[{"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"448","_id":"1681","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:12Z","date_updated":"2023-10-17T11:42:52Z","ddc":["000"],"scopus_import":"1","month":"09","intvolume":" 6","abstract":[{"lang":"eng","text":"In many social situations, individuals endeavor to find the single best possible partner, but are constrained to evaluate the candidates in sequence. Examples include the search for mates, economic partnerships, or any other long-term ties where the choice to interact involves two parties. Surprisingly, however, previous theoretical work on mutual choice problems focuses on finding equilibrium solutions, while ignoring the evolutionary dynamics of decisions. Empirically, this may be of high importance, as some equilibrium solutions can never be reached unless the population undergoes radical changes and a sufficient number of individuals change their decisions simultaneously. To address this question, we apply a mutual choice sequential search problem in an evolutionary game-theoretical model that allows one to find solutions that are favored by evolution. As an example, we study the influence of sequential search on the evolutionary dynamics of cooperation. For this, we focus on the classic snowdrift game and the prisoner’s dilemma game."}],"oa_version":"Published Version","issue":"4","volume":6,"ec_funded":1,"license":"https://creativecommons.org/licenses/by/4.0/","publication_identifier":{"eissn":["2073-4336"]},"publication_status":"published","file":[{"date_created":"2018-12-12T10:12:41Z","file_name":"IST-2016-448-v1+1_games-06-00413.pdf","date_updated":"2020-07-14T12:45:12Z","file_size":518832,"creator":"system","checksum":"912e1acbaf201100f447a43e4d5958bd","file_id":"4959","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"author":[{"id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas","full_name":"Priklopil, Tadeas","last_name":"Priklopil"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"publist_id":"5467","article_processing_charge":"No","title":"Evolution of decisions in population games with sequentially searching individuals","citation":{"ista":"Priklopil T, Chatterjee K. 2015. Evolution of decisions in population games with sequentially searching individuals. Games. 6(4), 413–437.","chicago":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games. MDPI, 2015. https://doi.org/10.3390/g6040413.","ama":"Priklopil T, Chatterjee K. Evolution of decisions in population games with sequentially searching individuals. Games. 2015;6(4):413-437. doi:10.3390/g6040413","apa":"Priklopil, T., & Chatterjee, K. (2015). Evolution of decisions in population games with sequentially searching individuals. Games. MDPI. https://doi.org/10.3390/g6040413","short":"T. Priklopil, K. Chatterjee, Games 6 (2015) 413–437.","ieee":"T. Priklopil and K. Chatterjee, “Evolution of decisions in population games with sequentially searching individuals,” Games, vol. 6, no. 4. MDPI, pp. 413–437, 2015.","mla":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games, vol. 6, no. 4, MDPI, 2015, pp. 413–37, doi:10.3390/g6040413."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"MDPI","oa":1,"page":"413 - 437","date_published":"2015-09-29T00:00:00Z","doi":"10.3390/g6040413","date_created":"2018-12-11T11:53:26Z","has_accepted_license":"1","year":"2015","day":"29","publication":"Games"},{"author":[{"last_name":"Martius","full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S"},{"first_name":"Eckehard","full_name":"Olbrich, Eckehard","last_name":"Olbrich"}],"publist_id":"5495","article_processing_charge":"No","title":"Quantifying emergent behavior of autonomous robots","citation":{"mla":"Martius, Georg S., and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” Entropy, vol. 17, no. 10, MDPI, 2015, pp. 7266–97, doi:10.3390/e17107266.","ieee":"G. S. Martius and E. Olbrich, “Quantifying emergent behavior of autonomous robots,” Entropy, vol. 17, no. 10. MDPI, pp. 7266–7297, 2015.","short":"G.S. Martius, E. Olbrich, Entropy 17 (2015) 7266–7297.","apa":"Martius, G. S., & Olbrich, E. (2015). Quantifying emergent behavior of autonomous robots. Entropy. MDPI. https://doi.org/10.3390/e17107266","ama":"Martius GS, Olbrich E. Quantifying emergent behavior of autonomous robots. Entropy. 2015;17(10):7266-7297. doi:10.3390/e17107266","chicago":"Martius, Georg S, and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” Entropy. MDPI, 2015. https://doi.org/10.3390/e17107266.","ista":"Martius GS, Olbrich E. 2015. Quantifying emergent behavior of autonomous robots. Entropy. 17(10), 7266–7297."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"page":"7266 - 7297","date_published":"2015-10-23T00:00:00Z","doi":"10.3390/e17107266","date_created":"2018-12-11T11:53:17Z","has_accepted_license":"1","year":"2015","day":"23","publication":"Entropy","quality_controlled":"1","publisher":"MDPI","oa":1,"acknowledgement":"This work was supported by the DFG priority program 1527 (Autonomous Learning) and by the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 318723 (MatheMACS) and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734.","file_date_updated":"2020-07-14T12:45:08Z","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"date_updated":"2023-10-17T11:42:00Z","ddc":["000"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"464","_id":"1655","volume":17,"issue":"10","ec_funded":1,"publication_status":"published","file":[{"checksum":"945d99631a96e0315acb26dc8541dcf9","file_id":"4943","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:12:25Z","file_name":"IST-2016-464-v1+1_entropy-17-07266.pdf","creator":"system","date_updated":"2020-07-14T12:45:08Z","file_size":6455007}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 17","abstract":[{"text":"Quantifying behaviors of robots which were generated autonomously from task-independent objective functions is an important prerequisite for objective comparisons of algorithms and movements of animals. The temporal sequence of such a behavior can be considered as a time series and hence complexity measures developed for time series are natural candidates for its quantification. The predictive information and the excess entropy are such complexity measures. They measure the amount of information the past contains about the future and thus quantify the nonrandom structure in the temporal sequence. However, when using these measures for systems with continuous states one has to deal with the fact that their values will depend on the resolution with which the systems states are observed. For deterministic systems both measures will diverge with increasing resolution. We therefore propose a new decomposition of the excess entropy in resolution dependent and resolution independent parts and discuss how they depend on the dimensionality of the dynamics, correlations and the noise level. For the practical estimation we propose to use estimates based on the correlation integral instead of the direct estimation of the mutual information based on next neighbor statistics because the latter allows less control of the scale dependencies. Using our algorithm we are able to show how autonomous learning generates behavior of increasing complexity with increasing learning duration.","lang":"eng"}],"oa_version":"Published Version"},{"publication":"ASN Neuro","day":"13","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:54:16Z","doi":"10.1177/1759091415575845","date_published":"2015-04-13T00:00:00Z","oa":1,"publisher":"SAGE Publications","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Chen C, Wang C, Zhao X, et al. Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. 2015;7(2). doi:10.1177/1759091415575845","apa":"Chen, C., Wang, C., Zhao, X., Zhou, T., Xu, D., Wang, Z., & Wang, Y. (2015). Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. SAGE Publications. https://doi.org/10.1177/1759091415575845","ieee":"C. Chen et al., “Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats,” ASN Neuro, vol. 7, no. 2. SAGE Publications, 2015.","short":"C. Chen, C. Wang, X. Zhao, T. Zhou, D. Xu, Z. Wang, Y. Wang, ASN Neuro 7 (2015).","mla":"Chen, Chong, et al. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” ASN Neuro, vol. 7, no. 2, SAGE Publications, 2015, doi:10.1177/1759091415575845.","ista":"Chen C, Wang C, Zhao X, Zhou T, Xu D, Wang Z, Wang Y. 2015. Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. 7(2).","chicago":"Chen, Chong, Chao Wang, Xuan Zhao, Tao Zhou, Dao Xu, Zhi Wang, and Ying Wang. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” ASN Neuro. SAGE Publications, 2015. https://doi.org/10.1177/1759091415575845."},"title":"Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats","article_processing_charge":"No","author":[{"last_name":"Chen","full_name":"Chen, Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong"},{"first_name":"Chao","full_name":"Wang, Chao","last_name":"Wang"},{"first_name":"Xuan","full_name":"Zhao, Xuan","last_name":"Zhao"},{"last_name":"Zhou","full_name":"Zhou, Tao","first_name":"Tao"},{"first_name":"Dao","full_name":"Xu, Dao","last_name":"Xu"},{"first_name":"Zhi","full_name":"Wang, Zhi","last_name":"Wang"},{"last_name":"Wang","full_name":"Wang, Ying","first_name":"Ying"}],"publist_id":"5269","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:14:08Z","file_name":"IST-2016-456-v1+1_ASN_Neuro-2015-Chen-.pdf","date_updated":"2020-07-14T12:45:18Z","file_size":1146814,"creator":"system","checksum":"53e16bd3fc2ae2c0d7de9164626c37aa","file_id":"5057","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","license":"https://creativecommons.org/licenses/by/3.0/","volume":7,"issue":"2","oa_version":"Published Version","abstract":[{"text":"Huge body of evidences demonstrated that volatile anesthetics affect the hippocampal neurogenesis and neurocognitive functions, and most of them showed impairment at anesthetic dose. Here, we investigated the effect of low dose (1.8%) sevoflurane on hippocampal neurogenesis and dentate gyrus-dependent learning. Neonatal rats at postnatal day 4 to 6 (P4-6) were treated with 1.8% sevoflurane for 6 hours. Neurogenesis was quantified by bromodeoxyuridine labeling and electrophysiology recording. Four and seven weeks after treatment, the Morris water maze and contextual-fear discrimination learning tests were performed to determine the influence on spatial learning and pattern separation. A 6-hour treatment with 1.8% sevoflurane promoted hippocampal neurogenesis and increased the survival of newborn cells and the proportion of immature granular cells in the dentate gyrus of neonatal rats. Sevoflurane-treated rats performed better during the training days of the Morris water maze test and in contextual-fear discrimination learning test. These results suggest that a subanesthetic dose of sevoflurane promotes hippocampal neurogenesis in neonatal rats and facilitates their performance in dentate gyrus-dependent learning tasks.","lang":"eng"}],"intvolume":" 7","month":"04","scopus_import":"1","ddc":["570"],"date_updated":"2023-10-18T06:47:30Z","file_date_updated":"2020-07-14T12:45:18Z","department":[{"_id":"PeJo"}],"_id":"1834","pubrep_id":"456","status":"public","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"type":"journal_article","article_type":"original"},{"title":"Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models","author":[{"first_name":"Matthias","full_name":"Erbar, Matthias","last_name":"Erbar"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338"},{"last_name":"Tetali","full_name":"Tetali, Prasad","first_name":"Prasad"}],"publist_id":"5520","external_id":{"arxiv":["1409.8605"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Erbar, Matthias, et al. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” Annales de La Faculté Des Sciences de Toulouse, vol. 24, no. 4, Faculté des sciences de Toulouse, 2015, pp. 781–800, doi:10.5802/afst.1464.","ieee":"M. Erbar, J. Maas, and P. Tetali, “Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models,” Annales de la faculté des sciences de Toulouse, vol. 24, no. 4. Faculté des sciences de Toulouse, pp. 781–800, 2015.","short":"M. Erbar, J. Maas, P. Tetali, Annales de La Faculté Des Sciences de Toulouse 24 (2015) 781–800.","apa":"Erbar, M., Maas, J., & Tetali, P. (2015). Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de La Faculté Des Sciences de Toulouse. Faculté des sciences de Toulouse. https://doi.org/10.5802/afst.1464","ama":"Erbar M, Maas J, Tetali P. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de la faculté des sciences de Toulouse. 2015;24(4):781-800. doi:10.5802/afst.1464","chicago":"Erbar, Matthias, Jan Maas, and Prasad Tetali. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” Annales de La Faculté Des Sciences de Toulouse. Faculté des sciences de Toulouse, 2015. https://doi.org/10.5802/afst.1464.","ista":"Erbar M, Maas J, Tetali P. 2015. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de la faculté des sciences de Toulouse. 24(4), 781–800."},"quality_controlled":"1","publisher":"Faculté des sciences de Toulouse","oa":1,"date_published":"2015-01-01T00:00:00Z","doi":"10.5802/afst.1464","date_created":"2018-12-11T11:53:10Z","page":"781 - 800","day":"01","publication":"Annales de la faculté des sciences de Toulouse","year":"2015","status":"public","article_type":"original","type":"journal_article","_id":"1635","department":[{"_id":"JaMa"}],"date_updated":"2023-10-18T07:48:28Z","month":"01","intvolume":" 24","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1409.8605"}],"oa_version":"Preprint","abstract":[{"text":"We calculate a Ricci curvature lower bound for some classical examples of random walks, namely, a chain on a slice of the n-dimensional discrete cube (the so-called Bernoulli-Laplace model) and the random transposition shuffle of the symmetric group of permutations on n letters.","lang":"eng"}],"issue":"4","volume":24,"language":[{"iso":"eng"}],"publication_status":"published"},{"_id":"14303","article_type":"letter_note","type":"journal_article","status":"public","date_updated":"2023-11-07T11:56:32Z","extern":"1","abstract":[{"lang":"eng","text":"Scaffolded DNA origami enables the fabrication of a variety of complex nanostructures that promise utility in diverse fields of application, ranging from biosensing over advanced therapeutics to metamaterials. The broad applicability of DNA origami as a material beyond the level of proof-of-concept studies critically depends, among other factors, on the availability of large amounts of pure single-stranded scaffold DNA. Here, we present a method for the efficient production of M13 bacteriophage-derived genomic DNA using high-cell-density fermentation of Escherichia coli in stirred-tank bioreactors. We achieve phage titers of up to 1.6 × 1014 plaque-forming units per mL. Downstream processing yields up to 410 mg of high-quality single-stranded DNA per one liter reaction volume, thus upgrading DNA origami-based nanotechnology from the milligram to the gram scale."}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1021/acs.nanolett.5b01461","open_access":"1"}],"month":"06","intvolume":" 15","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"7","volume":15,"citation":{"ieee":"B. Kick, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Efficient production of single-stranded phage DNA as scaffolds for DNA origami,” Nano Letters, vol. 15, no. 7. ACS Publications, pp. 4672–4676, 2015.","short":"B. Kick, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Nano Letters 15 (2015) 4672–4676.","apa":"Kick, B., Praetorius, F. M., Dietz, H., & Weuster-Botz, D. (2015). Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. ACS Publications. https://doi.org/10.1021/acs.nanolett.5b01461","ama":"Kick B, Praetorius FM, Dietz H, Weuster-Botz D. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 2015;15(7):4672-4676. doi:10.1021/acs.nanolett.5b01461","mla":"Kick, B., et al. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” Nano Letters, vol. 15, no. 7, ACS Publications, 2015, pp. 4672–76, doi:10.1021/acs.nanolett.5b01461.","ista":"Kick B, Praetorius FM, Dietz H, Weuster-Botz D. 2015. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 15(7), 4672–4676.","chicago":"Kick, B, Florian M Praetorius, H Dietz, and D Weuster-Botz. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” Nano Letters. ACS Publications, 2015. https://doi.org/10.1021/acs.nanolett.5b01461."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Kick","full_name":"Kick, B","first_name":"B"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M","last_name":"Praetorius","full_name":"Praetorius, Florian M"},{"first_name":"H","last_name":"Dietz","full_name":"Dietz, H"},{"full_name":"Weuster-Botz, D","last_name":"Weuster-Botz","first_name":"D"}],"article_processing_charge":"No","external_id":{"pmid":["26028443"]},"title":"Efficient production of single-stranded phage DNA as scaffolds for DNA origami","quality_controlled":"1","publisher":"ACS Publications","oa":1,"year":"2015","day":"01","publication":"Nano Letters","page":"4672-4676","date_published":"2015-06-01T00:00:00Z","doi":"10.1021/acs.nanolett.5b01461","date_created":"2023-09-06T12:52:47Z"},{"date_updated":"2024-02-21T13:52:07Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"_id":"1603","type":"conference","conference":{"location":"San Francisco, CA, United States","end_date":"2015-07-24","start_date":"2015-07-18","name":"CAV: Computer Aided Verification"},"status":"public","publication_identifier":{"eisbn":["978-3-319-21690-4"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"5549","status":"public","relation":"research_paper"}]},"volume":9206,"ec_funded":1,"abstract":[{"lang":"eng","text":"For deterministic systems, a counterexample to a property can simply be an error trace, whereas counterexamples in probabilistic systems are necessarily more complex. For instance, a set of erroneous traces with a sufficient cumulative probability mass can be used. Since these are too large objects to understand and manipulate, compact representations such as subchains have been considered. In the case of probabilistic systems with non-determinism, the situation is even more complex. While a subchain for a given strategy (or scheduler, resolving non-determinism) is a straightforward choice, we take a different approach. Instead, we focus on the strategy itself, and extract the most important decisions it makes, and present its succinct representation.\r\nThe key tools we employ to achieve this are (1) introducing a concept of importance of a state w.r.t. the strategy, and (2) learning using decision trees. There are three main consequent advantages of our approach. Firstly, it exploits the quantitative information on states, stressing the more important decisions. Secondly, it leads to a greater variability and degree of freedom in representing the strategies. Thirdly, the representation uses a self-explanatory data structure. In summary, our approach produces more succinct and more explainable strategies, as opposed to e.g. binary decision diagrams. Finally, our experimental results show that we can extract several rules describing the strategy even for very large systems that do not fit in memory, and based on the rules explain the erroneous behaviour."}],"oa_version":"Preprint","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.02834"}],"month":"07","intvolume":" 9206","citation":{"mla":"Brázdil, Tomáš, et al. Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Vol. 9206, Springer, 2015, pp. 158–77, doi:10.1007/978-3-319-21690-4_10.","ieee":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, and J. Kretinsky, “Counterexample explanation by learning small strategies in Markov decision processes,” presented at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015, vol. 9206, pp. 158–177.","short":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, J. Kretinsky, in:, Springer, 2015, pp. 158–177.","ama":"Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. Counterexample explanation by learning small strategies in Markov decision processes. In: Vol 9206. Springer; 2015:158-177. doi:10.1007/978-3-319-21690-4_10","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Fellner, A., & Kretinsky, J. (2015). Counterexample explanation by learning small strategies in Markov decision processes (Vol. 9206, pp. 158–177). Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21690-4_10","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Andreas Fellner, and Jan Kretinsky. “Counterexample Explanation by Learning Small Strategies in Markov Decision Processes,” 9206:158–77. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_10.","ista":"Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. 2015. Counterexample explanation by learning small strategies in Markov decision processes. CAV: Computer Aided Verification, LNCS, vol. 9206, 158–177."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5564","author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chmelik, Martin","last_name":"Chmelik","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fellner, Andreas","last_name":"Fellner","id":"42BABFB4-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky"}],"title":"Counterexample explanation by learning small strategies in Markov decision processes","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"year":"2015","day":"16","page":"158 - 177","doi":"10.1007/978-3-319-21690-4_10","date_published":"2015-07-16T00:00:00Z","date_created":"2018-12-11T11:52:58Z","acknowledgement":"This research was funded in part by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE) and Z211-N23 (Wittgenstein Award), European Research Council (ERC) Grant No 279307 (Graph Games), ERC Grant No 267989 (QUAREM), the Czech Science Foundation Grant No P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) REA Grant No 291734.","quality_controlled":"1","publisher":"Springer","oa":1},{"project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"title":"Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes","article_processing_charge":"No","publist_id":"5564","author":[{"first_name":"Andreas","id":"42BABFB4-F248-11E8-B48F-1D18A9856A87","full_name":"Fellner, Andreas","last_name":"Fellner"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A. Fellner, (2015).","ieee":"A. Fellner, “Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015.","apa":"Fellner, A. (2015). Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:28","ama":"Fellner A. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. 2015. doi:10.15479/AT:ISTA:28","mla":"Fellner, Andreas. Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria, 2015, doi:10.15479/AT:ISTA:28.","ista":"Fellner A. 2015. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:28.","chicago":"Fellner, Andreas. “Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015. https://doi.org/10.15479/AT:ISTA:28."},"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2018-12-12T12:31:29Z","doi":"10.15479/AT:ISTA:28","date_published":"2015-08-13T00:00:00Z","day":"13","year":"2015","has_accepted_license":"1","keyword":["Markov Decision Process","Decision Tree","Probabilistic Verification","Counterexample Explanation"],"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","_id":"5549","file_date_updated":"2020-07-14T12:47:00Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"ddc":["004"],"date_updated":"2024-02-21T13:52:07Z","month":"08","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This repository contains the experimental part of the CAV 2015 publication Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.\r\nWe extended the probabilistic model checker PRISM to represent strategies of Markov Decision Processes as Decision Trees.\r\nThe archive contains a java executable version of the extended tool (prism_dectree.jar) together with a few examples of the PRISM benchmark library.\r\nTo execute the program, please have a look at the README.txt, which provides instructions and further information on the archive.\r\nThe archive contains scripts that (if run often enough) reproduces the data presented in the publication."}],"ec_funded":1,"license":"https://creativecommons.org/publicdomain/zero/1.0/","contributor":[{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Kretinsky"}],"related_material":{"record":[{"relation":"popular_science","status":"public","id":"1603"}]},"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/zip","checksum":"b8bcb43c0893023cda66c1b69c16ac62","file_id":"5597","creator":"system","file_size":49557109,"date_updated":"2020-07-14T12:47:00Z","file_name":"IST-2015-28-v1+2_Fellner_DataRep.zip","date_created":"2018-12-12T13:02:31Z"}],"datarep_id":"28"},{"title":"Bounding Helly numbers via Betti numbers","publist_id":"5665","author":[{"first_name":"Xavier","full_name":"Goaoc, Xavier","last_name":"Goaoc"},{"first_name":"Pavel","full_name":"Paták, Pavel","last_name":"Paták"},{"first_name":"Zuzana","full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","last_name":"Patakova"},{"first_name":"Martin","orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin","last_name":"Tancer"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Goaoc, Xavier, et al. Bounding Helly Numbers via Betti Numbers. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–21, doi:10.4230/LIPIcs.SOCG.2015.507.","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Bounding Helly numbers via Betti numbers. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:507-521. doi:10.4230/LIPIcs.SOCG.2015.507","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2015). Bounding Helly numbers via Betti numbers (Vol. 34, pp. 507–521). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.507","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Bounding Helly numbers via Betti numbers,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 507–521.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–521.","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Bounding Helly Numbers via Betti Numbers,” 34:507–21. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.507.","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2015. Bounding Helly numbers via Betti numbers. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 507–521."},"doi":"10.4230/LIPIcs.SOCG.2015.507","date_published":"2015-01-01T00:00:00Z","date_created":"2018-12-11T11:52:27Z","page":"507 - 521","day":"01","has_accepted_license":"1","year":"2015","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"acknowledgement":"PP, ZP and MT were partially supported by the Charles University Grant GAUK 421511. ZP was\r\npartially supported by the Charles University Grant SVV-2014-260103. ZP and MT were partially\r\nsupported by the ERC Advanced Grant No. 267165 and by the project CE-ITI (GACR P202/12/G061)\r\nof the Czech Science Foundation. UW was partially supported by the Swiss National Science Foundation\r\n(grants SNSF-200020-138230 and SNSF-PP00P2-138948). Part of this work was done when XG was affiliated with INRIA Nancy Grand-Est and when MT was affiliated with Institutionen för matematik, Kungliga Tekniska Högskolan, then IST Austria.","file_date_updated":"2020-07-14T12:45:00Z","department":[{"_id":"UlWa"}],"ddc":["510"],"date_updated":"2024-02-28T12:59:37Z","status":"public","pubrep_id":"501","type":"conference","conference":{"end_date":"2015-06-25","location":"Eindhoven, Netherlands","start_date":"2015-06-22","name":"SoCG: Symposium on Computational Geometry"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1512","volume":34,"related_material":{"record":[{"relation":"later_version","id":"424","status":"public"}]},"file":[{"file_name":"IST-2016-501-v1+1_46.pdf","date_created":"2018-12-12T10:10:09Z","creator":"system","file_size":633712,"date_updated":"2020-07-14T12:45:00Z","checksum":"e6881df44d87fe0c2529c9f7b2724614","file_id":"4794","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"01","intvolume":" 34","alternative_title":["LIPIcs"],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b,d) such that the following holds. If F is a finite family of subsets of R^d such that the ith reduced Betti number (with Z_2 coefficients in singular homology) of the intersection of any proper subfamily G of F is at most b for every non-negative integer i less or equal to (d-1)/2, then F has Helly number at most h(b,d). These topological conditions are sharp: not controlling any of these first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map from C_*(K) to C_*(R^d). Both techniques are of independent interest.","lang":"eng"}]},{"page":"203 - 234","doi":"10.1515/crelle-2014-0122","date_published":"2015-02-20T00:00:00Z","date_created":"2018-12-11T11:45:32Z","year":"2015","day":"20","publication":"Journal fur die Reine und Angewandte Mathematik","quality_controlled":"1","publisher":"Walter de Gruyter","oa":1,"acknowledgement":"While working on this paper the authors were supported by the Leverhulme Trust and ERC grant 306457.","author":[{"last_name":"Browning","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Prendiville, Sean","last_name":"Prendiville","first_name":"Sean"}],"publist_id":"7631","article_processing_charge":"No","external_id":{"arxiv":["1402.4489"]},"title":"Improvements in Birch's theorem on forms in many variables","citation":{"ista":"Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many variables. Journal fur die Reine und Angewandte Mathematik. 2017(731), 203–234.","chicago":"Browning, Timothy D, and Sean Prendiville. “Improvements in Birch’s Theorem on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter, n.d. https://doi.org/10.1515/crelle-2014-0122.","ieee":"T. D. Browning and S. Prendiville, “Improvements in Birch’s theorem on forms in many variables,” Journal fur die Reine und Angewandte Mathematik, vol. 2017, no. 731. Walter de Gruyter, pp. 203–234.","short":"T.D. Browning, S. Prendiville, Journal Fur Die Reine Und Angewandte Mathematik 2017 (n.d.) 203–234.","ama":"Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many variables. Journal fur die Reine und Angewandte Mathematik. 2017(731):203-234. doi:10.1515/crelle-2014-0122","apa":"Browning, T. D., & Prendiville, S. (n.d.). Improvements in Birch’s theorem on forms in many variables. Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle-2014-0122","mla":"Browning, Timothy D., and Sean Prendiville. “Improvements in Birch’s Theorem on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik, vol. 2017, no. 731, Walter de Gruyter, pp. 203–34, doi:10.1515/crelle-2014-0122."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":2017,"related_material":{"record":[{"id":"256","status":"public","relation":"later_version"}]},"issue":"731","publication_identifier":{"issn":["0075-4102"]},"publication_status":"submitted","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1402.4489"}],"month":"02","intvolume":" 2017","abstract":[{"lang":"eng","text":"We show that a non-singular integral form of degree d is soluble non-trivially over the integers if and only if it is soluble non-trivially over the reals and the p-adic numbers, provided that the form has at least (d-\\sqrt{d}/2)2^d variables. This improves on a longstanding result of Birch."