[{"year":"2015","publication_status":"published","publisher":"Faculté des sciences de Toulouse","department":[{"_id":"JaMa"}],"author":[{"full_name":"Erbar, Matthias","last_name":"Erbar","first_name":"Matthias"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan"},{"full_name":"Tetali, Prasad","first_name":"Prasad","last_name":"Tetali"}],"date_updated":"2023-10-18T07:48:28Z","date_created":"2018-12-11T11:53:10Z","volume":24,"publist_id":"5520","oa":1,"external_id":{"arxiv":["1409.8605"]},"main_file_link":[{"url":"http://arxiv.org/abs/1409.8605","open_access":"1"}],"quality_controlled":"1","doi":"10.5802/afst.1464","language":[{"iso":"eng"}],"month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1635","status":"public","title":"Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models","intvolume":" 24","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We calculate a Ricci curvature lower bound for some classical examples of random walks, namely, a chain on a slice of the n-dimensional discrete cube (the so-called Bernoulli-Laplace model) and the random transposition shuffle of the symmetric group of permutations on n letters.","lang":"eng"}],"issue":"4","publication":"Annales de la faculté des sciences de Toulouse","citation":{"apa":"Erbar, M., Maas, J., & Tetali, P. (2015). Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de La Faculté Des Sciences de Toulouse. Faculté des sciences de Toulouse. https://doi.org/10.5802/afst.1464","ieee":"M. Erbar, J. Maas, and P. Tetali, “Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models,” Annales de la faculté des sciences de Toulouse, vol. 24, no. 4. Faculté des sciences de Toulouse, pp. 781–800, 2015.","ista":"Erbar M, Maas J, Tetali P. 2015. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de la faculté des sciences de Toulouse. 24(4), 781–800.","ama":"Erbar M, Maas J, Tetali P. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de la faculté des sciences de Toulouse. 2015;24(4):781-800. doi:10.5802/afst.1464","chicago":"Erbar, Matthias, Jan Maas, and Prasad Tetali. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” Annales de La Faculté Des Sciences de Toulouse. Faculté des sciences de Toulouse, 2015. https://doi.org/10.5802/afst.1464.","short":"M. Erbar, J. Maas, P. Tetali, Annales de La Faculté Des Sciences de Toulouse 24 (2015) 781–800.","mla":"Erbar, Matthias, et al. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” Annales de La Faculté Des Sciences de Toulouse, vol. 24, no. 4, Faculté des sciences de Toulouse, 2015, pp. 781–800, doi:10.5802/afst.1464."},"article_type":"original","page":"781 - 800","date_published":"2015-01-01T00:00:00Z","day":"01","article_processing_charge":"No"},{"issue":"7","abstract":[{"text":"Scaffolded DNA origami enables the fabrication of a variety of complex nanostructures that promise utility in diverse fields of application, ranging from biosensing over advanced therapeutics to metamaterials. The broad applicability of DNA origami as a material beyond the level of proof-of-concept studies critically depends, among other factors, on the availability of large amounts of pure single-stranded scaffold DNA. Here, we present a method for the efficient production of M13 bacteriophage-derived genomic DNA using high-cell-density fermentation of Escherichia coli in stirred-tank bioreactors. We achieve phage titers of up to 1.6 × 1014 plaque-forming units per mL. Downstream processing yields up to 410 mg of high-quality single-stranded DNA per one liter reaction volume, thus upgrading DNA origami-based nanotechnology from the milligram to the gram scale.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","_id":"14303","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 15","title":"Efficient production of single-stranded phage DNA as scaffolds for DNA origami","status":"public","article_processing_charge":"No","day":"01","date_published":"2015-06-01T00:00:00Z","citation":{"ista":"Kick B, Praetorius FM, Dietz H, Weuster-Botz D. 2015. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 15(7), 4672–4676.","ieee":"B. Kick, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Efficient production of single-stranded phage DNA as scaffolds for DNA origami,” Nano Letters, vol. 15, no. 7. ACS Publications, pp. 4672–4676, 2015.","apa":"Kick, B., Praetorius, F. M., Dietz, H., & Weuster-Botz, D. (2015). Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. ACS Publications. https://doi.org/10.1021/acs.nanolett.5b01461","ama":"Kick B, Praetorius FM, Dietz H, Weuster-Botz D. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 2015;15(7):4672-4676. doi:10.1021/acs.nanolett.5b01461","chicago":"Kick, B, Florian M Praetorius, H Dietz, and D Weuster-Botz. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” Nano Letters. ACS Publications, 2015. https://doi.org/10.1021/acs.nanolett.5b01461.","mla":"Kick, B., et al. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” Nano Letters, vol. 15, no. 7, ACS Publications, 2015, pp. 4672–76, doi:10.1021/acs.nanolett.5b01461.","short":"B. Kick, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Nano Letters 15 (2015) 4672–4676."},"publication":"Nano Letters","page":"4672-4676","article_type":"letter_note","extern":"1","author":[{"last_name":"Kick","first_name":"B","full_name":"Kick, B"},{"full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","first_name":"Florian M"},{"full_name":"Dietz, H","last_name":"Dietz","first_name":"H"},{"first_name":"D","last_name":"Weuster-Botz","full_name":"Weuster-Botz, D"}],"volume":15,"date_created":"2023-09-06T12:52:47Z","date_updated":"2023-11-07T11:56:32Z","pmid":1,"year":"2015","publisher":"ACS Publications","publication_status":"published","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"month":"06","doi":"10.1021/acs.nanolett.5b01461","language":[{"iso":"eng"}],"external_id":{"pmid":["26028443"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1021/acs.nanolett.5b01461","open_access":"1"}],"quality_controlled":"1"},{"publication_identifier":{"eisbn":["978-3-319-21690-4"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-21690-4_10","conference":{"name":"CAV: Computer Aided Verification","end_date":"2015-07-24","location":"San Francisco, CA, United States","start_date":"2015-07-18"},"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1502.02834","open_access":"1"}],"ec_funded":1,"publist_id":"5564","volume":9206,"date_updated":"2024-02-21T13:52:07Z","date_created":"2018-12-11T11:52:58Z","related_material":{"record":[{"id":"5549","relation":"research_paper","status":"public"}]},"author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"id":"42BABFB4-F248-11E8-B48F-1D18A9856A87","last_name":"Fellner","first_name":"Andreas","full_name":"Fellner, Andreas"},{"full_name":"Kretinsky, Jan","first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881"}],"publisher":"Springer","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","year":"2015","acknowledgement":"This research was funded in part by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE) and Z211-N23 (Wittgenstein Award), European Research Council (ERC) Grant No 279307 (Graph Games), ERC Grant No 267989 (QUAREM), the Czech Science Foundation Grant No P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) REA Grant No 291734.","day":"16","scopus_import":1,"date_published":"2015-07-16T00:00:00Z","page":"158 - 177","citation":{"short":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, J. Kretinsky, in:, Springer, 2015, pp. 158–177.","mla":"Brázdil, Tomáš, et al. Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Vol. 9206, Springer, 2015, pp. 158–77, doi:10.1007/978-3-319-21690-4_10.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Andreas Fellner, and Jan Kretinsky. “Counterexample Explanation by Learning Small Strategies in Markov Decision Processes,” 9206:158–77. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_10.","ama":"Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. Counterexample explanation by learning small strategies in Markov decision processes. In: Vol 9206. Springer; 2015:158-177. doi:10.1007/978-3-319-21690-4_10","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Fellner, A., & Kretinsky, J. (2015). Counterexample explanation by learning small strategies in Markov decision processes (Vol. 9206, pp. 158–177). Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21690-4_10","ieee":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, and J. Kretinsky, “Counterexample explanation by learning small strategies in Markov decision processes,” presented at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015, vol. 9206, pp. 158–177.","ista":"Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. 2015. Counterexample explanation by learning small strategies in Markov decision processes. CAV: Computer Aided Verification, LNCS, vol. 9206, 158–177."},"abstract":[{"text":"For deterministic systems, a counterexample to a property can simply be an error trace, whereas counterexamples in probabilistic systems are necessarily more complex. For instance, a set of erroneous traces with a sufficient cumulative probability mass can be used. Since these are too large objects to understand and manipulate, compact representations such as subchains have been considered. In the case of probabilistic systems with non-determinism, the situation is even more complex. While a subchain for a given strategy (or scheduler, resolving non-determinism) is a straightforward choice, we take a different approach. Instead, we focus on the strategy itself, and extract the most important decisions it makes, and present its succinct representation.