date":"2018-04-30","name":"ICLR: International Conference on Learning Representations","end_date":"2018-05-03","location":"Vancouver, Canada"},"department":[{"_id":"DaAl"}],"_id":"7812","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","author":[{"last_name":"Polino","first_name":"Antonio","full_name":"Polino, Antonio"},{"last_name":"Pascanu","first_name":"Razvan","full_name":"Pascanu, Razvan"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"}],"language":[{"iso":"eng"}],"ddc":["000"],"file_date_updated":"2020-07-14T12:48:03Z","file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:48:03Z","file_size":308339,"access_level":"open_access","file_name":"2018_ICLR_Polino.pdf","creator":"dernst","checksum":"a4336c167978e81891970e4e4517a8c3","file_id":"7894","date_created":"2020-05-26T13:02:00Z"}],"publication_status":"published","oa":1,"year":"2018","date_created":"2020-05-10T22:00:51Z"},{"year":"2018","alternative_title":["LNCS"],"date_created":"2018-12-11T11:44:31Z","language":[{"iso":"eng"}],"author":[{"full_name":"Arming, Sebastian","first_name":"Sebastian","last_name":"Arming"},{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"4524F760-F248-11E8-B48F-1D18A9856A87","full_name":"Katoen, Joost P","first_name":"Joost P","last_name":"Katoen"},{"full_name":"Sokolova, Ana","last_name":"Sokolova","first_name":"Ana"}],"intvolume":"     11024","oa":1,"publication_status":"published","doi":"10.1007/978-3-319-99154-2_4","_id":"79","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"conference":{"start_date":"2018-09-04","end_date":"2018-09-07","name":"QEST: Quantitative Evaluation of Systems","location":"Beijing, China"},"page":"53-70","day":"15","publist_id":"7975","volume":11024,"arxiv":1,"date_published":"2018-08-15T00:00:00Z","article_processing_charge":"No","isi":1,"title":"Parameter-independent strategies for pMDPs via POMDPs","quality_controlled":"1","date_updated":"2023-09-13T09:38:28Z","external_id":{"arxiv":["1806.05126"],"isi":["000548912200004"]},"month":"08","abstract":[{"lang":"eng","text":"Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition probabilities to account for stochastic uncertainties of the environment such as noise or input disturbances. We study pMDPs with reachability objectives where the parameter values are unknown and impossible to measure directly during execution, but there is a probability distribution known over the parameter values. We study for the first time computing parameter-independent strategies that are expectation optimal, i.e., optimize the expected reachability probability under the probability distribution over the parameters. We present an encoding of our problem to partially observable MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating (repeated) learner model; a series of benchmarks of varying configurations of a robot moving on a grid; and a consensus protocol."}],"citation":{"ama":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:<a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">10.1007/978-3-319-99154-2_4</a>","ieee":"S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.","mla":"Arming, Sebastian, et al. <i>Parameter-Independent Strategies for PMDPs via POMDPs</i>. Vol. 11024, Springer, 2018, pp. 53–70, doi:<a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">10.1007/978-3-319-99154-2_4</a>.","ista":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11024, 53–70.","short":"S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer, 2018, pp. 53–70.","apa":"Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., &#38; Sokolova, A. (2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp. 53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">https://doi.org/10.1007/978-3-319-99154-2_4</a>","chicago":"Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen, and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">https://doi.org/10.1007/978-3-319-99154-2_4</a>."},"scopus_import":"1","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.05126"}],"publisher":"Springer","status":"public","type":"conference"},{"author":[{"orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christopher","last_name":"Pull","orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","full_name":"Pull, Christopher"},{"first_name":"Matthias","last_name":"Fürst","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias"}],"language":[{"iso":"eng"}],"doi":"10.1146/annurev-ento-020117-043110","publication_status":"published","intvolume":"        63","year":"2018","date_created":"2018-12-11T11:48:36Z","day":"07","corr_author":"1","publication":"Annual Review of Entomology","department":[{"_id":"SyCr"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"806","page":"105 - 123","external_id":{"isi":["000424633700008"]},"quality_controlled":"1","date_updated":"2026-04-08T14:19:10Z","month":"01","volume":63,"publist_id":"6844","title":"Social immunity: Emergence and evolution of colony-level disease