[{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"ToHe"}],"author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Samanta","full_name":"Samanta, Roopsha","first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87"}],"conference":{"name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","end_date":"2014-12-17","location":"Delhi, India","start_date":"2014-12-15"},"year":"2014","oa_version":"Published Version","doi":"10.4230/LIPIcs.FSTTCS.2014.431","day":"01","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","publication_status":"published","abstract":[{"text":"We investigate the problem of checking if a finite-state transducer is robust to uncertainty in its input. Our notion of robustness is based on the analytic notion of Lipschitz continuity - a transducer is K-(Lipschitz) robust if the perturbation in its output is at most K times the perturbation in its input. We quantify input and output perturbation using similarity functions. We show that K-robustness is undecidable even for deterministic transducers. We identify a class of functional transducers, which admits a polynomial time automata-theoretic decision procedure for K-robustness. This class includes Mealy machines and functional letter-to-letter transducers. We also study K-robustness of nondeterministic transducers. Since a nondeterministic transducer generates a set of output words for each input word, we quantify output perturbation using setsimilarity functions. We show that K-robustness of nondeterministic transducers is undecidable, even for letter-to-letter transducers. We identify a class of set-similarity functions which admit decidable K-robustness of letter-to-letter transducers.","lang":"eng"}],"publist_id":"5227","quality_controlled":"1","citation":{"apa":"Henzinger, T. A., Otop, J., &#38; Samanta, R. (2014). Lipschitz robustness of finite-state transducers. In <i>Leibniz International Proceedings in Informatics, LIPIcs</i> (Vol. 29, pp. 431–443). Delhi, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431\">https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431</a>","short":"T.A. Henzinger, J. Otop, R. Samanta, in:, Leibniz International Proceedings in Informatics, LIPIcs, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–443.","ieee":"T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of finite-state transducers,” in <i>Leibniz International Proceedings in Informatics, LIPIcs</i>, Delhi, India, 2014, vol. 29, pp. 431–443.","ama":"Henzinger TA, Otop J, Samanta R. Lipschitz robustness of finite-state transducers. In: <i>Leibniz International Proceedings in Informatics, LIPIcs</i>. Vol 29. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:431-443. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431\">10.4230/LIPIcs.FSTTCS.2014.431</a>","chicago":"Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness of Finite-State Transducers.” In <i>Leibniz International Proceedings in Informatics, LIPIcs</i>, 29:431–43. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431\">https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431</a>.","mla":"Henzinger, Thomas A., et al. “Lipschitz Robustness of Finite-State Transducers.” <i>Leibniz International Proceedings in Informatics, LIPIcs</i>, vol. 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–43, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431\">10.4230/LIPIcs.FSTTCS.2014.431</a>.","ista":"Henzinger TA, Otop J, Samanta R. 2014. Lipschitz robustness of finite-state transducers. Leibniz International Proceedings in Informatics, LIPIcs. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 29, 431–443."},"type":"conference","file":[{"relation":"main_file","checksum":"7b1aff1710a8bffb7080ec07f62d9a17","date_updated":"2020-07-14T12:45:19Z","content_type":"application/pdf","file_size":562151,"file_name":"IST-2017-804-v1+1_37.pdf","access_level":"open_access","file_id":"4734","date_created":"2018-12-12T10:09:11Z","creator":"system"}],"ddc":["004"],"month":"12","title":"Lipschitz robustness of finite-state transducers","date_updated":"2021-01-12T06:53:45Z","date_published":"2014-12-01T00:00:00Z","page":"431 - 443","file_date_updated":"2020-07-14T12:45:19Z","pubrep_id":"804","publication":"Leibniz International Proceedings in Informatics, LIPIcs","date_created":"2018-12-11T11:54:27Z","_id":"1870","volume":29,"alternative_title":["LIPIcs"],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"        29","license":"https://creativecommons.org/licenses/by/4.0/"},{"ec_funded":1,"date_published":"2014-01-01T00:00:00Z","month":"01","date_updated":"2021-01-12T06:53:45Z","title":"Extensional crisis and proving identity","date_created":"2018-12-11T11:54:28Z","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"}],"_id":"1872","page":"185 - 200","file_date_updated":"2020-07-14T12:45:19Z","pubrep_id":"641","publication":"ATVA 2014","acknowledgement":"This research was supported in part by the Austrian National Research Network RiSE (S11410-N23).","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"      8837","volume":8837,"alternative_title":["LNCS"],"scopus_import":1,"editor":[{"first_name":"Franck","last_name":"Cassez","full_name":"Cassez, Franck"},{"first_name":"Jean-François","full_name":"Raskin, Jean-François","last_name":"Raskin"}],"author":[{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kovács","full_name":"Kovács, Laura","first_name":"Laura"},{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl"},{"first_name":"Andrei","full_name":"Voronkov, Andrei","last_name":"Voronkov"}],"year":"2014","conference":{"end_date":"2014-11-07","location":"Sydney, Australia","start_date":"2014-11-03","name":"ATVA: Automated Technology for Verification and Analysis"},"department":[{"_id":"ToHe"}],"day":"01","publisher":"Springer","oa_version":"Submitted Version","doi":"10.1007/978-3-319-11936-6_14","quality_controlled":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","publication_status":"published","abstract":[{"text":"Extensionality axioms are common when reasoning about data collections, such as arrays and functions in program analysis, or sets in mathematics. An extensionality axiom asserts that two collections are equal if they consist of the same elements at the same indices. Using extensionality is often required to show that two collections are equal. A typical example is the set theory theorem (∀x)(∀y)x∪y = y ∪x. Interestingly, while humans have no problem with proving such set identities using extensionality, they are very hard for superposition theorem provers because of the calculi they use. In this paper we show how addition of a new inference rule, called extensionality resolution, allows first-order theorem provers to easily solve problems no modern first-order theorem prover can solve. We illustrate this by running the VAMPIRE theorem prover with extensionality resolution on a number of set theory and array problems. Extensionality resolution helps VAMPIRE to solve problems from the TPTP library of first-order problems that were never solved before by any prover.","lang":"eng"}],"publist_id":"5226","ddc":["000"],"citation":{"mla":"Gupta, Ashutosh, et al. “Extensional Crisis and Proving Identity.” <i>ATVA 2014</i>, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 185–200, doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_14\">10.1007/978-3-319-11936-6_14</a>.","ista":"Gupta A, Kovács L, Kragl B, Voronkov A. 2014. Extensional crisis and proving identity. ATVA 2014. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 185–200.","ama":"Gupta A, Kovács L, Kragl B, Voronkov A. Extensional crisis and proving identity. In: Cassez F, Raskin J-F, eds. <i>ATVA 2014</i>. Vol 8837. Springer; 2014:185-200. doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_14\">10.1007/978-3-319-11936-6_14</a>","chicago":"Gupta, Ashutosh, Laura Kovács, Bernhard Kragl, and Andrei Voronkov. “Extensional Crisis and Proving Identity.” In <i>ATVA 2014</i>, edited by Franck Cassez and Jean-François Raskin, 8837:185–200. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_14\">https://doi.org/10.1007/978-3-319-11936-6_14</a>.","ieee":"A. Gupta, L. Kovács, B. Kragl, and A. Voronkov, “Extensional crisis and proving identity,” in <i>ATVA 2014</i>, Sydney, Australia, 2014, vol. 8837, pp. 185–200.","short":"A. Gupta, L. Kovács, B. Kragl, A. Voronkov, in:, F. Cassez, J.-F. Raskin (Eds.), ATVA 2014, Springer, 2014, pp. 185–200.","apa":"Gupta, A., Kovács, L., Kragl, B., &#38; Voronkov, A. (2014). Extensional crisis and proving identity. In F. Cassez &#38; J.-F. Raskin (Eds.), <i>ATVA 2014</i> (Vol. 8837, pp. 185–200). Sydney, Australia: Springer. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_14\">https://doi.org/10.1007/978-3-319-11936-6_14</a>"},"type":"conference","file":[{"file_size":244294,"date_updated":"2020-07-14T12:45:19Z","content_type":"application/pdf","checksum":"af4bd3fc1f4c93075e4dc5cbf625fe7b","relation":"main_file","access_level":"open_access","file_name":"IST-2016-641-v1+1_atva2014.pdf","file_id":"4801","date_created":"2018-12-12T10:10:15Z","creator":"system"}]},{"oa_version":"Submitted Version","doi":"10.1007/978-3-319-10936-7_17","day":"01","publisher":"Springer","department":[{"_id":"ToHe"}],"editor":[{"full_name":"Müller-Olm, Markus","last_name":"Müller-Olm","first_name":"Markus"},{"first_name":"Helmut","last_name":"Seidl","full_name":"Seidl, Helmut"}],"author":[{"full_name":"Samanta, Roopsha","last_name":"Samanta","first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Oswaldo","last_name":"Olivo","full_name":"Olivo, Oswaldo"},{"full_name":"Allen, Emerson","last_name":"Allen","first_name":"Emerson"}],"year":"2014","conference":{"end_date":"2014-09-14","location":"Munich, Germany","start_date":"2014-09-11","name":"SAS: Static Analysis Symposium"},"type":"conference","citation":{"mla":"Samanta, Roopsha, et al. <i>Cost-Aware Automatic Program Repair</i>. Edited by Markus Müller-Olm and Helmut Seidl, vol. 8723, Springer, 2014, pp. 268–84, doi:<a href=\"https://doi.org/10.1007/978-3-319-10936-7_17\">10.1007/978-3-319-10936-7_17</a>.","ista":"Samanta R, Olivo O, Allen E. 2014. Cost-aware automatic program repair. SAS: Static Analysis Symposium, LNCS, vol. 8723, 268–284.","ama":"Samanta R, Olivo O, Allen E. Cost-aware automatic program repair. In: Müller-Olm M, Seidl H, eds. Vol 8723. Springer; 2014:268-284. doi:<a href=\"https://doi.org/10.1007/978-3-319-10936-7_17\">10.1007/978-3-319-10936-7_17</a>","chicago":"Samanta, Roopsha, Oswaldo Olivo, and Emerson Allen. “Cost-Aware Automatic Program Repair.” edited by Markus Müller-Olm and Helmut Seidl, 8723:268–84. