[{"language":[{"iso":"eng"}],"scopus_import":1,"title":"Mechanisms and principles of homology search during recombination","publisher":"Nature Publishing Group","date_published":"2014-05-14T00:00:00Z","doi":"10.1038/nrm3805","year":"2014","month":"05","date_created":"2018-12-11T11:56:22Z","department":[{"_id":"MiSi"}],"author":[{"first_name":"Jörg","full_name":"Renkawitz, Jörg","last_name":"Renkawitz","orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Claudio","last_name":"Lademann","full_name":"Lademann, Claudio"},{"full_name":"Jentsch, Stefan","last_name":"Jentsch","first_name":"Stefan"}],"status":"public","abstract":[{"text":"Homologous recombination is crucial for genome stability and for genetic exchange. Although our knowledge of the principle steps in recombination and its machinery is well advanced, homology search, the critical step of exploring the genome for homologous sequences to enable recombination, has remained mostly enigmatic. However, recent methodological advances have provided considerable new insights into this fundamental step in recombination that can be integrated into a mechanistic model. These advances emphasize the importance of genomic proximity and nuclear organization for homology search and the critical role of homology search mediators in this process. They also aid our understanding of how homology search might lead to unwanted and potentially disease-promoting recombination events.","lang":"eng"}],"intvolume":"        15","type":"journal_article","citation":{"chicago":"Renkawitz, Jörg, Claudio Lademann, and Stefan Jentsch. “Mechanisms and Principles of Homology Search during Recombination.” <i>Nature Reviews Molecular Cell Biology</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nrm3805\">https://doi.org/10.1038/nrm3805</a>.","ieee":"J. Renkawitz, C. Lademann, and S. Jentsch, “Mechanisms and principles of homology search during recombination,” <i>Nature Reviews Molecular Cell Biology</i>, vol. 15, no. 6. Nature Publishing Group, pp. 369–383, 2014.","apa":"Renkawitz, J., Lademann, C., &#38; Jentsch, S. (2014). Mechanisms and principles of homology search during recombination. <i>Nature Reviews Molecular Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nrm3805\">https://doi.org/10.1038/nrm3805</a>","short":"J. Renkawitz, C. Lademann, S. Jentsch, Nature Reviews Molecular Cell Biology 15 (2014) 369–383.","ista":"Renkawitz J, Lademann C, Jentsch S. 2014. Mechanisms and principles of homology search during recombination. Nature Reviews Molecular Cell Biology. 15(6), 369–383.","ama":"Renkawitz J, Lademann C, Jentsch S. Mechanisms and principles of homology search during recombination. <i>Nature Reviews Molecular Cell Biology</i>. 2014;15(6):369-383. doi:<a href=\"https://doi.org/10.1038/nrm3805\">10.1038/nrm3805</a>","mla":"Renkawitz, Jörg, et al. “Mechanisms and Principles of Homology Search during Recombination.” <i>Nature Reviews Molecular Cell Biology</i>, vol. 15, no. 6, Nature Publishing Group, 2014, pp. 369–83, doi:<a href=\"https://doi.org/10.1038/nrm3805\">10.1038/nrm3805</a>."},"day":"14","publication_status":"published","oa_version":"None","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"J.R. was supported by a Boehringer Ingelheim Fonds PhD stipend.","_id":"2215","page":"369 - 383","volume":15,"date_updated":"2021-01-12T06:56:03Z","publist_id":"4755","publication":"Nature Reviews Molecular Cell Biology","issue":"6"},{"publication_status":"published","citation":{"apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Majumdar, R. (2014). Edit distance for timed automata (pp. 303–312). Presented at the HSCC: Hybrid Systems - Computation and Control, Berlin, Germany: Springer. <a href=\"https://doi.org/10.1145/2562059.2562141\">https://doi.org/10.1145/2562059.2562141</a>","ieee":"K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, “Edit distance for timed automata,” presented at the HSCC: Hybrid Systems - Computation and Control, Berlin, Germany, 2014, pp. 303–312.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Ritankar Majumdar. “Edit Distance for Timed Automata,” 303–12. Springer, 2014. <a href=\"https://doi.org/10.1145/2562059.2562141\">https://doi.org/10.1145/2562059.2562141</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Edit Distance for Timed Automata</i>. Springer, 2014, pp. 303–12, doi:<a href=\"https://doi.org/10.1145/2562059.2562141\">10.1145/2562059.2562141</a>.","ama":"Chatterjee K, Ibsen-Jensen R, Majumdar R. Edit distance for timed automata. In: Springer; 2014:303-312. doi:<a href=\"https://doi.org/10.1145/2562059.2562141\">10.1145/2562059.2562141</a>","ista":"Chatterjee K, Ibsen-Jensen R, Majumdar R. 2014. Edit distance for timed automata. HSCC: Hybrid Systems - Computation and Control, 303–312.","short":"K. Chatterjee, R. Ibsen-Jensen, R. Majumdar, in:, Springer, 2014, pp. 303–312."},"day":"01","type":"conference","abstract":[{"text":"The edit distance between two (untimed) traces is the minimum cost of a sequence of edit operations (insertion, deletion, or substitution) needed to transform one trace to the other. Edit distances have been extensively studied in the untimed setting, and form the basis for approximate matching of sequences in different domains such as coding theory, parsing, and speech recognition. In this paper, we lift the study of edit distances from untimed languages to the timed setting. We define an edit distance between timed words which incorporates both the edit distance between the untimed words and the absolute difference in time stamps. Our edit distance between two timed words is computable in polynomial time. Further, we show that the edit distance between a timed word and a timed language generated by a timed automaton, defined as the edit distance between the word and the closest word in the language, is PSPACE-complete. While computing the edit distance between two timed automata is undecidable, we show that the approximate version, where we decide if the edit distance between two timed automata is either less than a given parameter or more than δ away from the parameter, for δ &gt; 0, can be solved in exponential space and is EXPSPACE-hard. Our definitions and techniques can be generalized to the setting of hybrid systems, and analogous decidability results hold for rectangular automata.","lang":"eng"}],"status":"public","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar"}],"publist_id":"4752","oa":1,"date_updated":"2023-02-23T12:25:01Z","page":"303 - 312","_id":"2216","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","oa_version":"Submitted Version","month":"01","doi":"10.1145/2562059.2562141","year":"2014","date_published":"2014-01-01T00:00:00Z","publisher":"Springer","title":"Edit distance for timed automata","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"main_file_link":[{"open_access":"1","url":"https://dl.acm.org/citation.cfm?doid=2562059.2562141"}],"conference":{"start_date":"2017-04-15","location":"Berlin, Germany","end_date":"2017-04-17","name":"HSCC: Hybrid Systems - Computation and Control"},"related_material":{"record":[{"relation":"earlier_version","id":"5409","status":"public"}]},"date_created":"2018-12-11T11:56:22Z"},{"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5416"}]},"title":"Model measuring for hybrid systems","year":"2014","doi":"10.1145/2562059.2562130","ec_funded":1,"_id":"2217","acknowledgement":"This  work  was  supported  in  part  by  the  Austrian  Science Fund  NFN  RiSE  (Rigorous  Systems  Engineering)  and  by the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling).\r\nA Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/171","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","publist_id":"4751","date_updated":"2023-02-23T12:25:23Z","article_processing_charge":"No","abstract":[{"lang":"eng","text":"As hybrid systems involve continuous behaviors, they should be evaluated by quantitative methods, rather than qualitative methods. In this paper we adapt a quantitative framework, called model measuring, to the hybrid systems domain. The model-measuring problem asks, given a model M and a specification, what is the maximal distance such that all models within that distance from M satisfy (or violate) the specification. A distance function on models is given as part of the input of the problem. Distances, especially related to continuous behaviors are more natural in the hybrid case than the discrete case. We are interested in distances represented by monotonic hybrid automata, a hybrid counterpart of (discrete) weighted automata, whose recognized timed languages are monotone (w.r.t. inclusion) in the values of parameters.\r\n\r\nThe contributions of this paper are twofold. First, we give sufficient conditions under which the model-measuring problem can be solved. Second, we discuss the modeling of distances and applications of the model-measuring problem."