[{"_id":"7117","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","file":[{"file_name":"xcad_sup_mat_siga19.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1673176,"date_created":"2019-11-26T14:24:26Z","checksum":"56a2fb019adcb556d2b022f5e5acb68c","date_updated":"2020-07-14T12:47:49Z","relation":"supplementary_material","file_id":"7119","creator":"bbickel","title":"X-CAD Supplemental Material"},{"content_type":"application/pdf","access_level":"open_access","description":"This is the author's version of the work.","file_name":"XCAD_authors_version.pdf","creator":"bbickel","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","file_id":"7120","relation":"main_file","date_updated":"2020-07-14T12:47:49Z","checksum":"5f29d76aceb5102e766cbab9b17d776e","date_created":"2019-11-26T14:24:27Z","file_size":14563618},{"file_id":"7121","creator":"bbickel","date_updated":"2020-07-14T12:47:49Z","relation":"main_file","file_size":259979129,"checksum":"0d31e123286cbec9e28b2001c2bb0d55","date_created":"2019-11-26T14:27:37Z","content_type":"video/mp4","access_level":"open_access","file_name":"XCAD_video.mp4"}],"isi":1,"project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"oa":1,"issue":"6","related_material":{"record":[{"id":"12897","status":"public","relation":"dissertation_contains"}]},"publication_identifier":{"issn":["0730-0301"]},"abstract":[{"text":"We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models.","lang":"eng"}],"ddc":["000"],"ec_funded":1,"external_id":{"isi":["000498397300007"]},"date_updated":"2024-03-29T23:30:45Z","publisher":"ACM","date_created":"2019-11-26T14:22:09Z","year":"2019","language":[{"iso":"eng"}],"day":"06","status":"public","has_accepted_license":"1","article_type":"original","author":[{"last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian","first_name":"Christian"},{"last_name":"Schumacher","first_name":"Christian","full_name":"Schumacher, Christian"},{"last_name":"Knoop","first_name":"Espen","full_name":"Knoop, Espen"},{"orcid":"0000-0002-1546-3265","first_name":"Thomas","full_name":"Auzinger, Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87","last_name":"Auzinger"},{"last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","first_name":"Bernd","orcid":"0000-0001-6511-9385"},{"last_name":"Bächer","full_name":"Bächer, Moritz","first_name":"Moritz"}],"article_number":"157","department":[{"_id":"BeBi"}],"volume":38,"publication_status":"published","article_processing_charge":"No","type":"journal_article","doi":"10.1145/3355089.3356576","file_date_updated":"2020-07-14T12:47:49Z","month":"11","intvolume":" 38","oa_version":"Submitted Version","scopus_import":"1","date_published":"2019-11-06T00:00:00Z","publication":"ACM Transactions on Graphics","citation":{"ieee":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” ACM Transactions on Graphics, vol. 38, no. 6. ACM, 2019.","mla":"Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics, vol. 38, no. 6, 157, ACM, 2019, doi:10.1145/3355089.3356576.","ista":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157.","chicago":"Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356576.","short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019).","apa":"Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., & Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356576","ama":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 2019;38(6). doi:10.1145/3355089.3356576"}},{"publisher":"American Physical Society","date_created":"2019-03-31T21:59:12Z","external_id":{"arxiv":["1809.06358"],"isi":["000461922000006"]},"date_updated":"2024-03-29T23:30:47Z","main_file_link":[{"url":"https://arxiv.org/abs/1809.06358","open_access":"1"}],"publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"abstract":[{"lang":"eng","text":"Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations."}],"oa":1,"issue":"11","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9728"}]},"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Transition to turbulence in particle laden flows","quality_controlled":"1","_id":"6189","intvolume":" 122","month":"03","oa_version":"Preprint","scopus_import":"1","publication":"Physical Review Letters","date_published":"2019-03-22T00:00:00Z","citation":{"short":"N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019).","ama":"Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. Physical Review Letters. 2019;122(11). doi:10.1103/PhysRevLett.122.114502","apa":"Agrawal, N., Choueiri, G. H., & Hof, B. (2019). Transition to turbulence in particle laden flows. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.114502","chicago":"Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.114502.","mla":"Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.114502.","ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502.","ieee":"N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” Physical Review Letters, vol. 122, no. 11. American Physical Society, 2019."},"article_processing_charge":"No","doi":"10.1103/PhysRevLett.122.114502","type":"journal_article","publication_status":"published","department":[{"_id":"BjHo"}],"volume":122,"author":[{"first_name":"Nishchal","full_name":"Agrawal, Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87","last_name":"Agrawal"},{"first_name":"George H","full_name":"Choueiri, George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","last_name":"Choueiri"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754"}],"article_number":"114502","day":"22","year":"2019","language":[{"iso":"eng"}],"status":"public"},{"keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"degree_awarded":"PhD","_id":"6371","alternative_title":["ISTA Thesis"],"file":[{"content_type":"application/pdf","access_level":"open_access","embargo":"2020-05-02","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","creator":"cigler","file_id":"6373","date_updated":"2021-02-11T11:17:13Z","relation":"main_file","date_created":"2019-05-03T11:54:52Z","checksum":"c0085d47c58c9cbcab1b0a783480f6da","file_size":12597663},{"relation":"source_file","date_updated":"2020-07-14T12:47:28Z","file_id":"6374","embargo_to":"open_access","creator":"cigler","file_size":34644426,"checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","date_created":"2019-05-03T11:54:54Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","publication_identifier":{"issn":["2663-337X"]},"ddc":["576","579"],"abstract":[{"text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation. \r\n","lang":"eng"}],"oa":1,"project":[{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"67"},{"relation":"popular_science","status":"public","id":"5585"}]},"date_created":"2019-05-03T11:55:51Z","publisher":"Institute of Science and Technology Austria","date_updated":"2024-02-21T13:45:52Z","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"day":"03","year":"2019","department":[{"_id":"CaGu"}],"supervisor":[{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052"}],"author":[{"first_name":"Claudia","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","last_name":"Igler"}],"article_processing_charge":"No","type":"dissertation","doi":"10.15479/AT:ISTA:6371","publication_status":"published","page":"152","oa_version":"Published Version","file_date_updated":"2021-02-11T11:17:13Z","month":"05","citation":{"short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","apa":"Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.","ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria.","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","mla":"Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371."},"date_published":"2019-05-03T00:00:00Z"},{"department":[{"_id":"KrPi"}],"volume":2018,"author":[{"last_name":"Allini","full_name":"Allini, Elie Noumon","first_name":"Elie Noumon"},{"first_name":"Maciej","full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski"},{"last_name":"Petura","full_name":"Petura, Oto","first_name":"Oto"},{"last_name":"Bernard","full_name":"Bernard, Florent","first_name":"Florent"},{"first_name":"Marek","full_name":"Laban, Marek","last_name":"Laban"},{"full_name":"Fischer, Viktor","first_name":"Viktor","last_name":"Fischer"}],"has_accepted_license":"1","article_type":"original","day":"01","language":[{"iso":"eng"}],"year":"2018","status":"public","month":"01","file_date_updated":"2021-11-15T10:27:29Z","intvolume":" 2018","oa_version":"Published Version","scopus_import":"1","publication":"IACR Transactions on Cryptographic Hardware and Embedded Systems","date_published":"2018-01-01T00:00:00Z","citation":{"chicago":"Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research, 2018. https://doi.org/10.13154/tches.v2018.i3.214-242.","apa":"Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., & Fischer, V. (2018). Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research. https://doi.org/10.13154/tches.v2018.i3.214-242","ama":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018;2018(3):214-242. doi:10.13154/tches.v2018.i3.214-242","short":"E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.","mla":"Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3, International Association for Cryptologic Research, 2018, pp. 214–42, doi:10.13154/tches.v2018.i3.214-242.","ista":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.","ieee":"E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer, “Evaluation and monitoring of free running oscillators serving as source of randomness,” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3. International Association for Cryptologic Research, pp. 214–242, 2018."},"article_processing_charge":"No","doi":"10.13154/tches.v2018.i3.214-242","type":"journal_article","page":"214-242","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","file":[{"creator":"cchlebak","file_id":"10289","relation":"main_file","date_updated":"2021-11-15T10:27:29Z","checksum":"b816b848f046c48a8357700d9305dce5","date_created":"2021-11-15T10:27:29Z","file_size":955755,"content_type":"application/pdf","success":1,"access_level":"open_access","file_name":"2018_IACR_Allini.pdf"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Evaluation and monitoring of free running oscillators serving as source of randomness","quality_controlled":"1","_id":"10286","publisher":"International Association for Cryptologic Research","date_created":"2021-11-14T23:01:25Z","date_updated":"2021-11-15T10:48:49Z","publication_identifier":{"eissn":["2569-2925"]},"abstract":[{"lang":"eng","text":"In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied."}],"ddc":["000"],"oa":1,"issue":"3"},{"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","title":"Quasipolynomial set-based symbolic algorithms for parity games","file":[{"relation":"main_file","date_updated":"2022-05-17T07:51:08Z","creator":"dernst","file_id":"11392","checksum":"1229aa8640bd6db610c85decf2265480","date_created":"2022-05-17T07:51:08Z","file_size":720893,"access_level":"open_access","success":1,"content_type":"application/pdf","file_name":"2018_EPiCs_Chatterjee.pdf"}],"_id":"10883","alternative_title":["EPiC Series in Computing"],"quality_controlled":"1","external_id":{"arxiv":["1909.04983"]},"date_updated":"2022-07-29T09:24:31Z","acknowledgement":"A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.","publisher":"EasyChair","date_created":"2022-03-18T12:46:32Z","conference":{"end_date":"2018-11-21","start_date":"2018-11-17","name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning","location":"Awassa, Ethiopia"},"oa":1,"project":[{"grant_number":"S11407","name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"publication_identifier":{"issn":["2398-7340"]},"abstract":[{"text":"Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space.","lang":"eng"}],"ddc":["000"],"ec_funded":1,"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dvořák","full_name":"Dvořák, Wolfgang","first_name":"Wolfgang"},{"full_name":"Henzinger, Monika H","first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Alexander","full_name":"Svozil, Alexander","last_name":"Svozil"}],"department":[{"_id":"KrCh"}],"volume":57,"year":"2018","day":"23","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","intvolume":" 57","file_date_updated":"2022-05-17T07:51:08Z","month":"10","oa_version":"Published Version","scopus_import":"1","publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","date_published":"2018-10-23T00:00:00Z","citation":{"ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53, doi:10.29007/5z5k.","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k.","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair; 2018:233-253. doi:10.29007/5z5k","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k"},"page":"233-253","publication_status":"published","article_processing_charge":"No","doi":"10.29007/5z5k","type":"conference"},{"type":"conference","doi":"10.1007/978-3-030-01602-9_9","publication_status":"published","page":"185 - 214","citation":{"ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214.","ieee":"N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.","mla":"Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp. 185–214, doi:10.1007/978-3-030-01602-9_9.","chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9.","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9","apa":"Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. https://doi.org/10.1007/978-3-030-01602-9_9","short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214."},"date_published":"2018-10-27T00:00:00Z","scopus_import":1,"oa_version":"Preprint","intvolume":" 270","month":"10","status":"public","day":"27","year":"2018","language":[{"iso":"eng"}],"volume":270,"department":[{"_id":"RoSe"}],"author":[{"full_name":"Leopold, Nikolai K","first_name":"Nikolai K","orcid":"0000-0002-0495-6822","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pickl","first_name":"Peter","full_name":"Pickl, Peter"}],"ec_funded":1,"abstract":[{"text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm.","lang":"eng"}],"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"oa":1,"conference":{"end_date":"2017-04-01","start_date":"2017-03-30","location":"Munich, Germany","name":"MaLiQS: Macroscopic Limits of Quantum Systems"},"publist_id":"8045","date_created":"2018-12-11T11:44:08Z","publisher":"Springer","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.10843"}],"date_updated":"2021-01-12T06:48:16Z","external_id":{"arxiv":["1806.10843"]},"quality_controlled":"1","_id":"11","title":"Mean-field limits of particles in interaction with quantised radiation fields","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"year":"2018","day":"01","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","pubrep_id":"712","author":[{"last_name":"Flandoli","first_name":"Franco","full_name":"Flandoli, Franco"},{"full_name":"Russo, Francesco","first_name":"Francesco","last_name":"Russo"},{"first_name":"Giovanni A","full_name":"Zanco, Giovanni A","id":"47491882-F248-11E8-B48F-1D18A9856A87","last_name":"Zanco"}],"volume":31,"department":[{"_id":"JaMa"}],"page":"789-826","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","doi":"10.1007/s10959-016-0724-2","type":"journal_article","article_processing_charge":"Yes (via OA deal)","date_published":"2018-06-01T00:00:00Z","publication":"Journal of Theoretical Probability","citation":{"short":"F. Flandoli, F. Russo, G.A. Zanco, Journal of Theoretical Probability 31 (2018) 789–826.","ama":"Flandoli F, Russo F, Zanco GA. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 2018;31(2):789-826. doi:10.1007/s10959-016-0724-2","apa":"Flandoli, F., Russo, F., & Zanco, G. A. (2018). Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. Springer. https://doi.org/10.1007/s10959-016-0724-2","chicago":"Flandoli, Franco, Francesco Russo, and Giovanni A Zanco. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability. Springer, 2018. https://doi.org/10.1007/s10959-016-0724-2.","ieee":"F. Flandoli, F. Russo, and G. A. Zanco, “Infinite-dimensional calculus under weak spatial regularity of the processes,” Journal of Theoretical Probability, vol. 31, no. 2. Springer, pp. 789–826, 2018.","mla":"Flandoli, Franco, et al. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability, vol. 31, no. 2, Springer, 2018, pp. 789–826, doi:10.1007/s10959-016-0724-2.","ista":"Flandoli F, Russo F, Zanco GA. 2018. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 31(2), 789–826."},"file_date_updated":"2020-07-14T12:44:39Z","month":"06","intvolume":" 31","oa_version":"Published Version","scopus_import":1,"_id":"1215","quality_controlled":"1","title":"Infinite-dimensional calculus under weak spatial regularity of the processes","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2016-712-v1+1_s10959-016-0724-2.pdf","content_type":"application/pdf","access_level":"open_access","file_size":671125,"date_created":"2018-12-12T10:17:13Z","checksum":"47686d58ec21c164540f1a980ff2163f","file_id":"5266","creator":"system","date_updated":"2020-07-14T12:44:39Z","relation":"main_file"}],"issue":"2","oa":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"ddc":["519"],"abstract":[{"text":"Two generalizations of Itô formula to infinite-dimensional spaces are given.\r\nThe first one, in Hilbert spaces, extends the classical one by taking advantage of\r\ncancellations when they occur in examples and it is applied to the case of a group\r\ngenerator. The second one, based on the previous one and a limit procedure, is an Itô\r\nformula in a special class of Banach spaces having a product structure with the noise\r\nin a Hilbert component; again the key point is the extension due to a cancellation. This\r\nextension to Banach spaces and in particular the specific cancellation are motivated\r\nby path-dependent Itô calculus.","lang":"eng"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The second named author benefited partially from the support of the “FMJH Program Gaspard Monge in Optimization and Operations Research” (Project 2014-1607H). He is also grateful for the invitation to the Department of Mathematics of the University of Pisa. The third named author is grateful for the invitation to ENSTA.","date_updated":"2021-01-12T06:49:09Z","publist_id":"6119","publisher":"Springer","date_created":"2018-12-11T11:50:45Z"},{"conference":{"end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary","start_date":"2018-06-11"},"publist_id":"7735","date_created":"2018-12-11T11:45:04Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_updated":"2021-01-12T06:53:36Z","ddc":["510"],"abstract":[{"text":"We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998), and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the setting of approximating maps of graphs on 2-dimensional surfaces by embeddings. Our proof of this result is constructive and almost immediately implies an efficient algorithm for testing whether a given piecewise linear map of a graph in a surface is approximable by an embedding. More precisely, an instance of this problem consists of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact surface M given as the union of a set of pairwise disjoint discs corresponding to the clusters and a set of pairwise disjoint "pipes" corresponding to the bundles, connecting certain pairs of these discs. We are to decide whether G can be embedded inside M so that the vertices in every cluster are drawn in the corresponding disc, the edges in every bundle pass only through its corresponding pipe, and every edge crosses the boundary of each disc at most once.","lang":"eng"}],"publication_identifier":{"isbn":["978-3-95977-066-8"]},"oa":1,"project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281"}],"file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"2018_LIPIcs_Fulek.pdf","creator":"dernst","file_id":"5701","relation":"main_file","date_updated":"2020-07-14T12:45:19Z","checksum":"f1b94f1a75b37c414a1f61d59fb2cd4c","date_created":"2018-12-17T12:33:52Z","file_size":718857}],"title":"Hanani-Tutte for approximating maps of graphs","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"_id":"185","citation":{"apa":"Fulek, R., & Kynčl, J. (2018). Hanani-Tutte for approximating maps of graphs (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.2018.39","ama":"Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.39","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","chicago":"Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.39.","ista":"Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 39.","ieee":"R. Fulek and J. Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","mla":"Fulek, Radoslav, and Jan Kynčl. Hanani-Tutte for Approximating Maps of Graphs. Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.39."},"date_published":"2018-01-01T00:00:00Z","scopus_import":1,"oa_version":"Published Version","month":"01","intvolume":" 99","file_date_updated":"2020-07-14T12:45:19Z","type":"conference","doi":"10.4230/LIPIcs.SoCG.2018.39","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":99,"department":[{"_id":"UlWa"}],"article_number":"39","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kynčl","first_name":"Jan","full_name":"Kynčl, Jan"}],"has_accepted_license":"1","status":"public","day":"01","year":"2018","language":[{"iso":"eng"}]},{"page":"35:1 - 35:13","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","doi":"10.4230/LIPIcs.SoCG.2018.35","type":"conference","intvolume":" 99","month":"06","file_date_updated":"2020-07-14T12:45:20Z","scopus_import":1,"oa_version":"Published Version","date_published":"2018-06-11T00:00:00Z","citation":{"mla":"Edelsbrunner, Herbert, et al. Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13, doi:10.4230/LIPIcs.SoCG.2018.35.","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13.","ista":"Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13.","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.35.","short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13.","ama":"Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:35:1-35:13. doi:10.4230/LIPIcs.SoCG.2018.35","apa":"Edelsbrunner, H., Virk, Z., & Wagner, H. (2018). Smallest enclosing spheres and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.35"},"year":"2018","language":[{"iso":"eng"}],"day":"11","status":"public","has_accepted_license":"1","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"first_name":"Ziga","full_name":"Virk, Ziga","last_name":"Virk"},{"last_name":"Wagner","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert","first_name":"Hubert"}],"department":[{"_id":"HeEd"}],"volume":99,"project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"oa":1,"ddc":["000"],"abstract":[{"lang":"eng","text":"Smallest enclosing spheres of finite point sets are central to methods in topological data analysis. Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex."}],"date_updated":"2021-01-12T06:53:48Z","acknowledgement":"This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_created":"2018-12-11T11:45:05Z","publist_id":"7733","conference":{"end_date":"2018-06-14","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary"},"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"_id":"188","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Smallest enclosing spheres and Chernoff points in Bregman geometry","file":[{"checksum":"7509403803b3ac1aee94bbc2ad293d21","date_created":"2018-12-17T16:31:31Z","file_size":489080,"relation":"main_file","date_updated":"2020-07-14T12:45:20Z","creator":"dernst","file_id":"5724","file_name":"2018_LIPIcs_Edelsbrunner.pdf","access_level":"open_access","content_type":"application/pdf"}]},{"_id":"306","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"An introduction to the maximum entropy approach and its application to inference problems in biology","file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"2018_Heliyon_DeMartino.pdf","date_updated":"2020-07-14T12:45:59Z","relation":"main_file","creator":"dernst","file_id":"5929","checksum":"67010cf5e3b3e0637c659371714a715a","date_created":"2019-02-06T07:36:24Z","file_size":994490}],"oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"issue":"4","ec_funded":1,"ddc":["530"],"abstract":[{"lang":"eng","text":"A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data."}],"date_updated":"2021-01-12T07:40:46Z","date_created":"2018-12-11T11:45:44Z","publisher":"Elsevier","status":"public","year":"2018","day":"01","language":[{"iso":"eng"}],"has_accepted_license":"1","author":[{"last_name":"De Martino","first_name":"Andrea","full_name":"De Martino, Andrea"},{"last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele"}],"article_number":"e00596","department":[{"_id":"GaTk"}],"volume":4,"publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","doi":"10.1016/j.heliyon.2018.e00596","scopus_import":1,"oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:59Z","intvolume":" 4","month":"04","citation":{"chicago":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon. Elsevier, 2018. https://doi.org/10.1016/j.heliyon.2018.e00596.","short":"A. De Martino, D. De Martino, Heliyon 4 (2018).","apa":"De Martino, A., & De Martino, D. (2018). An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. Elsevier. https://doi.org/10.1016/j.heliyon.2018.e00596","ama":"De Martino A, De Martino D. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 2018;4(4). doi:10.1016/j.heliyon.2018.e00596","mla":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon, vol. 4, no. 4, e00596, Elsevier, 2018, doi:10.1016/j.heliyon.2018.e00596.","ista":"De Martino A, De Martino D. 2018. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 4(4), e00596.","ieee":"A. De Martino and D. De Martino, “An introduction to the maximum entropy approach and its application to inference problems in biology,” Heliyon, vol. 4, no. 4. Elsevier, 2018."},"publication":"Heliyon","date_published":"2018-04-01T00:00:00Z"},{"quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"day":"08","year":"2018","_id":"3300","department":[{"_id":"ToHe"}],"title":"Handbook of Model Checking","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Edmund M.","full_name":"Clarke, Edmund M.","last_name":"Clarke"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"first_name":"Helmut","full_name":"Veith, Helmut","last_name":"Veith"},{"first_name":"Roderick","full_name":"Bloem, Roderick","last_name":"Bloem"}],"doi":"10.1007/978-3-319-10575-8","type":"book","abstract":[{"lang":"eng","text":"This book first explores the origins of this idea, grounded in theoretical work on temporal logic and automata. The editors and authors are among the world's leading researchers in this domain, and they contributed 32 chapters representing a thorough view of the development and application of the technique. Topics covered include binary decision diagrams, symbolic model checking, satisfiability modulo theories, partial-order reduction, abstraction, interpolation, concurrency, security protocols, games, probabilistic model checking, and process algebra, and chapters on the transfer of theory to industrial practice, property specification languages for hardware, and verification of real-time systems and hybrid systems.\r\n\r\nThe book will be valuable for researchers and graduate students engaged with the development of formal methods and verification tools."}],"article_processing_charge":"No","publication_identifier":{"isbn":["978-3-319-10574-1"],"eisbn":["978-3-319-10575-8"]},"publication_status":"published","page":"XLVIII, 1212","citation":{"chicago":"Clarke, Edmund M., Thomas A Henzinger, Helmut Veith, and Roderick Bloem. Handbook of Model Checking. 1st ed. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-10575-8.","short":"E.M. Clarke, T.A. Henzinger, H. Veith, R. Bloem, Handbook of Model Checking, 1st ed., Springer Nature, Cham, 2018.","apa":"Clarke, E. M., Henzinger, T. A., Veith, H., & Bloem, R. (2018). Handbook of Model Checking (1st ed.). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-10575-8","ama":"Clarke EM, Henzinger TA, Veith H, Bloem R. Handbook of Model Checking. 1st ed. Cham: Springer Nature; 2018. doi:10.1007/978-3-319-10575-8","ista":"Clarke EM, Henzinger TA, Veith H, Bloem R. 2018. Handbook of Model Checking 1st ed., Cham: Springer Nature, XLVIII, 1212p.","ieee":"E. M. Clarke, T. A. Henzinger, H. Veith, and R. Bloem, Handbook of Model Checking, 1st ed. Cham: Springer Nature, 2018.","mla":"Clarke, Edmund M., et al. Handbook of Model Checking. 1st ed., Springer Nature, 2018, doi:10.1007/978-3-319-10575-8."},"publist_id":"3340","date_published":"2018-06-08T00:00:00Z","scopus_import":"1","oa_version":"None","date_created":"2018-12-11T12:02:32Z","publisher":"Springer Nature","month":"06","date_updated":"2021-12-21T10:49:36Z","edition":"1","place":"Cham"},{"title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-10-13T14:20:37Z","relation":"main_file","file_id":"8656","creator":"dernst","file_size":4906815,"date_created":"2020-10-13T14:20:37Z","checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b","success":1,"access_level":"open_access","content_type":"application/pdf","file_name":"2018_MIMB_Zagorski.pdf"}],"alternative_title":["Methods in Molecular Biology"],"_id":"37","quality_controlled":"1","date_updated":"2021-01-12T07:49:03Z","publist_id":"8018","publisher":"Springer Nature","date_created":"2018-12-11T11:44:17Z","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"}],"oa":1,"ddc":["570"],"abstract":[{"text":"Developmental processes are inherently dynamic and understanding them requires quantitative measurements of gene and protein expression levels in space and time. While live imaging is a powerful approach for obtaining such data, it is still a challenge to apply it over long periods of time to large tissues, such as the embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression and signaling activity patterns in this organ can be studied by collecting tissue sections at different developmental stages. In combination with immunohistochemistry, this allows for measuring the levels of multiple developmental regulators in a quantitative manner with high spatiotemporal resolution. The mean protein expression levels over time, as well as embryo-to-embryo variability can be analyzed. A key aspect of the approach is the ability to compare protein levels across different samples. This requires a number of considerations in sample preparation, imaging and data analysis. Here we present a protocol for obtaining time course data of dorsoventral expression patterns from mouse and chick neural tube in the first 3 days of neural tube development. The described workflow starts from embryo dissection and ends with a processed dataset. Software scripts for data analysis are included. The protocol is adaptable and instructions that allow the user to modify different steps are provided. Thus, the procedure can be altered for analysis of time-lapse images and applied to systems other than the neural tube.","lang":"eng"}],"ec_funded":1,"publication_identifier":{"isbn":["978-1-4939-8771-9"],"issn":["1064-3745"]},"author":[{"full_name":"Zagórski, Marcin P","first_name":"Marcin P","orcid":"0000-0001-7896-7762","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","first_name":"Anna","orcid":"0000-0003-4509-4998"}],"volume":1863,"department":[{"_id":"AnKi"}],"language":[{"iso":"eng"}],"day":"16","year":"2018","status":"public","has_accepted_license":"1","date_published":"2018-10-16T00:00:00Z","publication":"Morphogen Gradients ","citation":{"ista":"Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods in Molecular Biology, vol. 1863, 47–63.","mla":"Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63, doi:10.1007/978-1-4939-8772-6_4.","ieee":"M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63.","short":"M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63.","apa":"Zagórski, M. P., & Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In Morphogen Gradients (Vol. 1863, pp. 47–63). Springer Nature. https://doi.org/10.1007/978-1-4939-8772-6_4","ama":"Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:10.1007/978-1-4939-8772-6_4","chicago":"Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In Morphogen Gradients , 1863:47–63. MIMB. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-8772-6_4."},"file_date_updated":"2020-10-13T14:20:37Z","intvolume":" 1863","month":"10","oa_version":"Submitted Version","scopus_import":"1","page":"47 - 63","publication_status":"published","series_title":"MIMB","type":"book_chapter","doi":"10.1007/978-1-4939-8772-6_4","article_processing_charge":"No"},{"date_created":"2018-12-11T11:45:43Z","publisher":"Springer","publist_id":"7574","date_updated":"2021-01-12T07:40:42Z","acknowledgement":"This work was financially supported by FP7 of the EU through the project “Body on a chip,” ICT-FET-296257, and the ERC Advanced Grant “NeuroCMOS” (contract 267351), as well as by an individual Ambizione Grant 142440 from the Swiss National Science Foundation for Olivier Frey. The research leading to these results also received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734]. We would like to thank Alexander Stettler, ETH Zurich for his expertise and support in the cleanroom, and we acknowledge the Single Cell Unit of D-BSSE, ETH Zurich for assistance in microscopy issues. M.L. is grateful to the members of the Guet and Tkačik groups, IST Austria, for valuable comments and support.","ec_funded":1,"abstract":[{"text":"The hanging-drop network (HDN) is a technology platform based on a completely open microfluidic network at the bottom of an inverted, surface-patterned substrate. The platform is predominantly used for the formation, culturing, and interaction of self-assembled spherical microtissues (spheroids) under precisely controlled flow conditions. Here, we describe design, fabrication, and operation of microfluidic hanging-drop networks.","lang":"eng"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Fabrication and operation of microfluidic hanging drop networks","quality_controlled":"1","_id":"305","alternative_title":["MIMB"],"scopus_import":1,"oa_version":"None","intvolume":" 1771","month":"01","citation":{"short":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular Biology 1771 (2018) 183–202.","apa":"Misun, P., Birchler, A., Lang, M., Hierlemann, A., & Frey, O. (2018). Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-4939-7792-5_15","ama":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 2018;1771:183-202. doi:10.1007/978-1-4939-7792-5_15","chicago":"Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology. Springer, 2018. https://doi.org/10.1007/978-1-4939-7792-5_15.","mla":"Misun, Patrick, et al. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology, vol. 1771, Springer, 2018, pp. 183–202, doi:10.1007/978-1-4939-7792-5_15.","ista":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. 2018. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 1771, 183–202.","ieee":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and operation of microfluidic hanging drop networks,” Methods in Molecular Biology, vol. 1771. Springer, pp. 183–202, 2018."