}],"oa_version":"Preprint","date_updated":"2024-03-05T12:09:22Z","extern":"1","type":"journal_article","article_type":"original","status":"public","_id":"271"},{"_id":"1675","type":"conference","conference":{"name":"CRYPTO: International Cryptology Conference","location":"Santa Barbara, CA, United States","end_date":"2015-08-20","start_date":"2015-08-16"},"status":"public","pubrep_id":"671","date_updated":"2024-03-20T08:31:49Z","department":[{"_id":"VlKo"},{"_id":"KrPi"}],"abstract":[{"lang":"eng","text":"Proofs of work (PoW) have been suggested by Dwork and Naor (Crypto’92) as protection to a shared resource. The basic idea is to ask the service requestor to dedicate some non-trivial amount of computational work to every request. The original applications included prevention of spam and protection against denial of service attacks. More recently, PoWs have been used to prevent double spending in the Bitcoin digital currency system. In this work, we put forward an alternative concept for PoWs - so-called proofs of space (PoS), where a service requestor must dedicate a significant amount of disk space as opposed to computation. We construct secure PoS schemes in the random oracle model (with one additional mild assumption required for the proof to go through), using graphs with high “pebbling complexity” and Merkle hash-trees. We discuss some applications, including follow-up work where a decentralized digital currency scheme called Spacecoin is constructed that uses PoS (instead of wasteful PoW like in Bitcoin) to prevent double spending. The main technical contribution of this work is the construction of (directed, loop-free) graphs on N vertices with in-degree O(log logN) such that even if one places Θ(N) pebbles on the nodes of the graph, there’s a constant fraction of nodes that needs Θ(N) steps to be pebbled (where in every step one can put a pebble on a node if all its parents have a pebble)."}],"oa_version":"Preprint","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2013/796.pdf"}],"month":"08","intvolume":" 9216","publication_identifier":{"issn":["0302-9743"],"isbn":["9783662479995"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":9216,"related_material":{"record":[{"relation":"earlier_version","id":"2274","status":"public"}]},"ec_funded":1,"project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"},{"grant_number":"259668","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ieee":"S. Dziembowski, S. Faust, V. Kolmogorov, and K. Z. Pietrzak, “Proofs of space,” in 35th Annual Cryptology Conference, Santa Barbara, CA, United States, 2015, vol. 9216, pp. 585–605.","short":"S. Dziembowski, S. Faust, V. Kolmogorov, K.Z. Pietrzak, in:, 35th Annual Cryptology Conference, Springer, 2015, pp. 585–605.","ama":"Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. Proofs of space. In: 35th Annual Cryptology Conference. Vol 9216. Springer; 2015:585-605. doi:10.1007/978-3-662-48000-7_29","apa":"Dziembowski, S., Faust, S., Kolmogorov, V., & Pietrzak, K. Z. (2015). Proofs of space. In 35th Annual Cryptology Conference (Vol. 9216, pp. 585–605). Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-48000-7_29","mla":"Dziembowski, Stefan, et al. “Proofs of Space.” 35th Annual Cryptology Conference, vol. 9216, Springer, 2015, pp. 585–605, doi:10.1007/978-3-662-48000-7_29.","ista":"Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. 2015. Proofs of space. 35th Annual Cryptology Conference. CRYPTO: International Cryptology Conference, LNCS, vol. 9216, 585–605.","chicago":"Dziembowski, Stefan, Sebastian Faust, Vladimir Kolmogorov, and Krzysztof Z Pietrzak. “Proofs of Space.” In 35th Annual Cryptology Conference, 9216:585–605. Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_29."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Dziembowski","full_name":"Dziembowski, Stefan","first_name":"Stefan"},{"last_name":"Faust","full_name":"Faust, Sebastian","first_name":"Sebastian"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"publist_id":"5474","article_processing_charge":"No","title":"Proofs of space","quality_controlled":"1","publisher":"Springer","oa":1,"year":"2015","day":"01","publication":"35th Annual Cryptology Conference","page":"585 - 605","doi":"10.1007/978-3-662-48000-7_29","date_published":"2015-08-01T00:00:00Z","date_created":"2018-12-11T11:53:24Z"},{"_id":"15160","type":"journal_article","article_type":"original","keyword":["Cell Biology","Molecular Biology"],"status":"public","date_updated":"2024-03-25T11:52:26Z","extern":"1","abstract":[{"text":"The circadian clock orchestrates global changes in transcriptional regulation on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven by other bHLH-PAS transcription factors have a homologous repressor that modulates activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1. We show here that the cancer/testis antigen PASD1 fulfills this role to suppress circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1 is restricted to germline tissues in healthy individuals but can be induced in cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human cancer cells significantly increases the amplitude of transcriptional oscillations to generate more robust circadian rhythms. Our results describe a function for a germline-specific protein in regulation of the circadian clock and provide a molecular link from oncogenic transformation to suppression of circadian rhythms.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molcel.2015.03.031"}],"scopus_import":"1","intvolume":" 58","month":"06","publication_status":"published","publication_identifier":{"issn":["1097-2765"]},"language":[{"iso":"eng"}],"volume":58,"issue":"5","citation":{"chicago":"Michael, Alicia K., Stacy L. Harvey, Patrick J. Sammons, Amanda P. Anderson, Hema M. Kopalle, Alison H. Banham, and Carrie L. Partch. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” Molecular Cell. Elsevier, 2015. https://doi.org/10.1016/j.molcel.2015.03.031.","ista":"Michael AK, Harvey SL, Sammons PJ, Anderson AP, Kopalle HM, Banham AH, Partch CL. 2015. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 58(5), 743–754.","mla":"Michael, Alicia K., et al. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” Molecular Cell, vol. 58, no. 5, Elsevier, 2015, pp. 743–54, doi:10.1016/j.molcel.2015.03.031.","apa":"Michael, A. K., Harvey, S. L., Sammons, P. J., Anderson, A. P., Kopalle, H. M., Banham, A. H., & Partch, C. L. (2015). Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2015.03.031","ama":"Michael AK, Harvey SL, Sammons PJ, et al. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 2015;58(5):743-754. doi:10.1016/j.molcel.2015.03.031","short":"A.K. Michael, S.L. Harvey, P.J. Sammons, A.P. Anderson, H.M. Kopalle, A.H. Banham, C.L. Partch, Molecular Cell 58 (2015) 743–754.","ieee":"A. K. Michael et al., “Cancer/Testis antigen PASD1 silences the circadian clock,” Molecular Cell, vol. 58, no. 5. Elsevier, pp. 743–754, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Michael","full_name":"Michael, Alicia Kathleen","first_name":"Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c"},{"full_name":"Harvey, Stacy L.","last_name":"Harvey","first_name":"Stacy L."},{"first_name":"Patrick J.","full_name":"Sammons, Patrick J.","last_name":"Sammons"},{"first_name":"Amanda P.","full_name":"Anderson, Amanda P.","last_name":"Anderson"},{"last_name":"Kopalle","full_name":"Kopalle, Hema M.","first_name":"Hema M."},{"first_name":"Alison H.","last_name":"Banham","full_name":"Banham, Alison H."},{"first_name":"Carrie L.","full_name":"Partch, Carrie L.","last_name":"Partch"}],"title":"Cancer/Testis antigen PASD1 silences the circadian clock","oa":1,"quality_controlled":"1","publisher":"Elsevier","year":"2015","publication":"Molecular Cell","day":"04","page":"743-754","date_created":"2024-03-21T07:58:08Z","doi":"10.1016/j.molcel.2015.03.031","date_published":"2015-06-04T00:00:00Z"},{"issue":"9","volume":40,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0968-0004"]},"intvolume":" 40","month":"09","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"It is widely recognized that BMAL1 is an essential subunit of the primary transcription factor that drives rhythmic circadian transcription in the nucleus. In a surprising turn, Lipton et al. now show that BMAL1 rhythmically interacts with translational machinery in the cytosol to stimulate protein synthesis in response to mTOR signaling."}],"extern":"1","date_updated":"2024-03-25T11:53:58Z","keyword":["Molecular Biology","Biochemistry"],"status":"public","article_type":"original","type":"journal_article","_id":"15159","date_created":"2024-03-21T07:57:44Z","doi":"10.1016/j.tibs.2015.07.006","date_published":"2015-09-01T00:00:00Z","page":"489-490","publication":"Trends in Biochemical Sciences","day":"01","year":"2015","quality_controlled":"1","publisher":"Elsevier","title":"Cytosolic BMAL1 moonlights as a translation factor","article_processing_charge":"No","author":[{"last_name":"Michael","full_name":"Michael, Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia Kathleen"},{"last_name":"Asimgil","full_name":"Asimgil, Hande","first_name":"Hande"},{"first_name":"Carrie L.","full_name":"Partch, Carrie L.","last_name":"Partch"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. K. Michael, H. Asimgil, and C. L. Partch, “Cytosolic BMAL1 moonlights as a translation factor,” Trends in Biochemical Sciences, vol. 40, no. 9. Elsevier, pp. 489–490, 2015.","short":"A.K. Michael, H. Asimgil, C.L. Partch, Trends in Biochemical Sciences 40 (2015) 489–490.","apa":"Michael, A. K., Asimgil, H., & Partch, C. L. (2015). Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. Elsevier. https://doi.org/10.1016/j.tibs.2015.07.006","ama":"Michael AK, Asimgil H, Partch CL. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 2015;40(9):489-490. doi:10.1016/j.tibs.2015.07.006","mla":"Michael, Alicia K., et al. “Cytosolic BMAL1 Moonlights as a Translation Factor.” Trends in Biochemical Sciences, vol. 40, no. 9, Elsevier, 2015, pp. 489–90, doi:10.1016/j.tibs.2015.07.006.","ista":"Michael AK, Asimgil H, Partch CL. 2015. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 40(9), 489–490.","chicago":"Michael, Alicia K., Hande Asimgil, and Carrie L. Partch. “Cytosolic BMAL1 Moonlights as a Translation Factor.” Trends in Biochemical Sciences. Elsevier, 2015. https://doi.org/10.1016/j.tibs.2015.07.006."}},{"_id":"1619","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"468","date_updated":"2024-03-27T23:30:28Z","ddc":["570"],"department":[{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:45:07Z","abstract":[{"text":"The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"11","intvolume":" 13","publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4723","checksum":"0e82e3279f50b15c6c170c042627802b","file_size":1387760,"date_updated":"2020-07-14T12:45:07Z","creator":"system","file_name":"IST-2016-468-v1+1_journal.pbio.1002299.pdf","date_created":"2018-12-12T10:09:00Z"}],"language":[{"iso":"eng"}],"volume":13,"issue":"11","related_material":{"record":[{"status":"public","id":"9711","relation":"research_data"},{"id":"9765","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"6263"}]},"ec_funded":1,"article_number":"e1002299","project":[{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"},{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"303507","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 13(11), e1002299.","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak, E., & Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 2015;13(11). doi:10.1371/journal.pbio.1002299","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak, M.T. Bollenbach, PLoS Biology 13 (2015).","ieee":"G. Chevereau et al., “Quantifying the determinants of evolutionary dynamics leading to drug resistance,” PLoS Biology, vol. 13, no. 11. Public Library of Science, 2015.","mla":"Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology, vol. 13, no. 11, e1002299, Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chevereau","full_name":"Chevereau, Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","first_name":"Guillaume"},{"last_name":"Dravecka","orcid":"0000-0002-2519-8004","full_name":"Dravecka, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta"},{"full_name":"Batur, Tugce","last_name":"Batur","first_name":"Tugce"},{"last_name":"Guvenek","full_name":"Guvenek, Aysegul","first_name":"Aysegul"},{"first_name":"Dilay","last_name":"Ayhan","full_name":"Ayhan, Dilay"},{"first_name":"Erdal","full_name":"Toprak, Erdal","last_name":"Toprak"},{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"}],"publist_id":"5547","title":"Quantifying the determinants of evolutionary dynamics leading to drug resistance","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2015","day":"18","publication":"PLoS Biology","date_published":"2015-11-18T00:00:00Z","doi":"10.1371/journal.pbio.1002299","date_created":"2018-12-11T11:53:04Z"},{"doi":"10.1073/pnas.1410159111","date_published":"2014-12-01T00:00:00Z","date_created":"2021-11-29T13:09:53Z","page":"17869-17874","day":"01","publication":"Proceedings of the National Academy of Sciences","year":"2014","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"acknowledgement":"We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs, for helpful discussions. A.Š. acknowledges support from the Human Frontier Science Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology and Biological Sciences Research Council. D.F. acknowledges European Research Council Advanced Grant 227758.","title":"Crucial role of nonspecific interactions in amyloid nucleation","author":[{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"first_name":"Yassmine C.","full_name":"Chebaro, Yassmine C.","last_name":"Chebaro"},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."},{"first_name":"Daan","full_name":"Frenkel, Daan","last_name":"Frenkel"}],"external_id":{"pmid":["25453085"],"arxiv":["1412.0897"]},"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"short":"A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National Academy of Sciences 111 (2014) 17869–17874.","ieee":"A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of nonspecific interactions in amyloid nucleation,” Proceedings of the National Academy of Sciences, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874, 2014.","ama":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 2014;111(50):17869-17874. doi:10.1073/pnas.1410159111","apa":"Šarić, A., Chebaro, Y. C., Knowles, T. P. J., & Frenkel, D. (2014). Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1410159111","mla":"Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings of the National Academy of Sciences, vol. 111, no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:10.1073/pnas.1410159111.","ista":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 111(50), 17869–17874.","chicago":"Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410159111."},"issue":"50","volume":111,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","month":"12","intvolume":" 111","scopus_import":"1","main_file_link":[{"url":"https://www.pnas.org/content/111/50/17869","open_access":"1"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory."}],"extern":"1","date_updated":"2021-11-29T13:29:05Z","status":"public","keyword":["multidisciplinary"],"article_type":"original","type":"journal_article","_id":"10382"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1310.0826"}],"scopus_import":"1","intvolume":" 89","month":"05","abstract":[{"lang":"eng","text":"We use numerical simulations to compute the equation of state of a suspension of spherical self-propelled nanoparticles in two and three dimensions. We study in detail the effect of excluded volume interactions and confinement as a function of the system's temperature, concentration, and strength of the propulsion. We find a striking nonmonotonic dependence of the pressure on the temperature and provide simple scaling arguments to predict and explain the occurrence of such anomalous behavior. We explicitly show how our results have important implications for the effective forces on passive components suspended in a bath of active particles."}],"pmid":1,"oa_version":"Preprint","issue":"5","volume":89,"publication_status":"published","publication_identifier":{"eissn":["1550-2376"],"issn":["1539-3755"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"10383","date_updated":"2021-11-29T13:29:01Z","extern":"1","oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_created":"2021-11-29T13:10:33Z","date_published":"2014-05-06T00:00:00Z","doi":"10.1103/physreve.89.052303","year":"2014","publication":"Physical Review E","day":"06","article_number":"052303","article_processing_charge":"No","external_id":{"pmid":["25353796"],"arxiv":["1310.0826"]},"author":[{"first_name":"S. A.","full_name":"Mallory, S. A.","last_name":"Mallory"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"first_name":"C.","last_name":"Valeriani","full_name":"Valeriani, C."},{"full_name":"Cacciuto, A.","last_name":"Cacciuto","first_name":"A."}],"title":"Anomalous thermomechanical properties of a self-propelled colloidal fluid","citation":{"short":"S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014).","ieee":"S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical properties of a self-propelled colloidal fluid,” Physical Review E, vol. 89, no. 5. American Physical Society, 2014.","apa":"Mallory, S. A., Šarić, A., Valeriani, C., & Cacciuto, A. (2014). Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.89.052303","ama":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 2014;89(5). doi:10.1103/physreve.89.052303","mla":"Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical Review E, vol. 89, no. 5, 052303, American Physical Society, 2014, doi:10.1103/physreve.89.052303.","ista":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303.","chicago":"Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.052303."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"type":"journal_article","status":"public","_id":"1058","article_processing_charge":"No","author":[{"full_name":"Jensen, Nickels","last_name":"Jensen","first_name":"Nickels"},{"last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Willig","full_name":"Willig, Katrin","first_name":"Katrin"},{"last_name":"Lavoie Cardinal","full_name":"Lavoie Cardinal, Flavie","first_name":"Flavie"},{"first_name":"Tanja","full_name":"Brakemann, Tanja","last_name":"Brakemann"},{"last_name":"Hell","full_name":"Hell, Stefan","first_name":"Stefan"},{"first_name":"Stefan","last_name":"Jakobs","full_name":"Jakobs, Stefan"}],"publist_id":"6332","title":"Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang","citation":{"mla":"Jensen, Nickels, et al. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem, vol. 15, no. 4, Wiley-Blackwell, 2014, pp. 756–62, doi:10.1002/cphc.201301034.","ieee":"N. Jensen et al., “Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang,” ChemPhysChem, vol. 15, no. 4. Wiley-Blackwell, pp. 756–762, 2014.","short":"N. Jensen, J.G. Danzl, K. Willig, F. Lavoie Cardinal, T. Brakemann, S. Hell, S. Jakobs, ChemPhysChem 15 (2014) 756–762.","apa":"Jensen, N., Danzl, J. G., Willig, K., Lavoie Cardinal, F., Brakemann, T., Hell, S., & Jakobs, S. (2014). Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. Wiley-Blackwell. https://doi.org/10.1002/cphc.201301034","ama":"Jensen N, Danzl JG, Willig K, et al. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 2014;15(4):756-762. doi:10.1002/cphc.201301034","chicago":"Jensen, Nickels, Johann G Danzl, Katrin Willig, Flavie Lavoie Cardinal, Tanja Brakemann, Stefan Hell, and Stefan Jakobs. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem. Wiley-Blackwell, 2014. https://doi.org/10.1002/cphc.201301034.","ista":"Jensen N, Danzl JG, Willig K, Lavoie Cardinal F, Brakemann T, Hell S, Jakobs S. 2014. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 15(4), 756–762."},"date_updated":"2021-01-12T06:47:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","publisher":"Wiley-Blackwell","intvolume":" 15","month":"03","abstract":[{"lang":"eng","text":"Diffraction-unlimited far-field super-resolution fluorescence (nanoscopy) methods typically rely on transiently transferring fluorophores between two states, whereby this transfer is usually laid out as a switch. However, depending on whether this is induced in a spatially controlled manner using a pattern of light (coordinate-targeted) or stochastically on a single-molecule basis, specific requirements on the fluorophores are imposed. Therefore, the fluorophores are usually utilized just for one class of methods only. In this study we demonstrate that the reversibly switchable fluorescent protein Dreiklang enables live-cell recordings in both spatially controlled and stochastic modes. We show that the Dreiklang chromophore entails three different light-induced switching mechanisms, namely a reversible photochemical one, off-switching by stimulated emission, and a reversible transfer to a long-lived dark state from the S1 state, all of which can be utilized to overcome the diffraction barrier. We also find that for the single-molecule- based stochastic GSDIM approach (ground-state depletion followed by individual molecule return), Dreiklang provides a larger number of on-off localization events as compared to its progenitor Citrine. Altogether, Dreiklang is a versatile probe for essentially all popular forms of live-cell fluorescence nanoscopy."}],"oa_version":"None","page":"756 - 762","date_created":"2018-12-11T11:49:55Z","doi":"10.1002/cphc.201301034","date_published":"2014-03-17T00:00:00Z","issue":"4","volume":15,"year":"2014","publication_status":"published","publication":"ChemPhysChem","language":[{"iso":"eng"}],"day":"17"},{"date_updated":"2022-03-04T08:26:05Z","department":[{"_id":"CaHe"}],"_id":"10815","article_type":"original","type":"journal_article","keyword":["Developmental Biology","Embryology","General Medicine","Pediatrics","Perinatology","and Child Health"],"status":"public","publication_status":"published","publication_identifier":{"issn":["0914-3505"]},"language":[{"iso":"eng"}],"issue":"1","volume":54,"abstract":[{"lang":"eng","text":"In the last several decades, developmental biology has clarified the molecular mechanisms of embryogenesis and organogenesis. In particular, it has demonstrated that the “tool-kit genes” essential for regulating developmental processes are not only highly conserved among species, but are also used as systems at various times and places in an organism to control distinct developmental events. Therefore, mutations in many of these tool-kit genes may cause congenital diseases involving morphological abnormalities. This link between genes and abnormal morphological phenotypes underscores the importance of understanding how cells behave and contribute to morphogenesis as a result of gene function. Recent improvements in live imaging and in quantitative analyses of cellular dynamics will advance our understanding of the cellular pathogenesis of congenital diseases associated with aberrant morphologies. In these studies, it is critical to select an appropriate model organism for the particular phenomenon of interest."}],"pmid":1,"oa_version":"None","main_file_link":[{"url":"https://doi.org/10.1111/cga.12039","open_access":"1"}],"scopus_import":"1","intvolume":" 54","month":"02","citation":{"ieee":"M. Hashimoto, H. Morita, and N. Ueno, “Molecular and cellular mechanisms of development underlying congenital diseases,” Congenital Anomalies, vol. 54, no. 1. Wiley, pp. 1–7, 2014.","short":"M. Hashimoto, H. Morita, N. Ueno, Congenital Anomalies 54 (2014) 1–7.","ama":"Hashimoto M, Morita H, Ueno N. Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. 2014;54(1):1-7. doi:10.1111/cga.12039","apa":"Hashimoto, M., Morita, H., & Ueno, N. (2014). Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. Wiley. https://doi.org/10.1111/cga.12039","mla":"Hashimoto, Masakazu, et al. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” Congenital Anomalies, vol. 54, no. 1, Wiley, 2014, pp. 1–7, doi:10.1111/cga.12039.","ista":"Hashimoto M, Morita H, Ueno N. 2014. Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. 54(1), 1–7.","chicago":"Hashimoto, Masakazu, Hitoshi Morita, and Naoto Ueno. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” Congenital Anomalies. Wiley, 2014. https://doi.org/10.1111/cga.12039."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["24666178"]},"article_processing_charge":"No","author":[{"last_name":"Hashimoto","full_name":"Hashimoto, Masakazu","first_name":"Masakazu"},{"first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","last_name":"Morita","full_name":"Morita, Hitoshi"},{"last_name":"Ueno","full_name":"Ueno, Naoto","first_name":"Naoto"}],"title":"Molecular and cellular mechanisms of development underlying congenital diseases","year":"2014","publication":"Congenital Anomalies","day":"01","page":"1-7","date_created":"2022-03-04T08:17:25Z","date_published":"2014-02-01T00:00:00Z","doi":"10.1111/cga.12039","acknowledgement":"The authors thank all the members of the Division of Morphogenesis, National Institute for Basic Biology, for their contributions to the research, their encouragement, and helpful discussions, particularly Dr M. Suzuki for his critical reading of the manuscript. We also thank the Model Animal Research and Spectrography and Bioimaging Facilities, NIBB Core Research Facilities, for technical support. M.H. was supported by a research fellowship from the Japan Society for the Promotion of Science (JSPS). Our work introduced in this review was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan, to N.U.","oa":1,"publisher":"Wiley","quality_controlled":"1"},{"article_processing_charge":"No","department":[{"_id":"EvBe"}],"editor":[{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"}],"title":"Auxin and Its Role in Plant Development","citation":{"ista":"Zažímalová E, Petrášek J, Benková E eds. 2014. Auxin and Its Role in Plant Development 1st ed., Vienna: Springer Nature, 444p.","chicago":"Zažímalová, Eva, Jan Petrášek, and Eva Benková, eds. Auxin and Its Role in Plant Development. 1st ed. Vienna: Springer Nature, 2014. https://doi.org/10.1007/978-3-7091-1526-8.","ieee":"E. Zažímalová, J. Petrášek, and E. Benková, Eds., Auxin and Its Role in Plant Development, 1st ed. Vienna: Springer Nature, 2014.","short":"E. Zažímalová, J. Petrášek, E. Benková, eds., Auxin and Its Role in Plant Development, 1st ed., Springer Nature, Vienna, 2014.","ama":"Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development. 1st ed. Vienna: Springer Nature; 2014. doi:10.1007/978-3-7091-1526-8","apa":"Zažímalová, E., Petrášek, J., & Benková, E. (Eds.). (2014). Auxin and Its Role in Plant Development (1st ed.). Vienna: Springer Nature. https://doi.org/10.1007/978-3-7091-1526-8","mla":"Zažímalová, Eva, et al., editors. Auxin and Its Role in Plant Development. 1st ed., Springer Nature, 2014, doi:10.1007/978-3-7091-1526-8."},"date_updated":"2022-03-04T07:38:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_editor","status":"public","_id":"10811","page":"444","doi":"10.1007/978-3-7091-1526-8","date_published":"2014-04-01T00:00:00Z","date_created":"2022-03-03T11:52:44Z","publication_identifier":{"eisbn":["9783709115268"],"isbn":["9783709115251"]},"publication_status":"published","year":"2014","day":"01","language":[{"iso":"eng"}],"scopus_import":"1","publisher":"Springer Nature","quality_controlled":"1","edition":"1","month":"04","place":"Vienna","abstract":[{"text":"Auxin is an important signaling compound in plants and vital for plant development and growth. The present book, Auxin and its Role in Plant Development, provides the reader with detailed and comprehensive insight into the functioning of the molecule on the whole and specifically in plant development. In the first part, the functioning, metabolism and signaling pathways of auxin in plants are explained, the second part depicts the specific role of auxin in plant development and the third part describes the interaction and functioning of the signaling compound upon stimuli of the environment. Each chapter is written by international experts in the respective field and designed for scientists and researchers in plant biology, plant development and cell biology to summarize the recent progress in understanding the role of auxin and suggest future perspectives for auxin research.","lang":"eng"}],"oa_version":"None"},{"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"title":"Parameterized model checking of token-passing systems","author":[{"last_name":"Aminof","full_name":"Aminof, Benjamin","first_name":"Benjamin","id":"4A55BD00-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jacobs","full_name":"Jacobs, Swen","first_name":"Swen"},{"first_name":"Ayrat","last_name":"Khalimov","full_name":"Khalimov, Ayrat"},{"id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha","last_name":"Rubin","full_name":"Rubin, Sasha"}],"external_id":{"arxiv":["1311.4425"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Aminof B, Jacobs S, Khalimov A, Rubin S. Parameterized model checking of token-passing systems. In: Verification, Model Checking, and Abstract Interpretation. Vol 8318. Springer Nature; 2014:262-281. doi:10.1007/978-3-642-54013-4_15","apa":"Aminof, B., Jacobs, S., Khalimov, A., & Rubin, S. (2014). Parameterized model checking of token-passing systems. In Verification, Model Checking, and Abstract Interpretation (Vol. 8318, pp. 262–281). San Diego, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_15","ieee":"B. Aminof, S. Jacobs, A. Khalimov, and S. Rubin, “Parameterized model checking of token-passing systems,” in Verification, Model Checking, and Abstract Interpretation, San Diego, CA, United States, 2014, vol. 8318, pp. 262–281.","short":"B. Aminof, S. Jacobs, A. Khalimov, S. Rubin, in:, Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 262–281.","mla":"Aminof, Benjamin, et al. “Parameterized Model Checking of Token-Passing Systems.” Verification, Model Checking, and Abstract Interpretation, vol. 8318, Springer Nature, 2014, pp. 262–81, doi:10.1007/978-3-642-54013-4_15.","ista":"Aminof B, Jacobs S, Khalimov A, Rubin S. 2014. Parameterized model checking of token-passing systems. Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 262–281.","chicago":"Aminof, Benjamin, Swen Jacobs, Ayrat Khalimov, and Sasha Rubin. “Parameterized Model Checking of Token-Passing Systems.” In Verification, Model Checking, and Abstract Interpretation, 8318:262–81. Springer Nature, 2014. https://doi.org/10.1007/978-3-642-54013-4_15."},"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"This work was supported by the Austrian Science Fund through grant P23499-N23\r\nand through the RiSE network (S11403, S11405, S11406, S11407-N23); ERC Starting Grant (279307: Graph Games); Vienna Science and Technology Fund (WWTF)\r\ngrants PROSEED, ICT12-059, and VRG11-005.","date_published":"2014-01-30T00:00:00Z","doi":"10.1007/978-3-642-54013-4_15","date_created":"2022-03-18T13:01:22Z","page":"262-281","day":"30","publication":"Verification, Model Checking, and Abstract Interpretation","year":"2014","status":"public","type":"conference","conference":{"location":"San Diego, CA, United States","end_date":"2014-01-21","start_date":"2014-01-19","name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation"},"_id":"10884","department":[{"_id":"KrCh"}],"date_updated":"2022-05-17T08:36:01Z","month":"01","intvolume":" 8318","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1311.4425"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We revisit the parameterized model checking problem for token-passing systems and specifications in indexed CTL ∗ \\X. Emerson and Namjoshi (1995, 2003) have shown that parameterized model checking of indexed CTL ∗ \\X in uni-directional token rings can be reduced to checking rings up to some cutoff size. Clarke et al. (2004) have shown a similar result for general topologies and indexed LTL \\X, provided processes cannot choose the directions for sending or receiving the token.