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-10936-7_17\">https://doi.org/10.1007/978-3-319-10936-7_17</a>.","ieee":"R. Samanta, O. Olivo, and E. Allen, “Cost-aware automatic program repair,” presented at the SAS: Static Analysis Symposium, Munich, Germany, 2014, vol. 8723, pp. 268–284.","apa":"Samanta, R., Olivo, O., &#38; Allen, E. (2014). Cost-aware automatic program repair. In M. Müller-Olm &#38; H. Seidl (Eds.) (Vol. 8723, pp. 268–284). Presented at the SAS: Static Analysis Symposium, Munich, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-319-10936-7_17\">https://doi.org/10.1007/978-3-319-10936-7_17</a>","short":"R. Samanta, O. Olivo, E. Allen, in:, M. Müller-Olm, H. Seidl (Eds.), Springer, 2014, pp. 268–284."},"file":[{"creator":"system","date_created":"2018-12-12T10:07:51Z","file_id":"4650","access_level":"open_access","file_name":"IST-2014-313-v1+1_SOE.SAS14.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:19Z","file_size":409485,"checksum":"78ec4ea1bdecc676cd3e8cad35c6182c","relation":"main_file"}],"ddc":["000","005"],"language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"We present a formal framework for repairing infinite-state, imperative, sequential programs, with (possibly recursive) procedures and multiple assertions; the framework can generate repaired programs by modifying the original erroneous program in multiple program locations, and can ensure the readability of the repaired program using user-defined expression templates; the framework also generates a set of inductive assertions that serve as a proof of correctness of the repaired program. As a step toward integrating programmer intent and intuition in automated program repair, we present a cost-aware formulation - given a cost function associated with permissible statement modifications, the goal is to ensure that the total program modification cost does not exceed a given repair budget. As part of our predicate abstractionbased solution framework, we present a sound and complete algorithm for repair of Boolean programs. We have developed a prototype tool based on SMT solving and used it successfully to repair diverse errors in benchmark C programs."}],"publist_id":"5221","quality_controlled":"1","page":"268 - 284","file_date_updated":"2020-07-14T12:45:19Z","pubrep_id":"313","date_created":"2018-12-11T11:54:29Z","_id":"1875","month":"09","title":"Cost-aware automatic program repair","date_updated":"2021-01-12T06:53:46Z","date_published":"2014-09-01T00:00:00Z","scopus_import":1,"volume":8723,"alternative_title":["LNCS"],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":"      8723","oa":1},{"month":"07","title":"Functionals on triangulations of delaunay sets","date_updated":"2022-03-03T11:47:09Z","date_published":"2014-07-01T00:00:00Z","article_processing_charge":"No","page":"491 - 504","publication":"Moscow Mathematical Journal","date_created":"2018-12-11T11:54:29Z","external_id":{"arxiv":["1211.7053"]},"_id":"1876","volume":14,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1211.7053"}],"issue":"3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"        14","scopus_import":"1","department":[{"_id":"HeEd"}],"publication_identifier":{"issn":["16093321"]},"author":[{"last_name":"Dolbilin","full_name":"Dolbilin, Nikolai","first_name":"Nikolai"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"last_name":"Glazyrin","full_name":"Glazyrin, Alexey","first_name":"Alexey"},{"full_name":"Musin, Oleg","last_name":"Musin","first_name":"Oleg"}],"year":"2014","oa_version":"Submitted Version","arxiv":1,"doi":"10.17323/1609-4514-2014-14-3-491-504","day":"01","publisher":"Independent University of Moscow","language":[{"iso":"eng"}],"status":"public","abstract":[{"text":"We study densities of functionals over uniformly bounded triangulations of a Delaunay set of vertices, and prove that the minimum is attained for the Delaunay triangulation if this is the case for finite sets.","lang":"eng"}],"publication_status":"published","publist_id":"5220","quality_controlled":"1","type":"journal_article","citation":{"ama":"Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. Functionals on triangulations of delaunay sets. <i>Moscow Mathematical Journal</i>. 2014;14(3):491-504. doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-3-491-504\">10.17323/1609-4514-2014-14-3-491-504</a>","chicago":"Dolbilin, Nikolai, Herbert Edelsbrunner, Alexey Glazyrin, and Oleg Musin. “Functionals on Triangulations of Delaunay Sets.” <i>Moscow Mathematical Journal</i>. Independent University of Moscow, 2014. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-3-491-504\">https://doi.org/10.17323/1609-4514-2014-14-3-491-504</a>.","mla":"Dolbilin, Nikolai, et al. “Functionals on Triangulations of Delaunay Sets.” <i>Moscow Mathematical Journal</i>, vol. 14, no. 3, Independent University of Moscow, 2014, pp. 491–504, doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-3-491-504\">10.17323/1609-4514-2014-14-3-491-504</a>.","ista":"Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. 2014. Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. 14(3), 491–504.","short":"N. Dolbilin, H. Edelsbrunner, A. Glazyrin, O. Musin, Moscow Mathematical Journal 14 (2014) 491–504.","apa":"Dolbilin, N., Edelsbrunner, H., Glazyrin, A., &#38; Musin, O. (2014). Functionals on triangulations of delaunay sets. <i>Moscow Mathematical Journal</i>. Independent University of Moscow. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-3-491-504\">https://doi.org/10.17323/1609-4514-2014-14-3-491-504</a>","ieee":"N. Dolbilin, H. Edelsbrunner, A. Glazyrin, and O. Musin, “Functionals on triangulations of delaunay sets,” <i>Moscow Mathematical Journal</i>, vol. 14, no. 3. Independent University of Moscow, pp. 491–504, 2014."},"article_type":"original"},{"page":"441 - 442","oa_version":"None","publication":"Nature","doi":"10.1038/514441a","day":"23","date_created":"2018-12-11T11:54:30Z","publisher":"Springer Nature","_id":"1877","month":"10","department":[{"_id":"MiSi"}],"title":"Physiology: Relax and come in","date_updated":"2021-01-12T06:53:47Z","year":"2014","date_published":"2014-10-23T00:00:00Z","author":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari","last_name":"Vaahtomeri"}],"scopus_import":1,"citation":{"apa":"Sixt, M. K., &#38; Vaahtomeri, K. (2014). Physiology: Relax and come in. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/514441a\">https://doi.org/10.1038/514441a</a>","short":"M.K. Sixt, K. Vaahtomeri, Nature 514 (2014) 441–442.","ieee":"M. K. Sixt and K. Vaahtomeri, “Physiology: Relax and come in,” <i>Nature</i>, vol. 514, no. 7523. Springer Nature, pp. 441–442, 2014.","chicago":"Sixt, Michael K, and Kari Vaahtomeri. “Physiology: Relax and Come In.” <i>Nature</i>. Springer Nature, 2014. <a href=\"https://doi.org/10.1038/514441a\">https://doi.org/10.1038/514441a</a>.","ama":"Sixt MK, Vaahtomeri K. Physiology: Relax and come in. <i>Nature</i>. 2014;514(7523):441-442. doi:<a href=\"https://doi.org/10.1038/514441a\">10.1038/514441a</a>","mla":"Sixt, Michael K., and Kari Vaahtomeri. “Physiology: Relax and Come In.” <i>Nature</i>, vol. 514, no. 7523, Springer Nature, 2014, pp. 441–42, doi:<a href=\"https://doi.org/10.1038/514441a\">10.1038/514441a</a>.","ista":"Sixt MK, Vaahtomeri K. 2014. Physiology: Relax and come in. Nature. 514(7523), 441–442."},"type":"journal_article","article_type":"letter_note","status":"public","language":[{"iso":"eng"}],"publist_id":"5219","publication_status":"published","volume":514,"abstract":[{"text":"During inflammation, lymph nodes swell with an influx of immune cells. New findings identify a signalling pathway that induces relaxation in the contractile cells that give structure to these organs.","lang":"eng"}],"intvolume":"       514","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"7523","quality_controlled":"1"},{"month":"12","department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T06:53:50Z","title":"Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples","year":"2014","date_published":"2014-12-04T00:00:00Z","author":[{"first_name":"Dan","full_name":"Landau, Dan","last_name":"Landau"},{"first_name":"Chip","full_name":"Stewart, Chip","last_name":"Stewart"},{"first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","last_name":"Reiter"},{"first_name":"Michael","last_name":"Lawrence","full_name":"Lawrence, Michael"},{"first_name":"Carrie","last_name":"Sougnez","full_name":"Sougnez, Carrie"},{"last_name":"Brown","full_name":"Brown, Jennifer","first_name":"Jennifer"},{"last_name":"Lopez Guillermo","full_name":"Lopez Guillermo, Armando","first_name":"Armando"},{"last_name":"Gabriel","full_name":"Gabriel, Stacey","first_name":"Stacey"},{"full_name":"Lander, Eric","last_name":"Lander","first_name":"Eric"},{"first_name":"Donna","last_name":"Neuberg","full_name":"Neuberg, Donna"},{"last_name":"López Otín","full_name":"López