[{"publication":"Genome Announcements","doi":"10.1128/genomeA.00216-13","oa":1,"volume":1,"has_accepted_license":"1","quality_controlled":"1","scopus_import":1,"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4516","pubrep_id":"398","day":"13","status":"public","year":"2013","language":[{"iso":"eng"}],"month":"06","file":[{"file_name":"IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf","date_created":"2018-12-12T10:17:36Z","content_type":"application/pdf","date_updated":"2020-07-14T12:45:40Z","checksum":"0751ec74b695567e0cdf02aaf9c26829","access_level":"open_access","relation":"main_file","file_size":130026,"file_id":"5291","creator":"system"}],"publisher":"American Society for Microbiology","department":[{"_id":"JoBo"},{"_id":"LifeSc"}],"citation":{"mla":"Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” <i>Genome Announcements</i>, vol. 1, no. 3, American Society for Microbiology, 2013, doi:<a href=\"https://doi.org/10.1128/genomeA.00216-13\">10.1128/genomeA.00216-13</a>.","chicago":"Fernandes Redondo, Rodrigo A, Anne Kupczok, Gertraud Stift, and Jonathan P Bollback. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” <i>Genome Announcements</i>. American Society for Microbiology, 2013. <a href=\"https://doi.org/10.1128/genomeA.00216-13\">https://doi.org/10.1128/genomeA.00216-13</a>.","short":"R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013).","ieee":"R. A. Fernandes Redondo, A. Kupczok, G. Stift, and J. P. Bollback, “Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis,” <i>Genome Announcements</i>, vol. 1, no. 3. American Society for Microbiology, 2013.","ama":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. <i>Genome Announcements</i>. 2013;1(3). doi:<a href=\"https://doi.org/10.1128/genomeA.00216-13\">10.1128/genomeA.00216-13</a>","apa":"Fernandes Redondo, R. A., Kupczok, A., Stift, G., &#38; Bollback, J. P. (2013). Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. <i>Genome Announcements</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/genomeA.00216-13\">https://doi.org/10.1128/genomeA.00216-13</a>","ista":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. 2013. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 1(3)."},"publication_status":"published","date_created":"2018-12-11T11:57:30Z","_id":"2410","date_published":"2013-06-13T00:00:00Z","title":"Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis","date_updated":"2021-01-12T06:57:19Z","abstract":[{"lang":"eng","text":"Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis, isolated from soil in Austria. It is the first phage to be discovered that infects this species. Here, we present the complete genome sequence of this podovirus. "}],"issue":"3","file_date_updated":"2020-07-14T12:45:40Z","author":[{"orcid":"0000-0002-5837-2793","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kupczok","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","full_name":"Kupczok, Anne"},{"full_name":"Stift, Gertraud","first_name":"Gertraud","last_name":"Stift","id":"2DB195CA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","first_name":"Jonathan P"}],"ddc":["576"],"intvolume":"         1","type":"journal_article"},{"type":"journal_article","intvolume":"        13","ddc":["576"],"issue":"1","file_date_updated":"2020-07-14T12:45:40Z","author":[{"last_name":"Kupczok","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Kupczok, Anne","first_name":"Anne"},{"last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","orcid":"0000-0002-4624-4612"}],"date_updated":"2021-01-12T06:57:20Z","abstract":[{"text":"Background: The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to invasive elements that carry the same or a similar sequence. Even in closely related strains, spacer content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot be applied to quantify its rate of change since processes other than single nucleotide changes determine its evolution.Methods We present probabilistic models that are specific for spacer content evolution. They account for the different processes of insertion and deletion. Insertions can be constrained to occur on one end only or are allowed to occur throughout the array. One deletion event can affect one spacer or a whole fragment of adjacent spacers. Parameters of the underlying models are estimated for a pair of arrays by maximum likelihood using explicit ancestor enumeration.Results Simulations show that parameters are well estimated on average under the models presented here. There is a bias in the rate estimation when including fragment deletions. The models also estimate times between pairs of strains. But with increasing time, spacer overlap goes to zero, and thus there is an upper bound on the distance that can be estimated. Spacer content similarities are displayed in a distance based phylogeny using the estimated times.We use the presented models to analyze different Yersinia pestis data sets and find that the results among them are largely congruent. The models also capture the variation in diversity of spacers among the data sets. A comparison of spacer-based phylogenies and Cas gene phylogenies shows that they resolve very different time scales for this data set.Conclusions The simulations and data analyses show that the presented models are useful for quantifying spacer content evolution and for displaying spacer content similarities of closely related strains in a phylogeny. This allows for comparisons of different CRISPR arrays or for comparisons between CRISPR arrays and nucleotide substitution rates.","lang":"eng"}],"page":"54 - 54","_id":"2412","date_published":"2013-02-26T00:00:00Z","title":"Probabilistic models for CRISPR spacer content evolution ","publication_status":"published","citation":{"ista":"Kupczok A, Bollback JP. 2013. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 13(1), 54–54.","apa":"Kupczok, A., &#38; Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-13-54\">https://doi.org/10.1186/1471-2148-13-54</a>","ama":"Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution . <i>BMC Evolutionary Biology</i>. 2013;13(1):54-54. doi:<a href=\"https://doi.org/10.1186/1471-2148-13-54\">10.1186/1471-2148-13-54</a>","ieee":"A. Kupczok and J. P. Bollback, “Probabilistic models for CRISPR spacer content evolution ,” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1. BioMed Central, pp. 54–54, 2013.","short":"A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54.","chicago":"Kupczok, Anne, and Jonathan P Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” <i>BMC Evolutionary Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2148-13-54\">https://doi.org/10.1186/1471-2148-13-54</a>.","mla":"Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1, BioMed Central, 2013, pp. 54–54, doi:<a href=\"https://doi.org/10.1186/1471-2148-13-54\">10.1186/1471-2148-13-54</a>."},"date_created":"2018-12-11T11:57:31Z","publisher":"BioMed Central","department":[{"_id":"JoBo"}],"file":[{"file_size":518729,"file_id":"5268","creator":"system","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:45:40Z","checksum":"029c7e0b198c19312b66ecce3cabb22f","content_type":"application/pdf","date_created":"2018-12-12T10:17:15Z","file_name":"IST-2015-397-v1+1_1471-2148-13-54.pdf"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2013","language":[{"iso":"eng"}],"status":"public","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"397","publist_id":"4514","day":"26","scopus_import":1,"oa_version":"Published Version","has_accepted_license":"1","quality_controlled":"1","oa":1,"volume":13,"doi":"10.1186/1471-2148-13-54","publication":"BMC Evolutionary Biology"},{"title":"Efficient synthesis for concurrency by semantics-preserving transformations","ec_funded":1,"date_published":"2013-07-01T00:00:00Z","_id":"2445","date_created":"2018-12-11T11:57:42Z","citation":{"ista":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2013. Efficient synthesis for concurrency by semantics-preserving transformations. CAV: Computer Aided Verification, LNCS, vol. 8044, 951–967.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer, 2013, pp. 951–967.","chicago":"Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and Thorsten Tarrach. “Efficient Synthesis for Concurrency by Semantics-Preserving Transformations,” 8044:951–67. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">https://doi.org/10.1007/978-3-642-39799-8_68</a>.","mla":"Cerny, Pavol, et al. <i>Efficient Synthesis for Concurrency by Semantics-Preserving Transformations</i>. Vol. 8044, Springer, 2013, pp. 951–67, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">10.1007/978-3-642-39799-8_68</a>.","apa":"Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., &#38; Tarrach, T. (2013). Efficient synthesis for concurrency by semantics-preserving transformations (Vol. 8044, pp. 951–967). Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">https://doi.org/10.1007/978-3-642-39799-8_68</a>","ieee":"P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Efficient synthesis for concurrency by semantics-preserving transformations,” presented at the CAV: Computer Aided Verification, St. Petersburg, Russia, 2013, vol. 8044, pp. 951–967.","ama":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Efficient synthesis for concurrency by semantics-preserving transformations. In: Vol 8044. Springer; 2013:951-967. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">10.1007/978-3-642-39799-8_68</a>"},"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","file":[{"date_updated":"2020-07-14T12:45:40Z","checksum":"70c70ca5487faba82262c63e1b678a27","access_level":"open_access","relation":"main_file","file_size":365548,"file_id":"5158","creator":"system","file_name":"IST-2014-199-v1+1_cav2013-final.pdf","date_created":"2018-12-12T10:15:37Z","content_type":"application/pdf"}],"type":"conference","intvolume":"      8044","ddc":["000","004"],"author":[{"full_name":"Cerny, Pavol","first_name":"Pavol","last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"full_name":"Radhakrishna, Arjun","first_name":"Arjun","last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ryzhyk","first_name":"Leonid","full_name":"Ryzhyk, Leonid"},{"orcid":"0000-0003-4409-8487","first_name":"Thorsten","full_name":"Tarrach, Thorsten","last_name":"Tarrach","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:45:40Z","abstract":[{"text":"We develop program synthesis techniques that can help programmers fix concurrency-related bugs. We make two new contributions to synthesis for concurrency, the first improving the efficiency of the synthesized code, and the second improving the efficiency of the synthesis procedure itself. The first contribution is to have the synthesis procedure explore a variety of (sequential) semantics-preserving program transformations. Classically, only one such transformation has been considered, namely, the insertion of synchronization primitives (such as locks). Based on common manual bug-fixing techniques used by Linux device-driver developers, we explore additional, more efficient transformations, such as the reordering of independent instructions. The second contribution is to speed up the counterexample-guided removal of concurrency bugs within the synthesis procedure by considering partial-order traces (instead of linear traces) as counterexamples. A partial-order error trace represents a set of linear (interleaved) traces of a concurrent program all of which lead to the same error. By eliminating a partial-order error trace, we eliminate in a single iteration of the synthesis procedure all linearizations of the partial-order trace. We evaluated our techniques on several simplified examples of real concurrency bugs that occurred in Linux device drivers.","lang":"eng"}],"page":"951 - 967","conference":{"location":"St. Petersburg, Russia","name":"CAV: Computer Aided Verification","end_date":"2013-07-19","start_date":"2013-07-13"},"date_updated":"2023-09-07T11:57:01Z","volume":8044,"oa":1,"project":[{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"}],"doi":"10.1007/978-3-642-39799-8_68","month":"07","language":[{"iso":"eng"}],"year":"2013","status":"public","day":"01","alternative_title":["LNCS"],"publist_id":"4458","pubrep_id":"199","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","related_material":{"record":[{"id":"1130","status":"public","relation":"dissertation_contains"}]},"scopus_import":1,"quality_controlled":"1","has_accepted_license":"1"},{"date_created":"2018-12-11T11:57:42Z","publication_status":"published","citation":{"short":"K. Chatterjee, A. Gaiser, J. Kretinsky, 8044 (2013) 559–575.","chicago":"Chatterjee, Krishnendu, Andreas Gaiser, and Jan Kretinsky. “Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">https://doi.org/10.1007/978-3-642-39799-8_37</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis</i>. Vol. 8044, Springer, 2013, pp. 559–75, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">10.1007/978-3-642-39799-8_37</a>.","apa":"Chatterjee, K., Gaiser, A., &#38; Kretinsky, J. (2013). Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">https://doi.org/10.1007/978-3-642-39799-8_37</a>","ama":"Chatterjee K, Gaiser A, Kretinsky J. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 2013;8044:559-575. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">10.1007/978-3-642-39799-8_37</a>","ieee":"K. Chatterjee, A. Gaiser, and J. Kretinsky, “Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis,” vol. 8044. Springer, pp. 559–575, 2013.","ista":"Chatterjee K, Gaiser A, Kretinsky J. 2013. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 8044, 559–575."},"_id":"2446","date_published":"2013-07-01T00:00:00Z","ec_funded":1,"title":"Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis","department":[{"_id":"KrCh"}],"publisher":"Springer","intvolume":"      8044","type":"conference","date_updated":"2020-08-11T10:09:47Z","abstract":[{"lang":"eng","text":"The model-checking problem for probabilistic systems crucially relies on the translation of LTL to deterministic Rabin automata (DRW). Our recent Safraless translation [KE12, GKE12] for the LTL(F,G) fragment produces smaller automata as compared to the traditional approach. In this work, instead of DRW we consider deterministic automata with acceptance condition given as disjunction of generalized Rabin pairs (DGRW). The Safraless translation of LTL(F,G) formulas to DGRW results in smaller automata as compared to DRW. We present algorithms for probabilistic model-checking as well as game solving for DGRW conditions. Our new algorithms lead to improvement both in terms of theoretical bounds as well as practical evaluation. We compare PRISM with and without our new translation, and show that the new translation leads to significant improvements."}],"page":"559 - 575","conference":{"name":"CAV: Computer Aided Verification","location":"St. Petersburg, Russia","start_date":"2013-07-13","end_date":"2013-07-19"},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Andreas","full_name":"Gaiser, Andreas","last_name":"Gaiser"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","full_name":"Kretinsky, Jan","first_name":"Jan","orcid":"0000-0002-8122-2881"}],"main_file_link":[{"url":"http://arxiv.org/abs/1304.5281","open_access":"1"}],"volume":8044,"oa":1,"arxiv":1,"project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"doi":"10.1007/978-3-642-39799-8_37","alternative_title":["LNCS"],"publist_id":"4457","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","language":[{"iso":"eng"}],"year":"2013","status":"public","month":"07","series_title":"Lecture Notes in Computer Science","external_id":{"arxiv":["1304.5281"]},"quality_controlled":"1","scopus_import":1,"oa_version":"Preprint"},{"publication_status":"published","citation":{"ieee":"R. Piskac, T. Wies, and D. Zufferey, “Automating separation logic using SMT,” vol. 8044. Springer, pp. 773–789, 2013.","ama":"Piskac R, Wies T, Zufferey D. Automating separation logic using SMT. 2013;8044:773-789. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">10.1007/978-3-642-39799-8_54</a>","apa":"Piskac, R., Wies, T., &#38; Zufferey, D. (2013). Automating separation logic using SMT. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">https://doi.org/10.1007/978-3-642-39799-8_54</a>","mla":"Piskac, Ruzica, et al. <i>Automating Separation Logic Using SMT</i>. Vol. 8044, Springer, 2013, pp. 773–89, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">10.1007/978-3-642-39799-8_54</a>.","chicago":"Piskac, Ruzica, Thomas Wies, and Damien Zufferey. “Automating Separation Logic Using SMT.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">https://doi.org/10.1007/978-3-642-39799-8_54</a>.","short":"R. Piskac, T. Wies, D. Zufferey, 8044 (2013) 773–789.","ista":"Piskac R, Wies T, Zufferey D. 2013. Automating separation logic using SMT. 8044, 773–789."},"date_created":"2018-12-11T11:57:43Z","title":"Automating separation logic using SMT","_id":"2447","date_published":"2013-07-01T00:00:00Z","file":[{"content_type":"application/pdf","date_created":"2020-05-15T11:13:01Z","file_name":"2013_CAV_Piskac.pdf","creator":"dernst","file_size":309182,"file_id":"7859","relation":"main_file","access_level":"open_access","checksum":"2e866932ab688f47ecd504acb4d5c7d4","date_updated":"2020-07-14T12:45:41Z"}],"publisher":"Springer","department":[{"_id":"ToHe"}],"ddc":["000"],"intvolume":"      8044","type":"conference","conference":{"location":"St. Petersburg, Russia","name":"CAV: Computer Aided Verification","end_date":"2013-07-19","start_date":"2013-07-13"},"page":"773 - 789","abstract":[{"text":"Separation logic (SL) has gained widespread popularity because of its ability to succinctly express complex invariants of a program’s heap configurations. Several specialized provers have been developed for decidable SL fragments. However, these provers cannot be easily extended or combined with solvers for other theories that are important in program verification, e.g., linear arithmetic. In this paper, we present a reduction of decidable SL fragments to a decidable first-order theory that fits well into the satisfiability modulo theories (SMT) framework. We show how to use this reduction to automate satisfiability, entailment, frame inference, and abduction problems for separation logic using SMT solvers. Our approach provides a simple method of integrating separation logic into existing verification tools that provide SMT backends, and an elegant way of combining SL fragments with other decidable first-order theories. We implemented this approach in a verification tool and applied it to heap-manipulating programs whose verification involves reasoning in theory combinations.