},"date_published":"2018-01-01T00:00:00Z","publication":"Methods in Molecular Biology","doi":"10.1007/978-1-4939-7792-5_15","type":"journal_article","publication_status":"published","page":"183 - 202","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"volume":1771,"author":[{"full_name":"Misun, Patrick","first_name":"Patrick","last_name":"Misun"},{"last_name":"Birchler","full_name":"Birchler, Axel","first_name":"Axel"},{"last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz","first_name":"Moritz"},{"first_name":"Andreas","full_name":"Hierlemann, Andreas","last_name":"Hierlemann"},{"full_name":"Frey, Olivier","first_name":"Olivier","last_name":"Frey"}],"status":"public","language":[{"iso":"eng"}],"day":"01","year":"2018"},{"title":"Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","_id":"325","publist_id":"7540","conference":{"start_date":"2018-01-07","name":"POPL: Principles of Programming Languages","location":"Los Angeles, CA, USA","end_date":"2018-01-13"},"publisher":"ACM","date_created":"2018-12-11T11:45:50Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.04037"}],"external_id":{"arxiv":["1709.04037"]},"date_updated":"2021-01-12T07:42:07Z","abstract":[{"text":"Probabilistic programs extend classical imperative programs with real-valued random variables and random branching. The most basic liveness property for such programs is the termination property. The qualitative (aka almost-sure) termination problem asks whether a given program program terminates with probability 1. While ranking functions provide a sound and complete method for non-probabilistic programs, the extension of them to probabilistic programs is achieved via ranking supermartingales (RSMs). Although deep theoretical results have been established about RSMs, their application to probabilistic programs with nondeterminism has been limited only to programs of restricted control-flow structure. For non-probabilistic programs, lexicographic ranking functions provide a compositional and practical approach for termination analysis of real-world programs. In this work we introduce lexicographic RSMs and show that they present a sound method for almost-sure termination of probabilistic programs with nondeterminism. We show that lexicographic RSMs provide a tool for compositional reasoning about almost-sure termination, and for probabilistic programs with linear arithmetic they can be synthesized efficiently (in polynomial time). We also show that with additional restrictions even asymptotic bounds on expected termination time can be obtained through lexicographic RSMs. Finally, we present experimental results on benchmarks adapted from previous work to demonstrate the effectiveness of our approach.","lang":"eng"}],"issue":"POPL","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"oa":1,"volume":2,"department":[{"_id":"KrCh"}],"article_number":"34","author":[{"last_name":"Agrawal","first_name":"Sheshansh","full_name":"Agrawal, Sheshansh"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Petr","full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny"}],"day":"01","year":"2018","language":[{"iso":"eng"}],"status":"public","date_published":"2018-01-01T00:00:00Z","citation":{"short":"S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018.","apa":"Agrawal, S., Chatterjee, K., & Novotný, P. (2018). Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs (Vol. 2). Presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/3158122","ama":"Agrawal S, Chatterjee K, Novotný P. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. In: Vol 2. ACM; 2018. doi:10.1145/3158122","chicago":"Agrawal, Sheshansh, Krishnendu Chatterjee, and Petr Novotný. “Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs,” Vol. 2. ACM, 2018. https://doi.org/10.1145/3158122.","ista":"Agrawal S, Chatterjee K, Novotný P. 2018. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. POPL: Principles of Programming Languages vol. 2, 34.","mla":"Agrawal, Sheshansh, et al. Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs. Vol. 2, no. POPL, 34, ACM, 2018, doi:10.1145/3158122.","ieee":"S. Agrawal, K. Chatterjee, and P. Novotný, “Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs,” presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA, 2018, vol. 2, no. POPL."},"month":"01","intvolume":" 2","oa_version":"Preprint","type":"conference","doi":"10.1145/3158122","publication_status":"published"},{"citation":{"mla":"Trinh, Hoang, et al. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102, doi:10.1007/978-1-4939-7747-5_7.","ista":"Trinh H, Verstraeten I, Geelen D. 2018.In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . MIMB, vol. 1761, 95–102.","ieee":"H. Trinh, I. Verstraeten, and D. Geelen, “In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls,” in Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102.","short":"H. Trinh, I. Verstraeten, D. Geelen, in:, Root Development , Springer Nature, 2018, pp. 95–102.","ama":"Trinh H, Verstraeten I, Geelen D. In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . Vol 1761. Springer Nature; 2018:95-102. doi:10.1007/978-1-4939-7747-5_7","apa":"Trinh, H., Verstraeten, I., & Geelen, D. (2018). In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In Root Development (Vol. 1761, pp. 95–102). Springer Nature. https://doi.org/10.1007/978-1-4939-7747-5_7","chicago":"Trinh, Hoang, Inge Verstraeten, and Danny Geelen. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” In Root Development , 1761:95–102. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-7747-5_7."},"date_published":"2018-03-01T00:00:00Z","publication":"Root Development ","oa_version":"None","scopus_import":"1","intvolume":" 1761","month":"03","publication_status":"published","page":"95 - 102","doi":"10.1007/978-1-4939-7747-5_7","type":"book_chapter","article_processing_charge":"No","author":[{"last_name":"Trinh","first_name":"Hoang","full_name":"Trinh, Hoang"},{"first_name":"Inge","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten"},{"last_name":"Geelen","full_name":"Geelen, Danny","first_name":"Danny"}],"volume":1761,"department":[{"_id":"JiFr"}],"pmid":1,"status":"public","day":"01","year":"2018","language":[{"iso":"eng"}],"date_updated":"2021-01-12T07:54:21Z","external_id":{"pmid":["29525951"]},"publist_id":"7421","date_created":"2018-12-11T11:46:18Z","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Adventitious roots (AR) are de novo formed roots that emerge from any part of the plant or from callus in tissue culture, except root tissue. The plant tissue origin and the method by which they are induced determine the physiological properties of emerged ARs. Hence, a standard method encompassing all types of AR does not exist. Here we describe a method for the induction and analysis of AR that emerge from the etiolated hypocotyl of dicot plants. The hypocotyl is formed during embryogenesis and shows a determined developmental pattern which usually does not involve AR formation. However, the hypocotyl shows propensity to form de novo roots under specific circumstances such as removal of the root system, high humidity or flooding, or during de-etiolation. The hypocotyl AR emerge from a pericycle-like cell layer surrounding the vascular tissue of the central cylinder, which is reminiscent to the developmental program of lateral roots. Here we propose an easy protocol for in vitro hypocotyl AR induction from etiolated Arabidopsis seedlings."}],"publication_identifier":{"issn":["1064-3745"]},"title":"In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["MIMB"],"_id":"408","quality_controlled":"1"},{"volume":1761,"department":[{"_id":"JiFr"}],"title":"Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia","editor":[{"last_name":"Ristova","full_name":"Ristova, Daniela","first_name":"Daniela"},{"last_name":"Barbez","full_name":"Barbez, Elke","first_name":"Elke"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Karampelias, Michael","first_name":"Michael","last_name":"Karampelias"},{"last_name":"Tejos","full_name":"Tejos, Ricardo","first_name":"Ricardo"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"}],"quality_controlled":"1","status":"public","year":"2018","day":"11","language":[{"iso":"eng"}],"alternative_title":["Methods in Molecular Biology"],"_id":"411","citation":{"chicago":"Karampelias, Michael, Ricardo Tejos, Jiří Friml, and Steffen Vanneste. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” In Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, 1761:131–43. MIMB. Springer, 2018. https://doi.org/10.1007/978-1-4939-7747-5_10.","apa":"Karampelias, M., Tejos, R., Friml, J., & Vanneste, S. (2018). Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In D. Ristova & E. Barbez (Eds.), Root Development. Methods and Protocols (Vol. 1761, pp. 131–143). Springer. https://doi.org/10.1007/978-1-4939-7747-5_10","ama":"Karampelias M, Tejos R, Friml J, Vanneste S. Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Ristova D, Barbez E, eds. Root Development. Methods and Protocols. Vol 1761. MIMB. Springer; 2018:131-143. doi:10.1007/978-1-4939-7747-5_10","short":"M. Karampelias, R. Tejos, J. Friml, S. Vanneste, in:, D. Ristova, E. Barbez (Eds.), Root Development. Methods and Protocols, Springer, 2018, pp. 131–143.","ista":"Karampelias M, Tejos R, Friml J, Vanneste S. 2018.Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Root Development. Methods and Protocols. Methods in Molecular Biology, vol. 1761, 131–143.","ieee":"M. Karampelias, R. Tejos, J. Friml, and S. Vanneste, “Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia,” in Root Development. Methods and Protocols, vol. 1761, D. Ristova and E. Barbez, Eds. Springer, 2018, pp. 131–143.","mla":"Karampelias, Michael, et al. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, vol. 1761, Springer, 2018, pp. 131–43, doi:10.1007/978-1-4939-7747-5_10."},"publication":"Root Development. Methods and Protocols","date_published":"2018-03-11T00:00:00Z","publist_id":"7418","date_created":"2018-12-11T11:46:20Z","oa_version":"None","scopus_import":1,"publisher":"Springer","intvolume":" 1761","month":"03","date_updated":"2021-01-12T07:54:34Z","type":"book_chapter","doi":"10.1007/978-1-4939-7747-5_10","abstract":[{"text":"Immunolocalization is a valuable tool for cell biology research that allows to rapidly determine the localization and expression levels of endogenous proteins. In plants, whole-mount in situ immunolocalization remains a challenging method, especially in tissues protected by waxy layers and complex cell wall carbohydrates. Here, we present a robust method for whole-mount in situ immunolocalization in primary root meristems and lateral root primordia in Arabidopsis thaliana. For good epitope preservation, fixation is done in an alkaline paraformaldehyde/glutaraldehyde mixture. This fixative is suitable for detecting a wide range of proteins, including integral transmembrane proteins and proteins peripherally attached to the plasma membrane. From initiation until emergence from the primary root, lateral root primordia are surrounded by several layers of differentiated tissues with a complex cell wall composition that interferes with the efficient penetration of all buffers. Therefore, immunolocalization in early lateral root primordia requires a modified method, including a strong solvent treatment for removal of hydrophobic barriers and a specific cocktail of cell wall-degrading enzymes. The presented method allows for easy, reliable, and high-quality in situ detection of the subcellular localization of endogenous proteins in primary and lateral root meristems without the need of time-consuming crosses or making translational fusions to fluorescent proteins.","lang":"eng"}],"publication_status":"published","page":"131 - 143","series_title":"MIMB"},{"quality_controlled":"1","_id":"456","status":"public","year":"2018","language":[{"iso":"eng"}],"day":"10","department":[{"_id":"GaNo"}],"volume":10,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"title":"Zika-associated microcephaly: Reduce the stress and race for the treatment","article_number":"eaar7514","type":"journal_article","doi":"10.1126/scitranslmed.aar7514","abstract":[{"lang":"eng","text":"Inhibition of the endoplasmic reticulum stress pathway may hold the key to Zika virus-associated microcephaly treatment. "}],"publication_status":"published","issue":"423","scopus_import":1,"date_created":"2018-12-11T11:46:34Z","oa_version":"None","month":"01","publisher":"American Association for the Advancement of Science","intvolume":" 10","citation":{"ista":"Novarino G. 2018. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 10(423), eaar7514.","ieee":"G. Novarino, “Zika-associated microcephaly: Reduce the stress and race for the treatment,” Science Translational Medicine, vol. 10, no. 423. American Association for the Advancement of Science, 2018.","mla":"Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” Science Translational Medicine, vol. 10, no. 423, eaar7514, American Association for the Advancement of Science, 2018, doi:10.1126/scitranslmed.aar7514.","apa":"Novarino, G. (2018). Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aar7514","ama":"Novarino G. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 2018;10(423). doi:10.1126/scitranslmed.aar7514","short":"G. Novarino, Science Translational Medicine 10 (2018).","chicago":"Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” Science Translational Medicine. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/scitranslmed.aar7514."},"publication":"Science Translational Medicine","publist_id":"7365","date_published":"2018-01-10T00:00:00Z","date_updated":"2021-01-12T07:59:42Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"IST PubRep and IST DataRep: the institutional repositories at IST Austria","file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"2018_VOEB_Petritsch.pdf","file_id":"5702","creator":"dernst","relation":"main_file","date_updated":"2020-07-14T12:46:38Z","file_size":509434,"date_created":"2018-12-17T12:40:27Z","checksum":"7ac61bade5f37db011ca435ebcf86797"}],"_id":"53","date_updated":"2021-01-12T08:01:26Z","date_created":"2018-12-11T11:44:22Z","publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","publist_id":"8001","oa":1,"issue":"1","abstract":[{"lang":"eng","text":"In 2013, a publication repository was implemented at IST Austria and 2015 after a thorough preparation phase a data repository was implemented - both based on the Open Source Software EPrints. In this text, designed as field report, we will reflect on our experiences with Open Source Software in general and specifically with EPrints regarding technical aspects but also regarding their characteristics of the user community. The second part is a pleading for including the end users in the process of implementation, adaption and evaluation."}],"ddc":["020"],"author":[{"orcid":"0000-0003-2724-4614","first_name":"Barbara","full_name":"Petritsch, Barbara","id":"406048EC-F248-11E8-B48F-1D18A9856A87","last_name":"Petritsch"},{"first_name":"Jana","full_name":"Porsche, Jana","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87","last_name":"Porsche"}],"department":[{"_id":"E-Lib"}],"volume":71,"status":"public","year":"2018","day":"01","language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":1,"oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:38Z","intvolume":" 71","month":"10","citation":{"mla":"Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen, vol. 71, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018, pp. 199–206, doi:10.31263/voebm.v71i1.1993.","ieee":"B. Petritsch and J. Porsche, “IST PubRep and IST DataRep: the institutional repositories at IST Austria,” VÖB Mitteilungen, vol. 71, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 199–206, 2018.","ista":"Petritsch B, Porsche J. 2018. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 71(1), 199–206.","ama":"Petritsch B, Porsche J. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 2018;71(1):199-206. doi:10.31263/voebm.v71i1.1993","apa":"Petritsch, B., & Porsche, J. (2018). IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v71i1.1993","short":"B. Petritsch, J. Porsche, VÖB Mitteilungen 71 (2018) 199–206.","chicago":"Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018. https://doi.org/10.31263/voebm.v71i1.1993."},"publication":"VÖB Mitteilungen","date_published":"2018-10-01T00:00:00Z","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"page":"199 - 206","type":"journal_article","doi":"10.31263/voebm.v71i1.1993"},{"year":"2018","day":"01","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Aspnes","full_name":"Aspnes, James","first_name":"James"},{"full_name":"King, Valerie","first_name":"Valerie","last_name":"King"},{"last_name":"Saia","first_name":"Jared","full_name":"Saia, Jared"}],"department":[{"_id":"DaAl"}],"volume":31,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"page":"489-501","publication_status":"published","article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s00446-017-0315-1","type":"journal_article","file_date_updated":"2020-07-14T12:46:38Z","intvolume":" 31","month":"11","scopus_import":1,"oa_version":"Published Version","publication":"Distributed Computing","date_published":"2018-11-01T00:00:00Z","citation":{"ista":"Alistarh D-A, Aspnes J, King V, Saia J. 2018. Communication-efficient randomized consensus. Distributed Computing. 31(6), 489–501.","ieee":"D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient randomized consensus,” Distributed Computing, vol. 31, no. 6. Springer, pp. 489–501, 2018.","mla":"Alistarh, Dan-Adrian, et al. “Communication-Efficient Randomized Consensus.” Distributed Computing, vol. 31, no. 6, Springer, 2018, pp. 489–501, doi:10.1007/s00446-017-0315-1.","apa":"Alistarh, D.-A., Aspnes, J., King, V., & Saia, J. (2018). Communication-efficient randomized consensus. Distributed Computing. Springer. https://doi.org/10.1007/s00446-017-0315-1","ama":"Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized consensus. Distributed Computing. 2018;31(6):489-501. doi:10.1007/s00446-017-0315-1","short":"D.-A. Alistarh, J. Aspnes, V. King, J. Saia, Distributed Computing 31 (2018) 489–501.","chicago":"Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient Randomized Consensus.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-017-0315-1."},"_id":"536","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Communication-efficient randomized consensus","file":[{"file_name":"2017_DistribComp_Alistarh.pdf","content_type":"application/pdf","access_level":"open_access","file_size":595707,"checksum":"69b46e537acdcac745237ddb853fcbb5","date_created":"2019-01-22T07:25:51Z","file_id":"5867","creator":"dernst","date_updated":"2020-07-14T12:46:38Z","relation":"main_file"}],"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"oa":1,"issue":"6","publication_identifier":{"issn":["01782770"]},"ddc":["000"],"abstract":[{"text":"We consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary. We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n / 2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(nlog3n) messages in expectation, which is again within logarithmic factors of optimal. We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt+t2log2t) total messages. Our approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model.","lang":"eng"}],"date_updated":"2023-02-23T12:23:25Z","publisher":"Springer","date_created":"2018-12-11T11:47:01Z","publist_id":"7281"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The Bogoliubov free energy functional II: The dilute Limit","_id":"554","quality_controlled":"1","date_updated":"2021-01-12T08:02:35Z","external_id":{"arxiv":["1511.05953"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.05953"}],"date_created":"2018-12-11T11:47:09Z","publisher":"Springer","publist_id":"7260","oa":1,"project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"issue":"1","publication_identifier":{"issn":["00103616"]},"abstract":[{"lang":"eng","text":"We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a first-order phase transition and, in the limit (Formula presented.), we determine the critical temperature to be (Formula presented.) to leading order. Here, (Formula presented.) is the critical temperature of the free Bose gas, ρ is the density of the gas and a is the scattering length of the pair-interaction potential V. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula in the limit (Formula presented.)."}],"author":[{"id":"4197AD04-F248-11E8-B48F-1D18A9856A87","last_name":"Napiórkowski","first_name":"Marcin M","full_name":"Napiórkowski, Marcin M"},{"first_name":"Robin","full_name":"Reuvers, Robin","last_name":"Reuvers"},{"first_name":"Jan","full_name":"Solovej, Jan","last_name":"Solovej"}],"department":[{"_id":"RoSe"}],"volume":360,"status":"public","language":[{"iso":"eng"}],"day":"01","year":"2018","scopus_import":1,"oa_version":"Submitted Version","intvolume":" 360","month":"05","citation":{"chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” Communications in Mathematical Physics. Springer, 2018. https://doi.org/10.1007/s00220-017-3064-x.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403.","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-017-3064-x","ama":"Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 2018;360(1):347-403. doi:10.1007/s00220-017-3064-x","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy functional II: The dilute Limit,” Communications in Mathematical Physics, vol. 360, no. 1. Springer, pp. 347–403, 2018.","mla":"Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” Communications in Mathematical Physics, vol. 360, no. 1, Springer, 2018, pp. 347–403, doi:10.1007/s00220-017-3064-x.","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 360(1), 347–403."},"publication":"Communications in Mathematical Physics","date_published":"2018-05-01T00:00:00Z","publication_status":"published","page":"347-403","doi":"10.1007/s00220-017-3064-x","type":"journal_article"},{"author":[{"first_name":"Dimitar","full_name":"Dimitrov, Dimitar","last_name":"Dimitrov"},{"last_name":"Guillaud","first_name":"Laurent","full_name":"Guillaud, Laurent"},{"full_name":"Eguchi, Kohgaku","first_name":"Kohgaku","orcid":"0000-0002-6170-2546","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki","last_name":"Takahashi"}],"editor":[{"full_name":"Skaper, Stephen D.","first_name":"Stephen D.","last_name":"Skaper"}],"pmid":1,"department":[{"_id":"RySh"}],"volume":1727,"day":"01","year":"2018","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","month":"01","file_date_updated":"2020-07-14T12:47:09Z","intvolume":" 1727","scopus_import":1,"oa_version":"Submitted Version","date_published":"2018-01-01T00:00:00Z","publication":"Neurotrophic Factors","citation":{"chicago":"Dimitrov, Dimitar, Laurent Guillaud, Kohgaku Eguchi, and Tomoyuki Takahashi. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” In Neurotrophic Factors, edited by Stephen D. Skaper, 1727:201–15. Springer, 2018. https://doi.org/10.1007/978-1-4939-7571-6_15.","apa":"Dimitrov, D., Guillaud, L., Eguchi, K., & Takahashi, T. (2018). Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In S. D. Skaper (Ed.), Neurotrophic Factors (Vol. 1727, pp. 201–215). Springer. https://doi.org/10.1007/978-1-4939-7571-6_15","ama":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Skaper SD, ed. Neurotrophic Factors. Vol 1727. Springer; 2018:201-215. doi:10.1007/978-1-4939-7571-6_15","short":"D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.), Neurotrophic Factors, Springer, 2018, pp. 201–215.","mla":"Dimitrov, Dimitar, et al. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” Neurotrophic Factors, edited by Stephen D. Skaper, vol. 1727, Springer, 2018, pp. 201–15, doi:10.1007/978-1-4939-7571-6_15.","ieee":"D. Dimitrov, L. Guillaud, K. Eguchi, and T. Takahashi, “Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses,” in Neurotrophic Factors, vol. 1727, S. D. Skaper, Ed. Springer, 2018, pp. 201–215.","ista":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. 2018.Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Neurotrophic Factors. Methods in Molecular Biology, vol. 1727, 201–215."},"page":"201 - 215","publication_status":"published","article_processing_charge":"No","doi":"10.1007/978-1-4939-7571-6_15","type":"book_chapter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses","file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"2018_NeurotrophicFactors_Dimitrov.pdf","creator":"dernst","file_id":"7046","date_updated":"2020-07-14T12:47:09Z","relation":"main_file","date_created":"2019-11-19T07:47:43Z","checksum":"8aa174ca65a56fbb19e9f88cff3ac3fd","file_size":787407}],"_id":"562","alternative_title":["Methods in Molecular Biology"],"quality_controlled":"1","external_id":{"pmid":["29222783"]},"date_updated":"2021-01-12T08:03:05Z","publisher":"Springer","date_created":"2018-12-11T11:47:11Z","publist_id":"7252","oa":1,"ddc":["570"],"abstract":[{"text":"Primary neuronal cell culture preparations are widely used to investigate synaptic functions. This chapter describes a detailed protocol for the preparation of a neuronal cell culture in which giant calyx-type synaptic terminals are formed. This chapter also presents detailed protocols for utilizing the main technical advantages provided by such a preparation, namely, labeling and imaging of synaptic organelles and electrophysiological recordings directly from presynaptic terminals.","lang":"eng"}]},{"publication_status":"published","page":"921 - 962","doi":"10.1007/978-3-319-10575-8_27","type":"book_chapter","abstract":[{"text":"Graph-based games are an important tool in computer science. They have applications in synthesis, verification, refinement, and far beyond. We review graphbased games with objectives on infinite plays. We give definitions and algorithms to solve the games and to give a winning strategy. The objectives we consider are mostly Boolean, but we also look at quantitative graph-based games and their objectives. Synthesis aims to turn temporal logic specifications into correct reactive systems. We explain the reduction of synthesis to graph-based games (or equivalently tree automata) using synthesis of LTL specifications as an example. We treat the classical approach that uses determinization of parity automata and more modern approaches.","lang":"eng"}],"publication_identifier":{"isbn":["978-3-319-10574-1"]},"date_updated":"2021-01-12T08:05:10Z","edition":"1","citation":{"ista":"Bloem R, Chatterjee K, Jobstmann B. 2018.Graph games and reactive synthesis. In: Handbook of Model Checking. , 921–962.","ieee":"R. Bloem, K. Chatterjee, and B. Jobstmann, “Graph games and reactive synthesis,” in Handbook of Model Checking, 1st ed., T. A. Henzinger, E. M. Clarke, H. Veith, and R. Bloem, Eds. Springer, 2018, pp. 921–962.","mla":"Bloem, Roderick, et al. “Graph Games and Reactive Synthesis.” Handbook of Model Checking, edited by Thomas A Henzinger et al., 1st ed., Springer, 2018, pp. 921–62, doi:10.1007/978-3-319-10575-8_27.","chicago":"Bloem, Roderick, Krishnendu Chatterjee, and Barbara Jobstmann. “Graph Games and Reactive Synthesis.” In Handbook of Model Checking, edited by Thomas A Henzinger, Edmund M. Clarke, Helmut Veith, and Roderick Bloem, 1st ed., 921–62. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_27.","apa":"Bloem, R., Chatterjee, K., & Jobstmann, B. (2018). Graph games and reactive synthesis. In T. A. Henzinger, E. M. Clarke, H. Veith, & R. Bloem (Eds.), Handbook of Model Checking (1st ed., pp. 921–962). Springer. https://doi.org/10.1007/978-3-319-10575-8_27","ama":"Bloem R, Chatterjee K, Jobstmann B. Graph games and reactive synthesis. In: Henzinger TA, Clarke EM, Veith H, Bloem R, eds. Handbook of Model Checking. 1st ed. Springer; 2018:921-962. doi:10.1007/978-3-319-10575-8_27","short":"R. Bloem, K. Chatterjee, B. Jobstmann, in:, T.A. Henzinger, E.M. Clarke, H. Veith, R. Bloem (Eds.), Handbook of Model Checking, 1st ed., Springer, 2018, pp. 921–962."},"publication":"Handbook of Model Checking","publist_id":"7995","date_published":"2018-05-19T00:00:00Z","oa_version":"None","date_created":"2018-12-11T11:44:24Z","scopus_import":1,"month":"05","publisher":"Springer","status":"public","day":"19","language":[{"iso":"eng"}],"year":"2018","_id":"59","quality_controlled":"1","title":"Graph games and reactive synthesis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","editor":[{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Edmund M.","full_name":"Clarke, Edmund M.","last_name":"Clarke"},{"last_name":"Veith","full_name":"Veith, Helmut","first_name":"Helmut"},{"first_name":"Roderick","full_name":"Bloem, Roderick","last_name":"Bloem"}],"author":[{"full_name":"Bloem, Roderick","first_name":"Roderick","last_name":"Bloem"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Jobstmann","full_name":"Jobstmann, Barbara","first_name":"Barbara"}],"department":[{"_id":"KrCh"}]},{"date_updated":"2021-01-12T08:05:35Z","citation":{"mla":"Clarke, Edmund, et al. “Introduction to Model Checking.” Handbook of Model Checking, edited by Thomas A Henzinger, Springer, 2018, pp. 1–26, doi:10.1007/978-3-319-10575-8_1.","ista":"Clarke E, Henzinger TA, Veith H. 2018.Introduction to model checking. In: Handbook of Model Checking. , 1–26.","ieee":"E. Clarke, T. A. Henzinger, and H. Veith, “Introduction to model checking,” in Handbook of Model Checking, T. A. Henzinger, Ed. Springer, 2018, pp. 1–26.","short":"E. Clarke, T.A. Henzinger, H. Veith, in:, T.A. Henzinger (Ed.), Handbook of Model Checking, Springer, 2018, pp. 1–26.","apa":"Clarke, E., Henzinger, T. A., & Veith, H. (2018). Introduction to model checking. In T. A. Henzinger (Ed.), Handbook of Model Checking (pp. 1–26). Springer. https://doi.org/10.1007/978-3-319-10575-8_1","ama":"Clarke E, Henzinger TA, Veith H. Introduction to model checking. In: Henzinger TA, ed. Handbook of Model Checking. Handbook of Model Checking. Springer; 2018:1-26. doi:10.1007/978-3-319-10575-8_1","chicago":"Clarke, Edmund, Thomas A Henzinger, and Helmut Veith. “Introduction to Model Checking.” In Handbook of Model Checking, edited by Thomas A Henzinger, 1–26. Handbook of Model Checking. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_1."},"publication":"Handbook of Model Checking","publist_id":"7994","date_published":"2018-05-19T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:44:25Z","oa_version":"None","month":"05","publisher":"Springer","publication_status":"published","page":"1 - 26","series_title":"Handbook of Model Checking","type":"book_chapter","doi":"10.1007/978-3-319-10575-8_1","abstract":[{"text":"Model checking is a computer-assisted method for the analysis of dynamical systems that can be modeled by state-transition systems. Drawing from research traditions in mathematical logic, programming languages, hardware design, and theoretical computer science, model checking is now widely used for the verification of hardware and software in industry. This chapter is an introduction and short survey of model checking. The chapter aims to motivate and link the individual chapters of the handbook, and to provide context for readers who are not familiar with model checking.","lang":"eng"}],"title":"Introduction to model checking","editor":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Edmund","full_name":"Clarke, Edmund","last_name":"Clarke"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Veith","first_name":"Helmut","full_name":"Veith, Helmut"}],"department":[{"_id":"ToHe"}],"status":"public","day":"19","language":[{"iso":"eng"}],"year":"2018","_id":"60","quality_controlled":"1"},{"extern":"1","oa_version":"Preprint","date_created":"2018-12-11T11:44:25Z","month":"05","publisher":"Springer","citation":{"ista":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. 2018.There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. , 131–134.","mla":"Bondarenko, Andriy, et al. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” Contemporary Computational Mathematics, Springer, 2018, pp. 131–34, doi:10.1007/978-3-319-72456-0_7.","ieee":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, and M. Viazovska, “There is no strongly regular graph with parameters (460; 153; 32; 60),” in Contemporary Computational Mathematics, Springer, 2018, pp. 131–134.","chicago":"Bondarenko, Andriy, Anton Mellit, Andriy Prymak, Danylo Radchenko, and Maryna Viazovska. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” In Contemporary Computational Mathematics, 131–34. Springer, 2018. https://doi.org/10.1007/978-3-319-72456-0_7.","short":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, M. Viazovska, in:, Contemporary Computational Mathematics, Springer, 2018, pp. 131–134.","apa":"Bondarenko, A., Mellit, A., Prymak, A., Radchenko, D., & Viazovska, M. (2018). There is no strongly regular graph with parameters (460; 153; 32; 60). In Contemporary Computational Mathematics (pp. 131–134). Springer. https://doi.org/10.1007/978-3-319-72456-0_7","ama":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. Springer; 2018:131-134. doi:10.1007/978-3-319-72456-0_7"},"date_published":"2018-05-23T00:00:00Z","publication":"Contemporary Computational Mathematics","publist_id":"7993","date_updated":"2021-01-12T08:06:06Z","external_id":{"arxiv":["1509.06286"]},"main_file_link":[{"url":"https://arxiv.org/abs/1509.06286","open_access":"1"}],"article_processing_charge":"No","doi":"10.1007/978-3-319-72456-0_7","type":"book_chapter","abstract":[{"lang":"eng","text":"We prove that there is no strongly regular graph (SRG) with parameters (460; 153; 32; 60). The proof is based on a recent lower bound on the number of 4-cliques in a SRG and some applications of Euclidean representation of SRGs. "}],"oa":1,"publication_status":"published","page":"131 - 134","department":[{"_id":"TaHa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Bondarenko","full_name":"Bondarenko, Andriy","first_name":"Andriy"},{"id":"388D3134-F248-11E8-B48F-1D18A9856A87","last_name":"Mellit","first_name":"Anton","full_name":"Mellit, Anton"},{"full_name":"Prymak, Andriy","first_name":"Andriy","last_name":"Prymak"},{"first_name":"Danylo","full_name":"Radchenko, Danylo","last_name":"Radchenko"},{"last_name":"Viazovska","full_name":"Viazovska, Maryna","first_name":"Maryna"}],"title":"There is no strongly regular graph with parameters (460; 153; 32; 60)","quality_controlled":"1","_id":"61","status":"public","language":[{"iso":"eng"}],"day":"23","year":"2018"},{"title":"Platelet migration and bacterial trapping assay under flow","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2018_BioProtocol_Fan.pdf","content_type":"application/pdf","access_level":"open_access","file_size":2928337,"date_created":"2019-04-30T08:04:33Z","checksum":"d4588377e789da7f360b553ae02c5119","file_id":"6360","creator":"dernst","date_updated":"2020-07-14T12:47:28Z","relation":"main_file"}],"_id":"6354","quality_controlled":"1","keyword":["Platelets","Cell migration","Bacteria","Shear flow","Fibrinogen","E. coli"],"acknowledgement":" FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.)","date_updated":"2021-01-12T08:07:12Z","publisher":"Bio-Protocol","date_created":"2019-04-29T09:40:33Z","issue":"18","oa":1,"project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"ddc":["570"],"abstract":[{"lang":"eng","text":"Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow."}],"ec_funded":1,"publication_identifier":{"issn":["2331-8325"]},"article_number":"e3018","author":[{"last_name":"Fan","full_name":"Fan, Shuxia","first_name":"Shuxia"},{"last_name":"Lorenz","first_name":"Michael","full_name":"Lorenz, Michael"},{"full_name":"Massberg, Steffen","first_name":"Steffen","last_name":"Massberg"},{"orcid":"0000-0001-6120-3723","first_name":"Florian R","full_name":"Gärtner, Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","last_name":"Gärtner"}],"volume":8,"department":[{"_id":"MiSi"}],"language":[{"iso":"eng"}],"day":"20","year":"2018","status":"public","has_accepted_license":"1","publication":"Bio-Protocol","date_published":"2018-09-20T00:00:00Z","citation":{"chicago":"Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol, 2018. https://doi.org/10.21769/bioprotoc.3018.","short":"S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).","ama":"Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018","apa":"Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018","ieee":"S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol, 2018.","ista":"Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018.","mla":"Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018."},"intvolume":" 8","month":"09","file_date_updated":"2020-07-14T12:47:28Z","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","doi":"10.21769/bioprotoc.3018","type":"journal_article"},{"_id":"6459","year":"2018","language":[{"iso":"eng"}],"day":"24","status":"public","has_accepted_license":"1","keyword":["Open Access","Publication Analysis"],"author":[{"orcid":"0000-0003-2724-4614","first_name":"Barbara","full_name":"Petritsch, Barbara","id":"406048EC-F248-11E8-B48F-1D18A9856A87","last_name":"Petritsch"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Open Access at IST Austria 2009-2017","file":[{"file_name":"Poster_Beitrag_125_Petritsch.