[{"month":"07","oa":1,"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"doi":"10.1007/978-3-319-95246-8_9","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:14Z","ec_funded":1,"publist_id":"7968","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.","year":"2018","publication_status":"published","editor":[{"first_name":"Marten","last_name":"Lohstroh","full_name":"Lohstroh, Marten"},{"full_name":"Derler, Patricia","first_name":"Patricia","last_name":"Derler"},{"first_name":"Marjan","last_name":"Sirjani","full_name":"Sirjani, Marjan"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","first_name":"Jan"}],"date_updated":"2021-01-12T08:20:14Z","date_created":"2018-12-11T11:44:33Z","volume":10760,"scopus_import":1,"day":"20","has_accepted_license":"1","publication":"Principles of Modeling","citation":{"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.” Principles of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:10.1007/978-3-319-95246-8_9.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer; 2018:143-161. doi:10.1007/978-3-319-95246-8_9","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161."},"page":"143 - 161","date_published":"2018-07-20T00:00:00Z","type":"book_chapter","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"86","ddc":["000"],"status":"public","title":"Computing average response time","intvolume":" 10760","file":[{"checksum":"9995c6ce6957333baf616fc4f20be597","date_updated":"2020-07-14T12:48:14Z","date_created":"2019-11-19T08:22:18Z","relation":"main_file","file_id":"7053","file_size":516307,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_PrinciplesModeling_Chatterjee.pdf"}],"oa_version":"Submitted Version"},{"month":"06","publication_identifier":{"issn":["2500-2287"],"eissn":["2500-2295"]},"doi":"10.20388/omp2018.00s1.001","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience","open_access":"1"}],"quality_controlled":"1","author":[{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G"}],"date_updated":"2021-12-03T07:31:05Z","date_created":"2021-03-07T23:01:25Z","volume":4,"year":"2018","publication_status":"published","department":[{"_id":"JoDa"}],"publisher":"Lobachevsky State University of Nizhny Novgorod","day":"30","article_processing_charge":"No","scopus_import":"1","date_published":"2018-06-30T00:00:00Z","publication":"Opera Medica et Physiologica","citation":{"chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod, 2018. https://doi.org/10.20388/omp2018.00s1.001.","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod. https://doi.org/10.20388/omp2018.00s1.001","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018.","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11.","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001"},"article_type":"letter_note","page":"11","issue":"S1","type":"journal_article","alternative_title":["Molecular and cellular neuroscience"],"oa_version":"Published Version","_id":"9229","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Diffraction-unlimited optical imaging for synaptic physiology","intvolume":" 4"},{"date_published":"2018-08-01T00:00:00Z","citation":{"short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks (Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2018.23","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom, 2018, vol. 117.","ista":"Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"creator":"dernst","content_type":"application/pdf","file_size":542889,"access_level":"open_access","file_name":"2018_LIPIcs_Avni.pdf","checksum":"41ab2ae9b63f5eb49fa995250c0ba128","date_updated":"2020-07-14T12:47:15Z","date_created":"2019-02-14T14:22:04Z","file_id":"6007","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6005","title":"Timed network games with clocks","ddc":["000"],"status":"public","intvolume":" 117","abstract":[{"text":"Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting.","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"conference":{"name":"MFCS: Mathematical Foundations of Computer Science","end_date":"2018-08-31","location":"Liverpool, United Kingdom","start_date":"2018-08-27"},"doi":"10.4230/LIPICS.MFCS.2018.23","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF"}],"month":"08","publication_identifier":{"issn":["1868-8969"]},"author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy"},{"first_name":"Shibashis","last_name":"Guha","full_name":"Guha, Shibashis"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"related_material":{"record":[{"id":"963","relation":"earlier_version","status":"public"}]},"date_created":"2019-02-14T14:12:09Z","date_updated":"2023-02-23T14:02:58Z","volume":117,"year":"2018","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-07-14T12:47:15Z","license":"https://creativecommons.org/licenses/by/4.0/","article_number":"23"},{"issue":"6","abstract":[{"text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":6968201,"content_type":"application/pdf","file_name":"2017_PLOS_Polechova.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:01Z","date_created":"2019-01-22T08:30:03Z","checksum":"908c52751bba30c55ed36789e5e4c84d","file_id":"5870","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"315","intvolume":" 16","status":"public","ddc":["576"],"title":"Is the sky the limit? On the expansion threshold of a species’ range","has_accepted_license":"1","day":"15","scopus_import":1,"date_published":"2018-06-15T00:00:00Z","citation":{"short":"J. Polechova, PLoS Biology 16 (2018).","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372."},"publication":"PLoS Biology","publist_id":"7550","file_date_updated":"2020-07-14T12:46:01Z","article_number":"e2005372","related_material":{"record":[{"id":"9839","relation":"research_data","status":"public"}]},"author":[{"orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka","full_name":"Polechova, Jitka"}],"volume":16,"date_created":"2018-12-11T11:45:46Z","date_updated":"2023-02-23T14:10:16Z","year":"2018","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"publication_status":"published","publication_identifier":{"issn":["15449173"]},"month":"06","doi":"10.1371/journal.pbio.2005372","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1"},{"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["29712855"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1713333115","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"05","department":[{"_id":"DaZi"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2018","volume":115,"date_updated":"2021-12-14T07:53:40Z","date_created":"2021-06-07T06:11:28Z","related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/187674 "}]},"author":[{"first_name":"Jennifer M.","last_name":"Frost","full_name":"Frost, Jennifer M."