protection","isi":1,"date_published":"2018-01-07T00:00:00Z","article_processing_charge":"No","related_material":{"record":[{"id":"819","relation":"dissertation_contains","status":"public"}]},"publication_identifier":{"issn":["1545-4487"]},"type":"journal_article","status":"public","oa_version":"None","abstract":[{"text":"Social insect colonies have evolved many collectively performed adaptations that reduce the impact of infectious disease and that are expected to maximize their fitness. This colony-level protection is termed social immunity, and it enhances the health and survival of the colony. In this review, we address how social immunity emerges from its mechanistic components to produce colony-level disease avoidance, resistance, and tolerance. To understand the evolutionary causes and consequences of social immunity, we highlight the need for studies that evaluate the effects of social immunity on colony fitness. We discuss the role that host life history and ecology have on predicted eco-evolutionary dynamics, which differ among the social insect lineages. Throughout the review, we highlight current gaps in our knowledge and promising avenues for future research, which we hope will bring us closer to an integrated understanding of socio-eco-evo-immunology.","lang":"eng"}],"citation":{"mla":"Cremer, Sylvia, et al. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” <i>Annual Review of Entomology</i>, vol. 63, Annual Reviews, 2018, pp. 105–23, doi:<a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">10.1146/annurev-ento-020117-043110</a>.","ista":"Cremer S, Pull C, Fürst M. 2018. Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. 63, 105–123.","short":"S. Cremer, C. Pull, M. Fürst, Annual Review of Entomology 63 (2018) 105–123.","apa":"Cremer, S., Pull, C., &#38; Fürst, M. (2018). Social immunity: Emergence and evolution of colony-level disease protection. <i>Annual Review of Entomology</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">https://doi.org/10.1146/annurev-ento-020117-043110</a>","chicago":"Cremer, Sylvia, Christopher Pull, and Matthias Fürst. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” <i>Annual Review of Entomology</i>. Annual Reviews, 2018. <a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">https://doi.org/10.1146/annurev-ento-020117-043110</a>.","ama":"Cremer S, Pull C, Fürst M. Social immunity: Emergence and evolution of colony-level disease protection. <i>Annual Review of Entomology</i>. 2018;63:105-123. doi:<a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">10.1146/annurev-ento-020117-043110</a>","ieee":"S. Cremer, C. Pull, and M. Fürst, “Social immunity: Emergence and evolution of colony-level disease protection,” <i>Annual Review of Entomology</i>, vol. 63. Annual Reviews, pp. 105–123, 2018."},"scopus_import":"1","publisher":"Annual Reviews"},{"ddc":["000"],"language":[{"iso":"eng"}],"author":[{"first_name":"Adrian","last_name":"Elgyütt","id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","full_name":"Elgyütt, Adrian"},{"last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"file_date_updated":"2020-10-09T06:24:21Z","intvolume":"     11022","oa":1,"publication_status":"published","doi":"10.1007/978-3-030-00151-3_4","file":[{"content_type":"application/pdf","date_updated":"2020-10-09T06:24:21Z","relation":"main_file","file_size":537219,"file_name":"2018_LNCS_Elgyuett.pdf","access_level":"open_access","checksum":"e5d81c9b50a6bd9d8a2c16953aad7e23","creator":"dernst","success":1,"file_id":"8638","date_created":"2020-10-09T06:24:21Z"}],"project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"}],"year":"2018","alternative_title":["LNCS"],"date_created":"2018-12-11T11:44:31Z","day":"26","_id":"81","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","end_date":"2018-09-06","start_date":"2018-09-04","location":"Beijing, China"},"department":[{"_id":"ToHe"}],"has_accepted_license":"1","page":"53 - 70","date_updated":"2025-04-15T06:26:03Z","quality_controlled":"1","external_id":{"isi":["000884993200004"]},"month":"08","publist_id":"7973","volume":11022,"article_processing_charge":"No","date_published":"2018-08-26T00:00:00Z","isi":1,"title":"Monitoring temporal logic with clock variables","status":"public","type":"conference","abstract":[{"text":"We solve the offline monitoring problem for timed propositional temporal logic (TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider extends linear temporal logic (LTL) with clock variables and reset quantifiers, providing a mechanism to specify real-time constraints. We first describe a general monitoring algorithm based on an exhaustive computation of the set of satisfying clock assignments as a finite union of zones. We then propose a specialized monitoring algorithm for the one-variable case using a partition of the time domain based on the notion of region equivalence, whose complexity is linear in the length of the signal, thereby generalizing a known result regarding the monitoring of metric temporal logic (MTL). The region and zone representations of time constraints are known from timed automata verification and can also be used in the discrete-time case. Our prototype