Otín, Carlos","first_name":"Carlos"},{"first_name":"Elias","last_name":"Campo","full_name":"Campo, Elias"},{"first_name":"Gad","full_name":"Getz, Gad","last_name":"Getz"},{"first_name":"Catherine","last_name":"Wu","full_name":"Wu, Catherine"}],"page":"1952 - 1952","oa_version":"None","publication":"Blood","day":"04","date_created":"2018-12-11T11:54:32Z","_id":"1884","publisher":"American Society of Hematology","status":"public","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://www.bloodjournal.org/content/124/21/1952?sso-checked=true"}],"publist_id":"5211","publication_status":"published","abstract":[{"lang":"eng","text":"Unbiased high-throughput massively parallel sequencing methods have transformed the process of discovery of novel putative driver gene mutations in cancer. In chronic lymphocytic leukemia (CLL), these methods have yielded several unexpected findings, including the driver genes SF3B1, NOTCH1 and POT1. Recent analysis, utilizing down-sampling of existing datasets, has shown that the discovery process of putative drivers is far from complete across cancer. In CLL, while driver gene mutations affecting >10% of patients were efficiently discovered with previously published CLL cohorts of up to 160 samples subjected to whole exome sequencing (WES), this sample size has only 0.78 power to detect drivers affecting 5% of patients, and only 0.12 power for drivers affecting 2% of patients. These calculations emphasize the need to apply unbiased WES to larger patient cohorts."}],"volume":124,"intvolume":"       124","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","issue":"21","citation":{"short":"D. Landau, C. Stewart, J. Reiter, M. Lawrence, C. Sougnez, J. Brown, A. Lopez Guillermo, S. Gabriel, E. Lander, D. Neuberg, C. López Otín, E. Campo, G. Getz, C. Wu, Blood 124 (2014) 1952–1952.","apa":"Landau, D., Stewart, C., Reiter, J., Lawrence, M., Sougnez, C., Brown, J., … Wu, C. (2014). Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. <i>Blood</i>. American Society of Hematology.","ieee":"D. Landau <i>et al.</i>, “Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples,” <i>Blood</i>, vol. 124, no. 21. American Society of Hematology, pp. 1952–1952, 2014.","chicago":"Landau, Dan, Chip Stewart, Johannes Reiter, Michael Lawrence, Carrie Sougnez, Jennifer Brown, Armando Lopez Guillermo, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” <i>Blood</i>. American Society of Hematology, 2014.","ama":"Landau D, Stewart C, Reiter J, et al. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. <i>Blood</i>. 2014;124(21):1952-1952.","mla":"Landau, Dan, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” <i>Blood</i>, vol. 124, no. 21, American Society of Hematology, 2014, pp. 1952–1952.","ista":"Landau D, Stewart C, Reiter J, Lawrence M, Sougnez C, Brown J, Lopez Guillermo A, Gabriel S, Lander E, Neuberg D, López Otín C, Campo E, Getz G, Wu C. 2014. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. 124(21), 1952–1952."},"type":"journal_article"},{"oa_version":"Published Version","doi":"10.7554/eLife.03722","day":"14","publisher":"eLife Sciences Publications","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"GaTk"}],"author":[{"last_name":"Hermundstad","full_name":"Hermundstad, Ann","first_name":"Ann"},{"full_name":"Briguglio, John","last_name":"Briguglio","first_name":"John"},{"first_name":"Mary","last_name":"Conte","full_name":"Conte, Mary"},{"full_name":"Victor, Jonathan","last_name":"Victor","first_name":"Jonathan"},{"last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay","first_name":"Vijay"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"year":"2014","type":"journal_article","citation":{"short":"A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkačik, ELife (2014).","apa":"Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V., &#38; Tkačik, G. (2014). Variance predicts salience in central sensory processing. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.03722\">https://doi.org/10.7554/eLife.03722</a>","ieee":"A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkačik, “Variance predicts salience in central sensory processing,” <i>eLife</i>, no. November. eLife Sciences Publications, 2014.","ama":"Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. Variance predicts salience in central sensory processing. <i>eLife</i>. 2014;(November). doi:<a href=\"https://doi.org/10.7554/eLife.03722\">10.7554/eLife.03722</a>","chicago":"Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian, and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.” <i>ELife</i>. eLife Sciences Publications, 2014. <a href=\"https://doi.org/10.7554/eLife.03722\">https://doi.org/10.7554/eLife.03722</a>.","ista":"Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. 2014. Variance predicts salience in central sensory processing. eLife. (November), e03722.","mla":"Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.” <i>ELife</i>, no. November, e03722, eLife Sciences Publications, 2014, doi:<a href=\"https://doi.org/10.7554/eLife.03722\">10.7554/eLife.03722</a>."},"file":[{"creator":"system","date_created":"2018-12-12T10:12:04Z","file_id":"4922","file_name":"IST-2016-420-v1+1_e03722.full.pdf","access_level":"open_access","relation":"main_file","checksum":"766ac8999ac6e3364f10065a06024b8f","content_type":"application/pdf","date_updated":"2020-07-14T12:45:20Z","file_size":5117086}],"ddc":["570"],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Information processing in the sensory periphery is shaped by natural stimulus statistics. In the periphery, a transmission bottleneck constrains performance; thus efficient coding implies that natural signal components with a predictably wider range should be compressed. In a different regime—when sampling limitations constrain performance—efficient coding implies that more resources should be allocated to informative features that are more variable. We propose that this regime is relevant for sensory cortex when it extracts complex features from limited numbers of sensory samples. To test this prediction, we use central visual processing as a model: we show that visual sensitivity for local multi-point spatial correlations, described by dozens of independently-measured parameters, can be quantitatively predicted from the structure of natural images. This suggests that efficient coding applies centrally, where it extends to higher-order sensory features and operates in a regime in which sensitivity increases with feature variability."}],"publist_id":"5209","quality_controlled":"1","pubrep_id":"420","file_date_updated":"2020-07-14T12:45:20Z","publication":"eLife","date_created":"2018-12-11T11:54:32Z","_id":"1886","project":[{"call_identifier":"FWF","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425","name":"Sensitivity to higher-order statistics in natural scenes"}],"month":"11","date_updated":"2021-01-12T06:53:50Z","title":"Variance predicts salience in central sensory processing","date_published":"2014-11-14T00:00:00Z","scopus_import":1,"issue":"November","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"article_number":"e03722"},{"citation":{"mla":"Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” <i>Zoologie</i>, Deutsche Zoologische Gesellschaft, 2014, pp. 23–30.","ista":"Cremer S. 2014. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie., 23–30.","chicago":"Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” <i>Zoologie</i>. Deutsche Zoologische Gesellschaft, 2014.","ama":"Cremer S. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. <i>Zoologie</i>. 2014:23-30.","ieee":"S. Cremer, “Gemeinsame Krankheitsabwehr in Ameisengesellschaften,” <i>Zoologie</i>. Deutsche Zoologische Gesellschaft, pp. 23–30, 2014.","short":"S. Cremer, Zoologie (2014) 23–30.","apa":"Cremer, S. (2014). Gemeinsame Krankheitsabwehr in Ameisengesellschaften. <i>Zoologie</i>. Deutsche Zoologische Gesellschaft."},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"status":"public","publication_status":"published","main_file_link":[{"url":"https://www.dzg-ev.de/wp-content/uploads/2019/05/zoologie2014.pdf","open_access":"1"}],"publist_id":"5208","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","page":"23 - 30","oa_version":"Published Version","publication":"Zoologie","date_created":"2018-12-11T11:54:33Z","day":"01","publisher":"Deutsche Zoologische Gesellschaft","_id":"1887","month":"01","date_updated":"2023-10-17T07:54:57Z","title":"Gemeinsame Krankheitsabwehr in Ameisengesellschaften","department":[{"_id":"SyCr"}],"date_published":"2014-01-01T00:00:00Z","author":[{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"year":"2014","article_processing_charge":"No"},{"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        43","publication_status":"published","abstract":[{"text":"Im Rahmen meiner Arbeit mit der kollektiven Krankheitsabwehr in Ameisengesellschaften interessiert mich vor allem, wie sich die Kolonien als Ganzes gegen Krankheiten wehren können. Warum ist dieses Thema der Krankheitsdynamik in Gruppen so wichtig? Ein Vergleich von solitär lebenden Individuen mit Individuen, die in sozialen Gruppen zusammenleben, zeigt die Kosten und die Vorteile des Gruppenlebens: Einerseits haben Individuen in sozialen Gruppen aufgrund der hohen Dichte, in der die Tiere zusammenleben, den hohen Interaktionsraten, die sie miteinander haben, und der engen Verwandtschaft, die sie verbindet, ein höheres Ansteckungsrisiko. Andererseits kann die individuelle Krankheitsabwehr durch die kollektive Abwehr in den Gruppen ergänzt werden.","lang":"ger"}],"alternative_title":["Rundgespräche der Kommission für Ökologie"],"volume":43,"publist_id":"5207","language":[{"iso":"eng"}],"status":"public","citation":{"ieee":"S. Cremer, “Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt  Bayerische Akademie der Wissenschaften,” in <i>Soziale Insekten in einer sich wandelnden Welt</i>, vol. 43, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.","apa":"Cremer, S. (2014). Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt  Bayerische Akademie der Wissenschaften. In <i>Soziale Insekten in einer sich wandelnden Welt</i> (Vol. 43, pp. 65–72). Verlag Dr. Friedrich Pfeil.","short":"S. Cremer, in:, Soziale Insekten in Einer Sich Wandelnden Welt, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.","ista":"Cremer S. 2014.Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt  Bayerische Akademie der Wissenschaften. In: Soziale Insekten in einer sich wandelnden Welt. Rundgespräche der Kommission für Ökologie, vol. 43, 65–72.","mla":"Cremer, Sylvia. “Soziale Immunität: Wie Sich Der Staat Gegen Pathogene Wehrt  Bayerische Akademie Der Wissenschaften.” <i>Soziale Insekten in Einer Sich Wandelnden Welt</i>, vol. 43, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.","ama":"Cremer S. Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt  Bayerische Akademie der Wissenschaften. In: <i>Soziale Insekten in Einer Sich Wandelnden Welt</i>. Vol 43. Verlag Dr. Friedrich Pfeil; 2014:65-72.","chicago":"Cremer, Sylvia. “Soziale Immunität: Wie Sich Der Staat Gegen Pathogene Wehrt  Bayerische Akademie Der Wissenschaften.” In <i>Soziale Insekten in Einer Sich Wandelnden Welt</i>, 43:65–72. Verlag Dr. Friedrich Pfeil, 2014."},"type":"book_chapter","author":[{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"date_published":"2014-01-01T00:00:00Z","year":"2014","article_processing_charge":"No","title":"Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt  Bayerische Akademie der Wissenschaften","date_updated":"2023-10-17T12:28:45Z","publication_identifier":{"issn":["2366-2875"]},"department":[{"_id":"SyCr"}],"month":"01","_id":"1888","publisher":"Verlag Dr. Friedrich Pfeil","date_created":"2018-12-11T11:54:33Z","day":"01","publication":"Soziale Insekten in einer sich wandelnden Welt","oa_version":"None","page":"65 - 72"},{"publisher":"World Scientific Publishing","day":"01","doi":"10.1142/S0129055X14500123","oa_version":"Submitted Version","arxiv":1,"author":[{"first_name":"Gerhard","full_name":"Bräunlich, Gerhard","last_name":"Bräunlich"},{"last_name":"Hainzl","full_name":"Hainzl, Christian","first_name":"Christian"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"year":"2014","department":[{"_id":"RoSe"}],"article_type":"original","citation":{"apa":"Bräunlich, G., Hainzl, C., &#38; Seiringer, R. (2014). Translation-invariant quasi-free states for fermionic systems and the BCS approximation. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129055X14500123\">https://doi.org/10.1142/S0129055X14500123</a>","short":"G. Bräunlich, C. Hainzl, R. Seiringer, Reviews in Mathematical Physics 26 (2014).","ieee":"G. Bräunlich, C. Hainzl, and R. Seiringer, “Translation-invariant quasi-free states for fermionic systems and the BCS approximation,” <i>Reviews in Mathematical Physics</i>, vol. 26, no. 7. World Scientific Publishing, 2014.","chicago":"Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2014. <a href=\"https://doi.org/10.1142/S0129055X14500123\">https://doi.org/10.1142/S0129055X14500123</a>.","ama":"Bräunlich G, Hainzl C, Seiringer R. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. <i>Reviews in Mathematical Physics</i>. 2014;26(7). doi:<a href=\"https://doi.org/10.1142/S0129055X14500123\">10.1142/S0129055X14500123</a>","ista":"Bräunlich G, Hainzl C, Seiringer R. 2014. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. 26(7), 1450012.","mla":"Bräunlich, Gerhard, et al. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” <i>Reviews in Mathematical Physics</i>, vol. 26, no. 7, 1450012, World Scientific Publishing, 2014, doi:<a href=\"https://doi.org/10.1142/S0129055X14500123\">10.1142/S0129055X14500123</a>."},"type":"journal_article","quality_controlled":"1","publication_status":"published","abstract":[{"text":"We study translation-invariant quasi-free states for a system of fermions with two-particle interactions. The associated energy functional is similar to the BCS functional but also includes direct and exchange energies. We show that for suitable short-range interactions, these latter terms only lead to a renormalization of the chemical potential, with the usual properties of the BCS functional left unchanged. Our analysis thus represents a rigorous justification of part of the BCS approximation. We give bounds on the critical temperature below which the system displays superfluidity.","lang":"eng"}],"publist_id":"5206","language":[{"iso":"eng"}],"status":"public","_id":"1889","date_created":"2018-12-11T11:54:33Z","external_id":{"arxiv":["1305.5135"]},"publication":"Reviews in Mathematical Physics","date_published":"2014-08-01T00:00:00Z","article_processing_charge":"No","title":"Translation-invariant quasi-free states for fermionic systems and the BCS approximation","date_updated":"2022-06-07T09:03:09Z","month":"08","scopus_import":"1","article_number":"1450012","acknowledgement":"We would like to thank Max Lein and Andreas Deuchert for valuable suggestions and remarks. Partial financial support by the NSERC (R.S.) is gratefully acknowledged.","issue":"7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"        26","volume":26,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1305.5135"}]},{"doi":"10.1111/psyp.12062","oa_version":"Published Version","publisher":"Wiley-Blackwell","day":"11","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Körner, Christof","last_name":"Körner","first_name":"Christof"},{"full_name":"Braunstein, Verena","last_name":"Braunstein","first_name":"Verena"},{"last_name":"Stangl","full_name":"Stangl, Matthias","first_name":"Matthias"},{"first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl"},{"first_name":"Christa","full_name":"Neuper, Christa","last_name":"Neuper"},{"first_name":"Anja","last_name":"Ischebeck","full_name":"Ischebeck, Anja"}],"year":"2014","file":[{"file_id":"5233","date_created":"2018-12-12T10:16:44Z","creator":"system","checksum":"4255b6185e774acce1d99f8e195c564d","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:45:20Z","file_size":543243,"file_name":"IST-2016-442-v1+1_K-rner_et_al-2014-Psychophysiology.pdf","access_level":"open_access"}],"citation":{"ieee":"C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, and A. Ischebeck, “Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection,” <i>Psychophysiology</i>, vol. 51, no. 4. Wiley-Blackwell, pp. 385–395, 2014.","short":"C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, A. Ischebeck, Psychophysiology 51 (2014) 385–395.","apa":"Körner, C., Braunstein, V., Stangl, M., Schlögl, A., Neuper, C., &#38; Ischebeck, A. (2014). Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. <i>Psychophysiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/psyp.12062\">https://doi.org/10.1111/psyp.12062</a>","mla":"Körner, Christof, et al. “Sequential Effects in Continued Visual Search: Using Fixation-Related Potentials to Compare Distractor Processing before and after Target Detection.” <i>Psychophysiology</i>, vol. 51, no. 4, Wiley-Blackwell, 2014, pp. 385–95, doi:<a href=\"https://doi.org/10.1111/psyp.12062\">10.1111/psyp.12062</a>.","ista":"Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. 2014. Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. Psychophysiology. 51(4), 385–395.","ama":"Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. <i>Psychophysiology</i>. 2014;51(4):385-395. doi:<a href=\"https://doi.org/10.1111/psyp.12062\">10.1111/psyp.12062</a>","chicago":"Körner, Christof, Verena Braunstein, Matthias Stangl, Alois Schlögl, Christa Neuper, and Anja Ischebeck. “Sequential Effects in Continued Visual Search: Using Fixation-Related Potentials to Compare Distractor Processing before and after Target Detection.” <i>Psychophysiology</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/psyp.12062\">https://doi.org/10.1111/psyp.12062</a>."},"type":"journal_article","ddc":["000"],"abstract":[{"lang":"eng","text":"To search for a target in a complex environment is an everyday behavior that ends with finding the target. When we search for two identical targets, however, we must continue the search after finding the first target and memorize its location. We used fixation-related potentials to investigate the neural correlates of different stages of the search, that is, before and after finding the first target. Having found the first target influenced subsequent distractor processing. Compared to distractor fixations before the first target fixation, a negative shift was observed for three subsequent distractor fixations. These results suggest that processing a target in continued search modulates the brain's response, either transiently by reflecting temporary working memory processes or permanently by reflecting working memory retention."