[{"date_published":"2014-01-01T00:00:00Z","oa_version":"None","date_created":"2018-12-12T11:39:14Z","citation":{"ieee":"J. Porsche, <i>Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland</i>. none, 2014.","apa":"Porsche, J. (2014). <i>Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland</i>. none.","ama":"Porsche J. <i>Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland</i>. none; 2014.","short":"J. Porsche, Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland, none, 2014.","ista":"Porsche J. 2014. Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland, none,p.","chicago":"Porsche, Jana. <i>Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland</i>. none, 2014.","mla":"Porsche, Jana. <i>Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland</i>. none, 2014."},"pubrep_id":"254","department":[{"_id":"E-Lib"}],"file_date_updated":"2020-07-14T12:46:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["020"],"has_accepted_license":"1","type":"report","language":[{"iso":"eng"}],"publisher":"none","file":[{"file_id":"5501","date_created":"2018-12-12T11:53:40Z","file_name":"IST-2014-254-v1+1_Dublin_Day_3.pdf","creator":"system","relation":"main_file","file_size":648585,"date_updated":"2020-07-14T12:46:50Z","access_level":"open_access","checksum":"3954896648ce8afa8f7c4425e71cff08","content_type":"application/pdf"},{"creator":"system","file_size":221339,"relation":"main_file","file_name":"IST-2014-254-v1+2_Dublin_Day_1.pdf","date_updated":"2020-07-14T12:46:50Z","checksum":"9a0d42b0b832dfe7e4b22fb6816bcbba","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T11:53:41Z","file_id":"5502"},{"relation":"main_file","creator":"system","file_size":187778,"file_name":"IST-2014-254-v1+3_Dublin_Day_2.pdf","date_updated":"2020-07-14T12:46:50Z","checksum":"498b8d629fb1bd17bff1dc43700a93e6","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T11:53:42Z","file_id":"5503"}],"abstract":[{"lang":"eng","text":"Notes from the Third Plenary for the Research Data Alliance in Dublin, Ireland on March 26 to 28, 2014 with focus on starting an institutional research data repository."}],"year":"2014","title":"Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland","oa":1,"author":[{"last_name":"Porsche","full_name":"Porsche, Jana","first_name":"Jana","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87"}],"_id":"5422","status":"public","date_updated":"2020-07-14T23:04:56Z"},{"ddc":["005"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:46:50Z","month":"07","department":[{"_id":"KrCh"}],"day":"29","citation":{"chicago":"Chatterjee, Krishnendu, Alexander Kössler, Andreas Pavlogiannis, and Ulrich Schmid. <i>A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks</i>. IST Austria, 2014. <a href=\"https://doi.org/10.15479/AT:IST-2014-300-v1-1\">https://doi.org/10.15479/AT:IST-2014-300-v1-1</a>.","mla":"Chatterjee, Krishnendu, et al. <i>A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks</i>. IST Austria, 2014, doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-300-v1-1\">10.15479/AT:IST-2014-300-v1-1</a>.","ista":"Chatterjee K, Kössler A, Pavlogiannis A, Schmid U. 2014. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks, IST Austria, 14p.","short":"K. Chatterjee, A. Kössler, A. Pavlogiannis, U. Schmid, A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks, IST Austria, 2014.","ama":"Chatterjee K, Kössler A, Pavlogiannis A, Schmid U. <i>A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks</i>. IST Austria; 2014. doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-300-v1-1\">10.15479/AT:IST-2014-300-v1-1</a>","apa":"Chatterjee, K., Kössler, A., Pavlogiannis, A., &#38; Schmid, U. (2014). <i>A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2014-300-v1-1\">https://doi.org/10.15479/AT:IST-2014-300-v1-1</a>","ieee":"K. Chatterjee, A. Kössler, A. Pavlogiannis, and U. Schmid, <i>A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks</i>. IST Austria, 2014."},"pubrep_id":"300","date_created":"2018-12-12T11:39:15Z","oa_version":"Published Version","date_published":"2014-07-29T00:00:00Z","file":[{"content_type":"application/pdf","checksum":"4b8fde4d9ef6653837f6803921d83032","access_level":"open_access","date_updated":"2020-07-14T12:46:50Z","relation":"main_file","file_size":1270021,"creator":"system","file_name":"IST-2014-300-v1+1_main.pdf","date_created":"2018-12-12T11:53:53Z","file_id":"5514"}],"publisher":"IST Austria","language":[{"iso":"eng"}],"type":"technical_report","has_accepted_license":"1","_id":"5423","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Kössler, Alexander","last_name":"Kössler","first_name":"Alexander"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"first_name":"Ulrich","full_name":"Schmid, Ulrich","last_name":"Schmid"}],"oa":1,"title":"A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks","doi":"10.15479/AT:IST-2014-300-v1-1","year":"2014","alternative_title":["IST Austria Technical Report"],"abstract":[{"text":"We present a flexible framework for the automated competitive analysis of on-line scheduling algorithms for firm- deadline real-time tasks based on multi-objective graphs: Given a taskset and an on-line scheduling algorithm specified as a labeled transition system, along with some optional safety, liveness, and/or limit-average constraints for the adversary, we automatically compute the competitive ratio of the algorithm w.r.t. a clairvoyant scheduler. We demonstrate the flexibility and power of our approach by comparing the competitive ratio of several on-line algorithms, including D(over), that have been proposed in the past, for various tasksets. Our experimental results reveal that none of these algorithms is universally optimal, in the sense that there are tasksets where other schedulers provide better performance. Our framework is hence a very useful design tool for selecting optimal algorithms for a given application. ","lang":"eng"}],"date_updated":"2023-02-23T10:11:15Z","publication_identifier":{"issn":["2664-1690"]},"page":"14","status":"public","publication_status":"published","related_material":{"record":[{"id":"1714","status":"public","relation":"later_version"}]}},{"year":"2014","alternative_title":["IST Austria Technical Report"],"abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs), that are a standard framework for robotics applications to model uncertainties present in the real world, with temporal logic specifications. All temporal logic specifications in linear-time temporal logic (LTL) can be expressed as parity objectives. We study the qualitative analysis problem for POMDPs with parity objectives that asks whether there is a controller (policy) to ensure that the objective holds with probability 1 (almost-surely). While the qualitative analysis of POMDPs with parity objectives is undecidable, recent results show that when restricted to finite-memory policies the problem is EXPTIME-complete. While the problem is intractable in theory, we present a practical approach to solve the qualitative analysis problem. We designed several heuristics to deal with the exponential complexity, and have used our implementation on a number of well-known POMDP examples for robotics applications. Our results provide the first practical approach to solve the qualitative analysis of robot motion planning with LTL properties in the presence of uncertainty."}],"doi":"10.15479/AT:IST-2014-305-v1-1","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"full_name":"Gupta, Raghav","last_name":"Gupta","first_name":"Raghav"},{"first_name":"Ayush","last_name":"Kanodia","full_name":"Kanodia, Ayush"}],"title":"Qualitative analysis of POMDPs with temporal logic specifications for robotics applications","oa":1,"_id":"5424","status":"public","publication_status":"published","related_material":{"record":[{"status":"public","relation":"later_version","id":"1732"},{"id":"5426","relation":"later_version","status":"public"}]},"page":"12","publication_identifier":{"issn":["2664-1690"]},"date_updated":"2023-02-23T12:25:52Z","date_published":"2014-09-09T00:00:00Z","date_created":"2018-12-12T11:39:15Z","oa_version":"Published Version","day":"09","department":[{"_id":"KrCh"}],"citation":{"short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications, IST Austria, 2014.","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2014. Qualitative analysis of POMDPs with temporal logic specifications for robotics applications, IST Austria, 12p.