implementation appears to outperform previous discrete-time implementations of TPTL monitoring,","lang":"eng"}],"scopus_import":"1","citation":{"ama":"Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables. In: Vol 11022. Springer; 2018:53-70. doi:<a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">10.1007/978-3-030-00151-3_4</a>","ieee":"A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.","short":"A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.","ista":"Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 53–70.","mla":"Elgyütt, Adrian, et al. <i>Monitoring Temporal Logic with Clock Variables</i>. Vol. 11022, Springer, 2018, pp. 53–70, doi:<a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">10.1007/978-3-030-00151-3_4</a>.","chicago":"Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal Logic with Clock Variables,” 11022:53–70. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">https://doi.org/10.1007/978-3-030-00151-3_4</a>.","apa":"Elgyütt, A., Ferrere, T., &#38; Henzinger, T. A. (2018). Monitoring temporal logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">https://doi.org/10.1007/978-3-030-00151-3_4</a>"},"oa_version":"Submitted Version","publisher":"Springer"},{"date_created":"2018-12-11T11:44:32Z","year":"2018","intvolume":"        16","file":[{"file_size":4007095,"content_type":"application/pdf","date_updated":"2020-07-14T12:48:10Z","relation":"main_file","creator":"dernst","checksum":"527076f78265cd4ea192cd1569851587","access_level":"open_access","file_name":"2018_Plos_Chaudhry.pdf","date_created":"2018-12-17T12:55:31Z","file_id":"5706"}],"doi":"10.1371/journal.pbio.2005971","publication_status":"published","oa":1,"author":[{"full_name":"Chaudhry, Waqas","first_name":"Waqas","last_name":"Chaudhry"},{"orcid":"0000-0001-7460-7479","first_name":"Maros","last_name":"Pleska","full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shah","first_name":"Nilang","full_name":"Shah, Nilang"},{"last_name":"Weiss","first_name":"Howard","full_name":"Weiss, Howard"},{"full_name":"Mccall, Ingrid","last_name":"Mccall","first_name":"Ingrid"},{"full_name":"Meyer, Justin","first_name":"Justin","last_name":"Meyer"},{"first_name":"Animesh","last_name":"Gupta","full_name":"Gupta, Animesh"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"},{"last_name":"Levin","first_name":"Bruce","full_name":"Levin, Bruce"}],"language":[{"iso":"eng"}],"ddc":["570"],"file_date_updated":"2020-07-14T12:48:10Z","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"CaGu"}],"issue":"8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"82","publication":"PLoS Biology","day":"16","isi":1,"article_processing_charge":"Yes","date_published":"2018-08-16T00:00:00Z","title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","publist_id":"7972","volume":16,"month":"08","date_updated":"2023-09-13T08:45:41Z","quality_controlled":"1","external_id":{"isi":["000443383300024"]},"publisher":"Public Library of Science","oa_version":"Published Version","article_number":"2005971","abstract":[{"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.”.","lang":"eng"}],"scopus_import":"1","citation":{"short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","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.","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>.","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>.","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>","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>","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."},"status":"public","type":"journal_article","related_material":{"record":[{"status":"public","id":"9810","relation":"research_data"}]}},{"publisher":"Springer","oa_version":"Preprint","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"}],"scopus_import":"1","citation":{"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>","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.","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>.","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.","short":"E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479.","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>","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>."},"status":"public","publication_identifier":{"issn":["0302-9743"]},"type":"conference","isi":1,"acknowledgement":"Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14) and by a NSERC post-doctoral fellowship.","date_published":"2018-08-01T00:00:00Z","article_processing_charge":"No","title":"Snapshot based synchronization: A fast replacement for Hand-over-Hand locking","publist_id":"7969","volume":11014,"month":"08","date_updated":"2026-04-16T09:53:41Z","quality_controlled":"1","external_id":{"isi":["000851042300031"]},"has_accepted_license":"1","page":"465 - 479","department":[{"_id":"DaAl"}],"conference":{"location":"Turin, Italy","start_date":"2018-08-27","name":"Euro-Par: European Conference on Parallel Processing","end_date":"2018-08-31"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"85","day":"01","alternative_title":["LNCS"],"date_created":"2018-12-11T11:44:33Z","year":"2018","intvolume":"     