\r\n","lang":"eng"}],"date_updated":"2020-08-11T10:09:47Z","author":[{"last_name":"Piskac","full_name":"Piskac, Ruzica","first_name":"Ruzica"},{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","last_name":"Wies","first_name":"Thomas","full_name":"Wies, Thomas"},{"orcid":"0000-0002-3197-8736","first_name":"Damien","full_name":"Zufferey, Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","last_name":"Zufferey"}],"file_date_updated":"2020-07-14T12:45:41Z","oa":1,"volume":8044,"doi":"10.1007/978-3-642-39799-8_54","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"publist_id":"4456","month":"07","article_processing_charge":"No","year":"2013","language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","series_title":"Lecture Notes in Computer Science","has_accepted_license":"1","oa_version":"Submitted Version","scopus_import":1},{"quality_controlled":"1","external_id":{"pmid":["23857365"]},"oa_version":"Submitted Version","scopus_import":"1","pmid":1,"day":"10","publist_id":"4455","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","year":"2013","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","publication":"Plant Signaling & Behavior","project":[{"call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"doi":"10.4161/psb.25688","volume":8,"oa":1,"abstract":[{"text":"Cell-to-cell directional flow of the phytohormone auxin is primarily established by polar localization of the PIN auxin transporters, a process tightly regulated at multiple levels by auxin itself. We recently reported that, in the context of strong auxin flows, activity of the vacuolar ZIFL1.1 transporter is required for fine-tuning of polar auxin transport rates in the Arabidopsis root. In particular, ZIFL1.1 function protects plasma-membrane stability of the PIN2 carrier in epidermal root tip cells under conditions normally triggering PIN2 degradation. Here, we show that ZIFL1.1 activity at the root tip also promotes PIN1 plasma-membrane abundance in central cylinder cells, thus supporting the notion that ZIFL1.1 acts as a general positive modulator of polar auxin transport in roots.","lang":"eng"}],"article_number":"e25688","article_type":"original","date_updated":"2025-05-07T11:12:32Z","author":[{"full_name":"Remy, Estelle","first_name":"Estelle","last_name":"Remy"},{"last_name":"Baster","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","full_name":"Baster, Pawel"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"Duque","full_name":"Duque, Paula","first_name":"Paula"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091088/"}],"issue":"10","type":"journal_article","intvolume":"         8","department":[{"_id":"JiFr"}],"publisher":"Taylor & Francis","date_created":"2018-12-11T11:57:43Z","publication_status":"published","citation":{"ama":"Remy E, Baster P, Friml J, Duque P. ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. <i>Plant Signaling &#38; Behavior</i>. 2013;8(10). doi:<a href=\"https://doi.org/10.4161/psb.25688\">10.4161/psb.25688</a>","ieee":"E. Remy, P. Baster, J. Friml, and P. Duque, “ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip,” <i>Plant Signaling &#38; Behavior</i>, vol. 8, no. 10. Taylor &#38; Francis, 2013.","apa":"Remy, E., Baster, P., Friml, J., &#38; Duque, P. (2013). ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.4161/psb.25688\">https://doi.org/10.4161/psb.25688</a>","chicago":"Remy, Estelle, Pawel Baster, Jiří Friml, and Paula Duque. “ZIFL1.1 Transporter Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis, 2013. <a href=\"https://doi.org/10.4161/psb.25688\">https://doi.org/10.4161/psb.25688</a>.","mla":"Remy, Estelle, et al. “ZIFL1.1 Transporter Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” <i>Plant Signaling &#38; Behavior</i>, vol. 8, no. 10, e25688, Taylor &#38; Francis, 2013, doi:<a href=\"https://doi.org/10.4161/psb.25688\">10.4161/psb.25688</a>.","short":"E. Remy, P. Baster, J. Friml, P. Duque, Plant Signaling &#38; Behavior 8 (2013).","ista":"Remy E, Baster P, Friml J, Duque P. 2013. ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. Plant Signaling &#38; Behavior. 8(10), e25688."},"title":"ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip","ec_funded":1,"date_published":"2013-07-10T00:00:00Z","_id":"2448"},{"type":"journal_article","status":"public","year":"2013","month":"07","publist_id":"7659","day":"01","issue":"680","author":[{"first_name":"Stephan","full_name":"Baier, Stephan","last_name":"Baier"},{"orcid":"0000-0002-8314-0177","first_name":"Timothy D","full_name":"Timothy Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning"}],"main_file_link":[{"url":"https://arxiv.org/abs/1011.3434","open_access":"1"}],"date_updated":"2021-01-12T06:57:33Z","page":"69 - 151","quality_controlled":0,"abstract":[{"lang":"eng","text":"For given non-zero integers a, b, q we investigate the density of solutions (x; y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined over ℚ."}],"_id":"245","date_published":"2013-07-01T00:00:00Z","extern":1,"title":"Inhomogeneous cubic congruences and rational points on del Pezzo surfaces","oa":1,"date_created":"2018-12-11T11:45:24Z","publication_status":"published","citation":{"ieee":"S. Baier and T. D. Browning, “Inhomogeneous cubic congruences and rational points on del Pezzo surfaces,” <i>Journal fur die Reine und Angewandte Mathematik</i>, no. 680. Walter de Gruyter, pp. 69–151, 2013.","ama":"Baier S, Browning TD. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. <i>Journal fur die Reine und Angewandte Mathematik</i>. 2013;(680):69-151. doi:<a href=\"https://doi.org/10.1515/crelle.2012.039\">10.1515/crelle.2012.039</a>","apa":"Baier, S., &#38; Browning, T. D. (2013). Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. <i>Journal Fur Die Reine Und Angewandte Mathematik</i>. Walter de Gruyter. <a href=\"https://doi.org/10.1515/crelle.2012.039\">https://doi.org/10.1515/crelle.2012.039</a>","chicago":"Baier, Stephan, and Timothy D Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” <i>Journal Fur Die Reine Und Angewandte Mathematik</i>. Walter de Gruyter, 2013. <a href=\"https://doi.org/10.1515/crelle.2012.039\">https://doi.org/10.1515/crelle.2012.039</a>.","mla":"Baier, Stephan, and Timothy D. Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” <i>Journal Fur Die Reine Und Angewandte Mathematik</i>, no. 680, Walter de Gruyter, 2013, pp. 69–151, doi:<a href=\"https://doi.org/10.1515/crelle.2012.039\">10.1515/crelle.2012.039</a>.","short":"S. Baier, T.D. Browning, Journal Fur Die Reine Und Angewandte Mathematik (2013) 69–151.","ista":"Baier S, Browning TD. 2013. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. (680), 69–151."},"doi":"10.1515/crelle.2012.039","publisher":"Walter de Gruyter","publication":"Journal fur die Reine und Angewandte Mathematik"},{"volume":32,"oa":1,"doi":"10.1145/2461912.2461982","publication":"ACM Transactions on Graphics","month":"07","status":"public","year":"2013","language":[{"iso":"eng"}],"article_processing_charge":"No","day":"01","pubrep_id":"605","publist_id":"4436","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","title":"Highly adaptive liquid simulations on tetrahedral meshes","date_published":"2013-07-01T00:00:00Z","_id":"2466","date_created":"2018-12-11T11:57:50Z","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM","file":[{"creator":"system","file_size":8601561,"file_id":"5279","checksum":"aeea6b0ff2b27c695aeb8408c7d2fc50","date_updated":"2020-07-14T12:45:41Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-605-v1+1_tetflip_fixed.pdf","date_created":"2018-12-12T10:17:25Z"}],"intvolume":"        32","type":"journal_article","ddc":["000"],"author":[{"last_name":"Ando","first_name":"Ryoichi","full_name":"Ando, Ryoichi"},{"last_name":"Thuerey","first_name":"Nils","full_name":"Thuerey, Nils"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J","orcid":"0000-0001-6646-5546"}],"file_date_updated":"2020-07-14T12:45:41Z","issue":"4","article_number":"103","abstract":[{"lang":"eng","text":"We introduce a new method for efficiently simulating liquid with extreme amounts of spatial adaptivity. Our method combines several key components to drastically speed up the simulation of large-scale fluid phenomena: We leverage an alternative Eulerian tetrahedral mesh discretization to significantly reduce the complexity of the pressure solve while increasing the robustness with respect to element quality and removing the possibility of locking. Next, we enable subtle free-surface phenomena by deriving novel second-order boundary conditions consistent with our discretization. We couple this discretization with a spatially adaptive Fluid-Implicit Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations that can undergo sharp changes in spatial resolution while minimizing artifacts. Along the way, we provide a new method for generating a smooth and detailed surface from a set of particles with variable sizes. Finally, we explore several new sizing functions for determining spatially adaptive simulation resolutions, and we show how to couple them to our simulator. We combine each of these elements to produce a simulation algorithm that is capable of creating animations at high maximum resolutions while avoiding common pitfalls like inaccurate boundary conditions and inefficient computation."}],"date_updated":"2024-11-19T11:56:45Z"},{"_id":"2467","date_published":"2013-07-01T00:00:00Z","title":"Putting holes in holey geometry: Topology change for arbitrary surfaces","date_created":"2018-12-11T11:57:50Z","citation":{"ista":"Bernstein G, Wojtan C. 2013. Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. 