\r\nWe unify and substantially extend these results by systematically exploring fragments of indexed CTL ∗ \\X with respect to general topologies. For each fragment we establish whether a cutoff exists, and for some concrete topologies, such as rings, cliques and stars, we infer small cutoffs. Finally, we show that the problem becomes undecidable, and thus no cutoffs exist, if processes are allowed to choose the directions in which they send or from which they receive the token."}],"volume":8318,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9783642540134"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783642540127"]},"publication_status":"published"},{"series_title":"Mathematics and Visualization","_id":"10893","status":"public","type":"book_chapter","date_updated":"2022-06-21T12:01:47Z","department":[{"_id":"HeEd"}],"oa_version":"None","abstract":[{"text":"Saddle periodic orbits are an essential and stable part of the topological skeleton of a 3D vector field. Nevertheless, there is currently no efficient algorithm to robustly extract these features. In this chapter, we present a novel technique to extract saddle periodic orbits. Exploiting the analytic properties of such an orbit, we propose a scalar measure based on the finite-time Lyapunov exponent (FTLE) that indicates its presence. Using persistent homology, we can then extract the robust cycles of this field. These cycles thereby represent the saddle periodic orbits of the given vector field. We discuss the different existing FTLE approximation schemes regarding their applicability to this specific problem and propose an adapted version of FTLE called Normalized Velocity Separation. Finally, we evaluate our method using simple analytic vector field data.","lang":"eng"}],"intvolume":" 1","place":"Cham","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1612-3786"],"eissn":["2197-666X"],"isbn":["9783319040981"],"eisbn":["9783319040998"]},"ec_funded":1,"volume":1,"project":[{"name":"Topological Complex Systems","grant_number":"318493","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kasten, Jens, Jan Reininghaus, Wieland Reich, and Gerik Scheuermann. “Toward the Extraction of Saddle Periodic Orbits.” In Topological Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 1:55–69. Mathematics and Visualization. Cham: Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_4.","ista":"Kasten J, Reininghaus J, Reich W, Scheuermann G. 2014.Toward the extraction of saddle periodic orbits. In: Topological Methods in Data Analysis and Visualization III . vol. 1, 55–69.","mla":"Kasten, Jens, et al. “Toward the Extraction of Saddle Periodic Orbits.” Topological Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer et al., vol. 1, Springer, 2014, pp. 55–69, doi:10.1007/978-3-319-04099-8_4.","short":"J. Kasten, J. Reininghaus, W. Reich, G. Scheuermann, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III , Springer, Cham, 2014, pp. 55–69.","ieee":"J. Kasten, J. Reininghaus, W. Reich, and G. Scheuermann, “Toward the extraction of saddle periodic orbits,” in Topological Methods in Data Analysis and Visualization III , vol. 1, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Cham: Springer, 2014, pp. 55–69.","ama":"Kasten J, Reininghaus J, Reich W, Scheuermann G. Toward the extraction of saddle periodic orbits. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III . Vol 1. Mathematics and Visualization. Cham: Springer; 2014:55-69. doi:10.1007/978-3-319-04099-8_4","apa":"Kasten, J., Reininghaus, J., Reich, W., & Scheuermann, G. (2014). Toward the extraction of saddle periodic orbits. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III (Vol. 1, pp. 55–69). Cham: Springer. https://doi.org/10.1007/978-3-319-04099-8_4"},"editor":[{"first_name":"Peer-Timo","last_name":"Bremer","full_name":"Bremer, Peer-Timo"},{"first_name":"Ingrid","full_name":"Hotz, Ingrid","last_name":"Hotz"},{"full_name":"Pascucci, Valerio","last_name":"Pascucci","first_name":"Valerio"},{"first_name":"Ronald","last_name":"Peikert","full_name":"Peikert, Ronald"}],"title":"Toward the extraction of saddle periodic orbits","article_processing_charge":"No","author":[{"last_name":"Kasten","full_name":"Kasten, Jens","first_name":"Jens"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"full_name":"Reich, Wieland","last_name":"Reich","first_name":"Wieland"},{"first_name":"Gerik","full_name":"Scheuermann, Gerik","last_name":"Scheuermann"}],"acknowledgement":"First, we thank the reviewers of this paper for their ideas and critical comments. In addition, we thank Ronny Peikert and Filip Sadlo for a fruitful discussions. This research is supported by the European Commission under the TOPOSYS project FP7-ICT-318493-STREP, the European Social Fund (ESF App. No. 100098251), and the European Science Foundation under the ACAT Research Network Program.","quality_controlled":"1","publisher":"Springer","publication":"Topological Methods in Data Analysis and Visualization III ","day":"19","year":"2014","date_created":"2022-03-21T07:11:23Z","doi":"10.1007/978-3-319-04099-8_4","date_published":"2014-03-19T00:00:00Z","page":"55-69"},{"page":"868-869","date_published":"2014-02-27T00:00:00Z","doi":"10.1016/j.cell.2014.02.004","date_created":"2022-04-07T07:50:04Z","year":"2014","day":"27","publication":"Cell","quality_controlled":"1","publisher":"Elsevier","oa":1,"author":[{"last_name":"Buchwalter","full_name":"Buchwalter, Abigail","first_name":"Abigail"},{"last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"}],"article_processing_charge":"No","external_id":{"pmid":["24581486"]},"title":"Nuclear pores set the speed limit for mitosis","citation":{"mla":"Buchwalter, Abigail, and Martin Hetzer. “Nuclear Pores Set the Speed Limit for Mitosis.” Cell, vol. 156, no. 5, Elsevier, 2014, pp. 868–69, doi:10.1016/j.cell.2014.02.004.","ama":"Buchwalter A, Hetzer M. Nuclear pores set the speed limit for mitosis. Cell. 2014;156(5):868-869. doi:10.1016/j.cell.2014.02.004","apa":"Buchwalter, A., & Hetzer, M. (2014). Nuclear pores set the speed limit for mitosis. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.02.004","short":"A. Buchwalter, M. Hetzer, Cell 156 (2014) 868–869.","ieee":"A. Buchwalter and M. Hetzer, “Nuclear pores set the speed limit for mitosis,” Cell, vol. 156, no. 5. Elsevier, pp. 868–869, 2014.","chicago":"Buchwalter, Abigail, and Martin Hetzer. “Nuclear Pores Set the Speed Limit for Mitosis.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.02.004.","ista":"Buchwalter A, Hetzer M. 2014. Nuclear pores set the speed limit for mitosis. Cell. 156(5), 868–869."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","issue":"5","volume":156,"publication_identifier":{"issn":["0092-8674"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2014.02.004","open_access":"1"}],"month":"02","intvolume":" 156","abstract":[{"text":"The spindle assembly checkpoint prevents separation of sister chromatids until each kinetochore is attached to the mitotic spindle. Rodriguez-Bravo et al. report that the nuclear pore complex scaffolds spindle assembly checkpoint signaling in interphase, providing a store of inhibitory signals that limits the speed of the subsequent mitosis.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"date_updated":"2022-07-18T08:44:33Z","extern":"1","article_type":"original","type":"journal_article","status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology"],"_id":"11080"},{"date_updated":"2022-07-18T08:45:20Z","extern":"1","type":"journal_article","article_type":"original","keyword":["Cell Biology","Molecular Biology"],"status":"public","_id":"11082","issue":"16","volume":25,"publication_status":"published","publication_identifier":{"issn":["1059-1524","1939-4586"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1091/mbc.e14-04-0865"}],"scopus_import":"1","intvolume":" 25","month":"08","abstract":[{"lang":"eng","text":"The nuclear pore complex (NPC) plays a critical role in gene expression by mediating import of transcription regulators into the nucleus and export of RNA transcripts to the cytoplasm. Emerging evidence suggests that in addition to mediating transport, a subset of nucleoporins (Nups) engage in transcriptional activation and elongation at genomic loci that are not associated with NPCs. The underlying mechanism and regulation of Nup mobility on and off nuclear pores remain unclear. Here we show that Nup50 is a mobile Nup with a pronounced presence both at the NPC and in the nucleoplasm that can move between these different localizations. Strikingly, the dynamic behavior of Nup50 in both locations is dependent on active transcription by RNA polymerase II and requires the N-terminal half of the protein, which contains importin α– and Nup153-binding domains. However, Nup50 dynamics are independent of importin α, Nup153, and Nup98, even though the latter two proteins also exhibit transcription-dependent mobility. Of interest, depletion of Nup50 from C2C12 myoblasts does not affect cell proliferation but inhibits differentiation into myotubes. Taken together, our results suggest a transport-independent role for Nup50 in chromatin biology that occurs away from the NPC."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Buchwalter","full_name":"Buchwalter, Abigail L.","first_name":"Abigail L."},{"first_name":"Yun","last_name":"Liang","full_name":"Liang, Yun"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"title":"Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics","citation":{"ista":"Buchwalter AL, Liang Y, Hetzer M. 2014. Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. 25(16), 2472–2484.","chicago":"Buchwalter, Abigail L., Yun Liang, and Martin Hetzer. “Nup50 Is Required for Cell Differentiation and Exhibits Transcription-Dependent Dynamics.” Molecular Biology of the Cell. American Society for Cell Biology, 2014. https://doi.org/10.1091/mbc.e14-04-0865.","short":"A.L. Buchwalter, Y. Liang, M. Hetzer, Molecular Biology of the Cell 25 (2014) 2472–2484.","ieee":"A. L. Buchwalter, Y. Liang, and M. Hetzer, “Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics,” Molecular Biology of the Cell, vol. 25, no. 16. American Society for Cell Biology, pp. 2472–2484, 2014.","apa":"Buchwalter, A. L., Liang, Y., & Hetzer, M. (2014). Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.e14-04-0865","ama":"Buchwalter AL, Liang Y, Hetzer M. Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. 2014;25(16):2472-2484. doi:10.1091/mbc.e14-04-0865","mla":"Buchwalter, Abigail L., et al. “Nup50 Is Required for Cell Differentiation and Exhibits Transcription-Dependent Dynamics.” Molecular Biology of the Cell, vol. 25, no. 16, American Society for Cell Biology, 2014, pp. 2472–84, doi:10.1091/mbc.e14-04-0865."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","page":"2472-2484","date_created":"2022-04-07T07:50:24Z","date_published":"2014-08-15T00:00:00Z","doi":"10.1091/mbc.e14-04-0865","year":"2014","publication":"Molecular Biology of the Cell","day":"15","oa":1,"publisher":"American Society for Cell Biology","quality_controlled":"1"},{"author":[{"last_name":"Hatch","full_name":"Hatch, Emily","first_name":"Emily"},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"article_processing_charge":"No","external_id":{"pmid":["24751535"]},"title":"Breaching the nuclear envelope in development and disease","citation":{"ista":"Hatch E, Hetzer M. 2014. Breaching the nuclear envelope in development and disease. Journal of Cell Biology. 205(2), 133–141.","chicago":"Hatch, Emily, and Martin Hetzer. “Breaching the Nuclear Envelope in Development and Disease.” Journal of Cell Biology. Rockefeller University Press, 2014. https://doi.org/10.1083/jcb.201402003.","apa":"Hatch, E., & Hetzer, M. (2014). Breaching the nuclear envelope in development and disease. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201402003","ama":"Hatch E, Hetzer M. Breaching the nuclear envelope in development and disease. Journal of Cell Biology. 2014;205(2):133-141. doi:10.1083/jcb.201402003","ieee":"E. Hatch and M. Hetzer, “Breaching the nuclear envelope in development and disease,” Journal of Cell Biology, vol. 205, no. 2. Rockefeller University Press, pp. 133–141, 2014.","short":"E. Hatch, M. Hetzer, Journal of Cell Biology 205 (2014) 133–141.","mla":"Hatch, Emily, and Martin Hetzer. “Breaching the Nuclear Envelope in Development and Disease.” Journal of Cell Biology, vol. 205, no. 2, Rockefeller University Press, 2014, pp. 133–41, doi:10.1083/jcb.201402003."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","page":"133-141","date_published":"2014-04-21T00:00:00Z","doi":"10.1083/jcb.201402003","date_created":"2022-04-07T07:50:13Z","year":"2014","day":"21","publication":"Journal of Cell Biology","quality_controlled":"1","publisher":"Rockefeller University Press","oa":1,"date_updated":"2022-07-18T08:45:09Z","extern":"1","type":"journal_article","article_type":"review","status":"public","keyword":["Cell Biology"],"_id":"11081","issue":"2","volume":205,"publication_identifier":{"issn":["1540-8140","0021-9525"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1083/jcb.201402003","open_access":"1"}],"month":"04","intvolume":" 205","abstract":[{"lang":"eng","text":"In eukaryotic cells the nuclear genome is enclosed by the nuclear envelope (NE). In metazoans, the NE breaks down in mitosis and it has been assumed that the physical barrier separating nucleoplasm and cytoplasm remains intact during the rest of the cell cycle and cell differentiation. However, recent studies suggest that nonmitotic NE remodeling plays a critical role in development, virus infection, laminopathies, and cancer. Although the mechanisms underlying these NE restructuring events are currently being defined, one common theme is activation of protein kinase C family members in the interphase nucleus to disrupt the nuclear lamina, demonstrating the importance of the lamina in maintaining nuclear integrity."}],"pmid":1,"oa_version":"Published Version"},{"abstract":[{"text":"Candidate galaxies at redshifts of z ∼ 10 are now being found in extremely deep surveys, probing very small areas. As a consequence, candidates are very faint, making spectroscopic confirmation practically impossible. In order to overcome such limitations, we have undertaken the CF-HiZELS survey, which is a large-area, medium-depth near-infrared narrow-band survey targeted at z = 8.8 Lyman α (Lyα) emitters (LAEs) and covering 10 deg2 in part of the SSA22 field with the Canada–France–Hawaii Telescope (CFHT). We surveyed a comoving volume of 4.7 × 106 Mpc3 to a Lyα luminosity limit of 6.3 × 1043舁erg舁s−1. We look for Lyα candidates by applying the following criteria: (i) clear emission-line source, (ii) no optical detections (ugriz from CFHTLS), (iii) no visible detection in the optical stack (ugriz > 27), (iv) visually checked reliable NBJ and J detections and (v) J − K ≤ 0. We compute photometric redshifts and remove a significant amount of dusty lower redshift line-emitters at z ∼ 1.4 or 2.2. A total of 13 Lyα candidates were found, of which two are marked as strong candidates, but the majority have very weak constraints on their spectral energy distributions. Using follow-up observations with SINFONI/VLT, we are able to exclude the most robust candidates as LAEs. We put a strong constraint on the Lyα luminosity function at z ∼ 9 and make realistic predictions for ongoing and future surveys. Our results show that surveys for the highest redshift LAEs are susceptible of multiple contaminations and that spectroscopic follow-up is absolutely necessary.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1402.6697","open_access":"1"}],"month":"05","intvolume":" 440","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":440,"issue":"3","_id":"11583","type":"journal_article","article_type":"original","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","cosmology: observations","dark ages","reionization","first stars"],"date_updated":"2022-08-19T08:30:30Z","extern":"1","acknowledgement":"We thank the anonymous referee for the comments and suggestions which improved both the quality and clarity of this work. DS acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a Veni fellowship. IRS acknowledges support from STFC (ST/I001573/1), a Leverhulme Fellowship, the ERC Advanced Investigator programme DUSTYGAL 321334 and a Royal Society/Wolfson Merit Award. PNB acknowledges support from the Leverhulme Trust. JWK acknowledges the support from the Creative Research Initiative Program, no. 2008- 0060544, of the National Research Foundation of Korea (NRF) funded by the Korean government (MSIP). JPUF and BMJ acknowledge support from the ERC-StG grant EGGS-278202. The Dark Cosmology Centre is funded by the Danish National Research Foundation. This work is based in part on data obtained as part of the UKIRT Infrared Deep Sky Survey. Based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and CEA/IRFU, at the Canada–France–Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de l’Univers of the Centre National de la Recherche Scientifique (CNRS) of France and the University of Hawaii. This work is based in part on data products produced at Terapix available at the Canadian Astronomy Data Centre as part of the Canada-France-Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. This work was only possible due to OPTICON/FP7 and the access that it granted to the CFHT telescope. The authors also wish to acknowledge the CFHTLS and UKIDSS surveys for their excellent legacy and complementary value – without such high-quality data sets, this research would not have been possible.","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"year":"2014","day":"21","publication":"Monthly Notices of the Royal Astronomical Society","page":"2375-2387","doi":"10.1093/mnras/stu392","date_published":"2014-05-21T00:00:00Z","date_created":"2022-07-14T12:33:24Z","citation":{"ama":"Matthee JJ, Sobral D, Swinbank AM, et al. A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. 2014;440(3):2375-2387. doi:10.1093/mnras/stu392","apa":"Matthee, J. J., Sobral, D., Swinbank, A. M., Smail, I., Best, P. N., Kim, J.-W., … Fynbo, J. (2014). A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stu392","ieee":"J. J. Matthee et al., “A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys,” Monthly Notices of the Royal Astronomical Society, vol. 440, no. 3. Oxford University Press, pp. 2375–2387, 2014.","short":"J.J. Matthee, D. Sobral, A.M. Swinbank, I. Smail, P.N. Best, J.-W. Kim, M. Franx, B. Milvang-Jensen, J. Fynbo, Monthly Notices of the Royal Astronomical Society 440 (2014) 2375–2387.","mla":"Matthee, Jorryt J., et al. “A 10 Deg2 Lyman α Survey at Z=8.8 with Spectroscopic Follow-up: Strong Constraints on the Luminosity Function and Implications for Other Surveys.” Monthly Notices of the Royal Astronomical Society, vol. 440, no. 3, Oxford University Press, 2014, pp. 2375–87, doi:10.1093/mnras/stu392.","ista":"Matthee JJ, Sobral D, Swinbank AM, Smail I, Best PN, Kim J-W, Franx M, Milvang-Jensen B, Fynbo J. 2014. A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. 440(3), 2375–2387.","chicago":"Matthee, Jorryt J, David Sobral, A. M. Swinbank, Ian Smail, P. N. Best, Jae-Woo Kim, Marijn Franx, Bo Milvang-Jensen, and Johan Fynbo. “A 10 Deg2 Lyman α Survey at Z=8.8 with Spectroscopic Follow-up: Strong Constraints on the Luminosity Function and Implications for Other Surveys.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2014. https://doi.org/10.1093/mnras/stu392."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee"},{"last_name":"Sobral","full_name":"Sobral, David","first_name":"David"},{"first_name":"A. M.","last_name":"Swinbank","full_name":"Swinbank, A. M."},{"full_name":"Smail, Ian","last_name":"Smail","first_name":"Ian"},{"first_name":"P. N.","last_name":"Best","full_name":"Best, P. N."},{"first_name":"Jae-Woo","last_name":"Kim","full_name":"Kim, Jae-Woo"},{"first_name":"Marijn","last_name":"Franx","full_name":"Franx, Marijn"},{"first_name":"Bo","full_name":"Milvang-Jensen, Bo","last_name":"Milvang-Jensen"},{"first_name":"Johan","full_name":"Fynbo, Johan","last_name":"Fynbo"}],"article_processing_charge":"No","external_id":{"arxiv":["1402.6697"]},"title":"A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys"},{"_id":"11582","article_type":"original","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: abundances","galaxies: evolution","galaxies: kinematics and dynamics"],"status":"public","date_updated":"2022-08-19T08:27:25Z","extern":"1","abstract":[{"lang":"eng","text":"We have observed a sample of typical z ∼ 1 star-forming galaxies, selected from the HiZELS survey, with the new K-band Multi-Object Spectrograph (KMOS) near-infrared, multi-integral field unit instrument on the Very Large Telescope (VLT), in order to obtain their dynamics and metallicity gradients. The majority of our galaxies have a metallicity gradient consistent with being flat or negative (i.e. higher metallicity cores than outskirts). Intriguingly, we find a trend between metallicity gradient and specific star formation rate (sSFR), such that galaxies with a high sSFR tend to have relatively metal poor centres, a result which is strengthened when combined with data sets from the literature. This result appears to explain the discrepancies reported between different high-redshift studies and varying claims for evolution. From a galaxy evolution perspective, the trend we see would mean that a galaxy's sSFR is governed by the amount of metal-poor gas that can be funnelled into its core, triggered either by merging or through efficient accretion. In fact, merging may play a significant role as it is the starburst galaxies at all epochs, which have the more positive metallicity gradients. Our results may help to explain the origin of the fundamental metallicity relation, in which galaxies at a fixed mass are observed to have lower metallicities at higher star formation rates, especially if the metallicity is measured in an aperture encompassing only the central regions of the galaxy. Finally, we note that this study demonstrates the power of KMOS as an efficient instrument for large-scale resolved galaxy surveys."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1407.1047","open_access":"1"}],"scopus_import":"1","intvolume":" 443","month":"09","publication_status":"published","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"language":[{"iso":"eng"}],"volume":443,"issue":"3","citation":{"mla":"Stott, John P., et al. “A Relationship between Specific Star Formation Rate and Metallicity Gradient within z ∼ 1 Galaxies from KMOS-HiZELS.” Monthly Notices of the Royal Astronomical Society, vol. 443, no. 3, Oxford University Press, 2014, pp. 2695–704, doi:10.1093/mnras/stu1343.","ieee":"J. P. Stott et al., “A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS,” Monthly Notices of the Royal Astronomical Society, vol. 443, no. 3. Oxford University Press, pp. 2695–2704, 2014.","short":"J.P. Stott, D. Sobral, A.M. Swinbank, I. Smail, R. Bower, P.N. Best, R.M. Sharples, J.E. Geach, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 443 (2014) 2695–2704.","apa":"Stott, J. P., Sobral, D., Swinbank, A. M., Smail, I., Bower, R., Best, P. N., … Matthee, J. J. (2014). A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stu1343","ama":"Stott JP, Sobral D, Swinbank AM, et al. A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. 2014;443(3):2695-2704. doi:10.1093/mnras/stu1343","chicago":"Stott, John P., David Sobral, A. M. Swinbank, Ian Smail, Richard Bower, Philip N. Best, Ray M. Sharples, James E. Geach, and Jorryt J Matthee. “A Relationship between Specific Star Formation Rate and Metallicity Gradient within z ∼ 1 Galaxies from KMOS-HiZELS.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2014. https://doi.org/10.1093/mnras/stu1343.","ista":"Stott JP, Sobral D, Swinbank AM, Smail I, Bower R, Best PN, Sharples RM, Geach JE, Matthee JJ. 2014. A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. 443(3), 2695–2704."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1407.1047"]},"author":[{"first_name":"John P.","last_name":"Stott","full_name":"Stott, John P."},{"first_name":"David","last_name":"Sobral","full_name":"Sobral, David"},{"first_name":"A. M.","full_name":"Swinbank, A. M.","last_name":"Swinbank"},{"full_name":"Smail, Ian","last_name":"Smail","first_name":"Ian"},{"first_name":"Richard","last_name":"Bower","full_name":"Bower, Richard"},{"first_name":"Philip N.","last_name":"Best","full_name":"Best, Philip N."},{"full_name":"Sharples, Ray M.","last_name":"Sharples","first_name":"Ray M."},{"full_name":"Geach, James E.","last_name":"Geach","first_name":"James E."},{"last_name":"Matthee","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"}],"title":"A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS","acknowledgement":"First, we acknowledge the referee for their comments, which have improved the clarity of this paper. JPS and IRS acknowledge support from STFC (ST/I001573/1). IRS also acknowledges support from the ERC Advanced Investigator programme DUSTYGAL and a Royal Society/Wolfson Merit Award. DS acknowledges financial support from NWO through a Veni fellowship and from FCT through the award of an FCT-IF starting grant. PNB acknowledges STFC for financial support.","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","year":"2014","publication":"Monthly Notices of the Royal Astronomical Society","day":"21","page":"2695-2704","date_created":"2022-07-14T12:16:10Z","doi":"10.1093/mnras/stu1343","date_published":"2014-09-21T00:00:00Z"},{"article_type":"original","type":"journal_article","status":"public","_id":"11750","date_updated":"2022-08-11T09:51:22Z","extern":"1","scopus_import":"1","month":"05","intvolume":" 50","abstract":[{"lang":"eng","text":"We report on the magnetic properties of a hot-pressed FeSb 2 sample. We find a significant increase in the magnetic susceptibility in our sample when compared with the values previously reported for the polycrystalline sample. The pronounced Curie tail at low temperature corresponds to 0.2% of Fe 2+ impurities per mole. In the intrinsic conductivity region, the susceptibility due to free carriers shows thermally activated behavior and is consistent with the data reported for single crystal FeSb 2 . Based on our data and analysis, while the enhanced magnetic susceptibility in our sample comes mainly from a small amount of unreacted Fe, the contribution from the enhanced carrier density due to lattice and strain defects arising from the ball milling process is also significant. Existence of an unreacted Fe phase is evidenced by small coercivity values of ~100 observed at 50 and 300 K."}],"oa_version":"None","volume":50,"issue":"5","publication_identifier":{"issn":["0018-9464"],"eissn":["1941-0069"]},"publication_status":"published","language":[{"iso":"eng"}],"article_number":"6675864","author":[{"first_name":"Mani","full_name":"Pokharel, Mani","last_name":"Pokharel"},{"last_name":"Zhao","full_name":"Zhao, Huaizhou","first_name":"Huaizhou"},{"last_name":"Modic","full_name":"Modic, Kimberly A","orcid":"0000-0001-9760-3147","first_name":"Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425"},{"first_name":"Zhifeng","last_name":"Ren","full_name":"Ren, Zhifeng"},{"full_name":"Opeil, Cyril","last_name":"Opeil","first_name":"Cyril"}],"article_processing_charge":"No","title":"Magnetic properties of hot-pressed FeSb2","citation":{"ista":"Pokharel M, Zhao H, Modic KA, Ren Z, Opeil C. 2014. Magnetic properties of hot-pressed FeSb2. IEEE Transactions on Magnetics. 50(5), 6675864.","chicago":"Pokharel, Mani, Huaizhou Zhao, Kimberly A Modic, Zhifeng Ren, and Cyril Opeil. “Magnetic Properties of Hot-Pressed FeSb2.” IEEE Transactions on Magnetics. Institute of Electrical and Electronics Engineers, 2014. https://doi.org/10.1109/TMAG.2013.2292607.","ieee":"M. Pokharel, H. Zhao, K. A. Modic, Z. Ren, and C. Opeil, “Magnetic properties of hot-pressed FeSb2,” IEEE Transactions on Magnetics, vol. 50, no. 5. Institute of Electrical and Electronics Engineers, 2014.","short":"M. Pokharel, H. Zhao, K.A. Modic, Z. Ren, C. Opeil, IEEE Transactions on Magnetics 50 (2014).","apa":"Pokharel, M., Zhao, H., Modic, K. A., Ren, Z., & Opeil, C. (2014). Magnetic properties of hot-pressed FeSb2. IEEE Transactions on Magnetics. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/TMAG.2013.2292607","ama":"Pokharel M, Zhao H, Modic KA, Ren Z, Opeil C. Magnetic properties of hot-pressed FeSb2. IEEE Transactions on Magnetics. 2014;50(5). doi:10.1109/TMAG.2013.2292607","mla":"Pokharel, Mani, et al. “Magnetic Properties of Hot-Pressed FeSb2.” IEEE Transactions on Magnetics, vol. 50, no. 5, 6675864, Institute of Electrical and Electronics Engineers, 2014, doi:10.1109/TMAG.2013.2292607."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Institute of Electrical and Electronics Engineers","date_published":"2014-05-01T00:00:00Z","doi":"10.1109/TMAG.2013.2292607","date_created":"2022-08-08T08:26:02Z","year":"2014","day":"01","publication":"IEEE Transactions on Magnetics"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"isbn":["978-366244776-5"]},"publication_status":"published","volume":8737,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study a weighted online bipartite matching problem: G(V 1, V 2, E) is a weighted bipartite graph where V 1 is known beforehand and the vertices of V 2 arrive online. The goal is to match vertices of V 2 as they arrive to vertices in V 1, so as to maximize the sum of weights of edges in the matching. If assignments to V 1 cannot be changed, no bounded competitive ratio is achievable. We study the weighted online matching problem with free disposal, where vertices in V 1 can be assigned multiple times, but only get credit for the maximum weight edge assigned to them over the course of the algorithm. For this problem, the greedy algorithm is 0.5-competitive and determining whether a better competitive ratio is achievable is a well known open problem.\r\n\r\nWe identify an interesting special case where the edge weights are decomposable as the product of two factors, one corresponding to each end point of the edge. This is analogous to the well studied related machines model in the scheduling literature, although the objective functions are different. For this case of decomposable edge weights, we design a 0.5664 competitive randomized algorithm in complete bipartite graphs. We show that such instances with decomposable weights are non-trivial by establishing upper bounds of 0.618 for deterministic and 0.8 for randomized algorithms.