\r\nThe key tools we employ to achieve this are (1) introducing a concept of importance of a state w.r.t. the strategy, and (2) learning using decision trees. There are three main consequent advantages of our approach. Firstly, it exploits the quantitative information on states, stressing the more important decisions. Secondly, it leads to a greater variability and degree of freedom in representing the strategies. Thirdly, the representation uses a self-explanatory data structure. In summary, our approach produces more succinct and more explainable strategies, as opposed to e.g. binary decision diagrams. Finally, our experimental results show that we can extract several rules describing the strategy even for very large systems that do not fit in memory, and based on the rules explain the erroneous behaviour.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","intvolume":" 9206","title":"Counterexample explanation by learning small strategies in Markov decision processes","status":"public","_id":"1603","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"13","has_accepted_license":"1","article_processing_charge":"No","keyword":["Markov Decision Process","Decision Tree","Probabilistic Verification","Counterexample Explanation"],"date_published":"2015-08-13T00:00:00Z","citation":{"ama":"Fellner A. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. 2015. doi:10.15479/AT:ISTA:28","ista":"Fellner A. 2015. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:28.","ieee":"A. Fellner, “Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015.","apa":"Fellner, A. (2015). Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:28","mla":"Fellner, Andreas. Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria, 2015, doi:10.15479/AT:ISTA:28.","short":"A. Fellner, (2015).","chicago":"Fellner, Andreas. “Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015. https://doi.org/10.15479/AT:ISTA:28."},"abstract":[{"lang":"eng","text":"This repository contains the experimental part of the CAV 2015 publication Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.\r\nWe extended the probabilistic model checker PRISM to represent strategies of Markov Decision Processes as Decision Trees.\r\nThe archive contains a java executable version of the extended tool (prism_dectree.jar) together with a few examples of the PRISM benchmark library.\r\nTo execute the program, please have a look at the README.txt, which provides instructions and further information on the archive.\r\nThe archive contains scripts that (if run often enough) reproduces the data presented in the publication."}],"datarep_id":"28","type":"research_data","file":[{"checksum":"b8bcb43c0893023cda66c1b69c16ac62","date_created":"2018-12-12T13:02:31Z","date_updated":"2020-07-14T12:47:00Z","relation":"main_file","file_id":"5597","content_type":"application/zip","file_size":49557109,"creator":"system","access_level":"open_access","file_name":"IST-2015-28-v1+2_Fellner_DataRep.zip"}],"oa_version":"Published Version","_id":"5549","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes","ddc":["004"],"month":"08","doi":"10.15479/AT:ISTA:28","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:47:00Z","ec_funded":1,"publist_id":"5564","license":"https://creativecommons.org/publicdomain/zero/1.0/","author":[{"id":"42BABFB4-F248-11E8-B48F-1D18A9856A87","last_name":"Fellner","first_name":"Andreas","full_name":"Fellner, Andreas"}],"related_material":{"record":[{"id":"1603","status":"public","relation":"popular_science"}]},"contributor":[{"last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-12T12:31:29Z","date_updated":"2024-02-21T13:52:07Z","year":"2015","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria"},{"language":[{"iso":"eng"}],"conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2015-06-25","location":"Eindhoven, Netherlands","start_date":"2015-06-22"},"doi":"10.4230/LIPIcs.SOCG.2015.507","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,"month":"01","date_updated":"2024-02-28T12:59:37Z","date_created":"2018-12-11T11:52:27Z","volume":34,"author":[{"full_name":"Goaoc, Xavier","first_name":"Xavier","last_name":"Goaoc"},{"last_name":"Paták","first_name":"Pavel","full_name":"Paták, Pavel"},{"full_name":"Patakova, Zuzana","first_name":"Zuzana","last_name":"Patakova","orcid":"0000-0002-3975-1683"},{"last_name":"Tancer","first_name":"Martin","orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"424"}]},"publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2015","acknowledgement":"PP, ZP and MT were partially supported by the Charles University