32(4), 34.","short":"G. Bernstein, C. Wojtan, ACM Transactions on Graphics 32 (2013).","mla":"Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, 34, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2462027\">10.1145/2461912.2462027</a>.","chicago":"Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2462027\">https://doi.org/10.1145/2461912.2462027</a>.","apa":"Bernstein, G., &#38; Wojtan, C. (2013). Putting holes in holey geometry: Topology change for arbitrary surfaces. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2462027\">https://doi.org/10.1145/2461912.2462027</a>","ama":"Bernstein G, Wojtan C. Putting holes in holey geometry: Topology change for arbitrary surfaces. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2462027\">10.1145/2461912.2462027</a>","ieee":"G. Bernstein and C. Wojtan, “Putting holes in holey geometry: Topology change for arbitrary surfaces,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013."},"publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM","file":[{"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:45:41Z","checksum":"9c8425d62246996ca632c5a01870515b","file_id":"4768","file_size":3514674,"creator":"system","date_created":"2018-12-12T10:09:43Z","file_name":"IST-2016-604-v1+1_toptop2013.pdf","content_type":"application/pdf"}],"type":"journal_article","intvolume":"        32","ddc":["000"],"file_date_updated":"2020-07-14T12:45:41Z","issue":"4","author":[{"last_name":"Bernstein","full_name":"Bernstein, Gilbert","first_name":"Gilbert"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J","orcid":"0000-0001-6646-5546"}],"date_updated":"2023-02-23T10:44:16Z","article_number":"34","abstract":[{"lang":"eng","text":"This paper presents a method for computing topology changes for triangle meshes in an interactive geometric modeling environment. Most triangle meshes in practice do not exhibit desirable geometric properties, so we develop a solution that is independent of standard assumptions and robust to geometric errors. Specifically, we provide the first method for topology change applicable to arbitrary non-solid, non-manifold, non-closed, self-intersecting surfaces. We prove that this new method for topology change produces the expected conventional results when applied to solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a backwards-compatibility property relative to prior work. Beyond solid surfaces, we present empirical evidence that our method remains tolerant to a variety of surface aberrations through the incorporation of a novel error correction scheme. Finally, we demonstrate how topology change applied to non-solid objects enables wholly new and useful behaviors."}],"volume":32,"oa":1,"doi":"10.1145/2461912.2462027","publication":"ACM Transactions on Graphics","year":"2013","language":[{"iso":"eng"}],"status":"public","month":"07","publist_id":"4435","pubrep_id":"604","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","scopus_import":1,"oa_version":"Submitted Version","has_accepted_license":"1","quality_controlled":"1"},{"date_created":"2018-12-11T11:57:50Z","citation":{"ama":"Bojsen-Hansen M, Wojtan C. Liquid surface tracking with error compensation. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461991\">10.1145/2461912.2461991</a>","ieee":"M. Bojsen-Hansen and C. Wojtan, “Liquid surface tracking with error compensation,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","apa":"Bojsen-Hansen, M., &#38; Wojtan, C. (2013). Liquid surface tracking with error compensation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461991\">https://doi.org/10.1145/2461912.2461991</a>","chicago":"Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461991\">https://doi.org/10.1145/2461912.2461991</a>.","mla":"Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, 68, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461991\">10.1145/2461912.2461991</a>.","short":"M. Bojsen-Hansen, C. Wojtan, ACM Transactions on Graphics 32 (2013).","ista":"Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 32(4), 68."},"publication_status":"published","date_published":"2013-07-01T00:00:00Z","_id":"2468","title":"Liquid surface tracking with error compensation","file":[{"date_created":"2018-12-12T10:09:37Z","file_name":"IST-2016-603-v1+1_liquidError_web.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:45:41Z","checksum":"53d905e0180e23ef3e813b969ffed4e1","file_id":"4761","file_size":5813685,"creator":"system"}],"department":[{"_id":"ChWo"}],"publisher":"ACM","ddc":["000"],"intvolume":"        32","type":"journal_article","date_updated":"2023-02-23T10:44:18Z","abstract":[{"lang":"eng","text":"Our work concerns the combination of an Eulerian liquid simulation with a high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle mesh). The naive application of a high-resolution surface tracker to a low-resolution velocity field can produce many visually disturbing physical and topological artifacts that limit their use in practice. We address these problems by defining an error function which compares the current state of the surface tracker to the set of physically valid surface states. By reducing this error with a gradient descent technique, we introduce a novel physics-based surface fairing method. Similarly, by treating this error function as a potential energy, we derive a new surface correction force that mimics the vortex sheet equations. We demonstrate our results with both level set and mesh-based surface trackers."}],"article_number":"68","file_date_updated":"2020-07-14T12:45:41Z","issue":"4","author":[{"last_name":"Bojsen-Hansen","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","full_name":"Bojsen-Hansen, Morten","first_name":"Morten","orcid":"0000-0002-4417-3224"},{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"}],"volume":32,"oa":1,"publication":"ACM Transactions on Graphics","doi":"10.1145/2461912.2461991","pubrep_id":"603","publist_id":"4434","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","year":"2013","status":"public","language":[{"iso":"eng"}],"month":"07","has_accepted_license":"1","quality_controlled":"1","scopus_import":1,"oa_version":"Submitted Version"},{"pmid":1,"day":"22","publist_id":"4433","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","status":"public","year":"2013","language":[{"iso":"eng"}],"quality_controlled":"1","has_accepted_license":"1","external_id":{"pmid":["23885883"]},"oa_version":"Published Version","scopus_import":1,"volume":23,"oa":1,"publication":"Current Biology","doi":"10.1016/j.cub.2013.06.019","ddc":["570"],"intvolume":"        23","type":"journal_article","abstract":[{"text":"Cadherins are transmembrane proteins that mediate cell–cell adhesion in animals. By regulating contact formation and stability, cadherins play a crucial role in tissue morphogenesis and homeostasis. Here, we review the three major  unctions of cadherins in cell–cell contact formation and stability. Two of those functions lead to a decrease in interfacial ension at the forming cell–cell contact, thereby promoting contact expansion — first, by providing adhesion tension that lowers interfacial tension at the cell–cell contact, and second, by signaling to the actomyosin cytoskeleton in order to reduce cortex tension and thus interfacial tension at the contact. The third function of cadherins in cell–cell contact formation is to stabilize the contact by resisting mechanical forces that pull on the contact.","lang":"eng"}],"page":"R626 - R633","date_updated":"2021-01-12T06:57:40Z","author":[{"first_name":"Jean-Léon","full_name":"Maître, Jean-Léon","orcid":"0000-0002-3688-1474","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","last_name":"Maître"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"file_date_updated":"2020-07-14T12:45:41Z","issue":"14","date_created":"2018-12-11T11:57:51Z","citation":{"ama":"Maître J-L, Heisenberg C-PJ. Three functions of cadherins in cell adhesion. <i>Current Biology</i>. 2013;23(14):R626-R633. doi:<a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">10.1016/j.cub.2013.06.019</a>","ieee":"J.-L. Maître and C.-P. J. Heisenberg, “Three functions of cadherins in cell adhesion,” <i>Current Biology</i>, vol. 23, no. 14. Cell Press, pp. R626–R633, 2013.","apa":"Maître, J.-L., &#38; Heisenberg, C.-P. J. (2013). Three functions of cadherins in cell adhesion. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">https://doi.org/10.1016/j.cub.2013.06.019</a>","mla":"Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “Three Functions of Cadherins in Cell Adhesion.” <i>Current Biology</i>, vol. 23, no. 14, Cell Press, 2013, pp. R626–33, doi:<a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">10.1016/j.cub.2013.06.019</a>.","chicago":"Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “Three Functions of Cadherins in Cell Adhesion.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">https://doi.org/10.1016/j.cub.2013.06.019</a>.","short":"J.-L. Maître, C.-P.J. Heisenberg, Current Biology 23 (2013) R626–R633.","ista":"Maître J-L, Heisenberg C-PJ. 2013. Three functions of cadherins in cell adhesion. Current Biology. 23(14), R626–R633."