}],"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Jan","full_name":"Otop, Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","citation":{"apa":"Henzinger, T. A., &#38; Otop, J. (2014). Model measuring for hybrid systems. In <i>Proceedings of the 17th international conference on Hybrid systems: computation and control</i> (pp. 213–222). Berlin, Germany: Springer. <a href=\"https://doi.org/10.1145/2562059.2562130\">https://doi.org/10.1145/2562059.2562130</a>","ieee":"T. A. Henzinger and J. Otop, “Model measuring for hybrid systems,” in <i>Proceedings of the 17th international conference on Hybrid systems: computation and control</i>, Berlin, Germany, 2014, pp. 213–222.","chicago":"Henzinger, Thomas A, and Jan Otop. “Model Measuring for Hybrid Systems.” In <i>Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control</i>, 213–22. Springer, 2014. <a href=\"https://doi.org/10.1145/2562059.2562130\">https://doi.org/10.1145/2562059.2562130</a>.","ama":"Henzinger TA, Otop J. Model measuring for hybrid systems. In: <i>Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control</i>. Springer; 2014:213-222. doi:<a href=\"https://doi.org/10.1145/2562059.2562130\">10.1145/2562059.2562130</a>","mla":"Henzinger, Thomas A., and Jan Otop. “Model Measuring for Hybrid Systems.” <i>Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control</i>, Springer, 2014, pp. 213–22, doi:<a href=\"https://doi.org/10.1145/2562059.2562130\">10.1145/2562059.2562130</a>.","ista":"Henzinger TA, Otop J. 2014. Model measuring for hybrid systems. Proceedings of the 17th international conference on Hybrid systems: computation and control. HSCC: Hybrid Systems - Computation and Control, 213–222.","short":"T.A. Henzinger, J. Otop, in:, Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control, Springer, 2014, pp. 213–222."},"conference":{"start_date":"2014-04-15","end_date":"2014-04-17","name":"HSCC: Hybrid Systems - Computation and Control","location":"Berlin, Germany"},"date_created":"2018-12-11T11:56:23Z","department":[{"_id":"ToHe"}],"publisher":"Springer","scopus_import":1,"language":[{"iso":"eng"}],"month":"04","date_published":"2014-04-01T00:00:00Z","publication":"Proceedings of the 17th international conference on Hybrid systems: computation and control","page":"213 - 222","status":"public","day":"01","type":"conference"},{"file_date_updated":"2020-07-14T12:45:33Z","page":"568 - 584","status":"public","intvolume":"      8559","type":"conference","day":"22","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:45:33Z","checksum":"a631d3105509f239724644e77a1212e2","date_created":"2018-12-12T10:13:14Z","file_size":416732,"file_name":"IST-2014-297-v1+1_cav14-final.pdf","file_id":"4995","creator":"system","relation":"main_file","content_type":"application/pdf"},{"creator":"system","file_id":"4996","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:13:15Z","checksum":"f8b0f748cc9fa697ca992cc56c87bc4e","file_name":"IST-2014-297-v2+1_cav14-final2.pdf","file_size":616293,"date_updated":"2020-07-14T12:45:33Z","access_level":"open_access"}],"date_created":"2018-12-11T11:56:23Z","conference":{"end_date":"2014-07-22","name":"CAV: Computer Aided Verification","location":"Vienna, Austria","start_date":"2014-07-18"},"department":[{"_id":"ToHe"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"publisher":"Springer","date_published":"2014-07-22T00:00:00Z","month":"07","quality_controlled":"1","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"},{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["978-331908866-2"]},"_id":"2218","volume":8559,"publist_id":"4749","date_updated":"2023-09-07T11:57:01Z","oa":1,"author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","first_name":"Pavol"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","first_name":"Arjun"},{"first_name":"Leonid","last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid"},{"orcid":"0000-0003-4409-8487","last_name":"Tarrach","full_name":"Tarrach, Thorsten","first_name":"Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"While fixing concurrency bugs, program repair algorithms may introduce new concurrency bugs. We present an algorithm that avoids such regressions. The solution space is given by a set of program transformations we consider in the repair process. These include reordering of instructions within a thread and inserting atomic sections. The new algorithm learns a constraint on the space of candidate solutions, from both positive examples (error-free traces) and counterexamples (error traces). From each counterexample, the algorithm learns a constraint necessary to remove the errors. From each positive examples, it learns a constraint that is necessary in order to prevent the repair from turning the trace into an error trace. We implemented the algorithm and evaluated it on simplified Linux device drivers with known bugs."}],"citation":{"mla":"Cerny, Pavol, et al. <i>Regression-Free Synthesis for Concurrency</i>. Vol. 8559, Springer, 2014, pp. 568–84, doi:<a href=\"https://doi.org/10.1007/978-3-319-08867-9_38\">10.1007/978-3-319-08867-9_38</a>.","ama":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Regression-free synthesis for concurrency. In: Vol 8559. Springer; 2014:568-584. doi:<a href=\"https://doi.org/10.1007/978-3-319-08867-9_38\">10.1007/978-3-319-08867-9_38</a>","ista":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2014. Regression-free synthesis for concurrency. CAV: Computer Aided Verification, LNCS, vol. 8559, 568–584.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer, 2014, pp. 568–584.","apa":"Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., &#38; Tarrach, T. (2014). Regression-free synthesis for concurrency (Vol. 8559, pp. 568–584). Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-319-08867-9_38\">https://doi.org/10.1007/978-3-319-08867-9_38</a>","ieee":"P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Regression-free synthesis for concurrency,” presented at the CAV: Computer Aided Verification, Vienna, Austria, 2014, vol. 8559, pp. 568–584.","chicago":"Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and Thorsten Tarrach. “Regression-Free Synthesis for Concurrency,” 8559:568–84. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-08867-9_38\">https://doi.org/10.1007/978-3-319-08867-9_38</a>."},"publication_status":"published","ddc":["000"],"related_material":{"record":[{"id":"1130","relation":"dissertation_contains","status":"public"}]},"main_file_link":[{"open_access":"1","url":"https://link.springer.com/chapter/10.1007%2F978-3-319-08867-9_38"}],"alternative_title":["LNCS"],"title":"Regression-free synthesis for concurrency","pubrep_id":"297","ec_funded":1,"doi":"10.1007/978-3-319-08867-9_38","year":"2014"},{"department":[{"_id":"KrPi"}],"date_created":"2018-12-11T11:56:24Z","conference":{"name":"IACR: International Conference on Practice and Theory in Public-Key Cryptography"},"date_published":"2014-03-01T00:00:00Z","month":"03","language":[{"iso":"eng"}],"publisher":"Springer","scopus_import":1,"page":"1 - 18","type":"conference","day":"01","status":"public","intvolume":"      8383","main_file_link":[{"url":"https://eprint.iacr.org/2015/401","open_access":"1"}],"alternative_title":["LNCS"],"year":"2014","doi":"10.1007/978-3-642-54631-0_1","title":"Simple chosen-ciphertext security from low noise LPN","publist_id":"4748","volume":8383,"oa":1,"date_updated":"2021-01-12T06:56:05Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","oa_version":"Submitted Version","_id":"2219","publication_identifier":{"isbn":["978-364254630-3"]},"publication_status":"published","citation":{"ama":"Kiltz E, Masny D, Pietrzak KZ. Simple chosen-ciphertext security from low noise LPN. In: Vol 8383. Springer; 2014:1-18. doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_1\">10.1007/978-3-642-54631-0_1</a>","mla":"Kiltz, Eike, et al. <i>Simple Chosen-Ciphertext Security from Low Noise LPN</i>. Vol. 8383, Springer, 2014, pp. 1–18, doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_1\">10.1007/978-3-642-54631-0_1</a>.","ista":"Kiltz E, Masny D, Pietrzak KZ. 2014. Simple chosen-ciphertext security from low noise LPN. IACR: International Conference on Practice and Theory in Public-Key Cryptography, LNCS, vol. 8383, 1–18.","short":"E. Kiltz, D. Masny, K.Z. Pietrzak, in:, Springer, 2014, pp. 1–18.","ieee":"E. Kiltz, D. Masny, and K. Z. Pietrzak, “Simple chosen-ciphertext security from low noise LPN,” presented at the IACR: International Conference on Practice and Theory in Public-Key Cryptography, 2014, vol. 8383, pp. 1–18.","apa":"Kiltz, E., Masny, D., &#38; Pietrzak, K. Z. (2014). Simple chosen-ciphertext security from low noise LPN (Vol. 8383, pp. 1–18). Presented at the IACR: International Conference on Practice and Theory in Public-Key Cryptography, Springer. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_1\">https://doi.org/10.1007/978-3-642-54631-0_1</a>","chicago":"Kiltz, Eike, Daniel Masny, and Krzysztof Z Pietrzak. “Simple Chosen-Ciphertext Security from Low Noise LPN,” 8383:1–18. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_1\">https://doi.org/10.1007/978-3-642-54631-0_1</a>."},"author":[{"last_name":"Kiltz","full_name":"Kiltz, Eike","first_name":"Eike"},{"first_name":"Daniel","full_name":"Masny, Daniel","last_name":"Masny"},{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"Recently, Döttling et al. (ASIACRYPT 2012) proposed the first chosen-ciphertext (IND-CCA) secure public-key encryption scheme from the learning parity with noise (LPN) assumption. In this work we give an alternative scheme which is conceptually simpler and more efficient. At the core of our construction is a trapdoor technique originally proposed for lattices by Micciancio and Peikert (EUROCRYPT 2012), which we adapt to the LPN setting. The main technical tool is a new double-trapdoor mechanism, together with a trapdoor switching lemma based on a computational variant of the leftover hash lemma."}]},{"publist_id":"4747","volume":21,"oa":1,"date_updated":"2021-01-12T06:56:06Z","quality_controlled":"1","oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["10745521"]},"pmid":1,"_id":"2220","citation":{"apa":"de Vos, M., &#38; Bollenbach, M. T. (2014). Suppressive drug interactions between antifungals. <i>Chemistry and Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.chembiol.2014.04.004\">https://doi.org/10.1016/j.chembiol.2014.04.004</a>","ieee":"M. de Vos and M. T. Bollenbach, “Suppressive drug interactions between antifungals,” <i>Chemistry and Biology</i>, vol. 21, no. 4. Cell Press, pp. 439–440, 2014.","chicago":"Vos, Marjon de, and Mark Tobias Bollenbach. “Suppressive Drug Interactions between Antifungals.” <i>Chemistry and Biology</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.chembiol.2014.04.004\">https://doi.org/10.1016/j.chembiol.2014.04.004</a>.","ama":"de Vos M, Bollenbach MT. Suppressive drug interactions between antifungals. <i>Chemistry and Biology</i>. 