\r\n\r\nA tight competitive ratio of 1 − 1/e ≈ 0.632 was known previously for both the 0-1 case as well as the case where edge weights depend on the offline vertices only, but for these cases, reassignments cannot change the quality of the solution. Beating 0.5 for weighted matching where reassignments are necessary has been a significant challenge. We thus give the first online algorithm with competitive ratio strictly better than 0.5 for a non-trivial case of weighted matching with free disposal."}],"month":"09","intvolume":" 8737","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1409.2139"}],"extern":"1","date_updated":"2023-02-13T11:16:24Z","_id":"11789","status":"public","type":"conference","conference":{"end_date":"2014-09-10","location":"Wroclaw, Poland","start_date":"2014-09-08","name":"ESA: Annual European Symposium on Algorithms"},"day":"01","publication":"22nd Annual European Symposium on Algorithms","year":"2014","date_published":"2014-09-01T00:00:00Z","doi":"10.1007/978-3-662-44777-2_22","date_created":"2022-08-11T10:41:47Z","page":"260 - 271","publisher":"Springer Nature","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Charikar, Moses, et al. “Online Bipartite Matching with Decomposable Weights.” 22nd Annual European Symposium on Algorithms, vol. 8737, Springer Nature, 2014, pp. 260–71, doi:10.1007/978-3-662-44777-2_22.","apa":"Charikar, M., Henzinger, M. H., & Nguyễn, H. L. (2014). Online bipartite matching with decomposable weights. In 22nd Annual European Symposium on Algorithms (Vol. 8737, pp. 260–271). Wroclaw, Poland: Springer Nature. https://doi.org/10.1007/978-3-662-44777-2_22","ama":"Charikar M, Henzinger MH, Nguyễn HL. Online bipartite matching with decomposable weights. In: 22nd Annual European Symposium on Algorithms. Vol 8737. Springer Nature; 2014:260-271. doi:10.1007/978-3-662-44777-2_22","short":"M. Charikar, M.H. Henzinger, H.L. Nguyễn, in:, 22nd Annual European Symposium on Algorithms, Springer Nature, 2014, pp. 260–271.","ieee":"M. Charikar, M. H. Henzinger, and H. L. Nguyễn, “Online bipartite matching with decomposable weights,” in 22nd Annual European Symposium on Algorithms, Wroclaw, Poland, 2014, vol. 8737, pp. 260–271.","chicago":"Charikar, Moses, Monika H Henzinger, and Huy L. Nguyễn. “Online Bipartite Matching with Decomposable Weights.” In 22nd Annual European Symposium on Algorithms, 8737:260–71. Springer Nature, 2014. https://doi.org/10.1007/978-3-662-44777-2_22.","ista":"Charikar M, Henzinger MH, Nguyễn HL. 2014. Online bipartite matching with decomposable weights. 22nd Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LNCS, vol. 8737, 260–271."},"title":"Online bipartite matching with decomposable weights","author":[{"last_name":"Charikar","full_name":"Charikar, Moses","first_name":"Moses"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"full_name":"Nguyễn, Huy L.","last_name":"Nguyễn","first_name":"Huy L."}],"article_processing_charge":"No","external_id":{"arxiv":["1409.2139"]}},{"abstract":[{"text":"Assume a seller wants to sell a digital product in a social network where a buyer’s valuation of the item has positive network externalities from her neighbors that already have the item. The goal of the seller is to maximize his revenue. Previous work on this problem [7] studies the case where clients are offered the item in sequence and have to pay personalized prices. This is highly infeasible in large scale networks such as the Facebook graph: (1) Offering items to the clients one after the other consumes a large amount of time, and (2) price-discrimination of clients could appear unfair to them and result in negative client reaction or could conflict with legal requirements.\r\n\r\nWe study a setting dealing with these issues. Specifically, the item is offered in parallel to multiple clients at the same time and at the same price. This is called a round. We show that with O(logn) rounds, where n is the number of clients, a constant factor of the revenue with price discrimination can be achieved and that this is not possible with o(logn) rounds. Moreover we show that it is APX-hard to maximize the revenue and we give constant factor approximation algorithms for various further settings of limited price discrimination.","lang":"eng"}],"oa_version":"None","scopus_import":"1","alternative_title":["LNCS"],"publisher":"Springer Nature","quality_controlled":"1","month":"12","intvolume":" 8877","publication_identifier":{"issn":["0302-9743"]},"year":"2014","publication_status":"published","day":"01","publication":"10th International Conference of Web and Internet Economics","language":[{"iso":"eng"}],"page":"44 - 57","doi":"10.1007/978-3-319-13129-0_4","volume":8877,"date_published":"2014-12-01T00:00:00Z","date_created":"2022-08-11T10:58:44Z","_id":"11790","type":"conference","conference":{"location":"Beijing, China","end_date":"2014-12-17","start_date":"2014-12-14","name":"WINE: International Conference on Web and Internet Economics"},"status":"public","date_updated":"2023-02-13T11:18:30Z","citation":{"chicago":"Cigler, Luděk, Wolfgang Dvořák, Monika H Henzinger, and Martin Starnberger. “Limiting Price Discrimination When Selling Products with Positive Network Externalities.” In 10th International Conference of Web and Internet Economics, 8877:44–57. Springer Nature, 2014. https://doi.org/10.1007/978-3-319-13129-0_4.","ista":"Cigler L, Dvořák W, Henzinger MH, Starnberger M. 2014. Limiting price discrimination when selling products with positive network externalities. 10th International Conference of Web and Internet Economics. WINE: International Conference on Web and Internet Economics, LNCS, vol. 8877, 44–57.","mla":"Cigler, Luděk, et al. “Limiting Price Discrimination When Selling Products with Positive Network Externalities.” 10th International Conference of Web and Internet Economics, vol. 8877, Springer Nature, 2014, pp. 44–57, doi:10.1007/978-3-319-13129-0_4.","short":"L. Cigler, W. Dvořák, M.H. Henzinger, M. Starnberger, in:, 10th International Conference of Web and Internet Economics, Springer Nature, 2014, pp. 44–57.","ieee":"L. Cigler, W. Dvořák, M. H. Henzinger, and M. Starnberger, “Limiting price discrimination when selling products with positive network externalities,” in 10th International Conference of Web and Internet Economics, Beijing, China, 2014, vol. 8877, pp. 44–57.","ama":"Cigler L, Dvořák W, Henzinger MH, Starnberger M. Limiting price discrimination when selling products with positive network externalities. In: 10th International Conference of Web and Internet Economics. Vol 8877. Springer Nature; 2014:44-57. doi:10.1007/978-3-319-13129-0_4","apa":"Cigler, L., Dvořák, W., Henzinger, M. H., & Starnberger, M. (2014). Limiting price discrimination when selling products with positive network externalities. In 10th International Conference of Web and Internet Economics (Vol. 8877, pp. 44–57). Beijing, China: Springer Nature. https://doi.org/10.1007/978-3-319-13129-0_4"},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Luděk","full_name":"Cigler, Luděk","last_name":"Cigler"},{"last_name":"Dvořák","full_name":"Dvořák, Wolfgang","first_name":"Wolfgang"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Starnberger","full_name":"Starnberger, Martin","first_name":"Martin"}],"article_processing_charge":"No","title":"Limiting price discrimination when selling products with positive network externalities"},{"acknowledgement":"The Spanish MINECO project FIS2011-26675, the PIUNA program (U. Navarra), and the Project 29942WL (Fonds de Solidarité Prioritaire France-Cuba) have partially supported this research. ","oa_version":"None","abstract":[{"lang":"eng","text":"While the penetration of objects into granular media is well-studied, there is little understanding of how objects settle in gravities, geff, different from that of Earth - a scenario potentially relevant to the geomorphology of planets and asteroids and also to their exploration using man-made devices. By conducting experiments in an accelerating frame, we explore geff ranging from 0.4 g to 1.2 g. Surprisingly, we find that the rest depth is independent of geff and also that the time required for the object to come to rest scales like geff-1/2. With discrete element modeling simulations, we reproduce the experimental results and extend the range of geff to objects as small as asteroids and as large as Jupiter. Our results shed light on the initial stage of sedimentation into dry granular media across a range of celestial bodies and also have implications for the design of man-made, extraterrestrial vehicles and structures. Key Points The settling depth in granular media is independent of gravity The settling time scales like g-1/2 Layering driven by granular sedimentation should be similar."}],"intvolume":" 41","month":"05","publisher":"Wiley-Blackwell","quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Geophysical Research Letters","day":"16","year":"2014","publication_status":"published","date_created":"2018-12-11T11:44:43Z","volume":41,"date_published":"2014-05-16T00:00:00Z","issue":"9","doi":"10.1002/2014GL059229","page":"3032 - 3037","_id":"118","status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T06:48:53Z","citation":{"mla":"Altshuler, Ernesto, et al. “Settling into Dry Granular Media in Different Gravities.” Geophysical Research Letters, vol. 41, no. 9, Wiley-Blackwell, 2014, pp. 3032–37, doi:10.1002/2014GL059229.","ama":"Altshuler E, Torres H, González_Pita A, et al. Settling into dry granular media in different gravities. Geophysical Research Letters. 2014;41(9):3032-3037. doi:10.1002/2014GL059229","apa":"Altshuler, E., Torres, H., González_Pita, A., Sánchez, C. G., Pérez Penichet, C., Waitukaitis, S. R., & Hidalgo, R. (2014). Settling into dry granular media in different gravities. Geophysical Research Letters. Wiley-Blackwell. https://doi.org/10.1002/2014GL059229","ieee":"E. Altshuler et al., “Settling into dry granular media in different gravities,” Geophysical Research Letters, vol. 41, no. 9. Wiley-Blackwell, pp. 3032–3037, 2014.","short":"E. Altshuler, H. Torres, A. González_Pita, C.G. Sánchez, C. Pérez Penichet, S.R. Waitukaitis, R. Hidalgo, Geophysical Research Letters 41 (2014) 3032–3037.","chicago":"Altshuler, Ernesto, H Torres, A González_Pita, Colina G Sánchez, Carlos Pérez Penichet, Scott R Waitukaitis, and Rauól Hidalgo. “Settling into Dry Granular Media in Different Gravities.” Geophysical Research Letters. Wiley-Blackwell, 2014. https://doi.org/10.1002/2014GL059229.","ista":"Altshuler E, Torres H, González_Pita A, Sánchez CG, Pérez Penichet C, Waitukaitis SR, Hidalgo R. 2014. Settling into dry granular media in different gravities. Geophysical Research Letters. 41(9), 3032–3037."},"title":"Settling into dry granular media in different gravities","author":[{"full_name":"Altshuler, Ernesto","last_name":"Altshuler","first_name":"Ernesto"},{"last_name":"Torres","full_name":"Torres, H","first_name":"H"},{"first_name":"A","last_name":"González_Pita","full_name":"González_Pita, A"},{"last_name":"Sánchez","full_name":"Sánchez, Colina G","first_name":"Colina G"},{"first_name":"Carlos","last_name":"Pérez Penichet","full_name":"Pérez Penichet, Carlos"},{"last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rauól","last_name":"Hidalgo","full_name":"Hidalgo, Rauól"}],"publist_id":"7936"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Henzinger MH, Krinninger S, Nanongkai D. 2014. Decremental single-source shortest paths on undirected graphs in near-linear total update time. 55th Annual Symposium on Foundations of Computer Science. FOCS: Annual Symposium on Foundations of Computer Science, 146–155.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” In 55th Annual Symposium on Foundations of Computer Science, 146–55. Institute of Electrical and Electronics Engineers, 2014. https://doi.org/10.1109/focs.2014.24.","ama":"Henzinger MH, Krinninger S, Nanongkai D. Decremental single-source shortest paths on undirected graphs in near-linear total update time. In: 55th Annual Symposium on Foundations of Computer Science. Institute of Electrical and Electronics Engineers; 2014:146-155. doi:10.1109/focs.2014.24","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Decremental single-source shortest paths on undirected graphs in near-linear total update time. In 55th Annual Symposium on Foundations of Computer Science (pp. 146–155). Philadelphia, PA, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/focs.2014.24","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Decremental single-source shortest paths on undirected graphs in near-linear total update time,” in 55th Annual Symposium on Foundations of Computer Science, Philadelphia, PA, United States, 2014, pp. 146–155.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 55th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2014, pp. 146–155.","mla":"Henzinger, Monika H., et al. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” 55th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2014, pp. 146–55, doi:10.1109/focs.2014.24."},"title":"Decremental single-source shortest paths on undirected graphs in near-linear total update time","author":[{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"first_name":"Sebastian","full_name":"Krinninger, Sebastian","last_name":"Krinninger"},{"first_name":"Danupon","full_name":"Nanongkai, Danupon","last_name":"Nanongkai"}],"article_processing_charge":"No","external_id":{"arxiv":["1402.0054"]},"day":"01","publication":"55th Annual Symposium on Foundations of Computer Science","year":"2014","doi":"10.1109/focs.2014.24","date_published":"2014-10-01T00:00:00Z","date_created":"2022-08-16T08:14:33Z","page":"146-155","publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","oa":1,"extern":"1","date_updated":"2023-02-21T16:27:34Z","_id":"11855","status":"public","type":"conference","conference":{"name":"FOCS: Annual Symposium on Foundations of Computer Science","start_date":"2014-10-18","end_date":"2014-10-21","location":"Philadelphia, PA, United States"},"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["978-1-4799-6517-5"],"issn":["0272-5428"]},"publication_status":"published","related_material":{"record":[{"relation":"later_version","status":"public","id":"11768"}]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The decremental single-source shortest paths (SSSP) problem concerns maintaining the distances between a given source node s to every node in an n-node m-edge graph G undergoing edge deletions. While its static counterpart can be easily solved in near-linear time, this decremental problem is much more challenging even in the undirected unweighted case. In this case, the classic O(mn) total update time of Even and Shiloach (JACM 1981) has been the fastest known algorithm for three decades. With the loss of a (1 + ε)-approximation factor, the running time was recently improved to O(n 2+o(1) ) by Bernstein and Roditty (SODA 2011), and more recently to O(n 1.8+o(1) + m 1+o(1) ) by Henzinger, Krinninger, and Nanongkai (SODA 2014). In this paper, we finally bring the running time of this case down to near-linear: We give a (1 + ε)-approximation algorithm with O(m 1+o(1) ) total update time, thus obtaining near-linear time. Moreover, we obtain O(m 1+o(1) log W) time for the weighted case, where the edge weights are integers from 1 to W. The only prior work on weighted graphs in o(mn log W) time is the O(mn 0.986 log W)-time algorithm by Henzinger, Krinninger, and Nanongkai (STOC 2014) which works for the general weighted directed case. In contrast to the previous results which rely on maintaining a sparse emulator, our algorithm relies on maintaining a so-called sparse (d, ε)-hop set introduced by Cohen (JACM 2000) in the PRAM literature. A (d, ε)-hop set of a graph G = (V, E) is a set E' of weighted edges such that the distance between any pair of nodes in G can be (1 + ε)-approximated by their d-hop distance (given by a path containing at most d edges) on G'=(V, E∪E'). Our algorithm can maintain an (n o(1) , ε)-hop set of near-linear size in near-linear time under edge deletions. It is the first of its kind to the best of our knowledge. To maintain the distances on this hop set, we develop a monotone bounded-hop Even-Shiloach tree. It results from extending and combining the monotone Even-Shiloach tree of Henzinger, Krinninger, and Nanongkai (FOCS 2013) with the bounded-hop SSSP technique of Bernstein (STOC 2013). These two new tools might be of independent interest."}],"month":"10","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1402.0054"}]},{"_id":"11870","article_number":"674 - 683","type":"conference","conference":{"start_date":"2014-05-31","end_date":"2014-06-03","location":"New York, NY, United States","name":"STOC: Symposium on Theory of Computing"},"status":"public","date_updated":"2023-02-17T11:18:52Z","citation":{"short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 46th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2014.","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs,” in 46th Annual ACM Symposium on Theory of Computing, New York, NY, United States, 2014.","ama":"Henzinger MH, Krinninger S, Nanongkai D. Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. In: 46th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2014. doi:10.1145/2591796.2591869","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. In 46th Annual ACM Symposium on Theory of Computing. New York, NY, United States: Association for Computing Machinery. https://doi.org/10.1145/2591796.2591869","mla":"Henzinger, Monika H., et al. “Sublinear-Time Decremental Algorithms for Single-Source Reachability and Shortest Paths on Directed Graphs.” 46th Annual ACM Symposium on Theory of Computing, 674–683, Association for Computing Machinery, 2014, doi:10.1145/2591796.2591869.","ista":"Henzinger MH, Krinninger S, Nanongkai D. 2014. Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. 46th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 674–683.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time Decremental Algorithms for Single-Source Reachability and Shortest Paths on Directed Graphs.” In 46th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery, 2014. https://doi.org/10.1145/2591796.2591869."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"first_name":"Sebastian","last_name":"Krinninger","full_name":"Krinninger, Sebastian"},{"full_name":"Nanongkai, Danupon","last_name":"Nanongkai","first_name":"Danupon"}],"external_id":{"arxiv":["1504.07959"]},"article_processing_charge":"No","title":"Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs","abstract":[{"text":"We consider dynamic algorithms for maintaining Single-Source Reachability (SSR) and approximate Single-Source Shortest Paths (SSSP) on n-node m-edge directed graphs under edge deletions (decremental algorithms). The previous fastest algorithm for SSR and SSSP goes back three decades to Even and Shiloach (JACM 1981); it has O(1) query time and O(mn) total update time (i.e., linear amortized update time if all edges are deleted). This algorithm serves as a building block for several other dynamic algorithms. The question whether its total update time can be improved is a major, long standing, open problem.\r\n\r\nIn this paper, we answer this question affirmatively. We obtain a randomized algorithm which, in a simplified form, achieves an Õ(mn0.984) expected total update time for SSR and (1 + ε)-approximate SSSP, where Õ(·) hides poly log n. We also extend our algorithm to achieve roughly the same running time for Strongly Connected Components (SCC), improving the algorithm of Roditty and Zwick (FOCS 2002), and an algorithm that improves the Õ (mn log W)-time algorithm of Bernstein (STOC 2013) for approximating SSSP on weighted directed graphs, where the edge weights are integers from 1 to W. All our algorithms have constant query time in the worst case.","lang":"eng"}],"oa_version":"Preprint","publisher":"Association for Computing Machinery","scopus_import":"1","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1504.07959","open_access":"1"}],"month":"05","publication_identifier":{"issn":["0737-8017"],"isbn":["978-145032710-7"]},"publication_status":"published","year":"2014","day":"01","publication":"46th Annual ACM Symposium on Theory of Computing","language":[{"iso":"eng"}],"date_published":"2014-05-01T00:00:00Z","doi":"10.1145/2591796.2591869","date_created":"2022-08-16T09:41:57Z"},{"date_created":"2022-08-16T12:58:31Z","date_published":"2014-01-01T00:00:00Z","doi":"10.1137/1.9781611973402.79","page":"1053-1072","language":[{"iso":"eng"}],"publication":"25th Annual ACM-SIAM Symposium on Discrete Algorithms","day":"01","publication_status":"published","year":"2014","publication_identifier":{"isbn":["978-1-61197-338-9"],"eisbn":["978-1-61197-340-2"]},"month":"01","oa":1,"main_file_link":[{"url":"https://doi.org/10.1137/1.9781611973402.79","open_access":"1"}],"publisher":"Society for Industrial and Applied Mathematics","scopus_import":"1","quality_controlled":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We study dynamic (1 + ∊)-approximation algorithms for the single-source shortest paths problem in an unweighted undirected n-node m-edge graph under edge deletions. The fastest algorithm for this problem is an algorithm with O(n2+o(1)) total update time and constant query time by Bernstein and Roditty (SODA 2011). In this paper, we improve the total update time to O(n1.8+o(1) + m1+o(1)) while keeping the query time constant. This running time is essentially tight when m = Ω(n1.8) since we need Ω(m) time even in the static setting. For smaller values of m, the running time of our algorithm is subquadratic, and is the first that breaks through the quadratic time barrier.\r\n\r\nIn obtaining this result, we develop a fast algorithm for what we call center cover data structure. We also make non-trivial extensions to our previous techniques called lazy-update and monotone Even-Shiloach trees (ICALP 2013 and FOCS 2013). As by-products of our new techniques, we obtain two new results for the decremental all-pairs shortest-paths problem. Our first result is the first approximation algorithm whose total update time is faster than Õ(mn) for all values of m. Our second result is a new trade-off between the total update time and the additive approximation guarantee."}],"title":"A subquadratic-time algorithm for decremental single-source shortest paths","article_processing_charge":"No","author":[{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"first_name":"Sebastian","full_name":"Krinninger, Sebastian","last_name":"Krinninger"},{"last_name":"Nanongkai","full_name":"Nanongkai, Danupon","first_name":"Danupon"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2023-02-17T11:58:42Z","citation":{"ista":"Henzinger MH, Krinninger S, Nanongkai D. 2014. A subquadratic-time algorithm for decremental single-source shortest paths. 25th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1053–1072.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “A Subquadratic-Time Algorithm for Decremental Single-Source Shortest Paths.” In 25th Annual ACM-SIAM Symposium on Discrete Algorithms, 1053–72. Society for Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973402.79.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 1053–1072.","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “A subquadratic-time algorithm for decremental single-source shortest paths,” in 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Portland, OR, United States, 2014, pp. 1053–1072.","ama":"Henzinger MH, Krinninger S, Nanongkai D. A subquadratic-time algorithm for decremental single-source shortest paths. In: 25th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2014:1053-1072. doi:10.1137/1.9781611973402.79","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). A subquadratic-time algorithm for decremental single-source shortest paths. In 25th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1053–1072). Portland, OR, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973402.79","mla":"Henzinger, Monika H., et al. “A Subquadratic-Time Algorithm for Decremental Single-Source Shortest Paths.” 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 1053–72, doi:10.1137/1.9781611973402.79."},"status":"public","conference":{"end_date":"2014-01-07","location":"Portland, OR, United States","start_date":"2014-01-05","name":"SODA: Symposium on Discrete Algorithms"},"type":"conference","_id":"11876"},{"date_published":"2014-01-01T00:00:00Z","doi":"10.1137/1.9781611973730.54","date_created":"2022-08-16T12:36:42Z","page":"785-804","day":"01","publication":"26th Annual ACM-SIAM Symposium on Discrete Algorithms","year":"2014","publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","oa":1,"title":"Deterministic fully dynamic data structures for vertex cover and matching","author":[{"last_name":"Bhattacharya","full_name":"Bhattacharya, Sayan","first_name":"Sayan"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger"},{"full_name":"Italiano, Giuseppe F.","last_name":"Italiano","first_name":"Giuseppe F."}],"article_processing_charge":"No","external_id":{"arxiv":["1412.1318"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bhattacharya S, Henzinger MH, Italiano GF. 2014. Deterministic fully dynamic data structures for vertex cover and matching. 26th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 785–804.","chicago":"Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe F. Italiano. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” In 26th Annual ACM-SIAM Symposium on Discrete Algorithms, 785–804. Society for Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973730.54.","short":"S. Bhattacharya, M.H. Henzinger, G.F. Italiano, in:, 26th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 785–804.","ieee":"S. Bhattacharya, M. H. Henzinger, and G. F. Italiano, “Deterministic fully dynamic data structures for vertex cover and matching,” in 26th Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States, 2014, pp. 785–804.","apa":"Bhattacharya, S., Henzinger, M. H., & Italiano, G. F. (2014). Deterministic fully dynamic data structures for vertex cover and matching. In 26th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 785–804). San Diego, CA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973730.54","ama":"Bhattacharya S, Henzinger MH, Italiano GF. Deterministic fully dynamic data structures for vertex cover and matching. In: 26th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2014:785-804. doi:10.1137/1.9781611973730.54","mla":"Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” 26th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 785–804, doi:10.1137/1.9781611973730.54."},"related_material":{"record":[{"status":"public","id":"11890","relation":"later_version"}]},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-61197-374-7"],"eisbn":["978-1-61197-373-0"]},"publication_status":"published","month":"01","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1412.1318","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We present the first deterministic data structures for maintaining approximate minimum vertex cover and maximum matching in a fully dynamic graph in time per update. In particular, for minimum vertex cover we provide deterministic data structures for maintaining a (2 + ε) approximation in O(log n/ε2) amortized time per update. For maximum matching, we show how to maintain a (3 + e) approximation in O(m1/3/ε2) amortized time per update, and a (4 + ε) approximation in O(m1/3/ε2) worst-case time per update. Our data structure for fully dynamic minimum vertex cover is essentially near-optimal and settles an open problem by Onak and Rubinfeld [13].","lang":"eng"}],"extern":"1","date_updated":"2023-02-21T16:32:06Z","status":"public","type":"conference","conference":{"location":"San Diego, CA, United States","end_date":"2015-01-06","start_date":"2015-01-04","name":"SODA: Symposium on Discrete Algorithms"},"_id":"11875"},{"status":"public","type":"journal_article","_id":"119","extern":"1","date_updated":"2021-01-12T06:48:58Z","intvolume":" 112","month":"05","main_file_link":[{"url":"https://arxiv.org/abs/1309.2578","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Observations of flowing granular matter have suggested that same-material tribocharging depends on particle size, typically rendering large grains positive and small ones negative. Models assuming the transfer of trapped electrons can account for this trend, but have not been validated. Tracking individual grains in an electric field, we show quantitatively that charge is transferred based on size between materially identical grains. However, the surface density of trapped electrons, measured independently by thermoluminescence techniques, is orders of magnitude too small to account for the scale of charge transferred. This reveals that trapped electrons are not a necessary ingredient for same-material tribocharging."}],"volume":112,"issue":"21","language":[{"iso":"eng"}],"publication_status":"published","article_number":"218001","title":"Size-dependent same-material tribocharging in insulating grains","external_id":{"arxiv":["1309.2578"]},"author":[{"last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lee, Victor","last_name":"Lee","first_name":"Victor"},{"first_name":"James","full_name":"Pierson, James","last_name":"Pierson"},{"first_name":"Steven","last_name":"Forman","full_name":"Forman, Steven"},{"last_name":"Jaeger","full_name":"Jaeger, Heinrich","first_name":"Heinrich"}],"publist_id":"7935","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Waitukaitis SR, Lee V, Pierson J, Forman S, Jaeger H. 2014. Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. 112(21), 218001.","chicago":"Waitukaitis, Scott R, Victor Lee, James Pierson, Steven Forman, and Heinrich Jaeger. “Size-Dependent Same-Material Tribocharging in Insulating Grains.” APS Physics, Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.112.218001.","apa":"Waitukaitis, S. R., Lee, V., Pierson, J., Forman, S., & Jaeger, H. (2014). Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.112.218001","ama":"Waitukaitis SR, Lee V, Pierson J, Forman S, Jaeger H. Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. 2014;112(21). doi:10.1103/PhysRevLett.112.218001","ieee":"S. R. Waitukaitis, V. Lee, J. Pierson, S. Forman, and H. Jaeger, “Size-dependent same-material tribocharging in insulating grains,” APS Physics, Physical Review Letters, vol. 112, no. 21. American Physical Society, 2014.","short":"S.R. Waitukaitis, V. Lee, J. Pierson, S. Forman, H. Jaeger, APS Physics, Physical Review Letters 112 (2014).","mla":"Waitukaitis, Scott R., et al. “Size-Dependent Same-Material Tribocharging in Insulating Grains.” APS Physics, Physical Review Letters, vol. 112, no. 21, 218001, American Physical Society, 2014, doi:10.1103/PhysRevLett.112.218001."},"oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"This work was supported by the NSF through DMR-1309611. Access to the shared experimental facilities provided by the NSF-supported Chicago MRSEC (DMR-0820054) is gratefully acknowledged. S. L. F. and J. L. P. acknowledge funding from UIC NSF Grants No. 0850830 and No. 0602308. S. R. W. acknowledges support from a University of Chicago Millikan Fellowship and from Mrs. Joan Winstein through the Winstein Prize for Instrumentation.","date_created":"2018-12-11T11:44:44Z","doi":"10.1103/PhysRevLett.112.218001","date_published":"2014-05-30T00:00:00Z","publication":"APS Physics, Physical Review Letters","day":"30","year":"2014"},{"citation":{"mla":"Hofbauer, Harald F., et al. “Regulation of Gene Expression through a Transcriptional Repressor That Senses Acyl-Chain Length in Membrane Phospholipids.” Developmental Cell, vol. 29, no. 6, Elsevier, 2014, pp. P729-739, doi:10.1016/j.devcel.2014.04.025.","ama":"Hofbauer HF, Schopf FH, Schleifer H, et al. Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. 2014;29(6):P729-739. doi:10.1016/j.devcel.2014.04.025","apa":"Hofbauer, H. F., Schopf, F. H., Schleifer, H., Knittelfelder, O. L., Pieber, B., Rechberger, G. N., … Kohlwein, S. D. (2014). Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2014.04.025","short":"H.F. Hofbauer, F.H. Schopf, H. Schleifer, O.L. Knittelfelder, B. Pieber, G.N. Rechberger, H. Wolinski, M.L. Gaspar, C.O. Kappe, J. Stadlmann, K. Mechtler, A. Zenz, K. Lohner, O. Tehlivets, S.A. Henry, S.D. Kohlwein, Developmental Cell 29 (2014) P729-739.","ieee":"H. F. Hofbauer et al., “Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids,” Developmental Cell, vol. 29, no. 6. Elsevier, pp. P729-739, 2014.","chicago":"Hofbauer, Harald F., Florian H. Schopf, Hannes Schleifer, Oskar L. Knittelfelder, Bartholomäus Pieber, Gerald N. Rechberger, Heimo Wolinski, et al. “Regulation of Gene Expression through a Transcriptional Repressor That Senses Acyl-Chain Length in Membrane Phospholipids.” Developmental Cell. Elsevier, 2014. https://doi.org/10.1016/j.devcel.2014.04.025.","ista":"Hofbauer HF, Schopf FH, Schleifer H, Knittelfelder OL, Pieber B, Rechberger GN, Wolinski H, Gaspar ML, Kappe CO, Stadlmann J, Mechtler K, Zenz A, Lohner K, Tehlivets O, Henry SA, Kohlwein SD. 2014. Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. 29(6), P729-739."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Harald F.","full_name":"Hofbauer, Harald F.","last_name":"Hofbauer"},{"first_name":"Florian H.","last_name":"Schopf","full_name":"Schopf, Florian H."},{"first_name":"Hannes","full_name":"Schleifer, Hannes","last_name":"Schleifer"},{"full_name":"Knittelfelder, Oskar L.","last_name":"Knittelfelder","first_name":"Oskar L."},{"id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus","last_name":"Pieber","full_name":"Pieber, Bartholomäus","orcid":"0000-0001-8689-388X"},{"full_name":"Rechberger, Gerald N.","last_name":"Rechberger","first_name":"Gerald N."},{"first_name":"Heimo","last_name":"Wolinski","full_name":"Wolinski, Heimo"},{"first_name":"Maria L.","last_name":"Gaspar","full_name":"Gaspar, Maria L."},{"last_name":"Kappe","full_name":"Kappe, C. Oliver","first_name":"C. Oliver"},{"first_name":"Johannes","full_name":"Stadlmann, Johannes","last_name":"Stadlmann"},{"full_name":"Mechtler, Karl","last_name":"Mechtler","first_name":"Karl"},{"first_name":"Alexandra","full_name":"Zenz, Alexandra","last_name":"Zenz"},{"full_name":"Lohner, Karl","last_name":"Lohner","first_name":"Karl"},{"first_name":"Oksana","last_name":"Tehlivets","full_name":"Tehlivets, Oksana"},{"first_name":"Susan A.","last_name":"Henry","full_name":"Henry, Susan A."},{"first_name":"Sepp D.","full_name":"Kohlwein, Sepp D.","last_name":"Kohlwein"}],"external_id":{"pmid":["24960695"]},"article_processing_charge":"No","title":"Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids","quality_controlled":"1","publisher":"Elsevier","oa":1,"year":"2014","day":"23","publication":"Developmental Cell","page":"P729-739","doi":"10.1016/j.devcel.2014.04.025","date_published":"2014-06-23T00:00:00Z","date_created":"2022-08-25T08:42:42Z","_id":"11968","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-02-21T10:09:45Z","extern":"1","abstract":[{"text":"Membrane phospholipids typically contain fatty acids (FAs) of 16 and 18 carbon atoms. This particular chain length is evolutionarily highly conserved and presumably provides maximum stability and dynamic properties to biological membranes in response to nutritional or environmental cues. Here, we show that the relative proportion of C16 versus C18 FAs is regulated by the activity of acetyl-CoA carboxylase (Acc1), the first and rate-limiting enzyme of FA de novo synthesis. Acc1 activity is attenuated by AMPK/Snf1-dependent phosphorylation, which is required to maintain an appropriate acyl-chain length distribution. Moreover, we find that the transcriptional repressor Opi1 preferentially binds to C16 over C18 phosphatidic acid (PA) species: thus, C16-chain containing PA sequesters Opi1 more effectively to the ER, enabling AMPK/Snf1 control of PA acyl-chain length to determine the degree of derepression of Opi1 target genes. These findings reveal an unexpected regulatory link between the major energy-sensing kinase, membrane lipid composition, and transcription.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2014.04.025","open_access":"1"}],"month":"06","intvolume":" 29","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":29,"issue":"6"},{"type":"journal_article","article_type":"original","status":"public","_id":"11967","date_updated":"2023-02-21T10:09:42Z","extern":"1","scopus_import":"1","intvolume":" 7","month":"11","abstract":[{"lang":"eng","text":"An experimentally easy to perform method for the generation of alumina-supported Fe3O4 nanoparticles [(6±1) nm size, 0.67 wt %]and the use of this material in hydrazine-mediated heterogeneously catalyzed reductions of nitroarenes to anilines under batch and continuous-flow conditions is presented. The bench-stable, reusable nano-Fe3O4@Al2O3 catalyst can selectively reduce functionalized nitroarenes at 1 mol % catalyst loading by using a 20 mol % excess of hydrazine hydrate in an elevated temperature regime (150 °C, reaction time 2–6 min in batch). For continuous-flow processing, the catalyst material is packed into dedicated cartridges and used in a commercially available high-temperature/-pressure flow device. In continuous mode, reaction times can be reduced to less than 1 min at 150 °C (30 bar back pressure) in a highly intensified process. The nano-Fe3O4@Al2O3 catalyst demonstrated stable reduction of nitrobenzene (0.5 M in MeOH) for more than 10 h on stream at a productivity of 30 mmol h−1 (0.72 mol per day). Importantly, virtually no leaching of the catalytically active material could be observed by inductively coupled plasma MS monitoring."}],"oa_version":"None","pmid":1,"volume":7,"issue":"11","publication_status":"published","publication_identifier":{"issn":["1864-5631"],"eissn":["1864-564X"]},"language":[{"iso":"eng"}],"external_id":{"pmid":["25209099"]},"article_processing_charge":"No","author":[{"first_name":"Mojtaba Mirhosseini","last_name":"Moghaddam","full_name":"Moghaddam, Mojtaba Mirhosseini"},{"last_name":"Pieber","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus","first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726"},{"first_name":"Toma","full_name":"Glasnov, Toma","last_name":"Glasnov"},{"first_name":"C. Oliver","full_name":"Kappe, C. Oliver","last_name":"Kappe"}],"title":"Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow","citation":{"mla":"Moghaddam, Mojtaba Mirhosseini, et al. “Immobilized Iron Oxide Nanoparticles as Stable and Reusable Catalysts for Hydrazine-Mediated Nitro Reductions in Continuous Flow.” ChemSusChem, vol. 7, no. 11, Wiley, 2014, pp. 3122–31, doi:10.1002/cssc.201402455.","ieee":"M. M. Moghaddam, B. Pieber, T. Glasnov, and C. O. Kappe, “Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow,” ChemSusChem, vol. 7, no. 11. Wiley, pp. 3122–3131, 2014.","short":"M.M. Moghaddam, B. Pieber, T. Glasnov, C.O. Kappe, ChemSusChem 7 (2014) 3122–3131.","ama":"Moghaddam MM, Pieber B, Glasnov T, Kappe CO. Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow. ChemSusChem. 2014;7(11):3122-3131. doi:10.1002/cssc.201402455","apa":"Moghaddam, M. M., Pieber, B., Glasnov, T., & Kappe, C. O. (2014). Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow. ChemSusChem. Wiley. https://doi.org/10.1002/cssc.201402455","chicago":"Moghaddam, Mojtaba Mirhosseini, Bartholomäus Pieber, Toma Glasnov, and C. Oliver Kappe. “Immobilized Iron Oxide Nanoparticles as Stable and Reusable Catalysts for Hydrazine-Mediated Nitro Reductions in Continuous Flow.” ChemSusChem. Wiley, 2014. https://doi.org/10.1002/cssc.201402455.","ista":"Moghaddam MM, Pieber B, Glasnov T, Kappe CO. 2014. Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow. ChemSusChem. 7(11), 3122–3131."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Wiley","page":"3122-3131","date_created":"2022-08-25T08:36:54Z","doi":"10.1002/cssc.201402455","date_published":"2014-11-01T00:00:00Z","year":"2014","publication":"ChemSusChem","day":"01"},{"article_type":"letter_note","type":"journal_article","status":"public","_id":"11987","article_number":"13430","article_processing_charge":"No","author":[{"full_name":"Pieber, Bartholomäus","orcid":"0000-0001-8689-388X","last_name":"Pieber","first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726"},{"first_name":"Toma","last_name":"Glasnov","full_name":"Glasnov, Toma"},{"first_name":"C. O.","full_name":"Kappe, C. O.","last_name":"Kappe"}],"title":"Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow","date_updated":"2023-02-21T10:10:31Z","citation":{"ieee":"B. Pieber, T. Glasnov, and C. O. Kappe, “Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow,” RSC Advances, vol. 4, no. 26. Royal Society of Chemistry, 2014.","short":"B. Pieber, T. Glasnov, C.O. Kappe, RSC Advances 4 (2014).","ama":"Pieber B, Glasnov T, Kappe CO. Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow. RSC Advances. 2014;4(26). doi:10.1039/c4ra01442a","apa":"Pieber, B., Glasnov, T., & Kappe, C. O. (2014). Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow. RSC Advances. Royal Society of Chemistry. https://doi.org/10.1039/c4ra01442a","mla":"Pieber, Bartholomäus, et al. “Flash Carboxylation: Fast Lithiation–Carboxylation Sequence at Room Temperature in Continuous Flow.” RSC Advances, vol. 4, no. 26, 13430, Royal Society of Chemistry, 2014, doi:10.1039/c4ra01442a.","ista":"Pieber B, Glasnov T, Kappe CO. 2014. Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow. RSC Advances. 4(26), 13430.","chicago":"Pieber, Bartholomäus, Toma Glasnov, and C. O. Kappe. “Flash Carboxylation: Fast Lithiation–Carboxylation Sequence at Room Temperature in Continuous Flow.” RSC Advances. Royal Society of Chemistry, 2014. https://doi.org/10.1039/c4ra01442a."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","publisher":"Royal Society of Chemistry","quality_controlled":"1","scopus_import":"1","intvolume":" 4","month":"03","abstract":[{"lang":"eng","text":"A method for the direct lithiation of terminal alkynes and heterocycles with subsequent carboxylation in a continuous flow format was developed. This method provides carboxylic acids at ambient conditions within less than five seconds with only little excess of the organometallic base and CO2."}],"oa_version":"None","date_created":"2022-08-25T11:48:19Z","issue":"26","doi":"10.1039/c4ra01442a","volume":4,"date_published":"2014-03-03T00:00:00Z","year":"2014","publication_status":"published","publication_identifier":{"eissn":["2046-2069"]},"language":[{"iso":"eng"}],"publication":"RSC Advances","day":"03"},{"_id":"1309","type":"journal_article","status":"public","citation":{"mla":"Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations and Applications, vol. 21, no. 1, Birkhäuser, 2014, pp. 27–50, doi:10.1007/s00030-013-0235-0.","ama":"Fischer JL. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. 2014;21(1):27-50. doi:10.1007/s00030-013-0235-0","apa":"Fischer, J. L. (2014). Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. Birkhäuser. https://doi.org/10.1007/s00030-013-0235-0","ieee":"J. L. Fischer, “Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models,” Nonlinear Differential Equations and Applications, vol. 21, no. 1. Birkhäuser, pp. 27–50, 2014.","short":"J.L. Fischer, Nonlinear Differential Equations and Applications 21 (2014) 27–50.","chicago":"Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations and Applications. Birkhäuser, 2014. https://doi.org/10.1007/s00030-013-0235-0.","ista":"Fischer JL. 2014. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. 21(1), 27–50."},"date_updated":"2021-01-12T06:49:47Z","extern":1,"author":[{"last_name":"Fischer","full_name":"Julian Fischer","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"}],"publist_id":"5960","title":"Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models","abstract":[{"text":"We show that weak solutions of the Derrida-Lebowitz-Speer-Spohn (DLSS) equation display infinite speed of support propagation. We apply our method to the case of the quantum drift-diffusion equation which augments the DLSS equation with a drift term and possibly a second-order diffusion term. The proof is accomplished using weighted entropy estimates, Hardy's inequality and a family of singular weight functions to derive a differential inequality; the differential inequality shows exponential growth of the weighted entropy, with the growth constant blowing up very fast as the singularity of the weight becomes sharper. To the best of our knowledge, this is the first example of a nonnegativity-preserving higher-order parabolic equation displaying infinite speed of support propagation.","lang":"eng"}],"publisher":"Birkhäuser","quality_controlled":0,"intvolume":" 21","month":"01","publication_status":"published","year":"2014","publication":"Nonlinear Differential Equations and Applications","day":"01","page":"27 - 50","date_created":"2018-12-11T11:51:17Z","doi":"10.1007/s00030-013-0235-0","issue":"1","volume":21,"date_published":"2014-01-01T00:00:00Z"},{"abstract":[{"lang":"eng","text":"We derive upper bounds on the waiting time of solutions to the thin-film equation in the regime of weak slippage n ∈ [2, 32\\11). In particular, we give sufficient conditions on the initial data for instantaneous forward motion of the free boundary. For n ∈ (2, 32\\11), our estimates are sharp, for n = 2, they are sharp up to a logarithmic correction term. Note that the case n = 2 corresponds-with a grain of salt-to the assumption of the Navier slip condition at the fluid-solid interface. We also obtain results in the regime of strong slippage n ∈ (1,2); however, in this regime we expect them not to be optimal. Our method is based on weighted backward entropy estimates, Hardy's inequality and singular weight functions; we deduce a differential inequality which would enforce blowup of the weighted entropy if the contact line were to remain stationary for too long."}],"quality_controlled":0,"publisher":"Springer","intvolume":" 211","month":"01","year":"2014","publication_status":"published","publication":"Archive for Rational Mechanics and Analysis","day":"01","page":"771 - 818","date_created":"2018-12-11T11:51:18Z","volume":211,"date_published":"2014-01-01T00:00:00Z","issue":"3","doi":"10.1007/s00205-013-0690-0","_id":"1312","type":"journal_article","status":"public","date_updated":"2021-01-12T06:49:48Z","citation":{"chicago":"Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation: The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis. Springer, 2014. https://doi.org/10.1007/s00205-013-0690-0.","ista":"Fischer JL. 2014. Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. 211(3), 771–818.","mla":"Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation: The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis, vol. 211, no. 3, Springer, 2014, pp. 771–818, doi:10.1007/s00205-013-0690-0.","apa":"Fischer, J. L. (2014). Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-013-0690-0","ama":"Fischer JL. Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. 2014;211(3):771-818. doi:10.1007/s00205-013-0690-0","ieee":"J. L. Fischer, “Upper bounds on waiting times for the Thin-film equation: The case of weak slippage,” Archive for Rational Mechanics and Analysis, vol. 211, no. 3. Springer, pp. 771–818, 2014.","short":"J.L. Fischer, Archive for Rational Mechanics and Analysis 211 (2014) 771–818."},"extern":1,"publist_id":"5959","author":[{"orcid":"0000-0002-0479-558X","full_name":"Julian Fischer","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"title":"Upper bounds on waiting times for the Thin-film equation: The case of weak slippage"},{"year":"2014","publication":"Theoretical Computer Science","day":"28","page":"104 - 116","date_created":"2018-12-11T11:51:40Z","doi":"10.1016/j.tcs.2014.06.031","date_published":"2014-08-28T00:00:00Z","oa":1,"publisher":"Elsevier","quality_controlled":"1","citation":{"short":"K. Chatterjee, M.H. Henzinger, S. Krinninger, V. Loitzenbauer, M. Raskin, Theoretical Computer Science 547 (2014) 104–116.","ieee":"K. Chatterjee, M. H. Henzinger, S. Krinninger, V. Loitzenbauer, and M. Raskin, “Approximating the minimum cycle mean,” Theoretical Computer Science, vol. 547, no. C. Elsevier, pp. 104–116, 2014.","apa":"Chatterjee, K., Henzinger, M. H., Krinninger, S., Loitzenbauer, V., & Raskin, M. (2014). Approximating the minimum cycle mean. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2014.06.031","ama":"Chatterjee K, Henzinger MH, Krinninger S, Loitzenbauer V, Raskin M. Approximating the minimum cycle mean. Theoretical Computer Science. 2014;547(C):104-116. doi:10.1016/j.tcs.2014.06.031","mla":"Chatterjee, Krishnendu, et al. “Approximating the Minimum Cycle Mean.” Theoretical Computer Science, vol. 547, no. C, Elsevier, 2014, pp. 104–16, doi:10.1016/j.tcs.2014.06.031.","ista":"Chatterjee K, Henzinger MH, Krinninger S, Loitzenbauer V, Raskin M. 2014. Approximating the minimum cycle mean. Theoretical Computer Science. 547(C), 104–116.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, Veronika Loitzenbauer, and Michael Raskin. “Approximating the Minimum Cycle Mean.” Theoretical Computer Science. Elsevier, 2014. https://doi.org/10.1016/j.tcs.2014.06.031."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1307.4473"]},"article_processing_charge":"No","publist_id":"5836","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Sebastian","full_name":"Krinninger, Sebastian","last_name":"Krinninger"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"},{"first_name":"Michael","last_name":"Raskin","full_name":"Raskin, Michael"}],"title":"Approximating the minimum cycle mean","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"issue":"C","volume":547,"abstract":[{"text":"We consider directed graphs where each edge is labeled with an integer weight and study the fundamental algorithmic question of computing the value of a cycle with minimum mean weight. Our contributions are twofold: (1) First we show that the algorithmic question is reducible to the problem of a logarithmic number of min-plus matrix multiplications of n×n-matrices, where n is the number of vertices of the graph. (2) Second, when the weights are nonnegative, we present the first (1+ε)-approximation algorithm for the problem and the running time of our algorithm is Õ(nωlog3(nW/ε)/ε),1 where O(nω) is the time required for the classic n×n-matrix multiplication and W is the maximum value of the weights. With an additional O(log(nW/ε)) factor in space a cycle with approximately optimal weight can be computed within the same time bound.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.4473"}],"scopus_import":"1","intvolume":" 547","month":"08","date_updated":"2022-09-09T11:50:58Z","department":[{"_id":"KrCh"}],"_id":"1375","type":"journal_article","article_type":"original","status":"public"},{"abstract":[{"text":"Fault-tolerant distributed algorithms play an important role in ensuring the reliability of many software applications. In this paper we consider distributed algorithms whose computations are organized in rounds. To verify the correctness of such algorithms, we reason about (i) properties (such as invariants) of the state, (ii) the transitions controlled by the algorithm, and (iii) the communication graph. We introduce a logic that addresses these points, and contains set comprehensions with cardinality constraints, function symbols to describe the local states of each process, and a limited form of quantifier alternation to express the verification conditions. We show its use in automating the verification of consensus algorithms. In particular, we give a semi-decision procedure for the unsatisfiability problem of the logic and identify a decidable fragment. We successfully applied our framework to verify the correctness of a variety of consensus algorithms tolerant to both benign faults (message loss, process crashes) and value faults (message corruption).","lang":"eng"}],"oa_version":"Submitted Version","alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 8318","month":"01","publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:44:48Z","file_size":444138,"date_created":"2018-12-12T10:11:06Z","file_name":"IST-2014-179-v1+1_vmcai14.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"bffa33d39be77df0da39defe97eabf84","file_id":"4859"}],"ec_funded":1,"volume":8318,"_id":"1392","conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation","location":"San Diego, USA","end_date":"2014-01-21","start_date":"2014-01-19"},"type":"conference","pubrep_id":"179","status":"public","date_updated":"2021-01-12T06:50:22Z","ddc":["000","005"],"file_date_updated":"2020-07-14T12:44:48Z","department":[{"_id":"ToHe"}],"acknowledgement":"Supported by the Vienna Science and Technology Fund (WWTF) through grant PROSEED.","oa":1,"publisher":"Springer","quality_controlled":"1","year":"2014","has_accepted_license":"1","day":"01","page":"161 - 181","date_created":"2018-12-11T11:51:45Z","doi":"10.1007/978-3-642-54013-4_10","date_published":"2014-01-01T00:00:00Z","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ieee":"C. Dragoi, T. A. Henzinger, H. Veith, J. Widder, and D. Zufferey, “A logic-based framework for verifying consensus algorithms,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, San Diego, USA, 2014, vol. 8318, pp. 161–181.","short":"C. Dragoi, T.A. Henzinger, H. Veith, J. Widder, D. Zufferey, in:, Springer, 2014, pp. 161–181.","apa":"Dragoi, C., Henzinger, T. A., Veith, H., Widder, J., & Zufferey, D. (2014). A logic-based framework for verifying consensus algorithms (Vol. 8318, pp. 161–181). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, San Diego, USA: Springer. https://doi.org/10.1007/978-3-642-54013-4_10","ama":"Dragoi C, Henzinger TA, Veith H, Widder J, Zufferey D. A logic-based framework for verifying consensus algorithms. In: Vol 8318. Springer; 2014:161-181. doi:10.1007/978-3-642-54013-4_10","mla":"Dragoi, Cezara, et al. A Logic-Based Framework for Verifying Consensus Algorithms. Vol. 8318, Springer, 2014, pp. 161–81, doi:10.1007/978-3-642-54013-4_10.","ista":"Dragoi C, Henzinger TA, Veith H, Widder J, Zufferey D. 2014. A logic-based framework for verifying consensus algorithms. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 8318, 161–181.","chicago":"Dragoi, Cezara, Thomas A Henzinger, Helmut Veith, Josef Widder, and Damien Zufferey. “A Logic-Based Framework for Verifying Consensus Algorithms,” 8318:161–81. Springer, 2014. https://doi.org/10.1007/978-3-642-54013-4_10."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Dragoi, Cezara","last_name":"Dragoi","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"last_name":"Veith","full_name":"Veith, Helmut","first_name":"Helmut"},{"first_name":"Josef","full_name":"Widder, Josef","last_name":"Widder"},{"id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien","last_name":"Zufferey","full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736"}],"publist_id":"5817","title":"A logic-based framework for verifying consensus algorithms"},{"_id":"1393","type":"conference","conference":{"start_date":"2014-05-31","location":"Hyderabad, India","end_date":"2014-06-07","name":"FOSE: Future of Software Engineering"},"status":"public","date_updated":"2021-01-12T06:50:22Z","department":[{"_id":"ToHe"}],"abstract":[{"text":"Probabilistic programs are usual functional or imperative programs with two added constructs: (1) the ability to draw values at random from distributions, and (2) the ability to condition values of variables in a program via observations. Models from diverse application areas such as computer vision, coding theory, cryptographic protocols, biology and reliability analysis can be written as probabilistic programs. Probabilistic inference is the problem of computing an explicit representation of the probability distribution implicitly specified by a probabilistic program. Depending on the application, the desired output from inference may vary-we may want to estimate the expected value of some function f with respect to the distribution, or the mode of the distribution, or simply a set of samples drawn from the distribution. In this paper, we describe connections this research area called \\Probabilistic Programming" has with programming languages and software engineering, and this includes language design, and the static and dynamic analysis of programs. We survey current state of the art and speculate on promising directions for future research.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"main_file_link":[{"url":"https://doi.org/10.1145/2593882.2593900","open_access":"1"}],"month":"05","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"citation":{"ista":"Gordon A, Henzinger TA, Nori A, Rajamani S. 2014. Probabilistic programming. Proceedings of the on Future of Software Engineering. FOSE: Future of Software Engineering, 167–181.","chicago":"Gordon, Andrew, Thomas A Henzinger, Aditya Nori, and Sriram Rajamani. “Probabilistic Programming.” In Proceedings of the on Future of Software Engineering, 167–81. ACM, 2014. https://doi.org/10.1145/2593882.2593900.","ama":"Gordon A, Henzinger TA, Nori A, Rajamani S. Probabilistic programming. In: Proceedings of the on Future of Software Engineering. ACM; 2014:167-181. doi:10.1145/2593882.2593900","apa":"Gordon, A., Henzinger, T. A., Nori, A., & Rajamani, S. (2014). Probabilistic programming. In Proceedings of the on Future of Software Engineering (pp. 167–181). Hyderabad, India: ACM. https://doi.org/10.1145/2593882.2593900","ieee":"A. Gordon, T. A. Henzinger, A. Nori, and S. Rajamani, “Probabilistic programming,” in Proceedings of the on Future of Software Engineering, Hyderabad, India, 2014, pp. 167–181.","short":"A. Gordon, T.A. Henzinger, A. Nori, S. Rajamani, in:, Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–181.","mla":"Gordon, Andrew, et al. “Probabilistic Programming.” Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–81, doi:10.1145/2593882.2593900."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5816","author":[{"first_name":"Andrew","full_name":"Gordon, Andrew","last_name":"Gordon"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Nori","full_name":"Nori, Aditya","first_name":"Aditya"},{"last_name":"Rajamani","full_name":"Rajamani, Sriram","first_name":"Sriram"}],"article_processing_charge":"No","title":"Probabilistic programming","publisher":"ACM","quality_controlled":"1","oa":1,"year":"2014","day":"31","publication":"Proceedings of the on Future of Software Engineering","page":"167 - 181","date_published":"2014-05-31T00:00:00Z","doi":"10.1145/2593882.2593900","date_created":"2018-12-11T11:51:45Z"},{"publication_status":"published","year":"2014","day":"01","language":[{"iso":"eng"}],"page":"101","date_published":"2014-04-01T00:00:00Z","date_created":"2018-12-11T11:51:49Z","abstract":[{"text":"The co-evolution of hosts and pathogens is characterized by continuous adaptations of both parties. Pathogens of social insects need to adapt towards disease defences at two levels: 1) individual immunity of each colony member consisting of behavioural defence strategies as well as humoral and cellular immune responses and 2) social immunity that is collectively performed by all group members comprising behavioural, physiological and organisational defence strategies.\r\n\r\nTo disentangle the selection pressure on pathogens by the collective versus individual level of disease defence in social insects, we performed an evolution experiment using the Argentine Ant, Linepithema humile, as a host and a mixture of the general insect pathogenic fungus Metarhizium spp. (6 strains) as a pathogen. We allowed pathogen evolution over 10 serial host passages to two different evolution host treatments: (1) only individual host immunity in a single host treatment, and (2) simultaneously acting individual and social immunity in a social host treatment, in which an exposed ant was accompanied by two untreated nestmates.\r\n\r\nBefore starting the pathogen evolution experiment, the 6 Metarhizium spp. strains were characterised concerning conidiospore size killing rates in singly and socially reared ants, their competitiveness under coinfecting conditions and their influence on ant behaviour. We analysed how the ancestral atrain mixture changed in conidiospere size, killing rate and strain composition dependent on host treatment (single or social hosts) during 10 passages and found that killing rate and conidiospere size of the pathogen increased under both evolution regimes, but different depending on host treatment.\r\n\r\nTesting the evolved strain mixtures that evolved under either the single or social host treatment under both single and social current rearing conditions in a full factorial design experiment revealed that the additional collective defences in insect societies add new selection pressure for their coevolving pathogens that compromise their ability to adapt to its host at the group level. To our knowledge, this is the first study directly measuring the influence of social immunity on pathogen evolution.","lang":"eng"}],"oa_version":"None","acknowledgement":"This work was funded by the DFG and the ERC.","publisher":"IST Austria","alternative_title":["IST Austria Thesis"],"month":"04","supervisor":[{"last_name":"Cremer","full_name":"Cremer, Sylvia M","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia M"}],"citation":{"mla":"Stock, Miriam. Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants. IST Austria, 2014.","short":"M. Stock, Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants, IST Austria, 2014.","ieee":"M. Stock, “Evolution of a fungal pathogen towards individual versus social immunity in ants,” IST Austria, 2014.","ama":"Stock M. Evolution of a fungal pathogen towards individual versus social immunity in ants. 2014.","apa":"Stock, M. (2014). Evolution of a fungal pathogen towards individual versus social immunity in ants. IST Austria.","chicago":"Stock, Miriam. “Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants.” IST Austria, 2014.","ista":"Stock M. 2014. Evolution of a fungal pathogen towards individual versus social immunity in ants. IST Austria."