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(2016). <i>Termination and worst-case analysis of recursive programs</i>. IST Austria.","ama":"Anonymous 1, Anonymous 2, Anonymous 3. <i>Termination and Worst-Case Analysis of Recursive Programs</i>. IST Austria; 2016.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, Termination and Worst-Case Analysis of Recursive Programs, IST Austria, 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3. 2016. Termination and worst-case analysis of recursive programs, IST Austria, 26p.","chicago":"Anonymous, 1, 2 Anonymous, and 3 Anonymous. <i>Termination and Worst-Case Analysis of Recursive Programs</i>. IST Austria, 2016.","mla":"Anonymous, 1, et al. <i>Termination and Worst-Case Analysis of Recursive Programs</i>. IST Austria, 2016.","ieee":"1 Anonymous, 2 Anonymous, and 3 Anonymous, <i>Termination and worst-case analysis of recursive programs</i>. IST Austria, 2016."},"date_published":"2016-07-15T00:00:00Z","oa":1,"date_updated":"2020-07-14T23:05:05Z","date_created":"2018-12-12T11:39:23Z","abstract":[{"text":"We study the problem of developing efficient approaches for proving termination of recursive programs with one-dimensional arrays. Ranking functions serve as a sound and complete approach for proving termination of non-recursive programs without array operations. First, we generalize ranking functions to the notion of measure functions, and prove that measure functions (i) provide a sound method to prove termination of recursive programs (with one-dimensional arrays), and (ii) is both sound and complete over recursive programs without array operations. Our second contribution is the synthesis of measure functions of specific forms in polynomial time. More precisely, we prove that (i) polynomial measure functions over recursive programs can be synthesized in polynomial time through Farkas’ Lemma and Handelman’s Theorem, and (ii) measure functions involving logarithm and exponentiation can be synthesized in polynomial time through abstraction of logarithmic or exponential terms and Handelman’s Theorem. A key application of our method is the worst-case analysis of recursive programs. While previous methods obtain worst-case polynomial bounds of the form O(n^k), where k is an integer, our polynomial time methods can synthesize bounds of the form O(n log n), as well as O(n^x), where x is not an integer. We show the applicability of our automated technique to obtain worst-case complexity of classical recursive algorithms such as (i) Merge-Sort, the divideand-\r\nconquer algorithm for the Closest-Pair problem, where we obtain O(n log n) worst-case bound, and (ii) Karatsuba’s algorithm for polynomial multiplication and Strassen’s algorithm for matrix multiplication, where we obtain O(n^x) bound, where x is not an integer and close to the best-known bounds for the respective algorithms. Finally, we present experimental results to demonstrate the\r\neffectiveness of our approach.","lang":"eng"}],"language":[{"iso":"eng"}]},{"year":"2016","status":"public","publication_identifier":{"issn":["2664-1690"]},"title":"Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds","page":"20","file":[{"file_size":281,"checksum":"cf53cdb6d092e68db0b4a0a1506ef8fb","date_created":"2019-05-10T13:32:16Z","file_name":"listofauthors.txt","creator":"dernst","access_level":"closed","relation":"main_file","date_updated":"2020-07-14T12:46:58Z","file_id":"6406","content_type":"text/plain"},{"creator":"dernst","file_name":"popl2017b.pdf","date_created":"2019-05-10T13:32:16Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:46:58Z","file_id":"6407","file_size":563642,"checksum":"7bdd94ba13aa0dec9c46887fcf13870b"}],"type":"technical_report","has_accepted_license":"1","ddc":["000"],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","file_date_updated":"2020-07-14T12:46:58Z","date_published":"2016-07-15T00:00:00Z","oa":1,"date_updated":"2020-07-14T23:05:06Z","date_created":"2018-12-12T11:39:23Z","abstract":[{"text":"We consider the problem of developing automated techniques to aid the average-case complexity analysis of programs. Several classical textbook algorithms have quite efficient average-case complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., QUICK-SORT), or completely ineffective (e.g., COUPONCOLLECTOR). Since the main focus of average-case analysis is to obtain efficient bounds, we consider bounds that are either logarithmic,\r\nlinear, or almost-linear (O(log n), O(n), O(n · log n),\r\nrespectively, where n represents the size of the input). Our main contribution is a sound approach for deriving such average-case bounds for randomized recursive programs. Our approach is efficient (a simple linear-time algorithm), and it is based on (a) the analysis of recurrence relations induced by randomized algorithms, and (b) a guess-and-check technique. Our approach can infer the asymptotically optimal average-case bounds for classical randomized algorithms, including RANDOMIZED-SEARCH, QUICKSORT, QUICK-SELECT, COUPON-COLLECTOR, where the worstcase\r\nbounds are either inefficient (such as linear as compared to logarithmic of average-case, or quadratic as compared to linear or almost-linear of average-case), or ineffective. We have implemented our approach, and the experimental results show that we obtain the bounds efficiently for various classical algorithms.","lang":"eng"}],"language":[{"iso":"eng"}],"alternative_title":["IST Austria Technical Report"],"day":"15","_id":"5447","publisher":"IST Austria","pubrep_id":"619","month":"07","author":[{"first_name":"1","full_name":"Anonymous, 1","last_name":"Anonymous"},{"last_name":"Anonymous","full_name":"Anonymous, 2","first_name":"2"},{"first_name":"3","full_name":"Anonymous, 3","last_name":"Anonymous"}],"citation":{"ieee":"1 Anonymous, 2 Anonymous, and 3 Anonymous, <i>Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds</i>. IST Austria, 2016.","mla":"Anonymous, 1, et al. <i>Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds</i>. IST Austria, 2016.","chicago":"Anonymous, 1, 2 Anonymous, and 3 Anonymous. <i>Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds</i>. IST Austria, 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3. 