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. <i>Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications</i>. IST Austria; 2014. doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-305-v1-1\">10.15479/AT:IST-2014-305-v1-1</a>","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, <i>Qualitative analysis of POMDPs with temporal logic specifications for robotics applications</i>. IST Austria, 2014.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., &#38; Kanodia, A. (2014). <i>Qualitative analysis of POMDPs with temporal logic specifications for robotics applications</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2014-305-v1-1\">https://doi.org/10.15479/AT:IST-2014-305-v1-1</a>","mla":"Chatterjee, Krishnendu, et al. <i>Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications</i>. IST Austria, 2014, doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-305-v1-1\">10.15479/AT:IST-2014-305-v1-1</a>.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. <i>Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications</i>. IST Austria, 2014. <a href=\"https://doi.org/10.15479/AT:IST-2014-305-v1-1\">https://doi.org/10.15479/AT:IST-2014-305-v1-1</a>."},"pubrep_id":"305","ddc":["005"],"month":"09","file_date_updated":"2020-07-14T12:46:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","type":"technical_report","language":[{"iso":"eng"}],"file":[{"creator":"system","relation":"main_file","file_size":655774,"file_name":"IST-2014-305-v1+1_main.pdf","checksum":"35009d5fad01198341e6c1a3353481b7","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:51Z","date_created":"2018-12-12T11:53:51Z","file_id":"5512"}],"publisher":"IST Austria"},{"language":[{"iso":"eng"}],"type":"technical_report","has_accepted_license":"1","publisher":"IST Austria","file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"730c0a8e97cf2712a884b2cc423f3919","date_updated":"2020-07-14T12:46:51Z","file_name":"IST-2014-305-v2+1_main2.pdf","creator":"system","relation":"main_file","file_size":656019,"file_id":"5537","date_created":"2018-12-12T11:54:15Z"}],"date_created":"2018-12-12T11:39:16Z","oa_version":"Published Version","date_published":"2014-09-29T00:00:00Z","month":"09","file_date_updated":"2020-07-14T12:46:51Z","ddc":["005"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"311","citation":{"chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. <i>Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications</i>. IST Austria, 2014. <a href=\"https://doi.org/10.15479/AT:IST-2014-305-v2-1\">https://doi.org/10.15479/AT:IST-2014-305-v2-1</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications</i>. IST Austria, 2014, doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-305-v2-1\">10.15479/AT:IST-2014-305-v2-1</a>.","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2014. Qualitative analysis of POMDPs with temporal logic specifications for robotics applications, IST Austria, 10p.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. <i>Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications</i>. IST Austria; 2014. doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-305-v2-1\">10.15479/AT:IST-2014-305-v2-1</a>","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications, IST Austria, 2014.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., &#38; Kanodia, A. (2014). <i>Qualitative analysis of POMDPs with temporal logic specifications for robotics applications</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2014-305-v2-1\">https://doi.org/10.15479/AT:IST-2014-305-v2-1</a>","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, <i>Qualitative analysis of POMDPs with temporal logic specifications for robotics applications</i>. IST Austria, 2014."},"day":"29","department":[{"_id":"KrCh"}],"page":"10","related_material":{"record":[{"status":"public","relation":"later_version","id":"1732"},{"status":"public","relation":"earlier_version","id":"5424"}]},"publication_status":"published","status":"public","date_updated":"2023-02-23T12:25:47Z","publication_identifier":{"issn":["2664-1690"]},"doi":"10.15479/AT:IST-2014-305-v2-1","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs), that are a standard framework for robotics applications to model uncertainties present in the real world, with temporal logic specifications. All temporal logic specifications in linear-time temporal logic (LTL) can be expressed as parity objectives. We study the qualitative analysis problem for POMDPs with parity objectives that asks whether there is a controller (policy) to ensure that the objective holds with probability 1 (almost-surely). While the qualitative analysis of POMDPs with parity objectives is undecidable, recent results show that when restricted to finite-memory policies the problem is EXPTIME-complete. While the problem is intractable in theory, we present a practical approach to solve the qualitative analysis problem. We designed several heuristics to deal with the exponential complexity, and have used our implementation on a number of well-known POMDP examples for robotics applications. Our results provide the first practical approach to solve the qualitative analysis of robot motion planning with LTL properties in the presence of uncertainty.","lang":"eng"}],"alternative_title":["IST Austria Technical Report"],"year":"2014","_id":"5426","oa":1,"title":"Qualitative analysis of POMDPs with temporal logic specifications for robotics applications","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","full_name":"Chmelik, Martin"},{"last_name":"Gupta","full_name":"Gupta, Raghav","first_name":"Raghav"},{"first_name":"Ayush","full_name":"Kanodia, Ayush","last_name":"Kanodia"}]},{"abstract":[{"lang":"eng","text":"We consider graphs with n nodes together with their tree-decomposition that has b = O ( n ) bags and width t , on the standard RAM computational model with wordsize W = Θ (log n ) . Our contributions are two-fold: Our first contribution is an algorithm that given a graph and its tree-decomposition as input, computes a binary and balanced tree-decomposition of width at most 4 · t + 3 of the graph in O ( b ) time and space, improving a long-standing (from 1992) bound of O ( n · log n ) time for constant treewidth graphs. Our second contribution is on reachability queries for low treewidth graphs. We build on our tree-balancing algorithm and present a data-structure for graph reachability that requires O ( n · t 2 ) preprocessing time, O ( n · t ) space, and O ( d t/ log n e ) time for pair queries, and O ( n · t · log t/ log n ) time for single-source queries. For constant t our data-structure uses O ( n ) time for preprocessing, O (1) time for pair queries, and O ( n/ log n ) time for single-source queries. This is (asymptotically) optimal and is faster than DFS/BFS when answering more than a constant number of single-source queries."}],"year":"2014","alternative_title":["IST Austria Technical Report"],"doi":"10.15479/AT:IST-2014-314-v1-1","title":"Optimal tree-decomposition balancing and reachability on low treewidth graphs","oa":1,"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis"}],"_id":"5427","status":"public","publication_status":"published","page":"24","publication_identifier":{"issn":["2664-1690"]},"date_updated":"2021-01-12T08:02:09Z","date_published":"2014-11-05T00:00:00Z","date_created":"2018-12-12T11:39:16Z","oa_version":"Published Version","citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. <i>Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs</i>. IST Austria, 2014. <a href=\"https://doi.org/10.15479/AT:IST-2014-314-v1-1\">https://doi.org/10.15479/AT:IST-2014-314-v1-1</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs</i>. IST Austria, 2014, doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-314-v1-1\">10.15479/AT:IST-2014-314-v1-1</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs, IST Austria, 2014.