},"date_updated":"2021-01-12T06:50:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5803","author":[{"full_name":"Stock, Miriam","last_name":"Stock","id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam"}],"department":[{"_id":"SyCr"}],"title":"Evolution of a fungal pathogen towards individual versus social immunity in ants","_id":"1404","type":"dissertation","status":"public"},{"department":[{"_id":"RoSe"}],"title":"On the BCS gap equation for superfluid fermionic gases","author":[{"last_name":"Bräunlich","full_name":"Bräunlich, Gerhard","first_name":"Gerhard"},{"last_name":"Hainzl","full_name":"Hainzl, Christian","first_name":"Christian"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"publist_id":"5661","article_processing_charge":"No","external_id":{"arxiv":["1403.2563"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"G. Bräunlich, C. Hainzl, R. Seiringer, in:, Proceedings of the QMath12 Conference, World Scientific Publishing, 2014, pp. 127–137.","ieee":"G. Bräunlich, C. Hainzl, and R. Seiringer, “On the BCS gap equation for superfluid fermionic gases,” in Proceedings of the QMath12 Conference, Berlin, Germany, 2014, pp. 127–137.","ama":"Bräunlich G, Hainzl C, Seiringer R. On the BCS gap equation for superfluid fermionic gases. In: Proceedings of the QMath12 Conference. World Scientific Publishing; 2014:127-137. doi:10.1142/9789814618144_0007","apa":"Bräunlich, G., Hainzl, C., & Seiringer, R. (2014). On the BCS gap equation for superfluid fermionic gases. In Proceedings of the QMath12 Conference (pp. 127–137). Berlin, Germany: World Scientific Publishing. https://doi.org/10.1142/9789814618144_0007","mla":"Bräunlich, Gerhard, et al. “On the BCS Gap Equation for Superfluid Fermionic Gases.” Proceedings of the QMath12 Conference, World Scientific Publishing, 2014, pp. 127–37, doi:10.1142/9789814618144_0007.","ista":"Bräunlich G, Hainzl C, Seiringer R. 2014. On the BCS gap equation for superfluid fermionic gases. Proceedings of the QMath12 Conference. QMath: Mathematical Results in Quantum Physics, 127–137.","chicago":"Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “On the BCS Gap Equation for Superfluid Fermionic Gases.” In Proceedings of the QMath12 Conference, 127–37. World Scientific Publishing, 2014. https://doi.org/10.1142/9789814618144_0007."},"date_updated":"2021-01-12T06:51:19Z","status":"public","type":"conference","conference":{"start_date":"2013-09-10","end_date":"2013-09-13","location":"Berlin, Germany","name":"QMath: Mathematical Results in Quantum Physics"},"_id":"1516","doi":"10.1142/9789814618144_0007","date_published":"2014-01-01T00:00:00Z","date_created":"2018-12-11T11:52:28Z","page":"127 - 137","day":"01","publication":"Proceedings of the QMath12 Conference","language":[{"iso":"eng"}],"publication_status":"published","year":"2014","month":"01","quality_controlled":"1","publisher":"World Scientific Publishing","main_file_link":[{"url":"https://arxiv.org/abs/1403.2563","open_access":"1"}],"oa":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We present a rigorous derivation of the BCS gap equation for superfluid fermionic gases with point interactions. Our starting point is the BCS energy functional, whose minimizer we investigate in the limit when the range of the interaction potential goes to zero.\r\n"}]},{"has_accepted_license":"1","year":"2014","day":"01","publication":"ACM Transactions on Graphics","doi":"10.1145/2591010","date_published":"2014-03-01T00:00:00Z","date_created":"2018-12-11T11:53:08Z","publisher":"ACM","quality_controlled":"1","oa":1,"citation":{"ieee":"P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Edit propagation using geometric relationship functions,” ACM Transactions on Graphics, vol. 33, no. 2. ACM, 2014.","short":"P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, ACM Transactions on Graphics 33 (2014).","apa":"Guerrero, P., Jeschke, S., Wimmer, M., & Wonka, P. (2014). Edit propagation using geometric relationship functions. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2591010","ama":"Guerrero P, Jeschke S, Wimmer M, Wonka P. Edit propagation using geometric relationship functions. ACM Transactions on Graphics. 2014;33(2). doi:10.1145/2591010","mla":"Guerrero, Paul, et al. “Edit Propagation Using Geometric Relationship Functions.” ACM Transactions on Graphics, vol. 33, no. 2, 15, ACM, 2014, doi:10.1145/2591010.","ista":"Guerrero P, Jeschke S, Wimmer M, Wonka P. 2014. Edit propagation using geometric relationship functions. ACM Transactions on Graphics. 33(2), 15.","chicago":"Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Edit Propagation Using Geometric Relationship Functions.” ACM Transactions on Graphics. ACM, 2014. https://doi.org/10.1145/2591010."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5526","author":[{"full_name":"Guerrero, Paul","last_name":"Guerrero","first_name":"Paul"},{"first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","last_name":"Jeschke","full_name":"Jeschke, Stefan"},{"full_name":"Wimmer, Michael","last_name":"Wimmer","first_name":"Michael"},{"last_name":"Wonka","full_name":"Wonka, Peter","first_name":"Peter"}],"title":"Edit propagation using geometric relationship functions","article_number":"15","publication_status":"published","file":[{"checksum":"7f91e588a4e888610313b98271e6418e","file_id":"4876","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-577-v1+1_2014.TOG.Paul.EditingPropagation.final.pdf","date_created":"2018-12-12T10:11:22Z","creator":"system","file_size":9832561,"date_updated":"2020-07-14T12:45:07Z"}],"language":[{"iso":"eng"}],"volume":33,"issue":"2","abstract":[{"text":"We propose a method for propagating edit operations in 2D vector graphics, based on geometric relationship functions. These functions quantify the geometric relationship of a point to a polygon, such as the distance to the boundary or the direction to the closest corner vertex. The level sets of the relationship functions describe points with the same relationship to a polygon. For a given query point, we first determine a set of relationships to local features, construct all level sets for these relationships, and accumulate them. The maxima of the resulting distribution are points with similar geometric relationships. We show extensions to handle mirror symmetries, and discuss the use of relationship functions as local coordinate systems. Our method can be applied, for example, to interactive floorplan editing, and it is especially useful for large layouts, where individual edits would be cumbersome. We demonstrate populating 2D layouts with tens to hundreds of objects by propagating relatively few edit operations.","lang":"eng"}],"oa_version":"Submitted Version","month":"03","intvolume":" 33","date_updated":"2021-01-12T06:52:06Z","ddc":["000"],"file_date_updated":"2020-07-14T12:45:07Z","department":[{"_id":"ChWo"}],"_id":"1629","type":"journal_article","status":"public","pubrep_id":"577"},{"abstract":[{"lang":"eng","text":"The Hanani–Tutte theorem is a classical result proved for the first time in the 1930s that characterizes planar graphs as graphs that admit a drawing in the plane in which every pair of edges not sharing a vertex cross an even number of times. We generalize this classical result to clustered graphs with two disjoint clusters, and show that a straightforward extension of our result to flat clustered graphs with three or more disjoint clusters is not possible.\r\n\r\nWe also give a new and short proof for a related result by Di Battista and Frati based on the matroid intersection algorithm."}],"oa_version":"Preprint","scopus_import":"1","alternative_title":["LNCS"],"place":"Cham","month":"01","intvolume":" 8871","publication_identifier":{"issn":["0302-9743"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"1642","status":"public","relation":"later_version"}]},"volume":8871,"_id":"10793","type":"conference","status":"public","date_updated":"2023-02-23T10:08:04Z","department":[{"_id":"UlWa"}],"quality_controlled":"1","publisher":"Springer Nature","year":"2014","day":"01","publication":"International Symposium on Graph Drawing","page":"428-436","doi":"10.1007/978-3-662-45803-7_36","date_published":"2014-01-01T00:00:00Z","date_created":"2022-02-25T10:32:14Z","citation":{"mla":"Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” International Symposium on Graph Drawing, vol. 8871, Springer Nature, 2014, pp. 428–36, doi:10.1007/978-3-662-45803-7_36.","apa":"Fulek, R., Kynčl, J., Malinović, I., & Pálvölgyi, D. (2014). Clustered planarity testing revisited. In International Symposium on Graph Drawing (Vol. 8871, pp. 428–436). Cham: Springer Nature. https://doi.org/10.1007/978-3-662-45803-7_36","ama":"Fulek R, Kynčl J, Malinović I, Pálvölgyi D. Clustered planarity testing revisited. In: International Symposium on Graph Drawing. Vol 8871. Cham: Springer Nature; 2014:428-436. doi:10.1007/978-3-662-45803-7_36","short":"R. Fulek, J. Kynčl, I. Malinović, D. Pálvölgyi, in:, International Symposium on Graph Drawing, Springer Nature, Cham, 2014, pp. 428–436.","ieee":"R. Fulek, J. Kynčl, I. Malinović, and D. Pálvölgyi, “Clustered planarity testing revisited,” in International Symposium on Graph Drawing, 2014, vol. 8871, pp. 428–436.","chicago":"Fulek, Radoslav, Jan Kynčl, Igor Malinović, and Dömötör Pálvölgyi. “Clustered Planarity Testing Revisited.” In International Symposium on Graph Drawing, 8871:428–36. Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-662-45803-7_36.","ista":"Fulek R, Kynčl J, Malinović I, Pálvölgyi D. 2014. Clustered planarity testing revisited. International Symposium on Graph Drawing. , LNCS, vol. 8871, 428–436."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"last_name":"Kynčl","full_name":"Kynčl, Jan","first_name":"Jan"},{"full_name":"Malinović, Igor","last_name":"Malinović","first_name":"Igor"},{"full_name":"Pálvölgyi, Dömötör","last_name":"Pálvölgyi","first_name":"Dömötör"}],"external_id":{"arxiv":["1305.4519"]},"article_processing_charge":"No","title":"Clustered planarity testing revisited"},{"language":[{"iso":"eng"}],"publication_status":"published","volume":8642,"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We extend the notion of verifiable random functions (VRF) to constrained VRFs, which generalize the concept of constrained pseudorandom functions, put forward by Boneh and Waters (Asiacrypt’13), and independently by Kiayias et al. (CCS’13) and Boyle et al. (PKC’14), who call them delegatable PRFs and functional PRFs, respectively. In a standard VRF the secret key sk allows one to evaluate a pseudorandom function at any point of its domain; in addition, it enables computation of a non-interactive proof that the function value was computed correctly. In a constrained VRF from the key sk one can derive constrained keys skS for subsets S of the domain, which allow computation of function values and proofs only at points in S. After formally defining constrained VRFs, we derive instantiations from the multilinear-maps-based constrained PRFs by Boneh and Waters, yielding a VRF with constrained keys for any set that can be decided by a polynomial-size circuit. Our VRFs have the same function values as the Boneh-Waters PRFs and are proved secure under the same hardness assumption, showing that verifiability comes at no cost. Constrained (functional) VRFs were stated as an open problem by Boyle et al."}],"month":"01","intvolume":" 8642","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"url":"http://eprint.iacr.org/2014/537","open_access":"1"}],"date_updated":"2021-01-12T06:52:12Z","department":[{"_id":"KrPi"}],"_id":"1643","status":"public","type":"conference","conference":{"start_date":"2014-09-03","location":"Amalfi, Italy","end_date":"2014-09-05","name":"SCN: Security and Cryptography for Networks"},"day":"01","publication":"SCN 2014","year":"2014","doi":"10.1007/978-3-319-10879-7_7","date_published":"2014-01-01T00:00:00Z","date_created":"2018-12-11T11:53:13Z","page":"95 - 114","publisher":"Springer","oa":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Fuchsbauer G. Constrained Verifiable Random Functions . In: Abdalla M, De Prisco R, eds. SCN 2014. Vol 8642. Springer; 2014:95-114. doi:10.1007/978-3-319-10879-7_7","apa":"Fuchsbauer, G. (2014). Constrained Verifiable Random Functions . In M. Abdalla & R. De Prisco (Eds.), SCN 2014 (Vol. 8642, pp. 95–114). Amalfi, Italy: Springer. https://doi.org/10.1007/978-3-319-10879-7_7","ieee":"G. Fuchsbauer, “Constrained Verifiable Random Functions ,” in SCN 2014, Amalfi, Italy, 2014, vol. 8642, pp. 95–114.","short":"G. Fuchsbauer, in:, M. Abdalla, R. De Prisco (Eds.), SCN 2014, Springer, 2014, pp. 95–114.","mla":"Fuchsbauer, Georg. “Constrained Verifiable Random Functions .” SCN 2014, edited by Michel Abdalla and Roberto De Prisco, vol. 8642, Springer, 2014, pp. 95–114, doi:10.1007/978-3-319-10879-7_7.","ista":"Fuchsbauer G. 2014. Constrained Verifiable Random Functions . SCN 2014. SCN: Security and Cryptography for Networks, LNCS, vol. 8642, 95–114.","chicago":"Fuchsbauer, Georg. “Constrained Verifiable Random Functions .” In SCN 2014, edited by Michel Abdalla and Roberto De Prisco, 8642:95–114. Springer, 2014. https://doi.org/10.1007/978-3-319-10879-7_7."},"title":"Constrained Verifiable Random Functions ","editor":[{"last_name":"Abdalla","full_name":"Abdalla, Michel","first_name":"Michel"},{"first_name":"Roberto","last_name":"De Prisco","full_name":"De Prisco, Roberto"}],"publist_id":"5509","author":[{"first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"}],"project":[{"grant_number":"259668","name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425"}]},{"year":"2014","publication_status":"published","publication":"Electronic Proceedings in Theoretical Computer Science, EPTCS","language":[{"iso":"eng"}],"day":"02","page":"31 - 38","date_created":"2018-12-11T11:53:33Z","doi":"10.4204/EPTCS.169.5","volume":169,"date_published":"2014-12-02T00:00:00Z","abstract":[{"lang":"eng","text":"In this paper we present INTERHORN, a solver for recursion-free Horn clauses. The main application domain of INTERHORN lies in solving interpolation problems arising in software verification. We show how a range of interpolation problems, including path, transition, nested, state/transition and well-founded interpolation can be handled directly by INTERHORN. By detailing these interpolation problems and their Horn clause representations, we hope to encourage the emergence of a common back-end interpolation interface useful for diverse verification tools."}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.7378v2"}],"oa":1,"publisher":"Open Publishing","quality_controlled":"1","alternative_title":["EPTCS"],"intvolume":" 169","month":"12","date_updated":"2021-01-12T06:52:38Z","citation":{"mla":"Gupta, Ashutosh, et al. “Generalised Interpolation by Solving Recursion Free-Horn Clauses.” Electronic Proceedings in Theoretical Computer Science, EPTCS, vol. 169, Open Publishing, 2014, pp. 31–38, doi:10.4204/EPTCS.169.5.","apa":"Gupta, A., Popeea, C., & Rybalchenko, A. (2014). Generalised interpolation by solving recursion free-horn clauses. In Electronic Proceedings in Theoretical Computer Science, EPTCS (Vol. 169, pp. 31–38). Vienna, Austria: Open Publishing. https://doi.org/10.4204/EPTCS.169.5","ama":"Gupta A, Popeea C, Rybalchenko A. Generalised interpolation by solving recursion free-horn clauses. In: Electronic Proceedings in Theoretical Computer Science, EPTCS. Vol 169. Open Publishing; 2014:31-38. doi:10.4204/EPTCS.169.5","short":"A. Gupta, C. Popeea, A. Rybalchenko, in:, Electronic Proceedings in Theoretical Computer Science, EPTCS, Open Publishing, 2014, pp. 31–38.","ieee":"A. Gupta, C. Popeea, and A. Rybalchenko, “Generalised interpolation by solving recursion free-horn clauses,” in Electronic Proceedings in Theoretical Computer Science, EPTCS, Vienna, Austria, 2014, vol. 169, pp. 31–38.","chicago":"Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Generalised Interpolation by Solving Recursion Free-Horn Clauses.” In Electronic Proceedings in Theoretical Computer Science, EPTCS, 169:31–38. Open Publishing, 2014. https://doi.org/10.4204/EPTCS.169.5.","ista":"Gupta A, Popeea C, Rybalchenko A. 2014. Generalised interpolation by solving recursion free-horn clauses. Electronic Proceedings in Theoretical Computer Science, EPTCS. HCVS: Horn Clauses for Verification and Synthesis, EPTCS, vol. 169, 31–38."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5435","author":[{"last_name":"Gupta","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh"},{"first_name":"Corneliu","full_name":"Popeea, Corneliu","last_name":"Popeea"},{"last_name":"Rybalchenko","full_name":"Rybalchenko, Andrey","first_name":"Andrey"}],"title":"Generalised interpolation by solving recursion free-horn clauses","department":[{"_id":"ToHe"}],"_id":"1702","conference":{"start_date":"2014-07-17","end_date":"2014-07-17","location":"Vienna, Austria","name":"HCVS: Horn Clauses for Verification and Synthesis"},"type":"conference","status":"public"},{"_id":"1708","conference":{"name":"NIPS: Neural Information Processing Systems","start_date":"2014-12-08","location":"Montreal, Canada","end_date":"2014-12-13"},"type":"conference","status":"public","date_updated":"2021-01-12T06:52:40Z","citation":{"chicago":"Savin, Cristina, and Sophie Denève. “Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks,” 3:2024–32. Neural Information Processing Systems, 2014.","ista":"Savin C, Denève S. 2014. Spatio-temporal representations of uncertainty in spiking neural networks. NIPS: Neural Information Processing Systems vol. 3, 2024–2032.","mla":"Savin, Cristina, and Sophie Denève. Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks. Vol. 3, no. January, Neural Information Processing Systems, 2014, pp. 2024–32.","ieee":"C. Savin and S. Denève, “Spatio-temporal representations of uncertainty in spiking neural networks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2014, vol. 3, no. January, pp. 2024–2032.","short":"C. Savin, S. Denève, in:, Neural Information Processing Systems, 2014, pp. 2024–2032.","apa":"Savin, C., & Denève, S. (2014). Spatio-temporal representations of uncertainty in spiking neural networks (Vol. 3, pp. 2024–2032). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.","ama":"Savin C, Denève S. Spatio-temporal representations of uncertainty in spiking neural networks. In: Vol 3. Neural Information Processing Systems; 2014:2024-2032."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","full_name":"Savin, Cristina"},{"full_name":"Denève, Sophie","last_name":"Denève","first_name":"Sophie"}],"publist_id":"5427","department":[{"_id":"GaTk"}],"title":"Spatio-temporal representations of uncertainty in spiking neural networks","abstract":[{"lang":"eng","text":"It has been long argued that, because of inherent ambiguity and noise, the brain needs to represent uncertainty in the form of probability distributions. The neural encoding of such distributions remains however highly controversial. Here we present a novel circuit model for representing multidimensional real-valued distributions using a spike based spatio-temporal code. Our model combines the computational advantages of the currently competing models for probabilistic codes and exhibits realistic neural responses along a variety of classic measures. Furthermore, the model highlights the challenges associated with interpreting neural activity in relation to behavioral uncertainty and points to alternative population-level approaches for the experimental validation of distributed representations."}],"oa_version":"None","main_file_link":[{"url":"http://papers.nips.cc/paper/5343-spatio-temporal-representations-of-uncertainty-in-spiking-neural-networks.pdf"}],"quality_controlled":"1","publisher":"Neural Information Processing Systems","scopus_import":1,"intvolume":" 3","month":"01","year":"2014","publication_status":"published","language":[{"iso":"eng"}],"day":"01","page":"2024 - 2032","date_created":"2018-12-11T11:53:35Z","date_published":"2014-01-01T00:00:00Z","volume":3,"issue":"January"},{"date_updated":"2021-01-12T06:53:02Z","citation":{"chicago":"Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Silvano De Franceschi, Pascal Gentile, Riccardo Rurali, and Xavier Cartoixà. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.” Physical Review X. American Physical Society, 2014. https://doi.org/10.1103/PhysRevX.3.041025.","ista":"Mongillo M, Spathis P, Katsaros G, De Franceschi S, Gentile P, Rurali R, Cartoixà X. 2014. PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. 3(4).","mla":"Mongillo, Massimo, et al. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.” Physical Review X, vol. 3, no. 4, American Physical Society, 2014, doi:10.1103/PhysRevX.3.041025.","short":"M. Mongillo, P. Spathis, G. Katsaros, S. De Franceschi, P. Gentile, R. Rurali, X. Cartoixà, Physical Review X 3 (2014).","ieee":"M. Mongillo et al., “PtSi clustering in silicon probed by transport spectroscopy,” Physical Review X, vol. 3, no. 4. American Physical Society, 2014.","ama":"Mongillo M, Spathis P, Katsaros G, et al. PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. 2014;3(4). doi:10.1103/PhysRevX.3.041025","apa":"Mongillo, M., Spathis, P., Katsaros, G., De Franceschi, S., Gentile, P., Rurali, R., & Cartoixà, X. (2014). PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.3.041025"},"extern":1,"publist_id":"5363","author":[{"first_name":"Massimo","last_name":"Mongillo","full_name":"Mongillo, Massimo"},{"full_name":"Spathis, Panayotis N","last_name":"Spathis","first_name":"Panayotis"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","full_name":"Georgios Katsaros"},{"full_name":"De Franceschi, Silvano","last_name":"De Franceschi","first_name":"Silvano"},{"full_name":"Gentile, Pascal","last_name":"Gentile","first_name":"Pascal"},{"last_name":"Rurali","full_name":"Rurali, Riccardo","first_name":"Riccardo"},{"first_name":"Xavier","last_name":"Cartoixà","full_name":"Cartoixà, Xavier"}],"title":"PtSi clustering in silicon probed by transport spectroscopy","_id":"1761","type":"journal_article","status":"public","publication_status":"published","year":"2014","day":"01","publication":"Physical Review X","doi":"10.1103/PhysRevX.3.041025","volume":3,"date_published":"2014-01-01T00:00:00Z","issue":"4","date_created":"2018-12-11T11:53:52Z","abstract":[{"lang":"eng","text":"Metal silicides formed by means of thermal annealing processes are employed as contact materials in microelectronics. Control of the structure of silicide/silicon interfaces becomes a critical issue when the characteristic size of the device is reduced below a few tens of nanometers. Here, we report on silicide clustering occurring within the channel of PtSi/Si/PtSi Schottky-barrier transistors. This phenomenon is investigated through atomistic simulations and low-temperature resonant-tunneling spectroscopy. Our results provide evidence for the segregation of a PtSi cluster with a diameter of a few nanometers from the silicide contact. The cluster acts as a metallic quantum dot giving rise to distinct signatures of quantum transport through its discrete energy states."}],"acknowledgement":"This work was supported by the Agence Nationale de la Recherche and by the EU through the ERC Starting Grant HybridNano","publisher":"American Physical Society","quality_controlled":0,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.5413"}],"oa":1,"month":"01","intvolume":" 3"},{"day":"18","publication":"Neuron","publication_status":"published","year":"2014","date_published":"2014-06-18T00:00:00Z","issue":"6","doi":"10.1016/j.neuron.2014.04.036","volume":82,"date_created":"2018-12-11T11:54:01Z","page":"1255 - 1262","acknowledgement":"This work was supported by the National Institutes of Health R01NS41537. G.K. was supported by an EMBO Long Term Fellowship, S.L.B. by the A.P. Giannini Fellowship, and A.G.F. by the Brain Behavior Research Foundation","abstract":[{"lang":"eng","text":"Acute gene inactivation using short hairpin RNA (shRNA, knockdown) in developing brain is a powerful technique to study genetic function; however, discrepancies between knockdown and knockout murine phenotypes have left unanswered questions. For example, doublecortin (Dcx) knockdown but not knockout shows a neocortical neuronal migration phenotype. Here we report that in utero electroporation of shRNA, but not siRNA or miRNA, to Dcx demonstrates a migration phenotype in Dcx knockouts akin to the effect in wild-type mice, suggestingshRNA-mediated off-target toxicity. This effect wasnot limited to Dcx, as it was observed in Dclk1 knockouts, as well as with a fraction of scrambled shRNAs, suggesting a sequence-dependent but not sequence-specific effect. Profiling RNAs from electroporated cells showed a defect in endogenous let7 miRNA levels, and disruption of let7 or Dicer recapitulated the migration defect. The results suggest that shRNA-mediated knockdown can produce untoward migration effects by altering endogenous miRNA pathways."}],"month":"06","intvolume":" 82","quality_controlled":0,"publisher":"Elsevier","extern":1,"citation":{"ista":"Baek S, Kerjan G, Bielas S, Lee J, Fenstermaker A, Novarino G, Gleeson J. 2014. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 82(6), 1255–1262.","chicago":"Baek, Seungtae, Géraldine Kerjan, Stephanie Bielas, Jieun Lee, Ali Fenstermaker, Gaia Novarino, and Joseph Gleeson. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.036.","ama":"Baek S, Kerjan G, Bielas S, et al. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 2014;82(6):1255-1262. doi:10.1016/j.neuron.2014.04.036","apa":"Baek, S., Kerjan, G., Bielas, S., Lee, J., Fenstermaker, A., Novarino, G., & Gleeson, J. (2014). Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.036","ieee":"S. Baek et al., “Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation,” Neuron, vol. 82, no. 6. Elsevier, pp. 1255–1262, 2014.","short":"S. Baek, G. Kerjan, S. Bielas, J. Lee, A. Fenstermaker, G. Novarino, J. Gleeson, Neuron 82 (2014) 1255–1262.","mla":"Baek, Seungtae, et al. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron, vol. 82, no. 6, Elsevier, 2014, pp. 1255–62, doi:10.1016/j.neuron.2014.04.036."},"date_updated":"2021-01-12T06:53:13Z","title":"Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation","publist_id":"5322","author":[{"last_name":"Baek","full_name":"Baek, SeungTae","first_name":"Seungtae"},{"full_name":"Kerjan, Géraldine","last_name":"Kerjan","first_name":"Géraldine"},{"last_name":"Bielas","full_name":"Bielas, Stephanie L","first_name":"Stephanie"},{"first_name":"Jieun","full_name":"Lee, Jieun","last_name":"Lee"},{"first_name":"Ali","full_name":"Fenstermaker, Ali G","last_name":"Fenstermaker"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","full_name":"Gaia Novarino","orcid":"0000-0002-7673-7178"},{"last_name":"Gleeson","full_name":"Gleeson, Joseph G","first_name":"Joseph"}],"_id":"1791","status":"public","type":"journal_article"},{"type":"book_chapter","status":"public","_id":"1806","publist_id":"5304","author":[{"first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","last_name":"Baster","full_name":"Baster, Pawel"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"editor":[{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"}],"title":"Auxin on the road navigated by cellular PIN polarity","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:53:19Z","citation":{"ista":"Baster P, Friml J. 2014.Auxin on the road navigated by cellular PIN polarity. In: Auxin and Its Role in Plant Development. , 143–170.","chicago":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” In Auxin and Its Role in Plant Development, edited by Eva Zažímalová, Jan Petrášek, and Eva Benková, 143–70. Springer, 2014. https://doi.org/10.1007/978-3-7091-1526-8_8.","apa":"Baster, P., & Friml, J. (2014). Auxin on the road navigated by cellular PIN polarity. In E. Zažímalová, J. Petrášek, & E. Benková (Eds.), Auxin and Its Role in Plant Development (pp. 143–170). Springer. https://doi.org/10.1007/978-3-7091-1526-8_8","ama":"Baster P, Friml J. Auxin on the road navigated by cellular PIN polarity. In: Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development. Springer; 2014:143-170. doi:10.1007/978-3-7091-1526-8_8","short":"P. Baster, J. Friml, in:, E. Zažímalová, J. Petrášek, E. Benková (Eds.), Auxin and Its Role in Plant Development, Springer, 2014, pp. 143–170.","ieee":"P. Baster and J. Friml, “Auxin on the road navigated by cellular PIN polarity,” in Auxin and Its Role in Plant Development, E. Zažímalová, J. Petrášek, and E. Benková, Eds. Springer, 2014, pp. 143–170.","mla":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” Auxin and Its Role in Plant Development, edited by Eva Zažímalová et al., Springer, 2014, pp. 143–70, doi:10.1007/978-3-7091-1526-8_8."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"quality_controlled":"1","publisher":"Springer","month":"04","abstract":[{"text":"The generation of asymmetry, at both cellular and tissue level, is one of the most essential capabilities of all eukaryotic organisms. It mediates basically all multicellular development ranging from embryogenesis and de novo organ formation till responses to various environmental stimuli. In plants, the awe-inspiring number of such processes is regulated by phytohormone auxin and its directional, cell-to-cell transport. The mediators of this transport, PIN auxin transporters, are asymmetrically localized at the plasma membrane, and this polar localization determines the directionality of intercellular auxin flow. Thus, auxin transport contributes crucially to the generation of local auxin gradients or maxima, which instruct given cell to change its developmental program. Here, we introduce and discuss the molecular components and cellular mechanisms regulating the generation and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity in plants.","lang":"eng"}],"oa_version":"None","page":"143 - 170","date_created":"2018-12-11T11:54:07Z","date_published":"2014-04-01T00:00:00Z","doi":"10.1007/978-3-7091-1526-8_8","publication_status":"published","year":"2014","publication":"Auxin and Its Role in Plant Development","language":[{"iso":"eng"}],"day":"01"},{"file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"HeEd"}],"ddc":["000"],"date_updated":"2021-01-12T06:53:23Z","pubrep_id":"443","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1816","volume":24,"issue":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:08:43Z","file_name":"IST-2016-443-v1+1_S0218195914500034.pdf","creator":"system","date_updated":"2020-07-14T12:45:17Z","file_size":991734,"checksum":"be45c133ab4d43351260e21beaa8f4b1","file_id":"4704","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","intvolume":" 24","month":"03","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Watermarking techniques for vector graphics dislocate vertices in order to embed imperceptible, yet detectable, statistical features into the input data. The embedding process may result in a change of the topology of the input data, e.g., by introducing self-intersections, which is undesirable or even disastrous for many applications. In this paper we present a watermarking framework for two-dimensional vector graphics that employs conventional watermarking techniques but still provides the guarantee that the topology of the input data is preserved. The geometric part of this framework computes so-called maximum perturbation regions (MPR) of vertices. We propose two efficient algorithms to compute MPRs based on Voronoi diagrams and constrained triangulations. Furthermore, we present two algorithms to conditionally correct the watermarked data in order to increase the watermark embedding capacity and still guarantee topological correctness. While we focus on the watermarking of input formed by straight-line segments, one of our approaches can also be extended to circular arcs. We conclude the paper by demonstrating and analyzing the applicability of our framework in conjunction with two well-known watermarking techniques."