2014;21(4):439-440. doi:<a href=\"https://doi.org/10.1016/j.chembiol.2014.04.004\">10.1016/j.chembiol.2014.04.004</a>","mla":"de Vos, Marjon, and Mark Tobias Bollenbach. “Suppressive Drug Interactions between Antifungals.” <i>Chemistry and Biology</i>, vol. 21, no. 4, Cell Press, 2014, pp. 439–40, doi:<a href=\"https://doi.org/10.1016/j.chembiol.2014.04.004\">10.1016/j.chembiol.2014.04.004</a>.","ista":"de Vos M, Bollenbach MT. 2014. Suppressive drug interactions between antifungals. Chemistry and Biology. 21(4), 439–440.","short":"M. de Vos, M.T. Bollenbach, Chemistry and Biology 21 (2014) 439–440."},"publication_status":"published","author":[{"first_name":"Marjon","full_name":"De Vos, Marjon","last_name":"De Vos","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"In this issue of Chemistry & Biology, Cokol and colleagues report a systematic study of drug interactions between antifungal compounds. Suppressive drug interactions occur more frequently than previously realized and come in different flavors with interesting implications."}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/24766845"}],"doi":"10.1016/j.chembiol.2014.04.004","year":"2014","title":"Suppressive drug interactions between antifungals","external_id":{"pmid":["24766845"]},"page":"439 - 440","publication":"Chemistry and Biology","issue":"4","type":"journal_article","day":"24","status":"public","intvolume":"        21","department":[{"_id":"ToBo"}],"date_created":"2018-12-11T11:56:24Z","date_published":"2014-04-24T00:00:00Z","month":"04","language":[{"iso":"eng"}],"scopus_import":1,"publisher":"Cell Press"},{"department":[{"_id":"JiFr"}],"date_created":"2018-12-11T11:56:24Z","date_published":"2014-04-01T00:00:00Z","month":"04","language":[{"iso":"eng"}],"publisher":"Oxford University Press","scopus_import":1,"page":"750 - 763","issue":"4","publication":"Plant and Cell Physiology","type":"journal_article","day":"01","status":"public","intvolume":"        55","ec_funded":1,"doi":"10.1093/pcp/pcu012","year":"2014","title":"VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis","publist_id":"4742","date_updated":"2021-01-12T06:56:06Z","volume":55,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","oa_version":"None","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"_id":"2222","publication_identifier":{"issn":["00320781"]},"publication_status":"published","citation":{"chicago":"Naramoto, Satoshi, Tomasz Nodzyński, Tomoko Dainobu, Hirotomo Takatsuka, Teruyo Okada, Jiří Friml, and Hiroo Fukuda. “VAN4 Encodes a Putative TRS120 That Is Required for Normal Cell Growth and Vein Development in Arabidopsis.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/pcp/pcu012\">https://doi.org/10.1093/pcp/pcu012</a>.","apa":"Naramoto, S., Nodzyński, T., Dainobu, T., Takatsuka, H., Okada, T., Friml, J., &#38; Fukuda, H. (2014). VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcu012\">https://doi.org/10.1093/pcp/pcu012</a>","ieee":"S. Naramoto <i>et al.</i>, “VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis,” <i>Plant and Cell Physiology</i>, vol. 55, no. 4. Oxford University Press, pp. 750–763, 2014.","ista":"Naramoto S, Nodzyński T, Dainobu T, Takatsuka H, Okada T, Friml J, Fukuda H. 2014. VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. Plant and Cell Physiology. 55(4), 750–763.","short":"S. Naramoto, T. Nodzyński, T. Dainobu, H. Takatsuka, T. Okada, J. Friml, H. Fukuda, Plant and Cell Physiology 55 (2014) 750–763.","mla":"Naramoto, Satoshi, et al. “VAN4 Encodes a Putative TRS120 That Is Required for Normal Cell Growth and Vein Development in Arabidopsis.” <i>Plant and Cell Physiology</i>, vol. 55, no. 4, Oxford University Press, 2014, pp. 750–63, doi:<a href=\"https://doi.org/10.1093/pcp/pcu012\">10.1093/pcp/pcu012</a>.","ama":"Naramoto S, Nodzyński T, Dainobu T, et al. VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. <i>Plant and Cell Physiology</i>. 2014;55(4):750-763. doi:<a href=\"https://doi.org/10.1093/pcp/pcu012\">10.1093/pcp/pcu012</a>"},"author":[{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"first_name":"Tomoko","full_name":"Dainobu, Tomoko","last_name":"Dainobu"},{"first_name":"Hirotomo","full_name":"Takatsuka, Hirotomo","last_name":"Takatsuka"},{"last_name":"Okada","full_name":"Okada, Teruyo","first_name":"Teruyo"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí"},{"first_name":"Hiroo","full_name":"Fukuda, Hiroo","last_name":"Fukuda"}],"abstract":[{"text":"Leaf venation develops complex patterns in angiosperms, but the mechanism underlying this process is largely unknown. To elucidate the molecular mechanisms governing vein pattern formation, we previously isolated vascular network defective (van) mutants that displayed venation discontinuities. Here, we report the phenotypic analysis of van4 mutants, and we identify and characterize the VAN4 gene. Detailed phenotypic analysis shows that van4 mutants are defective in procambium cell differentiation and subsequent vascular cell differentiation. Reduced shoot and root cell growth is observed in van4 mutants, suggesting that VAN4 function is important for cell growth and the establishment of venation continuity. Consistent with these phenotypes, the VAN4 gene is strongly expressed in vascular and meristematic cells. VAN4 encodes a putative TRS120, which is a known guanine nucleotide exchange factor (GEF) for Rab GTPase involved in regulating vesicle transport, and a known tethering factor that determines the specificity of membrane fusion. VAN4 protein localizes at the trans-Golgi network/early endosome (TGN/EE). Aberrant recycling of the auxin efflux carrier PIN proteins is observed in van4 mutants. These results suggest that VAN4-mediated exocytosis at the TGN plays important roles in plant vascular development and cell growth in shoot and root. Our identification of VAN4 as a putative TRS120 shows that Rab GTPases are crucial (in addition to ARF GTPases) for continuous vascular development, and provides further evidence for the importance of vesicle transport in leaf vascular formation.","lang":"eng"}]},{"pubrep_id":"431","title":"BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis","ec_funded":1,"year":"2014","doi":"10.1093/pcp/pct196","ddc":["570"],"main_file_link":[{"url":"http://repository.ist.ac.at/id/eprint/431","open_access":"1"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"author":[{"full_name":"Tanaka, Hirokazu","last_name":"Tanaka","first_name":"Hirokazu"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"full_name":"Kitakura, Saeko","last_name":"Kitakura","first_name":"Saeko"},{"last_name":"Feraru","full_name":"Feraru, Mugurel","first_name":"Mugurel"},{"first_name":"Michiko","full_name":"Sasabe, Michiko","last_name":"Sasabe"},{"first_name":"Tomomi","last_name":"Ishikawa","full_name":"Ishikawa, Tomomi"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen"},{"first_name":"Tatsuo","last_name":"Kakimoto","full_name":"Kakimoto, Tatsuo"},{"first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"Correct positioning of membrane proteins is an essential process in eukaryotic organisms. The plant hormone auxin is distributed through intercellular transport and triggers various cellular responses. Auxin transporters of the PIN-FORMED (PIN) family localize asymmetrically at the plasma membrane (PM) and mediate the directional transport of auxin between cells. A fungal toxin, brefeldin A (BFA), inhibits a subset of guanine nucleotide exchange factors for ADP-ribosylation factor small GTPases (ARF GEFs) including GNOM, which plays a major role in localization of PIN1 predominantly to the basal side of the PM. The Arabidopsis genome encodes 19 ARF-related putative GTPases. However, ARF components involved in PIN1 localization have been genetically poorly defined. Using a fluorescence imaging-based forward genetic approach, we identified an Arabidopsis mutant, bfa-visualized exocytic trafficking defective1 (bex1), in which PM localization of PIN1-green fluorescent protein (GFP) as well as development is hypersensitive to BFA. We found that in bex1 a member of the ARF1 gene family, ARF1A1C, was mutated. ARF1A1C localizes to the trans-Golgi network/early endosome and Golgi apparatus, acts synergistically to BEN1/MIN7 ARF GEF and is important for PIN recycling to the PM. Consistent with the developmental importance of PIN proteins, functional interference with ARF1 resulted in an impaired auxin response gradient and various developmental defects including embryonic patterning defects and growth arrest. Our results show that ARF1A1C is essential for recycling of PIN auxin transporters and for various auxin-dependent developmental processes.","lang":"eng"}],"publication_status":"published","citation":{"ista":"Tanaka H, Nodzyński T, Kitakura S, Feraru M, Sasabe M, Ishikawa T, Kleine Vehn J, Kakimoto T, Friml J. 2014. BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. Plant and Cell Physiology. 55(4), 737–749.","short":"H. Tanaka, T. Nodzyński, S. Kitakura, M. Feraru, M. Sasabe, T. Ishikawa, J. Kleine Vehn, T. Kakimoto, J. Friml, Plant and Cell Physiology 55 (2014) 737–749.","mla":"Tanaka, Hirokazu, et al. “BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling of PIN Auxin Transporters and Auxin-Mediated Development in Arabidopsis.” <i>Plant and Cell Physiology</i>, vol. 55, no. 4, Oxford University Press, 2014, pp. 737–49, doi:<a href=\"https://doi.org/10.1093/pcp/pct196\">10.1093/pcp/pct196</a>.","ama":"Tanaka H, Nodzyński T, Kitakura S, et al. BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. <i>Plant and Cell Physiology</i>. 