Grant GAUK 421511. ZP was\r\npartially supported by the Charles University Grant SVV-2014-260103. ZP and MT were partially\r\nsupported by the ERC Advanced Grant No. 267165 and by the project CE-ITI (GACR P202/12/G061)\r\nof the Czech Science Foundation. UW was partially supported by the Swiss National Science Foundation\r\n(grants SNSF-200020-138230 and SNSF-PP00P2-138948). Part of this work was done when XG was affiliated with INRIA Nancy Grand-Est and when MT was affiliated with Institutionen för matematik, Kungliga Tekniska Högskolan, then IST Austria.","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:45:00Z","publist_id":"5665","date_published":"2015-01-01T00:00:00Z","page":"507 - 521","citation":{"ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2015. Bounding Helly numbers via Betti numbers. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 507–521.","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2015). Bounding Helly numbers via Betti numbers (Vol. 34, pp. 507–521). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.507","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Bounding Helly numbers via Betti numbers,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 507–521.","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Bounding Helly numbers via Betti numbers. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:507-521. doi:10.4230/LIPIcs.SOCG.2015.507","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Bounding Helly Numbers via Betti Numbers,” 34:507–21. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.507.","mla":"Goaoc, Xavier, et al. Bounding Helly Numbers via Betti Numbers. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–21, doi:10.4230/LIPIcs.SOCG.2015.507.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–521."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","file":[{"file_name":"IST-2016-501-v1+1_46.pdf","access_level":"open_access","content_type":"application/pdf","file_size":633712,"creator":"system","relation":"main_file","file_id":"4794","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:10:09Z","checksum":"e6881df44d87fe0c2529c9f7b2724614"}],"pubrep_id":"501","status":"public","title":"Bounding Helly numbers via Betti numbers","ddc":["510"],"intvolume":" 34","_id":"1512","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b,d) such that the following holds. If F is a finite family of subsets of R^d such that the ith reduced Betti number (with Z_2 coefficients in singular homology) of the intersection of any proper subfamily G of F is at most b for every non-negative integer i less or equal to (d-1)/2, then F has Helly number at most h(b,d). These topological conditions are sharp: not controlling any of these first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map from C_*(K) to C_*(R^d). Both techniques are of independent interest."}],"alternative_title":["LIPIcs"],"type":"conference"},{"extern":"1","publist_id":"7631","publisher":"Walter de Gruyter","publication_status":"submitted","year":"2015","acknowledgement":"While working on this paper the authors were supported by the Leverhulme Trust and ERC grant 306457.","volume":2017,"date_updated":"2024-03-05T12:09:22Z","date_created":"2018-12-11T11:45:32Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"256"}]},"author":[{"first_name":"Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D"},{"first_name":"Sean","last_name":"Prendiville","full_name":"Prendiville, Sean"}],"publication_identifier":{"issn":["0075-4102"]},"month":"02","quality_controlled":"1","external_id":{"arxiv":["1402.4489"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1402.4489","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1515/crelle-2014-0122","type":"journal_article","issue":"731","abstract":[{"text":"We show that a non-singular integral form of degree d is soluble non-trivially over the integers if and only if it is soluble non-trivially over the reals and the p-adic numbers, provided that the form has at least (d-\\sqrt{d}/2)2^d variables. This improves on a longstanding result of Birch.","lang":"eng"}],"intvolume":" 2017","status":"public","title":"Improvements in Birch's theorem on forms in many variables","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"271","oa_version":"Preprint","article_processing_charge":"No","day":"20","page":"203 - 234","article_type":"original","citation":{"ieee":"T. D. Browning and S. Prendiville, “Improvements in Birch’s theorem on forms in many variables,” Journal fur die Reine und Angewandte Mathematik, vol. 2017, no. 731. Walter de Gruyter, pp. 203–234.","apa":"Browning, T. D., & Prendiville, S. (n.d.). Improvements in Birch’s theorem on forms in many variables. Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle-2014-0122","ista":"Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many variables. Journal fur die Reine und Angewandte Mathematik. 2017(731), 203–234.","ama":"Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many variables. Journal fur die Reine und Angewandte Mathematik. 2017(731):203-234. doi:10.1515/crelle-2014-0122","chicago":"Browning, Timothy D, and Sean Prendiville. “Improvements in Birch’s Theorem on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter, n.d. https://doi.org/10.1515/crelle-2014-0122.","short":"T.D. Browning, S. Prendiville, Journal Fur Die Reine Und Angewandte Mathematik 2017 (n.d.) 203–234.","mla":"Browning, Timothy D., and Sean Prendiville. “Improvements in Birch’s Theorem on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik, vol. 2017, no. 731, Walter de Gruyter, pp. 203–34, doi:10.1515/crelle-2014-0122."},"publication":"Journal fur die Reine und Angewandte Mathematik","date_published":"2015-02-20T00:00:00Z"},{"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2274"}]},"author":[{"first_name":"Stefan","last_name":"Dziembowski","full_name":"Dziembowski, Stefan"},{"last_name":"Faust","first_name":"Sebastian","full_name":"Faust, Sebastian"},{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"}],"volume":9216,"date_created":"2018-12-11T11:53:24Z","date_updated":"2024-03-20T08:31:49Z","year":"2015","publisher":"Springer","department":[{"_id":"VlKo"},{"_id":"KrPi"}],"publication_status":"published","publist_id":"5474","ec_funded":1,"doi":"10.1007/978-3-662-48000-7_29","conference":{"location":"Santa Barbara, CA, United States","start_date":"2015-08-16","end_date":"2015-08-20","name":"CRYPTO: International Cryptology Conference"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2013/796.pdf","open_access":"1"}],"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"},{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"}],"quality_controlled":"1","publication_identifier":{"isbn":["9783662479995"],"issn":["0302-9743"]},"month":"08","pubrep_id":"671","oa_version":"Preprint","_id":"1675","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 9216","status":"public","title":"Proofs of space","abstract":[{"text":"Proofs of work (PoW) have been suggested by Dwork and Naor (Crypto’92) as protection to a shared resource. The basic idea is to ask the service requestor to dedicate some non-trivial amount of computational work to every request. The original applications included prevention of spam and protection against denial of service attacks. More recently, PoWs have been used to prevent double spending in the Bitcoin digital currency system. In this work, we put forward an alternative concept for PoWs - so-called proofs of space (PoS), where a service requestor must dedicate a significant amount of disk space as opposed to computation. We construct secure PoS schemes in the random oracle model (with one additional mild assumption required for the proof to go through), using graphs with high “pebbling complexity” and Merkle hash-trees. We discuss some applications, including follow-up work where a decentralized digital currency scheme called Spacecoin is constructed that uses PoS (instead of wasteful PoW like in Bitcoin) to prevent double spending. The main technical contribution of this work is the construction of (directed, loop-free) graphs on N vertices with in-degree O(log logN) such that even if one places Θ(N) pebbles on the nodes of the graph, there’s a constant fraction of nodes that needs Θ(N) steps to be pebbled (where in every step one can put a pebble on a node if all its parents have a pebble).","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2015-08-01T00:00:00Z","citation":{"ista":"Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. 2015. Proofs of space. 35th Annual Cryptology Conference. CRYPTO: International Cryptology Conference, LNCS, vol. 9216, 585–605.","apa":"Dziembowski, S., Faust, S., Kolmogorov, V., & Pietrzak, K. Z. (2015). Proofs of space. In 35th Annual Cryptology Conference (Vol. 9216, pp. 585–605). Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-48000-7_29","ieee":"S. Dziembowski, S. Faust, V. Kolmogorov, and K. Z. Pietrzak, “Proofs of space,” in 35th Annual Cryptology Conference, Santa Barbara, CA, United States, 2015, vol. 9216, pp. 585–605.","ama":"Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. Proofs of space. In: 35th Annual Cryptology Conference. Vol 9216. Springer; 2015:585-605. doi:10.1007/978-3-662-48000-7_29","chicago":"Dziembowski, Stefan, Sebastian Faust, Vladimir Kolmogorov, and Krzysztof Z Pietrzak. “Proofs of Space.” In 35th Annual Cryptology Conference, 9216:585–605. Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_29.","mla":"Dziembowski, Stefan, et al. “Proofs of Space.” 