11014","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"file":[{"file_name":"2018_Brown.pdf","access_level":"open_access","creator":"dernst","checksum":"13a3f250be8878405e791b53c19722ad","file_id":"5954","date_created":"2019-02-12T07:40:40Z","content_type":"application/pdf","date_updated":"2020-07-14T12:48:14Z","relation":"main_file","file_size":665372}],"doi":"10.1007/978-3-319-96983-1_33","oa":1,"publication_status":"published","author":[{"full_name":"Gilad, Eran","last_name":"Gilad","first_name":"Eran"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A","first_name":"Trevor A","last_name":"Brown"},{"first_name":"Mark","last_name":"Oskin","full_name":"Oskin, Mark"},{"first_name":"Yoav","last_name":"Etsion","full_name":"Etsion, Yoav"}],"ddc":["000"],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:14Z"},{"ddc":["000"],"language":[{"iso":"eng"}],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:48:14Z","intvolume":"     10760","oa":1,"publication_status":"published","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"file":[{"checksum":"9995c6ce6957333baf616fc4f20be597","creator":"dernst","file_name":"2018_PrinciplesModeling_Chatterjee.pdf","access_level":"open_access","date_created":"2019-11-19T08:22:18Z","file_id":"7053","file_size":516307,"date_updated":"2020-07-14T12:48:14Z","content_type":"application/pdf","relation":"main_file"}],"doi":"10.1007/978-3-319-95246-8_9","year":"2018","alternative_title":["LNCS"],"date_created":"2018-12-11T11:44:33Z","day":"20","publication":"Principles of Modeling","_id":"86","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"ec_funded":1,"has_accepted_license":"1","page":"143 - 161","date_updated":"2025-04-15T06:26:15Z","quality_controlled":"1","month":"07","publist_id":"7968","volume":10760,"date_published":"2018-07-20T00:00:00Z","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.","title":"Computing average response time","editor":[{"last_name":"Lohstroh","first_name":"Marten","full_name":"Lohstroh, Marten"},{"first_name":"Patricia","last_name":"Derler","full_name":"Derler, Patricia"},{"first_name":"Marjan","last_name":"Sirjani","full_name":"Sirjani, Marjan"}],"status":"public","type":"book_chapter","citation":{"ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 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.","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>.","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>.","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>","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>","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."},"scopus_import":1,"abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","publisher":"Springer"},{"year":"2018","date_created":"2020-10-06T16:33:37Z","article_type":"original","file_date_updated":"2020-10-06T16:35:16Z","language":[{"iso":"eng"}],"ddc":["570"],"author":[{"full_name":"Gregor, Carola","first_name":"Carola","last_name":"Gregor"},{"full_name":"Sidenstein, Sven C.","first_name":"Sven C.","last_name":"Sidenstein"},{"full_name":"Andresen, Martin","first_name":"Martin","last_name":"Andresen"},{"first_name":"Steffen J.","last_name":"Sahl","full_name":"Sahl, Steffen J."},{"first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"},{"full_name":"Hell, Stefan W.","last_name":"Hell","first_name":"Stefan W."}],"publication_status":"published","oa":1,"file":[{"file_size":2818077,"date_updated":"2020-10-06T16:35:16Z","relation":"main_file","content_type":"application/pdf","date_created":"2020-10-06T16:35:16Z","file_id":"8619","success":1,"creator":"dernst","checksum":"e642080fcbde9584c63544f587c74f03","access_level":"open_access","file_name":"2018_ScientificReports_Gregor.pdf"}],"doi":"10.1038/s41598-018-19947-1","intvolume":"         8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8618","department":[{"_id":"JoDa"}],"pmid":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","day":"09","publication":"Scientific Reports","volume":8,"title":"Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA","date_published":"2018-02-09T00:00:00Z","article_processing_charge":"No","isi":1,"external_id":{"isi":["000424630400037"],"pmid":["29426833"]},"quality_controlled":"1","date_updated":"2024-10-21T06:02:43Z","month":"02","keyword":["Multidisciplinary"],"article_number":"2724","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"citation":{"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>","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.","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>.","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.","short":"C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell, Scientific Reports 8 (2018).","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>","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>."},"oa_version":"Published Version","publisher":"Springer Nature","type":"journal_article","publication_identifier":{"issn":["2045-2322"]},"status":"public"}]