2014;55(4):737-749. doi:<a href=\"https://doi.org/10.1093/pcp/pct196\">10.1093/pcp/pct196</a>","chicago":"Tanaka, Hirokazu, Tomasz Nodzyński, Saeko Kitakura, Mugurel Feraru, Michiko Sasabe, Tomomi Ishikawa, Jürgen Kleine Vehn, Tatsuo Kakimoto, and Jiří Friml. “BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling of PIN Auxin Transporters and Auxin-Mediated Development in Arabidopsis.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/pcp/pct196\">https://doi.org/10.1093/pcp/pct196</a>.","ieee":"H. Tanaka <i>et al.</i>, “BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis,” <i>Plant and Cell Physiology</i>, vol. 55, no. 4. Oxford University Press, pp. 737–749, 2014.","apa":"Tanaka, H., Nodzyński, T., Kitakura, S., Feraru, M., Sasabe, M., Ishikawa, T., … Friml, J. (2014). BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pct196\">https://doi.org/10.1093/pcp/pct196</a>"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"},{"_id":"256BDAB0-B435-11E9-9278-68D0E5697425","name":"Innovationsförderung in der Grenzregion Österreich – Tschechische Republik durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur"}],"oa_version":"Published Version","quality_controlled":"1","_id":"2223","publication_identifier":{"issn":["00320781"]},"publist_id":"4741","oa":1,"volume":55,"date_updated":"2021-01-12T06:56:07Z","language":[{"iso":"eng"}],"publisher":"Oxford University Press","scopus_import":1,"date_published":"2014-04-01T00:00:00Z","month":"04","date_created":"2018-12-11T11:56:25Z","file":[{"relation":"main_file","content_type":"application/pdf","creator":"system","file_id":"5076","access_level":"open_access","date_updated":"2020-07-14T12:45:34Z","file_size":2028111,"file_name":"IST-2016-431-v1+1_Plant_Cell_Physiol-2014-Tanaka-737-49.pdf","checksum":"b781a76b32ac35a520256453c3ba9433","date_created":"2018-12-12T10:14:25Z"}],"department":[{"_id":"JiFr"}],"has_accepted_license":"1","status":"public","intvolume":"        55","type":"journal_article","day":"01","page":"737 - 749","file_date_updated":"2020-07-14T12:45:34Z","issue":"4","publication":"Plant and Cell Physiology"},{"language":[{"iso":"eng"}],"publisher":"IOP Publishing Ltd.","scopus_import":1,"title":"On secondary instabilities generating footbridges between spiral vortex flow","date_published":"2014-04-01T00:00:00Z","doi":"10.1088/0169-5983/46/2/025503","year":"2014","month":"04","date_created":"2018-12-11T11:56:25Z","department":[{"_id":"BjHo"}],"article_number":"025503","status":"public","author":[{"last_name":"Altmeyer","full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203","first_name":"Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        46","abstract":[{"lang":"eng","text":"This work investigates the transition between different traveling helical waves (spirals, SPIs) in the setup of differentially independent rotating cylinders. We use direct numerical simulations to consider an infinite long and periodic Taylor-Couette apparatus with fixed axial periodicity length. We find so-called mixed-cross-spirals (MCSs), that can be seen as nonlinear superpositions of SPIs, to establish stable footbridges connecting SPI states. While bridging the bifurcation branches of SPIs, the corresponding contributions within the MCS vary continuously with the control parameters. Here discussed MCSs presenting footbridge solutions start and end in different SPI branches. Therefore they differ significantly from the already known MCSs that present bypass solutions (Altmeyer and Hoffmann 2010 New J. Phys. 12 113035). The latter start and end in the same SPI branch, while they always bifurcate out of those SPI branches with the larger mode amplitude. Meanwhile, these only appear within the coexisting region of both SPIs. In contrast, the footbridge solutions can also bifurcate out of the minor SPI contribution. We also find they exist in regions where only one of the SPIs contributions exists. In addition, MCS as footbridge solution can appear either stable or unstable. The latter detected transient solutions offer similar spatio-temporal characteristics to the flow establishing stable footbridges. Such transition processes are interesting for pattern-forming systems in general because they accomplish transitions between traveling waves of different azimuthal wave numbers and have not been described in the literature yet."}],"type":"journal_article","publication_status":"published","day":"01","citation":{"chicago":"Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between Spiral Vortex Flow.” <i>Fluid Dynamics Research</i>. IOP Publishing Ltd., 2014. <a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">https://doi.org/10.1088/0169-5983/46/2/025503</a>.","apa":"Altmeyer, S. (2014). On secondary instabilities generating footbridges between spiral vortex flow. <i>Fluid Dynamics Research</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">https://doi.org/10.1088/0169-5983/46/2/025503</a>","ieee":"S. Altmeyer, “On secondary instabilities generating footbridges between spiral vortex flow,” <i>Fluid Dynamics Research</i>, vol. 46, no. 2. IOP Publishing Ltd., 2014.","short":"S. Altmeyer, Fluid Dynamics Research 46 (2014).","ista":"Altmeyer S. 2014. On secondary instabilities generating footbridges between spiral vortex flow. Fluid Dynamics Research. 46(2), 025503.","mla":"Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between Spiral Vortex Flow.” <i>Fluid Dynamics Research</i>, vol. 46, no. 2, 025503, IOP Publishing Ltd., 2014, doi:<a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">10.1088/0169-5983/46/2/025503</a>.","ama":"Altmeyer S. On secondary instabilities generating footbridges between spiral vortex flow. <i>Fluid Dynamics Research</i>. 2014;46(2). doi:<a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">10.1088/0169-5983/46/2/025503</a>"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","oa_version":"None","_id":"2224","publication_identifier":{"issn":["01695983"]},"date_updated":"2021-01-12T06:56:07Z","publist_id":"4740","volume":46,"issue":"2","publication":"Fluid Dynamics Research"},{"date_created":"2018-12-11T11:56:25Z","file":[{"relation":"main_file","content_type":"application/pdf","creator":"system","file_id":"5055","file_size":810150,"file_name":"IST-2016-427-v1+1_3054-16624-4-PB.pdf","checksum":"7eb297ff367a2ee73b21b6dd1e1948e4","date_created":"2018-12-12T10:14:06Z","access_level":"open_access","date_updated":"2020-07-14T12:45:34Z"}],"department":[{"_id":"LaEr"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"publisher":"Institute of Mathematical Statistics","date_published":"2014-03-15T00:00:00Z","month":"03","file_date_updated":"2020-07-14T12:45:34Z","publication":"Electronic Journal of Probability","status":"public","intvolume":"        19","type":"journal_article","day":"15","ddc":["510"],"article_number":"33","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"title":"Isotropic local laws for sample covariance and generalized Wigner matrices","pubrep_id":"427","ec_funded":1,"doi":"10.1214/EJP.v19-3054","year":"2014","oa_version":"Published Version","quality_controlled":"1","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["10836489"]},"_id":"2225","date_updated":"2021-01-12T06:56:07Z","oa":1,"volume":19,"publist_id":"4739","author":[{"last_name":"Bloemendal","full_name":"Bloemendal, Alex","first_name":"Alex"},{"first_name":"László","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Antti","last_name":"Knowles","full_name":"Knowles, Antti"},{"last_name":"Yau","full_name":"Yau, Horng","first_name":"Horng"},{"first_name":"Jun","last_name":"Yin","full_name":"Yin, Jun"}],"abstract":[{"lang":"eng","text":"We consider sample covariance matrices of the form X∗X, where X is an M×N matrix with independent random entries.  We prove the isotropic local Marchenko-Pastur law, i.e. we prove that the resolvent (X∗X−z)−1 converges to a multiple of the identity in the sense of quadratic forms. More precisely, we establish sharp high-probability bounds on the quantity ⟨v,(X∗X−z)−1w⟩−⟨v,w⟩m(z), where m is the Stieltjes transform of the Marchenko-Pastur law and v,w∈CN. We require the logarithms of the dimensions M and N to be comparable. Our result holds down to scales Iz≥N−1+ε and throughout the entire spectrum away from 0. We also prove analogous results for generalized Wigner matrices.\r\n"}],"citation":{"ieee":"A. Bloemendal, L. Erdös, A. Knowles, H. Yau, and J. Yin, “Isotropic local laws for sample covariance and generalized Wigner matrices,” <i>Electronic Journal of Probability</i>, vol. 19. Institute of Mathematical Statistics, 2014.","apa":"Bloemendal, A., Erdös, L., Knowles, A., Yau, H., &#38; Yin, J. (2014). Isotropic local laws for sample covariance and generalized Wigner matrices. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/EJP.v19-3054\">https://doi.org/10.1214/EJP.v19-3054</a>","chicago":"Bloemendal, Alex, László Erdös, Antti Knowles, Horng Yau, and Jun Yin. “Isotropic Local Laws for Sample Covariance and Generalized Wigner Matrices.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2014. <a href=\"https://doi.org/10.1214/EJP.v19-3054\">https://doi.org/10.1214/EJP.v19-3054</a>.","mla":"Bloemendal, Alex, et al. “Isotropic Local Laws for Sample Covariance and Generalized Wigner Matrices.” <i>Electronic Journal of Probability</i>, vol. 19, 33, Institute of Mathematical Statistics, 2014, doi:<a href=\"https://doi.org/10.1214/EJP.v19-3054\">10.1214/EJP.v19-3054</a>.","ama":"Bloemendal A, Erdös L, Knowles A, Yau H, Yin J. Isotropic local laws for sample covariance and generalized Wigner matrices. <i>Electronic Journal of Probability</i>. 2014;19. doi:<a href=\"https://doi.org/10.1214/EJP.v19-3054\">10.1214/EJP.v19-3054</a>","ista":"Bloemendal A, Erdös L, Knowles A, Yau H, Yin J. 2014. Isotropic local laws for sample covariance and generalized Wigner matrices. Electronic Journal of Probability. 