35th Annual Cryptology Conference, vol. 9216, Springer, 2015, pp. 585–605, doi:10.1007/978-3-662-48000-7_29.","short":"S. Dziembowski, S. Faust, V. Kolmogorov, K.Z. Pietrzak, in:, 35th Annual Cryptology Conference, Springer, 2015, pp. 585–605."},"publication":"35th Annual Cryptology Conference","page":"585 - 605","article_processing_charge":"No","day":"01","scopus_import":"1"},{"publication_identifier":{"issn":["1097-2765"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1016/j.molcel.2015.03.031","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molcel.2015.03.031"}],"extern":"1","volume":58,"date_created":"2024-03-21T07:58:08Z","date_updated":"2024-03-25T11:52:26Z","author":[{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia Kathleen","last_name":"Michael","full_name":"Michael, Alicia Kathleen"},{"full_name":"Harvey, Stacy L.","last_name":"Harvey","first_name":"Stacy L."},{"first_name":"Patrick J.","last_name":"Sammons","full_name":"Sammons, Patrick J."},{"full_name":"Anderson, Amanda P.","first_name":"Amanda P.","last_name":"Anderson"},{"last_name":"Kopalle","first_name":"Hema M.","full_name":"Kopalle, Hema M."},{"last_name":"Banham","first_name":"Alison H.","full_name":"Banham, Alison H."},{"full_name":"Partch, Carrie L.","first_name":"Carrie L.","last_name":"Partch"}],"publisher":"Elsevier","publication_status":"published","year":"2015","article_processing_charge":"No","day":"04","keyword":["Cell Biology","Molecular Biology"],"scopus_import":"1","date_published":"2015-06-04T00:00:00Z","page":"743-754","article_type":"original","citation":{"mla":"Michael, Alicia K., et al. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” Molecular Cell, vol. 58, no. 5, Elsevier, 2015, pp. 743–54, doi:10.1016/j.molcel.2015.03.031.","short":"A.K. Michael, S.L. Harvey, P.J. Sammons, A.P. Anderson, H.M. Kopalle, A.H. Banham, C.L. Partch, Molecular Cell 58 (2015) 743–754.","chicago":"Michael, Alicia K., Stacy L. Harvey, Patrick J. Sammons, Amanda P. Anderson, Hema M. Kopalle, Alison H. Banham, and Carrie L. Partch. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” Molecular Cell. Elsevier, 2015. https://doi.org/10.1016/j.molcel.2015.03.031.","ama":"Michael AK, Harvey SL, Sammons PJ, et al. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 2015;58(5):743-754. doi:10.1016/j.molcel.2015.03.031","ista":"Michael AK, Harvey SL, Sammons PJ, Anderson AP, Kopalle HM, Banham AH, Partch CL. 2015. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 58(5), 743–754.","apa":"Michael, A. K., Harvey, S. L., Sammons, P. J., Anderson, A. P., Kopalle, H. M., Banham, A. H., & Partch, C. L. (2015). Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2015.03.031","ieee":"A. K. Michael et al., “Cancer/Testis antigen PASD1 silences the circadian clock,” Molecular Cell, vol. 58, no. 5. Elsevier, pp. 743–754, 2015."},"publication":"Molecular Cell","issue":"5","abstract":[{"lang":"eng","text":"The circadian clock orchestrates global changes in transcriptional regulation on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven by other bHLH-PAS transcription factors have a homologous repressor that modulates activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1. We show here that the cancer/testis antigen PASD1 fulfills this role to suppress circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1 is restricted to germline tissues in healthy individuals but can be induced in cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human cancer cells significantly increases the amplitude of transcriptional oscillations to generate more robust circadian rhythms. Our results describe a function for a germline-specific protein in regulation of the circadian clock and provide a molecular link from oncogenic transformation to suppression of circadian rhythms."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 58","title":"Cancer/Testis antigen PASD1 silences the circadian clock","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15160"},{"oa_version":"None","intvolume":" 40","status":"public","title":"Cytosolic BMAL1 moonlights as a translation factor","_id":"15159","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"9","abstract":[{"lang":"eng","text":"It is widely recognized that BMAL1 is an essential subunit of the primary transcription factor that drives rhythmic circadian transcription in the nucleus. In a surprising turn, Lipton et al. now show that BMAL1 rhythmically interacts with translational machinery in the cytosol to stimulate protein synthesis in response to mTOR signaling."