2016. Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds, IST Austria, 20p.","ama":"Anonymous 1, Anonymous 2, Anonymous 3. <i>Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds</i>. IST Austria; 2016.","apa":"Anonymous, 1, Anonymous, 2, &#38; Anonymous, 3. (2016). <i>Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds</i>. IST Austria.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds, IST Austria, 2016."}},{"date_updated":"2023-02-23T12:27:16Z","external_id":{"arxiv":["1610.01188"]},"date_published":"2016-07-15T00:00:00Z","oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes."}],"arxiv":1,"date_created":"2018-12-12T11:39:23Z","alternative_title":["IST Austria Technical Report"],"citation":{"ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, <i>Data-centric dynamic partial order reduction</i>. IST Austria, 2016.","chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria, 2016.","mla":"Anonymous, 1, et al. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria, 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2016. Data-centric dynamic partial order reduction, IST Austria, 20p.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2016.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria; 2016.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, &#38; Anonymous, 4. (2016). <i>Data-centric dynamic partial order reduction</i>. IST Austria."},"author":[{"full_name":"Anonymous, 1","first_name":"1","last_name":"Anonymous"},{"last_name":"Anonymous","first_name":"2","full_name":"Anonymous, 2"},{"last_name":"Anonymous","full_name":"Anonymous, 3","first_name":"3"},{"last_name":"Anonymous","first_name":"4","full_name":"Anonymous, 4"}],"month":"07","pubrep_id":"620","_id":"5448","publisher":"IST Austria","day":"15","type":"technical_report","has_accepted_license":"1","file":[{"creator":"system","file_name":"IST-2016-620-v1+1_main.pdf","date_created":"2018-12-12T11:53:45Z","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:46:58Z","file_id":"5506","content_type":"application/pdf","file_size":538881,"checksum":"1d69252d66bcdf782615ddfb911d2957"},{"date_updated":"2020-07-14T12:46:58Z","file_id":"6405","content_type":"text/plain","relation":"main_file","access_level":"closed","creator":"dernst","date_created":"2019-05-10T13:30:40Z","file_name":"authornames.txt","checksum":"deabb0eb8f237cae4f9542b28b0b6eb2","file_size":121}],"page":"20","status":"public","year":"2016","publication_identifier":{"issn":["2664-1690"]},"title":"Data-centric dynamic partial order reduction","related_material":{"record":[{"id":"10417","relation":"later_version","status":"public"},{"id":"5456","status":"public","relation":"later_version"}]},"ddc":["000"],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:58Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"alternative_title":["IST Austria Technical Report"],"department":[{"_id":"KrCh"}],"author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"first_name":"Josef","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"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"}],"month":"11","citation":{"short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Amplification on Undirected Population Structures: Comets Beat Stars, IST Austria, 2016.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria, 2016.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>.","mla":"Pavlogiannis, Andreas, et al. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Amplification on undirected population structures: Comets beat stars, IST Austria, 22p."},"day":"09","_id":"5449","publisher":"IST Austria","pubrep_id":"648","date_updated":"2023-02-23T12:22:21Z","oa":1,"date_published":"2016-11-09T00:00:00Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population.\r\nThe fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure.\r\nAmplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade.\r\nIn this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively."}],"date_created":"2018-12-12T11:39:24Z","oa_version":"Updated Version","file_date_updated":"2020-07-14T12:46:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","file":[{"file_id":"5529","content_type":"application/pdf","date_updated":"2020-07-14T12:46:58Z","relation":"main_file","access_level":"open_access","date_created":"2018-12-12T11:54:07Z","file_name":"IST-2016-648-v1+1_tr.pdf","creator":"system","checksum":"8345a8c1e7d7f0cd92516d182b7fc59e","file_size":1264221}],"has_accepted_license":"1","type":"technical_report","doi":"10.15479/AT:IST-2016-648-v1-1","title":"Amplification on undirected population structures: Comets beat stars","year":"2016","publication_identifier":{"issn":["2664-1690"]},"status":"public","page":"22","related_material":{"record":[{"id":"512","status":"public","relation":"later_version"}]},"ddc":["519"]},{"oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","has_accepted_license":"1","type":"technical_report","file":[{"access_level":"open_access","date_created":"2018-12-12T11:53:04Z","file_name":"IST-2016-728-v1+1_main.pdf","creator":"system","file_id":"5465","content_type":"application/pdf","date_updated":"2020-07-14T12:46:59Z","relation":"main_file","file_size":1014732,"checksum":"7b8bb17c322c0556acba6ac169fa71c1"}],"doi":"10.15479/AT:IST-2016-728-v1-1","status":"public","title":"Strong amplifiers of natural selection","publication_identifier":{"issn":["2664-1690"]},"year":"2016","page":"34","ddc":["000"],"alternative_title":["IST Austria Technical Report"],"department":[{"_id":"KrCh"}],"author":[{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis"},{"orcid":"0000-0002-1097-9684","first_name":"Josef","full_name":"Tkadlec, Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"month":"12","citation":{"ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Strong amplifiers of natural selection</i>. IST Austria, 2016.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">https://doi.org/10.15479/AT:IST-2016-728-v1-1</a>.","mla":"Pavlogiannis, Andreas, et al. <i>Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">10.15479/AT:IST-2016-728-v1-1</a>.