}],"publication_status":"published","publist_id":"5205","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","file_date_updated":"2020-07-14T12:45:20Z","pubrep_id":"442","publication":"Psychophysiology","page":"385 - 395","_id":"1890","date_created":"2018-12-11T11:54:34Z","date_updated":"2021-01-12T06:53:52Z","title":"Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection","month":"02","date_published":"2014-02-11T00:00:00Z","scopus_import":1,"volume":51,"issue":"4","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Funded by Austrian Science Fund (FWF) Grant Number: P 22189-B18; European Union within the 6th Framework Programme Grant Number: 517590; State government of Styria Grant Number: PN 4055","oa":1,"intvolume":"        51"},{"status":"public","language":[{"iso":"eng"}],"publist_id":"5204","publication_status":"published","abstract":[{"lang":"eng","text":"We provide theoretical tests of a novel experimental technique to determine mechanostability of proteins based on stretching a mechanically protected protein by single-molecule force spectroscopy. This technique involves stretching a homogeneous or heterogeneous chain of reference proteins (single-molecule markers) in which one of them acts as host to the guest protein under study. The guest protein is grafted into the host through genetic engineering. It is expected that unraveling of the host precedes the unraveling of the guest removing ambiguities in the reading of the force-extension patterns of the guest protein. We study examples of such systems within a coarse-grained structure-based model. We consider systems with various ratios of mechanostability for the host and guest molecules and compare them to experimental results involving cohesin I as the guest molecule. For a comparison, we also study the force-displacement patterns in proteins that are linked in a serial fashion. We find that the mechanostability of the guest is similar to that of the isolated or serially linked protein. We also demonstrate that the ideal configuration of this strategy would be one in which the host is much more mechanostable than the single-molecule markers. We finally show that it is troublesome to use the highly stable cystine knot proteins as a host to graft a guest in stretching studies because this would involve a cleaving procedure."}],"volume":82,"intvolume":"        82","issue":"5","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Grant Nr. 2011/01/N/ST3/02475","scopus_import":1,"citation":{"ama":"Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M, Cieplak M. Theoretical tests of the mechanical protection strategy in protein nanomechanics. <i>Proteins: Structure, Function and Bioinformatics</i>. 2014;82(5):717-726. doi:<a href=\"https://doi.org/10.1002/prot.24436\">10.1002/prot.24436</a>","chicago":"Chwastyk, Mateusz, Albert Galera Prat, Mateusz K Sikora, Àngel Gómez Sicilia, Mariano Carrión Vázquez, and Marek Cieplak. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” <i>Proteins: Structure, Function and Bioinformatics</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/prot.24436\">https://doi.org/10.1002/prot.24436</a>.","mla":"Chwastyk, Mateusz, et al. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” <i>Proteins: Structure, Function and Bioinformatics</i>, vol. 82, no. 5, Wiley-Blackwell, 2014, pp. 717–26, doi:<a href=\"https://doi.org/10.1002/prot.24436\">10.1002/prot.24436</a>.","ista":"Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M, Cieplak M. 2014. Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. 82(5), 717–726.","apa":"Chwastyk, M., Galera Prat, A., Sikora, M. K., Gómez Sicilia, À., Carrión Vázquez, M., &#38; Cieplak, M. (2014). Theoretical tests of the mechanical protection strategy in protein nanomechanics. <i>Proteins: Structure, Function and Bioinformatics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/prot.24436\">https://doi.org/10.1002/prot.24436</a>","short":"M. Chwastyk, A. Galera Prat, M.K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez, M. Cieplak, Proteins: Structure, Function and Bioinformatics 82 (2014) 717–726.","ieee":"M. Chwastyk, A. Galera Prat, M. K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez, and M. Cieplak, “Theoretical tests of the mechanical protection strategy in protein nanomechanics,” <i>Proteins: Structure, Function and Bioinformatics</i>, vol. 82, no. 5. Wiley-Blackwell, pp. 717–726, 2014."},"type":"journal_article","month":"05","department":[{"_id":"CaHe"}],"title":"Theoretical tests of the mechanical protection strategy in protein nanomechanics","date_updated":"2021-01-12T06:53:52Z","year":"2014","author":[{"first_name":"Mateusz","last_name":"Chwastyk","full_name":"Chwastyk, Mateusz"},{"full_name":"Galera Prat, Albert","last_name":"Galera Prat","first_name":"Albert"},{"last_name":"Sikora","full_name":"Sikora, Mateusz K","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gómez Sicilia","full_name":"Gómez Sicilia, Àngel","first_name":"Àngel"},{"last_name":"Carrión Vázquez","full_name":"Carrión Vázquez, Mariano","first_name":"Mariano"},{"first_name":"Marek","last_name":"Cieplak","full_name":"Cieplak, Marek"}],"date_published":"2014-05-01T00:00:00Z","page":"717 - 726","oa_version":"None","doi":"10.1002/prot.24436","publication":"Proteins: Structure, Function and Bioinformatics","day":"01","date_created":"2018-12-11T11:54:34Z","publisher":"Wiley-Blackwell","_id":"1891"},{"quality_controlled":"1","language":[{"iso":"eng"}],"pmid":1,"status":"public","publication_status":"published","abstract":[{"text":"Behavioural variation among conspecifics is typically contingent on individual state or environmental conditions. Sex-specific genetic polymorphisms are enigmatic because they lack conditionality, and genes causing adaptive trait variation in one sex may reduce Darwinian fitness in the other. One way to avoid such genetic antagonism is to control sex-specific traits by inheritance via sex chromosomes. Here, controlled laboratory crossings suggest that in snail-brooding cichlid fish a single locus, two-allele polymorphism located on a sex-linked chromosome of heterogametic males generates an extreme reproductive dimorphism. Both natural and sexual selection are responsible for exceptionally large body size of bourgeois males, creating a niche for a miniature male phenotype to evolve. This extreme intrasexual dimorphism results from selection on opposite size thresholds caused by a single ecological factor, empty snail shells used as breeding substrate. Paternity analyses reveal that in the field parasitic dwarf males sire the majority of offspring in direct sperm competition with large nest owners exceeding their size more than 40 times. Apparently, use of empty snail shells as breeding substrate and single locus sex-linked inheritance of growth are the major ecological and genetic mechanisms responsible for the extreme intrasexual diversity observed in Lamprologus callipterus.","lang":"eng"}],"publist_id":"5203","article_type":"original","type":"journal_article","citation":{"ieee":"S. Ocana, P. Meidl, D. Bonfils, and M. Taborsky, “Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 281, no. 1794. The Royal Society, 2014.","short":"S. Ocana, P. Meidl, D. Bonfils, M. Taborsky, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).","apa":"Ocana, S., Meidl, P., Bonfils, D., &#38; Taborsky, M. (2014). Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2014.0253\">https://doi.org/10.1098/rspb.2014.0253</a>","mla":"Ocana, Sabine, et al. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 281, no. 1794, 20140253, The Royal Society, 2014, doi:<a href=\"https://doi.org/10.1098/rspb.2014.0253\">10.1098/rspb.2014.0253</a>.","ista":"Ocana S, Meidl P, Bonfils D, Taborsky M. 2014. Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20140253.","ama":"Ocana S, Meidl P, Bonfils D, Taborsky M. Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2014;281(1794). doi:<a href=\"https://doi.org/10.1098/rspb.2014.0253\">10.1098/rspb.2014.0253</a>","chicago":"Ocana, Sabine, Patrick Meidl, Danielle Bonfils, and Michael Taborsky. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society, 2014. <a href=\"https://doi.org/10.1098/rspb.2014.0253\">https://doi.org/10.1098/rspb.2014.0253</a>."},"author":[{"first_name":"Sabine","last_name":"Ocana","full_name":"Ocana, Sabine"},{"last_name":"Meidl","full_name":"Meidl, Patrick","id":"4709BCE6-F248-11E8-B48F-1D18A9856A87","first_name":"Patrick"},{"first_name":"Danielle","last_name":"Bonfils","full_name":"Bonfils, Danielle"},{"last_name":"Taborsky","full_name":"Taborsky, Michael","first_name":"Michael"}],"year":"2014","department":[{"_id":"CampIT"}],"day":"07","publisher":"The Royal Society","oa_version":"Submitted Version","doi":"10.1098/rspb.2014.0253","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1794","acknowledgement":"This research was supported by grants of the Swiss National Science Foundation to M.T.\r\nWe thank Tetsu Sato for providing field samples, Olivier Goffinet for field assistance, Dolores Schütz for vital help in the field and with the manuscript, David Lank, Barbara Taborsky, Suzanne Alonzo and two anonymous referees for comments on earlier manuscript versions, and the Fisheries Department, Ministry of Agriculture and Livestock of Zambia, for permission and support.","oa":1,"intvolume":"       281","article_number":"20140253","volume":281,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211437/"}],"scopus_import":"1","date_published":"2014-11-07T00:00:00Z","article_processing_charge":"No","month":"11","title":"Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids","date_updated":"2022-06-07T09:12:32Z","date_created":"2018-12-11T11:54:34Z","external_id":{"pmid":["25232141"]},"_id":"1892","publication":"Proceedings of the Royal Society of London Series B Biological Sciences"},{"intvolume":"       111","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by grants from the Research Foundation-Flanders (Odysseus).","issue":"7","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932866/","open_access":"1"}],"volume":111,"scopus_import":1,"ec_funded":1,"date_published":"2014-02-18T00:00:00Z","month":"02","date_updated":"2021-01-12T06:53:53Z","title":"SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis","date_created":"2018-12-11T11:54:34Z","_id":"1893","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"page":"2818 - 2823","publication":"PNAS","status":"public","language":[{"iso":"eng"}],"publist_id":"5202","abstract":[{"text":"Phosphatidylinositol (PtdIns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, PtdIns3P and PtdIns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vacuolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with PtdIns3P, the presumable product of their activity. In SAC gain- and loss-of-function mutants, the levels of PtdIns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with PtdIns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants.","lang":"eng"}],"publication_status":"published","type":"journal_article","citation":{"mla":"Marhavá, Petra, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” <i>PNAS</i>, vol. 111, no. 7, National Academy of Sciences, 2014, pp. 2818–23, doi:<a href=\"https://doi.org/10.1073/pnas.1324264111\">10.1073/pnas.1324264111</a>.","ista":"Marhavá P, Hirsch S, Feraru E, Tejos R, Van Wijk R, Viaene T, Heilmann M, Lerche J, De Rycke R, Feraru M, Grones P, Van Montagu M, Heilmann I, Munnik T, Friml J. 2014. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 111(7), 2818–2823.","chicago":"Marhavá, Petra, Sibylle Hirsch, Elena Feraru, Ricardo Tejos, Ringo Van Wijk, Tom Viaene, Mareike Heilmann, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” <i>PNAS</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1324264111\">https://doi.org/10.1073/pnas.1324264111</a>.","ama":"Marhavá P, Hirsch S, Feraru E, et al. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. <i>PNAS</i>. 2014;111(7):2818-2823. doi:<a href=\"https://doi.org/10.1073/pnas.1324264111\">10.1073/pnas.1324264111</a>","ieee":"P. Marhavá <i>et al.</i>, “SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis,” <i>PNAS</i>, vol. 111, no. 7. National Academy of Sciences, pp. 2818–2823, 2014.","short":"P. Marhavá, S. Hirsch, E. Feraru, R. Tejos, R. Van Wijk, T. Viaene, M. Heilmann, J. Lerche, R. De Rycke, M. Feraru, P. Grones, M. Van Montagu, I. Heilmann, T. Munnik, J. Friml, PNAS 111 (2014) 2818–2823.","apa":"Marhavá, P., Hirsch, S., Feraru, E., Tejos, R., Van Wijk, R., Viaene, T., … Friml, J. (2014). SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1324264111\">https://doi.org/10.1073/pnas.1324264111</a>"},"year":"2014","author":[{"last_name":"Nováková","full_name":"Nováková, Petra","first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sibylle","last_name":"Hirsch","full_name":"Hirsch, Sibylle"},{"first_name":"Elena","last_name":"Feraru","full_name":"Feraru, Elena"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"first_name":"Ringo","full_name":"Van Wijk, Ringo","last_name":"Van Wijk"},{"first_name":"Tom","full_name":"Viaene, Tom","last_name":"Viaene"},{"full_name":"Heilmann, Mareike","last_name":"Heilmann","first_name":"Mareike"},{"last_name":"Lerche","full_name":"Lerche, Jennifer","first_name":"Jennifer"},{"first_name":"Riet","last_name":"De Rycke","full_name":"De Rycke, Riet"},{"last_name":"Feraru","full_name":"Feraru, Mugurel","first_name":"Mugurel"},{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Grones, Peter","last_name":"Grones"},{"first_name":"Marc","last_name":"Van Montagu","full_name":"Van Montagu, Marc"},{"full_name":"Heilmann, Ingo","last_name":"Heilmann","first_name":"Ingo"},{"full_name":"Munnik, Teun","last_name":"Munnik","first_name":"Teun"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"department":[{"_id":"JiFr"}],"day":"18","publisher":"National Academy of Sciences","oa_version":"Submitted Version","doi":"10.1073/pnas.1324264111"},{"doi":"10.1371/journal.pone.0106247","oa_version":"Published Version","publisher":"Public Library of Science","day":"02","department":[{"_id":"CaGu"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2014","author":[{"first_name":"Anna","full_name":"Grabowska, Anna","last_name":"Grabowska"},{"first_name":"Ewa","full_name":"Wywiał, Ewa","last_name":"Wywiał"},{"first_name":"Stanislaw","last_name":"Dunin Horkawicz","full_name":"Dunin Horkawicz, Stanislaw"},{"last_name":"Łasica","full_name":"Łasica, Anna","first_name":"Anna"},{"first_name":"Marc","full_name":"Wösten, Marc","last_name":"Wösten"},{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","full_name":"Nagy-Staron, Anna A","last_name":"Nagy-Staron"},{"full_name":"Godlewska, Renata","last_name":"Godlewska","first_name":"Renata"},{"full_name":"Bocian Ostrzycka, Katarzyna","last_name":"Bocian Ostrzycka","first_name":"Katarzyna"},{"first_name":"Katarzyna","last_name":"Pieńkowska","full_name":"Pieńkowska, Katarzyna"},{"first_name":"Paweł","last_name":"Łaniewski","full_name":"Łaniewski, Paweł"},{"last_name":"Bujnicki","full_name":"Bujnicki, Janusz","first_name":"Janusz"},{"last_name":"Van Putten","full_name":"Van Putten, Jos","first_name":"Jos"},{"first_name":"Elzbieta","last_name":"Jagusztyn Krynicka","full_name":"Jagusztyn Krynicka, Elzbieta"}],"file":[{"file_name":"IST-2016-438-v1+1_journal.pone.0106247.pdf","access_level":"open_access","relation":"main_file","checksum":"7d02c3da7f72b82bb5d7932d80c3251f","date_updated":"2020-07-14T12:45:20Z","content_type":"application/pdf","file_size":4248801,"date_created":"2018-12-12T10:16:19Z","creator":"system","file_id":"5205"}],"type":"journal_article","citation":{"ama":"Grabowska A, Wywiał E, Dunin Horkawicz S, et al. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. <i>PLoS One</i>. 2014;9(9). doi:<a href=\"https://doi.org/10.1371/journal.pone.0106247\">10.1371/journal.pone.0106247</a>","chicago":"Grabowska, Anna, Ewa Wywiał, Stanislaw Dunin Horkawicz, Anna Łasica, Marc Wösten, Anna A Nagy-Staron, Renata Godlewska, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” <i>PLoS One</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0106247\">https://doi.org/10.1371/journal.pone.0106247</a>.","ista":"Grabowska A, Wywiał E, Dunin Horkawicz S, Łasica A, Wösten M, Nagy-Staron AA, Godlewska R, Bocian Ostrzycka K, Pieńkowska K, Łaniewski P, Bujnicki J, Van Putten J, Jagusztyn Krynicka E. 2014. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 9(9), e106247.","mla":"Grabowska, Anna, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” <i>PLoS One</i>, vol. 9, no. 9, e106247, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0106247\">10.1371/journal.pone.0106247</a>.","short":"A. Grabowska, E. Wywiał, S. Dunin Horkawicz, A. Łasica, M. Wösten, A.A. Nagy-Staron, R. Godlewska, K. Bocian Ostrzycka, K. Pieńkowska, P. Łaniewski, J. Bujnicki, J. Van Putten, E. Jagusztyn Krynicka, PLoS One 9 (2014).","apa":"Grabowska, A., Wywiał, E., Dunin Horkawicz, S., Łasica, A., Wösten, M., Nagy-Staron, A. A., … Jagusztyn Krynicka, E. (2014). Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0106247\">https://doi.org/10.1371/journal.pone.0106247</a>","ieee":"A. Grabowska <i>et al.</i>, “Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA,” <i>PLoS One</i>, vol. 9, no. 9. Public Library of Science, 2014."},"ddc":["570"],"publist_id":"5201","publication_status":"published","abstract":[{"lang":"eng","text":"Background: Bacterial Dsb enzymes are involved in the oxidative folding of many proteins, through the formation of disulfide bonds between their cysteine residues. The Dsb protein network has been well characterized in cells of the model microorganism Escherichia coli. To gain insight into the functioning of the Dsb system in epsilon-Proteobacteria, where it plays an important role in the colonization process, we studied two homologs of the main Escherichia coli Dsb oxidase (EcDsbA) that are present in the cells of the enteric pathogen Campylobacter jejuni, the most frequently reported bacterial cause of human enteritis in the world. Methods and Results: Phylogenetic analysis suggests the horizontal transfer of the epsilon-Proteobacterial DsbAs from a common ancestor to gamma-Proteobacteria, which then gave rise to the DsbL lineage. Phenotype and enzymatic assays suggest that the two C. jejuni DsbAs play different roles in bacterial cells and have divergent substrate spectra. CjDsbA1 is essential for the motility and autoagglutination phenotypes, while CjDsbA2 has no impact on those processes. CjDsbA1 plays a critical role in the oxidative folding that ensures the activity of alkaline phosphatase CjPhoX, whereas CjDsbA2 is crucial for the activity of arylsulfotransferase CjAstA, encoded within the dsbA2-dsbB-astA operon. Conclusions: Our results show that CjDsbA1 is the primary thiol-oxidoreductase affecting life processes associated with bacterial spread and host colonization, as well as ensuring the oxidative folding of particular protein substrates. In contrast, CjDsbA2 activity does not affect the same processes and so far its oxidative folding activity has been demonstrated for one substrate, arylsulfotransferase CjAstA. The results suggest the cooperation between CjDsbA2 and CjDsbB. In the case of the CjDsbA1, this cooperation is not exclusive and there is probably another protein to be identified in C. jejuni cells that acts to re-oxidize CjDsbA1. Altogether the data presented here constitute the considerable insight to the Epsilonproteobacterial Dsb systems, which have been poorly understood so far."