}],"type":"journal_article","date_published":"2015-09-01T00:00:00Z","page":"489-490","article_type":"original","citation":{"mla":"Michael, Alicia K., et al. “Cytosolic BMAL1 Moonlights as a Translation Factor.” Trends in Biochemical Sciences, vol. 40, no. 9, Elsevier, 2015, pp. 489–90, doi:10.1016/j.tibs.2015.07.006.","short":"A.K. Michael, H. Asimgil, C.L. Partch, Trends in Biochemical Sciences 40 (2015) 489–490.","chicago":"Michael, Alicia K., Hande Asimgil, and Carrie L. Partch. “Cytosolic BMAL1 Moonlights as a Translation Factor.” Trends in Biochemical Sciences. Elsevier, 2015. https://doi.org/10.1016/j.tibs.2015.07.006.","ama":"Michael AK, Asimgil H, Partch CL. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 2015;40(9):489-490. doi:10.1016/j.tibs.2015.07.006","ista":"Michael AK, Asimgil H, Partch CL. 2015. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 40(9), 489–490.","ieee":"A. K. Michael, H. Asimgil, and C. L. Partch, “Cytosolic BMAL1 moonlights as a translation factor,” Trends in Biochemical Sciences, vol. 40, no. 9. Elsevier, pp. 489–490, 2015.","apa":"Michael, A. K., Asimgil, H., & Partch, C. L. (2015). Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. Elsevier. https://doi.org/10.1016/j.tibs.2015.07.006"},"publication":"Trends in Biochemical Sciences","article_processing_charge":"No","day":"01","keyword":["Molecular Biology","Biochemistry"],"scopus_import":"1","volume":40,"date_updated":"2024-03-25T11:53:58Z","date_created":"2024-03-21T07:57:44Z","author":[{"full_name":"Michael, Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael","first_name":"Alicia Kathleen"},{"first_name":"Hande","last_name":"Asimgil","full_name":"Asimgil, Hande"},{"full_name":"Partch, Carrie L.","first_name":"Carrie L.","last_name":"Partch"}],"publisher":"Elsevier","publication_status":"published","year":"2015","extern":"1","language":[{"iso":"eng"}],"doi":"10.1016/j.tibs.2015.07.006","quality_controlled":"1","publication_identifier":{"issn":["0968-0004"]},"month":"09"},{"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.1002299","quality_controlled":"1","project":[{"name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013"},{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","name":"Optimality principles in responses to antibiotics","call_identifier":"FP7"}],"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"},"month":"11","date_updated":"2024-03-28T23:30:28Z","date_created":"2018-12-11T11:53:04Z","volume":13,"author":[{"id":"424D78A0-F248-11E8-B48F-1D18A9856A87","last_name":"Chevereau","first_name":"Guillaume","full_name":"Chevereau, Guillaume"},{"first_name":"Marta","last_name":"Dravecka","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","full_name":"Dravecka, Marta"},{"first_name":"Tugce","last_name":"Batur","full_name":"Batur, Tugce"},{"last_name":"Guvenek","first_name":"Aysegul","full_name":"Guvenek, Aysegul"},{"first_name":"Dilay","last_name":"Ayhan","full_name":"Ayhan, Dilay"},{"full_name":"Toprak, Erdal","last_name":"Toprak","first_name":"Erdal"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9711"},{"id":"9765","relation":"research_data","status":"public"},{"relation":"dissertation_contains","status":"public","id":"6263"}]},"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"ToBo"}],"year":"2015","file_date_updated":"2020-07-14T12:45:07Z","ec_funded":1,"publist_id":"5547","article_number":"e1002299","date_published":"2015-11-18T00:00:00Z","publication":"PLoS Biology","citation":{"chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.","mla":"Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology, vol. 13, no. 11, e1002299, Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak, M.T. Bollenbach, PLoS Biology 13 (2015).","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 13(11), e1002299.","ieee":"G. Chevereau et al., “Quantifying the determinants of evolutionary dynamics leading to drug resistance,” PLoS Biology, vol. 13, no. 11. Public Library of Science, 2015.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak, E., & Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 2015;13(11). doi:10.1371/journal.pbio.1002299"},"day":"18","has_accepted_license":"1","scopus_import":1,"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4723","checksum":"0e82e3279f50b15c6c170c042627802b","date_created":"2018-12-12T10:09:00Z","date_updated":"2020-07-14T12:45:07Z","access_level":"open_access","file_name":"IST-2016-468-v1+1_journal.pbio.1002299.pdf","content_type":"application/pdf","file_size":1387760,"creator":"system"}],"pubrep_id":"468","status":"public","ddc":["570"],"title":"Quantifying the determinants of evolutionary dynamics leading to drug resistance","intvolume":" 13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1619","abstract":[{"text":"The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution.","lang":"eng"}],"issue":"11","type":"journal_article"}]