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Strong amplifiers of natural selection, IST Austria, 34p.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Strong Amplifiers of Natural Selection, IST Austria, 2016.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">10.15479/AT:IST-2016-728-v1-1</a>","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">https://doi.org/10.15479/AT:IST-2016-728-v1-1</a>"},"day":"30","_id":"5451","pubrep_id":"728","publisher":"IST Austria","date_updated":"2023-02-23T12:27:05Z","oa":1,"date_published":"2016-12-30T00:00:00Z","language":[{"iso":"eng"}],"date_created":"2018-12-12T11:39:24Z"},{"article_processing_charge":"No","publication_status":"published","oa_version":"Published Version","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"id":"5453","status":"public","relation":"later_version"},{"status":"public","relation":"popular_science","id":"5559"}]},"ddc":["000"],"file":[{"access_level":"open_access","creator":"system","date_created":"2018-12-12T11:52:59Z","file_name":"IST-2017-728-v2+1_main.pdf","content_type":"application/pdf","file_id":"5460","date_updated":"2020-07-14T12:46:59Z","relation":"main_file","checksum":"58e895f26c82f560c0f0989bf8b08599","file_size":811558}],"has_accepted_license":"1","doi":"10.15479/AT:IST-2017-728-v2-1","year":"2016","author":[{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"month":"12","date_published":"2016-12-30T00:00:00Z","ec_funded":1,"file_date_updated":"2020-07-14T12:46:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"technical_report","publication_identifier":{"issn":["2664-1690"]},"status":"public","title":"Arbitrarily strong amplifiers of natural selection","page":"32","citation":{"short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">https://doi.org/10.15479/AT:IST-2017-728-v2-1</a>","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">10.15479/AT:IST-2017-728-v2-1</a>","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">https://doi.org/10.15479/AT:IST-2017-728-v2-1</a>.","mla":"Pavlogiannis, Andreas, et al. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">10.15479/AT:IST-2017-728-v2-1</a>.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 32p.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria, 2016."},"day":"30","_id":"5452","publisher":"IST Austria","pubrep_id":"750","department":[{"_id":"KrCh"}],"alternative_title":["IST Austria Technical Report"],"language":[{"iso":"eng"}],"date_created":"2018-12-12T11:39:25Z","date_updated":"2024-02-21T13:48:42Z","oa":1},{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:46:59Z","oa_version":"Published Version","ddc":["000"],"related_material":{"record":[{"id":"5452","relation":"earlier_version","status":"public"}]},"page":"34","publication_identifier":{"issn":["2664-1690"]},"title":"Arbitrarily strong amplifiers of natural selection","status":"public","year":"2016","doi":"10.15479/AT:IST-2017-749-v3-1","file":[{"checksum":"83b0313dab3bff4bdb6ac38695026fda","file_size":1015647,"access_level":"open_access","creator":"system","date_created":"2018-12-12T11:53:13Z","file_name":"IST-2017-749-v3+1_main.pdf","content_type":"application/pdf","file_id":"5474","date_updated":"2020-07-14T12:46:59Z","relation":"main_file"}],"type":"technical_report","has_accepted_license":"1","pubrep_id":"755","_id":"5453","publisher":"IST Austria","day":"30","citation":{"ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 34p.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">https://doi.org/10.15479/AT:IST-2017-749-v3-1</a>.","mla":"Pavlogiannis, Andreas, et al. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">10.15479/AT:IST-2017-749-v3-1</a>.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria, 2016.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">https://doi.org/10.15479/AT:IST-2017-749-v3-1</a>","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">10.15479/AT:IST-2017-749-v3-1</a>"},"month":"12","author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"},{"last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef","full_name":"Tkadlec, Josef"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"alternative_title":["IST Austria Technical Report"],"department":[{"_id":"KrCh"}],"date_created":"2018-12-12T11:39:25Z","language":[{"iso":"eng"}],"date_published":"2016-12-30T00:00:00Z","oa":1,"date_updated":"2023-02-23T12:27:07Z"},{"date_updated":"2024-02-21T13:49:54Z","oa":1,"date_published":"2016-02-19T00:00:00Z","abstract":[{"lang":"eng","text":"We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)"}],"date_created":"2018-12-12T12:31:29Z","department":[{"_id":"NiBa"}],"month":"02","author":[{"first_name":"Thomas","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","orcid":"0000-0002-4014-8478","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"}],"citation":{"ama":"Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>","apa":"Ellis, T., &#38; Field, D. (2016). Flower colour data and phylogeny (NEXUS) files. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>","short":"T. Ellis, D. Field, (2016).","ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","chicago":"Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS) Files.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>.","ista":"Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","mla":"Ellis, Thomas, and David Field. <i>Flower Colour Data and Phylogeny (NEXUS) Files</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>."