19, 33.","short":"A. Bloemendal, L. Erdös, A. Knowles, H. Yau, J. Yin, Electronic Journal of Probability 19 (2014)."},"publication_status":"published"},{"publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","issue":"1","type":"journal_article","day":"06","status":"public","intvolume":"        89","department":[{"_id":"BjHo"}],"date_created":"2018-12-11T11:56:26Z","date_published":"2014-01-06T00:00:00Z","month":"01","language":[{"iso":"eng"}],"scopus_import":1,"publisher":"American Institute of Physics","oa":1,"date_updated":"2021-01-12T06:56:08Z","volume":89,"publist_id":"4737","project":[{"grant_number":"SFB-TR3-TP10B","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen"}],"oa_version":"Submitted Version","quality_controlled":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["15393755"]},"_id":"2226","citation":{"ieee":"L. Shi, B. Hof, and A. Tilgner, “Transient growth of Ekman-Couette flow,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 89, no. 1. American Institute of Physics, 2014.","apa":"Shi, L., Hof, B., &#38; Tilgner, A. (2014). Transient growth of Ekman-Couette flow. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.89.013001\">https://doi.org/10.1103/PhysRevE.89.013001</a>","chicago":"Shi, Liang, Björn Hof, and Andreas Tilgner. “Transient Growth of Ekman-Couette Flow.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2014. <a href=\"https://doi.org/10.1103/PhysRevE.89.013001\">https://doi.org/10.1103/PhysRevE.89.013001</a>.","mla":"Shi, Liang, et al. “Transient Growth of Ekman-Couette Flow.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 89, no. 1, 013001, American Institute of Physics, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevE.89.013001\">10.1103/PhysRevE.89.013001</a>.","ama":"Shi L, Hof B, Tilgner A. Transient growth of Ekman-Couette flow. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2014;89(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.89.013001\">10.1103/PhysRevE.89.013001</a>","short":"L. Shi, B. Hof, A. Tilgner, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","ista":"Shi L, Hof B, Tilgner A. 2014. Transient growth of Ekman-Couette flow. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(1), 013001."},"publication_status":"published","author":[{"first_name":"Liang","last_name":"Shi","full_name":"Shi, Liang"},{"first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tilgner, Andreas","last_name":"Tilgner","first_name":"Andreas"}],"abstract":[{"text":"Coriolis force effects on shear flows are important in geophysical and astrophysical contexts. We report a study on the linear stability and the transient energy growth of the plane Couette flow with system rotation perpendicular to the shear direction. External rotation causes linear instability. At small rotation rates, the onset of linear instability scales inversely with the rotation rate and the optimal transient growth in the linearly stable region is slightly enhanced ∼Re2. The corresponding optimal initial perturbations are characterized by roll structures inclined in the streamwise direction and are twisted under external rotation. At large rotation rates, the transient growth is significantly inhibited and hence linear stability analysis is a reliable indicator for instability.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1312.5095"}],"article_number":"013001","year":"2014","doi":"10.1103/PhysRevE.89.013001","title":"Transient growth of Ekman-Couette flow"},{"type":"journal_article","day":"01","citation":{"ieee":"E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, and J. Prieto, “Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences,” <i>Organisms Diversity and Evolution</i>, vol. 14, no. 1. Springer, pp. 1–10, 2014.","apa":"Cires Rodriguez, E., Baltisberger, M., Cuesta, C., Vargas, P., &#38; Prieto, J. (2014). Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. <i>Organisms Diversity and Evolution</i>. Springer. <a href=\"https://doi.org/10.1007/s13127-013-0150-6\">https://doi.org/10.1007/s13127-013-0150-6</a>","chicago":"Cires Rodriguez, Eduardo, Matthias Baltisberger, Candela Cuesta, Pablo Vargas, and José Prieto. “Allopolyploid Origin of the Balkan Endemic Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.” <i>Organisms Diversity and Evolution</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s13127-013-0150-6\">https://doi.org/10.1007/s13127-013-0150-6</a>.","ama":"Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. <i>Organisms Diversity and Evolution</i>. 2014;14(1):1-10. doi:<a href=\"https://doi.org/10.1007/s13127-013-0150-6\">10.1007/s13127-013-0150-6</a>","mla":"Cires Rodriguez, Eduardo, et al. “Allopolyploid Origin of the Balkan Endemic Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.” <i>Organisms Diversity and Evolution</i>, vol. 14, no. 1, Springer, 2014, pp. 1–10, doi:<a href=\"https://doi.org/10.1007/s13127-013-0150-6\">10.1007/s13127-013-0150-6</a>.","short":"E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, J. Prieto, Organisms Diversity and Evolution 14 (2014) 1–10.","ista":"Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. 2014. Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. Organisms Diversity and Evolution. 14(1), 1–10."},"publication_status":"published","status":"public","author":[{"first_name":"Eduardo","last_name":"Cires Rodriguez","full_name":"Cires Rodriguez, Eduardo","id":"2AD56A7A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","full_name":"Baltisberger, Matthias","last_name":"Baltisberger"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410","last_name":"Cuesta","full_name":"Cuesta, Candela","first_name":"Candela"},{"first_name":"Pablo","last_name":"Vargas","full_name":"Vargas, Pablo"},{"last_name":"Prieto","full_name":"Prieto, José","first_name":"José"}],"intvolume":"        14","abstract":[{"text":"The Balkan Peninsula, characterized by high rates of endemism, is recognised as one of the most diverse and species-rich areas of Europe. However, little is known about the origin of Balkan endemics. The present study addresses the phylogenetic position of the Balkan endemic Ranunculus wettsteinii, as well as its taxonomic status and relationship with the widespread R. parnassiifolius, based on nuclear DNA (internal transcribed spacer, ITS) and plastid regions (rpl32-trnL, rps16-trnQ, trnK-matK and ycf6-psbM). Maximum parsimony and Bayesian inference analyses revealed a well-supported clade formed by accessions of R. wettsteinii. Furthermore, our phylogenetic and network analyses supported previous hypotheses of a likely allopolyploid origin for R. wettsteinii between R. montenegrinus and R. parnassiifolius, with the latter as the maternal parent.","lang":"eng"}],"page":"1 - 10","article_processing_charge":"No","volume":14,"date_updated":"2022-08-25T14:42:46Z","publist_id":"4734","publication":"Organisms Diversity and Evolution","issue":"1","quality_controlled":"1","oa_version":"None","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["14396092"]},"_id":"2227","date_published":"2014-03-01T00:00:00Z","month":"03","doi":"10.1007/s13127-013-0150-6","year":"2014","language":[{"iso":"eng"}],"title":"Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences","scopus_import":"1","publisher":"Springer","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"date_created":"2018-12-11T11:56:26Z"},{"department":[{"_id":"PeJo"}],"date_created":"2018-12-11T11:56:26Z","month":"03","date_published":"2014-03-23T00:00:00Z","publisher":"Nature Publishing Group","scopus_import":1,"language":[{"iso":"eng"}],"issue":"5","publication":"Nature Neuroscience","page":"686-693","day":"23","type":"journal_article","intvolume":"        17","status":"public","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286295/"}],"year":"2014","doi":"10.1038/nn.3678","ec_funded":1,"title":"A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons","publist_id":"4733","volume":17,"oa":1,"date_updated":"2021-01-12T06:56:08Z","_id":"2228","publication_identifier":{"issn":["10976256"]},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","project":[{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548"},{"_id":"25C26B1E-B435-11E9-9278-68D0E5697425","name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF","grant_number":"P24909-B24"}],"quality_controlled":"1","publication_status":"published","citation":{"chicago":"Hu, Hua, and Peter M Jonas. “A Supercritical Density of Na^+ Channels Ensures Fast Signaling in GABAergic Interneuron Axons.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nn.3678\">https://doi.org/10.1038/nn.3678</a>.","apa":"Hu, H., &#38; Jonas, P. M. (2014). A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.3678\">https://doi.org/10.1038/nn.3678</a>","ieee":"H. Hu and P. M. Jonas, “A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons,” <i>Nature Neuroscience</i>, vol. 17, no. 5. Nature Publishing Group, pp. 686–693, 2014.","ista":"Hu H, Jonas PM. 2014. A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. Nature Neuroscience. 17(5), 686–693.","short":"H. Hu, P.M. Jonas, Nature Neuroscience 17 (2014) 686–693.","mla":"Hu, Hua, and Peter M. Jonas. “A Supercritical Density of Na^+ Channels Ensures Fast Signaling in GABAergic Interneuron Axons.” <i>Nature Neuroscience</i>, vol. 17, no. 5, Nature Publishing Group, 2014, pp. 686–93, doi:<a href=\"https://doi.org/10.1038/nn.3678\">10.1038/nn.3678</a>.","ama":"Hu H, Jonas PM. A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. <i>Nature Neuroscience</i>. 