},{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"last_name":"Park","first_name":"Guen Tae","full_name":"Park, Guen Tae"},{"full_name":"Hsieh, Ping-Hung","last_name":"Hsieh","first_name":"Ping-Hung"},{"full_name":"Nakamura, Miyuki","first_name":"Miyuki","last_name":"Nakamura"},{"full_name":"Lin, Samuel J. H.","last_name":"Lin","first_name":"Samuel J. H."},{"full_name":"Yoo, Hyunjin","first_name":"Hyunjin","last_name":"Yoo"},{"full_name":"Choi, Jaemyung","last_name":"Choi","first_name":"Jaemyung"},{"first_name":"Yoko","last_name":"Ikeda","full_name":"Ikeda, Yoko"},{"last_name":"Kinoshita","first_name":"Tetsu","full_name":"Kinoshita, Tetsu"},{"first_name":"Yeonhee","last_name":"Choi","full_name":"Choi, Yeonhee"},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","extern":"1","file_date_updated":"2021-06-07T06:16:38Z","page":"E4720-E4729","article_type":"original","citation":{"short":"J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H. Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 115 (2018) E4720–E4729.","mla":"Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the National Academy of Sciences, vol. 115, no. 20, National Academy of Sciences, 2018, pp. E4720–29, doi:10.1073/pnas.1713333115.","chicago":"Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713333115.","ama":"Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 2018;115(20):E4720-E4729. doi:10.1073/pnas.1713333115","apa":"Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S. J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1713333115","ieee":"J. M. Frost et al., “FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis,” Proceedings of the National Academy of Sciences, vol. 115, no. 20. National Academy of Sciences, pp. E4720–E4729, 2018.","ista":"Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J, Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 115(20), E4720–E4729."},"publication":"Proceedings of the National Academy of Sciences","date_published":"2018-05-15T00:00:00Z","keyword":["Multidisciplinary"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"15","intvolume":" 115","status":"public","title":"FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis","ddc":["580"],"_id":"9471","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","file":[{"file_name":"2018_PNAS_Frost.pdf","access_level":"open_access","creator":"asandaue","content_type":"application/pdf","file_size":3045260,"file_id":"9472","relation":"main_file","date_created":"2021-06-07T06:16:38Z","date_updated":"2021-06-07T06:16:38Z","success":1,"checksum":"810260dc0e3cc3033e15c19ad0dc123e"}],"type":"journal_article","issue":"20","abstract":[{"lang":"eng","text":"The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin."}]},{"oa_version":"Submitted Version","intvolume":" 99","status":"public","title":"The ℤ2-Genus of Kuratowski minors","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"186","abstract":[{"text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces.","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","date_published":"2018-06-11T00:00:00Z","page":"40.1 - 40.14","citation":{"chicago":"Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.40.","mla":"Fulek, Radoslav, and Jan Kynčl. The ℤ2-Genus of Kuratowski Minors. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:10.4230/LIPIcs.SoCG.2018.40.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14.","ista":"Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14.","ieee":"R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 40.1-40.14.","apa":"Fulek, R., & Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol. 99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.40","ama":"Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:10.4230/LIPIcs.SoCG.2018.40"},"article_processing_charge":"No","day":"11","scopus_import":"1","volume":99,"date_updated":"2023-08-14T12:43:51Z","date_created":"2018-12-11T11:45:05Z","related_material":{"record":[{"id":"11593","status":"public","relation":"later_version"}]},"author":[{"full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2018","publist_id":"7734","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2018.40","conference":{"start_date":"2018-06-11","location":"Budapest, Hungary","end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry"},"project":[{"name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF","grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1803.05085"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.05085"}],"month":"06"},{"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound is best possible for infinitely many values of n."}],"_id":"433","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Thrackles: An improved upper bound","status":"public","intvolume":" 10692","oa_version":"Submitted Version","scopus_import":1,"day":"21","citation":{"ama":"Fulek R, Pach J. Thrackles: An improved upper bound. In: Vol 10692. Springer; 2018:160-166. doi:10.1007/978-3-319-73915-1_14","apa":"Fulek, R., & Pach, J. (2018). Thrackles: An improved upper bound (Vol. 10692, pp. 160–166). Presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States: Springer. https://doi.org/10.1007/978-3-319-73915-1_14","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States, 2018, vol. 10692, pp. 160–166.","ista":"Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph Drawing and Network Visualization, LNCS, vol. 10692, 160–166.","short":"R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166.","mla":"Fulek, Radoslav, and János Pach. Thrackles: An Improved Upper Bound. Vol. 10692, Springer, 2018, pp. 160–66, doi:10.1007/978-3-319-73915-1_14.","chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound,” 10692:160–66. Springer, 2018. https://doi.org/10.1007/978-3-319-73915-1_14."