},"day":"19","_id":"5550","publisher":"Institute of Science and Technology Austria","file":[{"creator":"system","date_created":"2018-12-12T13:02:27Z","file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","date_updated":"2020-07-14T12:47:00Z","file_id":"5594","file_size":4468543,"checksum":"950f85b80427d357bfeff09608ba02e9"}],"publist_id":"5828","type":"research_data","has_accepted_license":"1","doi":"10.15479/AT:ISTA:34","status":"public","title":"Flower colour data and phylogeny (NEXUS) files","year":"2016","related_material":{"record":[{"status":"public","relation":"research_paper","id":"1382"}]},"ddc":["576"],"license":"https://creativecommons.org/publicdomain/zero/1.0/","oa_version":"Published Version","datarep_id":"34","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"}},{"oa_version":"Published Version","datarep_id":"35","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:01Z","status":"public","year":"2016","title":"Data on pollinator observations and offpsring phenotypes","type":"research_data","file":[{"content_type":"application/zip","file_id":"5640","date_updated":"2020-07-14T12:47:01Z","relation":"main_file","access_level":"open_access","date_created":"2018-12-12T13:05:12Z","file_name":"IST-2016-35-v1+1_array_data.zip","creator":"system","checksum":"aa3eb85d52b110cd192aa23147c4d4f3","file_size":32775}],"has_accepted_license":"1","doi":"10.15479/AT:ISTA:35","related_material":{"record":[{"id":"1398","status":"public","relation":"research_paper"}]},"department":[{"_id":"NiBa"}],"day":"19","_id":"5551","publisher":"Institute of Science and Technology Austria","contributor":[{"last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"month":"02","author":[{"full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"}],"citation":{"mla":"Ellis, Thomas. <i>Data on Pollinator Observations and Offpsring Phenotypes</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>.","ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>.","chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>.","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>","ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>","short":"T. Ellis, (2016)."},"oa":1,"date_published":"2016-02-19T00:00:00Z","date_updated":"2024-02-21T13:51:27Z","date_created":"2018-12-12T12:31:29Z","abstract":[{"text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.","lang":"eng"}]},{"status":"public","title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","year":"2016","type":"research_data","has_accepted_license":"1","file":[{"checksum":"cbc61b523d4d475a04a737d50dc470ef","file_size":44905,"relation":"main_file","date_updated":"2020-07-14T12:47:01Z","file_id":"5625","content_type":"application/zip","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","date_created":"2018-12-12T13:03:07Z","creator":"system","access_level":"open_access"}],"doi":"10.15479/AT:ISTA:36","related_material":{"record":[{"id":"1398","status":"public","relation":"research_paper"}]},"oa_version":"Published Version","datarep_id":"36","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:01Z","date_published":"2016-02-19T00:00:00Z","oa":1,"date_updated":"2024-02-21T13:51:40Z","date_created":"2018-12-12T12:31:30Z","abstract":[{"lang":"eng","text":"Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation."}],"department":[{"_id":"NiBa"}],"day":"19","publisher":"Institute of Science and Technology Austria","_id":"5552","contributor":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"author":[{"last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","full_name":"Ellis, Thomas"}],"month":"02","citation":{"ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.","ista":"Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data., Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>.","mla":"Ellis, Thomas. <i>Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>.","chicago":"Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:36\">https://doi.org/10.15479/AT:ISTA:36</a>.","short":"T. Ellis, (2016).","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>","apa":"Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:36\">https://doi.org/10.15479/AT:ISTA:36</a>"}},{"oa_version":"Published Version","datarep_id":"37","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:01Z","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","file":[{"relation":"main_file","content_type":"application/zip","file_id":"5620","date_updated":"2020-07-14T12:47:01Z","creator":"system","file_name":"IST-2016-37-v1+1_paternity_archive.zip","date_created":"2018-12-12T13:03:02Z","access_level":"open_access","checksum":"4ae751b1fa4897fa216241f975a57313","file_size":132808}],"type":"research_data","doi":"10.15479/AT:ISTA:37","status":"public","year":"2016","title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","related_material":{"record":[{"id":"1398","status":"public","relation":"research_paper"}]},"ddc":["576"],"keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"department":[{"_id":"NiBa"}],"author":[{"full_name":"Field, David","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"},{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","first_name":"Thomas"}],"month":"02","citation":{"short":"D. Field, T. Ellis, (2016).","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>","apa":"Field, D., &#38; Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016.","mla":"Field, David, and Thomas Ellis. <i>Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>."},"day":"19","publisher":"Institute of Science and Technology Austria","_id":"5553","contributor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","contributor_type":"project_manager","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"date_updated":"2024-02-21T13:51:14Z","oa":1,"date_published":"2016-02-19T00:00:00Z","date_created":"2018-12-12T12:31:30Z","abstract":[{"lang":"eng","text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org."