}],"status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"quality_controlled":"1","publication":"PLoS One","pubrep_id":"438","file_date_updated":"2020-07-14T12:45:20Z","_id":"1894","date_created":"2018-12-11T11:54:35Z","title":"Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA","date_updated":"2021-01-12T06:53:54Z","month":"09","date_published":"2014-09-02T00:00:00Z","scopus_import":1,"volume":9,"article_number":"e106247","intvolume":"         9","oa":1,"issue":"9","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"volume":9,"article_number":"e107099","issue":"9","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported in part by a Grant-in-Aid for Scientific Research on Innovative Areas (Comprehensive Brain Science Network) and (B) 17330153, from the Ministry of Education, Culture, Sports, Science and Technology of Japan.","oa":1,"intvolume":"         9","scopus_import":1,"date_updated":"2021-01-12T06:53:54Z","title":"Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice","month":"09","date_published":"2014-09-30T00:00:00Z","pubrep_id":"439","file_date_updated":"2020-07-14T12:45:20Z","publication":"PLoS One","_id":"1895","date_created":"2018-12-11T11:54:35Z","publication_status":"published","abstract":[{"text":"Major histocompatibility complex class I (MHCI) molecules were recently identified as novel regulators of synaptic plasticity. These molecules are expressed in various brain areas, especially in regions undergoing activity-dependent synaptic plasticity, but their role in the nucleus accumbens (NAc) is unknown. In this study, we investigated the effects of genetic disruption of MHCI function, through deletion of β2-microblobulin, which causes lack of cell surface expression of MHCI. First, we confirmed that MHCI molecules are expressed in the NAc core in wild-type mice. Second, we performed electrophysiological recordings with NAc core slices from wild-type and β2-microglobulin knock-out mice lacking cell surface expression of MHCI. We found that low frequency stimulation induced long-term depression in wild-type but not knock-out mice, whereas high frequency stimulation induced long-term potentiation in both genotypes, with a larger magnitude in knock-out mice. Furthermore, we demonstrated that knock-out mice showed more persistent behavioral sensitization to cocaine, which is a NAc-related behavior. Using this model, we analyzed the density of total AMPA receptors and their subunits GluR1 and GluR2 in the NAc core, by SDS-digested freeze-fracture replica labeling. After repeated cocaine exposure, the density of GluR1 was increased, but there was no change in total AMPA receptors and GluR2 levels in wildtype mice. In contrast, following repeated cocaine exposure, increased densities of total AMPA receptors, GluR1 and GluR2 were observed in knock-out mice. These results indicate that functional deficiency of MHCI enhances synaptic potentiation, induced by electrical and pharmacological stimulation.","lang":"eng"}],"publist_id":"5200","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","file":[{"access_level":"open_access","file_name":"IST-2016-439-v1+1_journal.pone.0107099.pdf","file_size":6262085,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:20Z","checksum":"1f3be936be93114596d61ba44cacee69","relation":"main_file","date_created":"2018-12-12T10:09:01Z","creator":"system","file_id":"4724"}],"type":"journal_article","citation":{"ista":"Edamura M, Murakami G, Meng H, Itakura M, Shigemoto R, Fukuda A, Nakahara D. 2014. Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. 9(9), e107099.","mla":"Edamura, Mitsuhiro, et al. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” <i>PLoS One</i>, vol. 9, no. 9, e107099, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0107099\">10.1371/journal.pone.0107099</a>.","chicago":"Edamura, Mitsuhiro, Gen Murakami, Hongrui Meng, Makoto Itakura, Ryuichi Shigemoto, Atsuo Fukuda, and Daiichiro Nakahara. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” <i>PLoS One</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0107099\">https://doi.org/10.1371/journal.pone.0107099</a>.","ama":"Edamura M, Murakami G, Meng H, et al. Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. <i>PLoS One</i>. 2014;9(9). doi:<a href=\"https://doi.org/10.1371/journal.pone.0107099\">10.1371/journal.pone.0107099</a>","ieee":"M. Edamura <i>et al.</i>, “Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice,” <i>PLoS One</i>, vol. 9, no. 9. Public Library of Science, 2014.","short":"M. Edamura, G. Murakami, H. Meng, M. Itakura, R. Shigemoto, A. Fukuda, D. Nakahara, PLoS One 9 (2014).","apa":"Edamura, M., Murakami, G., Meng, H., Itakura, M., Shigemoto, R., Fukuda, A., &#38; Nakahara, D. (2014). Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0107099\">https://doi.org/10.1371/journal.pone.0107099</a>"},"ddc":["570"],"department":[{"_id":"RySh"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"first_name":"Mitsuhiro","full_name":"Edamura, Mitsuhiro","last_name":"Edamura"},{"last_name":"Murakami","full_name":"Murakami, Gen","first_name":"Gen"},{"last_name":"Meng","full_name":"Meng, Hongrui","first_name":"Hongrui"},{"first_name":"Makoto","full_name":"Itakura, Makoto","last_name":"Itakura"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"first_name":"Atsuo","last_name":"Fukuda","full_name":"Fukuda, Atsuo"},{"first_name":"Daiichiro","full_name":"Nakahara, Daiichiro","last_name":"Nakahara"}],"year":"2014","doi":"10.1371/journal.pone.0107099","oa_version":"Published Version","publisher":"Public Library of Science","day":"30"},{"type":"journal_article","citation":{"chicago":"Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2014. <a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">https://doi.org/10.1103/PhysRevE.89.032701</a>.","ama":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2014;89(3). doi:<a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">10.1103/PhysRevE.89.032701</a>","mla":"Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">10.1103/PhysRevE.89.032701</a>.","ista":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701.","apa":"Kollár, R., Bodova, K., Nosek, J., &#38; Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">https://doi.org/10.1103/PhysRevE.89.032701</a>","short":"R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","ieee":"R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 89, no. 3. American Institute of Physics, 2014."},"language":[{"iso":"eng"}],"status":"public","abstract":[{"text":"Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings.","lang":"eng"}],"publication_status":"published","publist_id":"5198","day":"04","publisher":"American Institute of Physics","oa_version":"Submitted Version","doi":"10.1103/PhysRevE.89.032701","author":[{"full_name":"Kollár, Richard","last_name":"Kollár","first_name":"Richard"},{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína","last_name":"Bod'ová","full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171"},{"first_name":"Jozef","last_name":"Nosek","full_name":"Nosek, Jozef"},{"first_name":"Ľubomír","full_name":"Tomáška, Ľubomír","last_name":"Tomáška"}],"year":"2014","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"scopus_import":"1","acknowledgement":"The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.).","issue":"3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"        89","article_number":"032701","volume":89,"main_file_link":[{"url":"http://arxiv.org/abs/1402.0430","open_access":"1"}],"date_created":"2018-12-11T11:54:35Z","_id":"1896","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","date_published":"2014-03-04T00:00:00Z","article_processing_charge":"No","month":"03","title":"Mathematical model of alternative mechanism of telomere length maintenance","date_updated":"2022-08-01T10:50:10Z"},{"day":"01","date_created":"2018-12-11T11:54:36Z","publisher":"American Society of Plant Biologists","_id":"1897","page":"3062 - 3076","oa_version":"Submitted Version","publication":"Plant Cell","doi":"10.1105/tpc.114.125880","year":"2014","author":[{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"last_name":"Otegui","full_name":"Otegui, Marisa","first_name":"Marisa"},{"full_name":"Kutsuna, Natsumaro","last_name":"Kutsuna","first_name":"Natsumaro"},{"first_name":"Riet","full_name":"De Rycke, Riet","last_name":"De Rycke"},{"last_name":"Dainobu","full_name":"Dainobu, Tomoko","first_name":"Tomoko"},{"full_name":"Karampelias, Michael","last_name":"Karampelias","first_name":"Michael"},{"first_name":"Masaru","last_name":"Fujimoto","full_name":"Fujimoto, Masaru"},{"last_name":"Feraru","full_name":"Feraru, Elena","first_name":"Elena"},{"first_name":"Daisuke","full_name":"Miki, Daisuke","last_name":"Miki"},{"full_name":"Fukuda, Hiroo","last_name":"Fukuda","first_name":"Hiroo"},{"first_name":"Akihiko","full_name":"Nakano, Akihiko","last_name":"Nakano"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2014-07-01T00:00:00Z","month":"07","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:53:55Z","title":"Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis","citation":{"apa":"Naramoto, S., Otegui, M., Kutsuna, N., De Rycke, R., Dainobu, T., Karampelias, M., … Friml, J. (2014). Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.114.125880\">https://doi.org/10.1105/tpc.114.125880</a>","short":"S. Naramoto, M. Otegui, N. Kutsuna, R. De Rycke, T. Dainobu, M. Karampelias, M. Fujimoto, E. Feraru, D. Miki, H. Fukuda, A. Nakano, J. Friml, Plant Cell 26 (2014) 3062–3076.","ieee":"S. Naramoto <i>et al.</i>, “Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis,” <i>Plant Cell</i>, vol. 26, no. 7. American Society of Plant Biologists, pp. 3062–3076, 2014.","ama":"Naramoto S, Otegui M, Kutsuna N, et al. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. <i>Plant Cell</i>. 2014;26(7):3062-3076. doi:<a href=\"https://doi.org/10.1105/tpc.114.125880\">10.1105/tpc.114.125880</a>","chicago":"Naramoto, Satoshi, Marisa Otegui, Natsumaro Kutsuna, Riet De Rycke, Tomoko Dainobu, Michael Karampelias, Masaru Fujimoto, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2014. <a href=\"https://doi.org/10.1105/tpc.114.125880\">https://doi.org/10.1105/tpc.114.125880</a>.","ista":"Naramoto S, Otegui M, Kutsuna N, De Rycke R, Dainobu T, Karampelias M, Fujimoto M, Feraru E, Miki D, Fukuda H, Nakano A, Friml J. 2014. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 26(7), 3062–3076.","mla":"Naramoto, Satoshi, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” <i>Plant Cell</i>, vol. 26, no. 7, American Society of Plant Biologists, 2014, pp. 3062–76, doi:<a href=\"https://doi.org/10.1105/tpc.114.125880\">10.1105/tpc.114.125880</a>."