},"page":"160 - 166","date_published":"2018-01-21T00:00:00Z","publist_id":"7390","year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"UlWa"}],"author":[{"full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav"},{"full_name":"Pach, János","first_name":"János","last_name":"Pach"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"5857"}]},"date_created":"2018-12-11T11:46:27Z","date_updated":"2023-08-24T14:39:32Z","volume":10692,"month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08037"}],"external_id":{"arxiv":["1708.08037"]},"oa":1,"quality_controlled":"1","conference":{"name":"GD 2017: Graph Drawing and Network Visualization","end_date":"2017-09-27","location":"Boston, MA, United States","start_date":"201-09-25"},"doi":"10.1007/978-3-319-73915-1_14","language":[{"iso":"eng"}]},{"article_processing_charge":"No","day":"09","month":"10","date_published":"2018-10-09T00:00:00Z","doi":"10.5061/dryad.72cg113","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.72cg113"}],"citation":{"ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, 10.5061/dryad.72cg113.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113","ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.","mla":"Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018)."},"abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_updated":"2023-08-24T14:50:26Z","date_created":"2021-08-09T12:46:39Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6095"}]},"author":[{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Chaube, Pragya","last_name":"Chaube","first_name":"Pragya"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"full_name":"Lemmon, Alan R.","first_name":"Alan R.","last_name":"Lemmon"},{"first_name":"Emily M.","last_name":"Lemmon","full_name":"Lemmon, Emily M."},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"full_name":"Panova, Marina","first_name":"Marina","last_name":"Panova"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"department":[{"_id":"NiBa"}],"publisher":"Dryad","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9837","year":"2018"},{"place":"Cham","editor":[{"full_name":"Czelakowski, J","last_name":"Czelakowski","first_name":"J"}],"publisher":"Springer Nature","department":[{"_id":"VlKo"}],"publication_status":"published","acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","year":"2018","volume":16,"date_created":"2022-03-18T10:30:32Z","date_updated":"2023-09-05T15:37:18Z","author":[{"full_name":"Kazda, Alexandr","last_name":"Kazda","first_name":"Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kozik, Marcin","last_name":"Kozik","first_name":"Marcin"},{"full_name":"McKenzie, Ralph","first_name":"Ralph","last_name":"McKenzie"},{"full_name":"Moore, Matthew","last_name":"Moore","first_name":"Matthew"}],"publication_identifier":{"eisbn":["9783319747729"],"issn":["2211-2758"],"eissn":["2211-2766"],"isbn":["9783319747712"]},"month":"03","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1502.01072"]},"main_file_link":[{"url":"https://arxiv.org/abs/1502.01072","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-74772-9_7","type":"book_chapter","abstract":[{"text":"We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k.","lang":"eng"}],"intvolume":" 16","title":"Absorption and directed Jónsson terms","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10864","oa_version":"Preprint","series_title":"OCTR","scopus_import":"1","article_processing_charge":"No","day":"21","page":"203-220","citation":{"short":"A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, Springer Nature, Cham, 2018, pp. 203–220.","mla":"Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:10.1007/978-3-319-74772-9_7.","chicago":"Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-74772-9_7.","ama":"Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:10.1007/978-3-319-74772-9_7","apa":"Kazda, A., Kozik, M., McKenzie, R., & Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science (Vol. 16, pp. 203–220). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-74772-9_7","ieee":"A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.","ista":"Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. vol. 16, 203–220."},"publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","date_published":"2018-03-21T00:00:00Z"},{"publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2018","acknowledgement":"Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration.","date_created":"2018-12-11T11:45:04Z","date_updated":"2023-09-06T11:10:57Z","volume":99,"author":[{"first_name":"Xavier","last_name":"Goaoc","full_name":"Goaoc, Xavier"},{"full_name":"Paták, Pavel","first_name":"Pavel","last_name":"Paták"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","first_name":"Zuzana"},{"full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","last_name":"Tancer","first_name":"Martin"},{"full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"7108"}]},"file_date_updated":"2020-07-14T12:45:18Z","publist_id":"7736","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2018-06-14","start_date":"2018-06-11","location":"Budapest, Hungary"},"doi":"10.4230/LIPIcs.SoCG.2018.41","month":"06","status":"public","ddc":["516","000"],"title":"Shellability is NP-complete","intvolume":" 99","_id":"184","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"checksum":"d12bdd60f04a57307867704b5f930afd","date_created":"2018-12-17T16:35:02Z","date_updated":"2020-07-14T12:45:18Z","file_id":"5725","relation":"main_file","creator":"dernst","file_size":718414,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_LIPIcs_Goaoc.pdf"}],"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"type":"conference","abstract":[{"text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes.","lang":"eng"}],"page":"41:1 - 41:16","citation":{"chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete,” 99:41:1-41:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.41.","mla":"Goaoc, Xavier, et al. Shellability Is NP-Complete. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16, doi:10.4230/LIPIcs.SoCG.2018.41.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16.","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2018. Shellability is NP-complete. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 41:1-41:16.","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2018). Shellability is NP-complete (Vol. 99, p. 41:1-41:16). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.41","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 41:1-41:16.","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:41:1-41:16. doi:10.4230/LIPIcs.SoCG.2018.41"},"date_published":"2018-06-11T00:00:00Z","scopus_import":1,"day":"11","has_accepted_license":"1"},{"scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.46.","mla":"Huszár, Kristóf, et al. On the Treewidth of Triangulated 3-Manifolds. Vol. 99, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.46.","short":"K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ista":"Huszár K, Spreer J, Wagner U. 2018. On the treewidth of triangulated 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 46.","apa":"Huszár, K., Spreer, J., & Wagner, U. (2018). On the treewidth of triangulated 3-manifolds (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.46","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.46"},"date_published":"2018-06-01T00:00:00Z","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how "simple" or "thin" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol and of Scharlemann and Thompson, by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1))."}],"_id":"285","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 99","status":"public","title":"On the treewidth of triangulated 3-manifolds","ddc":["516","000"],"file":[{"relation":"main_file","file_id":"5713","date_updated":"2020-07-14T12:45:51Z","date_created":"2018-12-17T15:32:38Z","checksum":"530d084116778135d5bffaa317479cac","file_name":"2018_LIPIcs_Huszar.pdf","access_level":"open_access","file_size":642522,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Submitted Version","publication_identifier":{"issn":["18688969"]},"month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1712.00434"]},"quality_controlled":"1","doi":"10.4230/LIPIcs.SoCG.2018.46","conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11"},"language":[{"iso":"eng"}],"article_number":"46","publist_id":"7614","file_date_updated":"2020-07-14T12:45:51Z","year":"2018","acknowledgement":"Research of the second author was supported by the Einstein Foundation (project “Einstein Visiting Fellow Santos”) and by the Simons Foundation (“Simons Visiting Professors” program).","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"publication_status":"published","related_material":{"record":[{"id":"7093","relation":"later_version","status":"public"}]},"author":[{"full_name":"Huszár, Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5445-5057","first_name":"Kristóf","last_name":"Huszár"},{"full_name":"Spreer, Jonathan","first_name":"Jonathan","last_name":"Spreer"},{"last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"}],"volume":99,"date_created":"2018-12-11T11:45:37Z","date_updated":"2023-09-06T11:13:41Z"},{"citation":{"chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.2025846.","mla":"Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846.","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, 10.5281/ZENODO.2025846.","ieee":"E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. https://doi.org/10.5281/ZENODO.2025846","ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:10.5281/ZENODO.2025846"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.3271452"}],"oa":1,"doi":"10.5281/ZENODO.2025846","date_published":"2018-12-07T00:00:00Z","article_processing_charge":"No","day":"07","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13059","year":"2018","department":[{"_id":"FyKo"}],"publisher":"Zenodo","title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","status":"public","ddc":["570"],"related_material":{"record":[{"id":"7181","status":"public","relation":"used_in_publication"}]},"author":[{"last_name":"Garriga","first_name":"Edgar","full_name":"Garriga, Edgar"},{"last_name":"di Tommaso","first_name":"Paolo","full_name":"di Tommaso, Paolo"},{"full_name":"Magis, Cedrik","first_name":"Cedrik","last_name":"Magis"},{"first_name":"Ionas","last_name":"Erb","full_name":"Erb, Ionas"},{"first_name":"Leila","last_name":"Mansouri","full_name":"Mansouri, Leila"},{"first_name":"Athanasios","last_name":"Baltzis","full_name":"Baltzis, Athanasios"},{"full_name":"Laayouni, Hafid","last_name":"Laayouni","first_name":"Hafid"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"last_name":"Floden","first_name":"Evan","full_name":"Floden, Evan"},{"full_name":"Notredame, Cedric","last_name":"Notredame","first_name":"Cedric"}],"oa_version":"Published Version","date_created":"2023-05-23T16:08:20Z","date_updated":"2023-09-06T14:32:51Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee)."}]},{"file_date_updated":"2020-07-14T12:46:35Z","publist_id":"8005","date_created":"2018-12-11T11:44:21Z","date_updated":"2023-09-07T12:27:43Z","author":[{"id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","last_name":"Watzinger","first_name":"Hannes","full_name":"Watzinger, Hannes"}],"publication_status":"published","department":[{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","year":"2018","month":"07","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_1033","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"lang":"eng","text":"Nowadays, quantum computation is receiving more and more attention as an alternative to the classical way of computing. For realizing a quantum computer, different devices are investigated as potential quantum bits. In this thesis, the focus is on Ge hut wires, which turned out to be promising candidates for implementing hole spin quantum bits. The advantages of Ge as a material system are the low hyperfine interaction for holes and the strong spin orbit coupling, as well as the compatibility with the highly developed CMOS processes in industry. In addition, Ge can also be isotopically purified which is expected to boost the spin coherence times. The strong spin orbit interaction for holes in Ge on the one hand enables the full electrical control of the quantum bit and on the other hand should allow short spin manipulation times. Starting with a bare Si wafer, this work covers the entire process reaching from growth over the fabrication and characterization of hut wire devices up to the demonstration of hole spin resonance. From experiments with single quantum dots, a large g-factor anisotropy between the in-plane and the out-of-plane direction was found. A comparison to a theoretical model unveiled the heavy-hole character of the lowest energy states. The second part of the thesis addresses double quantum dot devices, which were realized by adding two gate electrodes to a hut wire. In such devices, Pauli spin blockade was observed, which can serve as a read-out mechanism for spin quantum bits. Applying oscillating electric fields in spin blockade allowed the demonstration of continuous spin rotations and the extraction of a lower bound for the spin dephasing time. Despite the strong spin orbit coupling in Ge, the obtained value for the dephasing time is comparable to what has been recently reported for holes in Si. All in all, the presented results point out the high potential of Ge hut wires as a platform for long-lived, fast and fully electrically tunable hole spin quantum bits."