}]},{"year":"2016","title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","status":"public","type":"research_data","file":[{"file_size":1123495,"checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","date_created":"2018-12-12T13:03:08Z","creator":"system","access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"5626","date_updated":"2020-07-14T12:47:01Z"}],"has_accepted_license":"1","doi":"10.15479/AT:ISTA:43","related_material":{"record":[{"id":"1131","status":"public","relation":"used_in_publication"}]},"oa_version":"Published Version","datarep_id":"43","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:01Z","oa":1,"date_published":"2016-05-12T00:00:00Z","date_updated":"2024-02-21T13:50:34Z","date_created":"2018-12-12T12:31:30Z","abstract":[{"text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution.","lang":"eng"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"day":"12","publisher":"Institute of Science and Technology Austria","_id":"5554","contributor":[{"contributor_type":"researcher","first_name":"Magdalena","last_name":"Steinrück","id":"2C023F40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jesse","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Fabienne"}],"author":[{"first_name":"Murat","orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat","last_name":"Tugrul","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"}],"month":"05","citation":{"short":"M. Tugrul, (2016).","apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>","ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>","ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>.","mla":"Tugrul, Murat. <i>Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>.","chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>.","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016."}},{"ddc":["570"],"year":"2016","status":"public","title":"Fiji script to determine average speed and direction of migration of cells","type":"research_data","has_accepted_license":"1","file":[{"file_size":20692,"checksum":"9f96cddbcd4ed689f48712ffe234d5e5","relation":"main_file","date_updated":"2020-07-14T12:47:02Z","file_id":"5621","content_type":"application/zip","file_name":"IST-2016-44-v1+1_migrationAnalyzer.zip","date_created":"2018-12-12T13:03:03Z","creator":"system","access_level":"open_access"}],"doi":"10.15479/AT:ISTA:44","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:02Z","oa_version":"Published Version","datarep_id":"44","abstract":[{"text":"This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies.","lang":"eng"}],"date_created":"2018-12-12T12:31:31Z","date_published":"2016-07-08T00:00:00Z","oa":1,"date_updated":"2024-02-21T13:50:06Z","day":"08","_id":"5555","publisher":"Institute of Science and Technology Austria","month":"07","author":[{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"}],"citation":{"short":"R. Hauschild, (2016).","apa":"Hauschild, R. (2016). Fiji script to determine average speed and direction of migration of cells. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:44\">https://doi.org/10.15479/AT:ISTA:44</a>","ama":"Hauschild R. Fiji script to determine average speed and direction of migration of cells. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>","mla":"Hauschild, Robert. <i>Fiji Script to Determine Average Speed and Direction of Migration of Cells</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>.","chicago":"Hauschild, Robert. “Fiji Script to Determine Average Speed and Direction of Migration of Cells.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:44\">https://doi.org/10.15479/AT:ISTA:44</a>.","ista":"Hauschild R. 2016. Fiji script to determine average speed and direction of migration of cells, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>.","ieee":"R. Hauschild, “Fiji script to determine average speed and direction of migration of cells.” Institute of Science and Technology Austria, 2016."},"department":[{"_id":"Bio"}],"keyword":["cell migration","wide field microscopy","FIJI"]},{"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"license":"https://creativecommons.org/licenses/by-sa/4.0/","oa_version":"Published Version","datarep_id":"45","related_material":{"record":[{"id":"8431","relation":"used_in_publication","status":"deleted"},{"id":"1029","relation":"research_paper","status":"public"}]},"ddc":["571"],"file":[{"file_name":"IST-2016-45-v1+1_PaperCode.zip","date_created":"2018-12-12T13:02:58Z","creator":"system","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:47:02Z","file_id":"5616","content_type":"application/zip","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","file_size":296722548}],"has_accepted_license":"1","type":"research_data","doi":"10.15479/AT:ISTA:45","status":"public","title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","year":"2016","month":"08","author":[{"full_name":"Lukacisin, Martin","orcid":"0000-0001-6549-4177","first_name":"Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisin"},{"full_name":"Landon, Matthieu","first_name":"Matthieu","last_name":"Landon"},{"last_name":"Jajoo","full_name":"Jajoo, Rishi","first_name":"Rishi"}],"citation":{"ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016.","ista":"Lukacisin M, Landon M, Jajoo R. 2016. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>.","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:45\">https://doi.org/10.15479/AT:ISTA:45</a>.","mla":"Lukacisin, Martin, et al. <i>MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.”</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>.","ama":"Lukacisin M, Landon M, Jajoo R. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>","apa":"Lukacisin, M., Landon, M., &#38; Jajoo, R. (2016). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:45\">https://doi.org/10.15479/AT:ISTA:45</a>","short":"M. Lukacisin, M. Landon, R. Jajoo, (2016)."},"day":"25","_id":"5556","publisher":"Institute of Science and Technology Austria","keyword":["transcription","pausing","backtracking","polymerase","RNA","NET-seq","nucleosome","basepairing"],"department":[{"_id":"ToBo"}],"date_created":"2018-12-12T12:31:31Z","abstract":[{"text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions","lang":"eng"}],"date_updated":"2024-02-21T13:51:53Z","oa":1,"date_published":"2016-08-25T00:00:00Z"},{"keyword":["discrete tomography"],"department":[{"_id":"VlKo"}],"month":"09","author":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","full_name":"Swoboda, Paul","first_name":"Paul"}],"citation":{"chicago":"Swoboda, Paul. “Synthetic Discrete Tomography Problems.