},"scopus_import":1,"type":"journal_article","oa":1,"intvolume":"        26","acknowledgement":"This work was supported by the Odysseus Program of the Research Foundation-Flanders (J.F.).","issue":"7","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","language":[{"iso":"eng"}],"publist_id":"5199","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145132/"}],"volume":26,"publication_status":"published","abstract":[{"lang":"eng","text":"GNOM is one of the most characterized membrane trafficking regulators in plants, with crucial roles in development. GNOM encodes an ARF-guanine nucleotide exchange factor (ARF-GEF) that activates small GTPases of the ARF (ADP ribosylation factor) class to mediate vesicle budding at endomembranes. The crucial role of GNOM in recycling of PIN auxin transporters and other proteins to the plasma membrane was identified in studies using the ARF-GEF inhibitor brefeldin A (BFA). GNOM, the most prominent regulator of recycling in plants, has been proposed to act and localize at so far elusive recycling endosomes. Here, we report the GNOM localization in context of its cellular function in Arabidopsis thaliana. State-of-the-art imaging, pharmacological interference, and ultrastructure analysis show that GNOM predominantly localizes to Golgi apparatus. Super-resolution confocal live imaging microscopy identified GNOM and its closest homolog GNOM-like 1 at distinct subdomains on Golgi cisternae. Short-term BFA treatment stabilizes GNOM at the Golgi apparatus, whereas prolonged exposures results in GNOM translocation to trans-Golgi network (TGN)/early endosomes (EEs). Malformed TGN/EE in gnom mutants suggests a role for GNOM in maintaining TGN/EE function. Our results redefine the subcellular action of GNOM and reevaluate the identity and function of recycling endosomes in plants."}]},{"publisher":"Elsevier","_id":"1898","date_created":"2018-12-11T11:54:36Z","day":"01","publication":"Neuron","doi":"10.1016/j.neuron.2014.08.036","oa_version":"None","page":"152 - 163","date_published":"2014-10-01T00:00:00Z","author":[{"full_name":"Ritzau Jost, Andreas","last_name":"Ritzau Jost","first_name":"Andreas"},{"last_name":"Delvendahl","full_name":"Delvendahl, Igor","first_name":"Igor"},{"first_name":"Annika","full_name":"Rings, Annika","last_name":"Rings"},{"full_name":"Byczkowicz, Niklas","last_name":"Byczkowicz","first_name":"Niklas"},{"last_name":"Harada","orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"last_name":"Hirrlinger","full_name":"Hirrlinger, Johannes","first_name":"Johannes"},{"first_name":"Jens","full_name":"Eilers, Jens","last_name":"Eilers"},{"first_name":"Stefan","last_name":"Hallermann","full_name":"Hallermann, Stefan"}],"year":"2014","title":"Ultrafast action potentials mediate kilohertz signaling at a central synapse","date_updated":"2021-01-12T06:53:55Z","department":[{"_id":"RySh"}],"month":"10","scopus_import":1,"citation":{"ista":"Ritzau Jost A, Delvendahl I, Rings A, Byczkowicz N, Harada H, Shigemoto R, Hirrlinger J, Eilers J, Hallermann S. 2014. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 84(1), 152–163.","mla":"Ritzau Jost, Andreas, et al. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” <i>Neuron</i>, vol. 84, no. 1, Elsevier, 2014, pp. 152–63, doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.08.036\">10.1016/j.neuron.2014.08.036</a>.","ama":"Ritzau Jost A, Delvendahl I, Rings A, et al. Ultrafast action potentials mediate kilohertz signaling at a central synapse. <i>Neuron</i>. 2014;84(1):152-163. doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.08.036\">10.1016/j.neuron.2014.08.036</a>","chicago":"Ritzau Jost, Andreas, Igor Delvendahl, Annika Rings, Niklas Byczkowicz, Harumi Harada, Ryuichi Shigemoto, Johannes Hirrlinger, Jens Eilers, and Stefan Hallermann. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2014.08.036\">https://doi.org/10.1016/j.neuron.2014.08.036</a>.","ieee":"A. Ritzau Jost <i>et al.</i>, “Ultrafast action potentials mediate kilohertz signaling at a central synapse,” <i>Neuron</i>, vol. 84, no. 1. Elsevier, pp. 152–163, 2014.","short":"A. Ritzau Jost, I. Delvendahl, A. Rings, N. Byczkowicz, H. Harada, R. Shigemoto, J. Hirrlinger, J. Eilers, S. Hallermann, Neuron 84 (2014) 152–163.","apa":"Ritzau Jost, A., Delvendahl, I., Rings, A., Byczkowicz, N., Harada, H., Shigemoto, R., … Hallermann, S. (2014). Ultrafast action potentials mediate kilohertz signaling at a central synapse. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2014.08.036\">https://doi.org/10.1016/j.neuron.2014.08.036</a>"},"type":"journal_article","quality_controlled":"1","issue":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":"        84","publication_status":"published","abstract":[{"text":"Fast synaptic transmission is important for rapid information processing. To explore the maximal rate of neuronal signaling and to analyze the presynaptic mechanisms, we focused on the input layer of the cerebellar cortex, where exceptionally high action potential (AP) frequencies have been reported invivo. With paired recordings between presynaptic cerebellar mossy fiber boutons and postsynaptic granule cells, we demonstrate reliable neurotransmission upto ~1 kHz. Presynaptic APs are ultrafast, with ~100μs half-duration. Both Kv1 and Kv3 potassium channels mediate the fast repolarization, rapidly inactivating sodium channels ensure metabolic efficiency, and little AP broadening occurs during bursts of up to 1.5 kHz. Presynaptic Cav2.1 (P/Q-type) calcium channels open efficiently during ultrafast APs. Furthermore, a subset of synaptic vesicles is tightly coupled to Ca2+ channels, and vesicles are rapidly recruited to the release site. These data reveal mechanisms of presynaptic AP generation and transmitter release underlying neuronal kHz signaling.","lang":"eng"}],"volume":84,"publist_id":"5197","language":[{"iso":"eng"}],"status":"public"},{"publication":"Nature Cell Biology","page":"758 - 769","_id":"1899","external_id":{"pmid":["25016959"]},"date_created":"2018-12-11T11:54:36Z","title":"Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN","date_updated":"2021-01-12T06:53:55Z","month":"07","article_processing_charge":"No","date_published":"2014-07-13T00:00:00Z","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159251/"}],"volume":16,"oa":1,"intvolume":"        16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"8","doi":"10.1038/ncb3001","oa_version":"Submitted Version","publisher":"Nature Publishing Group","day":"13","department":[{"_id":"SiHi"}],"year":"2014","author":[{"first_name":"Scott","last_name":"Williams","full_name":"Williams, Scott"},{"full_name":"Ratliff, Lyndsay","last_name":"Ratliff","first_name":"Lyndsay"},{"first_name":"Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87","full_name":"Postiglione, Maria P","last_name":"Postiglione"},{"last_name":"Knoblich","full_name":"Knoblich, Juergen","first_name":"Juergen"},{"first_name":"Elaine","full_name":"Fuchs, Elaine","last_name":"Fuchs"}],"citation":{"apa":"Williams, S., Ratliff, L., Postiglione, M. P., Knoblich, J., &#38; Fuchs, E. (2014). Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb3001\">https://doi.org/10.1038/ncb3001</a>","short":"S. Williams, L. Ratliff, M.P. Postiglione, J. Knoblich, E. Fuchs, Nature Cell Biology 16 (2014) 758–769.","ieee":"S. Williams, L. Ratliff, M. P. Postiglione, J. Knoblich, and E. Fuchs, “Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN,” <i>Nature Cell Biology</i>, vol. 16, no. 8. Nature Publishing Group, pp. 758–769, 2014.","ama":"Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. <i>Nature Cell Biology</i>. 2014;16(8):758-769. doi:<a href=\"https://doi.org/10.1038/ncb3001\">10.1038/ncb3001</a>","chicago":"Williams, Scott, Lyndsay Ratliff, Maria P Postiglione, Juergen Knoblich, and Elaine Fuchs. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/ncb3001\">https://doi.org/10.1038/ncb3001</a>.","ista":"Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. 2014. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. 16(8), 758–769.","mla":"Williams, Scott, et al. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” <i>Nature Cell Biology</i>, vol. 16, no. 8, Nature Publishing Group, 2014, pp. 758–69, doi:<a href=\"https://doi.org/10.1038/ncb3001\">10.1038/ncb3001</a>."},"type":"journal_article","article_type":"original","publist_id":"5196","publication_status":"published","abstract":[{"text":"Asymmetric cell divisions allow stem cells to balance proliferation and differentiation. During embryogenesis, murine epidermis expands rapidly from a single layer of unspecified basal layer progenitors to a stratified, differentiated epithelium. Morphogenesis involves perpendicular (asymmetric) divisions and the spindle orientation protein LGN, but little is known about how the apical localization of LGN is regulated. Here, we combine conventional genetics and lentiviral-mediated in vivo RNAi to explore the functions of the LGN-interacting proteins Par3, mInsc and Gα i3. Whereas loss of each gene alone leads to randomized division angles, combined loss of Gnai3 and mInsc causes a phenotype of mostly planar divisions, akin to loss of LGN. These findings lend experimental support for the hitherto untested model that Par3-mInsc and Gα i3 act cooperatively to polarize LGN and promote perpendicular divisions. Finally, we uncover a developmental switch between delamination-driven early stratification and spindle-orientation-dependent differentiation that occurs around E15, revealing a two-step mechanism underlying epidermal maturation.","lang":"eng"}],"status":"public","pmid":1,"language":[{"iso":"eng"}],"quality_controlled":"1"}]