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. <i>Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs</i>. IST Austria; 2014. doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-314-v1-1\">10.15479/AT:IST-2014-314-v1-1</a>","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2014. Optimal tree-decomposition balancing and reachability on low treewidth graphs, IST Austria, 24p.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2014). <i>Optimal tree-decomposition balancing and reachability on low treewidth graphs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2014-314-v1-1\">https://doi.org/10.15479/AT:IST-2014-314-v1-1</a>","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, <i>Optimal tree-decomposition balancing and reachability on low treewidth graphs</i>. IST Austria, 2014."},"pubrep_id":"314","department":[{"_id":"KrCh"}],"day":"05","month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"file_date_updated":"2020-07-14T12:46:52Z","has_accepted_license":"1","type":"technical_report","language":[{"iso":"eng"}],"publisher":"IST Austria","file":[{"date_created":"2018-12-12T11:53:10Z","file_id":"5471","date_updated":"2020-07-14T12:46:52Z","checksum":"9d3b90bf4fff74664f182f2d95ef727a","content_type":"application/pdf","access_level":"open_access","file_size":405561,"creator":"system","relation":"main_file","file_name":"IST-2014-314-v1+1_long.pdf"}]},{"date_updated":"2023-09-20T12:07:48Z","publication_identifier":{"issn":["2664-1690"]},"page":"26","publication_status":"published","status":"public","related_material":{"record":[{"id":"1066","relation":"later_version","status":"public"}]},"_id":"5428","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Otop, Jan","last_name":"Otop"},{"first_name":"Yaron","full_name":"Velner, Yaron","last_name":"Velner"}],"oa":1,"title":"Quantitative fair simulation games","doi":"10.15479/AT:IST-2014-315-v1-1","alternative_title":["IST Austria Technical Report"],"year":"2014","abstract":[{"text":"Simulation is an attractive alternative for language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. For non-deterministic automata, while language inclusion is PSPACE-complete, simulation can be computed in polynomial time. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. Again, while fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable for mean-payoff automata and the decidability is open for discounted-sum automata, whereas the (quantitative) simulation reduce to mean-payoff games and discounted-sum games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games. For example, whereas for mean-payoff and discounted-sum games, the players do not need memory to play optimally; we show in contrast that for simulation games with Büchi acceptance conditions, (i) for mean-payoff objectives, optimal strategies for both players require infinite memory in general, and (ii) for discounted-sum objectives, optimal strategies need not exist for both players. While the simulation games with Büchi acceptance conditions are more complicated (e.g., due to infinite-memory requirements for mean-payoff objectives) as compared to their counterpart without Büchi acceptance conditions, we still present pseudo-polynomial time algorithms to solve simulation games with Büchi acceptance conditions for both weighted mean-payoff and weighted discounted-sum automata.","lang":"eng"}],"file":[{"relation":"main_file","file_size":531046,"creator":"system","file_name":"IST-2014-315-v1+1_report.pdf","date_updated":"2020-07-14T12:46:52Z","checksum":"b1d573bc04365625ff9974880c0aa807","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T11:53:59Z","file_id":"5521"}],"publisher":"IST Austria","language":[{"iso":"eng"}],"type":"technical_report","has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:52Z","ddc":["004"],"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"05","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"pubrep_id":"315","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. <i>Quantitative Fair Simulation Games</i>. IST Austria, 2014. <a href=\"https://doi.org/10.15479/AT:IST-2014-315-v1-1\">https://doi.org/10.15479/AT:IST-2014-315-v1-1</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Fair Simulation Games</i>. IST Austria, 2014, doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-315-v1-1\">10.15479/AT:IST-2014-315-v1-1</a>.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Velner, Y. (2014). <i>Quantitative fair simulation games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2014-315-v1-1\">https://doi.org/10.15479/AT:IST-2014-315-v1-1</a>","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, <i>Quantitative fair simulation games</i>. IST Austria, 2014.","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2014. Quantitative fair simulation games, IST Austria, 26p.","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. <i>Quantitative Fair Simulation Games</i>. IST Austria; 2014. doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-315-v1-1\">10.15479/AT:IST-2014-315-v1-1</a>","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Quantitative Fair Simulation Games, IST Austria, 2014."},"oa_version":"Published Version","date_created":"2018-12-12T11:39:16Z","date_published":"2014-12-05T00:00:00Z"},{"abstract":[{"lang":"eng","text":"Mechanically coupled cells can generate forces driving cell and tissue morphogenesis during development. Visualization and measuring of these forces is of major importance to better understand the complexity of the biomechanic processes that shape cells and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively assess mechanical tension in different tissues of the developing zebrafish and in cultures of primary germ layer progenitor cells ex vivo."}],"doi":"10.1007/978-1-4939-1164-6_15","author":[{"orcid":"0000-0002-5920-9090","last_name":"Smutny","full_name":"Smutny, Michael","first_name":"Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87"},{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Behrndt, Martin","last_name":"Behrndt"},{"orcid":"0000-0002-8526-5416","first_name":"Pedro","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","last_name":"Campinho","full_name":"Campinho, Pedro"},{"full_name":"Ruprecht, Verena","last_name":"Ruprecht","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","orcid":"0000-0003-4088-8633"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"title":"UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo","editor":[{"first_name":"Celeste","full_name":"Nelson, Celeste","last_name":"Nelson"}],"_id":"6178","status":"public","publication_status":"published","place":"New York, NY","publication_identifier":{"isbn":["9781493911639","9781493911646"],"issn":["1064-3745"],"eissn":["1940-6029"]},"oa_version":"None","day":"22","citation":{"ieee":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, and C.-P. J. Heisenberg, “UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo,” in <i>Tissue Morphogenesis</i>, vol. 1189, C. Nelson, Ed. New York, NY: Springer, 2014, pp. 219–235.","apa":"Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., &#38; Heisenberg, C.-P. J. (2014). UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In C. Nelson (Ed.), <i>Tissue Morphogenesis</i> (Vol. 1189, pp. 219–235). New York, NY: Springer. <a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">https://doi.org/10.1007/978-1-4939-1164-6_15</a>","ista":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. 2014.UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Tissue Morphogenesis. vol. 1189, 219–235.","short":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:, C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, NY, 2014, pp. 219–235.","ama":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Nelson C, ed. <i>Tissue Morphogenesis</i>. Vol 1189. Methods in Molecular Biology. New York, NY: Springer; 2014:219-235. doi:<a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">10.1007/978-1-4939-1164-6_15</a>","mla":"Smutny, Michael, et al. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” <i>Tissue Morphogenesis</i>, edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:<a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">10.1007/978-1-4939-1164-6_15</a>.","chicago":"Smutny, Michael, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and Carl-Philipp J Heisenberg. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” In <i>Tissue Morphogenesis</i>, edited by Celeste Nelson, 1189:219–35. Methods in Molecular Biology. New York, NY: Springer, 2014. <a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">https://doi.org/10.1007/978-1-4939-1164-6_15</a>."},"month":"08","pmid":1,"volume":1189,"article_processing_charge":"No","year":"2014","page":"219-235","publication":"Tissue Morphogenesis","date_updated":"2023-09-05T14:12:00Z","external_id":{"pmid":["25245697"]},"date_published":"2014-08-22T00:00:00Z","date_created":"2019-03-26T08:55:59Z","department":[{"_id":"CaHe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"book_chapter","language":[{"iso":"eng"}],"quality_controlled":"1","series_title":"Methods in Molecular Biology","intvolume":"      1189","publisher":"Springer"},{"abstract":[{"text":"The Wigner-Dyson-Gaudin-Mehta conjecture asserts that the local eigenvalue statistics of large real and complex Hermitian matrices with independent, identically distributed entries are universal in a sense that they depend only on the symmetry class of the matrix and otherwise are independent of the details of the distribution. We present the recent solution to this half-century old conjecture. We explain how stochastic tools, such as the Dyson Brownian motion, and PDE ideas, such as De Giorgi-Nash-Moser regularity theory, were combined in the solution. We also show related results for log-gases that represent a universal model for strongly correlated systems. Finally, in the spirit of Wigner’s original vision, we discuss the extensions of these universality results to more realistic physical systems such as random band matrices.","lang":"eng"}],"author":[{"orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László"}],"title":"Random matrices, log-gases and Hölder regularity","_id":"1507","acknowledgement":"The author is partially supported by SFB-TR 12 Grant of the German Research Council.","publication_status":"published","status":"public","ec_funded":1,"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"conference":{"end_date":"2014-08-21","location":"Seoul, Korea","start_date":"2014-08-13","name":"ICM: International Congress of Mathematicians"},"oa_version":"Submitted Version","day":"01","citation":{"chicago":"Erdös, László. “Random Matrices, Log-Gases and Hölder Regularity.” In <i>Proceedings of the International Congress of Mathematicians</i>, 3:214–36. International Congress of Mathematicians, 2014.","mla":"Erdös, László. “Random Matrices, Log-Gases and Hölder Regularity.” <i>Proceedings of the International Congress of Mathematicians</i>, vol. 3, International Congress of Mathematicians, 2014, pp. 214–36.","ista":"Erdös L. 2014. Random matrices, log-gases and Hölder regularity. Proceedings of the International Congress of Mathematicians. ICM: International Congress of Mathematicians vol. 3, 214–236.","short":"L. Erdös, in:, Proceedings of the International Congress of Mathematicians, International Congress of Mathematicians, 2014, pp. 214–236.","ama":"Erdös L. Random matrices, log-gases and Hölder regularity. In: <i>Proceedings of the International Congress of Mathematicians</i>. Vol 3. International Congress of Mathematicians; 2014:214-236.","ieee":"L. Erdös, “Random matrices, log-gases and Hölder regularity,” in <i>Proceedings of the International Congress of Mathematicians</i>, Seoul, Korea, 2014, vol. 3, pp. 214–236.","apa":"Erdös, L. (2014). Random matrices, log-gases and Hölder regularity. In <i>Proceedings of the International Congress of Mathematicians</i> (Vol. 3, pp. 214–236). Seoul, Korea: International Congress of Mathematicians."},"month":"08","article_processing_charge":"No","volume":3,"year":"2014","oa":1,"page":"214 - 236","publication":"Proceedings of the International Congress of Mathematicians","date_updated":"2023-10-17T11:12:55Z","date_published":"2014-08-01T00:00:00Z","scopus_import":"1","date_created":"2018-12-11T11:52:25Z","department":[{"_id":"LaEr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5670","quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","main_file_link":[{"url":"http://arxiv.org/abs/1407.5752","open_access":"1"}],"intvolume":"         3","publisher":"International Congress of Mathematicians"},{"date_updated":"2021-01-12T06:51:19Z","publication":"Proceedings of the QMath12 Conference","page":"127 - 137","publication_status":"published","status":"public","_id":"1516","title":"On the BCS gap equation for superfluid fermionic gases","oa":1,"author":[{"first_name":"Gerhard","full_name":"Bräunlich, Gerhard","last_name":"Bräunlich"},{"first_name":"Christian","full_name":"Hainzl, Christian","last_name":"Hainzl"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"doi":"10.1142/9789814618144_0007","abstract":[{"lang":"eng","text":"We present a rigorous derivation of the BCS gap equation for superfluid fermionic gases with point interactions. Our starting point is the BCS energy functional, whose minimizer we investigate in the limit when the range of the interaction potential goes to zero.\r\n"}],"year":"2014","publisher":"World Scientific Publishing","main_file_link":[{"url":"https://arxiv.org/abs/1403.2563","open_access":"1"}],"arxiv":1,"article_processing_charge":"No","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"month":"01","publist_id":"5661","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Bräunlich, G., Hainzl, C., &#38; Seiringer, R. (2014). On the BCS gap equation for superfluid fermionic gases. In <i>Proceedings of the QMath12 Conference</i> (pp. 127–137). Berlin, Germany: World Scientific Publishing. <a href=\"https://doi.org/10.1142/9789814618144_0007\">https://doi.org/10.1142/9789814618144_0007</a>","ieee":"G. Bräunlich, C. Hainzl, and R. Seiringer, “On the BCS gap equation for superfluid fermionic gases,” in <i>Proceedings of the QMath12 Conference</i>, Berlin, Germany, 2014, pp. 127–137.","ista":"Bräunlich G, Hainzl C, Seiringer R. 2014. On the BCS gap equation for superfluid fermionic gases. Proceedings of the QMath12 Conference. QMath: Mathematical Results in Quantum Physics, 127–137.","short":"G. Bräunlich, C. Hainzl, R. Seiringer, in:, Proceedings of the QMath12 Conference, World Scientific Publishing, 2014, pp. 127–137.","ama":"Bräunlich G, Hainzl C, Seiringer R. On the BCS gap equation for superfluid fermionic gases. In: <i>Proceedings of the QMath12 Conference</i>. World Scientific Publishing; 2014:127-137. doi:<a href=\"https://doi.org/10.1142/9789814618144_0007\">10.1142/9789814618144_0007</a>","mla":"Bräunlich, Gerhard, et al. “On the BCS Gap Equation for Superfluid Fermionic Gases.” <i>Proceedings of the QMath12 Conference</i>, World Scientific Publishing, 2014, pp. 127–37, doi:<a href=\"https://doi.org/10.1142/9789814618144_0007\">10.1142/9789814618144_0007</a>.","chicago":"Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “On the BCS Gap Equation for Superfluid Fermionic Gases.” In <i>Proceedings of the QMath12 Conference</i>, 127–37. World Scientific Publishing, 2014. <a href=\"https://doi.org/10.1142/9789814618144_0007\">https://doi.org/10.1142/9789814618144_0007</a>."},"day":"01","department":[{"_id":"RoSe"}],"oa_version":"Preprint","date_created":"2018-12-11T11:52:28Z","conference":{"start_date":"2013-09-10","location":"Berlin, Germany","end_date":"2013-09-13","name":"QMath: Mathematical Results in Quantum Physics"},"date_published":"2014-01-01T00:00:00Z","external_id":{"arxiv":["1403.2563"]}},{"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1307.4473","open_access":"1"}],"intvolume":"       547","publisher":"Elsevier","date_published":"2014-08-28T00:00:00Z","external_id":{"arxiv":["1307.4473"]},"scopus_import":"1","date_created":"2018-12-11T11:51:40Z","department":[{"_id":"KrCh"}],"publist_id":"5836","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","page":"104 - 116","publication":"Theoretical Computer Science","date_updated":"2022-09-09T11:50:58Z","year":"2014","oa":1,"article_processing_charge":"No","volume":547,"arxiv":1,"oa_version":"Preprint","day":"28","citation":{"mla":"Chatterjee, Krishnendu, et al. “Approximating the Minimum Cycle Mean.” <i>Theoretical Computer Science</i>, vol. 547, no. C, Elsevier, 2014, pp. 104–16, doi:<a href=\"https://doi.org/10.1016/j.tcs.2014.06.031\">10.1016/j.tcs.2014.06.031</a>.