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1967778,"date_created":"2019-05-16T07:26:25Z","checksum":"9063ab4d10ea93353c3a03bbf53fbcf1","date_updated":"2020-07-14T12:47:30Z","relation":"main_file","file_id":"6460","creator":"dernst"}],"department":[{"_id":"E-Lib"}],"oa":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","ddc":["020"],"type":"conference_poster","doi":"10.5281/zenodo.1410279","date_updated":"2020-07-14T23:06:21Z","month":"09","file_date_updated":"2020-07-14T12:47:30Z","publisher":"IST Austria","date_created":"2019-05-16T07:27:14Z","oa_version":"Published Version","date_published":"2018-09-24T00:00:00Z","citation":{"chicago":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018. https://doi.org/10.5281/zenodo.1410279.","ama":"Petritsch B. Open Access at IST Austria 2009-2017. IST Austria; 2018. doi:10.5281/zenodo.1410279","apa":"Petritsch, B. (2018). Open Access at IST Austria 2009-2017. Presented at the Open-Access-Tage, Graz, Austria: IST Austria. https://doi.org/10.5281/zenodo.1410279","short":"B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018.","ista":"Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.","mla":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018, doi:10.5281/zenodo.1410279.","ieee":"B. Petritsch, Open Access at IST Austria 2009-2017. IST Austria, 2018."},"conference":{"end_date":"2018-09-26","start_date":"2018-09-24","name":"Open-Access-Tage","location":"Graz, Austria"}},{"date_created":"2019-06-06T12:42:01Z","scopus_import":1,"oa_version":"None","publisher":"Oxford University Press","month":"01","citation":{"mla":"Hausel, Tamás, et al. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218, doi:10.1093/oso/9780198802013.003.0009.","ieee":"T. Hausel, A. Mellit, and D. Pei, “Mirror symmetry with branes by equivariant verlinde formulas,” in Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.","ista":"Hausel T, Mellit A, Pei D. 2018.Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. , 189–218.","apa":"Hausel, T., Mellit, A., & Pei, D. (2018). Mirror symmetry with branes by equivariant verlinde formulas. In Geometry and Physics: Volume I (pp. 189–218). Oxford University Press. https://doi.org/10.1093/oso/9780198802013.003.0009","ama":"Hausel T, Mellit A, Pei D. Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. Oxford University Press; 2018:189-218. doi:10.1093/oso/9780198802013.003.0009","short":"T. Hausel, A. Mellit, D. Pei, in:, Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.","chicago":"Hausel, Tamás, Anton Mellit, and Du Pei. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” In Geometry and Physics: Volume I, 189–218. Oxford University Press, 2018. https://doi.org/10.1093/oso/9780198802013.003.0009."},"publication":"Geometry and Physics: Volume I","date_published":"2018-01-01T00:00:00Z","date_updated":"2021-01-12T08:07:52Z","publication_identifier":{"isbn":["9780198802013","9780191840500"]},"type":"book_chapter","doi":"10.1093/oso/9780198802013.003.0009","abstract":[{"text":"This chapter finds an agreement of equivariant indices of semi-classical homomorphisms between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface. On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs bundles, whose mirror was proposed by Hitchin to be certain even exterior powers of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present. The agreement arises from a mysterious functional equation. This gives strong computational evidence for Hitchin’s proposal.","lang":"eng"}],"publication_status":"published","page":"189-218","department":[{"_id":"TaHa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Hausel, Tamás","first_name":"Tamás"},{"full_name":"Mellit, Anton","first_name":"Anton","last_name":"Mellit","id":"388D3134-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pei, Du","first_name":"Du","last_name":"Pei"}],"title":"Mirror symmetry with branes by equivariant verlinde formulas","quality_controlled":"1","_id":"6525","status":"public","day":"01","year":"2018","language":[{"iso":"eng"}]},{"main_file_link":[{"url":"https://arxiv.org/abs/1605.08767","open_access":"1"}],"date_updated":"2021-01-12T08:09:33Z","external_id":{"arxiv":["1605.08767"]},"publist_id":"7017","date_created":"2018-12-11T11:47:56Z","publisher":"Springer","issue":"1-2","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa":1,"ec_funded":1,"abstract":[{"text":"We consider spectral properties and the edge universality of sparse random matrices, the class of random matrices that includes the adjacency matrices of the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density up to the spectral edges. Under a suitable condition on the sparsity, we also prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations if a deterministic shift of the spectral edge due to the sparsity is included. For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom fluctuations of the second largest eigenvalue when p is much larger than N−2/3 with a deterministic shift of order (Np)−1.","lang":"eng"}],"title":"Local law and Tracy–Widom limit for sparse random matrices","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"690","quality_controlled":"1","citation":{"ieee":"J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer, 2018.","ista":"Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 171(1–2), 543–616.","mla":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616, Springer, 2018, doi:10.1007/s00440-017-0787-8.","chicago":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields. Springer, 2018. https://doi.org/10.1007/s00440-017-0787-8.","apa":"Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8","ama":"Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8","short":"J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018)."},"date_published":"2018-06-14T00:00:00Z","publication":"Probability Theory and Related Fields","oa_version":"Preprint","scopus_import":1,"intvolume":" 171","month":"06","publication_status":"published","type":"journal_article","doi":"10.1007/s00440-017-0787-8","article_number":"543-616","author":[{"first_name":"Jii","full_name":"Lee, Jii","last_name":"Lee"},{"id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli","orcid":"0000-0003-0954-3231","first_name":"Kevin","full_name":"Schnelli, Kevin"}],"volume":171,"department":[{"_id":"LaEr"}],"status":"public","day":"14","language":[{"iso":"eng"}],"year":"2018"},{"title":"Maximum persistency via iterative relaxed inference with graphical models","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"703","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1508.07902","open_access":"1"}],"date_updated":"2021-01-12T08:11:32Z","external_id":{"arxiv":["1508.07902"]},"publist_id":"6992","date_created":"2018-12-11T11:48:01Z","publisher":"IEEE","issue":"7","oa":1,"abstract":[{"text":"We consider the NP-hard problem of MAP-inference for undirected discrete graphical models. We propose a polynomial time and practically efficient algorithm for finding a part of its optimal solution. Specifically, our algorithm marks some labels of the considered graphical model either as (i) optimal, meaning that they belong to all optimal solutions of the inference problem; (ii) non-optimal if they provably do not belong to any solution. With access to an exact solver of a linear programming relaxation to the MAP-inference problem, our algorithm marks the maximal possible (in a specified sense) number of labels. We also present a version of the algorithm, which has access to a suboptimal dual solver only and still can ensure the (non-)optimality for the marked labels, although the overall number of the marked labels may decrease. We propose an efficient implementation, which runs in time comparable to a single run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art results on computational benchmarks from machine learning and computer vision.","lang":"eng"}],"publication_identifier":{"issn":["01628828"]},"author":[{"last_name":"Shekhovtsov","first_name":"Alexander","full_name":"Shekhovtsov, Alexander"},{"last_name":"Swoboda","id":"446560C6-F248-11E8-B48F-1D18A9856A87","full_name":"Swoboda, Paul","first_name":"Paul"},{"last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan","first_name":"Bogdan"}],"volume":40,"department":[{"_id":"VlKo"}],"status":"public","day":"01","year":"2018","language":[{"iso":"eng"}],"citation":{"short":"A. Shekhovtsov, P. Swoboda, B. Savchynskyy, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1668–1682.","ama":"Shekhovtsov A, Swoboda P, Savchynskyy B. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2018;40(7):1668-1682. doi:10.1109/TPAMI.2017.2730884","apa":"Shekhovtsov, A., Swoboda, P., & Savchynskyy, B. (2018). Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2017.2730884","chicago":"Shekhovtsov, Alexander, Paul Swoboda, and Bogdan Savchynskyy. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2017.2730884.","mla":"Shekhovtsov, Alexander, et al. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7, IEEE, 2018, pp. 1668–82, doi:10.1109/TPAMI.2017.2730884.","ista":"Shekhovtsov A, Swoboda P, Savchynskyy B. 2018. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(7), 1668–1682.","ieee":"A. Shekhovtsov, P. Swoboda, and B. Savchynskyy, “Maximum persistency via iterative relaxed inference with graphical models,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7. IEEE, pp. 1668–1682, 2018."},"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","date_published":"2018-07-01T00:00:00Z","oa_version":"Preprint","scopus_import":1,"intvolume":" 40","month":"07","publication_status":"published","page":"1668-1682","type":"journal_article","doi":"10.1109/TPAMI.2017.2730884"},{"ddc":["000"],"abstract":[{"lang":"eng","text":"Training deep learning models has received tremendous research interest recently. In particular, there has been intensive research on reducing the communication cost of training when using multiple computational devices, through reducing the precision of the underlying data representation. Naturally, such methods induce system trade-offs—lowering communication precision could de-crease communication overheads and improve scalability; but, on the other hand, it can also reduce the accuracy of training. In this paper, we study this trade-off space, and ask:Can low-precision communication consistently improve the end-to-end performance of training modern neural networks, with no accuracy loss?From the performance point of view, the answer to this question may appear deceptively easy: compressing communication through low precision should help when the ratio between communication and computation is high. However, this answer is less straightforward when we try to generalize this principle across various neural network architectures (e.g., AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g., EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL), and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is not clear how a realistic realization of all these factors maps to the speed up provided by low-precision communication. In this paper, we conduct an empirical study to answer this question and report the insights."}],"publication_identifier":{"issn":["2367-2005"],"isbn":["9783893180783"]},"oa":1,"conference":{"end_date":"2018-03-29","name":"EDBT: Conference on Extending Database Technology","location":"Vienna, Austria","start_date":"2018-03-26"},"date_created":"2019-11-26T14:19:11Z","publisher":"OpenProceedings","date_updated":"2023-02-23T12:59:17Z","quality_controlled":"1","_id":"7116","file":[{"creator":"dernst","file_id":"7118","relation":"main_file","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-26T14:23:04Z","checksum":"ec979b56abc71016d6e6adfdadbb4afe","file_size":1603204,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_OpenProceedings_Grubic.pdf"}],"title":"Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.5441/002/EDBT.2018.14","type":"conference","article_processing_charge":"No","publication_status":"published","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","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"},"page":"145-156","citation":{"ieee":"D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study,” in Proceedings of the 21st International Conference on Extending Database Technology, Vienna, Austria, 2018, pp. 145–156.","mla":"Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–56, doi:10.5441/002/EDBT.2018.14.","ista":"Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. Proceedings of the 21st International Conference on Extending Database Technology. EDBT: Conference on Extending Database Technology, 145–156.","chicago":"Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” In Proceedings of the 21st International Conference on Extending Database Technology, 145–56. OpenProceedings, 2018. https://doi.org/10.5441/002/EDBT.2018.14.","ama":"Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In: Proceedings of the 21st International Conference on Extending Database Technology. OpenProceedings; 2018:145-156. doi:10.5441/002/EDBT.2018.14","apa":"Grubic, D., Tam, L., Alistarh, D.-A., & Zhang, C. (2018). Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In Proceedings of the 21st International Conference on Extending Database Technology (pp. 145–156). Vienna, Austria: OpenProceedings. https://doi.org/10.5441/002/EDBT.2018.14","short":"D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–156."},"publication":"Proceedings of the 21st International Conference on Extending Database Technology","date_published":"2018-03-26T00:00:00Z","scopus_import":1,"oa_version":"Published Version","month":"03","file_date_updated":"2020-07-14T12:47:49Z","has_accepted_license":"1","status":"public","day":"26","year":"2018","language":[{"iso":"eng"}],"department":[{"_id":"DaAl"}],"author":[{"last_name":"Grubic","full_name":"Grubic, Demjan","first_name":"Demjan"},{"last_name":"Tam","first_name":"Leo","full_name":"Tam, Leo"},{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian"},{"first_name":"Ce","full_name":"Zhang, Ce","last_name":"Zhang"}]},{"oa_version":"Published Version","scopus_import":1,"file_date_updated":"2020-07-14T12:47:57Z","intvolume":" 124","month":"12","citation":{"chicago":"Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), 124:59:1-59:25. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ITCS.2019.59.","short":"K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25.","ama":"Pietrzak KZ. Proofs of catalytic space. In: 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:59:1-59:25. doi:10.4230/LIPICS.ITCS.2019.59","apa":"Pietrzak, K. Z. (2018). Proofs of catalytic space. In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019) (Vol. 124, p. 59:1-59:25). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.59","mla":"Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), vol. 124, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25, doi:10.4230/LIPICS.ITCS.2019.59.","ista":"Pietrzak KZ. 2018. Proofs of catalytic space. 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). ITCS: Innovations in theoretical Computer Science Conference, LIPIcs, vol. 124, 59:1-59:25.","ieee":"K. Z. Pietrzak, “Proofs of catalytic space,” in 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), San Diego, CA, United States, 2018, vol. 124, p. 59:1-59:25."},"publication":"10th Innovations in Theoretical Computer Science Conference (ITCS 2019)","date_published":"2018-12-31T00:00:00Z","article_processing_charge":"No","type":"conference","doi":"10.4230/LIPICS.ITCS.2019.59","publication_status":"published","page":"59:1-59:25","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"KrPi"}],"volume":124,"author":[{"first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"}],"has_accepted_license":"1","status":"public","day":"31","language":[{"iso":"eng"}],"year":"2018","date_created":"2020-01-30T09:16:05Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","conference":{"end_date":"2019-01-12","start_date":"2019-01-10","location":"San Diego, CA, United States","name":"ITCS: Innovations in theoretical Computer Science Conference"},"date_updated":"2021-01-12T08:13:26Z","main_file_link":[{"url":"https://eprint.iacr.org/2018/194","open_access":"1"}],"publication_identifier":{"isbn":["978-3-95977-095-8"],"issn":["1868-8969"]},"ec_funded":1,"abstract":[{"lang":"eng","text":"Proofs of space (PoS) [Dziembowski et al., CRYPTO'15] are proof systems where a prover can convince a verifier that he \"wastes\" disk space. PoS were introduced as a more ecological and economical replacement for proofs of work which are currently used to secure blockchains like Bitcoin. In this work we investigate extensions of PoS which allow the prover to embed useful data into the dedicated space, which later can be recovered. Our first contribution is a security proof for the original PoS from CRYPTO'15 in the random oracle model (the original proof only applied to a restricted class of adversaries which can store a subset of the data an honest prover would store). When this PoS is instantiated with recent constructions of maximally depth robust graphs, our proof implies basically optimal security. As a second contribution we show three different extensions of this PoS where useful data can be embedded into the space required by the prover. Our security proof for the PoS extends (non-trivially) to these constructions. We discuss how some of these variants can be used as proofs of catalytic space (PoCS), a notion we put forward in this work, and which basically is a PoS where most of the space required by the prover can be used to backup useful data. Finally we discuss how one of the extensions is a candidate construction for a proof of replication (PoR), a proof system recently suggested in the Filecoin whitepaper. "}],"ddc":["000"],"project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"oa":1,"file":[{"date_created":"2020-02-04T08:17:52Z","checksum":"5cebb7f7849a3beda898f697d755dd96","file_size":822884,"creator":"dernst","file_id":"7443","date_updated":"2020-07-14T12:47:57Z","relation":"main_file","file_name":"2018_LIPIcs_Pietrzak.pdf","content_type":"application/pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Proofs of catalytic space","quality_controlled":"1","alternative_title":["LIPIcs"],"_id":"7407"},{"month":"09","intvolume":" 4","publisher":"Association for Computing Machinery","date_created":"2019-02-14T13:24:11Z","scopus_import":1,"oa_version":"None","date_published":"2018-09-01T00:00:00Z","publication":"ACM Transactions on Parallel Computing","citation":{"mla":"Alistarh, Dan-Adrian, et al. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing, vol. 4, no. 4, 18, Association for Computing Machinery, 2018, doi:10.1145/3201897.","ieee":"D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “ThreadScan: Automatic and scalable memory reclamation,” ACM Transactions on Parallel Computing, vol. 4, no. 4. Association for Computing Machinery, 2018.","ista":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2018. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 4(4), 18.","short":"D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, ACM Transactions on Parallel Computing 4 (2018).","ama":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 2018;4(4). doi:10.1145/3201897","apa":"Alistarh, D.-A., Leiserson, W., Matveev, A., & Shavit, N. (2018). ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. Association for Computing Machinery. https://doi.org/10.1145/3201897","chicago":"Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing. Association for Computing Machinery, 2018. https://doi.org/10.1145/3201897."},"date_updated":"2023-02-23T13:17:54Z","publication_identifier":{"issn":["2329-4949"]},"abstract":[{"lang":"eng","text":"The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU are either prohibitively expensive or require significant programming expertise to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated.\r\nIn this article, we take a new approach to concurrent memory reclamation. Instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads.\r\nInitial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free."}],"doi":"10.1145/3201897","type":"journal_article","issue":"4","publication_status":"published","related_material":{"record":[{"id":"779","relation":"earlier_version","status":"public"}]},"department":[{"_id":"DaAl"}],"volume":4,"author":[{"first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"},{"last_name":"Leiserson","full_name":"Leiserson, William","first_name":"William"},{"last_name":"Matveev","first_name":"Alexander","full_name":"Matveev, Alexander"},{"first_name":"Nir","full_name":"Shavit, Nir","last_name":"Shavit"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"18","title":"ThreadScan: Automatic and scalable memory reclamation","quality_controlled":"1","_id":"6001","language":[{"iso":"eng"}],"year":"2018","day":"01","status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Polino, Antonio","first_name":"Antonio","last_name":"Polino"},{"last_name":"Pascanu","first_name":"Razvan","full_name":"Pascanu, Razvan"},{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"}],"title":"Model compression via distillation and quantization","department":[{"_id":"DaAl"}],"file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"2018_ICLR_Polino.pdf","date_updated":"2020-07-14T12:48:03Z","relation":"main_file","creator":"dernst","file_id":"7894","date_created":"2020-05-26T13:02:00Z","checksum":"a4336c167978e81891970e4e4517a8c3","file_size":308339}],"_id":"7812","status":"public","language":[{"iso":"eng"}],"year":"2018","day":"01","has_accepted_license":"1","quality_controlled":"1","date_updated":"2023-02-23T13:18:41Z","external_id":{"arxiv":["1802.05668"]},"oa_version":"Published Version","date_created":"2020-05-10T22:00:51Z","scopus_import":1,"file_date_updated":"2020-07-14T12:48:03Z","month":"05","citation":{"chicago":"Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In 6th International Conference on Learning Representations, 2018.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018.","apa":"Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via distillation and quantization. In 6th International Conference on Learning Representations. Vancouver, Canada.","ieee":"A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018.","mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 6th International Conference on Learning Representations, 2018.","ista":"Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations."},"conference":{"location":"Vancouver, Canada","name":"ICLR: International Conference on Learning Representations","start_date":"2018-04-30","end_date":"2018-05-03"},"publication":"6th International Conference on Learning Representations","date_published":"2018-05-01T00:00:00Z","oa":1,"publication_status":"published","article_processing_charge":"No","type":"conference","ddc":["000"],"abstract":[{"text":"Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices.","lang":"eng"}]},{"article_processing_charge":"No","abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex."}],"doi":"10.1101/494088","ec_funded":1,"type":"preprint","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"grant_number":"M02416","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425"}],"oa":1,"publication_status":"submitted","publisher":"Cold Spring Harbor Laboratory","month":"12","date_created":"2020-09-21T12:01:50Z","oa_version":"Preprint","publication":"bioRxiv","date_published":"2018-12-13T00:00:00Z","citation":{"ieee":"A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor Laboratory.","mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/494088.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, 10.1101/494088.","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/494088","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.).","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088."},"date_updated":"2021-01-12T08:20:00Z","acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","main_file_link":[{"url":"https://doi.org/10.1101/494088","open_access":"1"}],"_id":"8547","language":[{"iso":"eng"}],"day":"13","year":"2018","status":"public","department":[{"_id":"SiHi"}],"author":[{"last_name":"Llorca","first_name":"Alfredo","full_name":"Llorca, Alfredo"},{"full_name":"Ciceri, Gabriele","first_name":"Gabriele","last_name":"Ciceri"},{"first_name":"Robert J","full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie"},{"full_name":"Wong, Fong K.","first_name":"Fong K.","last_name":"Wong"},{"last_name":"Diana","full_name":"Diana, Giovanni","first_name":"Giovanni"},{"last_name":"Serafeimidou","first_name":"Eleni","full_name":"Serafeimidou, Eleni"},{"first_name":"Marian","full_name":"Fernández-Otero, Marian","last_name":"Fernández-Otero"},{"full_name":"Streicher, Carmen","first_name":"Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Arnold, Sebastian J.","first_name":"Sebastian J.","last_name":"Arnold"},{"full_name":"Meyer, Martin","first_name":"Martin","last_name":"Meyer"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon"},{"full_name":"Maravall, Miguel","first_name":"Miguel","last_name":"Maravall"},{"last_name":"Marín","first_name":"Oscar","full_name":"Marín, Oscar"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture"},{"status":"public","year":"2018","day":"20","language":[{"iso":"eng"}],"has_accepted_license":"1","editor":[{"full_name":"Lohstroh, Marten","first_name":"Marten","last_name":"Lohstroh"},{"last_name":"Derler","first_name":"Patricia","full_name":"Derler, Patricia"},{"last_name":"Sirjani","full_name":"Sirjani, Marjan","first_name":"Marjan"}],"author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","first_name":"Jan"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"volume":10760,"publication_status":"published","page":"143 - 161","doi":"10.1007/978-3-319-95246-8_9","type":"book_chapter","oa_version":"Submitted Version","scopus_import":1,"file_date_updated":"2020-07-14T12:48:14Z","month":"07","intvolume":" 10760","citation":{"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.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","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","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","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","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.","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."},"date_published":"2018-07-20T00:00:00Z","publication":"Principles of Modeling","alternative_title":["LNCS"],"_id":"86","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Computing average response time","file":[{"relation":"main_file","date_updated":"2020-07-14T12:48:14Z","file_id":"7053","creator":"dernst","file_size":516307,"date_created":"2019-11-19T08:22:18Z","checksum":"9995c6ce6957333baf616fc4f20be597","access_level":"open_access","content_type":"application/pdf","file_name":"2018_PrinciplesModeling_Chatterjee.pdf"}],"oa":1,"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"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."}],"ddc":["000"],"date_updated":"2021-01-12T08:20:14Z","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.","date_created":"2018-12-11T11:44:33Z","publisher":"Springer","publist_id":"7968"},{"year":"2018","language":[{"iso":"eng"}],"day":"30","status":"public","article_type":"letter_note","author":[{"first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"}],"volume":4,"department":[{"_id":"JoDa"}],"page":"11","publication_status":"published","type":"journal_article","doi":"10.20388/omp2018.00s1.001","article_processing_charge":"No","date_published":"2018-06-30T00:00:00Z","publication":"Opera Medica et Physiologica","citation":{"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.","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.","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.","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 2018;4(S1):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","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11."},"intvolume":" 4","month":"06","scopus_import":"1","oa_version":"Published Version","alternative_title":["Molecular and cellular neuroscience"],"_id":"9229","quality_controlled":"1","title":"Diffraction-unlimited optical imaging for synaptic physiology","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"S1","oa":1,"publication_identifier":{"issn":["2500-2287"],"eissn":["2500-2295"]},"main_file_link":[{"url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience","open_access":"1"}],"date_updated":"2021-12-03T07:31:05Z","publisher":"Lobachevsky State University of Nizhny Novgorod","date_created":"2021-03-07T23:01:25Z"},{"date_published":"2018-08-01T00:00:00Z","citation":{"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.","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.","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","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018."},"month":"08","file_date_updated":"2020-07-14T12:47:15Z","intvolume":" 117","oa_version":"Published Version","scopus_import":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","type":"conference","doi":"10.4230/LIPICS.MFCS.2018.23","article_processing_charge":"No","article_number":"23","author":[{"last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy","first_name":"Guy","orcid":"0000-0001-5588-8287"},{"last_name":"Guha","full_name":"Guha, Shibashis","first_name":"Shibashis"},{"last_name":"Kupferman","first_name":"Orna","full_name":"Kupferman, Orna"}],"volume":117,"department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"day":"01","year":"2018","status":"public","has_accepted_license":"1","date_updated":"2023-02-23T14:02:58Z","conference":{"end_date":"2018-08-31","start_date":"2018-08-27","location":"Liverpool, United Kingdom","name":"MFCS: Mathematical Foundations of Computer Science"},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_created":"2019-02-14T14:12:09Z","related_material":{"record":[{"id":"963","relation":"earlier_version","status":"public"}]},"oa":1,"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory","_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"ddc":["000"],"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"}],"publication_identifier":{"issn":["1868-8969"]},"title":"Timed network games with clocks","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","file_id":"6007","date_updated":"2020-07-14T12:47:15Z","relation":"main_file","date_created":"2019-02-14T14:22:04Z","checksum":"41ab2ae9b63f5eb49fa995250c0ba128","file_size":542889,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_LIPIcs_Avni.pdf"}],"alternative_title":["LIPIcs"],"_id":"6005","quality_controlled":"1"},{"quality_controlled":"1","_id":"315","file":[{"file_size":6968201,"date_created":"2019-01-22T08:30:03Z","checksum":"908c52751bba30c55ed36789e5e4c84d","relation":"main_file","date_updated":"2020-07-14T12:46:01Z","file_id":"5870","creator":"dernst","file_name":"2017_PLOS_Polechova.pdf","access_level":"open_access","content_type":"application/pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Is the sky the limit? On the expansion threshold of a species’ range","publication_identifier":{"issn":["15449173"]},"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"}],"ddc":["576"],"oa":1,"related_material":{"record":[{"status":"public","relation":"research_data","id":"9839"}]},"issue":"6","date_created":"2018-12-11T11:45:46Z","publisher":"Public Library of Science","publist_id":"7550","date_updated":"2023-02-23T14:10:16Z","has_accepted_license":"1","status":"public","day":"15","language":[{"iso":"eng"}],"year":"2018","department":[{"_id":"NiBa"}],"volume":16,"author":[{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112"}],"article_number":"e2005372","type":"journal_article","doi":"10.1371/journal.pbio.2005372","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","scopus_import":1,"month":"06","file_date_updated":"2020-07-14T12:46:01Z","intvolume":" 16","citation":{"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.","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","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","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.","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.","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372."},"date_published":"2018-06-15T00:00:00Z","publication":"PLoS Biology"},{"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.","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","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","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.","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.","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.","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."},"publication":"Proceedings of the National Academy of Sciences","date_published":"2018-05-15T00:00:00Z","oa_version":"Published Version","scopus_import":"1","file_date_updated":"2021-06-07T06:16:38Z","intvolume":" 115","month":"05","publication_status":"published","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","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"},"page":"E4720-E4729","type":"journal_article","doi":"10.1073/pnas.1713333115","article_processing_charge":"No","author":[{"first_name":"Jennifer M.","full_name":"Frost, Jennifer M.","last_name":"Frost"},{"full_name":"Kim, M. Yvonne","first_name":"M. Yvonne","last_name":"Kim"},{"full_name":"Park, Guen Tae","first_name":"Guen Tae","last_name":"Park"},{"last_name":"Hsieh","full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung"},{"last_name":"Nakamura","full_name":"Nakamura, Miyuki","first_name":"Miyuki"},{"last_name":"Lin","full_name":"Lin, Samuel J. H.","first_name":"Samuel J. H."},{"last_name":"Yoo","first_name":"Hyunjin","full_name":"Yoo, Hyunjin"},{"full_name":"Choi, Jaemyung","first_name":"Jaemyung","last_name":"Choi"},{"first_name":"Yoko","full_name":"Ikeda, Yoko","last_name":"Ikeda"},{"first_name":"Tetsu","full_name":"Kinoshita, Tetsu","last_name":"Kinoshita"},{"first_name":"Yeonhee","full_name":"Choi, Yeonhee","last_name":"Choi"},{"first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."}],"volume":115,"pmid":1,"department":[{"_id":"DaZi"}],"status":"public","language":[{"iso":"eng"}],"year":"2018","day":"15","article_type":"original","has_accepted_license":"1","date_updated":"2021-12-14T07:53:40Z","external_id":{"pmid":["29712855"]},"extern":"1","date_created":"2021-06-07T06:11:28Z","publisher":"National Academy of Sciences","related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/187674 "}]},"issue":"20","oa":1,"abstract":[{"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.","lang":"eng"}],"ddc":["580"],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"title":"FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_size":3045260,"checksum":"810260dc0e3cc3033e15c19ad0dc123e","date_created":"2021-06-07T06:16:38Z","relation":"main_file","date_updated":"2021-06-07T06:16:38Z","file_id":"9472","creator":"asandaue","file_name":"2018_PNAS_Frost.pdf","access_level":"open_access","success":1,"content_type":"application/pdf"}],"_id":"9471","quality_controlled":"1","keyword":["Multidisciplinary"]},{"quality_controlled":"1","alternative_title":["LIPIcs"],"_id":"186","title":"The ℤ2-Genus of Kuratowski minors","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"}],"related_material":{"record":[{"id":"11593","status":"public","relation":"later_version"}]},"project":[{"grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa":1,"publist_id":"7734","conference":{"end_date":"2018-06-14","start_date":"2018-06-11","location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry"},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_created":"2018-12-11T11:45:05Z","main_file_link":[{"url":"https://arxiv.org/abs/1803.05085","open_access":"1"}],"external_id":{"arxiv":["1803.05085"]},"date_updated":"2023-08-14T12:43:51Z","day":"11","language":[{"iso":"eng"}],"year":"2018","status":"public","volume":99,"department":[{"_id":"UlWa"}],"author":[{"last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav","first_name":"Radoslav","orcid":"0000-0001-8485-1774"},{"first_name":"Jan","full_name":"Kynčl, Jan","last_name":"Kynčl"}],"type":"conference","doi":"10.4230/LIPIcs.SoCG.2018.40","article_processing_charge":"No","page":"40.1 - 40.14","publication_status":"published","date_published":"2018-06-11T00:00:00Z","citation":{"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","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14.","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.","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.","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."