2014;17(5):686-693. doi:<a href=\"https://doi.org/10.1038/nn.3678\">10.1038/nn.3678</a>"},"abstract":[{"text":"Fast-spiking, parvalbumin-expressing GABAergic interneurons, a large proportion of which are basket cells (BCs), have a key role in feedforward and feedback inhibition, gamma oscillations and complex information processing. For these functions, fast propagation of action potentials (APs) from the soma to the presynaptic terminals is important. However, the functional properties of interneuron axons remain elusive. We examined interneuron axons by confocally targeted subcellular patch-clamp recording in rat hippocampal slices. APs were initiated in the proximal axon ∼20 μm from the soma and propagated to the distal axon with high reliability and speed. Subcellular mapping revealed a stepwise increase of Na^+ conductance density from the soma to the proximal axon, followed by a further gradual increase in the distal axon. Active cable modeling and experiments with partial channel block revealed that low axonal Na^+ conductance density was sufficient for reliability, but high Na^+ density was necessary for both speed of propagation and fast-spiking AP phenotype. Our results suggest that a supercritical density of Na^+ channels compensates for the morphological properties of interneuron axons (small segmental diameter, extensive branching and high bouton density), ensuring fast AP propagation and high-frequency repetitive firing.","lang":"eng"}],"author":[{"id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","first_name":"Hua","last_name":"Hu","full_name":"Hu, Hua"},{"first_name":"Peter M","full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}]},{"doi":"10.1126/science.1244811","year":"2014","ec_funded":1,"title":"Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617475/"}],"citation":{"chicago":"Vyleta, Nicholas, and Peter M Jonas. “Loose Coupling between Ca^2+ Channels and Release Sensors at a Plastic Hippocampal Synapse.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1244811\">https://doi.org/10.1126/science.1244811</a>.","ieee":"N. Vyleta and P. M. Jonas, “Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse,” <i>Science</i>, vol. 343, no. 6171. American Association for the Advancement of Science, pp. 665–670, 2014.","apa":"Vyleta, N., &#38; Jonas, P. M. (2014). Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1244811\">https://doi.org/10.1126/science.1244811</a>","short":"N. Vyleta, P.M. Jonas, Science 343 (2014) 665–670.","ista":"Vyleta N, Jonas PM. 2014. Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. Science. 343(6171), 665–670.","mla":"Vyleta, Nicholas, and Peter M. Jonas. “Loose Coupling between Ca^2+ Channels and Release Sensors at a Plastic Hippocampal Synapse.” <i>Science</i>, vol. 343, no. 6171, American Association for the Advancement of Science, 2014, pp. 665–70, doi:<a href=\"https://doi.org/10.1126/science.1244811\">10.1126/science.1244811</a>.","ama":"Vyleta N, Jonas PM. Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. <i>Science</i>. 2014;343(6171):665-670. doi:<a href=\"https://doi.org/10.1126/science.1244811\">10.1126/science.1244811</a>"},"publication_status":"published","abstract":[{"lang":"eng","text":"The distance between Ca^2+ channels and release sensors determines the speed and efficacy of synaptic transmission. Tight &quot;nanodomain&quot; channel-sensor coupling initiates transmitter release at synapses in the mature brain, whereas loose &quot;microdomain&quot; coupling appears restricted to early developmental stages. To probe the coupling configuration at a plastic synapse in the mature central nervous system, we performed paired recordings between mossy fiber terminals and CA3 pyramidal neurons in rat hippocampus. Millimolar concentrations of both the fast Ca^2+ chelator BAPTA [1,2-bis(2-aminophenoxy)ethane- N,N, N′,N′-tetraacetic acid] and the slow chelator EGTA efficiently suppressed transmitter release, indicating loose coupling between Ca^2+ channels and release sensors. Loose coupling enabled the control of initial release probability by fast endogenous Ca^2+ buffers and the generation of facilitation by buffer saturation. Thus, loose coupling provides the molecular framework for presynaptic plasticity."}],"author":[{"last_name":"Vyleta","full_name":"Vyleta, Nicholas","first_name":"Nicholas","id":"36C4978E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T06:56:09Z","publist_id":"4732","volume":343,"oa":1,"publication_identifier":{"issn":["00368075"]},"_id":"2229","quality_controlled":"1","project":[{"grant_number":"P24909-B24","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","name":"Mechanisms of transmitter release at GABAergic synapses"},{"grant_number":"268548","call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"02","date_published":"2014-02-01T00:00:00Z","scopus_import":1,"publisher":"American Association for the Advancement of Science","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"date_created":"2018-12-11T11:56:27Z","day":"01","type":"journal_article","intvolume":"       343","status":"public","publication":"Science","issue":"6171","page":"665 - 670"},{"abstract":[{"lang":"eng","text":"Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals."}],"author":[{"first_name":"José","full_name":"Guzmán, José","last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schlögl, Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schmidt Hieber","full_name":"Schmidt Hieber, Christoph","first_name":"Christoph"}],"citation":{"ista":"Guzmán J, Schlögl A, Schmidt Hieber C. 2014. Stimfit: Quantifying electrophysiological data with Python. Frontiers in Neuroinformatics. 8(FEB), 16.","short":"J. Guzmán, A. Schlögl, C. Schmidt Hieber, Frontiers in Neuroinformatics 8 (2014).","ama":"Guzmán J, Schlögl A, Schmidt Hieber C. Stimfit: Quantifying electrophysiological data with Python. <i>Frontiers in Neuroinformatics</i>. 2014;8(FEB). doi:<a href=\"https://doi.org/10.3389/fninf.2014.00016\">10.3389/fninf.2014.00016</a>","mla":"Guzmán, José, et al. “Stimfit: Quantifying Electrophysiological Data with Python.” <i>Frontiers in Neuroinformatics</i>, vol. 8, no. FEB, 16, Frontiers Research Foundation, 2014, doi:<a href=\"https://doi.org/10.3389/fninf.2014.00016\">10.3389/fninf.2014.00016</a>.","chicago":"Guzmán, José, Alois Schlögl, and Christoph Schmidt Hieber. “Stimfit: Quantifying Electrophysiological Data with Python.” <i>Frontiers in Neuroinformatics</i>. Frontiers Research Foundation, 2014. <a href=\"https://doi.org/10.3389/fninf.2014.00016\">https://doi.org/10.3389/fninf.2014.00016</a>.","ieee":"J. Guzmán, A. Schlögl, and C. Schmidt Hieber, “Stimfit: Quantifying electrophysiological data with Python,” <i>Frontiers in Neuroinformatics</i>, vol. 8, no. FEB. Frontiers Research Foundation, 2014.","apa":"Guzmán, J., Schlögl, A., &#38; Schmidt Hieber, C. (2014). Stimfit: Quantifying electrophysiological data with Python. <i>Frontiers in Neuroinformatics</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fninf.2014.00016\">https://doi.org/10.3389/fninf.2014.00016</a>"},"publication_status":"published","publication_identifier":{"issn":["16625196"]},"_id":"2230","oa_version":"Published Version","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":8,"date_updated":"2021-01-12T06:56:09Z","publist_id":"4731","oa":1,"title":"Stimfit: Quantifying electrophysiological data with Python","pubrep_id":"425","year":"2014","doi":"10.3389/fninf.2014.00016","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"16","intvolume":"         8","status":"public","day":"21","type":"journal_article","publication":"Frontiers in Neuroinformatics","issue":"FEB","file_date_updated":"2020-07-14T12:45:34Z","scopus_import":1,"publisher":"Frontiers Research Foundation","language":[{"iso":"eng"}],"month":"02","date_published":"2014-02-21T00:00:00Z","file":[{"creator":"system","file_id":"4935","relation":"main_file","content_type":"application/pdf","checksum":"eeca00bba7232ff7d27db83321f6ea30","date_created":"2018-12-12T10:12:17Z","file_size":2883372,"file_name":"IST-2016-425-v1+1_fninf-08-00016.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:34Z"}],"date_created":"2018-12-11T11:56:27Z","has_accepted_license":"1","department":[{"_id":"ScienComp"},{"_id":"PeJo"}]},{"day":"04","type":"journal_article","intvolume":"       106","status":"public","issue":"5","publication":"Biophysical Journal","page":"1194 - 1204","month":"03","date_published":"2014-03-04T00:00:00Z","publisher":"Biophysical Society","scopus_import":1,"language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"date_created":"2018-12-11T11:56:28Z","publication_status":"published","citation":{"apa":"Rieckh, G., &#38; Tkačik, G. (2014). Noise and information transmission in promoters with multiple internal states. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">https://doi.org/10.1016/j.bpj.2014.01.014</a>","ieee":"G. Rieckh and G. Tkačik, “Noise and information transmission in promoters with multiple internal states,” <i>Biophysical Journal</i>, vol. 106, no. 5. Biophysical Society, pp. 1194–1204, 2014.","chicago":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” <i>Biophysical Journal</i>. Biophysical Society, 2014. <a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">https://doi.org/10.1016/j.bpj.2014.01.014</a>.","mla":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” <i>Biophysical Journal</i>, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:<a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">10.1016/j.bpj.2014.01.014</a>.","ama":"Rieckh G, Tkačik G. Noise and information transmission in promoters with multiple internal states. <i>Biophysical Journal</i>. 2014;106(5):1194-1204. doi:<a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">10.1016/j.bpj.2014.01.014</a>","short":"G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.","ista":"Rieckh G, Tkačik G. 2014. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 106(5), 1194–1204."