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:46\">https://doi.org/10.15479/AT:ISTA:46</a>.","ista":"Swoboda P. 2016. Synthetic discrete tomography problems, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>.","mla":"Swoboda, Paul. <i>Synthetic Discrete Tomography Problems</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>.","ieee":"P. Swoboda, “Synthetic discrete tomography problems.” Institute of Science and Technology Austria, 2016.","apa":"Swoboda, P. (2016). Synthetic discrete tomography problems. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:46\">https://doi.org/10.15479/AT:ISTA:46</a>","ama":"Swoboda P. Synthetic discrete tomography problems. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>","short":"P. Swoboda, (2016)."},"day":"20","publisher":"Institute of Science and Technology Austria","_id":"5557","contributor":[{"last_name":"Kuske","contributor_type":"data_collector","first_name":"Jan"}],"date_updated":"2024-02-21T13:50:21Z","oa":1,"date_published":"2016-09-20T00:00:00Z","abstract":[{"lang":"eng","text":"Small synthetic discrete tomography problems.\r\nSizes are 32x32, 64z64 and 256x256.\r\nProjection angles are 2, 4, and 6.\r\nNumber of labels are 3 and 5."}],"date_created":"2018-12-12T12:31:31Z","oa_version":"Published Version","datarep_id":"46","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"type":"research_data","file":[{"file_size":36058401,"checksum":"aa5a16a0dc888da7186fb8fc45e88439","relation":"main_file","file_id":"5645","date_updated":"2020-07-14T12:47:02Z","content_type":"application/zip","creator":"system","date_created":"2018-12-12T13:05:19Z","file_name":"IST-2016-46-v1+1_discrete_tomography_synthetic.zip","access_level":"open_access"}],"has_accepted_license":"1","doi":"10.15479/AT:ISTA:46","title":"Synthetic discrete tomography problems","status":"public","year":"2016","ddc":["006"]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:02Z","oa_version":"Published Version","datarep_id":"48","ddc":["004"],"related_material":{"record":[{"status":"public","relation":"other","id":"1122"}]},"year":"2016","status":"public","title":"Tracking, Correcting and Absorbing Water Surface Waves","has_accepted_license":"1","file":[{"checksum":"5b1b256ad796fbddb4b7729f5e45e444","file_size":55237885,"date_created":"2018-12-12T13:02:18Z","file_name":"IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2","creator":"system","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:47:02Z","content_type":"application/x-bzip2","file_id":"5589"}],"publist_id":"6238","type":"research_data","doi":"10.15479/AT:ISTA:48","day":"23","publisher":"Institute of Science and Technology Austria","_id":"5558","pubrep_id":"640","month":"09","author":[{"id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","last_name":"Bojsen-Hansen","first_name":"Morten","full_name":"Bojsen-Hansen, Morten","orcid":"0000-0002-4417-3224"}],"citation":{"ista":"Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>.","mla":"Bojsen-Hansen, Morten. <i>Tracking, Correcting and Absorbing Water Surface Waves</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>.","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:48\">https://doi.org/10.15479/AT:ISTA:48</a>.","ieee":"M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016.","short":"M. Bojsen-Hansen, (2016).","apa":"Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:48\">https://doi.org/10.15479/AT:ISTA:48</a>","ama":"Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>"},"department":[{"_id":"ChWo"}],"date_created":"2018-12-12T12:31:31Z","abstract":[{"text":"PhD thesis LaTeX source code","lang":"eng"}],"oa":1,"date_published":"2016-09-23T00:00:00Z","date_updated":"2024-02-21T13:50:48Z"},{"intvolume":"        33","month":"03","author":[{"last_name":"Wielgoss","full_name":"Wielgoss, Sébastien","first_name":"Sébastien"},{"full_name":"Bergmiller, Tobias","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller"},{"first_name":"Anna M.","full_name":"Bischofberger, Anna M.","last_name":"Bischofberger"},{"last_name":"Hall","first_name":"Alex R.","full_name":"Hall, Alex R."}],"quality_controlled":"1","pmid":1,"acknowledgement":"The authors thank three anonymous reviewers and the editor for helpful comments on the manuscript, as well as Dominique Schneider for feedback on an earlier draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824 to S.W.).","publication":"Molecular Biology and Evolution","external_id":{"pmid":["26609077"]},"date_published":"2016-03-01T00:00:00Z","article_processing_charge":"No","publication_status":"published","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"research_data","id":"9719"}]},"ddc":["576"],"doi":"10.1093/molbev/msv270","file":[{"relation":"main_file","date_updated":"2020-07-14T12:47:10Z","file_id":"5750","content_type":"application/pdf","creator":"dernst","date_created":"2018-12-18T13:21:45Z","file_name":"2016_MolBiolEvol_Wielgoss.pdf","access_level":"open_access","file_size":634037,"checksum":"47d9010690b6c5c17f2ac830cc63ac5c"}],"has_accepted_license":"1","year":"2016","citation":{"apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2016). Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. 2016;33(3):770-782. doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>","short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology and Evolution 33 (2016) 770–782.","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>.","mla":"Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>.","ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. 33(3), 770–782.","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria,” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3. Oxford University Press, pp. 770–782, 2016."