},"month":"06","intvolume":" 99","oa_version":"Submitted Version","scopus_import":"1"},{"alternative_title":["LNCS"],"_id":"433","quality_controlled":"1","title":"Thrackles: An improved upper bound","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"5857","relation":"later_version","status":"public"}]},"oa":1,"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."}],"main_file_link":[{"url":"https://arxiv.org/abs/1708.08037","open_access":"1"}],"date_updated":"2023-08-24T14:39:32Z","external_id":{"arxiv":["1708.08037"]},"conference":{"end_date":"2017-09-27","location":"Boston, MA, United States","name":"GD 2017: Graph Drawing and Network Visualization","start_date":"201-09-25"},"publist_id":"7390","date_created":"2018-12-11T11:46:27Z","publisher":"Springer","status":"public","language":[{"iso":"eng"}],"year":"2018","day":"21","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"last_name":"Pach","first_name":"János","full_name":"Pach, János"}],"volume":10692,"department":[{"_id":"UlWa"}],"publication_status":"published","page":"160 - 166","type":"conference","doi":"10.1007/978-3-319-73915-1_14","citation":{"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.","ista":"Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph Drawing and Network Visualization, LNCS, vol. 10692, 160–166.","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.","short":"R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166.","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","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."},"date_published":"2018-01-21T00:00:00Z","scopus_import":1,"oa_version":"Submitted Version","intvolume":" 10692","month":"01"},{"article_processing_charge":"No","abstract":[{"lang":"eng","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."}],"type":"research_data_reference","doi":"10.5061/dryad.72cg113","oa":1,"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6095"}]},"publisher":"Dryad","month":"10","date_created":"2021-08-09T12:46:39Z","oa_version":"Published Version","date_published":"2018-10-09T00:00:00Z","citation":{"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.","ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","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.","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).","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","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."},"date_updated":"2023-08-24T14:50:26Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.72cg113"}],"_id":"9837","day":"09","year":"2018","status":"public","department":[{"_id":"NiBa"}],"author":[{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Pragya","full_name":"Chaube, Pragya","last_name":"Chaube"},{"last_name":"Morales","first_name":"Hernán E.","full_name":"Morales, Hernán E."},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"full_name":"Lemmon, Alan R.","first_name":"Alan R.","last_name":"Lemmon"},{"last_name":"Lemmon","first_name":"Emily M.","full_name":"Lemmon, Emily M."},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"first_name":"Marina","full_name":"Panova, Marina","last_name":"Panova"},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Westram, Anja M","first_name":"Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes"},{"department":[{"_id":"VlKo"}],"volume":16,"editor":[{"full_name":"Czelakowski, J","first_name":"J","last_name":"Czelakowski"}],"author":[{"id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","last_name":"Kazda","first_name":"Alexandr","full_name":"Kazda, Alexandr"},{"last_name":"Kozik","first_name":"Marcin","full_name":"Kozik, Marcin"},{"full_name":"McKenzie, Ralph","first_name":"Ralph","last_name":"McKenzie"},{"last_name":"Moore","full_name":"Moore, Matthew","first_name":"Matthew"}],"status":"public","language":[{"iso":"eng"}],"day":"21","year":"2018","oa_version":"Preprint","scopus_import":"1","intvolume":" 16","month":"03","citation":{"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","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.","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.","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.","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.","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."},"publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","date_published":"2018-03-21T00:00:00Z","article_processing_charge":"No","doi":"10.1007/978-3-319-74772-9_7","type":"book_chapter","series_title":"OCTR","publication_status":"published","page":"203-220","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Absorption and directed Jónsson terms","quality_controlled":"1","_id":"10864","date_created":"2022-03-18T10:30:32Z","publisher":"Springer Nature","date_updated":"2023-09-05T15:37:18Z","external_id":{"arxiv":["1502.01072"]},"place":"Cham","main_file_link":[{"url":"https://arxiv.org/abs/1502.01072","open_access":"1"}],"acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","publication_identifier":{"eissn":["2211-2766"],"isbn":["9783319747712"],"eisbn":["9783319747729"],"issn":["2211-2758"]},"abstract":[{"lang":"eng","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."}],"oa":1},{"citation":{"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.","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.","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.","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","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","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."},"date_published":"2018-06-11T00:00:00Z","oa_version":"Published Version","scopus_import":1,"file_date_updated":"2020-07-14T12:45:18Z","intvolume":" 99","month":"06","doi":"10.4230/LIPIcs.SoCG.2018.41","type":"conference","publication_status":"published","page":"41:1 - 41:16","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":99,"department":[{"_id":"UlWa"}],"author":[{"full_name":"Goaoc, Xavier","first_name":"Xavier","last_name":"Goaoc"},{"last_name":"Paták","first_name":"Pavel","full_name":"Paták, Pavel"},{"first_name":"Zuzana","full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova"},{"id":"38AC689C-F248-11E8-B48F-1D18A9856A87","last_name":"Tancer","first_name":"Martin","full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714"},{"full_name":"Wagner, Uli","first_name":"Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","status":"public","year":"2018","language":[{"iso":"eng"}],"day":"11","conference":{"end_date":"2018-06-14","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary"},"publist_id":"7736","date_created":"2018-12-11T11:45:04Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration.","date_updated":"2023-09-06T11:10:57Z","ddc":["516","000"],"abstract":[{"lang":"eng","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."}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"7108"}]},"oa":1,"file":[{"file_name":"2018_LIPIcs_Goaoc.pdf","content_type":"application/pdf","access_level":"open_access","file_size":718414,"date_created":"2018-12-17T16:35:02Z","checksum":"d12bdd60f04a57307867704b5f930afd","file_id":"5725","creator":"dernst","relation":"main_file","date_updated":"2020-07-14T12:45:18Z"}],"title":"Shellability is NP-complete","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","_id":"184","alternative_title":["Leibniz International Proceedings in Information, LIPIcs"]},{"quality_controlled":"1","alternative_title":["LIPIcs"],"_id":"285","file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"2018_LIPIcs_Huszar.pdf","file_id":"5713","creator":"dernst","relation":"main_file","date_updated":"2020-07-14T12:45:51Z","file_size":642522,"date_created":"2018-12-17T15:32:38Z","checksum":"530d084116778135d5bffaa317479cac"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"On the treewidth of triangulated 3-manifolds","publication_identifier":{"issn":["18688969"]},"abstract":[{"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)).","lang":"eng"}],"ddc":["516","000"],"oa":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"7093"}]},"date_created":"2018-12-11T11:45:37Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","conference":{"end_date":"2018-06-14","location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry","start_date":"2018-06-11"},"publist_id":"7614","date_updated":"2023-09-06T11:13:41Z","external_id":{"arxiv":["1712.00434"]},"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).","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"year":"2018","day":"01","department":[{"_id":"UlWa"}],"volume":99,"author":[{"full_name":"Huszár, Kristóf","first_name":"Kristóf","orcid":"0000-0002-5445-5057","last_name":"Huszár","id":"33C26278-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jonathan","full_name":"Spreer, Jonathan","last_name":"Spreer"},{"last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","first_name":"Uli","orcid":"0000-0002-1494-0568"}],"article_number":"46","article_processing_charge":"No","doi":"10.4230/LIPIcs.SoCG.2018.46","type":"conference","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":1,"oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:45:51Z","month":"06","intvolume":" 99","citation":{"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.","ista":"Huszár K, Spreer J, Wagner U. 2018. On the treewidth of triangulated 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 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.","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","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","short":"K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","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."},"date_published":"2018-06-01T00:00:00Z"},{"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7181"}]},"oa":1,"abstract":[{"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).","lang":"eng"}],"ddc":["570"],"type":"research_data_reference","doi":"10.5281/ZENODO.2025846","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3271452","open_access":"1"}],"date_updated":"2023-09-06T14:32:51Z","date_published":"2018-12-07T00:00:00Z","citation":{"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.","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.","ieee":"E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","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","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","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."},"month":"12","publisher":"Zenodo","date_created":"2023-05-23T16:08:20Z","oa_version":"Published Version","day":"07","year":"2018","status":"public","_id":"13059","title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","author":[{"full_name":"Garriga, Edgar","first_name":"Edgar","last_name":"Garriga"},{"first_name":"Paolo","full_name":"di Tommaso, Paolo","last_name":"di Tommaso"},{"last_name":"Magis","first_name":"Cedrik","full_name":"Magis, Cedrik"},{"last_name":"Erb","full_name":"Erb, Ionas","first_name":"Ionas"},{"last_name":"Mansouri","first_name":"Leila","full_name":"Mansouri, Leila"},{"last_name":"Baltzis","full_name":"Baltzis, Athanasios","first_name":"Athanasios"},{"last_name":"Laayouni","full_name":"Laayouni, Hafid","first_name":"Hafid"},{"orcid":"0000-0001-8243-4694","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov"},{"first_name":"Evan","full_name":"Floden, Evan","last_name":"Floden"},{"last_name":"Notredame","first_name":"Cedric","full_name":"Notredame, Cedric"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"FyKo"}]},{"publication_status":"published","page":"77","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","type":"dissertation","doi":"10.15479/AT:ISTA:th_1033","oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:35Z","month":"07","citation":{"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.","short":"H. Watzinger, Ge Hut Wires - from Growth to Hole Spin Resonance, Institute of Science and Technology Austria, 2018.","ama":"Watzinger H. Ge hut wires - from growth to hole spin resonance. 2018. doi:10.15479/AT:ISTA:th_1033","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","ista":"Watzinger H. 2018. Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria.","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."},"date_published":"2018-07-30T00:00:00Z","status":"public","language":[{"iso":"eng"}],"year":"2018","day":"30","pubrep_id":"1033","has_accepted_license":"1","author":[{"first_name":"Hannes","full_name":"Watzinger, Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","last_name":"Watzinger"}],"department":[{"_id":"GeKa"}],"supervisor":[{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","first_name":"Georgios","orcid":"0000-0001-8342-202X"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"abstract":[{"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.","lang":"eng"}],"ddc":["530"],"date_updated":"2023-09-07T12:27:43Z","date_created":"2018-12-11T11:44:21Z","publisher":"Institute of Science and Technology Austria","publist_id":"8005","degree_awarded":"PhD","_id":"49","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Ge hut wires - from growth to hole spin resonance","file":[{"file_name":"2018_Thesis_Watzinger.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2019-04-09T07:13:28Z","checksum":"b653b5216251f938ddbeafd1de88667c","file_size":85539748,"date_updated":"2020-07-14T12:46:35Z","relation":"main_file","creator":"dernst","file_id":"6249"},{"content_type":"application/zip","access_level":"closed","file_name":"2018_Thesis_Watzinger_source.zip","creator":"dernst","file_id":"6250","relation":"source_file","date_updated":"2020-07-14T12:46:35Z","date_created":"2019-04-09T07:13:27Z","checksum":"39bcf8de7ac5b1bb516b11ce2f966785","file_size":21830697}]},{"status":"public","year":"2018","day":"11","language":[{"iso":"eng"}],"pubrep_id":"1026","has_accepted_license":"1","author":[{"first_name":"Mabel","full_name":"Iglesias Ham, Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","last_name":"Iglesias Ham"}],"department":[{"_id":"HeEd"}],"supervisor":[{"orcid":"0000-0002-9823-6833","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"}],"publication_status":"published","page":"171","article_processing_charge":"No","type":"dissertation","doi":"10.15479/AT:ISTA:th_1026","oa_version":"Published Version","month":"06","file_date_updated":"2020-07-14T12:45:24Z","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.","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.","ama":"Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026","apa":"Iglesias Ham, M. (2018). Multiple covers with balls. Institute of Science and Technology Austria. https://doi.org/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."},"date_published":"2018-06-11T00:00:00Z","degree_awarded":"PhD","_id":"201","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Multiple covers with balls","file":[{"content_type":"application/zip","access_level":"closed","file_name":"IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip","file_id":"5918","creator":"kschuh","date_updated":"2020-07-14T12:45:24Z","relation":"source_file","file_size":11827713,"date_created":"2019-02-05T07:43:31Z","checksum":"dd699303623e96d1478a6ae07210dd05"},{"access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf","relation":"main_file","date_updated":"2020-07-14T12:45:24Z","creator":"kschuh","file_id":"5919","date_created":"2019-02-05T07:43:45Z","checksum":"ba163849a190d2b41d66fef0e4983294","file_size":4783846}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"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."}],"ddc":["514","516"],"date_updated":"2023-09-07T12:25:32Z","date_created":"2018-12-11T11:45:10Z","publisher":"Institute of Science and Technology Austria","publist_id":"7712"},{"publist_id":"7986","publisher":"Institute of Science and Technology Austria","date_created":"2018-12-11T11:44:27Z","date_updated":"2023-09-07T12:29:07Z","abstract":[{"lang":"eng","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."}],"ddc":["004","519"],"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"oa":1,"project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"2018_Thesis_Zimin.pdf","relation":"main_file","date_updated":"2020-07-14T12:47:40Z","file_id":"6253","creator":"dernst","file_size":1036137,"checksum":"e849dd40a915e4d6c5572b51b517f098","date_created":"2019-04-09T07:32:47Z"},{"file_name":"2018_Thesis_Zimin_Source.zip","content_type":"application/zip","access_level":"closed","checksum":"da092153cec55c97461bd53c45c5d139","date_created":"2019-04-09T07:32:47Z","file_size":637490,"creator":"dernst","file_id":"6254","relation":"source_file","date_updated":"2020-07-14T12:47:40Z"}],"title":"Learning from dependent data","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","degree_awarded":"PhD","_id":"68","alternative_title":["ISTA Thesis"],"date_published":"2018-09-01T00:00:00Z","citation":{"ieee":"A. Zimin, “Learning from dependent data,” Institute of Science and Technology Austria, 2018.","ista":"Zimin A. 2018. Learning from dependent data. Institute of Science and Technology Austria.","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.","apa":"Zimin, A. (2018). Learning from dependent data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH1048","ama":"Zimin A. Learning from dependent data. 2018. doi:10.15479/AT:ISTA:TH1048","chicago":"Zimin, Alexander. “Learning from Dependent Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH1048."},"month":"09","file_date_updated":"2020-07-14T12:47:40Z","oa_version":"Published Version","doi":"10.15479/AT:ISTA:TH1048","type":"dissertation","article_processing_charge":"No","page":"92","publication_status":"published","supervisor":[{"last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887"}],"department":[{"_id":"ChLa"}],"author":[{"id":"37099E9C-F248-11E8-B48F-1D18A9856A87","last_name":"Zimin","first_name":"Alexander","full_name":"Zimin, Alexander"}],"has_accepted_license":"1","pubrep_id":"1048","language":[{"iso":"eng"}],"day":"01","year":"2018","status":"public"},{"page":"59","publication_status":"published","doi":"10.15479/AT:ISTA:TH_1046","type":"dissertation","article_processing_charge":"No","date_published":"2018-09-05T00:00:00Z","citation":{"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.","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.","short":"H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018.","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","ama":"Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:10.15479/AT:ISTA:TH_1046"},"file_date_updated":"2020-07-14T12:48:11Z","month":"09","oa_version":"Published Version","day":"05","year":"2018","language":[{"iso":"eng"}],"status":"public","pubrep_id":"1046","has_accepted_license":"1","author":[{"id":"40297222-F248-11E8-B48F-1D18A9856A87","last_name":"Abusalah","first_name":"Hamza M","full_name":"Abusalah, Hamza M"}],"supervisor":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"}],"department":[{"_id":"KrPi"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1229"},{"id":"1235","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"1236"},{"id":"559","relation":"part_of_dissertation","status":"public"}]},"oa":1,"project":[{"call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","grant_number":"259668"},{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"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"}],"ddc":["004"],"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-07T12:30:23Z","publist_id":"7971","publisher":"Institute of Science and Technology Austria","date_created":"2018-12-11T11:44:32Z","_id":"83","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","title":"Proof systems for sustainable decentralized cryptocurrencies","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"2018_Thesis_Abusalah.pdf","file_id":"6245","creator":"dernst","relation":"main_file","date_updated":"2020-07-14T12:48:11Z","file_size":876241,"date_created":"2019-04-09T06:43:41Z","checksum":"c4b5f7d111755d1396787f41886fc674"},{"access_level":"closed","content_type":"application/x-gzip","file_name":"2018_Thesis_Abusalah_source.tar.gz","date_updated":"2020-07-14T12:48:11Z","relation":"source_file","file_id":"6246","creator":"dernst","file_size":2029190,"date_created":"2019-04-09T06:43:41Z","checksum":"0f382ac56b471c48fd907d63eb87dafe"}]},{"degree_awarded":"PhD","_id":"197","alternative_title":["ISTA Thesis"],"file":[{"date_created":"2018-12-12T10:14:57Z","checksum":"bc678e02468d8ebc39dc7267dfb0a1c4","file_size":12918758,"creator":"system","file_id":"5113","relation":"main_file","date_updated":"2020-07-14T12:45:22Z","file_name":"IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf","content_type":"application/pdf","access_level":"open_access"},{"file_name":"2018_Thesis_Kolesnikov_source.zip","access_level":"closed","content_type":"application/zip","file_size":55973760,"checksum":"bc66973b086da5a043f1162dcfb1fde4","date_created":"2019-04-05T09:34:49Z","date_updated":"2020-07-14T12:45:22Z","relation":"source_file","file_id":"6225","creator":"dernst"}],"title":"Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"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.","lang":"eng"}],"ddc":["004"],"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"oa":1,"project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publist_id":"7718","publisher":"Institute of Science and Technology Austria","date_created":"2018-12-11T11:45:09Z","acknowledgement":"I also gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research.","date_updated":"2023-09-07T12:51:46Z","has_accepted_license":"1","pubrep_id":"1021","year":"2018","day":"25","language":[{"iso":"eng"}],"status":"public","supervisor":[{"full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"ChLa"}],"author":[{"last_name":"Kolesnikov","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander","first_name":"Alexander"}],"doi":"10.15479/AT:ISTA:th_1021","type":"dissertation","article_processing_charge":"No","page":"113","publication_status":"published","date_published":"2018-05-25T00:00:00Z","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.","short":"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","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.","ieee":"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."},"file_date_updated":"2020-07-14T12:45:22Z","month":"05","oa_version":"Published Version"},{"date_updated":"2023-09-07T13:10:36Z","date_created":"2019-08-08T06:47:40Z","publisher":"Springer","related_material":{"record":[{"id":"6681","status":"public","relation":"dissertation_contains"}]},"issue":"3-4","project":[{"name":"Robust invariants of Nonlinear Systems","grant_number":"M01980","call_identifier":"FWF","_id":"25F8B9BC-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"oa":1,"abstract":[{"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) .","lang":"eng"}],"ddc":["514"],"publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"title":"Computing simplicial representatives of homotopy group elements","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","date_updated":"2020-07-14T12:47:40Z","creator":"dernst","file_id":"6775","date_created":"2019-08-08T06:55:21Z","checksum":"cf9e7fcd2a113dd4828774fc75cdb7e8","file_size":1056278,"access_level":"open_access","content_type":"application/pdf","file_name":"2018_JourAppliedComputTopology_Filakovsky.pdf"}],"_id":"6774","quality_controlled":"1","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.","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","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","short":"M. Filakovský, P. Franek, U. Wagner, S.Y. Zhechev, Journal of Applied and Computational Topology 2 (2018) 177–231.","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.","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.","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."},"date_published":"2018-12-01T00:00:00Z","publication":"Journal of Applied and Computational Topology","oa_version":"Published Version","intvolume":" 2","file_date_updated":"2020-07-14T12:47:40Z","month":"12","publication_status":"published","page":"177-231","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1007/s41468-018-0021-5","type":"journal_article","author":[{"last_name":"Filakovský","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","full_name":"Filakovský, Marek","first_name":"Marek"},{"last_name":"Franek","id":"473294AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8878-8397","full_name":"Franek, Peter","first_name":"Peter"},{"last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","first_name":"Uli","orcid":"0000-0002-1494-0568"},{"first_name":"Stephan Y","full_name":"Zhechev, Stephan Y","id":"3AA52972-F248-11E8-B48F-1D18A9856A87","last_name":"Zhechev"}],"volume":2,"department":[{"_id":"UlWa"}],"status":"public","day":"01","language":[{"iso":"eng"}],"year":"2018","article_type":"original","has_accepted_license":"1"},{"related_material":{"record":[{"id":"6426","status":"public","relation":"earlier_version"},{"status":"public","relation":"dissertation_contains","id":"8332"}]},"project":[{"call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S11402-N23"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"oa":1,"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."}],"ddc":["000"],"publication_identifier":{"issn":["18688969"]},"date_updated":"2023-09-07T13:18:00Z","conference":{"end_date":"2018-09-07","location":"Beijing, China","name":"CONCUR: International Conference on Concurrency Theory","start_date":"2018-09-04"},"publist_id":"7790","date_created":"2018-12-11T11:44:48Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"],"_id":"133","quality_controlled":"1","title":"Synchronizing the asynchronous","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-853-v2+2_concur2018.pdf","file_id":"5368","creator":"system","relation":"main_file","date_updated":"2020-07-14T12:44:44Z","file_size":745438,"checksum":"c90895f4c5fafc18ddc54d1c8848077e","date_created":"2018-12-12T10:18:46Z"}],"publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.4230/LIPIcs.CONCUR.2018.21","type":"conference","citation":{"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","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","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","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.","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.","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.","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","oa_version":"Published Version","scopus_import":1,"intvolume":" 118","month":"08","file_date_updated":"2020-07-14T12:44:44Z","status":"public","language":[{"iso":"eng"}],"year":"2018","day":"13","pubrep_id":"1039","has_accepted_license":"1","article_number":"21","author":[{"orcid":"0000-0001-7745-9117","first_name":"Bernhard","full_name":"Kragl, Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl"},{"first_name":"Shaz","full_name":"Qadeer, Shaz","last_name":"Qadeer"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"volume":118,"department":[{"_id":"ToHe"}]},{"date_published":"2018-06-11T00:00:00Z","citation":{"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","short":"H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","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.","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.","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."},"file_date_updated":"2020-07-14T12:45:19Z","month":"06","intvolume":" 99","scopus_import":1,"oa_version":"Published Version","type":"conference","doi":"10.4230/LIPIcs.SoCG.2018.34","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","volume":99,"department":[{"_id":"HeEd"}],"article_number":"34","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"orcid":"0000-0002-8882-5116","first_name":"Georg F","full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"year":"2018","day":"11","status":"public","publist_id":"7732","conference":{"end_date":"2018-06-14","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary"},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","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).","date_updated":"2023-09-07T13:29:00Z","abstract":[{"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. ","lang":"eng"}],"ddc":["516"],"related_material":{"record":[{"status":"public","relation":"later_version","id":"9317"},{"id":"9056","status":"public","relation":"dissertation_contains"}]},"project":[{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"oa":1,"file":[{"file_name":"2018_LIPIcs_Edelsbrunner_Osang.pdf","content_type":"application/pdf","access_level":"open_access","file_size":528018,"checksum":"d8c0533ad0018eb4ed1077475eb8fc18","date_created":"2018-12-18T09:27:22Z","file_id":"5738","creator":"dernst","date_updated":"2020-07-14T12:45:19Z","relation":"main_file"}],"title":"The multi-cover persistence of Euclidean balls","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","alternative_title":["LIPIcs"],"_id":"187"},{"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"page":"55 - 64","publication_status":"published","doi":"10.1007/s10711-017-0265-6","type":"journal_article","article_processing_charge":"Yes (via OA deal)","date_published":"2018-06-01T00:00:00Z","publication":"Geometriae Dedicata","citation":{"ieee":"A. Akopyan, “3-Webs generated by confocal conics and circles,” Geometriae Dedicata, vol. 194, no. 1. Springer, pp. 55–64, 2018.","ista":"Akopyan A. 2018. 3-Webs generated by confocal conics and circles. Geometriae Dedicata. 194(1), 55–64.","mla":"Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae Dedicata, vol. 194, no. 1, Springer, 2018, pp. 55–64, doi:10.1007/s10711-017-0265-6.","short":"A. Akopyan, Geometriae Dedicata 194 (2018) 55–64.","apa":"Akopyan, A. (2018). 3-Webs generated by confocal conics and circles. Geometriae Dedicata. Springer. https://doi.org/10.1007/s10711-017-0265-6","ama":"Akopyan A. 3-Webs generated by confocal conics and circles. Geometriae Dedicata. 2018;194(1):55-64. doi:10.1007/s10711-017-0265-6","chicago":"Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae Dedicata. Springer, 2018. https://doi.org/10.1007/s10711-017-0265-6."},"month":"06","file_date_updated":"2020-07-14T12:47:44Z","intvolume":" 194","scopus_import":"1","oa_version":"Published Version","day":"01","language":[{"iso":"eng"}],"year":"2018","status":"public","article_type":"original","has_accepted_license":"1","author":[{"orcid":"0000-0002-2548-617X","first_name":"Arseniy","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan"}],"volume":194,"department":[{"_id":"HeEd"}],"issue":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"oa":1,"abstract":[{"text":"We consider families of confocal conics and two pencils of Apollonian circles having the same foci. We will show that these families of curves generate trivial 3-webs and find the exact formulas describing them.","lang":"eng"}],"ddc":["510"],"ec_funded":1,"external_id":{"isi":["000431418800004"]},"date_updated":"2023-09-08T11:40:29Z","publist_id":"7014","publisher":"Springer","date_created":"2018-12-11T11:47:57Z","_id":"692","quality_controlled":"1","title":"3-Webs generated by confocal conics and circles","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"2018_Springer_Akopyan.pdf","date_updated":"2020-07-14T12:47:44Z","relation":"main_file","creator":"kschuh","file_id":"7222","checksum":"1febcfc1266486053a069e3425ea3713","date_created":"2020-01-03T11:35:08Z","file_size":1140860}],"isi":1},{"isi":1,"file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"2018_NatureComm_Watzinger.pdf","file_id":"5687","creator":"dernst","relation":"main_file","date_updated":"2020-07-14T12:48:02Z","file_size":1063469,"date_created":"2018-12-17T10:28:30Z","checksum":"e7148c10a64497e279c4de570b6cc544"}],"title":"A germanium hole spin qubit","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","_id":"77","date_created":"2018-12-11T11:44:30Z","publisher":"Nature Publishing Group","date_updated":"2023-09-08T11:44:02Z","external_id":{"isi":["000445560800010"]},"ec_funded":1,"ddc":["530"],"abstract":[{"text":"Holes confined in quantum dots have gained considerable interest in the past few years due to their potential as spin qubits. Here we demonstrate two-axis control of a spin 3/2 qubit in natural Ge. The qubit is formed in a hut wire double quantum dot device. The Pauli spin blockade principle allowed us to demonstrate electric dipole spin resonance by applying a radio frequency electric field to one of the electrodes defining the double quantum dot. Coherent hole spin oscillations with Rabi frequencies reaching 140 MHz are demonstrated and dephasing times of 130 ns are measured. The reported results emphasize the potential of Ge as a platform for fast and electrically tunable hole spin qubit devices.","lang":"eng"}],"related_material":{"record":[{"id":"7977","relation":"popular_science"},{"status":"public","relation":"dissertation_contains","id":"7996"}]},"issue":"3902 ","project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497"},{"name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","grant_number":"Y00715","_id":"2552F888-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa":1,"volume":9,"department":[{"_id":"GeKa"}],"author":[{"id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","last_name":"Watzinger","first_name":"Hannes","full_name":"Watzinger, Hannes"},{"first_name":"Josip","full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka"},{"last_name":"Vukusic","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","full_name":"Vukusic, Lada","first_name":"Lada","orcid":"0000-0003-2424-8636"},{"full_name":"Gao, Fei","first_name":"Fei","last_name":"Gao"},{"last_name":"Wang","first_name":"Ting","full_name":"Wang, Ting"},{"first_name":"Friedrich","full_name":"Schäffler, Friedrich","last_name":"Schäffler"},{"first_name":"Jian","full_name":"Zhang, Jian","last_name":"Zhang"},{"orcid":"0000-0001-8342-202X","first_name":"Georgios","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"}],"article_type":"original","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"day":"25","year":"2018","citation":{"ieee":"H. Watzinger et al., “A germanium hole spin qubit,” Nature Communications, vol. 9, no. 3902. Nature Publishing Group, 2018.","mla":"Watzinger, Hannes, et al. “A Germanium Hole Spin Qubit.” Nature Communications, vol. 9, no. 3902, Nature Publishing Group, 2018, doi:10.1038/s41467-018-06418-4.","ista":"Watzinger H, Kukucka J, Vukušić L, Gao F, Wang T, Schäffler F, Zhang J, Katsaros G. 2018. A germanium hole spin qubit. Nature Communications. 9(3902).","ama":"Watzinger H, Kukucka J, Vukušić L, et al. A germanium hole spin qubit. Nature Communications. 2018;9(3902). doi:10.1038/s41467-018-06418-4","apa":"Watzinger, H., Kukucka, J., Vukušić, L., Gao, F., Wang, T., Schäffler, F., … Katsaros, G. (2018). A germanium hole spin qubit. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-06418-4","short":"H. Watzinger, J. Kukucka, L. Vukušić, F. Gao, T. Wang, F. Schäffler, J. Zhang, G. Katsaros, Nature Communications 9 (2018).","chicago":"Watzinger, Hannes, Josip Kukucka, Lada Vukušić, Fei Gao, Ting Wang, Friedrich Schäffler, Jian Zhang, and Georgios Katsaros. “A Germanium Hole Spin Qubit.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-06418-4."},"date_published":"2018-09-25T00:00:00Z","publication":"Nature Communications","oa_version":"Published Version","scopus_import":"1","month":"09","intvolume":" 9","file_date_updated":"2020-07-14T12:48:02Z","type":"journal_article","doi":"10.1038/s41467-018-06418-4","article_processing_charge":"Yes","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}]},{"article_processing_charge":"No","type":"journal_article","doi":"10.1038/s41467-018-03574-5","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","scopus_import":"1","file_date_updated":"2020-07-14T12:46:22Z","intvolume":" 9","month":"03","citation":{"ieee":"X. Qin et al., “A biochemical network controlling basal myosin oscillation,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","mla":"Qin, Xiang, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications, vol. 9, no. 1, 1210, Nature Publishing Group, 2018, doi:10.1038/s41467-018-03574-5.","ista":"Qin X, Hannezo EB, Mangeat T, Liu C, Majumder P, Liu J, Choesmel Cadamuro V, Mcdonald J, Liu Y, Yi B, Wang X. 2018. A biochemical network controlling basal myosin oscillation. Nature Communications. 