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, Veronika Loitzenbauer, and Michael Raskin. “Approximating the Minimum Cycle Mean.” <i>Theoretical Computer Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tcs.2014.06.031\">https://doi.org/10.1016/j.tcs.2014.06.031</a>.","apa":"Chatterjee, K., Henzinger, M. H., Krinninger, S., Loitzenbauer, V., &#38; Raskin, M. (2014). Approximating the minimum cycle mean. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2014.06.031\">https://doi.org/10.1016/j.tcs.2014.06.031</a>","ieee":"K. Chatterjee, M. H. Henzinger, S. Krinninger, V. Loitzenbauer, and M. Raskin, “Approximating the minimum cycle mean,” <i>Theoretical Computer Science</i>, vol. 547, no. C. Elsevier, pp. 104–116, 2014.","ista":"Chatterjee K, Henzinger MH, Krinninger S, Loitzenbauer V, Raskin M. 2014. Approximating the minimum cycle mean. Theoretical Computer Science. 547(C), 104–116.","short":"K. Chatterjee, M.H. Henzinger, S. Krinninger, V. Loitzenbauer, M. Raskin, Theoretical Computer Science 547 (2014) 104–116.","ama":"Chatterjee K, Henzinger MH, Krinninger S, Loitzenbauer V, Raskin M. Approximating the minimum cycle mean. <i>Theoretical Computer Science</i>. 2014;547(C):104-116. doi:<a href=\"https://doi.org/10.1016/j.tcs.2014.06.031\">10.1016/j.tcs.2014.06.031</a>"},"month":"08","publication_status":"published","status":"public","ec_funded":1,"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"issue":"C","abstract":[{"text":"We consider directed graphs where each edge is labeled with an integer weight and study the fundamental algorithmic question of computing the value of a cycle with minimum mean weight. Our contributions are twofold: (1) First we show that the algorithmic question is reducible to the problem of a logarithmic number of min-plus matrix multiplications of n×n-matrices, where n is the number of vertices of the graph. (2) Second, when the weights are nonnegative, we present the first (1+ε)-approximation algorithm for the problem and the running time of our algorithm is Õ(nωlog3(nW/ε)/ε),1 where O(nω) is the time required for the classic n×n-matrix multiplication and W is the maximum value of the weights. With an additional O(log(nW/ε)) factor in space a cycle with approximately optimal weight can be computed within the same time bound.","lang":"eng"}],"doi":"10.1016/j.tcs.2014.06.031","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","orcid":"0000-0002-5008-6530"},{"first_name":"Sebastian","full_name":"Krinninger, Sebastian","last_name":"Krinninger"},{"last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika","first_name":"Veronika"},{"full_name":"Raskin, Michael","last_name":"Raskin","first_name":"Michael"}],"title":"Approximating the minimum cycle mean","_id":"1375"},{"file":[{"file_name":"IST-2014-179-v1+1_vmcai14.pdf","relation":"main_file","file_size":444138,"creator":"system","date_updated":"2020-07-14T12:44:48Z","access_level":"open_access","content_type":"application/pdf","checksum":"bffa33d39be77df0da39defe97eabf84","file_id":"4859","date_created":"2018-12-12T10:11:06Z"}],"volume":8318,"has_accepted_license":"1","file_date_updated":"2020-07-14T12:44:48Z","month":"01","ddc":["000","005"],"day":"01","pubrep_id":"179","citation":{"chicago":"Dragoi, Cezara, Thomas A Henzinger, Helmut Veith, Josef Widder, and Damien Zufferey. “A Logic-Based Framework for Verifying Consensus Algorithms,” 8318:161–81. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54013-4_10\">https://doi.org/10.1007/978-3-642-54013-4_10</a>.","mla":"Dragoi, Cezara, et al. <i>A Logic-Based Framework for Verifying Consensus Algorithms</i>. Vol. 8318, Springer, 2014, pp. 161–81, doi:<a href=\"https://doi.org/10.1007/978-3-642-54013-4_10\">10.1007/978-3-642-54013-4_10</a>.","ama":"Dragoi C, Henzinger TA, Veith H, Widder J, Zufferey D. A logic-based framework for verifying consensus algorithms. In: Vol 8318. Springer; 2014:161-181. doi:<a href=\"https://doi.org/10.1007/978-3-642-54013-4_10\">10.1007/978-3-642-54013-4_10</a>","short":"C. Dragoi, T.A. Henzinger, H. Veith, J. Widder, D. Zufferey, in:, Springer, 2014, pp. 161–181.","ista":"Dragoi C, Henzinger TA, Veith H, Widder J, Zufferey D. 2014. A logic-based framework for verifying consensus algorithms. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 8318, 161–181.","ieee":"C. Dragoi, T. A. Henzinger, H. Veith, J. Widder, and D. Zufferey, “A logic-based framework for verifying consensus algorithms,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, San Diego, USA, 2014, vol. 8318, pp. 161–181.","apa":"Dragoi, C., Henzinger, T. A., Veith, H., Widder, J., &#38; Zufferey, D. (2014). A logic-based framework for verifying consensus algorithms (Vol. 8318, pp. 161–181). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, San Diego, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-54013-4_10\">https://doi.org/10.1007/978-3-642-54013-4_10</a>"},"conference":{"location":"San Diego, USA","start_date":"2014-01-19","end_date":"2014-01-21","name":"VMCAI: Verification, Model Checking and Abstract Interpretation"},"oa_version":"Submitted Version","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"}],"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"Supported by the Vienna Science and Technology Fund (WWTF) through grant PROSEED.","_id":"1392","author":[{"last_name":"Dragoi","full_name":"Dragoi, Cezara","first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"},{"first_name":"Josef","full_name":"Widder, Josef","last_name":"Widder"},{"last_name":"Zufferey","full_name":"Zufferey, Damien","first_name":"Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736"}],"title":"A logic-based framework for verifying consensus algorithms","doi":"10.1007/978-3-642-54013-4_10","abstract":[{"lang":"eng","text":"Fault-tolerant distributed algorithms play an important role in ensuring the reliability of many software applications. In this paper we consider distributed algorithms whose computations are organized in rounds. To verify the correctness of such algorithms, we reason about (i) properties (such as invariants) of the state, (ii) the transitions controlled by the algorithm, and (iii) the communication graph. We introduce a logic that addresses these points, and contains set comprehensions with cardinality constraints, function symbols to describe the local states of each process, and a limited form of quantifier alternation to express the verification conditions. We show its use in automating the verification of consensus algorithms. In particular, we give a semi-decision procedure for the unsatisfiability problem of the logic and identify a decidable fragment. We successfully applied our framework to verify the correctness of a variety of consensus algorithms tolerant to both benign faults (message loss, process crashes) and value faults (message corruption)."