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"access_level":"open_access","file_name":"2018_Thesis_Watzinger.pdf","file_size":85539748,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6249","checksum":"b653b5216251f938ddbeafd1de88667c","date_created":"2019-04-09T07:13:28Z","date_updated":"2020-07-14T12:46:35Z"},{"file_id":"6250","relation":"source_file","date_created":"2019-04-09T07:13:27Z","date_updated":"2020-07-14T12:46:35Z","checksum":"39bcf8de7ac5b1bb516b11ce2f966785","file_name":"2018_Thesis_Watzinger_source.zip","access_level":"closed","creator":"dernst","file_size":21830697,"content_type":"application/zip"}],"oa_version":"Published Version","pubrep_id":"1033","ddc":["530"],"title":"Ge hut wires - from growth to hole spin resonance","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"49","day":"30","article_processing_charge":"No","has_accepted_license":"1","date_published":"2018-07-30T00:00:00Z","page":"77","citation":{"ama":"Watzinger H. Ge hut wires - from growth to hole spin resonance. 2018. doi:10.15479/AT:ISTA:th_1033","ista":"Watzinger H. 2018. Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria.","apa":"Watzinger, H. (2018). Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1033","ieee":"H. Watzinger, “Ge hut wires - from growth to hole spin resonance,” Institute of Science and Technology Austria, 2018.","mla":"Watzinger, Hannes. Ge Hut Wires - from Growth to Hole Spin Resonance. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1033.","short":"H. Watzinger, Ge Hut Wires - from Growth to Hole Spin Resonance, Institute of Science and Technology Austria, 2018.","chicago":"Watzinger, Hannes. “Ge Hut Wires - from Growth to Hole Spin Resonance.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1033."}},{"article_processing_charge":"No","has_accepted_license":"1","day":"11","date_published":"2018-06-11T00:00:00Z","page":"171","citation":{"ista":"Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and Technology Austria.","ieee":"M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology Austria, 2018.","apa":"Iglesias Ham, M. (2018). Multiple covers with balls. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1026","ama":"Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026","chicago":"Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1026.","mla":"Iglesias Ham, Mabel. Multiple Covers with Balls. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1026.","short":"M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology Austria, 2018."},"abstract":[{"lang":"eng","text":"We describe arrangements of three-dimensional spheres from a geometrical and topological point of view. Real data (fitting this setup) often consist of soft spheres which show certain degree of deformation while strongly packing against each other. In this context, we answer the following questions: If we model a soft packing of spheres by hard spheres that are allowed to overlap, can we measure the volume in the overlapped areas? Can we be more specific about the overlap volume, i.e. quantify how much volume is there covered exactly twice, three times, or k times? What would be a good optimization criteria that rule the arrangement of soft spheres while making a good use of the available space? Fixing a particular criterion, what would be the optimal sphere configuration? The first result of this thesis are short formulas for the computation of volumes covered by at least k of the balls. The formulas exploit information contained in the order-k Voronoi diagrams and its closely related Level-k complex. The used complexes lead to a natural generalization into poset diagrams, a theoretical formalism that contains the order-k and degree-k diagrams as special cases. In parallel, we define different criteria to determine what could be considered an optimal arrangement from a geometrical point of view. Fixing a criterion, we find optimal soft packing configurations in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools from computational topology on real physical data, to show the potentials of higher-order diagrams in the description of melting crystals. The results of the experiments leaves us with an open window to apply the theories developed in this thesis in real applications."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"access_level":"closed","file_name":"IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip","creator":"kschuh","content_type":"application/zip","file_size":11827713,"file_id":"5918","relation":"source_file","checksum":"dd699303623e96d1478a6ae07210dd05","date_updated":"2020-07-14T12:45:24Z","date_created":"2019-02-05T07:43:31Z"},{"access_level":"open_access","file_name":"IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf","creator":"kschuh","content_type":"application/pdf","file_size":4783846,"file_id":"5919","relation":"main_file","checksum":"ba163849a190d2b41d66fef0e4983294","date_updated":"2020-07-14T12:45:24Z","date_created":"2019-02-05T07:43:45Z"}],"pubrep_id":"1026","ddc":["514","516"],"title":"Multiple covers with balls","status":"public","_id":"201","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"month":"06","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"}],"doi":"10.15479/AT:ISTA:th_1026","oa":1,"publist_id":"7712","file_date_updated":"2020-07-14T12:45:24Z","date_updated":"2023-09-07T12:25:32Z","date_created":"2018-12-11T11:45:10Z","author":[{"first_name":"Mabel","last_name":"Iglesias Ham","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","full_name":"Iglesias Ham, Mabel"}],"department":[{"_id":"HeEd"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018"},{"file_date_updated":"2020-07-14T12:47:40Z","ec_funded":1,"publist_id":"7986","author":[{"id":"37099E9C-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","last_name":"Zimin","full_name":"Zimin, Alexander"}],"date_created":"2018-12-11T11:44:27Z","date_updated":"2023-09-07T12:29:07Z","year":"2018","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ChLa"}],"month":"09","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:TH1048","supervisor":[{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"abstract":[{"text":"The most common assumption made in statistical learning theory