9(1), 1210.","apa":"Qin, X., Hannezo, E. B., Mangeat, T., Liu, C., Majumder, P., Liu, J., … Wang, X. (2018). A biochemical network controlling basal myosin oscillation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-03574-5","ama":"Qin X, Hannezo EB, Mangeat T, et al. A biochemical network controlling basal myosin oscillation. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-03574-5","short":"X. Qin, E.B. Hannezo, T. Mangeat, C. Liu, P. Majumder, J. Liu, V. Choesmel Cadamuro, J. Mcdonald, Y. Liu, B. Yi, X. Wang, Nature Communications 9 (2018).","chicago":"Qin, Xiang, Edouard B Hannezo, Thomas Mangeat, Chang Liu, Pralay Majumder, Jjiaying Liu, Valerie Choesmel Cadamuro, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-03574-5."},"publication":"Nature Communications","date_published":"2018-03-23T00:00:00Z","pubrep_id":"996","has_accepted_license":"1","status":"public","year":"2018","day":"23","language":[{"iso":"eng"}],"department":[{"_id":"EdHa"}],"volume":9,"author":[{"first_name":"Xiang","full_name":"Qin, Xiang","last_name":"Qin"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"last_name":"Mangeat","full_name":"Mangeat, Thomas","first_name":"Thomas"},{"first_name":"Chang","full_name":"Liu, Chang","last_name":"Liu"},{"last_name":"Majumder","full_name":"Majumder, Pralay","first_name":"Pralay"},{"first_name":"Jjiaying","full_name":"Liu, Jjiaying","last_name":"Liu"},{"first_name":"Valerie","full_name":"Choesmel Cadamuro, Valerie","last_name":"Choesmel Cadamuro"},{"full_name":"Mcdonald, Jocelyn","first_name":"Jocelyn","last_name":"Mcdonald"},{"last_name":"Liu","full_name":"Liu, Yinyao","first_name":"Yinyao"},{"last_name":"Yi","full_name":"Yi, Bin","first_name":"Bin"},{"last_name":"Wang","full_name":"Wang, Xiaobo","first_name":"Xiaobo"}],"article_number":"1210","ddc":["539","570"],"abstract":[{"lang":"eng","text":"The actomyosin cytoskeleton, a key stress-producing unit in epithelial cells, oscillates spontaneously in a wide variety of systems. Although much of the signal cascade regulating myosin activity has been characterized, the origin of such oscillatory behavior is still unclear. Here, we show that basal myosin II oscillation in Drosophila ovarian epithelium is not controlled by actomyosin cortical tension, but instead relies on a biochemical oscillator involving ROCK and myosin phosphatase. Key to this oscillation is a diffusive ROCK flow, linking junctional Rho1 to medial actomyosin cortex, and dynamically maintained by a self-activation loop reliant on ROCK kinase activity. In response to the resulting myosin II recruitment, myosin phosphatase is locally enriched and shuts off ROCK and myosin II signals. Coupling Drosophila genetics, live imaging, modeling, and optogenetics, we uncover an intrinsic biochemical oscillator at the core of myosin II regulatory network, shedding light on the spatio-temporal dynamics of force generation."}],"oa":1,"issue":"1","date_created":"2018-12-11T11:46:16Z","publisher":"Nature Publishing Group","publist_id":"7427","date_updated":"2023-09-08T11:41:45Z","external_id":{"isi":["000428165400009"]},"quality_controlled":"1","_id":"401","isi":1,"file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-996-v1+1_2018_Hannezo_A-biochemical.pdf","relation":"main_file","date_updated":"2020-07-14T12:46:22Z","creator":"system","file_id":"4902","date_created":"2018-12-12T10:11:45Z","checksum":"87a427bc2e8724be3dd22a4efdd21a33","file_size":3780491}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"A biochemical network controlling basal myosin oscillation"},{"citation":{"chicago":"Casano, Alessandra M, and Michael K Sixt. “A Fat Lot of Good for Wound Healing.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.02.009.","apa":"Casano, A. M., & Sixt, M. K. (2018). A fat lot of good for wound healing. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.02.009","ama":"Casano AM, Sixt MK. A fat lot of good for wound healing. Developmental Cell. 2018;44(4):405-406. doi:10.1016/j.devcel.2018.02.009","short":"A.M. Casano, M.K. Sixt, Developmental Cell 44 (2018) 405–406.","ista":"Casano AM, Sixt MK. 2018. A fat lot of good for wound healing. Developmental Cell. 44(4), 405–406.","ieee":"A. M. Casano and M. K. Sixt, “A fat lot of good for wound healing,” Developmental Cell, vol. 44, no. 4. Cell Press, pp. 405–406, 2018.","mla":"Casano, Alessandra M., and Michael K. Sixt. “A Fat Lot of Good for Wound Healing.” Developmental Cell, vol. 44, no. 4, Cell Press, 2018, pp. 405–06, doi:10.1016/j.devcel.2018.02.009."},"publication":"Developmental Cell","date_published":"2018-02-26T00:00:00Z","oa_version":"Published Version","scopus_import":"1","intvolume":" 44","month":"02","publication_status":"published","page":"405 - 406","type":"journal_article","doi":"10.1016/j.devcel.2018.02.009","article_processing_charge":"No","author":[{"first_name":"Alessandra M","full_name":"Casano, Alessandra M","orcid":"0000-0002-6009-6804","id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87","last_name":"Casano"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"volume":44,"pmid":1,"department":[{"_id":"MiSi"}],"status":"public","language":[{"iso":"eng"}],"year":"2018","day":"26","acknowledgement":"Short Survey","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29486189","open_access":"1"}],"date_updated":"2023-09-08T11:42:28Z","external_id":{"pmid":["29486189"],"isi":["000426150700002"]},"publist_id":"7547","date_created":"2018-12-11T11:45:47Z","publisher":"Cell Press","issue":"4","oa":1,"abstract":[{"text":"The insect’s fat body combines metabolic and immunological functions. In this issue of Developmental Cell, Franz et al. (2018) show that in Drosophila, cells of the fat body are not static, but can actively “swim” toward sites of epithelial injury, where they physically clog the wound and locally secrete antimicrobial peptides.","lang":"eng"}],"title":"A fat lot of good for wound healing","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"_id":"318","quality_controlled":"1"},{"has_accepted_license":"1","pubrep_id":"994","day":"26","language":[{"iso":"eng"}],"year":"2018","status":"public","department":[{"_id":"MaJö"}],"volume":8,"author":[{"full_name":"Masís, Javier","first_name":"Javier","last_name":"Masís"},{"first_name":"David","full_name":"Mankus, David","last_name":"Mankus"},{"last_name":"Wolff","full_name":"Wolff, Steffen","first_name":"Steffen"},{"full_name":"Guitchounts, Grigori","first_name":"Grigori","last_name":"Guitchounts"},{"orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","full_name":"Cox, David","last_name":"Cox"}],"article_number":"5184","article_processing_charge":"No","doi":"10.1038/s41598-018-23247-z","type":"journal_article","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","file_date_updated":"2020-07-14T12:46:23Z","month":"03","intvolume":" 8","oa_version":"Published Version","scopus_import":"1","publication":"Scientific Reports","date_published":"2018-03-26T00:00:00Z","citation":{"chicago":"Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-23247-z.","ama":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-23247-z","apa":"Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox, D. (2018). A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-23247-z","short":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Scientific Reports 8 (2018).","mla":"Masís, Javier, et al. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” Scientific Reports, vol. 8, no. 1, 5184, Nature Publishing Group, 2018, doi:10.1038/s41598-018-23247-z.","ista":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 8(1), 5184.","ieee":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for quantitative brain lesion characterization and electrode localization,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018."},"quality_controlled":"1","_id":"410","file":[{"file_name":"IST-2018-994-v1+1_2018_Joesch_A-micro-CT-based.pdf","content_type":"application/pdf","access_level":"open_access","checksum":"653fcb852f899c75b00ceee2a670d738","date_created":"2018-12-12T10:10:42Z","file_size":2359430,"creator":"system","file_id":"4831","date_updated":"2020-07-14T12:46:23Z","relation":"main_file"}],"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"A micro-CT-based method for quantitative brain lesion characterization and electrode localization","ddc":["571","572"],"abstract":[{"text":"Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12–15 and 5–6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods.","lang":"eng"}],"oa":1,"issue":"1","publisher":"Nature Publishing Group","date_created":"2018-12-11T11:46:19Z","publist_id":"7419","external_id":{"isi":["000428234100005"]},"date_updated":"2023-09-08T11:48:39Z"},{"publist_id":"7625","date_created":"2018-12-11T11:45:34Z","publisher":"Springer","date_updated":"2023-09-08T13:21:05Z","external_id":{"isi":["000438981700009"]},"ddc":["580"],"abstract":[{"text":"Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein–protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions.","lang":"eng"}],"issue":"5","oa":1,"isi":1,"file":[{"checksum":"451ae47616e6af2533099f596b2a47fb","date_created":"2020-05-14T12:23:08Z","file_size":1150679,"creator":"dernst","file_id":"7834","relation":"main_file","date_updated":"2020-07-14T12:45:45Z","file_name":"2018_PlantMolecBio_Dokladal.pdf","content_type":"application/pdf","access_level":"open_access"}],"title":"An armadillo-domain protein participates in a telomerase interaction network","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","_id":"277","citation":{"short":"L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová, Plant Molecular Biology 97 (2018) 407–420.","ama":"Dokládal L, Benková E, Honys D, et al. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 2018;97(5):407-420. doi:10.1007/s11103-018-0747-4","apa":"Dokládal, L., Benková, E., Honys, D., Dupláková, N., Lee, L., Gelvin, S., & Sýkorová, E. (2018). An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-018-0747-4","chicago":"Dokládal, Ladislav, Eva Benková, David Honys, Nikoleta Dupláková, Lan Lee, Stanton Gelvin, and Eva Sýkorová. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” Plant Molecular Biology. Springer, 2018. https://doi.org/10.1007/s11103-018-0747-4.","ista":"Dokládal L, Benková E, Honys D, Dupláková N, Lee L, Gelvin S, Sýkorová E. 2018. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 97(5), 407–420.","ieee":"L. Dokládal et al., “An armadillo-domain protein participates in a telomerase interaction network,” Plant Molecular Biology, vol. 97, no. 5. Springer, pp. 407–420, 2018.","mla":"Dokládal, Ladislav, et al. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” Plant Molecular Biology, vol. 97, no. 5, Springer, 2018, pp. 407–20, doi:10.1007/s11103-018-0747-4."},"publication":"Plant Molecular Biology","date_published":"2018-06-12T00:00:00Z","scopus_import":"1","oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:45:45Z","intvolume":" 97","month":"06","type":"journal_article","doi":"10.1007/s11103-018-0747-4","article_processing_charge":"No","publication_status":"published","page":"407 - 420","volume":97,"department":[{"_id":"EvBe"}],"author":[{"last_name":"Dokládal","full_name":"Dokládal, Ladislav","first_name":"Ladislav"},{"first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"last_name":"Honys","first_name":"David","full_name":"Honys, David"},{"first_name":"Nikoleta","full_name":"Dupláková, Nikoleta","last_name":"Dupláková"},{"last_name":"Lee","full_name":"Lee, Lan","first_name":"Lan"},{"full_name":"Gelvin, Stanton","first_name":"Stanton","last_name":"Gelvin"},{"first_name":"Eva","full_name":"Sýkorová, Eva","last_name":"Sýkorová"}],"article_type":"original","has_accepted_license":"1","status":"public","year":"2018","day":"12","language":[{"iso":"eng"}]},{"date_published":"2018-04-14T00:00:00Z","citation":{"apa":"Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2018). AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. In D. Beyer & M. Huisman (Eds.) (Vol. 10806, pp. 303–319). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89963-3_18","ama":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. In: Beyer D, Huisman M, eds. Vol 10806. Springer; 2018:303-319. doi:10.1007/978-3-319-89963-3_18","short":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, in:, D. Beyer, M. Huisman (Eds.), Springer, 2018, pp. 303–319.","chicago":"Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” edited by Dirk Beyer and Marieke Huisman, 10806:303–19. Springer, 2018. https://doi.org/10.1007/978-3-319-89963-3_18.","ieee":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10806, pp. 303–319.","ista":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2018. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10806, 303–319.","mla":"Nickovic, Dejan, et al. AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic. Edited by Dirk Beyer and Marieke Huisman, vol. 10806, Springer, 2018, pp. 303–19, doi:10.1007/978-3-319-89963-3_18."},"month":"04","intvolume":" 10806","file_date_updated":"2020-07-14T12:45:58Z","scopus_import":"1","oa_version":"Published Version","type":"conference","doi":"10.1007/978-3-319-89963-3_18","article_processing_charge":"No","page":"303 - 319","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","volume":10806,"department":[{"_id":"ToHe"}],"author":[{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","first_name":"Dejan","full_name":"Nickovic, Dejan"},{"last_name":"Lebeltel","full_name":"Lebeltel, Olivier","first_name":"Olivier"},{"last_name":"Maler","full_name":"Maler, Oded","first_name":"Oded"},{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143"},{"last_name":"Ulus","first_name":"Dogan","full_name":"Ulus, Dogan"}],"editor":[{"full_name":"Beyer, Dirk","first_name":"Dirk","last_name":"Beyer"},{"last_name":"Huisman","first_name":"Marieke","full_name":"Huisman, Marieke"}],"has_accepted_license":"1","year":"2018","language":[{"iso":"eng"}],"day":"14","status":"public","publist_id":"7582","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Thessaloniki, Greece","start_date":"2018-04-14","end_date":"2018-04-20"},"publisher":"Springer","date_created":"2018-12-11T11:45:41Z","external_id":{"isi":["00445822600018"]},"date_updated":"2023-09-08T11:52:02Z","abstract":[{"text":"We introduce in this paper AMT 2.0 , a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended Signal Temporal Logic (xSTL), which integrates Timed Regular Expressions (TRE) within Signal Temporal Logic (STL). The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal.","lang":"eng"}],"ddc":["000"],"related_material":{"record":[{"status":"public","relation":"later_version","id":"10861"}]},"oa":1,"file":[{"date_updated":"2020-07-14T12:45:58Z","relation":"main_file","creator":"dernst","file_id":"5928","date_created":"2019-02-06T07:33:05Z","checksum":"e11db3b9c8e27a1c7d1c738cc5e4d25a","file_size":3267209,"access_level":"open_access","content_type":"application/pdf","file_name":"2018_LNCS_Nickovic.pdf"}],"isi":1,"title":"AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","_id":"299","alternative_title":["LNCS"]},{"quality_controlled":"1","_id":"413","isi":1,"title":"Ants avoid superinfections by performing risk-adjusted sanitary care","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Being cared for when sick is a benefit of sociality that can reduce disease and improve survival of group members. However, individuals providing care risk contracting infectious diseases themselves. If they contract a low pathogen dose, they may develop low-level infections that do not cause disease but still affect host immunity by either decreasing or increasing the host’s vulnerability to subsequent infections. Caring for contagious individuals can thus significantly alter the future disease susceptibility of caregivers. Using ants and their fungal pathogens as a model system, we tested if the altered disease susceptibility of experienced caregivers, in turn, affects their expression of sanitary care behavior. We found that low-level infections contracted during sanitary care had protective or neutral effects on secondary exposure to the same (homologous) pathogen but consistently caused high mortality on superinfection with a different (heterologous) pathogen. In response to this risk, the ants selectively adjusted the expression of their sanitary care. Specifically, the ants performed less grooming and more antimicrobial disinfection when caring for nestmates contaminated with heterologous pathogens compared with homologous ones. By modulating the components of sanitary care in this way the ants acquired less infectious particles of the heterologous pathogens, resulting in reduced superinfection. The performance of risk-adjusted sanitary care reveals the remarkable capacity of ants to react to changes in their disease susceptibility, according to their own infection history and to flexibly adjust collective care to individual risk.","lang":"eng"}],"ec_funded":1,"issue":"11","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/helping-in-spite-of-risk-ants-perform-risk-averse-sanitary-care-of-infectious-nest-mates/"}]},"project":[{"call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"}],"oa":1,"publist_id":"7416","publisher":"National Academy of Sciences","date_created":"2018-12-11T11:46:20Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29463746"}],"external_id":{"isi":["000427245400069"],"pmid":["29463746"]},"date_updated":"2023-09-08T13:22:21Z","year":"2018","day":"13","language":[{"iso":"eng"}],"status":"public","volume":115,"pmid":1,"department":[{"_id":"SyCr"}],"author":[{"id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad","first_name":"Matthias","full_name":"Konrad, Matthias"},{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","orcid":"0000-0003-1122-3982","first_name":"Christopher","full_name":"Pull, Christopher"},{"last_name":"Metzler","id":"48204546-F248-11E8-B48F-1D18A9856A87","full_name":"Metzler, Sina","first_name":"Sina","orcid":"0000-0002-9547-2494"},{"full_name":"Seif, Katharina","first_name":"Katharina","last_name":"Seif","id":"90F7894A-02CF-11E9-976E-E38CFE5CBC1D"},{"id":"31757262-F248-11E8-B48F-1D18A9856A87","last_name":"Naderlinger","first_name":"Elisabeth","full_name":"Naderlinger, Elisabeth"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V","full_name":"Grasse, Anna V"},{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"type":"journal_article","doi":"10.1073/pnas.1713501115","article_processing_charge":"No","page":"2782 - 2787","publication_status":"published","publication":"PNAS","date_published":"2018-03-13T00:00:00Z","citation":{"ista":"Konrad M, Pull C, Metzler S, Seif K, Naderlinger E, Grasse AV, Cremer S. 2018. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 115(11), 2782–2787.","mla":"Konrad, Matthias, et al. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” PNAS, vol. 115, no. 11, National Academy of Sciences, 2018, pp. 2782–87, doi:10.1073/pnas.1713501115.","ieee":"M. Konrad et al., “Ants avoid superinfections by performing risk-adjusted sanitary care,” PNAS, vol. 115, no. 11. National Academy of Sciences, pp. 2782–2787, 2018.","ama":"Konrad M, Pull C, Metzler S, et al. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 2018;115(11):2782-2787. doi:10.1073/pnas.1713501115","apa":"Konrad, M., Pull, C., Metzler, S., Seif, K., Naderlinger, E., Grasse, A. V., & Cremer, S. (2018). Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713501115","short":"M. Konrad, C. Pull, S. Metzler, K. Seif, E. Naderlinger, A.V. Grasse, S. Cremer, PNAS 115 (2018) 2782–2787.","chicago":"Konrad, Matthias, Christopher Pull, Sina Metzler, Katharina Seif, Elisabeth Naderlinger, Anna V Grasse, and Sylvia Cremer. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713501115."},"intvolume":" 115","month":"03","scopus_import":"1","oa_version":"Published Version"},{"title":"Anyonic statistics of quantum impurities in two dimensions","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"_id":"195","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1712.00308","open_access":"1"}],"external_id":{"arxiv":["1712.00308"],"isi":["000436939100007"]},"date_updated":"2023-09-08T13:22:57Z","publisher":"American Physical Society","date_created":"2018-12-11T11:45:08Z","issue":"4","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"}],"oa":1,"abstract":[{"text":"We demonstrate that identical impurities immersed in a two-dimensional many-particle bath can be viewed as flux-tube-charged-particle composites described by fractional statistics. In particular, we find that the bath manifests itself as an external magnetic flux tube with respect to the impurities, and hence the time-reversal symmetry is broken for the effective Hamiltonian describing the impurities. The emerging flux tube acts as a statistical gauge field after a certain critical coupling. This critical coupling corresponds to the intersection point between the quasiparticle state and the phonon wing, where the angular momentum is transferred from the impurity to the bath. This amounts to a novel configuration with emerging anyons. The proposed setup paves the way to realizing anyons using electrons interacting with superfluid helium or lattice phonons, as well as using atomic impurities in ultracold gases.","lang":"eng"}],"ec_funded":1,"article_number":"045402","author":[{"id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","first_name":"Enderalp","full_name":"Yakaboylu, Enderalp"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"}],"volume":98,"department":[{"_id":"MiLe"}],"year":"2018","language":[{"iso":"eng"}],"day":"15","status":"public","publication":"Physical Review B - Condensed Matter and Materials Physics","date_published":"2018-07-15T00:00:00Z","citation":{"ieee":"E. Yakaboylu and M. Lemeshko, “Anyonic statistics of quantum impurities in two dimensions,” Physical Review B - Condensed Matter and Materials Physics, vol. 98, no. 4. American Physical Society, 2018.","ista":"Yakaboylu E, Lemeshko M. 2018. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 98(4), 045402.","mla":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” Physical Review B - Condensed Matter and Materials Physics, vol. 98, no. 4, 045402, American Physical Society, 2018, doi:10.1103/PhysRevB.98.045402.","chicago":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.045402.","ama":"Yakaboylu E, Lemeshko M. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 2018;98(4). doi:10.1103/PhysRevB.98.045402","apa":"Yakaboylu, E., & Lemeshko, M. (2018). Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.98.045402","short":"E. Yakaboylu, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 98 (2018)."},"intvolume":" 98","month":"07","scopus_import":"1","oa_version":"Submitted Version","publication_status":"published","type":"journal_article","doi":"10.1103/PhysRevB.98.045402","article_processing_charge":"No"},{"quality_controlled":"1","_id":"144","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"status":"public","day":"09","language":[{"iso":"eng"}],"year":"2018","isi":1,"department":[{"_id":"ToHe"}],"volume":"Part F138033","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0001-5199-3143","first_name":"Thomas","full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Saraç","full_name":"Saraç, Ege","first_name":"Ege"}],"title":"A theory of register monitors","article_processing_charge":"No","doi":"10.1145/3209108.3209194","type":"conference","abstract":[{"lang":"eng","text":"The task of a monitor is to watch, at run-time, the execution of a reactive system, and signal the occurrence of a safety violation in the observed sequence of events. While finite-state monitors have been studied extensively, in practice, monitoring software also makes use of unbounded memory. We define a model of automata equipped with integer-valued registers which can execute only a bounded number of instructions between consecutive events, and thus can form the theoretical basis for the study of infinite-state monitors. We classify these register monitors according to the number k of available registers, and the type of register instructions. In stark contrast to the theory of computability for register machines, we prove that for every k 1, monitors with k + 1 counters (with instruction set 〈+1, =〉) are strictly more expressive than monitors with k counters. We also show that adder monitors (with instruction set 〈1, +, =〉) are strictly more expressive than counter monitors, but are complete for monitoring all computable safety -languages for k = 6. Real-time monitors are further required to signal the occurrence of a safety violation as soon as it occurs. The expressiveness hierarchy for counter monitors carries over to real-time monitors. We then show that 2 adders cannot simulate 3 counters in real-time. Finally, we show that real-time adder monitors with inequalities are as expressive as real-time Turing machines."}],"publication_status":"published","page":"394 - 403","oa_version":"None","date_created":"2018-12-11T11:44:52Z","scopus_import":"1","month":"07","publisher":"IEEE","citation":{"ista":"Ferrere T, Henzinger TA, Saraç E. 2018. A theory of register monitors. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. Part F138033, 394–403.","mla":"Ferrere, Thomas, et al. A Theory of Register Monitors. Vol. Part F138033, IEEE, 2018, pp. 394–403, doi:10.1145/3209108.3209194.","ieee":"T. Ferrere, T. A. Henzinger, and E. Saraç, “A theory of register monitors,” presented at the LICS: Logic in Computer Science, Oxford, UK, 2018, vol. Part F138033, pp. 394–403.","chicago":"Ferrere, Thomas, Thomas A Henzinger, and Ege Saraç. “A Theory of Register Monitors,” Part F138033:394–403. IEEE, 2018. https://doi.org/10.1145/3209108.3209194.","short":"T. Ferrere, T.A. Henzinger, E. Saraç, in:, IEEE, 2018, pp. 394–403.","ama":"Ferrere T, Henzinger TA, Saraç E. A theory of register monitors. In: Vol Part F138033. IEEE; 2018:394-403. doi:10.1145/3209108.3209194","apa":"Ferrere, T., Henzinger, T. A., & Saraç, E. (2018). A theory of register monitors (Vol. Part F138033, pp. 394–403). Presented at the LICS: Logic in Computer Science, Oxford, UK: IEEE. https://doi.org/10.1145/3209108.3209194"},"conference":{"end_date":"2018-07-12","start_date":"2018-07-09","location":"Oxford, UK","name":"LICS: Logic in Computer Science"},"date_published":"2018-07-09T00:00:00Z","publist_id":"7779","date_updated":"2023-09-08T11:49:13Z","external_id":{"isi":["000545262800041"]}},{"author":[{"last_name":"Abbas","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87","full_name":"Abbas, Mohamad","first_name":"Mohamad"},{"last_name":"Hernández","first_name":"García J","full_name":"Hernández, García J"},{"first_name":"Stephan","full_name":"Pollmann, Stephan","last_name":"Pollmann"},{"full_name":"Samodelov, Sophia L","first_name":"Sophia L","last_name":"Samodelov"},{"last_name":"Kolb","first_name":"Martina","full_name":"Kolb, Martina"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Hammes, Ulrich Z","first_name":"Ulrich Z","last_name":"Hammes"},{"first_name":"Matias D","full_name":"Zurbriggen, Matias D","last_name":"Zurbriggen"},{"last_name":"Blázquez","first_name":"Miguel","full_name":"Blázquez, Miguel"},{"last_name":"Alabadí","full_name":"Alabadí, David","first_name":"David"}],"department":[{"_id":"JiFr"}],"volume":115,"status":"public","year":"2018","language":[{"iso":"eng"}],"day":"26","scopus_import":"1","oa_version":"None","month":"06","intvolume":" 115","citation":{"apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1806565115","ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 2018;115(26):6864-6869. doi:10.1073/pnas.1806565115","short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869.","chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1806565115.","ieee":"M. Abbas et al., “Auxin methylation is required for differential growth in Arabidopsis,” PNAS, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018.","ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.","mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:10.1073/pnas.1806565115."},"publication":"PNAS","date_published":"2018-06-26T00:00:00Z","publication_status":"published","page":"6864-6869","article_processing_charge":"No","doi":"10.1073/pnas.1806565115","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Auxin methylation is required for differential growth in Arabidopsis","isi":1,"_id":"203","quality_controlled":"1","date_updated":"2023-09-08T13:24:40Z","external_id":{"isi":["000436245000096"]},"main_file_link":[{"url":"http://eprints.nottingham.ac.uk/52388/","open_access":"1"}],"date_created":"2018-12-11T11:45:11Z","publisher":"National Academy of Sciences","publist_id":"7710","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa":1,"issue":"26","ec_funded":1,"abstract":[{"text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses.","lang":"eng"}]},{"oa":1,"project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"issue":"1","abstract":[{"lang":"eng","text":"Following an earlier calculation in 3D, we calculate the 2D critical temperature of a dilute, translation-invariant Bose gas using a variational formulation of the Bogoliubov approximation introduced by Critchley and Solomon in 1976. This provides the first analytical calculation of the Kosterlitz-Thouless transition temperature that includes the constant in the logarithm."}],"date_updated":"2023-09-08T13:30:51Z","external_id":{"isi":["000460003000003"],"arxiv":["1706.01822"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.01822"}],"acknowledgement":"We thank Robert Seiringer and Daniel Ueltschi for bringing the issue of the change in critical temperature to our attention. We also thank the Erwin Schrödinger Institute (all authors) and the Department of Mathematics, University of Copenhagen (MN) for the hospitality during the period this work was carried out. We gratefully acknowledge the financial support by the European Unions Seventh Framework Programme under the ERC Grant Agreement Nos. 321029 (JPS and RR) and 337603 (RR) as well as support by the VIL-LUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059) (JPS and RR), by the National Science Center (NCN) under grant No. 2016/21/D/ST1/02430 and the Austrian Science Fund (FWF) through project No. P 27533-N27 (MN).","date_created":"2018-12-11T11:46:15Z","publisher":"IOP Publishing Ltd.","publist_id":"7432","_id":"399","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation","isi":1,"publication_status":"published","article_processing_charge":"No","type":"journal_article","doi":"10.1209/0295-5075/121/10007","scopus_import":"1","oa_version":"Preprint","month":"01","intvolume":" 121","citation":{"ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation,” EPL, vol. 121, no. 1. IOP Publishing Ltd., 2018.","mla":"Napiórkowski, Marcin M., et al. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL, vol. 121, no. 1, 10007, IOP Publishing Ltd., 2018, doi:10.1209/0295-5075/121/10007.","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 121(1), 10007.","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL. IOP Publishing Ltd., 2018. https://doi.org/10.1209/0295-5075/121/10007.","ama":"Napiórkowski MM, Reuvers R, Solovej J. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 2018;121(1). doi:10.1209/0295-5075/121/10007","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/121/10007","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, EPL 121 (2018)."},"date_published":"2018-01-01T00:00:00Z","publication":"EPL","status":"public","language":[{"iso":"eng"}],"day":"01","year":"2018","article_type":"original","author":[{"full_name":"Napiórkowski, Marcin M","first_name":"Marcin M","last_name":"Napiórkowski","id":"4197AD04-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reuvers, Robin","first_name":"Robin","last_name":"Reuvers"},{"full_name":"Solovej, Jan","first_name":"Jan","last_name":"Solovej"}],"article_number":"10007","department":[{"_id":"RoSe"}],"volume":121},{"publication_status":"epub_ahead","oa":1,"type":"journal_article","doi":"10.1111/pce.13475","abstract":[{"text":"CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress. CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants, indicating that ABA is required for CLE9-medaited guard cell signalling. We further deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABA-dependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants.","lang":"eng"}],"publication_identifier":{"issn":["01407791"]},"article_processing_charge":"No","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30378140","open_access":"1"}],"date_updated":"2023-09-11T12:43:31Z","external_id":{"isi":["000459014800021"],"pmid":["30378140"]},"citation":{"chicago":"Zhang, Luosha, Xiong Shi, Yutao Zhang, Jiajing Wang, Jingwei Yang, Takashi Ishida, Wenqian Jiang, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment. Wiley, 2018. https://doi.org/10.1111/pce.13475.","short":"L. Zhang, X. Shi, Y. Zhang, J. Wang, J. Yang, T. Ishida, W. Jiang, X. Han, J. Kang, X. Wang, L. Pan, S. Lv, B. Cao, Y. Zhang, J. Wu, H. Han, Z. Hu, L. Cui, S. Sawa, J. He, G. Wang, Plant Cell and Environment (2018).","ama":"Zhang L, Shi X, Zhang Y, et al. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. 2018. doi:10.1111/pce.13475","apa":"Zhang, L., Shi, X., Zhang, Y., Wang, J., Yang, J., Ishida, T., … Wang, G. (2018). CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. Wiley. https://doi.org/10.1111/pce.13475","ieee":"L. Zhang et al., “CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana,” Plant Cell and Environment. Wiley, 2018.","mla":"Zhang, Luosha, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment, Wiley, 2018, doi:10.1111/pce.13475.","ista":"Zhang L, Shi X, Zhang Y, Wang J, Yang J, Ishida T, Jiang W, Han X, Kang J, Wang X, Pan L, Lv S, Cao B, Zhang Y, Wu J, Han H, Hu Z, Cui L, Sawa S, He J, Wang G. 2018. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment."},"publication":"Plant Cell and Environment","date_published":"2018-10-31T00:00:00Z","oa_version":"Published Version","date_created":"2019-01-13T22:59:11Z","scopus_import":"1","month":"10","publisher":"Wiley","status":"public","language":[{"iso":"eng"}],"day":"31","year":"2018","_id":"5830","quality_controlled":"1","title":"CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Luosha","full_name":"Zhang, Luosha","last_name":"Zhang"},{"last_name":"Shi","full_name":"Shi, Xiong","first_name":"Xiong"},{"last_name":"Zhang","first_name":"Yutao","full_name":"Zhang, Yutao"},{"first_name":"Jiajing","full_name":"Wang, Jiajing","last_name":"Wang"},{"last_name":"Yang","full_name":"Yang, Jingwei","first_name":"Jingwei"},{"last_name":"Ishida","full_name":"Ishida, Takashi","first_name":"Takashi"},{"full_name":"Jiang, Wenqian","first_name":"Wenqian","last_name":"Jiang"},{"first_name":"Xiangyu","full_name":"Han, Xiangyu","last_name":"Han"},{"full_name":"Kang, Jingke","first_name":"Jingke","last_name":"Kang"},{"first_name":"Xuening","full_name":"Wang, Xuening","last_name":"Wang"},{"first_name":"Lixia","full_name":"Pan, Lixia","last_name":"Pan"},{"full_name":"Lv, Shuo","first_name":"Shuo","last_name":"Lv"},{"first_name":"Bing","full_name":"Cao, Bing","last_name":"Cao"},{"first_name":"Yonghong","full_name":"Zhang, Yonghong","last_name":"Zhang"},{"last_name":"Wu","first_name":"Jinbin","full_name":"Wu, Jinbin"},{"first_name":"Huibin","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han"},{"last_name":"Hu","full_name":"Hu, Zhubing","first_name":"Zhubing"},{"first_name":"Langjun","full_name":"Cui, Langjun","last_name":"Cui"},{"last_name":"Sawa","full_name":"Sawa, Shinichiro","first_name":"Shinichiro"},{"first_name":"Junmin","full_name":"He, Junmin","last_name":"He"},{"full_name":"Wang, Guodong","first_name":"Guodong","last_name":"Wang"}],"isi":1,"pmid":1,"department":[{"_id":"JiFr"}]},{"pmid":1,"department":[{"_id":"EdHa"}],"volume":20,"author":[{"last_name":"Lilja","full_name":"Lilja, Anna","first_name":"Anna"},{"full_name":"Rodilla, Veronica","first_name":"Veronica","last_name":"Rodilla"},{"last_name":"Huyghe","first_name":"Mathilde","full_name":"Huyghe, Mathilde"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B"},{"full_name":"Landragin, Camille","first_name":"Camille","last_name":"Landragin"},{"full_name":"Renaud, Olivier","first_name":"Olivier","last_name":"Renaud"},{"last_name":"Leroy","full_name":"Leroy, Olivier","first_name":"Olivier"},{"first_name":"Steffen","full_name":"Rulands, Steffen","last_name":"Rulands"},{"first_name":"Benjamin","full_name":"Simons, Benjamin","last_name":"Simons"},{"first_name":"Silvia","full_name":"Fré, Silvia","last_name":"Fré"}],"article_type":"original","year":"2018","language":[{"iso":"eng"}],"day":"21","status":"public","month":"05","intvolume":" 20","scopus_import":"1","oa_version":"Submitted Version","publication":"Nature Cell Biology","date_published":"2018-05-21T00:00:00Z","citation":{"ama":"Lilja A, Rodilla V, Huyghe M, et al. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 2018;20(6):677-687. doi:10.1038/s41556-018-0108-1","apa":"Lilja, A., Rodilla, V., Huyghe, M., Hannezo, E. B., Landragin, C., Renaud, O., … Fré, S. (2018). Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0108-1","short":"A. Lilja, V. Rodilla, M. Huyghe, E.B. Hannezo, C. Landragin, O. Renaud, O. Leroy, S. Rulands, B. Simons, S. Fré, Nature Cell Biology 20 (2018) 677–687.","chicago":"Lilja, Anna, Veronica Rodilla, Mathilde Huyghe, Edouard B Hannezo, Camille Landragin, Olivier Renaud, Olivier Leroy, Steffen Rulands, Benjamin Simons, and Silvia Fré. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41556-018-0108-1.","ieee":"A. Lilja et al., “Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland,” Nature Cell Biology, vol. 20, no. 6. Nature Publishing Group, pp. 677–687, 2018.","mla":"Lilja, Anna, et al. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology, vol. 20, no. 6, Nature Publishing Group, 2018, pp. 677–87, doi:10.1038/s41556-018-0108-1.","ista":"Lilja A, Rodilla V, Huyghe M, Hannezo EB, Landragin C, Renaud O, Leroy O, Rulands S, Simons B, Fré S. 2018. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 20(6), 677–687."},"article_processing_charge":"No","doi":"10.1038/s41556-018-0108-1","type":"journal_article","page":"677 - 687","publication_status":"published","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland","quality_controlled":"1","_id":"288","publisher":"Nature Publishing Group","date_created":"2018-12-11T11:45:38Z","publist_id":"7594","external_id":{"pmid":["29784917"],"isi":["000433237300003"]},"date_updated":"2023-09-11T12:44:08Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6984964"}],"abstract":[{"lang":"eng","text":"Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer."}],"oa":1,"issue":"6"},{"publisher":"ACM","date_created":"2018-12-11T11:45:43Z","external_id":{"isi":["000448185000120"]},"date_updated":"2023-09-11T12:46:13Z","acknowledgement":"This work was in part supported by King Abdullah University of Science and Technology Baseline Funding.","abstract":[{"text":"Additive manufacturing has recently seen drastic improvements in resolution, making it now possible to fabricate features at scales of hundreds or even dozens of nanometers, which previously required very expensive lithographic methods.\r\nAs a result, additive manufacturing now seems poised for optical applications, including those relevant to computer graphics, such as material design, as well as display and imaging applications.\r\n \r\nIn this work, we explore the use of additive manufacturing for generating structural colors, where the structures are designed using a fabrication-aware optimization process.\r\nThis requires a combination of full-wave simulation, a feasible parameterization of the design space, and a tailored optimization procedure.\r\nMany of these components should be re-usable for the design of other optical structures at this scale.\r\n \r\nWe show initial results of material samples fabricated based on our designs.\r\nWhile these suffer from the prototype character of state-of-the-art fabrication hardware, we believe they clearly demonstrate the potential of additive nanofabrication for structural colors and other graphics applications.","lang":"eng"}],"ddc":["000","535","680"],"ec_funded":1,"project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and 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Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 37(4), 159.","ieee":"T. Auzinger, W. Heidrich, and B. Bickel, “Computational design of nanostructural color for additive manufacturing,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","mla":"Auzinger, Thomas, et al. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics, vol. 37, no. 4, 159, ACM, 2018, doi:10.1145/3197517.3201376.","short":"T. Auzinger, W. Heidrich, B. Bickel, ACM Transactions on Graphics 37 (2018).","ama":"Auzinger T, Heidrich W, Bickel B. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201376","apa":"Auzinger, T., Heidrich, W., & Bickel, B. (2018). Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201376","chicago":"Auzinger, Thomas, Wolfgang Heidrich, and Bernd Bickel. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201376."},"article_processing_charge":"No","type":"journal_article","doi":"10.1145/3197517.3201376","publication_status":"published","department":[{"_id":"BeBi"}],"volume":37,"author":[{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","last_name":"Auzinger","orcid":"0000-0002-1546-3265","first_name":"Thomas","full_name":"Auzinger, Thomas"},{"full_name":"Heidrich, Wolfgang","first_name":"Wolfgang","last_name":"Heidrich"},{"first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"}],"article_number":"159","pubrep_id":"1028","has_accepted_license":"1","day":"01","year":"2018","language":[{"iso":"eng"}],"status":"public"},{"quality_controlled":"1","_id":"12","isi":1,"file":[{"creator":"system","file_id":"5360","date_updated":"2020-07-14T12:44:38Z","relation":"main_file","checksum":"6a5368bc86c4e1a9fcfe588fd1f14ee8","date_created":"2018-12-12T10:18:38Z","file_size":104225664,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-1037-v1+1_CoreCavity-AuthorVersion.pdf"},{"date_created":"2018-12-12T10:18:39Z","checksum":"3861e693ba47c51f3ec7b7867d573a61","file_size":377743553,"creator":"system","file_id":"5361","relation":"main_file","date_updated":"2020-07-14T12:44:38Z","file_name":"IST-2018-1037-v1+2_CoreCavity-Supplemental.zip","content_type":"application/zip","access_level":"open_access"},{"date_updated":"2020-07-14T12:44:38Z","relation":"main_file","creator":"system","file_id":"5362","date_created":"2018-12-12T10:18:41Z","checksum":"490040c685ed869536e2a18f5a906b94","file_size":162634396,"access_level":"open_access","content_type":"video/vnd.objectvideo","file_name":"IST-2018-1037-v1+3_CoreCavity-Video.mp4"},{"access_level":"open_access","content_type":"image/jpeg","file_name":"IST-2018-1037-v1+4_CoreCavity-RepresentativeImage.jpg","date_updated":"2020-07-14T12:44:38Z","relation":"main_file","file_id":"5363","creator":"system","file_size":527972,"date_created":"2018-12-12T10:18:42Z","checksum":"be7fc8b229adda727419b6504b3b9352"}],"title":"CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"abstract":[{"lang":"eng","text":"Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects."}],"ddc":["004","516","670"],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/","relation":"press_release","description":"News on IST Homepage"}]},"issue":"4","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Distributed 3D Object Design","grant_number":"642841","call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425"}],"oa":1,"publist_id":"8044","date_created":"2018-12-11T11:44:09Z","publisher":"ACM","date_updated":"2023-09-11T12:48:09Z","external_id":{"isi":["000448185000096"]},"has_accepted_license":"1","pubrep_id":"1037","status":"public","year":"2018","day":"04","language":[{"iso":"eng"}],"volume":37,"department":[{"_id":"BeBi"}],"article_number":"135","author":[{"last_name":"Nakashima","first_name":"Kazutaka","full_name":"Nakashima, Kazutaka"},{"orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","first_name":"Thomas","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Iarussi, Emmanuel","first_name":"Emmanuel","last_name":"Iarussi","id":"33F19F16-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhang","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3808-281X","full_name":"Zhang, Ran","first_name":"Ran"},{"first_name":"Takeo","full_name":"Igarashi, Takeo","last_name":"Igarashi"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"}],"doi":"10.1145/3197517.3201341","type":"journal_article","article_processing_charge":"No","publication_status":"published","citation":{"short":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel, ACM Transaction on Graphics 37 (2018).","apa":"Nakashima, K., Auzinger, T., Iarussi, E., Zhang, R., Igarashi, T., & Bickel, B. (2018). CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. ACM. https://doi.org/10.1145/3197517.3201341","ama":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 2018;37(4). doi:10.1145/3197517.3201341","chicago":"Nakashima, Kazutaka, Thomas Auzinger, Emmanuel Iarussi, Ran Zhang, Takeo Igarashi, and Bernd Bickel. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201341.","ista":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. 2018. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 37(4), 135.","ieee":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, and B. Bickel, “CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds,” ACM Transaction on Graphics, vol. 37, no. 4. ACM, 2018.","mla":"Nakashima, Kazutaka, et al. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics, vol. 37, no. 4, 135, ACM, 2018, doi:10.1145/3197517.3201341."},"date_published":"2018-08-04T00:00:00Z","publication":"ACM Transaction on Graphics","scopus_import":"1","oa_version":"Submitted Version","month":"08","file_date_updated":"2020-07-14T12:44:38Z","intvolume":" 37"},{"isi":1,"file":[{"date_created":"2018-12-12T10:09:18Z","checksum":"b6b90367545b4c615891c960ab0567f1","file_size":843646,"relation":"main_file","date_updated":"2020-07-14T12:46:31Z","creator":"system","file_id":"4741","file_name":"IST-2018-964-v1+1_2018_Hilbe_Crosstalk_in.pdf","access_level":"open_access","content_type":"application/pdf"}],"title":"Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","_id":"454","publist_id":"7368","date_created":"2018-12-11T11:46:34Z","publisher":"Nature Publishing Group","acknowledgement":"This work was supported by the European Research Council (ERC) start grant 279307: Graph Games (C.K.), Austrian Science Fund (FWF) grant no P23499-N23 (C.K.), FWF\r\nNFN grant no S11407-N23 RiSE/SHiNE (C.K.), Office of Naval Research grant N00014-16-1-2914 (M.A.N.), National Cancer Institute grant CA179991 (M.A.N.) and by the John Templeton Foundation. J.G.R. is supported by an Erwin Schrödinger fellowship\r\n(Austrian Science Fund FWF J-3996). C.H. acknowledges generous support from the\r\nISTFELLOW program. The Program for Evolutionary Dynamics is supported in part by\r\na gift from B Wu and Eric Larson.","date_updated":"2023-09-11T12:51:03Z","external_id":{"isi":["000424318200001"]},"ec_funded":1,"ddc":["004"],"abstract":[{"lang":"eng","text":"Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze “crosstalk” between a player’s concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person’s decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games."}],"issue":"1","project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"oa":1,"volume":9,"department":[{"_id":"KrCh"}],"article_number":"555","author":[{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","first_name":"Johannes","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","first_name":"Christian","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X"},{"last_name":"Rand","first_name":"David","full_name":"Rand, David"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"has_accepted_license":"1","pubrep_id":"964","status":"public","year":"2018","day":"07","language":[{"iso":"eng"}],"citation":{"chicago":"Reiter, Johannes, Christian Hilbe, David Rand, Krishnendu Chatterjee, and Martin Nowak. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-017-02721-8.","apa":"Reiter, J., Hilbe, C., Rand, D., Chatterjee, K., & Nowak, M. (2018). Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02721-8","ama":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 2018;9(1). doi:10.1038/s41467-017-02721-8","short":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, M. Nowak, Nature Communications 9 (2018).","mla":"Reiter, Johannes, et al. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications, vol. 9, no. 1, 555, Nature Publishing Group, 2018, doi:10.1038/s41467-017-02721-8.","ieee":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, and M. Nowak, “Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","ista":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. 2018. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 9(1), 555."},"publication":"Nature Communications","date_published":"2018-02-07T00:00:00Z","scopus_import":"1","oa_version":"Published Version","intvolume":" 9","file_date_updated":"2020-07-14T12:46:31Z","month":"02","type":"journal_article","doi":"10.1038/s41467-017-02721-8","article_processing_charge":"No","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"month":"04","file_date_updated":"2020-07-14T12:46:03Z","intvolume":" 98","oa_version":"Published Version","scopus_import":"1","date_published":"2018-04-04T00:00:00Z","publication":"Neuron","citation":{"mla":"Hu, Hua, et al. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” Neuron, vol. 98, no. 1, Elsevier, 2018, pp. 156–65, doi:10.1016/j.neuron.2018.02.024.","ieee":"H. Hu, F. Roth, D. H. Vandael, and P. M. Jonas, “Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons,” Neuron, vol. 98, no. 1. Elsevier, pp. 156–165, 2018.","ista":"Hu H, Roth F, Vandael DH, Jonas PM. 2018. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 98(1), 156–165.","chicago":"Hu, Hua, Fabian Roth, David H Vandael, and Peter M Jonas. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.02.024.","short":"H. Hu, F. Roth, D.H. Vandael, P.M. Jonas, Neuron 98 (2018) 156–165.","apa":"Hu, H., Roth, F., Vandael, D. H., & Jonas, P. M. (2018). Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.02.024","ama":"Hu H, Roth F, Vandael DH, Jonas PM. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 2018;98(1):156-165. doi:10.1016/j.neuron.2018.02.024"},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"page":"156 - 165","publication_status":"published","article_processing_charge":"Yes (in subscription journal)","doi":"10.1016/j.neuron.2018.02.024","type":"journal_article","author":[{"id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","last_name":"Hu","first_name":"Hua","full_name":"Hu, Hua"},{"full_name":"Roth, Fabian","first_name":"Fabian","last_name":"Roth"},{"orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","first_name":"David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M"}],"department":[{"_id":"PeJo"}],"volume":98,"day":"04","language":[{"iso":"eng"}],"year":"2018","status":"public","has_accepted_license":"1","external_id":{"isi":["000429192100016"]},"date_updated":"2023-09-11T12:45:10Z","publisher":"Elsevier","date_created":"2018-12-11T11:45:48Z","publist_id":"7545","oa":1,"project":[{"grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"issue":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/a-certain-type-of-neurons-is-more-energy-efficient-than-previously-assumed/","relation":"press_release","description":"News on IST Homepage"}]},"ddc":["570"],"abstract":[{"text":"Fast-spiking, parvalbumin-expressing GABAergic interneurons (PV+-BCs) express a complex machinery of rapid signaling mechanisms, including specialized voltage-gated ion channels to generate brief action potentials (APs). However, short APs are associated with overlapping Na+ and K+ fluxes and are therefore energetically expensive. How the potentially vicious combination of high AP frequency and inefficient spike generation can be reconciled with limited energy supply is presently unclear. To address this question, we performed direct recordings from the PV+-BC axon, the subcellular structure where active conductances for AP initiation and propagation are located. Surprisingly, the energy required for the AP was, on average, only ∼1.6 times the theoretical minimum. High energy efficiency emerged from the combination of fast inactivation of Na+ channels and delayed activation of Kv3-type K+ channels, which minimized ion flux overlap during APs. Thus, the complementary tuning of axonal Na+ and K+ channel gating optimizes both fast signaling properties and metabolic efficiency. Hu et al. demonstrate that action potentials in parvalbumin-expressing GABAergic interneuron axons are energetically efficient, which is highly unexpected given their brief duration. High energy efficiency emerges from the combination of fast inactivation of voltage-gated Na+ channels and delayed activation of Kv3 channels in the axon. ","lang":"eng"}],"ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons","file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"2018_Neuron_Hu.pdf","date_updated":"2020-07-14T12:46:03Z","relation":"main_file","creator":"dernst","file_id":"5690","date_created":"2018-12-17T10:37:50Z","checksum":"76070f3729f9c603e1080d0151aa2b11","file_size":3180444}],"isi":1,"_id":"320","quality_controlled":"1"},{"publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","type":"journal_article","doi":"10.7554/eLife.32035","oa_version":"Published Version","scopus_import":"1","month":"03","file_date_updated":"2020-07-14T12:46:25Z","intvolume":" 7","citation":{"chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” eLife, vol. 7. eLife Sciences Publications, 2018.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035.","mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035."},"date_published":"2018-03-09T00:00:00Z","publication":"eLife","status":"public","day":"09","language":[{"iso":"eng"}],"year":"2018","has_accepted_license":"1","author":[{"id":"35F78294-F248-11E8-B48F-1D18A9856A87","last_name":"Payne","first_name":"Pavel","full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453"},{"last_name":"Geyrhofer","first_name":"Lukas","full_name":"Geyrhofer, Lukas"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"}],"article_number":"e32035","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"volume":7,"oa":1,"project":[{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9840"}]},"ec_funded":1,"abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"ddc":["576"],"date_updated":"2023-09-11T12:49:17Z","external_id":{"isi":["000431035800001"]},"acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","date_created":"2018-12-11T11:46:23Z","publisher":"eLife Sciences Publications","publist_id":"7400","_id":"423","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","isi":1,"file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"2018_eLife_Payne.pdf","creator":"dernst","file_id":"5689","relation":"main_file","date_updated":"2020-07-14T12:46:25Z","checksum":"447cf6e680bdc3c01062a8737d876569","date_created":"2018-12-17T10:36:07Z","file_size":3533881}]},{"quality_controlled":"1","alternative_title":["LNCS"],"_id":"5791","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Crossing minimization in perturbed drawings","publication_identifier":{"isbn":["9783030044138"]},"abstract":[{"lang":"eng","text":"Due to data compression or low resolution, nearby vertices and edges of a graph drawing may be bundled to a common node or arc. We model such a “compromised” drawing by a piecewise linear map φ:G → ℝ. We wish to perturb φ by an arbitrarily small ε>0 into a proper drawing (in which the vertices are distinct points, any two edges intersect in finitely many points, and no three edges have a common interior point) that minimizes the number of crossings. An ε-perturbation, for every ε>0, is given by a piecewise linear map (Formula Presented), where with ||·|| is the uniform norm (i.e., sup norm). We present a polynomial-time solution for this optimization problem when G is a cycle and the map φ has no spurs (i.e., no two adjacent edges are mapped to overlapping arcs). We also show that the problem becomes NP-complete (i) when G is an arbitrary graph and φ has no spurs, and (ii) when φ may have spurs and G is a cycle or a union of disjoint paths."}],"oa":1,"publisher":"Springer","date_created":"2018-12-30T22:59:15Z","conference":{"end_date":"2018-09-28","name":"Graph Drawing and Network Visualization","location":"Barcelona, Spain","start_date":"2018-09-26"},"external_id":{"isi":["000672802500016"],"arxiv":["1808.07608"]},"date_updated":"2023-09-11T12:49:55Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.07608"}],"language":[{"iso":"eng"}],"year":"2018","day":"18","status":"public","department":[{"_id":"UlWa"}],"volume":"11282 ","author":[{"first_name":"Radoslav","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek"},{"last_name":"Tóth","first_name":"Csaba D.","full_name":"Tóth, Csaba D."}],"article_processing_charge":"No","type":"conference","doi":"10.1007/978-3-030-04414-5_16","page":"229-241","publication_status":"published","month":"12","oa_version":"Preprint","scopus_import":"1","date_published":"2018-12-18T00:00:00Z","citation":{"short":"R. Fulek, C.D. Tóth, in:, Springer, 2018, pp. 229–241.","apa":"Fulek, R., & Tóth, C. D. (2018). Crossing minimization in perturbed drawings (Vol. 11282, pp. 229–241). Presented at the Graph Drawing and Network Visualization, Barcelona, Spain: Springer. https://doi.org/10.1007/978-3-030-04414-5_16","ama":"Fulek R, Tóth CD. Crossing minimization in perturbed drawings. In: Vol 11282. Springer; 2018:229-241. doi:10.1007/978-3-030-04414-5_16","chicago":"Fulek, Radoslav, and Csaba D. Tóth. “Crossing Minimization in Perturbed Drawings,” 11282:229–41. Springer, 2018. https://doi.org/10.1007/978-3-030-04414-5_16.","mla":"Fulek, Radoslav, and Csaba D. Tóth. Crossing Minimization in Perturbed Drawings. Vol. 11282, Springer, 2018, pp. 229–41, doi:10.1007/978-3-030-04414-5_16.","ieee":"R. Fulek and C. D. Tóth, “Crossing minimization in perturbed drawings,” presented at the Graph Drawing and Network Visualization, Barcelona, Spain, 2018, vol. 11282, pp. 229–241.","ista":"Fulek R, Tóth CD. 2018. Crossing minimization in perturbed drawings. Graph Drawing and Network Visualization, LNCS, vol. 11282, 229–241."}},{"doi":"10.1103/PhysRevFluids.3.054401","type":"journal_article","article_processing_charge":"No","publication_status":"published","publication":"Physical Review Fluids","date_published":"2018-05-30T00:00:00Z","citation":{"short":"N.B. Budanur, B. Hof, Physical Review Fluids 3 (2018).","apa":"Budanur, N. B., & Hof, B. (2018). Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.054401","ama":"Budanur NB, Hof B. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 2018;3(5). doi:10.1103/PhysRevFluids.3.054401","chicago":"Budanur, Nazmi B, and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.054401.","mla":"Budanur, Nazmi B., and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” Physical Review Fluids, vol. 3, no. 5, 054401, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.054401.","ista":"Budanur NB, Hof B. 2018. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 3(5), 054401.","ieee":"N. B. Budanur and B. Hof, “Complexity of the laminar-turbulent boundary in pipe flow,” Physical Review Fluids, vol. 3, no. 5. American Physical Society, 2018."},"month":"05","intvolume":" 3","scopus_import":"1","oa_version":"Preprint","day":"30","year":"2018","language":[{"iso":"eng"}],"status":"public","volume":3,"department":[{"_id":"BjHo"}],"article_number":"054401","author":[{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","first_name":"Nazmi B","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"Over the past decade, the edge of chaos has proven to be a fruitful starting point for investigations of shear flows when the laminar base flow is linearly stable. Numerous computational studies of shear flows demonstrated the existence of states that separate laminar and turbulent regions of the state space. In addition, some studies determined invariant solutions that reside on this edge. In this paper, we study the unstable manifold of one such solution with the aid of continuous symmetry reduction, which we formulate here for the simultaneous quotiening of axial and azimuthal symmetries. Upon our investigation of the unstable manifold, we discover a previously unknown traveling-wave solution on the laminar-turbulent boundary with a relatively complex structure. By means of low-dimensional projections, we visualize different dynamical paths that connect these solutions to the turbulence. Our numerical experiments demonstrate that the laminar-turbulent boundary exhibits qualitatively different regions whose properties are influenced by the nearby invariant solutions."}],"issue":"5","oa":1,"publist_id":"7590","publisher":"American Physical Society","date_created":"2018-12-11T11:45:39Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.01918"}],"external_id":{"arxiv":["1802.01918"],"isi":["000433426200001"]},"date_updated":"2023-09-11T12:45:44Z","quality_controlled":"1","_id":"291","isi":1,"title":"Complexity of the laminar-turbulent boundary in pipe flow","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"language":[{"iso":"eng"}],"day":"06","year":"2018","status":"public","department":[{"_id":"HeEd"}],"volume":32,"author":[{"full_name":"Akopyan, Arseniy","first_name":"Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Segal Halevi","full_name":"Segal Halevi, Erel","first_name":"Erel"}],"article_processing_charge":"No","type":"journal_article","doi":"10.1137/16M110407X","page":"2242 - 2257","publication_status":"published","intvolume":" 32","month":"09","scopus_import":"1","oa_version":"Preprint","publication":"SIAM Journal on Discrete Mathematics","date_published":"2018-09-06T00:00:00Z","citation":{"ieee":"A. Akopyan and E. Segal Halevi, “Counting blanks in polygonal arrangements,” SIAM Journal on Discrete Mathematics, vol. 32, no. 3. Society for Industrial and Applied Mathematics , pp. 2242–2257, 2018.","mla":"Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics, vol. 32, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 2242–57, doi:10.1137/16M110407X.","ista":"Akopyan A, Segal Halevi E. 2018. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 32(3), 2242–2257.","short":"A. Akopyan, E. Segal Halevi, SIAM Journal on Discrete Mathematics 32 (2018) 2242–2257.","apa":"Akopyan, A., & Segal Halevi, E. (2018). Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M110407X","ama":"Akopyan A, Segal Halevi E. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 2018;32(3):2242-2257. doi:10.1137/16M110407X","chicago":"Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M110407X."},"quality_controlled":"1","_id":"58","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Counting blanks in polygonal arrangements","abstract":[{"text":"Inside a two-dimensional region (``cake""), there are m nonoverlapping tiles of a certain kind (``toppings""). We want to expand the toppings while keeping them nonoverlapping, and possibly add some blank pieces of the same ``certain kind,"" such that the entire cake is covered. How many blanks must we add? We study this question in several cases: (1) The cake and toppings are general polygons. (2) The cake and toppings are convex figures. (3) The cake and toppings are axis-parallel rectangles. (4) The cake is an axis-parallel rectilinear polygon and the toppings are axis-parallel rectangles. In all four cases, we provide tight bounds on the number of blanks.","lang":"eng"}],"ec_funded":1,"oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"issue":"3","publisher":"Society for Industrial and Applied Mathematics ","date_created":"2018-12-11T11:44:24Z","publist_id":"7996","external_id":{"arxiv":["1604.00960"],"isi":["000450810500036"]},"date_updated":"2023-09-11T12:48:39Z","main_file_link":[{"url":"https://arxiv.org/abs/1604.00960","open_access":"1"}]},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"423"}]},"oa":1,"doi":"10.5061/dryad.42n44","type":"research_data_reference","abstract":[{"text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.","lang":"eng"}],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.42n44"}],"date_updated":"2023-09-11T12:49:17Z","citation":{"chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. https://doi.org/10.5061/dryad.42n44.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. https://doi.org/10.5061/dryad.42n44","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","mla":"Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44."},"date_published":"2018-03-12T00:00:00Z","date_created":"2021-08-09T13:10:02Z","oa_version":"Published Version","month":"03","publisher":"Dryad","status":"public","year":"2018","day":"12","_id":"9840","title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Payne","id":"35F78294-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2711-9453","full_name":"Payne, Pavel","first_name":"Pavel"},{"last_name":"Geyrhofer","full_name":"Geyrhofer, Lukas","first_name":"Lukas"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"first_name":"Jonathan P","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}]},{"author":[{"full_name":"Pull, Christopher","first_name":"Christopher","orcid":"0000-0003-1122-3982","last_name":"Pull","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","orcid":"0000-0003-1832-8883","first_name":"Line V","full_name":"Ugelvig, Line V"},{"id":"39523C54-F248-11E8-B48F-1D18A9856A87","last_name":"Wiesenhofer","first_name":"Florian","full_name":"Wiesenhofer, Florian"},{"full_name":"Grasse, Anna V","first_name":"Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tragust, Simon","first_name":"Simon","last_name":"Tragust","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schmitt","full_name":"Schmitt, Thomas","first_name":"Thomas"},{"full_name":"Brown, Mark","first_name":"Mark","last_name":"Brown"},{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia"}],"article_number":"e32073","department":[{"_id":"SyCr"}],"volume":7,"status":"public","year":"2018","day":"09","language":[{"iso":"eng"}],"pubrep_id":"978","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","intvolume":" 7","file_date_updated":"2020-07-14T12:47:20Z","month":"01","citation":{"chicago":"Pull, Christopher, Line V Ugelvig, Florian Wiesenhofer, Anna V Grasse, Simon Tragust, Thomas Schmitt, Mark Brown, and Sylvia Cremer. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32073.","short":"C. Pull, L.V. Ugelvig, F. Wiesenhofer, A.V. Grasse, S. Tragust, T. Schmitt, M. Brown, S. Cremer, ELife 7 (2018).","ama":"Pull C, Ugelvig LV, Wiesenhofer F, et al. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 2018;7. doi:10.7554/eLife.32073","apa":"Pull, C., Ugelvig, L. V., Wiesenhofer, F., Grasse, A. V., Tragust, S., Schmitt, T., … Cremer, S. (2018). Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32073","mla":"Pull, Christopher, et al. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife, vol. 7, e32073, eLife Sciences Publications, 2018, doi:10.7554/eLife.32073.","ieee":"C. Pull et al., “Destructive disinfection of infected brood prevents systemic disease spread in ant colonies,” eLife, vol. 7. eLife Sciences Publications, 2018.","ista":"Pull C, Ugelvig LV, Wiesenhofer F, Grasse AV, Tragust S, Schmitt T, Brown M, Cremer S. 2018. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 7, e32073."},"publication":"eLife","date_published":"2018-01-09T00:00:00Z","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes","type":"journal_article","doi":"10.7554/eLife.32073","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Destructive disinfection of infected brood prevents systemic disease spread in ant colonies","isi":1,"file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-978-v1+1_elife-32073-v1.pdf","date_updated":"2020-07-14T12:47:20Z","relation":"main_file","creator":"system","file_id":"4832","date_created":"2018-12-12T10:10:43Z","checksum":"540f941e8d3530a9441e4affd94f07d7","file_size":1435585}],"_id":"616","quality_controlled":"1","date_updated":"2023-09-11T12:54:26Z","external_id":{"isi":["000419601300001"]},"date_created":"2018-12-11T11:47:31Z","publisher":"eLife Sciences Publications","publist_id":"7188","oa":1,"project":[{"grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","name":"Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","grant_number":"302004"}],"related_material":{"record":[{"id":"819","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"ddc":["570","590"],"abstract":[{"lang":"eng","text":"Social insects protect their colonies from infectious disease through collective defences that result in social immunity. In ants, workers first try to prevent infection of colony members. Here, we show that if this fails and a pathogen establishes an infection, ants employ an efficient multicomponent behaviour − "destructive disinfection" − to prevent further spread of disease through the colony. Ants specifically target infected pupae during the pathogen's non-contagious incubation period, relying on chemical 'sickness cues' emitted by pupae. They then remove the pupal cocoon, perforate its cuticle and administer antimicrobial poison, which enters the body and prevents pathogen replication from the inside out. Like the immune system of a body that specifically targets and eliminates infected cells, this social immunity measure sacrifices infected brood to stop the pathogen completing its lifecycle, thus protecting the rest of the colony. Hence, the same principles of disease defence apply at different levels of biological organisation."}]},{"_id":"132","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Defining lineage potential and fate behavior of precursors during pancreas development","file":[{"relation":"main_file","date_updated":"2020-07-14T12:44:43Z","file_id":"5694","creator":"dernst","file_size":8948384,"date_created":"2018-12-17T10:49:49Z","checksum":"78d2062b9e3c3b90fe71545aeb6d2f65","access_level":"open_access","content_type":"application/pdf","file_name":"2018_DevelopmentalCell_Sznurkowska.pdf"}],"isi":1,"oa":1,"issue":"3","abstract":[{"lang":"eng","text":"Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments."}],"ddc":["570"],"external_id":{"isi":["000441327300012"]},"date_updated":"2023-09-11T12:52:41Z","acknowledgement":"E.H. is funded by a Junior Research Fellowship from Trinity College, Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller Young Researcher Prize for support.","publisher":"Cell Press","date_created":"2018-12-11T11:44:48Z","publist_id":"7791","day":"06","language":[{"iso":"eng"}],"year":"2018","status":"public","has_accepted_license":"1","article_type":"original","author":[{"last_name":"Sznurkowska","first_name":"Magdalena","full_name":"Sznurkowska, Magdalena"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B"},{"last_name":"Azzarelli","full_name":"Azzarelli, Roberta","first_name":"Roberta"},{"full_name":"Rulands, Steffen","first_name":"Steffen","last_name":"Rulands"},{"last_name":"Nestorowa","first_name":"Sonia","full_name":"Nestorowa, Sonia"},{"full_name":"Hindley, Christopher","first_name":"Christopher","last_name":"Hindley"},{"last_name":"Nichols","first_name":"Jennifer","full_name":"Nichols, Jennifer"},{"full_name":"Göttgens, Berthold","first_name":"Berthold","last_name":"Göttgens"},{"full_name":"Huch, Meritxell","first_name":"Meritxell","last_name":"Huch"},{"last_name":"Philpott","first_name":"Anna","full_name":"Philpott, Anna"},{"last_name":"Simons","full_name":"Simons, Benjamin","first_name":"Benjamin"}],"department":[{"_id":"EdHa"}],"volume":46,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"page":"360 - 375","publication_status":"published","article_processing_charge":"No","doi":"10.1016/j.devcel.2018.06.028","type":"journal_article","file_date_updated":"2020-07-14T12:44:43Z","month":"08","intvolume":" 46","scopus_import":"1","oa_version":"Published Version","date_published":"2018-08-06T00:00:00Z","publication":"Developmental Cell","citation":{"ista":"Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C, Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 46(3), 360–375.","ieee":"M. Sznurkowska et al., “Defining lineage potential and fate behavior of precursors during pancreas development,” Developmental Cell, vol. 46, no. 3. Cell Press, pp. 360–375, 2018.","mla":"Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell, vol. 46, no. 3, Cell Press, 2018, pp. 360–75, doi:10.1016/j.devcel.2018.06.028.","chicago":"Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.06.028.","short":"M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C. Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental Cell 46 (2018) 360–375.","apa":"Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S., Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.06.028","ama":"Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 2018;46(3):360-375. doi:10.1016/j.devcel.2018.06.028"}},{"_id":"42","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis","file":[{"checksum":"ca3b6711040b1662488aeb3d1f961f13","date_created":"2018-12-17T10:44:16Z","file_size":1292128,"relation":"main_file","date_updated":"2020-07-14T12:46:25Z","creator":"dernst","file_id":"5691","file_name":"2018_JournalExperimBotany_Cucinotta.pdf","access_level":"open_access","content_type":"application/pdf"}],"isi":1,"oa":1,"issue":"21","ddc":["575"],"abstract":[{"lang":"eng","text":"Seeds derive from ovules upon fertilization and therefore the total number of ovules determines the final seed yield, a fundamental trait in crop plants. Among the factors that co-ordinate the process of ovule formation, the transcription factors CUP-SHAPED COTYLEDON 1 (CUC1) and CUC2 and the hormone cytokinin (CK) have a particularly prominent role. Indeed, the absence of both CUC1 and CUC2 causes a severe reduction in ovule number, a phenotype that can be rescued by CK treatment. In this study, we combined CK quantification with an integrative genome-wide target identification approach to select Arabidopsis genes regulated by CUCs that are also involved in CK metabolism. We focused our attention on the functional characterization of UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) and UGT73C1, which are up-regulated in the absence of CUC1 and CUC2 and encode enzymes able to catalyse CK inactivation by O-glucosylation. Our results demonstrate a role for these UGTs as a link between CUCs and CK homeostasis, and highlight the importance of CUCs and CKs in the determination of seed yield."}],"external_id":{"isi":["000448163900015"]},"date_updated":"2023-09-11T12:52:03Z","acknowledgement":"This work was funded by the Ministry of Education, Youth and Sports of the Czech Republic through the National Program of Sustainability (grant no. LO1204).","publisher":"Oxford University Press","date_created":"2018-12-11T11:44:19Z","publist_id":"8012","day":"26","year":"2018","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","author":[{"first_name":"Mara","full_name":"Cucinotta, Mara","last_name":"Cucinotta"},{"first_name":"Silvia","full_name":"Manrique, Silvia","last_name":"Manrique"},{"orcid":"0000-0003-1923-2410","first_name":"Candela","full_name":"Cuesta, Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","last_name":"Cuesta"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"full_name":"Colombo, Lucia","first_name":"Lucia","last_name":"Colombo"}],"department":[{"_id":"EvBe"}],"volume":69,"page":"5169 - 5176","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","article_processing_charge":"No","type":"journal_article","doi":"10.1093/jxb/ery281","file_date_updated":"2020-07-14T12:46:25Z","month":"07","intvolume":" 69","scopus_import":"1","oa_version":"Published Version","publication":"Journal of Experimental Botany","date_published":"2018-07-26T00:00:00Z","citation":{"ieee":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, and L. Colombo, “Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis,” Journal of Experimental Botany, vol. 69, no. 21. Oxford University Press, pp. 5169–5176, 2018.","ista":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. 2018. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 69(21), 5169–5176.","mla":"Cucinotta, Mara, et al. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany, vol. 69, no. 21, Oxford University Press, 2018, pp. 5169–76, doi:10.1093/jxb/ery281.","chicago":"Cucinotta, Mara, Silvia Manrique, Candela Cuesta, Eva Benková, Ondřej Novák, and Lucia Colombo. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery281.","short":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, L. Colombo, Journal of Experimental Botany 69 (2018) 5169–5176.","ama":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 2018;69(21):5169-5176. doi:10.1093/jxb/ery281","apa":"Cucinotta, M., Manrique, S., Cuesta, C., Benková, E., Novák, O., & Colombo, L. (2018). Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery281"}},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins","isi":1,"_id":"407","quality_controlled":"1","date_updated":"2023-09-11T12:53:11Z","external_id":{"isi":["000435623400001"]},"acknowledgement":"This work was supported by the Ministry of Education Youth and Sports, Czech Republic (grant LO1204 from the National Program of Sustainability I and Agricultural Research ) and by Czech Science Foundation grants 16-04184S , 501/10/1450 and 13-39982S and by IGA projects IGA_PrF_2018_033 and IGA_PrF_2018_023 . We would like to thank Jarmila Balonová, Olga Hustáková and Miroslava Šubová for their skillful technical assistance and Mgr. Tomáš Pospíšil, Ph.D. for his measurement of 1 H NMR and analysis of some 2D NMR spectral data. \r\n","date_created":"2018-12-11T11:46:18Z","publisher":"Elsevier","publist_id":"7422","abstract":[{"lang":"eng","text":"Isoprenoid cytokinins play a number of crucial roles in the regulation of plant growth and development. To study cytokinin receptor properties in plants, we designed and prepared fluorescent derivatives of 6-[(3-methylbut-2-en-1-yl)amino]purine (N6-isopentenyladenine, iP) with several fluorescent labels attached to the C2 or N9 atom of the purine moiety via a 2- or 6-carbon linker. The fluorescent labels included dansyl (DS), fluorescein (FC), 7-nitrobenzofurazan (NBD), rhodamine B (RhoB), coumarin (Cou), 7-(diethylamino)coumarin (DEAC) and cyanine 5 dye (Cy5). All prepared compounds were screened for affinity for the Arabidopsis thaliana cytokinin receptor (CRE1/AHK4). Although the attachment of the fluorescent labels to iP via the linkers mostly disrupted binding to the receptor, several fluorescent derivatives interacted well. For this reason, three derivatives, two rhodamine B and one 4-chloro-7-nitrobenzofurazan labeled iP were tested for their interaction with CRE1/AHK4 and Zea mays cytokinin receptors in detail. We further showed that the three derivatives were able to activate transcription of cytokinin response regulator ARR5 in Arabidopsis seedlings. The activity of fluorescently labeled cytokinins was compared with corresponding 6-dimethylaminopurine fluorescently labeled negative controls. Selected rhodamine B C2-labeled compounds 17, 18 and 4-chloro-7-nitrobenzofurazan N9-labeled compound 28 and their respective negative controls (19, 20 and 29, respectively) were used for in planta staining experiments in Arabidopsis thaliana cell suspension culture using live cell confocal microscopy."}],"author":[{"first_name":"Karolina","full_name":"Kubiasová, Karolina","last_name":"Kubiasová"},{"first_name":"Václav","full_name":"Mik, Václav","last_name":"Mik"},{"first_name":"Jaroslav","full_name":"Nisler, Jaroslav","last_name":"Nisler"},{"last_name":"Hönig","first_name":"Martin","full_name":"Hönig, Martin"},{"first_name":"Alexandra","full_name":"Husičková, Alexandra","last_name":"Husičková"},{"last_name":"Spíchal","full_name":"Spíchal, Lukáš","first_name":"Lukáš"},{"last_name":"Pěkná","full_name":"Pěkná, Zuzana","first_name":"Zuzana"},{"first_name":"Olga","full_name":"Šamajová, Olga","last_name":"Šamajová"},{"first_name":"Karel","full_name":"Doležal, Karel","last_name":"Doležal"},{"first_name":"Ondřej","full_name":"Plíhal, Ondřej","last_name":"Plíhal"},{"first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"last_name":"Strnad","first_name":"Miroslav","full_name":"Strnad, Miroslav"},{"last_name":"Plíhalová","full_name":"Plíhalová, Lucie","first_name":"Lucie"}],"department":[{"_id":"EvBe"}],"volume":150,"status":"public","year":"2018","day":"01","language":[{"iso":"eng"}],"oa_version":"None","scopus_import":"1","intvolume":" 150","month":"06","citation":{"chicago":"Kubiasová, Karolina, Václav Mik, Jaroslav Nisler, Martin Hönig, Alexandra Husičková, Lukáš Spíchal, Zuzana Pěkná, et al. “Design, Synthesis and Perception of Fluorescently Labeled Isoprenoid Cytokinins.” Phytochemistry. Elsevier, 2018. https://doi.org/10.1016/j.phytochem.2018.02.015.","apa":"Kubiasová, K., Mik, V., Nisler, J., Hönig, M., Husičková, A., Spíchal, L., … Plíhalová, L. (2018). Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. Elsevier. https://doi.org/10.1016/j.phytochem.2018.02.015","ama":"Kubiasová K, Mik V, Nisler J, et al. Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. 2018;150:1-11. doi:10.1016/j.phytochem.2018.02.015","short":"K. Kubiasová, V. Mik, J. Nisler, M. Hönig, A. Husičková, L. Spíchal, Z. Pěkná, O. Šamajová, K. Doležal, O. Plíhal, E. Benková, M. Strnad, L. Plíhalová, Phytochemistry 150 (2018) 1–11.","ista":"Kubiasová K, Mik V, Nisler J, Hönig M, Husičková A, Spíchal L, Pěkná Z, Šamajová O, Doležal K, Plíhal O, Benková E, Strnad M, Plíhalová L. 2018. Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. 150, 1–11.","ieee":"K. Kubiasová et al., “Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins,” Phytochemistry, vol. 150. Elsevier, pp. 1–11, 2018.","mla":"Kubiasová, Karolina, et al. “Design, Synthesis and Perception of Fluorescently Labeled Isoprenoid Cytokinins.” Phytochemistry, vol. 150, Elsevier, 2018, pp. 1–11, doi:10.1016/j.phytochem.2018.02.015."},"date_published":"2018-06-01T00:00:00Z","publication":"Phytochemistry","publication_status":"published","page":"1-11","article_processing_charge":"No","type":"journal_article","doi":"10.1016/j.phytochem.2018.02.015"},{"oa":1,"issue":"16","abstract":[{"text":"We analyze a disordered central spin model, where a central spin interacts equally with each spin in a periodic one-dimensional (1D) random-field Heisenberg chain. If the Heisenberg chain is initially in the many-body localized (MBL) phase, we find that the coupling to the central spin suffices to delocalize the chain for a substantial range of coupling strengths. We calculate the phase diagram of the model and identify the phase boundary between the MBL and ergodic phase. Within the localized phase, the central spin significantly enhances the rate of the logarithmic entanglement growth and its saturation value. We attribute the increase in entanglement entropy to a nonextensive enhancement of magnetization fluctuations induced by the central spin. Finally, we demonstrate that correlation functions of the central spin can be utilized to distinguish between MBL and ergodic phases of the 1D chain. Hence, we propose the use of a central spin as a possible experimental probe to identify the MBL phase.","lang":"eng"}],"date_updated":"2023-09-11T12:55:03Z","external_id":{"arxiv":["1806.08316"],"isi":["000448596500002"]},"acknowledgement":"F.P. acknowledges the sup- port of the DFG Research Unit FOR 1807 through Grants No. PO 1370/2-1 and No. TRR80, the Nanosystems Initiative Munich (NIM) by the German Excellence Initiative, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 771537). N.Y.Y. acknowledges support from the NSF (PHY-1654740), the ARO STIR program, and a Google research award.","main_file_link":[{"url":"https://arxiv.org/abs/1806.08316","open_access":"1"}],"date_created":"2018-12-11T11:44:20Z","publisher":"American Physical Society","publist_id":"8008","_id":"46","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Detection and characterization of many-body localization in central spin models","isi":1,"publication_status":"published","article_processing_charge":"No","type":"journal_article","doi":"10.1103/PhysRevB.98.161122","scopus_import":"1","oa_version":"Preprint","intvolume":" 98","month":"10","citation":{"ieee":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, and B. Trauzettel, “Detection and characterization of many-body localization in central spin models,” Physical Review B, vol. 98, no. 16. American Physical Society, 2018.","ista":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. 2018. Detection and characterization of many-body localization in central spin models. Physical Review B. 98(16), 161122.","mla":"Hetterich, Daniel, et al. “Detection and Characterization of Many-Body Localization in Central Spin Models.” Physical Review B, vol. 98, no. 16, 161122, American Physical Society, 2018, doi:10.1103/PhysRevB.98.161122.","short":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, B. Trauzettel, Physical Review B 98 (2018).","ama":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. Detection and characterization of many-body localization in central spin models. Physical Review B. 2018;98(16). doi:10.1103/PhysRevB.98.161122","apa":"Hetterich, D., Yao, N., Serbyn, M., Pollmann, F., & Trauzettel, B. (2018). Detection and characterization of many-body localization in central spin models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.98.161122","chicago":"Hetterich, Daniel, Norman Yao, Maksym Serbyn, Frank Pollmann, and Björn Trauzettel. “Detection and Characterization of Many-Body Localization in Central Spin Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.161122."},"publication":"Physical Review B","date_published":"2018-10-15T00:00:00Z","status":"public","day":"15","year":"2018","language":[{"iso":"eng"}],"article_type":"original","author":[{"last_name":"Hetterich","first_name":"Daniel","full_name":"Hetterich, Daniel"},{"last_name":"Yao","first_name":"Norman","full_name":"Yao, Norman"},{"first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"},{"last_name":"Pollmann","full_name":"Pollmann, Frank","first_name":"Frank"},{"last_name":"Trauzettel","first_name":"Björn","full_name":"Trauzettel, Björn"}],"article_number":"161122","department":[{"_id":"MaSe"}],"volume":98},{"publication_status":"published","acknowledged_ssus":[{"_id":"SSU"}],"page":"331 - 346","doi":"10.1016/j.devcel.2018.04.002","type":"journal_article","article_processing_charge":"No","citation":{"apa":"Ratheesh, A., Bicher, J., Smutny, M., Veselá, J., Papusheva, E., Krens, G., … Siekhaus, D. E. (2018). Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2018.04.002","ama":"Ratheesh A, Bicher J, Smutny M, et al. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 2018;45(3):331-346. doi:10.1016/j.devcel.2018.04.002","short":"A. Ratheesh, J. Bicher, M. Smutny, J. Veselá, E. Papusheva, G. Krens, W. Kaufmann, A. György, A.M. Casano, D.E. Siekhaus, Developmental Cell 45 (2018) 331–346.","chicago":"Ratheesh, Aparna, Julia Bicher, Michael Smutny, Jana Veselá, Ekaterina Papusheva, Gabriel Krens, Walter Kaufmann, Attila György, Alessandra M Casano, and Daria E Siekhaus. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell. Elsevier, 2018. https://doi.org/10.1016/j.devcel.2018.04.002.","mla":"Ratheesh, Aparna, et al. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell, vol. 45, no. 3, Elsevier, 2018, pp. 331–46, doi:10.1016/j.devcel.2018.04.002.","ista":"Ratheesh A, Bicher J, Smutny M, Veselá J, Papusheva E, Krens G, Kaufmann W, György A, Casano AM, Siekhaus DE. 2018. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 45(3), 331–346.","ieee":"A. Ratheesh et al., “Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration,” Developmental Cell, vol. 45, no. 3. Elsevier, pp. 331–346, 2018."},"date_published":"2018-05-07T00:00:00Z","publication":"Developmental Cell","scopus_import":"1","oa_version":"Published Version","month":"05","intvolume":" 45","status":"public","year":"2018","language":[{"iso":"eng"}],"day":"07","article_type":"original","author":[{"full_name":"Ratheesh, Aparna","first_name":"Aparna","orcid":"0000-0001-7190-0776","last_name":"Ratheesh","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Biebl","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","full_name":"Biebl, Julia","first_name":"Julia"},{"last_name":"Smutny","full_name":"Smutny, Michael","first_name":"Michael"},{"full_name":"Veselá, Jana","first_name":"Jana","last_name":"Veselá","id":"433253EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Papusheva, Ekaterina","first_name":"Ekaterina","last_name":"Papusheva","id":"41DB591E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","first_name":"Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","full_name":"György, Attila","first_name":"Attila","orcid":"0000-0002-1819-198X"},{"orcid":"0000-0002-6009-6804","full_name":"Casano, Alessandra M","first_name":"Alessandra M","last_name":"Casano","id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8323-8353","first_name":"Daria E","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus"}],"volume":45,"department":[{"_id":"DaSi"},{"_id":"CaHe"},{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"MiSi"}],"pmid":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/cells-change-tension-to-make-tissue-barriers-easier-to-get-through/","description":"News on IST Homepage","relation":"press_release"}]},"issue":"3","project":[{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29638","name":"Drosophila TNFa´s Funktion in Immunzellen"},{"_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions"}],"oa":1,"ec_funded":1,"abstract":[{"text":"Migrating cells penetrate tissue barriers during development, inflammatory responses, and tumor metastasis. We study if migration in vivo in such three-dimensionally confined environments requires changes in the mechanical properties of the surrounding cells using embryonic Drosophila melanogaster hemocytes, also called macrophages, as a model. We find that macrophage invasion into the germband through transient separation of the apposing ectoderm and mesoderm requires cell deformations and reductions in apical tension in the ectoderm. Interestingly, the genetic pathway governing these mechanical shifts acts downstream of the only known tumor necrosis factor superfamily member in Drosophila, Eiger, and its receptor, Grindelwald. Eiger-Grindelwald signaling reduces levels of active Myosin in the germband ectodermal cortex through the localization of a Crumbs complex component, Patj (Pals-1-associated tight junction protein). We therefore elucidate a distinct molecular pathway that controls tissue tension and demonstrate the importance of such regulation for invasive migration in vivo.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2018.04.002"}],"date_updated":"2023-09-11T13:22:13Z","external_id":{"isi":["000432461400009"],"pmid":["29738712"]},"date_created":"2018-12-11T11:45:44Z","publisher":"Elsevier","_id":"308","quality_controlled":"1","title":"Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1},{"status":"public","day":"15","language":[{"iso":"eng"}],"year":"2018","has_accepted_license":"1","pubrep_id":"1061","author":[{"orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul","first_name":"Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Steinberg","full_name":"Steinberg, Victor","first_name":"Victor"}],"article_number":"103302 ","department":[{"_id":"BjHo"}],"volume":3,"publication_status":"published","article_processing_charge":"No","type":"journal_article","doi":"10.1103/PhysRevFluids.3.103302","scopus_import":"1","oa_version":"Published Version","month":"10","file_date_updated":"2020-07-14T12:45:12Z","intvolume":" 3","citation":{"short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","ama":"Varshney A, Steinberg V. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103302","apa":"Varshney, A., & Steinberg, V. (2018). Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103302","chicago":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103302.","ieee":"A. Varshney and V. Steinberg, “Drag enhancement and drag reduction in viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018.","ista":"Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 3(10), 103302.","mla":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103302, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103302."},"date_published":"2018-10-15T00:00:00Z","publication":"Physical Review Fluids","_id":"17","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Drag enhancement and drag reduction in viscoelastic flow","isi":1,"file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf","file_id":"4800","creator":"system","relation":"main_file","date_updated":"2020-07-14T12:45:12Z","file_size":1409040,"checksum":"e1445be33e8165114e96246275600750","date_created":"2018-12-12T10:10:14Z"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa":1,"issue":"10","ec_funded":1,"ddc":["532"],"abstract":[{"lang":"eng","text":"Creeping flow of polymeric fluid without inertia exhibits elastic instabilities and elastic turbulence accompanied by drag enhancement due to elastic stress produced by flow-stretched polymers. However, in inertia-dominated flow at high Re and low fluid elasticity El, a reduction in turbulent frictional drag is caused by an intricate competition between inertial and elastic stresses. Here we explore the effect of inertia on the stability of viscoelastic flow in a broad range of control parameters El and (Re,Wi). We present the stability diagram of observed flow regimes in Wi-Re coordinates and find that the instabilities' onsets show an unexpectedly nonmonotonic dependence on El. Further, three distinct regions in the diagram are identified based on El. Strikingly, for high-elasticity fluids we discover a complete relaminarization of flow at Reynolds number in the range of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive effects may be explained by a finite polymer extensibility and a suppression of vorticity at high Wi. Our results call for further theoretical and numerical development to uncover the role of inertial effect on elastic turbulence in a viscoelastic flow."}],"date_updated":"2023-09-11T12:59:28Z","external_id":{"isi":["000447311500001"]},"date_created":"2018-12-11T11:44:11Z","publisher":"American Physical Society","publist_id":"8038"},{"scopus_import":"1","oa_version":"Preprint","month":"06","intvolume":" 115","citation":{"chicago":"Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1716659115.","apa":"Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G., & Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1716659115","ama":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. PNAS. 2018;115(23):6088-6093. doi:10.1073/pnas.1716659115","short":"A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093.","ieee":"A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018.","mla":"Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.","ista":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093."},"date_published":"2018-06-05T00:00:00Z","publication":"PNAS","publication_status":"published","page":"6088 - 6093","article_processing_charge":"No","type":"journal_article","doi":"10.1073/pnas.1716659115","author":[{"last_name":"Granados","first_name":"Alejandro","full_name":"Granados, Alejandro"},{"full_name":"Pietsch, Julian","first_name":"Julian","last_name":"Pietsch"},{"first_name":"Sarah A","full_name":"Cepeda Humerez, Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez"},{"first_name":"Isebail","full_name":"Farquhar, Isebail","last_name":"Farquhar"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","full_name":"Tkacik, Gasper"},{"last_name":"Swain","full_name":"Swain, Peter","first_name":"Peter"}],"pmid":1,"department":[{"_id":"GaTk"}],"volume":115,"status":"public","year":"2018","day":"05","language":[{"iso":"eng"}],"article_type":"original","date_updated":"2023-09-11T12:58:24Z","external_id":{"pmid":["29784812"],"isi":["000434114900071"]},"acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to G.T.).","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/early/2017/09/21/192039"}],"date_created":"2018-12-11T11:45:35Z","publisher":"National Academy of Sciences","publist_id":"7618","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6473"}]},"issue":"23","abstract":[{"lang":"eng","text":"Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Distributed and dynamic intracellular organization of extracellular information","isi":1,"_id":"281","quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis requires the coordinated assembly of various endocytic proteins and lipids at the plasma membrane. Accumulating evidence demonstrates a crucial role for phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) in endocytosis, but specific roles for PtdIns(4)P other than as the biosynthetic precursor of PtdIns(4,5)P2 have not been clarified. In this study we investigated the role of PtdIns(4)P or PtdIns(4,5)P2 in receptor-mediated endocytosis through the construction of temperature-sensitive (ts) mutants for the PI 4-kinases Stt4p and Pik1p and the PtdIns(4) 5-kinase Mss4p. Quantitative analyses of endocytosis revealed that both the stt4(ts)pik1(ts) and mss4(ts) mutants have a severe defect in endocytic internalization. Live-cell imaging of endocytic protein dynamics in stt4(ts)pik1(ts) and mss4(ts) mutants revealed that PtdIns(4)P is required for the recruitment of the alpha-factor receptor Ste2p to clathrin-coated pits whereas PtdIns(4,5)P2 is required for membrane internalization. We also found that the localization to endocytic sites of the ENTH/ANTH domain-bearing clathrin adaptors, Ent1p/Ent2p and Yap1801p/Yap1802p, is significantly impaired in the stt4(ts)pik1(ts) mutant, but not in the mss4(ts) mutant. These results suggest distinct roles in successive steps for PtdIns(4)P and PtdIns(4,5)P2 during receptor-mediated endocytosis."}],"oa":1,"issue":"1","date_created":"2018-12-11T11:47:32Z","publisher":"Company of Biologists","publist_id":"7184","date_updated":"2023-09-11T12:57:13Z","external_id":{"pmid":["29192062"],"isi":["000424786900012"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29192062","open_access":"1"}],"quality_controlled":"1","_id":"620","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis","article_processing_charge":"No","type":"journal_article","doi":"10.1242/jcs.207696","publication_status":"published","scopus_import":"1","oa_version":"Published Version","month":"01","intvolume":" 131","citation":{"ieee":"W. Yamamoto et al., “Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis,” Journal of Cell Science, vol. 131, no. 1. Company of Biologists, 2018.","mla":"Yamamoto, Wataru, et al. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science, vol. 131, no. 1, jcs207696, Company of Biologists, 2018, doi:10.1242/jcs.207696.","ista":"Yamamoto W, Wada S, Nagano M, Aoshima K, Siekhaus DE, Toshima J, Toshima J. 2018. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 131(1), jcs207696.","chicago":"Yamamoto, Wataru, Suguru Wada, Makoto Nagano, Kaito Aoshima, Daria E Siekhaus, Junko Toshima, and Jiro Toshima. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.207696.","short":"W. Yamamoto, S. Wada, M. Nagano, K. Aoshima, D.E. Siekhaus, J. Toshima, J. Toshima, Journal of Cell Science 131 (2018).","apa":"Yamamoto, W., Wada, S., Nagano, M., Aoshima, K., Siekhaus, D. E., Toshima, J., & Toshima, J. (2018). Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.207696","ama":"Yamamoto W, Wada S, Nagano M, et al. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 2018;131(1). doi:10.1242/jcs.207696"},"date_published":"2018-01-04T00:00:00Z","publication":"Journal of Cell Science","status":"public","day":"04","language":[{"iso":"eng"}],"year":"2018","department":[{"_id":"DaSi"}],"pmid":1,"volume":131,"author":[{"last_name":"Yamamoto","full_name":"Yamamoto, Wataru","first_name":"Wataru"},{"full_name":"Wada, Suguru","first_name":"Suguru","last_name":"Wada"},{"full_name":"Nagano, Makoto","first_name":"Makoto","last_name":"Nagano"},{"first_name":"Kaito","full_name":"Aoshima, Kaito","last_name":"Aoshima"},{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Toshima","full_name":"Toshima, Junko","first_name":"Junko"},{"full_name":"Toshima, Jiro","first_name":"Jiro","last_name":"Toshima"}],"article_number":"jcs207696"},{"abstract":[{"lang":"eng","text":"We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a densetime real-valued signal w and a parameterized temporal logic formula φ, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on φ and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of φ relative to w. Our implementation and experiments demonstrate that this approach can work well in practice."}],"ddc":["000"],"publication_identifier":{"isbn":["978-1-4503-5642-8 "]},"oa":1,"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"conference":{"end_date":"2018-04-13","location":"Porto, Portugal","name":"HSCC: Hybrid Systems: Computation and Control","start_date":"2018-04-11"},"publist_id":"7739","date_created":"2018-12-11T11:45:04Z","publisher":"ACM","date_updated":"2023-09-11T13:30:51Z","external_id":{"isi":["000474781600020"]},"quality_controlled":"1","_id":"182","alternative_title":["HSCC Proceedings"],"isi":1,"file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"2018_HSCC_Bakhirkin.pdf","date_updated":"2020-07-14T12:45:17Z","relation":"main_file","creator":"dernst","file_id":"7833","date_created":"2020-05-14T12:18:29Z","checksum":"81eabc96430e84336ea88310ac0a1ad0","file_size":5900421}],"title":"Efficient parametric identification for STL","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"conference","doi":"10.1145/3178126.3178132","article_processing_charge":"No","publication_status":"published","page":"177 - 186","citation":{"mla":"Bakhirkin, Alexey, et al. “Efficient Parametric Identification for STL.” Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–86, doi:10.1145/3178126.3178132.","ieee":"A. Bakhirkin, T. Ferrere, and O. Maler, “Efficient parametric identification for STL,” in Proceedings of the 21st International Conference on Hybrid Systems, Porto, Portugal, 2018, pp. 177–186.","ista":"Bakhirkin A, Ferrere T, Maler O. 2018. Efficient parametric identification for STL. Proceedings of the 21st International Conference on Hybrid Systems. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 177–186.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, and Oded Maler. “Efficient Parametric Identification for STL.” In Proceedings of the 21st International Conference on Hybrid Systems, 177–86. ACM, 2018. https://doi.org/10.1145/3178126.3178132.","apa":"Bakhirkin, A., Ferrere, T., & Maler, O. (2018). Efficient parametric identification for STL. In Proceedings of the 21st International Conference on Hybrid Systems (pp. 177–186). Porto, Portugal: ACM. https://doi.org/10.1145/3178126.3178132","ama":"Bakhirkin A, Ferrere T, Maler O. Efficient parametric identification for STL. In: Proceedings of the 21st International Conference on Hybrid Systems. ACM; 2018:177-186. doi:10.1145/3178126.3178132","short":"A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–186."},"date_published":"2018-04-11T00:00:00Z","publication":"Proceedings of the 21st International Conference on Hybrid Systems","scopus_import":"1","oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:45:17Z","month":"04","has_accepted_license":"1","status":"public","day":"11","year":"2018","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"author":[{"first_name":"Alexey","full_name":"Bakhirkin, Alexey","last_name":"Bakhirkin"},{"orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","first_name":"Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Maler","full_name":"Maler, Oded","first_name":"Oded"}]},{"volume":"F138033","department":[{"_id":"KrCh"}],"author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Kučera","first_name":"Antonín","full_name":"Kučera, Antonín"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny","first_name":"Petr","full_name":"Novotny, Petr"},{"first_name":"Dominik","full_name":"Velan, Dominik","last_name":"Velan"},{"first_name":"Florian","full_name":"Zuleger, Florian","last_name":"Zuleger"}],"status":"public","year":"2018","language":[{"iso":"eng"}],"day":"09","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS,” F138033:185–94. IEEE, 2018. https://doi.org/10.1145/3209108.3209191.","ama":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033. IEEE; 2018:185-194. doi:10.1145/3209108.3209191","apa":"Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., & Zuleger, F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS (Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science, Oxford, United Kingdom: IEEE. https://doi.org/10.1145/3209108.3209191","short":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:, IEEE, 2018, pp. 185–194.","ieee":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger, “Efficient algorithms for asymptotic bounds on termination time in VASS,” presented at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033, pp. 185–194.","ista":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194.","mla":"Brázdil, Tomáš, et al. Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS. Vol. F138033, IEEE, 2018, pp. 185–94, doi:10.1145/3209108.3209191."},"date_published":"2018-07-09T00:00:00Z","oa_version":"Preprint","scopus_import":"1","month":"07","doi":"10.1145/3209108.3209191","type":"conference","article_processing_charge":"No","publication_status":"published","page":"185 - 194","isi":1,"title":"Efficient algorithms for asymptotic bounds on termination time in VASS","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","_id":"143","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"conference":{"location":"Oxford, United Kingdom","name":"LICS: Logic in Computer Science","start_date":"2018-07-09","end_date":"2018-07-12"},"publist_id":"7780","date_created":"2018-12-11T11:44:51Z","publisher":"IEEE","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.10985"}],"date_updated":"2023-09-11T13:23:42Z","external_id":{"isi":["000545262800020"]},"ec_funded":1,"abstract":[{"text":"Vector Addition Systems with States (VASS) provide a well-known and fundamental model for the analysis of concurrent processes, parameterized systems, and are also used as abstract models of programs in resource bound analysis. In this paper we study the problem of obtaining asymptotic bounds on the termination time of a given VASS. In particular, we focus on the practically important case of obtaining polynomial bounds on termination time. Our main contributions are as follows: First, we present a polynomial-time algorithm for deciding whether a given VASS has a linear asymptotic complexity. We also show that if the complexity of a VASS is not linear, it is at least quadratic. Second, we classify VASS according to quantitative properties of their cycles. We show that certain singularities in these properties are the key reason for non-polynomial asymptotic complexity of VASS. In absence of singularities, we show that the asymptotic complexity is always polynomial and of the form Θ(nk), for some integer k d, where d is the dimension of the VASS. We present a polynomial-time algorithm computing the optimal k. For general VASS, the same algorithm, which is based on a complete technique for the construction of ranking functions in VASS, produces a valid lower bound, i.e., a k such that the termination complexity is (nk). Our results are based on new insights into the geometry of VASS dynamics, which hold the potential for further applicability to VASS analysis.","lang":"eng"}],"publication_identifier":{"isbn":["978-1-4503-5583-4"]},"oa":1,"project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}]},{"department":[{"_id":"VlKo"}],"author":[{"last_name":"Mohapatra","full_name":"Mohapatra, Pritish","first_name":"Pritish"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","last_name":"Rolinek","first_name":"Michal","full_name":"Rolinek, Michal"},{"last_name":"Jawahar","full_name":"Jawahar, C V","first_name":"C V"},{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"},{"full_name":"Kumar, M Pawan","first_name":"M Pawan","last_name":"Kumar"}],"status":"public","language":[{"iso":"eng"}],"day":"28","year":"2018","oa_version":"Preprint","scopus_import":"1","month":"06","citation":{"short":"P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–3701.","apa":"Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., & Kumar, M. P. (2018). Efficient optimization for rank-based loss functions. In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 3693–3701). Salt Lake City, UT, USA: IEEE. https://doi.org/10.1109/cvpr.2018.00389","ama":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization for rank-based loss functions. In: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2018:3693-3701. doi:10.1109/cvpr.2018.00389","chicago":"Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 3693–3701. IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00389.","ieee":"P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient optimization for rank-based loss functions,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, USA, 2018, pp. 3693–3701.","ista":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 3693–3701.","mla":"Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.” 