},"publication_status":"published","title":"Three functions of cadherins in cell adhesion","_id":"2469","date_published":"2013-07-22T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2013_CurrentBiology_Maitre.pdf","date_created":"2019-01-24T15:40:22Z","content_type":"application/pdf","checksum":"6a424b2f007b41d4955a9135793b2162","date_updated":"2020-07-14T12:45:41Z","access_level":"open_access","relation":"main_file","file_id":"5881","file_size":247320,"creator":"dernst"}],"department":[{"_id":"CaHe"}],"publisher":"Cell Press"},{"day":"23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4432","pubrep_id":"413","month":"07","status":"public","language":[{"iso":"eng"}],"year":"2013","quality_controlled":"1","has_accepted_license":"1","oa_version":"Published Version","scopus_import":1,"oa":1,"volume":8,"publication":"PLoS One","doi":"10.1371/journal.pone.0070050","ddc":["570"],"type":"journal_article","intvolume":"         8","abstract":[{"lang":"eng","text":"Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and its function is indispensable for plant growth and development. ABP1 has been shown to be involved in auxin-dependent regulation of cell division and expansion, in plasma-membrane-related processes such as changes in transmembrane potential, and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated downstream pathway remains elusive.Methodology/Principal Findings:Using auxin transport assays and quantitative analysis of cellular morphology we show that ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can counterbalance increased auxin efflux and auxin starvation phenotypes caused by the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the ABP1-controlled vesicle trafficking processes, including positive regulation of endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The findings indicate the involvement of ABP1 in control of rate of auxin transport across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity at the plasma membrane, and highlighting the relevance of ABP1 for the formation of developmentally important, PIN-dependent auxin gradients."}],"article_number":"e70050","date_updated":"2021-01-12T06:57:40Z","author":[{"last_name":"Čovanová","first_name":"Milada","full_name":"Čovanová, Milada"},{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"full_name":"Rychtář, Jan","first_name":"Jan","last_name":"Rychtář"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"}],"issue":"7","file_date_updated":"2020-07-14T12:45:41Z","citation":{"mla":"Čovanová, Milada, et al. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” <i>PLoS One</i>, vol. 8, no. 7, e70050, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0070050\">10.1371/journal.pone.0070050</a>.","chicago":"Čovanová, Milada, Michael Sauer, Jan Rychtář, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0070050\">https://doi.org/10.1371/journal.pone.0070050</a>.","short":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, E. Zažímalová, PLoS One 8 (2013).","ieee":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, and E. Zažímalová, “Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells,” <i>PLoS One</i>, vol. 8, no. 7. Public Library of Science, 2013.","ama":"Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. <i>PLoS One</i>. 2013;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0070050\">10.1371/journal.pone.0070050</a>","apa":"Čovanová, M., Sauer, M., Rychtář, J., Friml, J., Petrášek, J., &#38; Zažímalová, E. (2013). Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0070050\">https://doi.org/10.1371/journal.pone.0070050</a>","ista":"Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. 2013. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. 8(7), e70050."},"publication_status":"published","date_created":"2018-12-11T11:57:51Z","title":"Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells","date_published":"2013-07-23T00:00:00Z","_id":"2470","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"creator":"system","file_id":"4681","file_size":2294955,"date_updated":"2020-07-14T12:45:41Z","checksum":"2d47ef47616ef4de1d517d146548184e","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-413-v1+1_journal.pone.0070050.pdf","date_created":"2018-12-12T10:08:21Z"}],"publisher":"Public Library of Science","department":[{"_id":"JiFr"}]},{"month":"07","status":"public","language":[{"iso":"eng"}],"year":"2013","day":"30","publist_id":"4430","pubrep_id":"414","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","scopus_import":1,"quality_controlled":"1","has_accepted_license":"1","volume":8,"oa":1,"doi":"10.1371/journal.pone.0070013","publication":"PLoS One","intvolume":"         8","type":"journal_article","ddc":["570"],"author":[{"first_name":"Inmaculada","full_name":"Sanchez Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","last_name":"Sanchez Romero"},{"last_name":"Ariza","full_name":"Ariza, Antonio","first_name":"Antonio"},{"last_name":"Wilson","first_name":"Keith","full_name":"Wilson, Keith"},{"full_name":"Skjøt, Michael","first_name":"Michael","last_name":"Skjøt"},{"last_name":"Vind","first_name":"Jesper","full_name":"Vind, Jesper"},{"full_name":"De Maria, Leonardo","first_name":"Leonardo","last_name":"De Maria"},{"first_name":"Lars","full_name":"Skov, Lars","last_name":"Skov"},{"first_name":"Jose","full_name":"Sánchez Ruiz, Jose","last_name":"Sánchez Ruiz"}],"file_date_updated":"2020-07-14T12:45:41Z","issue":"7","abstract":[{"lang":"eng","text":"The impact of disulfide bonds on protein stability goes beyond simple equilibrium thermodynamics effects associated with the conformational entropy of the unfolded state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional association and strongly affect the rates of irreversible enzyme inactivation, highly relevant in biotechnological applications. While these kinetic-stability effects remain poorly understood, by analogy with proposed mechanisms for processes of protein aggregation and fibrillogenesis, we propose that they may be determined by the properties of sparsely-populated, partially-unfolded intermediates. Here we report the successful design, on the basis of high temperature molecular-dynamics simulations, of six thermodynamically and kinetically stabilized variants of phytase from Citrobacter braakii (a biotechnologically important enzyme) with one, two or three engineered disulfides. Activity measurements and 3D crystal structure determination demonstrate that the engineered crosslinks do not cause dramatic alterations in the native structure. The inactivation kinetics for all the variants displays a strongly non-Arrhenius temperature dependence, with the time-scale for the irreversible denaturation process reaching a minimum at a given temperature within the range of the denaturation transition. We show this striking feature to be a signature of a key role played by a partially unfolded, intermediate state/ensemble. Energetic and mutational analyses confirm that the intermediate is highly unfolded (akin to a proposed critical intermediate in the misfolding of the prion protein), a result that explains the observed kinetic stabilization. Our results provide a rationale for the kinetic-stability consequences of disulfide-crosslink engineering and an experimental methodology to arrive at energetic/structural descriptions of the sparsely populated and elusive intermediates that play key roles in irreversible protein denaturation."}],"article_number":"e70013","date_updated":"2021-01-12T06:57:41Z","title":"Mechanism of protein kinetic stabilization by engineered disulfide crosslinks","date_published":"2013-07-30T00:00:00Z","_id":"2471","date_created":"2018-12-11T11:57:51Z","citation":{"ista":"Sanchez-Romero I, Ariza A, Wilson K, Skjøt M, Vind J, De Maria L, Skov L, Sánchez Ruiz J. 2013. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 8(7), e70013.","chicago":"Sanchez-Romero, Inmaculada, Antonio Ariza, Keith Wilson, Michael Skjøt, Jesper Vind, Leonardo De Maria, Lars Skov, and Jose Sánchez Ruiz. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0070013\">https://doi.org/10.1371/journal.pone.0070013</a>.","mla":"Sanchez-Romero, Inmaculada, et al. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” <i>PLoS One</i>, vol. 8, no. 7, e70013, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0070013\">10.1371/journal.pone.0070013</a>.","short":"I. Sanchez-Romero, A. Ariza, K. Wilson, M. Skjøt, J. Vind, L. De Maria, L. Skov, J. Sánchez Ruiz, PLoS One 8 (2013).","ieee":"I. Sanchez-Romero <i>et al.</i>, “Mechanism of protein kinetic stabilization by engineered disulfide crosslinks,” <i>PLoS One</i>, vol. 8, no. 7. Public Library of Science, 2013.","ama":"Sanchez-Romero I, Ariza A, Wilson K, et al. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. <i>PLoS One</i>. 2013;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0070013\">10.1371/journal.pone.0070013</a>","apa":"Sanchez-Romero, I., Ariza, A., Wilson, K., Skjøt, M., Vind, J., De Maria, L., … Sánchez Ruiz, J. (2013). Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0070013\">https://doi.org/10.1371/journal.pone.0070013</a>"},"publication_status":"published","department":[{"_id":"HaJa"}],"publisher":"Public Library of Science","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"content_type":"application/pdf","file_name":"IST-2016-414-v1+1_journal.pone.0070013.pdf","date_created":"2018-12-12T10:15:07Z","file_size":1323666,"file_id":"5124","creator":"system","date_updated":"2020-07-14T12:45:41Z","checksum":"c0c96cc76ed7ef0d036a31a7e33c9a37","access_level":"open_access","relation":"main_file"}]},{"oa":1,"volume":8,"publication":"PLoS One","doi":"10.1371/journal.pone.0070069","project":[{"name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362","call_identifier":"FP7"},{"grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4431","pubrep_id":"393","day":"29","status":"public","language":[{"iso":"eng"}],"year":"2013","month":"07","has_accepted_license":"1","quality_controlled":"1","scopus_import":1,"oa_version":"Published Version","publication_status":"published","citation":{"ista":"Cazzonelli C, Vanstraelen M, Simon S, Yin K, Carron Arthur A, Nisar N, Tarle G, Cuttriss A, Searle I, Benková E, Mathesius U, Masle J, Friml J, Pogson B. 2013. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. 8(7), e70069.","ieee":"C. Cazzonelli <i>et al.</i>, “Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development,” <i>PLoS One</i>, vol. 8, no. 7. Public Library of Science, 2013.","ama":"Cazzonelli C, Vanstraelen M, Simon S, et al. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. <i>PLoS One</i>. 2013;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0070069\">10.1371/journal.pone.0070069</a>","apa":"Cazzonelli, C., Vanstraelen, M., Simon, S., Yin, K., Carron Arthur, A., Nisar, N., … Pogson, B. (2013). Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0070069\">https://doi.org/10.1371/journal.pone.0070069</a>","chicago":"Cazzonelli, Christopher, Marleen Vanstraelen, Sibu Simon, Kuide Yin, Ashley Carron Arthur, Nazia Nisar, Gauri Tarle, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0070069\">https://doi.org/10.1371/journal.pone.0070069</a>.","mla":"Cazzonelli, Christopher, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” <i>PLoS One</i>, vol. 8, no. 7, e70069, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0070069\">10.1371/journal.pone.0070069</a>.","short":"C. Cazzonelli, M. Vanstraelen, S. Simon, K. Yin, A. Carron Arthur, N. Nisar, G. Tarle, A. Cuttriss, I. Searle, E. Benková, U. Mathesius, J. Masle, J. Friml, B. Pogson, PLoS One 8 (2013)."},"date_created":"2018-12-11T11:57:52Z","_id":"2472","date_published":"2013-07-29T00:00:00Z","title":"Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development","ec_funded":1,"file":[{"file_id":"5222","file_size":9003465,"creator":"system","date_updated":"2020-07-14T12:45:41Z","checksum":"3be71828b6c2ba9c90eb7056e3f7f57a","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"IST-2015-393-v1+1_journal.pone.0070069.pdf","date_created":"2018-12-12T10:16:34Z"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Public Library of Science","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"ddc":["580","570"],"type":"journal_article","intvolume":"         8","date_updated":"2021-01-12T06:57:41Z","article_number":"e70069","abstract":[{"text":"Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone auxin are required for tissue-specific directional auxin transport and cellular auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important roles in developmental processes such as embryogenesis, organogenesis, vascular tissue differentiation, root meristem patterning and tropic growth. Here we analyzed roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible and is expressed during multiple auxin-regulated developmental processes. Loss of pin6 function interfered with primary root growth and lateral root development. Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis in other growth processes such as shoot apical dominance, lateral root primordia development, adventitious root formation, root hair outgrowth and root waving. These changes in auxin-regulated growth correlated with a reduction in total auxin transport as well as with an altered activity of DR5-GUS auxin response reporter. Overall, the data indicate that PIN6 regulates auxin homeostasis during plant development.","lang":"eng"}],"issue":"7","file_date_updated":"2020-07-14T12:45:41Z","author":[{"last_name":"Cazzonelli","first_name":"Christopher","full_name":"Cazzonelli, Christopher"},{"first_name":"Marleen","full_name":"Vanstraelen, Marleen","last_name":"Vanstraelen"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","first_name":"Sibu"},{"last_name":"Yin","first_name":"Kuide","full_name":"Yin, Kuide"},{"last_name":"Carron Arthur","first_name":"Ashley","full_name":"Carron Arthur, Ashley"},{"last_name":"Nisar","full_name":"Nisar, Nazia","first_name":"Nazia"},{"last_name":"Tarle","first_name":"Gauri","full_name":"Tarle, Gauri"},{"last_name":"Cuttriss","first_name":"Abby","full_name":"Cuttriss, Abby"},{"full_name":"Searle, Iain","first_name":"Iain","last_name":"Searle"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva"},{"first_name":"Ulrike","full_name":"Mathesius, Ulrike","last_name":"Mathesius"},{"full_name":"Masle, Josette","first_name":"Josette","last_name":"Masle"},{"full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pogson","full_name":"Pogson, Barry","first_name":"Barry"}]},{"ddc":["570"],"intvolume":"        87","type":"journal_article","date_updated":"2021-01-12T06:57:42Z","page":"75 - 89","abstract":[{"text":"When a mutation with selective advantage s spreads through a panmictic population, it may cause two lineages at a linked locus to coalesce; the probability of coalescence is exp(−2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid individuals, and r is the recombination rate. Population structure delays fixation, and so weakens the effect of a selective sweep. However, favourable alleles spread through a spatially continuous population behind a narrow wavefront; ancestral lineages are confined at the tip of this front, and so coalesce rapidly. In extremely dense populations, coalescence is dominated by rare fluctuations ahead of the front. However, we show that for moderate densities, a simple quasi-deterministic approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ), where ρ is the population density and  is the characteristic scale of the wavefront; g(η) depends only on the strength of random drift,  . The net effect of a sweep on coalescence also depends crucially on whether two lineages are ever both within the wavefront at the same time: even in the extreme case when coalescence within the front is instantaneous, the net rate of coalescence may be lower than in a single panmictic population. Sweeps can also have a substantial impact on the rate of gene flow. A single lineage will jump to a new location when it is hit by a sweep, with mean square displacement  ; this can be substantial if the species’ range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R, is small. This effect is half as strong in two dimensions. In contrast, the rate of coalescence between lineages, at random locations in space and on the genetic map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average, one-dimensional structure is likely to reduce coalescence due to sweeps, relative to panmixis. In two dimensions, genes must move along the front before they can coalesce; this process is rapid, being dominated by rare fluctuations. This leads to a dramatically higher rate of coalescence within the wavefront than if lineages simply diffused along the front. Nevertheless, the net rate of coalescence due to a sweep through a two-dimensional population is likely to be lower than it would be with panmixis.","lang":"eng"}],"issue":"8","file_date_updated":"2020-07-14T12:45:41Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"},{"last_name":"Kelleher","first_name":"Jerome","full_name":"Kelleher, Jerome"},{"first_name":"Amandine","full_name":"Véber, Amandine","last_name":"Véber"}],"publication_status":"published","citation":{"ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 87(8), 75–89.","short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 75–89.","mla":"Barton, Nicholas H., et al. “Genetic Hitch-Hiking in Spatially Extended Populations.” <i>Theoretical Population Biology</i>, vol. 87, no. 8, Elsevier, 2013, pp. 75–89, doi:<a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">10.1016/j.tpb.2012.12.001</a>.","chicago":"Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Genetic Hitch-Hiking in Spatially Extended Populations.” <i>Theoretical Population Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">https://doi.org/10.1016/j.tpb.2012.12.001</a>.","apa":"Barton, N. H., Etheridge, A., Kelleher, J., &#38; Véber, A. (2013). Genetic hitch-hiking in spatially extended populations. <i>Theoretical Population Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">https://doi.org/10.1016/j.tpb.2012.12.001</a>","ieee":"N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Genetic hitch-hiking in spatially extended populations,” <i>Theoretical Population Biology</i>, vol. 87, no. 8. Elsevier, pp. 75–89, 2013.","ama":"Barton NH, Etheridge A, Kelleher J, Véber A. Genetic hitch-hiking in spatially extended populations. <i>Theoretical Population Biology</i>. 2013;87(8):75-89. doi:<a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">10.1016/j.tpb.2012.12.001</a>"},"date_created":"2018-12-11T11:57:52Z","date_published":"2013-01-03T00:00:00Z","_id":"2473","title":"Genetic hitch-hiking in spatially extended populations","ec_funded":1,"file":[{"content_type":"application/pdf","file_name":"IST-2013-118-v1+1_bartonetalRevision.pdf","date_created":"2018-12-12T10:18:54Z","creator":"system","file_size":1706282,"file_id":"5376","checksum":"4274ec1f433b838a7d5b941cc9684ca7","date_updated":"2020-07-14T12:45:41Z","relation":"main_file","access_level":"open_access"}],"publisher":"Elsevier","department":[{"_id":"NiBa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"118","publist_id":"4428","day":"03","status":"public","language":[{"iso":"eng"}],"year":"2013","month":"01","has_accepted_license":"1","quality_controlled":"1","scopus_import":1,"oa_version":"Submitted Version","oa":1,"volume":87,"publication":"Theoretical Population Biology","doi":"10.1016/j.tpb.2012.12.001","project":[{"grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}]},{"date_updated":"2021-01-12T06:57:51Z","abstract":[{"lang":"eng","text":"Châtelet surfaces provide a rich source of geometrically rational surfaces that do not always satisfy the Hasse principle. Restricting attention to a special class of Châtelet surfaces, we investigate the frequency that such counter-examples arise over the rational numbers."