},"pubrep_id":"587","_id":"5749","publisher":"Oxford University Press","day":"01","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"abstract":[{"text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance.","lang":"eng"}],"date_created":"2018-12-18T13:18:10Z","volume":33,"date_updated":"2023-09-05T13:46:05Z","oa":1,"file_date_updated":"2020-07-14T12:47:10Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","license":"https://creativecommons.org/licenses/by-nc/4.0/","issue":"3","type":"journal_article","page":"770-782","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"title":"Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria","status":"public","scopus_import":"1"},{"language":[{"iso":"eng"}],"date_created":"2018-12-20T21:13:59Z","volume":18,"abstract":[{"lang":"eng","text":"Retroviruses such as HIV-1 assemble and bud from infected cells in an immature, non-infectious form. Subsequently, a series of proteolytic cleavages catalysed by the viral protease leads to a spectacular structural rearrangement of the viral particle into a mature form that is competent to fuse with and infect a new cell. Maturation involves changes in the structures of protein domains, in the interactions between protein domains, and in the architecture of the viral components that are assembled by the proteins. Tight control of proteolytic cleavages at different sites is required for successful maturation, and the process is a major target of antiretroviral drugs. Here we will describe what is known about the structures of immature and mature retrovirus particles, and about the maturation process by which one transitions into the other. Despite a wealth of available data, fundamental questions about retroviral maturation remain unanswered."}],"date_updated":"2021-01-12T08:03:22Z","oa":1,"citation":{"ieee":"S. Mattei, F. K. Schur, and J. A. Briggs, “Retrovirus maturation—an extraordinary structural transformation,” <i>Current Opinion in Virology</i>, vol. 18, no. 6. Elsevier, pp. 27–35, 2016.","chicago":"Mattei, Simone, Florian KM Schur, and John AG Briggs. “Retrovirus Maturation—an Extraordinary Structural Transformation.” <i>Current Opinion in Virology</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.coviro.2016.02.008\">https://doi.org/10.1016/j.coviro.2016.02.008</a>.","mla":"Mattei, Simone, et al. “Retrovirus Maturation—an Extraordinary Structural Transformation.” <i>Current Opinion in Virology</i>, vol. 18, no. 6, Elsevier, 2016, pp. 27–35, doi:<a href=\"https://doi.org/10.1016/j.coviro.2016.02.008\">10.1016/j.coviro.2016.02.008</a>.","ista":"Mattei S, Schur FK, Briggs JA. 2016. Retrovirus maturation—an extraordinary structural transformation. Current Opinion in Virology. 18(6), 27–35.","short":"S. Mattei, F.K. Schur, J.A. Briggs, Current Opinion in Virology 18 (2016) 27–35.","ama":"Mattei S, Schur FK, Briggs JA. Retrovirus maturation—an extraordinary structural transformation. <i>Current Opinion in Virology</i>. 2016;18(6):27-35. doi:<a href=\"https://doi.org/10.1016/j.coviro.2016.02.008\">10.1016/j.coviro.2016.02.008</a>","apa":"Mattei, S., Schur, F. K., &#38; Briggs, J. A. (2016). Retrovirus maturation—an extraordinary structural transformation. <i>Current Opinion in Virology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coviro.2016.02.008\">https://doi.org/10.1016/j.coviro.2016.02.008</a>"},"_id":"5771","publisher":"Elsevier","day":"22","type":"journal_article","page":"27-35","status":"public","publication_identifier":{"issn":["1879-6257"]},"title":"Retrovirus maturation—an extraordinary structural transformation","file_date_updated":"2020-07-14T12:47:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","publication":"Current Opinion in Virology","date_published":"2016-03-22T00:00:00Z","intvolume":"        18","author":[{"last_name":"Mattei","full_name":"Mattei, Simone","first_name":"Simone"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian","first_name":"Florian","orcid":"0000-0003-4790-8078"},{"last_name":"Briggs","full_name":"Briggs, John AG","first_name":"John AG"}],"month":"03","extern":"1","quality_controlled":"1","ddc":["570"],"doi":"10.1016/j.coviro.2016.02.008","has_accepted_license":"1","file":[{"creator":"dernst","file_name":"2016_CurrentOpinion_Mattei.pdf","date_created":"2019-01-09T13:05:44Z","access_level":"open_access","relation":"main_file","file_id":"5812","date_updated":"2020-07-14T12:47:11Z","content_type":"application/pdf","file_size":1773842,"checksum":"320939d28ebd1adfb122338019892508"}],"year":"2016","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version"},{"date_published":"2016-06-24T00:00:00Z","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1601.07683","open_access":"1"}],"date_updated":"2021-01-12T08:05:06Z","publication":"Science","abstract":[{"text":"Quantum metrology exploits entangled states of particles to improve sensing precision beyond the limit achievable with uncorrelated particles. All previous methods required detection noise levels below this standard quantum limit to realize the benefits of the intrinsic sensitivity provided by these states.We experimentally demonstrate a widely applicable method for entanglement-enhanced measurements without low-noise detection. The method involves an intermediate quantum phase magnification step that eases implementation complexity. We used it to perform squeezed-state metrology 8 decibels below the standard quantum limit with a detection system that has a noise floor 10 decibels above the standard quantum limit.","lang":"eng"}],"volume":352,"date_created":"2018-12-11T11:47:21Z","quality_controlled":0,"extern":1,"_id":"587","publisher":"American Association for the Advancement of Science","day":"24","citation":{"short":"O. Hosten, R. Krishnakumar, N. Engelsen, M. Kasevich, Science 352 (2016) 1552–1555.","ama":"Hosten O, Krishnakumar R, Engelsen N, Kasevich M. Quantum phase magnification. <i>Science</i>. 2016;352(6293):1552-1555. doi:<a href=\"https://doi.org/10.1126/science.aaf3397\">10.1126/science.aaf3397</a>","apa":"Hosten, O., Krishnakumar, R., Engelsen, N., &#38; Kasevich, M. (2016). Quantum phase magnification. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaf3397\">https://doi.org/10.1126/science.aaf3397</a>","ieee":"O. Hosten, R. Krishnakumar, N. Engelsen, and M. Kasevich, “Quantum phase magnification,” <i>Science</i>, vol. 352, no. 6293. American Association for the Advancement of Science, pp. 1552–1555, 2016.","mla":"Hosten, Onur, et al. “Quantum Phase Magnification.” <i>Science</i>, vol. 352, no. 6293, American Association for the Advancement of Science, 2016, pp. 1552–55, doi:<a href=\"https://doi.org/10.1126/science.aaf3397\">10.1126/science.aaf3397</a>.","chicago":"Hosten, Onur, Rajiv Krishnakumar, Nils Engelsen, and Mark Kasevich. “Quantum Phase Magnification.” <i>Science</i>. American Association for the Advancement of Science, 2016. <a href=\"https://doi.org/10.1126/science.aaf3397\">https://doi.org/10.1126/science.aaf3397</a>.","ista":"Hosten O, Krishnakumar R, Engelsen N, Kasevich M. 2016. Quantum phase magnification. Science. 