is the assumption of the independent and identically distributed (i.i.d.) data. While being very convenient mathematically, it is often very clearly violated in practice. This disparity between the machine learning theory and applications underlies a growing demand in the development of algorithms that learn from dependent data and theory that can provide generalization guarantees similar to the independent situations. This thesis is dedicated to two variants of dependencies that can arise in practice. One is a dependence on the level of samples in a single learning task. Another dependency type arises in the multi-task setting when the tasks are dependent on each other even though the data for them can be i.i.d. In both cases we model the data (samples or tasks) as stochastic processes and introduce new algorithms for both settings that take into account and exploit the resulting dependencies. We prove the theoretical guarantees on the performance of the introduced algorithms under different evaluation criteria and, in addition, we compliment the theoretical study by the empirical one, where we evaluate some of the algorithms on two real world datasets to highlight their practical applicability.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"1048","oa_version":"Published Version","file":[{"creator":"dernst","file_size":1036137,"content_type":"application/pdf","file_name":"2018_Thesis_Zimin.pdf","access_level":"open_access","date_created":"2019-04-09T07:32:47Z","date_updated":"2020-07-14T12:47:40Z","checksum":"e849dd40a915e4d6c5572b51b517f098","file_id":"6253","relation":"main_file"},{"file_size":637490,"content_type":"application/zip","creator":"dernst","file_name":"2018_Thesis_Zimin_Source.zip","access_level":"closed","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-04-09T07:32:47Z","checksum":"da092153cec55c97461bd53c45c5d139","relation":"source_file","file_id":"6254"}],"_id":"68","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["004","519"],"status":"public","title":"Learning from dependent data","day":"01","has_accepted_license":"1","article_processing_charge":"No","date_published":"2018-09-01T00:00:00Z","citation":{"mla":"Zimin, Alexander. Learning from Dependent Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH1048.","short":"A. Zimin, Learning from Dependent Data, Institute of Science and Technology Austria, 2018.","chicago":"Zimin, Alexander. “Learning from Dependent Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH1048.","ama":"Zimin A. Learning from dependent data. 2018. doi:10.15479/AT:ISTA:TH1048","ista":"Zimin A. 2018. Learning from dependent data. Institute of Science and Technology Austria.","ieee":"A. Zimin, “Learning from dependent data,” Institute of Science and Technology Austria, 2018.","apa":"Zimin, A. (2018). Learning from dependent data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH1048"},"page":"92"},{"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"doi":"10.15479/AT:ISTA:TH_1046","project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"},{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"09","date_created":"2018-12-11T11:44:32Z","date_updated":"2023-09-07T12:30:23Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1229"},{"id":"1235","relation":"part_of_dissertation","status":"public"},{"id":"1236","status":"public","relation":"part_of_dissertation"},{"id":"559","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Abusalah, Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","last_name":"Abusalah","first_name":"Hamza M"}],"department":[{"_id":"KrPi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018","ec_funded":1,"publist_id":"7971","file_date_updated":"2020-07-14T12:48:11Z","date_published":"2018-09-05T00:00:00Z","page":"59","citation":{"ama":"Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:10.15479/AT:ISTA:TH_1046","apa":"Abusalah, H. M. (2018). Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1046","ieee":"H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018.","ista":"Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria.","short":"H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018.","mla":"Abusalah, Hamza M. Proof Systems for Sustainable Decentralized Cryptocurrencies. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1046.","chicago":"Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1046."},"has_accepted_license":"1","article_processing_charge":"No","day":"05","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":876241,"creator":"dernst","access_level":"open_access","file_name":"2018_Thesis_Abusalah.pdf","checksum":"c4b5f7d111755d1396787f41886fc674","date_updated":"2020-07-14T12:48:11Z","date_created":"2019-04-09T06:43:41Z","relation":"main_file","file_id":"6245"},{"creator":"dernst","content_type":"application/x-gzip","file_size":2029190,"file_name":"2018_Thesis_Abusalah_source.tar.gz","access_level":"closed","date_created":"2019-04-09T06:43:41Z","date_updated":"2020-07-14T12:48:11Z","checksum":"0f382ac56b471c48fd907d63eb87dafe","file_id":"6246","relation":"source_file"}],"pubrep_id":"1046","title":"Proof systems for sustainable decentralized cryptocurrencies","ddc":["004"],"status":"public","_id":"83","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work.\r\nProofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"page":"113","citation":{"chicago":"Kolesnikov, Alexander. “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1021.","mla":"Kolesnikov, Alexander. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1021.","short":"A. Kolesnikov, Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images, Institute of Science and Technology Austria, 2018.","ista":"Kolesnikov A. 2018. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria.","ieee":"A. Kolesnikov, “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images,” Institute of Science and Technology Austria, 2018.","apa":"Kolesnikov, A. (2018). Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1021","ama":"Kolesnikov A. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. 