}],"quality_controlled":0,"page":"1030 - 1078","issue":"4","acknowledgement":"While working on this paper, the first author was supported by an IUF Junior and ANR while the second author was supported by ERC grant 306457.","author":[{"full_name":"de la Bretèche, Régis","first_name":"Régis","last_name":"De La Bretèche"},{"last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Timothy Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177"}],"main_file_link":[{"url":"https://arxiv.org/abs/1210.4010","open_access":"1"}],"publist_id":"7652","day":"29","intvolume":"       108","type":"journal_article","year":"2013","status":"public","month":"11","publication":"Proceedings of the London Mathematical Society","publisher":"Oxford University Press","doi":"10.1112/plms/pdt060","date_created":"2018-12-11T11:45:26Z","citation":{"ista":"De La Bretèche R, Browning TD. 2013. Density of Châtelet surfaces failing the Hasse principle. Proceedings of the London Mathematical Society. 108(4), 1030–1078.","apa":"De La Bretèche, R., &#38; Browning, T. D. (2013). Density of Châtelet surfaces failing the Hasse principle. <i>Proceedings of the London Mathematical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1112/plms/pdt060\">https://doi.org/10.1112/plms/pdt060</a>","ama":"De La Bretèche R, Browning TD. Density of Châtelet surfaces failing the Hasse principle. <i>Proceedings of the London Mathematical Society</i>. 2013;108(4):1030-1078. doi:<a href=\"https://doi.org/10.1112/plms/pdt060\">10.1112/plms/pdt060</a>","ieee":"R. De La Bretèche and T. D. Browning, “Density of Châtelet surfaces failing the Hasse principle,” <i>Proceedings of the London Mathematical Society</i>, vol. 108, no. 4. Oxford University Press, pp. 1030–1078, 2013.","short":"R. De La Bretèche, T.D. Browning, Proceedings of the London Mathematical Society 108 (2013) 1030–1078.","chicago":"De La Bretèche, Régis, and Timothy D Browning. “Density of Châtelet Surfaces Failing the Hasse Principle.” <i>Proceedings of the London Mathematical Society</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1112/plms/pdt060\">https://doi.org/10.1112/plms/pdt060</a>.","mla":"De La Bretèche, Régis, and Timothy D. Browning. “Density of Châtelet Surfaces Failing the Hasse Principle.” <i>Proceedings of the London Mathematical Society</i>, vol. 108, no. 4, Oxford University Press, 2013, pp. 1030–78, doi:<a href=\"https://doi.org/10.1112/plms/pdt060\">10.1112/plms/pdt060</a>."},"publication_status":"published","_id":"250","date_published":"2013-11-29T00:00:00Z","extern":1,"volume":108,"title":"Density of Châtelet surfaces failing the Hasse principle","oa":1},{"alternative_title":["LNCS"],"publist_id":"4384","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","status":"public","language":[{"iso":"eng"}],"year":"2013","article_processing_charge":"No","month":"07","has_accepted_license":"1","series_title":"Lecture Notes in Computer Science","quality_controlled":"1","scopus_import":1,"oa_version":"Submitted Version","volume":7966,"oa":1,"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/978-3-642-39212-2_3","ddc":["000"],"intvolume":"      7966","type":"conference","date_updated":"2020-08-11T10:09:47Z","page":"15 - 27","abstract":[{"text":"Traditional formal methods are based on a Boolean satisfaction notion: a reactive system satisfies, or not, a given specification. We generalize formal methods to also address the quality of systems. As an adequate specification formalism we introduce the linear temporal logic LTL[F]. The satisfaction value of an LTL[F] formula is a number between 0 and 1, describing the quality of the satisfaction. The logic generalizes traditional LTL by augmenting it with a (parameterized) set F of arbitrary functions over the interval [0,1]. For example, F may contain the maximum or minimum between the satisfaction values of subformulas, their product, and their average. The classical decision problems in formal methods, such as satisfiability, model checking, and synthesis, are generalized to search and optimization problems in the quantitative setting. For example, model checking asks for the quality in which a specification is satisfied, and synthesis returns a system satisfying the specification with the highest quality. Reasoning about quality gives rise to other natural questions, like the distance between specifications. We formalize these basic questions and study them for LTL[F]. By extending the automata-theoretic approach for LTL to a setting that takes quality into an account, we are able to solve the above problems and show that reasoning about LTL[F] has roughly the same complexity as reasoning about traditional LTL.","lang":"eng"}],"conference":{"name":"ICALP: Automata, Languages and Programming","location":"Riga, Latvia","end_date":"2013-07-12","start_date":"2013-07-08"},"file_date_updated":"2020-07-14T12:45:42Z","issue":"Part 2","author":[{"last_name":"Almagor","full_name":"Almagor, Shaull","first_name":"Shaull"},{"last_name":"Boker","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi","first_name":"Udi"},{"first_name":"Orna","full_name":"Kupferman, Orna","last_name":"Kupferman"}],"acknowledgement":"ERC Grant QUALITY. ","date_created":"2018-12-11T11:58:08Z","publication_status":"published","citation":{"apa":"Almagor, S., Boker, U., &#38; Kupferman, O. (2013). Formalizing and reasoning about quality. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">https://doi.org/10.1007/978-3-642-39212-2_3</a>","ieee":"S. Almagor, U. Boker, and O. Kupferman, “Formalizing and reasoning about quality,” vol. 7966, no. Part 2. Springer, pp. 15–27, 2013.","ama":"Almagor S, Boker U, Kupferman O. Formalizing and reasoning about quality. 2013;7966(Part 2):15-27. doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">10.1007/978-3-642-39212-2_3</a>","short":"S. Almagor, U. Boker, O. Kupferman, 7966 (2013) 15–27.","chicago":"Almagor, Shaull, Udi Boker, and Orna Kupferman. “Formalizing and Reasoning about Quality.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">https://doi.org/10.1007/978-3-642-39212-2_3</a>.","mla":"Almagor, Shaull, et al. <i>Formalizing and Reasoning about Quality</i>. Vol. 7966, no. Part 2, Springer, 2013, pp. 15–27, doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">10.1007/978-3-642-39212-2_3</a>.","ista":"Almagor S, Boker U, Kupferman O. 2013. Formalizing and reasoning about quality. 7966(Part 2), 15–27."},"_id":"2517","date_published":"2013-07-01T00:00:00Z","title":"Formalizing and reasoning about quality","ec_funded":1,"file":[{"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:45:42Z","checksum":"85afbf6c18a2c7e377c52c9410e2d824","file_size":363031,"file_id":"7860","creator":"dernst","date_created":"2020-05-15T11:16:12Z","file_name":"2013_ICALP_Almagor.pdf","content_type":"application/pdf"}],"department":[{"_id":"ToHe"}],"publisher":"Springer"},{"date_updated":"2023-02-23T10:35:42Z","abstract":[{"lang":"eng","text":"A class of valued constraint satisfaction problems (VCSPs) is characterised by a valued constraint language, a fixed set of cost functions on a finite domain. An instance of the problem is specified by a sum of cost functions from the language with the goal to minimise the sum. We study which classes of finite-valued languages can be solved exactly by the basic linear programming relaxation (BLP). Thapper and Živný showed [20] that if BLP solves the language then the language admits a binary commutative fractional polymorphism. We prove that the converse is also true. This leads to a necessary and a sufficient condition which can be checked in polynomial time for a given language. In contrast, the previous necessary and sufficient condition due to [20] involved infinitely many inequalities. More recently, Thapper and Živný [21] showed (using, in particular, a technique introduced in this paper) that core languages that do not satisfy our condition are NP-hard. Taken together, these results imply that a finite-valued language can either be solved using Linear Programming or is NP-hard."}],"page":"625 - 636","conference":{"start_date":"2013-07-08","end_date":"2013-07-12","name":"ICALP: Automata, Languages and Programming","location":"Riga, Latvia"},"issue":"1","main_file_link":[{"url":"http://arxiv.org/abs/1207.7213","open_access":"1"}],"author":[{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"}],"type":"conference","intvolume":"      7965","department":[{"_id":"VlKo"}],"publisher":"Springer","date_created":"2018-12-11T11:58:08Z","citation":{"ista":"Kolmogorov V. 2013. The power of linear programming for finite-valued CSPs: A constructive characterization. ICALP: Automata, Languages and Programming, LNCS, vol. 7965, 625–636.","mla":"Kolmogorov, Vladimir. <i>The Power of Linear Programming for Finite-Valued CSPs: A Constructive Characterization</i>. Vol. 7965, no. 1, Springer, 2013, pp. 625–36, doi:<a href=\"https://doi.org/10.1007/978-3-642-39206-1_53\">10.1007/978-3-642-39206-1_53</a>.","chicago":"Kolmogorov, Vladimir. “The Power of Linear Programming for Finite-Valued CSPs: A Constructive Characterization,” 7965:625–36. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39206-1_53\">https://doi.org/10.1007/978-3-642-39206-1_53</a>.","short":"V. Kolmogorov, in:, Springer, 2013, pp. 625–636.","ama":"Kolmogorov V. The power of linear programming for finite-valued CSPs: A constructive characterization. In: Vol 7965. Springer; 2013:625-636. doi:<a href=\"https://doi.org/10.1007/978-3-642-39206-1_53\">10.1007/978-3-642-39206-1_53</a>","ieee":"V. Kolmogorov, “The power of linear programming for finite-valued CSPs: A constructive characterization,” presented at the ICALP: Automata, Languages and Programming, Riga, Latvia, 2013, vol. 7965, no. 1, pp. 625–636.","apa":"Kolmogorov, V. (2013). The power of linear programming for finite-valued CSPs: A constructive characterization (Vol. 7965, pp. 625–636). Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39206-1_53\">https://doi.org/10.1007/978-3-642-39206-1_53</a>"},"publication_status":"published","_id":"2518","date_published":"2013-07-01T00:00:00Z","title":"The power of linear programming for finite-valued CSPs: A constructive characterization","external_id":{"arxiv":["1207.7213"]},"quality_controlled":"1","related_material":{"record":[{"relation":"later_version","id":"2271","status":"public"}]},"scopus_import":1,"oa_version":"Preprint","alternative_title":["LNCS"],"publist_id":"4383","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","language":[{"iso":"eng"}],"year":"2013","status":"public","month":"07","arxiv":1,"doi":"10.1007/978-3-642-39206-1_53","volume":7965,"oa":1},{"month":"07","language":[{"iso":"eng"}],"status":"public","year":"2013","day":"11","pubrep_id":"137","publist_id":"4381","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":1,"quality_controlled":"1","has_accepted_license":"1","oa":1,"publication":"Proceedings of the 29th conference uncertainty in Artificial Intelligence","type":"conference","ddc":["000"],"publication_identifier":{"isbn":["9780974903996"]},"author":[{"last_name":"Quadrianto","first_name":"Novi","full_name":"Quadrianto, Novi"},{"last_name":"Sharmanska","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308","full_name":"Sharmanska, Viktoriia","first_name":"Viktoriia"},{"last_name":"Knowles","first_name":"David","full_name":"Knowles, David"},{"full_name":"Ghahramani, Zoubin","first_name":"Zoubin","last_name":"Ghahramani"}],"file_date_updated":"2020-07-14T12:45:42Z","page":"527 - 536","abstract":[{"text":"We propose a probabilistic model to infer supervised latent variables in\r\nthe Hamming space from observed data. Our model allows simultaneous\r\ninference of the number of binary latent variables, and their values. The\r\nlatent variables preserve neighbourhood structure of the data in a sense\r\nthat objects in the same semantic concept have similar latent values, and\r\nobjects in different concepts have dissimilar latent values. We formulate\r\nthe supervised infinite latent variable problem based on an intuitive\r\nprinciple of pulling objects together if they are of the same type, and\r\npushing them apart if they are not. We then combine this principle with a\r\nflexible Indian Buffet Process prior on the latent variables. We show that\r\nthe inferred supervised latent variables can be directly used to perform a\r\nnearest neighbour search for the purpose of retrieval.  We introduce a new\r\napplication of dynamically extending hash codes, and show how to\r\neffectively couple the structure of the hash codes with continuously\r\ngrowing structure of the neighbourhood preserving infinite latent feature\r\nspace.","lang":"eng"}],"conference":{"start_date":"2013-07-11","end_date":"2013-07-15","location":"Bellevue, WA, United States","name":"UAI: Uncertainty in Artificial Intelligence"},"date_updated":"2023-02-23T10:46:36Z","title":"The supervised IBP: Neighbourhood preserving infinite latent feature models","_id":"2520","date_published":"2013-07-11T00:00:00Z","date_created":"2018-12-11T11:58:09Z","publication_status":"published","citation":{"ista":"Quadrianto N, Sharmanska V, Knowles D, Ghahramani Z. 2013. The supervised IBP: Neighbourhood preserving infinite latent feature models. Proceedings of the 29th conference uncertainty in Artificial Intelligence. UAI: Uncertainty in Artificial Intelligence, 527–536.","apa":"Quadrianto, N., Sharmanska, V., Knowles, D., &#38; Ghahramani, Z. (2013). The supervised IBP: Neighbourhood preserving infinite latent feature models. In <i>Proceedings of the 29th conference uncertainty in Artificial Intelligence</i> (pp. 527–536). Bellevue, WA, United States: AUAI Press.","ama":"Quadrianto N, Sharmanska V, Knowles D, Ghahramani Z. The supervised IBP: Neighbourhood preserving infinite latent feature models. In: <i>Proceedings of the 29th Conference Uncertainty in Artificial Intelligence</i>. AUAI Press; 2013:527-536.","ieee":"N. Quadrianto, V. Sharmanska, D. Knowles, and Z. Ghahramani, “The supervised IBP: Neighbourhood preserving infinite latent feature models,” in <i>Proceedings of the 29th conference uncertainty in Artificial Intelligence</i>, Bellevue, WA, United States, 2013, pp. 527–536.","short":"N. Quadrianto, V. Sharmanska, D. Knowles, Z. Ghahramani, in:, Proceedings of the 29th Conference Uncertainty in Artificial Intelligence, AUAI Press, 2013, pp. 527–536.","chicago":"Quadrianto, Novi, Viktoriia Sharmanska, David Knowles, and Zoubin Ghahramani. “The Supervised IBP: Neighbourhood Preserving Infinite Latent Feature Models.” In <i>Proceedings of the 29th Conference Uncertainty in Artificial Intelligence</i>, 527–36. AUAI Press, 2013.","mla":"Quadrianto, Novi, et al. “The Supervised IBP: Neighbourhood Preserving Infinite Latent Feature Models.” <i>Proceedings of the 29th Conference Uncertainty in Artificial Intelligence</i>, AUAI Press, 2013, pp. 527–36."},"department":[{"_id":"ChLa"}],"publisher":"AUAI Press","file":[{"creator":"system","file_id":"5134","file_size":1117100,"checksum":"325f20c4b926bd74d39006b97df572bd","date_updated":"2020-07-14T12:45:42Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2013-137-v1+1_QuaShaKnoGha13.pdf","date_created":"2018-12-12T10:15:16Z"}]},{"citation":{"short":"L. Erdös, A. Knowles, H. Yau, J. Yin, Communications in Mathematical Physics 323 (2013) 367–416.","mla":"Erdös, László, et al. “Delocalization and Diffusion Profile for Random Band Matrices.” <i>Communications in Mathematical Physics</i>, vol. 323, no. 1, Springer, 2013, pp. 367–416, doi:<a href=\"https://doi.org/10.1007/s00220-013-1773-3\">10.1007/s00220-013-1773-3</a>.","chicago":"Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “Delocalization and Diffusion Profile for Random Band Matrices.” <i>Communications in Mathematical Physics</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s00220-013-1773-3\">https://doi.org/10.1007/s00220-013-1773-3</a>.","apa":"Erdös, L., Knowles, A., Yau, H., &#38; Yin, J. (2013). Delocalization and diffusion profile for random band matrices. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-013-1773-3\">https://doi.org/10.1007/s00220-013-1773-3</a>","ieee":"L. Erdös, A. Knowles, H. Yau, and J. Yin, “Delocalization and diffusion profile for random band matrices,” <i>Communications in Mathematical Physics</i>, vol. 323, no. 1. Springer, pp. 367–416, 2013.","ama":"Erdös L, Knowles A, Yau H, Yin J. Delocalization and diffusion profile for random band matrices. <i>Communications in Mathematical Physics</i>. 2013;323(1):367-416. doi:<a href=\"https://doi.org/10.1007/s00220-013-1773-3\">10.1007/s00220-013-1773-3</a>","ista":"Erdös L, Knowles A, Yau H, Yin J. 2013. Delocalization and diffusion profile for random band matrices. Communications in Mathematical Physics. 323(1), 367–416."},"publication_status":"published","date_created":"2018-12-11T11:59:07Z","oa":1,"title":"Delocalization and diffusion profile for random band matrices","volume":323,"_id":"2697","date_published":"2013-10-01T00:00:00Z","extern":1,"publication":"Communications in Mathematical Physics","publisher":"Springer","doi":"10.1007/s00220-013-1773-3","day":"01","publist_id":"4199","month":"10","status":"public","type":"journal_article","year":"2013","intvolume":"       323","page":"367 - 416","quality_controlled":0,"abstract":[{"lang":"eng","text":"We consider Hermitian and symmetric random band matrices H = (h xy ) in d⩾1 d ⩾ 1 dimensions. The matrix entries h xy , indexed by x,y∈(Z/LZ)d x , y ∈ ( Z / L Z ) d , are independent, centred random variables with variances sxy=E|hxy|2 s x y = E | h x y | 2 . We assume that s xy is negligible if |x − y| exceeds the band width W. In one dimension we prove that the eigenvectors of H are delocalized if W≫L4/5 W ≫ L 4 / 5 . We also show that the magnitude of the matrix entries |Gxy|2 | G x y | 2 of the resolvent G=G(z)=(H−z)−1 G = G ( z ) = ( H - z ) - 1 is self-averaging and we compute E|Gxy|2 E | G x y | 2 . We show that, as L→∞ L → ∞ and W≫L4/5 W ≫ L 4 / 5 , the behaviour of E|Gxy|2 E | G x y | 2 is governed by a diffusion operator whose diffusion constant we compute. Similar results are obtained in higher dimensions."}],"date_updated":"2021-01-12T06:59:07Z","author":[{"full_name":"László Erdös","first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Knowles, Antti","first_name":"Antti","last_name":"Knowles"},{"full_name":"Yau, Horng-Tzer","first_name":"Horng","last_name":"Yau"},{"last_name":"Yin","full_name":"Yin, Jun","first_name":"Jun"}],"main_file_link":[{"url":"http://arxiv.org/abs/1205.5669","open_access":"1"}],"issue":"1"}]