}],"intvolume":"      8318","publisher":"Springer","language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","publist_id":"5817","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"scopus_import":1,"date_created":"2018-12-11T11:51:45Z","date_published":"2014-01-01T00:00:00Z","date_updated":"2021-01-12T06:50:22Z","page":"161 - 181","oa":1,"year":"2014","alternative_title":["LNCS"]},{"article_processing_charge":"No","oa_version":"Published Version","conference":{"end_date":"2014-06-07","start_date":"2014-05-31","location":"Hyderabad, India","name":"FOSE: Future of Software Engineering"},"citation":{"apa":"Gordon, A., Henzinger, T. A., Nori, A., &#38; Rajamani, S. (2014). Probabilistic programming. In <i>Proceedings of the on Future of Software Engineering</i> (pp. 167–181). Hyderabad, India: ACM. <a href=\"https://doi.org/10.1145/2593882.2593900\">https://doi.org/10.1145/2593882.2593900</a>","ieee":"A. Gordon, T. A. Henzinger, A. Nori, and S. Rajamani, “Probabilistic programming,” in <i>Proceedings of the on Future of Software Engineering</i>, Hyderabad, India, 2014, pp. 167–181.","ista":"Gordon A, Henzinger TA, Nori A, Rajamani S. 2014. Probabilistic programming. Proceedings of the on Future of Software Engineering. FOSE: Future of Software Engineering, 167–181.","short":"A. Gordon, T.A. Henzinger, A. Nori, S. Rajamani, in:, Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–181.","ama":"Gordon A, Henzinger TA, Nori A, Rajamani S. Probabilistic programming. In: <i>Proceedings of the on Future of Software Engineering</i>. ACM; 2014:167-181. doi:<a href=\"https://doi.org/10.1145/2593882.2593900\">10.1145/2593882.2593900</a>","chicago":"Gordon, Andrew, Thomas A Henzinger, Aditya Nori, and Sriram Rajamani. “Probabilistic Programming.” In <i>Proceedings of the on Future of Software Engineering</i>, 167–81. ACM, 2014. <a href=\"https://doi.org/10.1145/2593882.2593900\">https://doi.org/10.1145/2593882.2593900</a>.","mla":"Gordon, Andrew, et al. “Probabilistic Programming.” <i>Proceedings of the on Future of Software Engineering</i>, ACM, 2014, pp. 167–81, doi:<a href=\"https://doi.org/10.1145/2593882.2593900\">10.1145/2593882.2593900</a>."},"day":"31","month":"05","publication_status":"published","status":"public","ec_funded":1,"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"abstract":[{"text":"Probabilistic programs are usual functional or imperative programs with two added constructs: (1) the ability to draw values at random from distributions, and (2) the ability to condition values of variables in a program via observations. Models from diverse application areas such as computer vision, coding theory, cryptographic protocols, biology and reliability analysis can be written as probabilistic programs. Probabilistic inference is the problem of computing an explicit representation of the probability distribution implicitly specified by a probabilistic program. Depending on the application, the desired output from inference may vary-we may want to estimate the expected value of some function f with respect to the distribution, or the mode of the distribution, or simply a set of samples drawn from the distribution. In this paper, we describe connections this research area called \\Probabilistic Programming&quot; has with programming languages and software engineering, and this includes language design, and the static and dynamic analysis of programs. We survey current state of the art and speculate on promising directions for future research.","lang":"eng"}],"doi":"10.1145/2593882.2593900","title":"Probabilistic programming","author":[{"first_name":"Andrew","last_name":"Gordon","full_name":"Gordon, Andrew"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Nori, Aditya","last_name":"Nori","first_name":"Aditya"},{"first_name":"Sriram","last_name":"Rajamani","full_name":"Rajamani, Sriram"}],"_id":"1393","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"ACM","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/2593882.2593900"}],"date_published":"2014-05-31T00:00:00Z","date_created":"2018-12-11T11:51:45Z","scopus_import":1,"department":[{"_id":"ToHe"}],"publist_id":"5816","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"167 - 181","publication":"Proceedings of the on Future of Software Engineering","date_updated":"2021-01-12T06:50:22Z","year":"2014","oa":1},{"publication_status":"published","status":"public","page":"131","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-07T11:38:56Z","year":"2014","alternative_title":["ISTA Thesis"],"abstract":[{"text":"In this thesis I studied various individual and social immune defences employed by the invasive garden ant Lasius neglectus mostly against entomopathogenic fungi.  The first two chapters of this thesis address the phenomenon of 'social immunisation'. Social immunisation, that is the immunological protection of group members due to social contact to a pathogen-exposed nestmate, has been described in various social insect species against different types of pathogens. However, in the case of entomopathogenic fungi it has, so far, only been demonstrated that social immunisation exists at all. Its underlying mechanisms r any other properties were, however, unknown. In the first chapter of this thesis I identified the mechanistic basis of social immunisation in L. neglectus against the entomopathogenous fungus Metarhizium. I could show that nestmates of a pathogen-exposed individual contract low-level infections due to social interactions. These low-level infections are, however, non-lethal and cause an active stimulation of the immune system, which protects the nestmates upon subsequent pathogen encounters. In the second chapter of this thesis I investigated the specificity and colony level effects of social immunisation. I demonstrated that the protection conferred by social immunisation is highly specific, protecting ants only against the same pathogen strain. In addition, depending on the respective context, social immunisation may even cause fitness costs. I further showed that social immunisation crucially affects sanitary behaviour and disease dynamics within ant groups. In the third chapter of this thesis I studied the effects of the ectosymbiotic fungus Laboulbenia formicarum on its host L. neglectus. Although Laboulbeniales are the largest order of insect-parasitic fungi, research concerning host fitness consequence is sparse. I showed that highly Laboulbenia-infected ants sustain fitness costs under resource limitation, however, gain fitness benefits when exposed to an entomopathogenus fungus. These effects are probably cause by a prophylactic upregulation of behavioural as well as physiological immune defences in highly infected ants.","lang":"eng"}],"author":[{"full_name":"Konrad, Matthias","last_name":"Konrad","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"}],"title":"Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus","supervisor":[{"full_name":"Cremer, Sylvia M","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia M","orcid":"0000-0002-2193-3868"}],"_id":"1395","language":[{"iso":"eng"}],"type":"dissertation","article_processing_charge":"No","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","date_published":"2014-02-01T00:00:00Z","oa_version":"None","date_created":"2018-12-11T11:51:46Z","day":"01","department":[{"_id":"SyCr"}],"citation":{"ieee":"M. Konrad, “Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus,” Institute of Science and Technology Austria, 2014.","apa":"Konrad, M. (2014). <i>Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus</i>. Institute of Science and Technology Austria.","ista":"Konrad M. 2014. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science and Technology Austria.","ama":"Konrad M. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. 2014.","short":"M. Konrad, Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus, Institute of Science and Technology Austria, 2014.","mla":"Konrad, Matthias. <i>Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus</i>. Institute of Science and Technology Austria, 2014.","chicago":"Konrad, Matthias. “Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus.” Institute of Science and Technology Austria, 2014."},"publist_id":"5814","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"02"},{"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","article_processing_charge":"No","type":"dissertation","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"12","publist_id":"5805","citation":{"mla":"Marhavá, Petra. <i>Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2014.","chicago":"Marhavá, Petra. “Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2014.","ieee":"P. Marhavá, “Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2014.","apa":"Marhavá, P. (2014). <i>Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana</i>. Institute of Science and Technology Austria.","ama":"Marhavá P. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. 2014.","short":"P. Marhavá, Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2014.","ista":"Marhavá P. 2014. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria."},"day":"01","department":[{"_id":"JiFr"}],"date_created":"2018-12-11T11:51:49Z","oa_version":"None","date_published":"2014-12-01T00:00:00Z","date_updated":"2023-09-07T11:39:38Z","publication_identifier":{"issn":["2663-337X"]},"page":"90","status":"public","publication_status":"published","_id":"1402","supervisor":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"title":"Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana","author":[{"first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavá","full_name":"Marhavá, Petra"}],"abstract":[{"lang":"eng","text":"Phosphatidylinositol (Ptdlns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, Ptdlns3P and Ptdlns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vauolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with Ptdlns3P, the presumable product of their activity. in SAC gain- and loss-of-function mutants, the levels of Ptdlns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with Ptdlns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants."}],"alternative_title":["ISTA Thesis"],"year":"2014"},{"date_updated":"2023-10-17T12:16:58Z","page":"91","publication_status":"published","status":"public","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"2282"},{"status":"public","relation":"part_of_dissertation","id":"2950"},{"relation":"part_of_dissertation","status":"public","id":"3373"}]},"_id":"1403","author":[{"full_name":"Behrndt, Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"title":"Forces driving epithelial spreading in zebrafish epiboly","supervisor":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"alternative_title":["IST Austria Thesis"],"year":"2014","abstract":[{"lang":"eng","text":"A variety of developmental and disease related processes depend on epithelial cell sheet spreading. In order to gain insight into the biophysical mechanism(s) underlying the tissue morphogenesis we studied the spreading of an epithelium during the early development of the zebrafish embryo. In zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the yolk cell to completely engulf it at the end of gastrulation. Previous studies have proposed that an actomyosin ring forming within the yolk syncytial layer (YSL) acts as purse string that through constriction along its circumference pulls on the margin of the EVL. Direct biophysical evidence for this hypothesis has however been missing. The aim of the thesis was to understand how the actomyosin ring may generate pulling forces onto the EVL and what cellular mechanism(s) may facilitate the spreading of the epithelium. Using laser ablation to measure cortical tension within the actomyosin ring we found an anisotropic tension distribution, which was highest along the circumference of the ring. However the low degree of anisotropy was incompatible with the actomyosin ring functioning as a purse string only. Additionally, we observed retrograde cortical flow from vegetal parts of the ring into the EVL margin. Interpreting the experimental data using a theoretical distribution that models  the tissues as active viscous gels led us to proposen that the actomyosin ring has a twofold contribution to EVL epiboly. It not only acts as a purse string through constriction along its circumference, but in addition constriction along the width of the ring generates pulling forces through friction-resisted cortical flow. Moreover, when rendering the purse string mechanism unproductive EVL epiboly proceeded normally indicating that the flow-friction mechanism is sufficient to drive the process. Aiming to understand what cellular mechanism(s) may facilitate the spreading of the epithelium we found that tension-oriented EVL cell divisions limit tissue anisotropy by releasing tension along the division axis and promote epithelial spreading. Notably, EVL cells undergo ectopic cell fusion in conditions in which oriented-cell division is impaired or the epithelium is mechanically challenged. Taken together our study of EVL epiboly suggests a novel mechanism of force generation for actomyosin rings through friction-resisted cortical flow and highlights the importance of tension-oriented cell divisions in epithelial morphogenesis."}],"publisher":"IST Austria","language":[{"iso":"eng"}],"type":"dissertation","month":"08","publist_id":"5804","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaHe"}],"day":"01","citation":{"ieee":"M. Behrndt, “Forces driving epithelial spreading in zebrafish epiboly,” IST Austria, 2014.","apa":"Behrndt, M. (2014). <i>Forces driving epithelial spreading in zebrafish epiboly</i>. IST Austria.","short":"M. Behrndt, Forces Driving Epithelial Spreading in Zebrafish Epiboly, IST Austria, 2014.","ama":"Behrndt M. Forces driving epithelial spreading in zebrafish epiboly. 2014.","ista":"Behrndt M. 2014. Forces driving epithelial spreading in zebrafish epiboly. IST Austria.","chicago":"Behrndt, Martin. “Forces Driving Epithelial Spreading in Zebrafish Epiboly.” IST Austria, 2014.","mla":"Behrndt, Martin. <i>Forces Driving Epithelial Spreading in Zebrafish Epiboly</i>. IST Austria, 2014."},"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"None","date_created":"2018-12-11T11:51:49Z","date_published":"2014-08-01T00:00:00Z"},{"language":[{"iso":"eng"}],"type":"dissertation","publisher":"IST Austria","date_published":"2014-04-01T00:00:00Z","date_created":"2018-12-11T11:51:49Z","oa_version":"None","day":"01","department":[{"_id":"SyCr"}],"citation":{"ieee":"M. Stock, “Evolution of a fungal pathogen towards individual versus social immunity in ants,” IST Austria, 2014.","apa":"Stock, M. (2014). <i>Evolution of a fungal pathogen towards individual versus social immunity in ants</i>. IST Austria.","ama":"Stock M. Evolution of a fungal pathogen towards individual versus social immunity in ants. 2014.","short":"M. Stock, Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants, IST Austria, 2014.","ista":"Stock M. 2014. Evolution of a fungal pathogen towards individual versus social immunity in ants. IST Austria.","chicago":"Stock, Miriam. “Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants.” IST Austria, 2014.","mla":"Stock, Miriam. <i>Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants</i>. IST Austria, 2014."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","publist_id":"5803","acknowledgement":"This work was funded by the DFG and the ERC.","publication_status":"published","status":"public","page":"101","date_updated":"2021-01-12T06:50:30Z","alternative_title":["IST Austria Thesis"],"year":"2014","abstract":[{"lang":"eng","text":"The co-evolution of hosts and pathogens is characterized by continuous adaptations of both parties. Pathogens of social insects need to adapt towards disease defences at two levels: 1) individual immunity of each colony member consisting of behavioural defence strategies as well as humoral and cellular immune responses and 2) social immunity that is collectively performed by all group members comprising behavioural, physiological and organisational defence strategies.\r\n\r\nTo disentangle the selection pressure on pathogens by the collective versus individual level of disease defence in social insects, we performed an evolution experiment using the Argentine Ant, Linepithema humile, as a host and a mixture of the general insect pathogenic fungus Metarhizium spp. (6 strains) as a pathogen. We allowed pathogen evolution over 10 serial host passages to two different evolution host treatments: (1) only individual host immunity in a single host treatment, and (2) simultaneously acting individual and social immunity in a social host treatment, in which an exposed ant was accompanied by two untreated nestmates.\r\n\r\nBefore starting the pathogen evolution experiment, the 6 Metarhizium spp. strains were characterised concerning conidiospore size killing rates in singly and socially reared ants, their competitiveness under coinfecting conditions and their influence on ant behaviour. We analysed how the ancestral atrain mixture changed in conidiospere size, killing rate and strain composition dependent on host treatment (single or social hosts) during 10 passages and found that killing rate and conidiospere size of the pathogen increased under both evolution regimes, but different depending on host treatment.