2018. doi:10.15479/AT:ISTA:th_1021"},"date_published":"2018-05-25T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"25","status":"public","title":"Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images","ddc":["004"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"197","oa_version":"Published Version","file":[{"file_name":"IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":12918758,"file_id":"5113","relation":"main_file","date_created":"2018-12-12T10:14:57Z","date_updated":"2020-07-14T12:45:22Z","checksum":"bc678e02468d8ebc39dc7267dfb0a1c4"},{"content_type":"application/zip","file_size":55973760,"creator":"dernst","access_level":"closed","file_name":"2018_Thesis_Kolesnikov_source.zip","checksum":"bc66973b086da5a043f1162dcfb1fde4","date_created":"2019-04-05T09:34:49Z","date_updated":"2020-07-14T12:45:22Z","relation":"source_file","file_id":"6225"}],"pubrep_id":"1021","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Modern computer vision systems heavily rely on statistical machine learning models, which typically require large amounts of labeled data to be learned reliably. Moreover, very recently computer vision research widely adopted techniques for representation learning, which further increase the demand for labeled data. However, for many important practical problems there is relatively small amount of labeled data available, so it is problematic to leverage full potential of the representation learning methods. One way to overcome this obstacle is to invest substantial resources into producing large labelled datasets. Unfortunately, this can be prohibitively expensive in practice. In this thesis we focus on the alternative way of tackling the aforementioned issue. We concentrate on methods, which make use of weakly-labeled or even unlabeled data. Specifically, the first half of the thesis is dedicated to the semantic image segmentation task. We develop a technique, which achieves competitive segmentation performance and only requires annotations in a form of global image-level labels instead of dense segmentation masks. Subsequently, we present a new methodology, which further improves segmentation performance by leveraging tiny additional feedback from a human annotator. By using our methods practitioners can greatly reduce the amount of data annotation effort, which is required to learn modern image segmentation models. In the second half of the thesis we focus on methods for learning from unlabeled visual data. We study a family of autoregressive models for modeling structure of natural images and discuss potential applications of these models. Moreover, we conduct in-depth study of one of these applications, where we develop the state-of-the-art model for the probabilistic image colorization task."}],"project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036"}],"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:th_1021","publication_identifier":{"issn":["2663-337X"]},"month":"05","department":[{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","acknowledgement":"I also gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research.","year":"2018","date_updated":"2023-09-07T12:51:46Z","date_created":"2018-12-11T11:45:09Z","author":[{"full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov","first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"publist_id":"7718","file_date_updated":"2020-07-14T12:45:22Z"},{"month":"12","publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Robust invariants of Nonlinear Systems","_id":"25F8B9BC-B435-11E9-9278-68D0E5697425","grant_number":"M01980"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"doi":"10.1007/s41468-018-0021-5","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:40Z","year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"UlWa"}],"author":[{"full_name":"Filakovský, Marek","first_name":"Marek","last_name":"Filakovský","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","last_name":"Franek","id":"473294AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8878-8397","full_name":"Franek, Peter"},{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stephan Y","last_name":"Zhechev","id":"3AA52972-F248-11E8-B48F-1D18A9856A87","full_name":"Zhechev, Stephan Y"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6681"}]},"date_created":"2019-08-08T06:47:40Z","date_updated":"2023-09-07T13:10:36Z","volume":2,"day":"01","has_accepted_license":"1","publication":"Journal of Applied and Computational Topology","citation":{"chicago":"Filakovský, Marek, Peter Franek, Uli Wagner, and Stephan Y Zhechev. “Computing Simplicial Representatives of Homotopy Group Elements.” Journal of Applied and Computational Topology. Springer, 2018. https://doi.org/10.1007/s41468-018-0021-5.","mla":"Filakovský, Marek, et al. “Computing Simplicial Representatives of Homotopy Group Elements.” Journal of Applied and Computational Topology, vol. 2, no. 3–4, Springer, 2018, pp. 177–231, doi:10.1007/s41468-018-0021-5.","short":"M. Filakovský, P. Franek, U. Wagner, S.Y. Zhechev, Journal of Applied and Computational Topology 2 (2018) 177–231.","ista":"Filakovský M, Franek P, Wagner U, Zhechev SY. 2018. Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. 2(3–4), 177–231.","apa":"Filakovský, M., Franek, P., Wagner, U., & Zhechev, S. Y. (2018). Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. Springer. https://doi.org/10.1007/s41468-018-0021-5","ieee":"M. Filakovský, P. Franek, U. Wagner, and S. Y. Zhechev, “Computing simplicial representatives of homotopy group elements,” Journal of Applied and Computational Topology, vol. 2, no. 3–4. Springer, pp. 177–231, 2018.","ama":"Filakovský M, Franek P, Wagner U, Zhechev SY. Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. 2018;2(3-4):177-231. doi:10.1007/s41468-018-0021-5"},"article_type":"original","page":"177-231","date_published":"2018-12-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"A central problem of algebraic topology is to understand the homotopy groups 𝜋𝑑(𝑋) of a topological space X. For the computational version of the problem, it is well known that there is no algorithm to decide whether the fundamental group 𝜋1(𝑋) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with 𝜋1(𝑋) trivial), compute the higher homotopy group 𝜋𝑑(𝑋) for any given 𝑑≥2 . However, these algorithms come with a caveat: They compute the isomorphism type of 𝜋𝑑(𝑋) , 𝑑≥2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of 𝜋𝑑(𝑋) . Converting elements of this abstract group into explicit geometric maps from the d-dimensional sphere 𝑆𝑑 to X has been one of the main unsolved problems in the emerging field of computational homotopy theory. Here we present an algorithm that, given a simply connected space X, computes 𝜋𝑑(𝑋) and represents its elements as simplicial maps from a suitable triangulation of the d-sphere 𝑆𝑑 to X. For fixed d, the algorithm runs in time exponential in size(𝑋) , the number of simplices of X. Moreover, we prove that this is optimal: For every fixed 𝑑≥2 , we construct a family of simply connected spaces X such that for any simplicial map representing a generator of 𝜋𝑑(𝑋) , the size of the triangulation of 𝑆𝑑 on which the map is defined, is exponential in size(𝑋) ."