},"abstract":[{"text":"Based on the measurements of noise in gene expression performed during the past decade, it has become customary to think of gene regulation in terms of a two-state model, where the promoter of a gene can stochastically switch between an ON and an OFF state. As experiments are becoming increasingly precise and the deviations from the two-state model start to be observable, we ask about the experimental signatures of complex multistate promoters, as well as the functional consequences of this additional complexity. In detail, we i), extend the calculations for noise in gene expression to promoters described by state transition diagrams with multiple states, ii), systematically compute the experimentally accessible noise characteristics for these complex promoters, and iii), use information theory to evaluate the channel capacities of complex promoter architectures and compare them with the baseline provided by the two-state model. We find that adding internal states to the promoter generically decreases channel capacity, except in certain cases, three of which (cooperativity, dual-role regulation, promoter cycling) we analyze in detail.","lang":"eng"}],"author":[{"last_name":"Rieckh","full_name":"Rieckh, Georg","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","first_name":"Gasper"}],"publist_id":"4730","volume":106,"date_updated":"2021-01-12T06:56:10Z","oa":1,"pmid":1,"_id":"2231","publication_identifier":{"issn":["00063495"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","oa_version":"Submitted Version","doi":"10.1016/j.bpj.2014.01.014","year":"2014","external_id":{"pmid":["24606943"]},"title":"Noise and information transmission in promoters with multiple internal states","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026790/"}]},{"month":"02","date_published":"2014-02-01T00:00:00Z","article_type":"original","publisher":"IOP Publishing","language":[{"iso":"eng"}],"department":[{"_id":"BjHo"}],"date_created":"2018-12-11T11:56:28Z","day":"01","type":"journal_article","intvolume":"      2014","status":"public","issue":"2","publication":"Journal of Statistical Mechanics Theory and Experiment","year":"2014","doi":"10.1088/1742-5468/2014/02/P02001","title":"Deterministic and stochastic aspects of the transition to turbulence","external_id":{"arxiv":["1403.4516"]},"main_file_link":[{"url":"http://arxiv.org/abs/1403.4516","open_access":"1"}],"article_number":"P02001","publication_status":"published","citation":{"ama":"Song B, Hof B. Deterministic and stochastic aspects of the transition to turbulence. <i>Journal of Statistical Mechanics Theory and Experiment</i>. 2014;2014(2). doi:<a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">10.1088/1742-5468/2014/02/P02001</a>","mla":"Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of the Transition to Turbulence.” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2014, no. 2, P02001, IOP Publishing, 2014, doi:<a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">10.1088/1742-5468/2014/02/P02001</a>.","short":"B. Song, B. Hof, Journal of Statistical Mechanics Theory and Experiment 2014 (2014).","ista":"Song B, Hof B. 2014. Deterministic and stochastic aspects of the transition to turbulence. Journal of Statistical Mechanics Theory and Experiment. 2014(2), P02001.","ieee":"B. Song and B. Hof, “Deterministic and stochastic aspects of the transition to turbulence,” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2014, no. 2. IOP Publishing, 2014.","apa":"Song, B., &#38; Hof, B. (2014). Deterministic and stochastic aspects of the transition to turbulence. <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">https://doi.org/10.1088/1742-5468/2014/02/P02001</a>","chicago":"Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of the Transition to Turbulence.” <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing, 2014. <a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">https://doi.org/10.1088/1742-5468/2014/02/P02001</a>."},"abstract":[{"text":"The purpose of this contribution is to summarize and discuss recent advances regarding the onset of turbulence in shear flows. The absence of a clear-cut instability mechanism, the spatio-temporal intermittent character and extremely long lived transients are some of the major difficulties encountered in these flows and have hindered progress towards understanding the transition process. We will show for the case of pipe flow that concepts from nonlinear dynamics and statistical physics can help to explain the onset of turbulence. In particular, the turbulent structures (puffs) observed close to onset are spatially localized chaotic transients and their lifetimes increase super-exponentially with Reynolds number. At the same time fluctuations of individual turbulent puffs can (although very rarely) lead to the nucleation of new puffs. The competition between these two stochastic processes gives rise to a non-equilibrium phase transition where turbulence changes from a super-transient to a sustained state.","lang":"eng"}],"author":[{"first_name":"Baofang","last_name":"Song","full_name":"Song, Baofang","id":"a79e57f5-e8a5-11ec-9dc9-83fb8c81cf72"},{"first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"arxiv":1,"publist_id":"4729","oa":1,"volume":2014,"date_updated":"2022-06-10T10:13:15Z","article_processing_charge":"No","_id":"2232","publication_identifier":{"issn":["17425468"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","quality_controlled":"1"},{"file_date_updated":"2020-07-14T12:45:34Z","issue":"1","publication":"Logical Methods in Computer Science","type":"journal_article","day":"13","status":"public","intvolume":"        10","department":[{"_id":"ToHe"}],"has_accepted_license":"1","date_created":"2018-12-11T11:56:28Z","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:45:34Z","checksum":"9f6ea2e2d8d4a32ff0becc29d835bbf8","date_created":"2018-12-12T10:07:45Z","file_size":550936,"file_name":"IST-2015-389-v1+1_1401.3957.pdf","file_id":"4643","creator":"system","relation":"main_file","content_type":"application/pdf"}],"date_published":"2014-02-13T00:00:00Z","month":"02","language":[{"iso":"eng"}],"publisher":"International Federation of Computational Logic","scopus_import":1,"volume":10,"publist_id":"4728","oa":1,"date_updated":"2021-01-12T06:56:11Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"quality_controlled":"1","oa_version":"Published Version","_id":"2233","publication_identifier":{"issn":["18605974"]},"publication_status":"published","citation":{"apa":"Boker, U., &#38; Henzinger, T. A. (2014). Exact and approximate determinization of discounted-sum automata. <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic. <a href=\"https://doi.org/10.2168/LMCS-10(1:10)2014\">https://doi.org/10.2168/LMCS-10(1:10)2014</a>","ieee":"U. Boker and T. A. Henzinger, “Exact and approximate determinization of discounted-sum automata,” <i>Logical Methods in Computer Science</i>, vol. 10, no. 1. International Federation of Computational Logic, 2014.","chicago":"Boker, Udi, and Thomas A Henzinger. “Exact and Approximate Determinization of Discounted-Sum Automata.” <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic, 2014. <a href=\"https://doi.org/10.2168/LMCS-10(1:10)2014\">https://doi.org/10.2168/LMCS-10(1:10)2014</a>.","ama":"Boker U, Henzinger TA. Exact and approximate determinization of discounted-sum automata. <i>Logical Methods in Computer Science</i>. 2014;10(1). doi:<a href=\"https://doi.org/10.2168/LMCS-10(1:10)2014\">10.2168/LMCS-10(1:10)2014</a>","mla":"Boker, Udi, and Thomas A. Henzinger. “Exact and Approximate Determinization of Discounted-Sum Automata.” <i>Logical Methods in Computer Science</i>, vol. 10, no. 1, International Federation of Computational Logic, 2014, doi:<a href=\"https://doi.org/10.2168/LMCS-10(1:10)2014\">10.2168/LMCS-10(1:10)2014</a>.","short":"U. Boker, T.A. Henzinger, Logical Methods in Computer Science 10 (2014).","ista":"Boker U, Henzinger TA. 2014. Exact and approximate determinization of discounted-sum automata. Logical Methods in Computer Science. 10(1)."},"author":[{"last_name":"Boker","full_name":"Boker, Udi","first_name":"Udi"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A"}],"abstract":[{"text":" A discounted-sum automaton (NDA) is a nondeterministic finite automaton with edge weights, valuing a run by the discounted sum of visited edge weights. More precisely, the weight in the i-th position of the run is divided by λi, where the discount factor λ is a fixed rational number greater than 1. The value of a word is the minimal value of the automaton runs on it. Discounted summation is a common and useful measuring scheme, especially for infinite sequences, reflecting the assumption that earlier weights are more important than later weights. Unfortunately, determinization of NDAs, which is often essential in formal verification, is, in general, not possible. We provide positive news, showing that every NDA with an integral discount factor is determinizable. We complete the picture by proving that the integers characterize exactly the discount factors that guarantee determinizability: for every nonintegral rational discount factor λ, there is a nondeterminizable λ-NDA. We also prove that the class of NDAs with integral discount factors enjoys closure under the algebraic operations min, max, addition, and subtraction, which is not the case for general NDAs nor for deterministic NDAs. For general NDAs, we look into approximate determinization, which is always possible as the influence of a word's suffix decays. We show that the naive approach, of unfolding the automaton computations up to a sufficient level, is doubly exponential in the discount factor. We provide an alternative construction for approximate determinization, which is singly exponential