\r\n\r\nTesting the evolved strain mixtures that evolved under either the single or social host treatment under both single and social current rearing conditions in a full factorial design experiment revealed that the additional collective defences in insect societies add new selection pressure for their coevolving pathogens that compromise their ability to adapt to its host at the group level. To our knowledge, this is the first study directly measuring the influence of social immunity on pathogen evolution."}],"author":[{"full_name":"Stock, Miriam","last_name":"Stock","id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam"}],"title":"Evolution of a fungal pathogen towards individual versus social immunity in ants","supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia M","full_name":"Cremer, Sylvia M","last_name":"Cremer","orcid":"0000-0002-2193-3868"}],"_id":"1404"},{"_id":"9458","title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","author":[{"first_name":"Jason T.","full_name":"Huff, Jason T.","last_name":"Huff"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"doi":"10.1016/j.cell.2014.01.029","abstract":[{"text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.","lang":"eng"}],"issue":"6","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"status":"public","publication_status":"published","month":"03","pmid":1,"citation":{"chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>.","mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>.","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” <i>Cell</i>, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014.","apa":"Huff, J. T., &#38; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. 2014;156(6):1286-1297. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297."},"day":"13","oa_version":"Published Version","article_processing_charge":"No","volume":156,"oa":1,"year":"2014","date_updated":"2021-12-14T08:22:36Z","publication":"Cell","page":"1286-1297","article_type":"original","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"date_created":"2021-06-04T12:00:16Z","scopus_import":"1","extern":"1","external_id":{"pmid":["24630728"]},"date_published":"2014-03-13T00:00:00Z","publisher":"Elsevier","intvolume":"       156","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2014.01.029"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1"},{"page":"16166-16171","article_type":"original","date_updated":"2021-12-14T08:23:26Z","publication":"Proceedings of the National Academy of Sciences","year":"2014","oa":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","intvolume":"       111","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1418564111","open_access":"1"}],"date_created":"2021-06-07T07:23:43Z","scopus_import":"1","extern":"1","external_id":{"pmid":["25344531"]},"date_published":"2014-11-11T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"status":"public","publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"doi":"10.1073/pnas.1418564111","abstract":[{"lang":"eng","text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction."}],"issue":"45","_id":"9479","title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","author":[{"first_name":"Zsuzsanna","full_name":"Mérai, Zsuzsanna","last_name":"Mérai"},{"last_name":"Chumak","full_name":"Chumak, Nina","first_name":"Nina"},{"last_name":"García-Aguilar","full_name":"García-Aguilar, Marcelina","first_name":"Marcelina"},{"first_name":"Tzung-Fu","last_name":"Hsieh","full_name":"Hsieh, Tzung-Fu"},{"first_name":"Toshiro","full_name":"Nishimura, Toshiro","last_name":"Nishimura"},{"last_name":"Schoft","full_name":"Schoft, Vera K.","first_name":"Vera K."},{"first_name":"János","last_name":"Bindics","full_name":"Bindics, János"},{"first_name":"Lucyna","full_name":"Ślusarz, Lucyna","last_name":"Ślusarz"},{"full_name":"Arnoux, Stéphanie","last_name":"Arnoux","first_name":"Stéphanie"},{"last_name":"Opravil","full_name":"Opravil, Susanne","first_name":"Susanne"},{"last_name":"Mechtler","full_name":"Mechtler, Karl","first_name":"Karl"},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."},{"first_name":"Hisashi","last_name":"Tamaru","full_name":"Tamaru, Hisashi"}],"volume":111,"article_processing_charge":"No","oa_version":"Published Version","pmid":1,"month":"11","citation":{"chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>.","mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>.","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.","ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(45):16166-16171. doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","ieee":"Z. Mérai <i>et al.</i>, “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>"},"day":"11"},{"status":"public","publication_status":"published","publication_identifier":{"issn":["1360-1385"],"eissn":["1878-4372"]},"doi":"10.1016/j.tplants.2014.01.014","abstract":[{"text":"Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression.","lang":"eng"}],"issue":"5","_id":"9519","title":"DNA methylation as a system of plant genomic immunity","author":[{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman"}],"article_processing_charge":"No","volume":19,"oa_version":"None","pmid":1,"month":"05","citation":{"mla":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>, vol. 19, no. 5, Elsevier, 2014, pp. 320–26, doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>.","chicago":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>.","ama":"Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. 2014;19(5):320-326. doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>","ista":"Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19(5), 320–326.","short":"M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.","apa":"Kim, M. Y., &#38; Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>","ieee":"M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” <i>Trends in Plant Science</i>, vol. 19, no. 5. Elsevier, pp. 320–326, 2014."},"day":"04","page":"320-326","article_type":"review","date_updated":"2021-12-14T08:24:48Z","publication":"Trends in Plant Science","year":"2014","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Elsevier","intvolume":"        19","date_created":"2021-06-07T14:38:09Z","scopus_import":"1","external_id":{"pmid":["24618094 "]},"date_published":"2014-05-04T00:00:00Z","extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}]},{"year":"2014","doi":"10.1371/journal.pone.0111430.s006","title":"Transition probability between TF expression states when Dbx2 inhibits Nkx2.2","author":[{"last_name":"Lovrics","full_name":"Lovrics, Anna","first_name":"Anna"},{"last_name":"Gao","full_name":"Gao, Yu","first_name":"Yu"},{"last_name":"Juhász","full_name":"Juhász, Bianka","first_name":"Bianka"},{"last_name":"Bock","full_name":"Bock, István","first_name":"István"},{"first_name":"Helen M.","full_name":"Byrne, Helen M.","last_name":"Byrne"},{"first_name":"András","full_name":"Dinnyés, András","last_name":"Dinnyés"},{"full_name":"Kovács, Krisztián","last_name":"Kovács","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztián"}],"_id":"9722","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2004"}]},"status":"public","date_updated":"2023-02-23T10:24:07Z","date_published":"2014-11-14T00:00:00Z","oa_version":"Published Version","date_created":"2021-07-26T14:35:00Z","citation":{"chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>.","mla":"Lovrics, Anna, et al. <i>Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2</i>. Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","ama":"Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. 2014. doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>","ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács, (2014).","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., &#38; Kovács, K. (2014). Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>","ieee":"A. Lovrics <i>et al.</i>, “Transition probability between TF expression states when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014."},"department":[{"_id":"JoCs"}],"day":"14","month":"11","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","type":"research_data_reference","publisher":"Public Library of Science"}]