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–701, doi:10.1109/cvpr.2018.00389."},"publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","date_published":"2018-06-28T00:00:00Z","article_processing_charge":"No","doi":"10.1109/cvpr.2018.00389","type":"conference","publication_status":"published","page":"3693-3701","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Efficient optimization for rank-based loss functions","quality_controlled":"1","_id":"273","date_created":"2018-12-11T11:45:33Z","publisher":"IEEE","conference":{"end_date":"2018-06-22","start_date":"2018-06-18","name":"CVPR: Conference on Computer Vision and Pattern Recognition","location":"Salt Lake City, UT, USA"},"date_updated":"2023-09-11T13:24:43Z","external_id":{"isi":["000457843603087"],"arxiv":["1604.08269"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.08269"}],"publication_identifier":{"isbn":["9781538664209"]},"ec_funded":1,"abstract":[{"text":"The accuracy of information retrieval systems is often measured using complex loss functions such as the average precision (AP) or the normalized discounted cumulative gain (NDCG). Given a set of positive and negative samples, the parameters of a retrieval system can be estimated by minimizing these loss functions. However, the non-differentiability and non-decomposability of these loss functions does not allow for simple gradient based optimization algorithms. This issue is generally circumvented by either optimizing a structured hinge-loss upper bound to the loss function or by using asymptotic methods like the direct-loss minimization framework. Yet, the high computational complexity of loss-augmented inference, which is necessary for both the frameworks, prohibits its use in large training data sets. To alleviate this deficiency, we present a novel quicksort flavored algorithm for a large class of non-decomposable loss functions. We provide a complete characterization of the loss functions that are amenable to our algorithm, and show that it includes both AP and NDCG based loss functions. Furthermore, we prove that no comparison based algorithm can improve upon the computational complexity of our approach asymptotically. We demonstrate the effectiveness of our approach in the context of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning models for a variety of vision tasks. We show that our approach provides significantly better results than simpler decomposable loss functions, while requiring a comparable training time.","lang":"eng"}],"project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"oa":1},{"_id":"289","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene","isi":1,"oa":1,"issue":"16","abstract":[{"lang":"eng","text":"We report on quantum capacitance measurements of high quality, graphite- and hexagonal boron nitride encapsulated Bernal stacked trilayer graphene devices. At zero applied magnetic field, we observe a number of electron density- and electrical displacement-tuned features in the electronic compressibility associated with changes in Fermi surface topology. At high displacement field and low density, strong trigonal warping gives rise to emergent Dirac gullies centered near the corners of the hexagonal Brillouin and related by three fold rotation symmetry. At low magnetic fields of B=1.25~T, the gullies manifest as a change in the degeneracy of the Landau levels from two to three. Weak incompressible states are also observed at integer filling within these triplets Landau levels, which a Hartree-Fock analysis indicates are associated with Coulomb-driven nematic phases that spontaneously break rotation symmetry."}],"external_id":{"isi":["000447307500007"],"arxiv":["1805.01038"]},"date_updated":"2023-09-11T13:39:50Z","main_file_link":[{"url":"https://arxiv.org/abs/1805.01038","open_access":"1"}],"acknowledgement":"The experimental work at UCSB was funded by the National Science Foundation under Grant No. DMR- 1654186. Work at Columbia was supported by the National Science Foundation under Grant No. DMR- 1507788. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the Ministry of Education, Culture, Sports, Science and Technology, Japan, and the Japan Society for the Promotion of Science KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Fellowship from the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard foundation and the Sloan Foundation. Measurements made use of a dilution refrigerator funded through the Major Research Instrumentation program of the U.S. National Science Foundation under Grant No. DMR- 1531389, and the MRL Shared Experimental Facilities, which are supported by the MRSEC Program of the U.S. National Science Foundation under Grant No. DMR- 1720256.","publisher":"American Physical Society","date_created":"2018-12-11T11:45:38Z","language":[{"iso":"eng"}],"day":"19","year":"2018","status":"public","article_type":"original","author":[{"first_name":"Alexander","full_name":"Zibrov, Alexander","last_name":"Zibrov"},{"id":"47C23AC6-02D0-11E9-BD0E-99399A5D3DEB","last_name":"Peng","orcid":"0000-0003-1250-0021","first_name":"Rao","full_name":"Peng, Rao"},{"full_name":"Kometter, Carlos","first_name":"Carlos","last_name":"Kometter"},{"first_name":"Jia","full_name":"Li, Jia","last_name":"Li"},{"first_name":"Cory","full_name":"Dean, Cory","last_name":"Dean"},{"last_name":"Taniguchi","full_name":"Taniguchi, Takashi","first_name":"Takashi"},{"last_name":"Watanabe","first_name":"Kenji","full_name":"Watanabe, Kenji"},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"},{"full_name":"Young, Andrea","first_name":"Andrea","last_name":"Young"}],"article_number":"167601","department":[{"_id":"MaSe"}],"volume":121,"publication_status":"published","article_processing_charge":"No","type":"journal_article","doi":"10.1103/PhysRevLett.121.167601","month":"10","intvolume":" 121","scopus_import":"1","oa_version":"Preprint","publication":"Physical Review Letters","date_published":"2018-10-19T00:00:00Z","citation":{"mla":"Zibrov, Alexander, et al. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters, vol. 121, no. 16, 167601, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.167601.","ista":"Zibrov A, Rao P, Kometter C, Li J, Dean C, Taniguchi T, Watanabe K, Serbyn M, Young A. 2018. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 121(16), 167601.","ieee":"A. Zibrov et al., “Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","chicago":"Zibrov, Alexander, Peng Rao, Carlos Kometter, Jia Li, Cory Dean, Takashi Taniguchi, Kenji Watanabe, Maksym Serbyn, and Andrea Young. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.167601.","apa":"Zibrov, A., Rao, P., Kometter, C., Li, J., Dean, C., Taniguchi, T., … Young, A. (2018). Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.167601","ama":"Zibrov A, Rao P, Kometter C, et al. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.167601","short":"A. Zibrov, P. Rao, C. Kometter, J. Li, C. Dean, T. Taniguchi, K. Watanabe, M. Serbyn, A. Young, Physical Review Letters 121 (2018)."}},{"issue":"8","project":[{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","grant_number":"707438","call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425"}],"oa":1,"abstract":[{"lang":"eng","text":"In this paper, we discuss biological effects of electromagnetic (EM) fields in the context of cancer biology. In particular, we review the nanomechanical properties of microtubules (MTs), the latter being one of the most successful targets for cancer therapy. We propose an investigation on the coupling of electromagnetic radiation to mechanical vibrations of MTs as an important basis for biological and medical applications. In our opinion, optomechanical methods can accurately monitor and control the mechanical properties of isolated MTs in a liquid environment. Consequently, studying nanomechanical properties of MTs may give useful information for future applications to diagnostic and therapeutic technologies involving non-invasive externally applied physical fields. For example, electromagnetic fields or high intensity ultrasound can be used therapeutically avoiding harmful side effects of chemotherapeutic agents or classical radiation therapy."}],"ec_funded":1,"main_file_link":[{"url":"https://www.bioscience.org/2018/v23/af/4651/fulltext.htm","open_access":"1"}],"acknowledgement":"The work of SB has been supported by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska Curie grant agreement No MSC-IF 707438 SUPEREOM. JAT gratefully acknowledges funding support from NSERC (Canada) for his research. MC acknowledges support from the Czech Science Foundation, projects 15-17102S and 17-11898S and he participates in COST Action BM1309, CA15211 and bilateral exchange project between Czech and Slovak Academies of Sciences, SAV-15-22.","external_id":{"pmid":["29293441"],"isi":["000439042800001"]},"date_updated":"2023-09-11T13:38:14Z","publisher":"Frontiers in Bioscience","date_created":"2018-12-11T11:45:37Z","_id":"287","quality_controlled":"1","title":"Electromagnetic fields and optomechanics In cancer diagnostics and treatment","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"page":"1391 - 1406","publication_status":"published","doi":"10.2741/4651","type":"journal_article","article_processing_charge":"No","date_published":"2018-03-01T00:00:00Z","publication":"Frontiers in Bioscience - Landmark","citation":{"chicago":"Salari, Vahid, Shabir Barzanjeh, Michal Cifra, Christoph Simon, Felix Scholkmann, Zahra Alirezaei, and Jack Tuszynski. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark. Frontiers in Bioscience, 2018. https://doi.org/10.2741/4651.","ama":"Salari V, Barzanjeh S, Cifra M, et al. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 2018;23(8):1391-1406. doi:10.2741/4651","apa":"Salari, V., Barzanjeh, S., Cifra, M., Simon, C., Scholkmann, F., Alirezaei, Z., & Tuszynski, J. (2018). Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. Frontiers in Bioscience. https://doi.org/10.2741/4651","short":"V. Salari, S. Barzanjeh, M. Cifra, C. Simon, F. Scholkmann, Z. Alirezaei, J. Tuszynski, Frontiers in Bioscience - Landmark 23 (2018) 1391–1406.","mla":"Salari, Vahid, et al. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark, vol. 23, no. 8, Frontiers in Bioscience, 2018, pp. 1391–406, doi:10.2741/4651.","ieee":"V. Salari et al., “Electromagnetic fields and optomechanics In cancer diagnostics and treatment,” Frontiers in Bioscience - Landmark, vol. 23, no. 8. Frontiers in Bioscience, pp. 1391–1406, 2018.","ista":"Salari V, Barzanjeh S, Cifra M, Simon C, Scholkmann F, Alirezaei Z, Tuszynski J. 2018. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 23(8), 1391–1406."},"intvolume":" 23","month":"03","oa_version":"Submitted Version","scopus_import":"1","day":"01","language":[{"iso":"eng"}],"year":"2018","status":"public","author":[{"last_name":"Salari","full_name":"Salari, Vahid","first_name":"Vahid"},{"orcid":"0000-0003-0415-1423","first_name":"Shabir","full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh"},{"last_name":"Cifra","full_name":"Cifra, Michal","first_name":"Michal"},{"first_name":"Christoph","full_name":"Simon, Christoph","last_name":"Simon"},{"first_name":"Felix","full_name":"Scholkmann, Felix","last_name":"Scholkmann"},{"last_name":"Alirezaei","first_name":"Zahra","full_name":"Alirezaei, Zahra"},{"full_name":"Tuszynski, Jack","first_name":"Jack","last_name":"Tuszynski"}],"volume":23,"department":[{"_id":"JoFi"}],"pmid":1},{"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"oa":1,"issue":"1","related_material":{"record":[{"id":"2157","status":"public","relation":"earlier_version"}]},"abstract":[{"lang":"eng","text":"We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in R3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, that is, an essential curve in the boundary of X bounding a disk in S3 \\ X with length bounded by a computable function of the number of tetrahedra of X."}],"ec_funded":1,"external_id":{"isi":["000425685900006"],"arxiv":["1402.0815"]},"date_updated":"2023-09-11T13:38:49Z","main_file_link":[{"url":"https://arxiv.org/abs/1402.0815","open_access":"1"}],"publisher":"ACM","date_created":"2018-12-11T11:46:24Z","publist_id":"7398","_id":"425","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Embeddability in the 3-Sphere is decidable","isi":1,"publication_status":"published","article_processing_charge":"No","type":"journal_article","doi":"10.1145/3078632","intvolume":" 65","month":"01","scopus_import":"1","oa_version":"Preprint","publication":"Journal of the ACM","date_published":"2018-01-01T00:00:00Z","citation":{"short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Journal of the ACM 65 (2018).","apa":"Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2018). Embeddability in the 3-Sphere is decidable. Journal of the ACM. ACM. https://doi.org/10.1145/3078632","ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 2018;65(1). doi:10.1145/3078632","chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability in the 3-Sphere Is Decidable.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3078632.","ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2018. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 65(1), 5.","mla":"Matoušek, Jiří, et al. “Embeddability in the 3-Sphere Is Decidable.” Journal of the ACM, vol. 65, no. 1, 5, ACM, 2018, doi:10.1145/3078632.","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the 3-Sphere is decidable,” Journal of the ACM, vol. 65, no. 1. ACM, 2018."},"language":[{"iso":"eng"}],"year":"2018","day":"01","status":"public","article_type":"original","author":[{"first_name":"Jiří","full_name":"Matoušek, Jiří","last_name":"Matoušek"},{"last_name":"Sedgwick","first_name":"Eric","full_name":"Sedgwick, Eric"},{"last_name":"Tancer","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin","first_name":"Martin"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568"}],"article_number":"5","department":[{"_id":"UlWa"}],"volume":65},{"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"}],"department":[{"_id":"NiBa"}],"volume":122,"status":"public","language":[{"iso":"eng"}],"day":"01","year":"2018","has_accepted_license":"1","article_type":"original","oa_version":"Submitted Version","scopus_import":"1","intvolume":" 122","file_date_updated":"2020-07-14T12:47:09Z","month":"07","citation":{"ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.","apa":"Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007","ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007","chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology. Academic Press, 2018. https://doi.org/10.1016/j.tpb.2017.11.007."},"publication":"Theoretical Population Biology","date_published":"2018-07-01T00:00:00Z","publication_status":"published","page":"110-127","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","article_processing_charge":"No","type":"journal_article","doi":"10.1016/j.tpb.2017.11.007","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Establishment in a new habitat by polygenic adaptation","isi":1,"file":[{"creator":"nbarton","file_id":"7199","relation":"main_file","date_updated":"2020-07-14T12:47:09Z","checksum":"0b96f6db47e3e91b5e7d103b847c239d","date_created":"2019-12-21T09:36:39Z","file_size":2287682,"content_type":"application/pdf","access_level":"open_access","file_name":"bartonetheridge.pdf"}],"_id":"564","quality_controlled":"1","date_updated":"2023-09-11T13:41:22Z","external_id":{"isi":["000440392900014"]},"date_created":"2018-12-11T11:47:12Z","publisher":"Academic Press","publist_id":"7250","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"oa":1,"related_material":{"record":[{"id":"9842","relation":"research_data","status":"public"}]},"issue":"7","ec_funded":1,"abstract":[{"lang":"eng","text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population."}],"ddc":["519","576"]},{"external_id":{"isi":["000438240900054"]},"date_updated":"2023-09-11T13:43:22Z","acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","publisher":"Nature Publishing Group","date_created":"2018-12-11T11:44:56Z","publist_id":"7764","oa":1,"project":[{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"issue":"7713","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/engineering-cooperation/"}]},"abstract":[{"text":"Social dilemmas occur when incentives for individuals are misaligned with group interests 1-7 . According to the 'tragedy of the commons', these misalignments can lead to overexploitation and collapse of public resources. The resulting behaviours can be analysed with the tools of game theory 8 . The theory of direct reciprocity 9-15 suggests that repeated interactions can alleviate such dilemmas, but previous work has assumed that the public resource remains constant over time. Here we introduce the idea that the public resource is instead changeable and depends on the strategic choices of individuals. An intuitive scenario is that cooperation increases the public resource, whereas defection decreases it. Thus, cooperation allows the possibility of playing a more valuable game with higher payoffs, whereas defection leads to a less valuable game. We analyse this idea using the theory of stochastic games 16-19 and evolutionary game theory. We find that the dependence of the public resource on previous interactions can greatly enhance the propensity for cooperation. For these results, the interaction between reciprocity and payoff feedback is crucial: neither repeated interactions in a constant environment nor single interactions in a changing environment yield similar cooperation rates. Our framework shows which feedbacks between exploitation and environment - either naturally occurring or designed - help to overcome social dilemmas.","lang":"eng"}],"ddc":["000"],"ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Evolution of cooperation in stochastic games","file":[{"file_name":"2018_Nature_Hilbe.pdf","content_type":"application/pdf","access_level":"open_access","date_created":"2019-11-19T08:09:57Z","checksum":"011ab905cf9a410bc2b96f15174d654d","file_size":2834442,"creator":"dernst","file_id":"7049","relation":"main_file","date_updated":"2020-07-14T12:45:02Z"}],"isi":1,"_id":"157","quality_controlled":"1","month":"07","intvolume":" 559","file_date_updated":"2020-07-14T12:45:02Z","scopus_import":"1","oa_version":"Submitted Version","date_published":"2018-07-04T00:00:00Z","publication":"Nature","citation":{"mla":"Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” Nature, vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:10.1038/s41586-018-0277-x.","ieee":"C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation in stochastic games,” Nature, vol. 559, no. 7713. Nature Publishing Group, pp. 246–249, 2018.","ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249.","chicago":"Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak. “Evolution of Cooperation in Stochastic Games.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0277-x.","ama":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic games. Nature. 2018;559(7713):246-249. doi:10.1038/s41586-018-0277-x","apa":"Hilbe, C., Šimsa, Š., Chatterjee, K., & Nowak, M. (2018). Evolution of cooperation in stochastic games. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0277-x","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249."},"page":"246 - 249","publication_status":"published","article_processing_charge":"No","doi":"10.1038/s41586-018-0277-x","type":"journal_article","author":[{"orcid":"0000-0001-5116-955X","first_name":"Christian","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe"},{"last_name":"Šimsa","first_name":"Štepán","full_name":"Šimsa, Štepán"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"department":[{"_id":"KrCh"}],"volume":559,"day":"04","language":[{"iso":"eng"}],"year":"2018","status":"public","has_accepted_license":"1"},{"publist_id":"7445","date_created":"2018-12-11T11:46:10Z","publisher":"Oxford University Press","acknowledgement":"his work was supported by the Deutsche Forschungsgemeinschaft (grant number FR 1411/9-1). This work was supported by the German Research Foundation (DFG) and the Technical University of Munich within the fund- ing programme Open Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont status of the organisms and Michael Galperin for\r\nuseful comments. T","date_updated":"2023-09-11T13:56:52Z","external_id":{"isi":["000429483700022"]},"ddc":["576"],"abstract":[{"lang":"eng","text":"Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification."}],"issue":"3","oa":1,"isi":1,"file":[{"date_updated":"2020-07-14T12:46:16Z","relation":"main_file","file_id":"4667","creator":"system","file_size":691602,"date_created":"2018-12-12T10:08:07Z","checksum":"458a7c2c2e79528567edfeb0f326cbe0","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf"}],"title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","_id":"384","citation":{"short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938.","apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., & Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evy049","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049","chicago":"Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy049.","ieee":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018.","ista":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 10(3), 928–938.","mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049."},"date_published":"2018-03-01T00:00:00Z","publication":"Genome Biology and Evolution","scopus_import":"1","oa_version":"Published Version","month":"03","intvolume":" 10","file_date_updated":"2020-07-14T12:46:16Z","doi":"10.1093/gbe/evy049","type":"journal_article","article_processing_charge":"No","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"page":"928 - 938","volume":10,"department":[{"_id":"FyKo"}],"author":[{"last_name":"Hönigschmid","first_name":"Peter","full_name":"Hönigschmid, Peter"},{"last_name":"Bykova","first_name":"Nadya","full_name":"Bykova, Nadya"},{"last_name":"Schneider","full_name":"Schneider, René","first_name":"René"},{"id":"49FF1036-F248-11E8-B48F-1D18A9856A87","last_name":"Ivankov","first_name":"Dmitry","full_name":"Ivankov, Dmitry"},{"first_name":"Dmitrij","full_name":"Frishman, Dmitrij","last_name":"Frishman"}],"pubrep_id":"999","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"day":"01","year":"2018"},{"oa_version":"Preprint","scopus_import":"1","month":"03","intvolume":" 208","citation":{"mla":"Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics, vol. 208, no. 3, Genetics Society of America, 2018, pp. 1231–45, doi:10.1534/genetics.117.300638.","ieee":"H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers to gene flow from distorted isolation-by-distance patterns,” Genetics, vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.","ista":"Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245.","chicago":"Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300638.","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.","ama":"Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 2018;208(3):1231-1245. doi:10.1534/genetics.117.300638","apa":"Ringbauer, H., Kolesnikov, A., Field, D., & Barton, N. H. (2018). Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300638"},"publication":"Genetics","date_published":"2018-03-01T00:00:00Z","article_processing_charge":"No","doi":"10.1534/genetics.117.300638","type":"journal_article","publication_status":"published","page":"1231-1245","department":[{"_id":"NiBa"},{"_id":"ChLa"}],"volume":208,"author":[{"last_name":"Ringbauer","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","full_name":"Ringbauer, Harald","first_name":"Harald","orcid":"0000-0002-4884-9682"},{"first_name":"Alexander","full_name":"Kolesnikov, Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov"},{"last_name":"Field","first_name":"David","full_name":"Field, David"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"status":"public","year":"2018","language":[{"iso":"eng"}],"day":"01","date_created":"2018-12-11T11:47:12Z","publisher":"Genetics Society of America","publist_id":"7251","date_updated":"2023-09-11T13:42:38Z","external_id":{"isi":["000426219600025"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/205484v1"}],"abstract":[{"lang":"eng","text":"In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes\r\nthan geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow."}],"oa":1,"related_material":{"record":[{"id":"200","relation":"dissertation_contains","status":"public"}]},"issue":"3","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","quality_controlled":"1","_id":"563"},{"publication_identifier":{"issn":["0167-7055"]},"abstract":[{"lang":"eng","text":"The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by combining particles with grids. To improve performance, the subsequent narrow band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid surface and a traditional grid‐based fluid simulation away from the surface. This spatially‐limited FLIP simulation significantly reduces the number of particles and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP idea even further, by allowing a simulation to transition between a FLIP‐like fluid simulation and a grid‐based simulation in arbitrary locations, not just near the surface. This approach leads to even more savings in memory and computation, because we can concentrate the particles only in areas where they are needed. More importantly, this new method allows us to seamlessly transition to smooth implicit surface geometry wherever the particle‐based simulation is unnecessary. Consequently, our method leads to a practical algorithm for avoiding the noisy surface artifacts associated with particle‐based liquid simulations, while simultaneously maintaining the benefits of a FLIP simulation in regions of dynamic motion."}],"ddc":["006"],"ec_funded":1,"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"}],"oa":1,"issue":"2","publisher":"Wiley","date_created":"2018-12-11T11:44:49Z","external_id":{"isi":["000434085600016"]},"date_updated":"2023-09-11T14:00:26Z","quality_controlled":"1","_id":"135","alternative_title":["Eurographics"],"file":[{"file_name":"exnbflip.pdf","success":1,"access_level":"open_access","content_type":"application/pdf","file_size":54309947,"checksum":"8edb90da8a72395eb5d970580e0925b6","date_created":"2020-10-08T08:38:23Z","relation":"main_file","date_updated":"2020-10-08T08:38:23Z","file_id":"8627","creator":"wojtan"}],"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Extended narrow band FLIP for liquid simulations","article_processing_charge":"No","type":"journal_article","doi":"10.1111/cgf.13351","page":"169 - 177","publication_status":"published","intvolume":" 37","file_date_updated":"2020-10-08T08:38:23Z","month":"05","scopus_import":"1","oa_version":"Submitted Version","date_published":"2018-05-22T00:00:00Z","publication":"Computer Graphics Forum","citation":{"mla":"Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:10.1111/cgf.13351.","ista":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177.","ieee":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow band FLIP for liquid simulations,” Computer Graphics Forum, vol. 37, no. 2. Wiley, pp. 169–177, 2018.","chicago":"Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13351.","ama":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 2018;37(2):169-177. doi:10.1111/cgf.13351","apa":"Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2018). Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13351","short":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum 37 (2018) 169–177."},"has_accepted_license":"1","article_type":"original","year":"2018","language":[{"iso":"eng"}],"day":"22","status":"public","department":[{"_id":"ChWo"}],"volume":37,"author":[{"full_name":"Sato, Takahiro","first_name":"Takahiro","last_name":"Sato"},{"orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"},{"first_name":"Nils","full_name":"Thuerey, Nils","last_name":"Thuerey"},{"first_name":"Takeo","full_name":"Igarashi, Takeo","last_name":"Igarashi"},{"full_name":"Ando, Ryoichi","first_name":"Ryoichi","last_name":"Ando"}]},{"year":"2018","day":"01","language":[{"iso":"eng"}],"status":"public","article_type":"original","author":[{"orcid":"0000-0002-7214-0171","first_name":"Katarina","full_name":"Bodova, Katarina","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bodova"},{"full_name":"Priklopil, Tadeas","first_name":"Tadeas","last_name":"Priklopil","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4014-8478","first_name":"David","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","first_name":"Melinda","orcid":"0000-0001-6118-0541"}],"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"volume":209,"page":"861-883","publication_status":"published","article_processing_charge":"No","doi":"10.1534/genetics.118.300748","type":"journal_article","intvolume":" 209","month":"07","oa_version":"Preprint","scopus_import":"1","date_published":"2018-07-01T00:00:00Z","publication":"Genetics","citation":{"ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.","mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300748.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300748","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748"},"_id":"316","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","isi":1,"oa":1,"project":[{"name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960","_id":"25B36484-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"issue":"3","related_material":{"link":[{"url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"status":"public","relation":"research_data","id":"9813"}]},"abstract":[{"lang":"eng","text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants."}],"ec_funded":1,"external_id":{"isi":["000437171700017"]},"date_updated":"2023-09-11T13:57:43Z","main_file_link":[{"url":"https://www.biorxiv.org/node/80098.abstract","open_access":"1"}],"publisher":"Genetics Society of America","date_created":"2018-12-11T11:45:47Z"},{"oa_version":"Submitted Version","scopus_import":"1","month":"07","intvolume":" 330","citation":{"apa":"Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer, E., … Schal, C. (2018). Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. Wiley. https://doi.org/10.1002/jez.b.22824","ama":"Harrison M, Arning N, Kremer L, et al. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 2018;330:254-264. doi:10.1002/jez.b.22824","short":"M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer, A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.","chicago":"Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles, Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. Wiley, 2018. https://doi.org/10.1002/jez.b.22824.","ista":"Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 330, 254–264.","ieee":"M. Harrison et al., “Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest,” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol. 330. Wiley, pp. 254–264, 2018.","mla":"Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol. 330, Wiley, 2018, pp. 254–64, doi:10.1002/jez.b.22824."},"date_published":"2018-07-11T00:00:00Z","publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","article_processing_charge":"No","doi":"10.1002/jez.b.22824","type":"journal_article","publication_status":"published","page":"254-264","pmid":1,"department":[{"_id":"BeVi"}],"volume":330,"author":[{"last_name":"Harrison","full_name":"Harrison, Mark","first_name":"Mark"},{"full_name":"Arning, Nicolas","first_name":"Nicolas","last_name":"Arning"},{"last_name":"Kremer","full_name":"Kremer, Lucas","first_name":"Lucas"},{"full_name":"Ylla, Guillem","first_name":"Guillem","last_name":"Ylla"},{"full_name":"Belles, Xavier","first_name":"Xavier","last_name":"Belles"},{"first_name":"Erich","full_name":"Bornberg Bauer, Erich","last_name":"Bornberg Bauer"},{"full_name":"Huylmans, Ann K","first_name":"Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jongepier, Evelien","first_name":"Evelien","last_name":"Jongepier"},{"first_name":"Maria","full_name":"Puilachs, Maria","last_name":"Puilachs"},{"last_name":"Richards","first_name":"Stephen","full_name":"Richards, Stephen"},{"last_name":"Schal","first_name":"Coby","full_name":"Schal, Coby"}],"article_type":"original","status":"public","year":"2018","language":[{"iso":"eng"}],"day":"11","date_created":"2018-12-11T11:45:06Z","publisher":"Wiley","publist_id":"7730","date_updated":"2023-09-11T13:59:54Z","external_id":{"isi":["000443231000002"],"pmid":["29998472"]},"main_file_link":[{"url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824","open_access":"1"}],"abstract":[{"lang":"eng","text":"The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control."}],"oa":1,"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","quality_controlled":"1","_id":"190"},{"date_published":"2018-01-30T00:00:00Z","publication":"SIAM Journal on Mathematical Analysis","citation":{"short":"J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 50 (2018) 411–455.","ama":"Fischer JL, Grün G. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 2018;50(1):411-455. doi:10.1137/16M1098796","apa":"Fischer, J. L., & Grün, G. (2018). Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1098796","chicago":"Fischer, Julian L, and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1098796.","ista":"Fischer JL, Grün G. 2018. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 50(1), 411–455.","mla":"Fischer, Julian L., and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 411–55, doi:10.1137/16M1098796.","ieee":"J. L. Fischer and G. Grün, “Existence of positive solutions to stochastic thin-film equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 1. Society for Industrial and Applied Mathematics , pp. 411–455, 2018."},"intvolume":" 50","month":"01","file_date_updated":"2020-07-14T12:46:22Z","scopus_import":"1","oa_version":"Published Version","page":"411 - 455","publication_status":"published","doi":"10.1137/16M1098796","type":"journal_article","article_processing_charge":"No","author":[{"orcid":"0000-0002-0479-558X","first_name":"Julian L","full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer"},{"last_name":"Grün","full_name":"Grün, Günther","first_name":"Günther"}],"volume":50,"department":[{"_id":"JuFi"}],"year":"2018","day":"30","language":[{"iso":"eng"}],"status":"public","article_type":"original","has_accepted_license":"1","external_id":{"isi":["000426630900015"]},"date_updated":"2023-09-11T13:59:22Z","publist_id":"7425","publisher":"Society for Industrial and Applied Mathematics ","date_created":"2018-12-11T11:46:17Z","issue":"1","oa":1,"abstract":[{"lang":"eng","text":"We construct martingale solutions to stochastic thin-film equations by introducing a (spatial) semidiscretization and establishing convergence. The discrete scheme allows for variants of the energy and entropy estimates in the continuous setting as long as the discrete energy does not exceed certain threshold values depending on the spatial grid size $h$. Using a stopping time argument to prolongate high-energy paths constant in time, arbitrary moments of coupled energy/entropy functionals can be controlled. Having established Hölder regularity of approximate solutions, the convergence proof is then based on compactness arguments---in particular on Jakubowski's generalization of Skorokhod's theorem---weak convergence methods, and recent tools on martingale convergence.\r\n\r\n"}],"ddc":["510"],"title":"Existence of positive solutions to stochastic thin-film equations","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"checksum":"89a8eae7c52bb356c04f52b44bff4b5a","date_created":"2019-11-07T12:20:25Z","file_size":557338,"date_updated":"2020-07-14T12:46:22Z","relation":"main_file","creator":"dernst","file_id":"6992","file_name":"2018_SIAM_Fischer.pdf","access_level":"open_access","content_type":"application/pdf"}],"isi":1,"_id":"404","quality_controlled":"1"}]