in the discount factor, in the precision, and in the number of states. We also prove matching lower bounds, showing that the exponential dependency on each of these three parameters cannot be avoided. All our results hold equally for automata over finite words and for automata over infinite words. ","lang":"eng"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"ec_funded":1,"doi":"10.2168/LMCS-10(1:10)2014","year":"2014","pubrep_id":"389","title":"Exact and approximate determinization of discounted-sum automata"},{"pubrep_id":"428","title":"Markov decision processes with multiple long-run average objectives","ec_funded":1,"year":"2014","doi":"10.2168/LMCS-10(1:13)2014","ddc":["000"],"main_file_link":[{"open_access":"1","url":"http://repository.ist.ac.at/id/eprint/428"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"author":[{"last_name":"Brázdil","full_name":"Brázdil, Tomáš","first_name":"Tomáš"},{"full_name":"Brožek, Václav","last_name":"Brožek","first_name":"Václav"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Forejt","full_name":"Forejt, Vojtěch","first_name":"Vojtěch"},{"first_name":"Antonín","full_name":"Kučera, Antonín","last_name":"Kučera"}],"abstract":[{"lang":"eng","text":"We study Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) functions. We consider two different objectives, namely, expectation and satisfaction objectives. Given an MDP with κ limit-average functions, in the expectation objective the goal is to maximize the expected limit-average value, and in the satisfaction objective the goal is to maximize the probability of runs such that the limit-average value stays above a given vector. We show that under the expectation objective, in contrast to the case of one limit-average function, both randomization and memory are necessary for strategies even for ε-approximation, and that finite-memory randomized strategies are sufficient for achieving Pareto optimal values. Under the satisfaction objective, in contrast to the case of one limit-average function, infinite memory is necessary for strategies achieving a specific value (i.e. randomized finite-memory strategies are not sufficient), whereas memoryless randomized strategies are sufficient for ε-approximation, for all ε &gt; 0. We further prove that the decision problems for both expectation and satisfaction objectives can be solved in polynomial time and the trade-off curve (Pareto curve) can be ε-approximated in time polynomial in the size of the MDP and 1/ε, and exponential in the number of limit-average functions, for all ε &gt; 0. Our analysis also reveals flaws in previous work for MDPs with multiple mean-payoff functions under the expectation objective, corrects the flaws, and allows us to obtain improved results."}],"publication_status":"published","citation":{"short":"T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, A. Kučera, Logical Methods in Computer Science 10 (2014).","ista":"Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. 2014. Markov decision processes with multiple long-run average objectives. Logical Methods in Computer Science. 10(1).","mla":"Brázdil, Tomáš, et al. “Markov Decision Processes with Multiple Long-Run Average Objectives.” <i>Logical Methods in Computer Science</i>, vol. 10, no. 1, International Federation of Computational Logic, 2014, doi:<a href=\"https://doi.org/10.2168/LMCS-10(1:13)2014\">10.2168/LMCS-10(1:13)2014</a>.","ama":"Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. Markov decision processes with multiple long-run average objectives. <i>Logical Methods in Computer Science</i>. 2014;10(1). doi:<a href=\"https://doi.org/10.2168/LMCS-10(1:13)2014\">10.2168/LMCS-10(1:13)2014</a>","chicago":"Brázdil, Tomáš, Václav Brožek, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Markov Decision Processes with Multiple Long-Run Average Objectives.” <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic, 2014. <a href=\"https://doi.org/10.2168/LMCS-10(1:13)2014\">https://doi.org/10.2168/LMCS-10(1:13)2014</a>.","apa":"Brázdil, T., Brožek, V., Chatterjee, K., Forejt, V., &#38; Kučera, A. (2014). Markov decision processes with multiple long-run average objectives. <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic. <a href=\"https://doi.org/10.2168/LMCS-10(1:13)2014\">https://doi.org/10.2168/LMCS-10(1:13)2014</a>","ieee":"T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, and A. Kučera, “Markov decision processes with multiple long-run average objectives,” <i>Logical Methods in Computer Science</i>, vol. 10, no. 1. International Federation of Computational Logic, 2014."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"_id":"2234","publication_identifier":{"issn":["18605974"]},"date_updated":"2021-01-12T06:56:11Z","publist_id":"4727","oa":1,"volume":10,"language":[{"iso":"eng"}],"publisher":"International Federation of Computational Logic","scopus_import":1,"date_published":"2014-02-14T00:00:00Z","month":"02","file":[{"file_id":"4656","creator":"system","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:07:57Z","checksum":"803edcc2d8c1acfba44a9ec43a5eb9f0","file_name":"IST-2016-428-v1+1_1104.3489.pdf","file_size":375388,"date_updated":"2020-07-14T12:45:34Z","access_level":"open_access"}],"date_created":"2018-12-11T11:56:29Z","department":[{"_id":"KrCh"}],"has_accepted_license":"1","status":"public","intvolume":"        10","type":"journal_article","day":"14","file_date_updated":"2020-07-14T12:45:34Z","issue":"1","publication":"Logical Methods in Computer Science"},{"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985068/","open_access":"1"}],"year":"2014","doi":"10.1038/nature12977","title":"Disease associations between honeybees and bumblebees as a threat to wild pollinators","oa":1,"date_updated":"2021-01-12T06:56:11Z","publist_id":"4726","volume":506,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","quality_controlled":"1","_id":"2235","publication_identifier":{"issn":["00280836"]},"publication_status":"published","citation":{"ista":"Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. 2014. Disease associations between honeybees and bumblebees as a threat to wild pollinators. Nature. 506(7488), 364–366.","short":"M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, M. Brown, Nature 506 (2014) 364–366.","mla":"Fürst, Matthias, et al. “Disease Associations between Honeybees and Bumblebees as a Threat to Wild Pollinators.” <i>Nature</i>, vol. 506, no. 7488, Nature Publishing Group, 2014, pp. 364–66, doi:<a href=\"https://doi.org/10.1038/nature12977\">10.1038/nature12977</a>.","ama":"Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. Disease associations between honeybees and bumblebees as a threat to wild pollinators. <i>Nature</i>. 2014;506(7488):364-366. doi:<a href=\"https://doi.org/10.1038/nature12977\">10.1038/nature12977</a>","chicago":"Fürst, Matthias, Dino Mcmahon, Juliet Osborne, Robert Paxton, and Mark Brown. “Disease Associations between Honeybees and Bumblebees as a Threat to Wild Pollinators.” <i>Nature</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nature12977\">https://doi.org/10.1038/nature12977</a>.","apa":"Fürst, M., Mcmahon, D., Osborne, J., Paxton, R., &#38; Brown, M. (2014). Disease associations between honeybees and bumblebees as a threat to wild pollinators. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature12977\">https://doi.org/10.1038/nature12977</a>","ieee":"M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, and M. Brown, “Disease associations between honeybees and bumblebees as a threat to wild pollinators,” <i>Nature</i>, vol. 506, no. 7488. Nature Publishing Group, pp. 364–366, 2014."},"author":[{"first_name":"Matthias","last_name":"Fürst","full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dino","full_name":"Mcmahon, Dino","last_name":"Mcmahon"},{"first_name":"Juliet","full_name":"Osborne, Juliet","last_name":"Osborne"},{"full_name":"Paxton, Robert","last_name":"Paxton","first_name":"Robert"},{"first_name":"Mark","last_name":"Brown","full_name":"Brown, Mark"}],"abstract":[{"lang":"eng","text":"Emerging infectious diseases (EIDs) pose a risk to human welfare, both directly and indirectly, by affecting managed livestock and wildlife that provide valuable resources and ecosystem services, such as the pollination of crops. Honeybees (Apis mellifera), the prevailing managed insect crop pollinator, suffer from a range of emerging and exotic high-impact pathogens, and population maintenance requires active management by beekeepers to control them. Wild pollinators such as bumblebees (Bombus spp.) are in global decline, one cause of which may be pathogen spillover from managed pollinators like honeybees or commercial colonies of bumblebees. Here we use a combination of infection experiments and landscape-scale field data to show that honeybee EIDs are indeed widespread infectious agents within the pollinator assemblage. The prevalence of deformed wing virus (DWV) and the exotic parasite Nosema ceranae in honeybees and bumblebees is linked; as honeybees have higher DWV prevalence, and sympatric bumblebees and honeybees are infected by the same DWV strains, Apis is the likely source of at least one major EID in wild pollinators. Lessons learned from vertebrates highlight the need for increased pathogen control in managed bee species to maintain wild pollinators, as declines in native pollinators may be caused by interspecies pathogen transmission originating from managed pollinators."}],"department":[{"_id":"SyCr"}],"date_created":"2018-12-11T11:56:29Z","date_published":"2014-02-20T00:00:00Z","month":"02","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","scopus_import":1,"page":"364 - 366","issue":"7488","publication":"Nature","type":"journal_article","day":"20","status":"public","intvolume":"       506"}]