}],"issue":"3-4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6774","status":"public","ddc":["514"],"title":"Computing simplicial representatives of homotopy group elements","intvolume":" 2","oa_version":"Published Version","file":[{"checksum":"cf9e7fcd2a113dd4828774fc75cdb7e8","date_created":"2019-08-08T06:55:21Z","date_updated":"2020-07-14T12:47:40Z","relation":"main_file","file_id":"6775","content_type":"application/pdf","file_size":1056278,"creator":"dernst","access_level":"open_access","file_name":"2018_JourAppliedComputTopology_Filakovsky.pdf"}]},{"_id":"133","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 118","title":"Synchronizing the asynchronous","status":"public","ddc":["000"],"pubrep_id":"1039","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":745438,"creator":"system","access_level":"open_access","file_name":"IST-2018-853-v2+2_concur2018.pdf","checksum":"c90895f4c5fafc18ddc54d1c8848077e","date_created":"2018-12-12T10:18:46Z","date_updated":"2020-07-14T12:44:44Z","relation":"main_file","file_id":"5368"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent computation threads. We present synchronization, a new proof rule that simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Modular verification is enabled via pending asynchronous calls in atomic summaries, and a complementary proof rule that eliminates pending asynchronous calls when components and their specifications are composed. We evaluate synchronization in the context of a multi-layer refinement verification methodology on a collection of benchmark programs."}],"citation":{"short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Kragl, Bernhard, et al. Synchronizing the Asynchronous. Vol. 118, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.CONCUR.2018.21.","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Synchronizing the Asynchronous,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21.","ama":"Kragl B, Qadeer S, Henzinger TA. Synchronizing the asynchronous. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.CONCUR.2018.21","ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Synchronizing the asynchronous,” presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","apa":"Kragl, B., Qadeer, S., & Henzinger, T. A. (2018). Synchronizing the asynchronous (Vol. 118). Presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21","ista":"Kragl B, Qadeer S, Henzinger TA. 2018. Synchronizing the asynchronous. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 118, 21."},"date_published":"2018-08-13T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"13","year":"2018","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}],"publication_status":"published","related_material":{"record":[{"id":"6426","relation":"earlier_version","status":"public"},{"id":"8332","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Kragl, Bernhard","first_name":"Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"}],"volume":118,"date_updated":"2023-09-07T13:18:00Z","date_created":"2018-12-11T11:44:48Z","article_number":"21","publist_id":"7790","file_date_updated":"2020-07-14T12:44:44Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"}],"quality_controlled":"1","doi":"10.4230/LIPIcs.CONCUR.2018.21","conference":{"end_date":"2018-09-07","start_date":"2018-09-04","location":"Beijing, China","name":"CONCUR: International Conference on Concurrency Theory"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["18688969"]},"month":"08"},{"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_LIPIcs_Edelsbrunner_Osang.pdf","file_size":528018,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5738","checksum":"d8c0533ad0018eb4ed1077475eb8fc18","date_created":"2018-12-18T09:27:22Z","date_updated":"2020-07-14T12:45:19Z"}],"_id":"187","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 99","title":"The multi-cover persistence of Euclidean balls","status":"public","ddc":["516"],"abstract":[{"lang":"eng","text":"Given a locally finite X ⊆ ℝd and a radius r ≥ 0, the k-fold cover of X and r consists of all points in ℝd that have k or more points of X within distance r. We consider two filtrations - one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k - and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in ℝd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module from Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. "}],"type":"conference","alternative_title":["LIPIcs"],"date_published":"2018-06-11T00:00:00Z","citation":{"short":"H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. The Multi-Cover Persistence of Euclidean Balls. Vol. 99, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.34.","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.34.","ama":"Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.34","apa":"Edelsbrunner, H., & Osang, G. F. (2018). The multi-cover persistence of Euclidean balls (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.34","ieee":"H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","ista":"Edelsbrunner H, Osang GF. 2018. The multi-cover persistence of Euclidean balls. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 34."},"has_accepted_license":"1","day":"11","scopus_import":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"9317"},{"status":"public","relation":"dissertation_contains","id":"9056"}]},"author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"full_name":"Osang, Georg F","first_name":"Georg F","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8882-5116"}],"volume":99,"date_updated":"2023-09-07T13:29:00Z","date_created":"2018-12-11T11:45:05Z","acknowledgement":"This work is partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","year":"2018","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"HeEd"}],"publication_status":"published","publist_id":"7732","file_date_updated":"2020-07-14T12:45:19Z","article_number":"34","doi":"10.4230/LIPIcs.SoCG.2018.34","conference":{"end_date":"2018-06-14","start_date":"2018-06-11","location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"}],"quality_controlled":"1","month":"06"}]