352(6293), 1552–1555."},"month":"06","author":[{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","orcid":"0000-0002-2031-204X","full_name":"Onur Hosten","first_name":"Onur"},{"last_name":"Krishnakumar","full_name":"Krishnakumar, Rajiv","first_name":"Rajiv"},{"full_name":"Engelsen, Nils J","first_name":"Nils","last_name":"Engelsen"},{"last_name":"Kasevich","first_name":"Mark","full_name":"Kasevich, Mark A"}],"intvolume":"       352","page":"1552 - 1555","status":"public","title":"Quantum phase magnification","year":"2016","doi":"10.1126/science.aaf3397","publist_id":"7214","type":"journal_article","issue":"6293","publication_status":"published"},{"page":"6698-6712","status":"public","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"title":"Unified scaling of polar codes: Error exponent, scaling exponent, moderate deviations, and error floors","type":"journal_article","issue":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_updated":"2021-01-12T08:08:44Z","main_file_link":[{"url":"https://arxiv.org/abs/1501.02444","open_access":"1"}],"article_type":"original","volume":62,"date_created":"2019-07-31T06:03:49Z","abstract":[{"lang":"eng","text":"Consider the transmission of a polar code of block length N and rate R over a binary memoryless symmetric channel W and let P e be the block error probability under successive cancellation decoding. In this paper, we develop new bounds that characterize the relationship of the parameters R, N, P e , and the quality of the channel W quantified by its capacity I(W) and its Bhattacharyya parameter Z(W). In previous work, two main regimes were studied. In the error exponent regime, the channel W and the rate R <; I(W) are fixed, and it was proved that the error probability Pe scales roughly as 2 -√N . In the scaling exponent approach, the channel W and the error probability Pe are fixed and it was proved that the gap to capacity I(W) - R scales as N -1/μ . Here, μ is called scaling exponent and this scaling exponent depends on the channel W. A heuristic computation for the binary erasure channel (BEC) gives μ = 3.627 and it was shown that, for any channel W, 3.579 ≤ μ ≤ 5.702. Our contributions are as follows. First, we provide the tighter upper bound μ <;≤ 4.714 valid for any W. With the same technique, we obtain the upper bound μ ≤ 3.639 for the case of the BEC; this upper bound approaches very closely the heuristically derived value for the scaling exponent of the erasure channel. Second, we develop a trade-off between the gap to capacity I(W)- R and the error probability Pe as the functions of the block length N. In other words, we neither fix the gap to capacity (error exponent regime) nor the error probability (scaling exponent regime), but we do consider a moderate deviations regime in which we study how fast both quantities, as the functions of the block length N, simultaneously go to 0. Third, we prove that polar codes are not affected by error floors. To do so, we fix a polar code of block length N and rate R. Then, we vary the channel W and study the impact of this variation on the error probability. We show that the error probability Pe scales as the Bhattacharyya parameter Z(W) raised to a power that scales roughly like VN. This agrees with the scaling in the error exponent regime."}],"language":[{"iso":"eng"}],"publisher":"IEEE","_id":"6732","day":"01","citation":{"ieee":"M. Mondelli, S. H. Hassani, and R. L. Urbanke, “Unified scaling of polar codes: Error exponent, scaling exponent, moderate deviations, and error floors,” <i>IEEE Transactions on Information Theory</i>, vol. 62, no. 12. IEEE, pp. 6698–6712, 2016.","chicago":"Mondelli, Marco, S. Hamed Hassani, and Rudiger L. Urbanke. “Unified Scaling of Polar Codes: Error Exponent, Scaling Exponent, Moderate Deviations, and Error Floors.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2016. <a href=\"https://doi.org/10.1109/tit.2016.2616117\">https://doi.org/10.1109/tit.2016.2616117</a>.","mla":"Mondelli, Marco, et al. “Unified Scaling of Polar Codes: Error Exponent, Scaling Exponent, Moderate Deviations, and Error Floors.” <i>IEEE Transactions on Information Theory</i>, vol. 62, no. 12, IEEE, 2016, pp. 6698–712, doi:<a href=\"https://doi.org/10.1109/tit.2016.2616117\">10.1109/tit.2016.2616117</a>.","ista":"Mondelli M, Hassani SH, Urbanke RL. 2016. Unified scaling of polar codes: Error exponent, scaling exponent, moderate deviations, and error floors. IEEE Transactions on Information Theory. 62(12), 6698–6712.","short":"M. Mondelli, S.H. Hassani, R.L. Urbanke, IEEE Transactions on Information Theory 62 (2016) 6698–6712.","ama":"Mondelli M, Hassani SH, Urbanke RL. Unified scaling of polar codes: Error exponent, scaling exponent, moderate deviations, and error floors. <i>IEEE Transactions on Information Theory</i>. 2016;62(12):6698-6712. doi:<a href=\"https://doi.org/10.1109/tit.2016.2616117\">10.1109/tit.2016.2616117</a>","apa":"Mondelli, M., Hassani, S. H., &#38; Urbanke, R. L. (2016). Unified scaling of polar codes: Error exponent, scaling exponent, moderate deviations, and error floors. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/tit.2016.2616117\">https://doi.org/10.1109/tit.2016.2616117</a>"},"year":"2016","doi":"10.1109/tit.2016.2616117","oa_version":"Preprint","publication_status":"published","date_published":"2016-12-01T00:00:00Z","publication":"IEEE Transactions on Information Theory","external_id":{"arxiv":["1501.02444"]},"arxiv":1,"quality_controlled":"1","extern":"1","month":"12","intvolume":"        62","author":[{"last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","first_name":"Marco"},{"full_name":"Hassani, S. Hamed","first_name":"S. Hamed","last_name":"Hassani"},{"full_name":"Urbanke, Rudiger L.","first_name":"Rudiger L.","last_name":"Urbanke"}]}]