}],"title":"Topology-preserving watermarking of vector graphics","publist_id":"5290","author":[{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Huber","orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan"},{"first_name":"Martin","last_name":"Held","full_name":"Held, Martin"},{"first_name":"Peter","last_name":"Meerwald","full_name":"Meerwald, Peter"},{"last_name":"Kwitt","full_name":"Kwitt, Roland","first_name":"Roland"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"S. Huber, M. Held, P. Meerwald, and R. Kwitt, “Topology-preserving watermarking of vector graphics,” International Journal of Computational Geometry and Applications, vol. 24, no. 1. World Scientific Publishing, pp. 61–86, 2014.","short":"S. Huber, M. Held, P. Meerwald, R. Kwitt, International Journal of Computational Geometry and Applications 24 (2014) 61–86.","apa":"Huber, S., Held, M., Meerwald, P., & Kwitt, R. (2014). Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195914500034","ama":"Huber S, Held M, Meerwald P, Kwitt R. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 2014;24(1):61-86. doi:10.1142/S0218195914500034","mla":"Huber, Stefan, et al. “Topology-Preserving Watermarking of Vector Graphics.” International Journal of Computational Geometry and Applications, vol. 24, no. 1, World Scientific Publishing, 2014, pp. 61–86, doi:10.1142/S0218195914500034.","ista":"Huber S, Held M, Meerwald P, Kwitt R. 2014. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 24(1), 61–86.","chicago":"Huber, Stefan, Martin Held, Peter Meerwald, and Roland Kwitt. “Topology-Preserving Watermarking of Vector Graphics.” International Journal of Computational Geometry and Applications. World Scientific Publishing, 2014. https://doi.org/10.1142/S0218195914500034."},"date_created":"2018-12-11T11:54:10Z","date_published":"2014-03-16T00:00:00Z","doi":"10.1142/S0218195914500034","page":"61 - 86","publication":"International Journal of Computational Geometry and Applications","day":"16","year":"2014","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"World Scientific Publishing","acknowledgement":"Work by Martin Held and Stefan Huber was supported by Austrian Science Fund (FWF): L367-N15 and P25816-N15."},{"scopus_import":1,"month":"06","intvolume":" 55","abstract":[{"text":"We review recent progress towards a rigorous understanding of the Bogoliubov approximation for bosonic quantum many-body systems. We focus, in particular, on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A list of open problems will be discussed at the end.","lang":"eng"}],"oa_version":"Submitted Version","issue":"7","volume":55,"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"ed0efc93c10f1341155f0316af617b82","file_id":"5172","creator":"system","file_size":269171,"date_updated":"2020-07-14T12:45:17Z","file_name":"IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf","date_created":"2018-12-12T10:15:49Z"}],"language":[{"iso":"eng"}],"type":"journal_article","status":"public","pubrep_id":"532","_id":"1821","file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T06:53:25Z","ddc":["510","530"],"quality_controlled":"1","publisher":"American Institute of Physics","oa":1,"doi":"10.1063/1.4881536","date_published":"2014-06-26T00:00:00Z","date_created":"2018-12-11T11:54:11Z","has_accepted_license":"1","year":"2014","day":"26","publication":"Journal of Mathematical Physics","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"article_number":"1.4881536","author":[{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5285","title":"Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation","citation":{"mla":"Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics, vol. 55, no. 7, 1.4881536, American Institute of Physics, 2014, doi:10.1063/1.4881536.","ieee":"R. Seiringer, “Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation,” Journal of Mathematical Physics, vol. 55, no. 7. American Institute of Physics, 2014.","short":"R. Seiringer, Journal of Mathematical Physics 55 (2014).","ama":"Seiringer R. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4881536","apa":"Seiringer, R. (2014). Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4881536","chicago":"Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4881536.","ista":"Seiringer R. 2014. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 55(7), 1.4881536."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"author":[{"last_name":"Jakšić","full_name":"Jakšić, Vojkan","first_name":"Vojkan"},{"full_name":"Pillet, Claude","last_name":"Pillet","first_name":"Claude"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"publist_id":"5284","department":[{"_id":"RoSe"}],"title":"Introduction","citation":{"mla":"Jakšić, Vojkan, et al. “Introduction.” Journal of Mathematical Physics, vol. 55, no. 7, 075101, American Institute of Physics, 2014, doi:10.1063/1.4884877.","ieee":"V. Jakšić, C. Pillet, and R. Seiringer, “Introduction,” Journal of Mathematical Physics, vol. 55, no. 7. American Institute of Physics, 2014.","short":"V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014).","ama":"Jakšić V, Pillet C, Seiringer R. Introduction. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4884877","apa":"Jakšić, V., Pillet, C., & Seiringer, R. (2014). Introduction. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4884877","chicago":"Jakšić, Vojkan, Claude Pillet, and Robert Seiringer. “Introduction.” Journal of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4884877.","ista":"Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical Physics. 55(7), 075101."},"date_updated":"2021-01-12T06:53:25Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1822","article_number":"075101","issue":"7","volume":55,"date_published":"2014-07-01T00:00:00Z","doi":"10.1063/1.4884877","date_created":"2018-12-11T11:54:12Z","publication_status":"published","year":"2014","day":"01","language":[{"iso":"eng"}],"publication":"Journal of Mathematical Physics","publisher":"American Institute of Physics","scopus_import":1,"quality_controlled":"1","month":"07","intvolume":" 55","oa_version":"None"},{"publist_id":"5274","author":[{"first_name":"Katharina","full_name":"Muelling, Katharina","last_name":"Muelling"},{"first_name":"Oliver","last_name":"Kroemer","full_name":"Kroemer, Oliver"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"}],"title":"Movement templates for learning of hitting and batting","department":[{"_id":"ChLa"}],"editor":[{"full_name":"Kober, Jens","last_name":"Kober","first_name":"Jens"},{"first_name":"Jan","last_name":"Peters","full_name":"Peters, Jan"}],"date_updated":"2021-01-12T06:53:28Z","citation":{"ama":"Muelling K, Kroemer O, Lampert C, Schölkopf B. Movement templates for learning of hitting and batting. In: Kober J, Peters J, eds. Learning Motor Skills. Vol 97. From Algorithms to Robot Experiments. Springer; 2014:69-82. doi:10.1007/978-3-319-03194-1_3","apa":"Muelling, K., Kroemer, O., Lampert, C., & Schölkopf, B. (2014). Movement templates for learning of hitting and batting. In J. Kober & J. Peters (Eds.), Learning Motor Skills (Vol. 97, pp. 69–82). Springer. https://doi.org/10.1007/978-3-319-03194-1_3","ieee":"K. Muelling, O. Kroemer, C. Lampert, and B. Schölkopf, “Movement templates for learning of hitting and batting,” in Learning Motor Skills, vol. 97, J. Kober and J. Peters, Eds. Springer, 2014, pp. 69–82.","short":"K. Muelling, O. Kroemer, C. Lampert, B. Schölkopf, in:, J. Kober, J. Peters (Eds.), Learning Motor Skills, Springer, 2014, pp. 69–82.","mla":"Muelling, Katharina, et al. “Movement Templates for Learning of Hitting and Batting.” Learning Motor Skills, edited by Jens Kober and Jan Peters, vol. 97, Springer, 2014, pp. 69–82, doi:10.1007/978-3-319-03194-1_3.","ista":"Muelling K, Kroemer O, Lampert C, Schölkopf B. 2014.Movement templates for learning of hitting and batting. In: Learning Motor Skills. Springer Tracts in Advanced Robotics, vol. 97, 69–82.","chicago":"Muelling, Katharina, Oliver Kroemer, Christoph Lampert, and Bernhard Schölkopf. “Movement Templates for Learning of Hitting and Batting.” In Learning Motor Skills, edited by Jens Kober and Jan Peters, 97:69–82. From Algorithms to Robot Experiments. Springer, 2014. https://doi.org/10.1007/978-3-319-03194-1_3."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","status":"public","_id":"1829","series_title":"From Algorithms to Robot Experiments","page":"69 - 82","date_created":"2018-12-11T11:54:14Z","date_published":"2014-01-01T00:00:00Z","doi":"10.1007/978-3-319-03194-1_3","volume":97,"year":"2014","publication_status":"published","publication":"Learning Motor Skills","language":[{"iso":"eng"}],"day":"01","alternative_title":["Springer Tracts in Advanced Robotics"],"quality_controlled":"1","publisher":"Springer","scopus_import":1,"intvolume":" 97","month":"01","abstract":[{"text":"Hitting and batting tasks, such as tennis forehands, ping-pong strokes, or baseball batting, depend on predictions where the ball can be intercepted and how it can properly be returned to the opponent. These predictions get more accurate over time, hence the behaviors need to be continuously modified. As a result, movement templates with a learned global shape need to be adapted during the execution so that the racket reaches a target position and velocity that will return the ball over to the other side of the net or court. It requires altering learned movements to hit a varying target with the necessary velocity at a specific instant in time. Such a task cannot be incorporated straightforwardly in most movement representations suitable for learning. For example, the standard formulation of the dynamical system based motor primitives (introduced by Ijspeert et al (2002b)) does not satisfy this property despite their flexibility which has allowed learning tasks ranging from locomotion to kendama. In order to fulfill this requirement, we reformulate the Ijspeert framework to incorporate the possibility of specifying a desired hitting point and a desired hitting velocity while maintaining all advantages of the original formulation.We show that the proposed movement template formulation works well in two scenarios, i.e., for hitting a ball on a string with a table tennis racket at a specified velocity and for returning balls launched by a ball gun successfully over the net using forehand movements.","lang":"eng"}],"oa_version":"None"},{"title":"Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history","publist_id":"5257","author":[{"last_name":"Risso","full_name":"Risso, Valeria","first_name":"Valeria"},{"first_name":"Fadia","full_name":"Manssour Triedo, Fadia","last_name":"Manssour Triedo"},{"full_name":"Delgado Delgado, Asuncion","last_name":"Delgado Delgado","first_name":"Asuncion"},{"last_name":"Arco","full_name":"Arco, Rocio","first_name":"Rocio"},{"first_name":"Alicia","last_name":"Barroso Deljesús","full_name":"Barroso Deljesús, Alicia"},{"last_name":"Inglés Prieto","full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571","first_name":"Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Raquel","last_name":"Godoy Ruiz","full_name":"Godoy Ruiz, Raquel"},{"first_name":"Josè","full_name":"Gavira, Josè","last_name":"Gavira"},{"first_name":"Eric","full_name":"Gaucher, Eric","last_name":"Gaucher"},{"last_name":"Ibarra Molero","full_name":"Ibarra Molero, Beatriz","first_name":"Beatriz"},{"first_name":"Jose","last_name":"Sánchez Ruiz","full_name":"Sánchez Ruiz, Jose"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"V. Risso et al., “Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 440–455, 2014.","short":"V. Risso, F. Manssour Triedo, A. Delgado Delgado, R. Arco, A. Barroso Deljesús, Á. Inglés Prieto, R. Godoy Ruiz, J. Gavira, E. Gaucher, B. Ibarra Molero, J. Sánchez Ruiz, Molecular Biology and Evolution 32 (2014) 440–455.","ama":"Risso V, Manssour Triedo F, Delgado Delgado A, et al. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 2014;32(2):440-455. doi:10.1093/molbev/msu312","apa":"Risso, V., Manssour Triedo, F., Delgado Delgado, A., Arco, R., Barroso Deljesús, A., Inglés Prieto, Á., … Sánchez Ruiz, J. (2014). Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu312","mla":"Risso, Valeria, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2014, pp. 440–55, doi:10.1093/molbev/msu312.","ista":"Risso V, Manssour Triedo F, Delgado Delgado A, Arco R, Barroso Deljesús A, Inglés Prieto Á, Godoy Ruiz R, Gavira J, Gaucher E, Ibarra Molero B, Sánchez Ruiz J. 2014. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 32(2), 440–455.","chicago":"Risso, Valeria, Fadia Manssour Triedo, Asuncion Delgado Delgado, Rocio Arco, Alicia Barroso Deljesús, Álvaro Inglés Prieto, Raquel Godoy Ruiz, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu312."},"quality_controlled":"1","publisher":"Oxford University Press","oa":1,"doi":"10.1093/molbev/msu312","date_published":"2014-11-12T00:00:00Z","date_created":"2018-12-11T11:54:19Z","page":"440 - 455","day":"12","publication":"Molecular Biology and Evolution","has_accepted_license":"1","year":"2014","status":"public","pubrep_id":"430","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"_id":"1844","department":[{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:45:19Z","ddc":["571"],"date_updated":"2021-01-12T06:53:34Z","month":"11","intvolume":" 32","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations.","lang":"eng"}],"issue":"2","volume":32,"license":"https://creativecommons.org/licenses/by-nc/4.0/","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5247","checksum":"06215318e66be8f3e0c33abb07e9d3da","creator":"system","file_size":1545246,"date_updated":"2020-07-14T12:45:19Z","file_name":"IST-2016-430-v1+1_Mol_Biol_Evol-2015-Risso-440-55.pdf","date_created":"2018-12-12T10:16:56Z"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"status":"public","type":"journal_article","_id":"1842","title":"On the geometric ramsey number of outerplanar graphs","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publist_id":"5260","author":[{"last_name":"Cibulka","full_name":"Cibulka, Josef","first_name":"Josef"},{"full_name":"Gao, Pu","last_name":"Gao","first_name":"Pu"},{"first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","last_name":"Krcál","full_name":"Krcál, Marek"},{"first_name":"Tomáš","full_name":"Valla, Tomáš","last_name":"Valla"},{"last_name":"Valtr","full_name":"Valtr, Pavel","first_name":"Pavel"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Cibulka, Josef, Pu Gao, Marek Krcál, Tomáš Valla, and Pavel Valtr. “On the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-014-9646-x.","ista":"Cibulka J, Gao P, Krcál M, Valla T, Valtr P. 2014. On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. 53(1), 64–79.","mla":"Cibulka, Josef, et al. “On the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational Geometry, vol. 53, no. 1, Springer, 2014, pp. 64–79, doi:10.1007/s00454-014-9646-x.","short":"J. Cibulka, P. Gao, M. Krcál, T. Valla, P. Valtr, Discrete & Computational Geometry 53 (2014) 64–79.","ieee":"J. Cibulka, P. Gao, M. Krcál, T. Valla, and P. Valtr, “On the geometric ramsey number of outerplanar graphs,” Discrete & Computational Geometry, vol. 53, no. 1. Springer, pp. 64–79, 2014.","apa":"Cibulka, J., Gao, P., Krcál, M., Valla, T., & Valtr, P. (2014). On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-014-9646-x","ama":"Cibulka J, Gao P, Krcál M, Valla T, Valtr P. On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. 2014;53(1):64-79. doi:10.1007/s00454-014-9646-x"},"date_updated":"2021-01-12T06:53:33Z","intvolume":" 53","month":"11","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1310.7004"}],"publisher":"Springer","scopus_import":1,"acknowledgement":"Marek Krčál was supported by the ERC Advanced Grant No. 267165.","oa_version":"Submitted Version","abstract":[{"text":"We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2 outerplanar triangulations in both convex and general cases. We also prove that the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by O(n3) and O(n10), in the convex and general case, respectively. We then apply similar methods to prove an (Formula presented.) upper bound on the Ramsey number of a path with n ordered vertices.","lang":"eng"}],"date_created":"2018-12-11T11:54:18Z","volume":53,"date_published":"2014-11-14T00:00:00Z","issue":"1","doi":"10.1007/s00454-014-9646-x","page":"64 - 79","language":[{"iso":"eng"}],"publication":"Discrete & Computational Geometry","day":"14","year":"2014","publication_status":"published"},{"oa":1,"publisher":"Wiley","quality_controlled":"1","date_created":"2018-12-11T11:54:22Z","doi":"10.1111/cgf.12509","date_published":"2014-11-05T00:00:00Z","page":"239 - 252","publication":"Computer Graphics Forum","day":"05","year":"2014","has_accepted_license":"1","title":"Partial shape matching using transformation parameter similarity","publist_id":"5246","author":[{"last_name":"Guerrero","full_name":"Guerrero, Paul","first_name":"Paul"},{"last_name":"Auzinger","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","full_name":"Wimmer, Michael","last_name":"Wimmer"},{"last_name":"Jeschke","full_name":"Jeschke, Stefan","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. 2014. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 34(1), 239–252.","chicago":"Guerrero, Paul, Thomas Auzinger, Michael Wimmer, and Stefan Jeschke. “Partial Shape Matching Using Transformation Parameter Similarity.” Computer Graphics Forum. Wiley, 2014. https://doi.org/10.1111/cgf.12509.","short":"P. Guerrero, T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum 34 (2014) 239–252.","ieee":"P. Guerrero, T. Auzinger, M. Wimmer, and S. Jeschke, “Partial shape matching using transformation parameter similarity,” Computer Graphics Forum, vol. 34, no. 1. Wiley, pp. 239–252, 2014.","ama":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 2014;34(1):239-252. doi:10.1111/cgf.12509","apa":"Guerrero, P., Auzinger, T., Wimmer, M., & Jeschke, S. (2014). Partial shape matching using transformation parameter similarity. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.12509","mla":"Guerrero, Paul, et al. “Partial Shape Matching Using Transformation Parameter Similarity.” Computer Graphics Forum, vol. 34, no. 1, Wiley, 2014, pp. 239–52, doi:10.1111/cgf.12509."},"intvolume":" 34","month":"11","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching. In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching.","lang":"eng"}],"volume":34,"issue":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5182","checksum":"91946bfc509c77f5fd3151a3ff2b2c8f","creator":"system","date_updated":"2020-07-14T12:45:19Z","file_size":24817484,"date_created":"2018-12-12T10:15:58Z","file_name":"IST-2016-574-v1+1_Guerrero-2014-TPS-paper.pdf"}],"publication_status":"published","pubrep_id":"574","status":"public","type":"journal_article","_id":"1854","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"ChWo"}],"ddc":["000"],"date_updated":"2021-01-12T06:53:38Z"},{"_id":"1852","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:37Z","department":[{"_id":"JiFr"}],"abstract":[{"lang":"eng","text":"To control morphogenesis, molecular regulatory networks have to interfere with the mechanical properties of the individual cells of developing organs and tissues, but how this is achieved is not well known. We study this issue here in the shoot meristem of higher plants, a group of undifferentiated cells where complex changes in growth rates and directions lead to the continuous formation of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important role in this process via a dual, local effect on the extracellular matrix, the cell wall, which determines cell shape. Our study reveals that auxin not only causes a limited reduction in wall stiffness but also directly interferes with wall anisotropy via the regulation of cortical microtubule dynamics. We further show that to induce growth isotropy and organ outgrowth, auxin somehow interferes with the cortical microtubule-ordering activity of a network of proteins, including AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate that the induced isotropy is sufficient to amplify the effects of the relatively minor changes in wall stiffness to promote organogenesis and the establishment of new growth axes in a robust manner."}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01074821","open_access":"1"}],"month":"10","intvolume":" 24","publication_status":"published","language":[{"iso":"eng"}],"volume":24,"issue":"19","citation":{"ista":"Sassi M, Ali O, Boudon F, Cloarec G, Abad U, Cellier C, Chen X, Gilles B, Milani P, Friml J, Vernoux T, Godin C, Hamant O, Traas J. 2014. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 24(19), 2335–2342.","chicago":"Sassi, Massimiliano, Olivier Ali, Frédéric Boudon, Gladys Cloarec, Ursula Abad, Coralie Cellier, Xu Chen, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.08.036.","short":"M. Sassi, O. Ali, F. Boudon, G. Cloarec, U. Abad, C. Cellier, X. Chen, B. Gilles, P. Milani, J. Friml, T. Vernoux, C. Godin, O. Hamant, J. Traas, Current Biology 24 (2014) 2335–2342.","ieee":"M. Sassi et al., “An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis,” Current Biology, vol. 24, no. 19. Cell Press, pp. 2335–2342, 2014.","ama":"Sassi M, Ali O, Boudon F, et al. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 2014;24(19):2335-2342. doi:10.1016/j.cub.2014.08.036","apa":"Sassi, M., Ali, O., Boudon, F., Cloarec, G., Abad, U., Cellier, C., … Traas, J. (2014). An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.08.036","mla":"Sassi, Massimiliano, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology, vol. 24, no. 19, Cell Press, 2014, pp. 2335–42, doi:10.1016/j.cub.2014.08.036."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Massimiliano","full_name":"Sassi, Massimiliano","last_name":"Sassi"},{"full_name":"Ali, Olivier","last_name":"Ali","first_name":"Olivier"},{"full_name":"Boudon, Frédéric","last_name":"Boudon","first_name":"Frédéric"},{"full_name":"Cloarec, Gladys","last_name":"Cloarec","first_name":"Gladys"},{"first_name":"Ursula","last_name":"Abad","full_name":"Abad, Ursula"},{"full_name":"Cellier, Coralie","last_name":"Cellier","first_name":"Coralie"},{"full_name":"Chen, Xu","last_name":"Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu"},{"full_name":"Gilles, Benjamin","last_name":"Gilles","first_name":"Benjamin"},{"full_name":"Milani, Pascale","last_name":"Milani","first_name":"Pascale"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Teva","last_name":"Vernoux","full_name":"Vernoux, Teva"},{"first_name":"Christophe","full_name":"Godin, Christophe","last_name":"Godin"},{"last_name":"Hamant","full_name":"Hamant, Olivier","first_name":"Olivier"},{"first_name":"Jan","last_name":"Traas","full_name":"Traas, Jan"}],"publist_id":"5248","title":"An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis","acknowledgement":"This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). ","publisher":"Cell Press","quality_controlled":"1","oa":1,"year":"2014","day":"06","publication":"Current Biology","page":"2335 - 2342","date_published":"2014-10-06T00:00:00Z","doi":"10.1016/j.cub.2014.08.036","date_created":"2018-12-11T11:54:22Z"},{"date_created":"2018-12-11T11:54:22Z","doi":"10.1109/IOT.2014.7030120","date_published":"2014-02-03T00:00:00Z","page":"85 - 90","language":[{"iso":"eng"}],"day":"03","year":"2014","publication_status":"published","month":"02","quality_controlled":"1","publisher":"IEEE","oa_version":"None","abstract":[{"text":"Wireless sensor networks (WSNs) composed of low-power, low-cost sensor nodes are expected to form the backbone of future intelligent networks for a broad range of civil, industrial and military applications. These sensor nodes are often deployed through random spreading, and function in dynamic environments. Many applications of WSNs such as pollution tracking, forest fire detection, and military surveillance require knowledge of the location of constituent nodes. But the use of technologies such as GPS on all nodes is prohibitive due to power and cost constraints. So, the sensor nodes need to autonomously determine their locations. Most localization techniques use anchor nodes with known locations to determine the position of remaining nodes. Localization techniques have two conflicting requirements. On one hand, an ideal localization technique should be computationally simple and on the other hand, it must be resistant to attacks that compromise anchor nodes. In this paper, we propose a computationally light-weight game theoretic secure localization technique and demonstrate its effectiveness in comparison to existing techniques.","lang":"eng"}],"title":"Game theoretic secure localization in wireless sensor networks","department":[{"_id":"KrCh"}],"author":[{"full_name":"Jha, Susmit","last_name":"Jha","first_name":"Susmit"},{"last_name":"Tripakis","full_name":"Tripakis, Stavros","first_name":"Stavros"},{"full_name":"Seshia, Sanjit","last_name":"Seshia","first_name":"Sanjit"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}],"publist_id":"5247","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Jha S, Tripakis S, Seshia S, Chatterjee K. Game theoretic secure localization in wireless sensor networks. In: IEEE; 2014:85-90. doi:10.1109/IOT.2014.7030120","apa":"Jha, S., Tripakis, S., Seshia, S., & Chatterjee, K. (2014). Game theoretic secure localization in wireless sensor networks (pp. 85–90). Presented at the IOT: Internet of Things, Cambridge, USA: IEEE. https://doi.org/10.1109/IOT.2014.7030120","short":"S. Jha, S. Tripakis, S. Seshia, K. Chatterjee, in:, IEEE, 2014, pp. 85–90.","ieee":"S. Jha, S. Tripakis, S. Seshia, and K. Chatterjee, “Game theoretic secure localization in wireless sensor networks,” presented at the IOT: Internet of Things, Cambridge, USA, 2014, pp. 85–90.","mla":"Jha, Susmit, et al. Game Theoretic Secure Localization in Wireless Sensor Networks. IEEE, 2014, pp. 85–90, doi:10.1109/IOT.2014.7030120.","ista":"Jha S, Tripakis S, Seshia S, Chatterjee K. 2014. Game theoretic secure localization in wireless sensor networks. IOT: Internet of Things, 85–90.","chicago":"Jha, Susmit, Stavros Tripakis, Sanjit Seshia, and Krishnendu Chatterjee. “Game Theoretic Secure Localization in Wireless Sensor Networks,” 85–90. IEEE, 2014. https://doi.org/10.1109/IOT.2014.7030120."},"date_updated":"2021-01-12T06:53:38Z","status":"public","conference":{"name":"IOT: Internet of Things","start_date":"2014-10-06","end_date":"2014-10-08","location":"Cambridge, USA"},"type":"conference","_id":"1853"},{"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"729","volume":516,"ec_funded":1,"abstract":[{"lang":"eng","text":"The prominent and evolutionarily ancient role of the plant hormone auxin is the regulation of cell expansion. Cell expansion requires ordered arrangement of the cytoskeleton but molecular mechanisms underlying its regulation by signalling molecules including auxin are unknown. Here we show in the model plant Arabidopsis thaliana that in elongating cells exogenous application of auxin or redistribution of endogenous auxin induces very rapid microtubule re-orientation from transverse to longitudinal, coherent with the inhibition of cell expansion. This fast auxin effect requires auxin binding protein 1 (ABP1) and involves a contribution of downstream signalling components such as ROP6 GTPase, ROP-interactive protein RIC1 and the microtubule-severing protein katanin. These components are required for rapid auxin-and ABP1-mediated re-orientation of microtubules to regulate cell elongation in roots and dark-grown hypocotyls as well as asymmetric growth during gravitropic responses."}],"pmid":1,"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257754/"}],"month":"12","intvolume":" 516","date_updated":"2022-05-23T08:26:44Z","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"EvBe"}],"_id":"1862","article_type":"original","type":"journal_article","status":"public","year":"2014","day":"04","publication":"Nature","page":"90 - 93","date_published":"2014-12-04T00:00:00Z","doi":"10.1038/nature13889","date_created":"2018-12-11T11:54:25Z","acknowledgement":"We thank R. Dixit for performing complementary experiments, D. W. Ehrhardt and T. Hashimoto for providing the seeds of TUB6–RFP and EB1b–GFP respectively, E. Zazimalova, J. Petrasek and M. Fendrych for discussing the manuscript and J. Leung for text optimization. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), ANR blanc AuxiWall project (ANR-11-BSV5-0007, to C.P.-R. and L.G.) and the Agency for Innovation by Science and Technology (IWT) (to H.R.). This work benefited from the facilities and expertise of the Imagif Cell Biology platform (http://www.imagif.cnrs.fr), which is supported by the Conseil Général de l’Essonne.","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"citation":{"mla":"Chen, Xu, et al. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” Nature, vol. 516, no. 729, Nature Publishing Group, 2014, pp. 90–93, doi:10.1038/nature13889.","short":"X. Chen, L. Grandont, H. Li, R. Hauschild, S. Paque, A. Abuzeineh, H. Rakusova, E. Benková, C. Perrot Rechenmann, J. Friml, Nature 516 (2014) 90–93.","ieee":"X. Chen et al., “Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules,” Nature, vol. 516, no. 729. Nature Publishing Group, pp. 90–93, 2014.","ama":"Chen X, Grandont L, Li H, et al. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. 2014;516(729):90-93. doi:10.1038/nature13889","apa":"Chen, X., Grandont, L., Li, H., Hauschild, R., Paque, S., Abuzeineh, A., … Friml, J. (2014). Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13889","chicago":"Chen, Xu, Laurie Grandont, Hongjiang Li, Robert Hauschild, Sébastien Paque, Anas Abuzeineh, Hana Rakusova, Eva Benková, Catherine Perrot Rechenmann, and Jiří Friml. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature13889.","ista":"Chen X, Grandont L, Li H, Hauschild R, Paque S, Abuzeineh A, Rakusova H, Benková E, Perrot Rechenmann C, Friml J. 2014. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. 516(729), 90–93."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu","last_name":"Chen","full_name":"Chen, Xu"},{"full_name":"Grandont, Laurie","last_name":"Grandont","first_name":"Laurie"},{"last_name":"Li","full_name":"Li, Hongjiang","orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Paque, Sébastien","last_name":"Paque","first_name":"Sébastien"},{"first_name":"Anas","full_name":"Abuzeineh, Anas","last_name":"Abuzeineh"},{"full_name":"Rakusova, Hana","last_name":"Rakusova","first_name":"Hana","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"full_name":"Perrot Rechenmann, Catherine","last_name":"Perrot Rechenmann","first_name":"Catherine"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"publist_id":"5237","article_processing_charge":"No","external_id":{"pmid":["25409144"]},"title":"Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}]},{"year":"2014","publication":"HVC 2014","day":"01","page":"68 - 74","date_created":"2018-12-11T11:54:27Z","doi":"10.1007/978-3-319-13338-6_6","date_published":"2014-01-01T00:00:00Z","acknowledgement":"The work presented in this paper was supported in part by the European Research Council (ERC) under grant agreement QUAINT (I774-N23)","publisher":"Springer","quality_controlled":"1","citation":{"chicago":"Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using Uninterpreted Functions.” In HVC 2014, edited by Eran Yahav, 8855:68–74. Springer, 2014. https://doi.org/10.1007/978-3-319-13338-6_6.","ista":"Hofferek G, Gupta A. 2014. Suraq - a controller synthesis tool using uninterpreted functions. HVC 2014. HVC: Haifa Verification Conference, LNCS, vol. 8855, 68–74.","mla":"Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using Uninterpreted Functions.” HVC 2014, edited by Eran Yahav, vol. 8855, Springer, 2014, pp. 68–74, doi:10.1007/978-3-319-13338-6_6.","short":"G. Hofferek, A. Gupta, in:, E. Yahav (Ed.), HVC 2014, Springer, 2014, pp. 68–74.","ieee":"G. Hofferek and A. Gupta, “Suraq - a controller synthesis tool using uninterpreted functions,” in HVC 2014, Haifa, Israel, 2014, vol. 8855, pp. 68–74.","apa":"Hofferek, G., & Gupta, A. (2014). Suraq - a controller synthesis tool using uninterpreted functions. In E. Yahav (Ed.), HVC 2014 (Vol. 8855, pp. 68–74). Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-13338-6_6","ama":"Hofferek G, Gupta A. Suraq - a controller synthesis tool using uninterpreted functions. In: Yahav E, ed. HVC 2014. Vol 8855. Springer; 2014:68-74. doi:10.1007/978-3-319-13338-6_6"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5228","author":[{"last_name":"Hofferek","full_name":"Hofferek, Georg","first_name":"Georg"},{"last_name":"Gupta","full_name":"Gupta, Ashutosh","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"}],"title":"Suraq - a controller synthesis tool using uninterpreted functions","editor":[{"first_name":"Eran","last_name":"Yahav","full_name":"Yahav, Eran"}],"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"S11407","name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":8855,"abstract":[{"lang":"eng","text":"Boolean controllers for systems with complex datapaths are often very difficult to implement correctly, in particular when concurrency is involved. Yet, in many instances it is easy to formally specify correctness. For example, the specification for the controller of a pipelined processor only has to state that the pipelined processor gives the same results as a non-pipelined reference design. This makes such controllers a good target for automated synthesis. However, an efficient abstraction for the complex datapath elements is needed, as a bit-precise description is often infeasible. We present Suraq, the first controller synthesis tool which uses uninterpreted functions for the abstraction. Quantified firstorder formulas (with specific quantifier structure) serve as the specification language from which Suraq synthesizes Boolean controllers. Suraq transforms the specification into an unsatisfiable SMT formula, and uses Craig interpolation to compute its results. Using Suraq, we were able to synthesize a controller (consisting of two Boolean signals) for a five-stage pipelined DLX processor in roughly one hour and 15 minutes."}],"oa_version":"None","alternative_title":["LNCS"],"intvolume":" 8855","month":"01","date_updated":"2021-01-12T06:53:44Z","department":[{"_id":"ToHe"}],"_id":"1869","conference":{"location":"Haifa, Israel","end_date":"2014-11-20","start_date":"2014-11-18","name":"HVC: Haifa Verification Conference"},"type":"conference","status":"public"},{"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"A. Gupta, L. Kovács, B. Kragl, A. Voronkov, in:, F. Cassez, J.-F. Raskin (Eds.), ATVA 2014, Springer, 2014, pp. 185–200.","ieee":"A. Gupta, L. Kovács, B. Kragl, and A. Voronkov, “Extensional crisis and proving identity,” in ATVA 2014, Sydney, Australia, 2014, vol. 8837, pp. 185–200.","apa":"Gupta, A., Kovács, L., Kragl, B., & Voronkov, A. (2014). Extensional crisis and proving identity. In F. Cassez & J.-F. Raskin (Eds.), ATVA 2014 (Vol. 8837, pp. 185–200). Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_14","ama":"Gupta A, Kovács L, Kragl B, Voronkov A. Extensional crisis and proving identity. In: Cassez F, Raskin J-F, eds. ATVA 2014. Vol 8837. Springer; 2014:185-200. doi:10.1007/978-3-319-11936-6_14","mla":"Gupta, Ashutosh, et al. “Extensional Crisis and Proving Identity.” ATVA 2014, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 185–200, doi:10.1007/978-3-319-11936-6_14.","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.","chicago":"Gupta, Ashutosh, Laura Kovács, Bernhard Kragl, and Andrei Voronkov. “Extensional Crisis and Proving Identity.” In ATVA 2014, edited by Franck Cassez and Jean-François Raskin, 8837:185–200. Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_14."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5226","author":[{"last_name":"Gupta","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh"},{"last_name":"Kovács","full_name":"Kovács, Laura","first_name":"Laura"},{"last_name":"Kragl","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard"},{"full_name":"Voronkov, Andrei","last_name":"Voronkov","first_name":"Andrei"}],"editor":[{"first_name":"Franck","last_name":"Cassez","full_name":"Cassez, Franck"},{"first_name":"Jean-François","full_name":"Raskin, Jean-François","last_name":"Raskin"}],"title":"Extensional crisis and proving identity","acknowledgement":"This research was supported in part by the Austrian National Research Network RiSE (S11410-N23).","oa":1,"publisher":"Springer","quality_controlled":"1","year":"2014","has_accepted_license":"1","publication":"ATVA 2014","day":"01","page":"185 - 200","date_created":"2018-12-11T11:54:28Z","doi":"10.1007/978-3-319-11936-6_14","date_published":"2014-01-01T00:00:00Z","_id":"1872","conference":{"start_date":"2014-11-03","location":"Sydney, Australia","end_date":"2014-11-07","name":"ATVA: Automated Technology for Verification and Analysis"},"type":"conference","pubrep_id":"641","status":"public","date_updated":"2021-01-12T06:53:45Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:19Z","abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 8837","month":"01","publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"af4bd3fc1f4c93075e4dc5cbf625fe7b","file_id":"4801","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:10:15Z","file_name":"IST-2016-641-v1+1_atva2014.pdf","creator":"system","date_updated":"2020-07-14T12:45:19Z","file_size":244294}],"ec_funded":1,"volume":8837},{"volume":29,"publication_status":"published","file":[{"checksum":"7b1aff1710a8bffb7080ec07f62d9a17","file_id":"4734","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:09:11Z","file_name":"IST-2017-804-v1+1_37.pdf","date_updated":"2020-07-14T12:45:19Z","file_size":562151,"creator":"system"}],"language":[{"iso":"eng"}],"alternative_title":["LIPIcs"],"month":"12","intvolume":" 29","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T06:53:45Z","ddc":["004"],"type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2014-12-15","location":"Delhi, India","end_date":"2014-12-17","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science"},"status":"public","pubrep_id":"804","_id":"1870","page":"431 - 443","doi":"10.4230/LIPIcs.FSTTCS.2014.431","date_published":"2014-12-01T00:00:00Z","date_created":"2018-12-11T11:54:27Z","has_accepted_license":"1","year":"2014","day":"01","publication":"Leibniz International Proceedings in Informatics, LIPIcs","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"author":[{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Otop, Jan","last_name":"Otop"},{"first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","full_name":"Samanta, Roopsha","last_name":"Samanta"}],"publist_id":"5227","title":"Lipschitz robustness of finite-state transducers","citation":{"chicago":"Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness of Finite-State Transducers.” In Leibniz International Proceedings in Informatics, LIPIcs, 29:431–43. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431.","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.","mla":"Henzinger, Thomas A., et al. “Lipschitz Robustness of Finite-State Transducers.” Leibniz International Proceedings in Informatics, LIPIcs, vol. 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–43, doi:10.4230/LIPIcs.FSTTCS.2014.431.","ama":"Henzinger TA, Otop J, Samanta R. Lipschitz robustness of finite-state transducers. In: Leibniz International Proceedings in Informatics, LIPIcs. Vol 29. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:431-443. doi:10.4230/LIPIcs.FSTTCS.2014.431","apa":"Henzinger, T. A., Otop, J., & Samanta, R. (2014). Lipschitz robustness of finite-state transducers. In Leibniz International Proceedings in Informatics, LIPIcs (Vol. 29, pp. 431–443). Delhi, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431","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 Leibniz International Proceedings in Informatics, LIPIcs, Delhi, India, 2014, vol. 29, pp. 431–443."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"_id":"1875","conference":{"name":"SAS: Static Analysis Symposium","start_date":"2014-09-11","end_date":"2014-09-14","location":"Munich, Germany"},"type":"conference","pubrep_id":"313","status":"public","date_updated":"2021-01-12T06:53:46Z","ddc":["000","005"],"file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"ToHe"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 8723","month":"09","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:19Z","file_size":409485,"creator":"system","date_created":"2018-12-12T10:07:51Z","file_name":"IST-2014-313-v1+1_SOE.SAS14.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4650","checksum":"78ec4ea1bdecc676cd3e8cad35c6182c"}],"volume":8723,"citation":{"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:10.1007/978-3-319-10936-7_17","apa":"Samanta, R., Olivo, O., & Allen, E. (2014). Cost-aware automatic program repair. In M. Müller-Olm & H. Seidl (Eds.) (Vol. 8723, pp. 268–284). Presented at the SAS: Static Analysis Symposium, Munich, Germany: Springer. https://doi.org/10.1007/978-3-319-10936-7_17","short":"R. Samanta, O. Olivo, E. Allen, in:, M. Müller-Olm, H. Seidl (Eds.), Springer, 2014, pp. 268–284.","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.","mla":"Samanta, Roopsha, et al. Cost-Aware Automatic Program Repair. Edited by Markus Müller-Olm and Helmut Seidl, vol. 8723, Springer, 2014, pp. 268–84, doi:10.1007/978-3-319-10936-7_17.","ista":"Samanta R, Olivo O, Allen E. 2014. Cost-aware automatic program repair. SAS: Static Analysis Symposium, LNCS, vol. 8723, 268–284.","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. https://doi.org/10.1007/978-3-319-10936-7_17."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5221","author":[{"last_name":"Samanta","full_name":"Samanta, Roopsha","first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Olivo, Oswaldo","last_name":"Olivo","first_name":"Oswaldo"},{"full_name":"Allen, Emerson","last_name":"Allen","first_name":"Emerson"}],"editor":[{"first_name":"Markus","last_name":"Müller-Olm","full_name":"Müller-Olm, Markus"},{"last_name":"Seidl","full_name":"Seidl, Helmut","first_name":"Helmut"}],"title":"Cost-aware automatic program repair","oa":1,"quality_controlled":"1","publisher":"Springer","year":"2014","has_accepted_license":"1","day":"01","page":"268 - 284","date_created":"2018-12-11T11:54:29Z","doi":"10.1007/978-3-319-10936-7_17","date_published":"2014-09-01T00:00:00Z"},{"title":"Functionals on triangulations of delaunay sets","publist_id":"5220","author":[{"last_name":"Dolbilin","full_name":"Dolbilin, Nikolai","first_name":"Nikolai"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Glazyrin","full_name":"Glazyrin, Alexey","first_name":"Alexey"},{"full_name":"Musin, Oleg","last_name":"Musin","first_name":"Oleg"}],"article_processing_charge":"No","external_id":{"arxiv":["1211.7053"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Dolbilin, Nikolai, Herbert Edelsbrunner, Alexey Glazyrin, and Oleg Musin. “Functionals on Triangulations of Delaunay Sets.” Moscow Mathematical Journal. Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-3-491-504.","ista":"Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. 2014. Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. 14(3), 491–504.","mla":"Dolbilin, Nikolai, et al. “Functionals on Triangulations of Delaunay Sets.” Moscow Mathematical Journal, vol. 14, no. 3, Independent University of Moscow, 2014, pp. 491–504, doi:10.17323/1609-4514-2014-14-3-491-504.","short":"N. Dolbilin, H. Edelsbrunner, A. Glazyrin, O. Musin, Moscow Mathematical Journal 14 (2014) 491–504.","ieee":"N. Dolbilin, H. Edelsbrunner, A. Glazyrin, and O. Musin, “Functionals on triangulations of delaunay sets,” Moscow Mathematical Journal, vol. 14, no. 3. Independent University of Moscow, pp. 491–504, 2014.","apa":"Dolbilin, N., Edelsbrunner, H., Glazyrin, A., & Musin, O. (2014). Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-3-491-504","ama":"Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. 2014;14(3):491-504. doi:10.17323/1609-4514-2014-14-3-491-504"},"date_published":"2014-07-01T00:00:00Z","doi":"10.17323/1609-4514-2014-14-3-491-504","date_created":"2018-12-11T11:54:29Z","page":"491 - 504","day":"01","publication":"Moscow Mathematical Journal","year":"2014","quality_controlled":"1","publisher":"Independent University of Moscow","oa":1,"department":[{"_id":"HeEd"}],"date_updated":"2022-03-03T11:47:09Z","status":"public","article_type":"original","type":"journal_article","_id":"1876","issue":"3","volume":14,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["16093321"]},"publication_status":"published","month":"07","intvolume":" 14","scopus_import":"1","main_file_link":[{"url":"http://arxiv.org/abs/1211.7053","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:47Z","citation":{"ama":"Sixt MK, Vaahtomeri K. Physiology: Relax and come in. Nature. 2014;514(7523):441-442. doi:10.1038/514441a","apa":"Sixt, M. K., & Vaahtomeri, K. (2014). Physiology: Relax and come in. Nature. Springer Nature. https://doi.org/10.1038/514441a","short":"M.K. Sixt, K. Vaahtomeri, Nature 514 (2014) 441–442.","ieee":"M. K. Sixt and K. Vaahtomeri, “Physiology: Relax and come in,” Nature, vol. 514, no. 7523. Springer Nature, pp. 441–442, 2014.","mla":"Sixt, Michael K., and Kari Vaahtomeri. “Physiology: Relax and Come In.” Nature, vol. 514, no. 7523, Springer Nature, 2014, pp. 441–42, doi:10.1038/514441a.","ista":"Sixt MK, Vaahtomeri K. 2014. Physiology: Relax and come in. Nature. 514(7523), 441–442.","chicago":"Sixt, Michael K, and Kari Vaahtomeri. “Physiology: Relax and Come In.” Nature. Springer Nature, 2014. https://doi.org/10.1038/514441a."},"title":"Physiology: Relax and come in","department":[{"_id":"MiSi"}],"publist_id":"5219","author":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"},{"last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari"}],"_id":"1877","status":"public","article_type":"letter_note","type":"journal_article","day":"23","language":[{"iso":"eng"}],"publication":"Nature","publication_status":"published","year":"2014","date_published":"2014-10-23T00:00:00Z","volume":514,"issue":"7523","doi":"10.1038/514441a","date_created":"2018-12-11T11:54:30Z","page":"441 - 442","oa_version":"None","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"}],"month":"10","intvolume":" 514","publisher":"Springer Nature","quality_controlled":"1","scopus_import":1},{"date_created":"2018-12-11T11:54:32Z","doi":"10.7554/eLife.03722","date_published":"2014-11-14T00:00:00Z","year":"2014","has_accepted_license":"1","publication":"eLife","day":"14","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","publist_id":"5209","author":[{"last_name":"Hermundstad","full_name":"Hermundstad, Ann","first_name":"Ann"},{"first_name":"John","last_name":"Briguglio","full_name":"Briguglio, John"},{"first_name":"Mary","last_name":"Conte","full_name":"Conte, Mary"},{"first_name":"Jonathan","last_name":"Victor","full_name":"Victor, 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"}],"title":"Variance predicts salience in central sensory processing","citation":{"chicago":"Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian, and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.” ELife. eLife Sciences Publications, 2014. https://doi.org/10.7554/eLife.03722.","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.” ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722.","short":"A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkačik, ELife (2014).","ieee":"A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkačik, “Variance predicts salience in central sensory processing,” eLife, 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. eLife. 2014;(November). doi:10.7554/eLife.03722","apa":"Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V., & Tkačik, G. (2014). Variance predicts salience in central sensory processing. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.03722"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"article_number":"e03722","issue":"November","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:12:04Z","file_name":"IST-2016-420-v1+1_e03722.full.pdf","creator":"system","date_updated":"2020-07-14T12:45:20Z","file_size":5117086,"file_id":"4922","checksum":"766ac8999ac6e3364f10065a06024b8f","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"scopus_import":1,"month":"11","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:20Z","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:53:50Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"420","status":"public","_id":"1886"},{"_id":"1890","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"442","date_updated":"2021-01-12T06:53:52Z","ddc":["000"],"department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:20Z","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."}],"oa_version":"Published Version","scopus_import":1,"month":"02","intvolume":" 51","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"4255b6185e774acce1d99f8e195c564d","file_id":"5233","creator":"system","file_size":543243,"date_updated":"2020-07-14T12:45:20Z","file_name":"IST-2016-442-v1+1_K-rner_et_al-2014-Psychophysiology.pdf","date_created":"2018-12-12T10:16:44Z"}],"language":[{"iso":"eng"}],"issue":"4","volume":51,"citation":{"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.","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.” Psychophysiology. Wiley-Blackwell, 2014. https://doi.org/10.1111/psyp.12062.","apa":"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. Wiley-Blackwell. https://doi.org/10.1111/psyp.12062","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. Psychophysiology. 2014;51(4):385-395. doi:10.1111/psyp.12062","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,” Psychophysiology, 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.","mla":"Körner, Christof, et al. “Sequential Effects in Continued Visual Search: Using Fixation-Related Potentials to Compare Distractor Processing before and after Target Detection.” Psychophysiology, vol. 51, no. 4, Wiley-Blackwell, 2014, pp. 385–95, doi:10.1111/psyp.12062."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Christof","full_name":"Körner, Christof","last_name":"Körner"},{"first_name":"Verena","full_name":"Braunstein, Verena","last_name":"Braunstein"},{"last_name":"Stangl","full_name":"Stangl, Matthias","first_name":"Matthias"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"full_name":"Neuper, Christa","last_name":"Neuper","first_name":"Christa"},{"first_name":"Anja","last_name":"Ischebeck","full_name":"Ischebeck, Anja"}],"publist_id":"5205","title":"Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection","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","publisher":"Wiley-Blackwell","oa":1,"has_accepted_license":"1","year":"2014","day":"11","publication":"Psychophysiology","page":"385 - 395","doi":"10.1111/psyp.12062","date_published":"2014-02-11T00:00:00Z","date_created":"2018-12-11T11:54:34Z"},{"department":[{"_id":"CampIT"}],"date_updated":"2022-06-07T09:12:32Z","status":"public","type":"journal_article","article_type":"original","_id":"1892","volume":281,"issue":"1794","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 281","month":"11","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211437/","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","pmid":1,"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"}],"title":"Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids","article_processing_charge":"No","external_id":{"pmid":["25232141"]},"publist_id":"5203","author":[{"last_name":"Ocana","full_name":"Ocana, Sabine","first_name":"Sabine"},{"first_name":"Patrick","id":"4709BCE6-F248-11E8-B48F-1D18A9856A87","full_name":"Meidl, Patrick","last_name":"Meidl"},{"first_name":"Danielle","full_name":"Bonfils, Danielle","last_name":"Bonfils"},{"first_name":"Michael","full_name":"Taborsky, Michael","last_name":"Taborsky"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","chicago":"Ocana, Sabine, Patrick Meidl, Danielle Bonfils, and Michael Taborsky. “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. The Royal Society, 2014. https://doi.org/10.1098/rspb.2014.0253.","ama":"Ocana S, Meidl P, Bonfils D, Taborsky M. 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. 2014;281(1794). doi:10.1098/rspb.2014.0253","apa":"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. The Royal Society. https://doi.org/10.1098/rspb.2014.0253","short":"S. Ocana, P. Meidl, D. Bonfils, M. Taborsky, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).","ieee":"S. Ocana, P. Meidl, D. Bonfils, and M. Taborsky, “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, vol. 281, no. 1794. The Royal Society, 2014.","mla":"Ocana, Sabine, et al. “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, vol. 281, no. 1794, 20140253, The Royal Society, 2014, doi:10.1098/rspb.2014.0253."},"article_number":"20140253","date_created":"2018-12-11T11:54:34Z","doi":"10.1098/rspb.2014.0253","date_published":"2014-11-07T00:00:00Z","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","day":"07","year":"2014","oa":1,"quality_controlled":"1","publisher":"The Royal Society","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."},{"_id":"1891","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:52Z","citation":{"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.” Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell, 2014. https://doi.org/10.1002/prot.24436.","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.","mla":"Chwastyk, Mateusz, et al. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics, vol. 82, no. 5, Wiley-Blackwell, 2014, pp. 717–26, doi:10.1002/prot.24436.","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,” Proteins: Structure, Function and Bioinformatics, vol. 82, no. 5. Wiley-Blackwell, pp. 717–726, 2014.","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.","apa":"Chwastyk, M., Galera Prat, A., Sikora, M. K., Gómez Sicilia, À., Carrión Vázquez, M., & Cieplak, M. (2014). Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.24436","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. Proteins: Structure, Function and Bioinformatics. 2014;82(5):717-726. doi:10.1002/prot.24436"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5204","author":[{"last_name":"Chwastyk","full_name":"Chwastyk, Mateusz","first_name":"Mateusz"},{"full_name":"Galera Prat, Albert","last_name":"Galera Prat","first_name":"Albert"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","full_name":"Sikora, Mateusz K","last_name":"Sikora"},{"first_name":"Àngel","full_name":"Gómez Sicilia, Àngel","last_name":"Gómez Sicilia"},{"last_name":"Carrión Vázquez","full_name":"Carrión Vázquez, Mariano","first_name":"Mariano"},{"first_name":"Marek","last_name":"Cieplak","full_name":"Cieplak, Marek"}],"title":"Theoretical tests of the mechanical protection strategy in protein nanomechanics","department":[{"_id":"CaHe"}],"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."}],"oa_version":"None","acknowledgement":"Grant Nr. 2011/01/N/ST3/02475","scopus_import":1,"publisher":"Wiley-Blackwell","month":"05","intvolume":" 82","publication_status":"published","year":"2014","day":"01","publication":"Proteins: Structure, Function and Bioinformatics","language":[{"iso":"eng"}],"page":"717 - 726","issue":"5","volume":82,"doi":"10.1002/prot.24436","date_published":"2014-05-01T00:00:00Z","date_created":"2018-12-11T11:54:34Z"},{"citation":{"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.” Blood. American Society of Hematology, 2014.","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.","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.” Blood, vol. 124, no. 21, American Society of Hematology, 2014, pp. 1952–1952.","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.","ieee":"D. Landau 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,” Blood, vol. 124, no. 21. American Society of Hematology, pp. 1952–1952, 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. Blood. 2014;124(21):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. Blood. American Society of Hematology."},"date_updated":"2021-01-12T06:53:50Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5211","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","last_name":"Reiter","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes"},{"first_name":"Michael","last_name":"Lawrence","full_name":"Lawrence, Michael"},{"first_name":"Carrie","full_name":"Sougnez, Carrie","last_name":"Sougnez"},{"full_name":"Brown, Jennifer","last_name":"Brown","first_name":"Jennifer"},{"full_name":"Lopez Guillermo, Armando","last_name":"Lopez Guillermo","first_name":"Armando"},{"last_name":"Gabriel","full_name":"Gabriel, Stacey","first_name":"Stacey"},{"last_name":"Lander","full_name":"Lander, Eric","first_name":"Eric"},{"full_name":"Neuberg, Donna","last_name":"Neuberg","first_name":"Donna"},{"first_name":"Carlos","full_name":"López Otín, Carlos","last_name":"López Otín"},{"first_name":"Elias","full_name":"Campo, Elias","last_name":"Campo"},{"last_name":"Getz","full_name":"Getz, Gad","first_name":"Gad"},{"first_name":"Catherine","full_name":"Wu, Catherine","last_name":"Wu"}],"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","department":[{"_id":"KrCh"}],"_id":"1884","type":"journal_article","status":"public","publication_status":"published","year":"2014","day":"04","language":[{"iso":"eng"}],"publication":"Blood","page":"1952 - 1952","volume":124,"issue":"21","date_published":"2014-12-04T00:00:00Z","date_created":"2018-12-11T11:54:32Z","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."}],"oa_version":"None","publisher":"American Society of Hematology","main_file_link":[{"url":"http://www.bloodjournal.org/content/124/21/1952?sso-checked=true"}],"month":"12","intvolume":" 124"},{"oa":1,"publisher":"World Scientific Publishing","quality_controlled":"1","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.","date_created":"2018-12-11T11:54:33Z","doi":"10.1142/S0129055X14500123","date_published":"2014-08-01T00:00:00Z","year":"2014","publication":"Reviews in Mathematical Physics","day":"01","article_number":"1450012","article_processing_charge":"No","external_id":{"arxiv":["1305.5135"]},"publist_id":"5206","author":[{"first_name":"Gerhard","last_name":"Bräunlich","full_name":"Bräunlich, Gerhard"},{"last_name":"Hainzl","full_name":"Hainzl, Christian","first_name":"Christian"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"title":"Translation-invariant quasi-free states for fermionic systems and the BCS approximation","citation":{"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,” Reviews in Mathematical Physics, vol. 26, no. 7. World Scientific Publishing, 2014.","apa":"Bräunlich, G., Hainzl, C., & Seiringer, R. (2014). Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X14500123","ama":"Bräunlich G, Hainzl C, Seiringer R. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. 2014;26(7). doi:10.1142/S0129055X14500123","mla":"Bräunlich, Gerhard, et al. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews in Mathematical Physics, vol. 26, no. 7, 1450012, World Scientific Publishing, 2014, doi:10.1142/S0129055X14500123.","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.","chicago":"Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X14500123."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1305.5135"}],"scopus_import":"1","intvolume":" 26","month":"08","abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","volume":26,"issue":"7","publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"1889","department":[{"_id":"RoSe"}],"date_updated":"2022-06-07T09:03:09Z"},{"intvolume":" 9","month":"09","scopus_import":1,"oa_version":"Published Version","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."}],"issue":"9","volume":9,"language":[{"iso":"eng"}],"file":[{"checksum":"7d02c3da7f72b82bb5d7932d80c3251f","file_id":"5205","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:16:19Z","file_name":"IST-2016-438-v1+1_journal.pone.0106247.pdf","creator":"system","date_updated":"2020-07-14T12:45:20Z","file_size":4248801}],"publication_status":"published","pubrep_id":"438","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1894","file_date_updated":"2020-07-14T12:45:20Z","department":[{"_id":"CaGu"}],"ddc":["570"],"date_updated":"2021-01-12T06:53:54Z","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","date_created":"2018-12-11T11:54:35Z","date_published":"2014-09-02T00:00:00Z","doi":"10.1371/journal.pone.0106247","publication":"PLoS One","day":"02","year":"2014","has_accepted_license":"1","article_number":"e106247","title":"Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA","author":[{"last_name":"Grabowska","full_name":"Grabowska, Anna","first_name":"Anna"},{"full_name":"Wywiał, Ewa","last_name":"Wywiał","first_name":"Ewa"},{"first_name":"Stanislaw","full_name":"Dunin Horkawicz, Stanislaw","last_name":"Dunin Horkawicz"},{"first_name":"Anna","last_name":"Łasica","full_name":"Łasica, Anna"},{"first_name":"Marc","last_name":"Wösten","full_name":"Wösten, Marc"},{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","full_name":"Nagy-Staron, Anna A","last_name":"Nagy-Staron"},{"last_name":"Godlewska","full_name":"Godlewska, Renata","first_name":"Renata"},{"first_name":"Katarzyna","last_name":"Bocian Ostrzycka","full_name":"Bocian Ostrzycka, Katarzyna"},{"full_name":"Pieńkowska, Katarzyna","last_name":"Pieńkowska","first_name":"Katarzyna"},{"full_name":"Łaniewski, Paweł","last_name":"Łaniewski","first_name":"Paweł"},{"first_name":"Janusz","full_name":"Bujnicki, Janusz","last_name":"Bujnicki"},{"first_name":"Jos","full_name":"Van Putten, Jos","last_name":"Van Putten"},{"first_name":"Elzbieta","last_name":"Jagusztyn Krynicka","full_name":"Jagusztyn Krynicka, Elzbieta"}],"publist_id":"5201","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Grabowska, Anna, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One, vol. 9, no. 9, e106247, Public Library of Science, 2014, doi:10.1371/journal.pone.0106247.","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. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0106247","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. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0106247","ieee":"A. Grabowska et al., “Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014.","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).","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.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0106247.","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."}},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Edamura, Mitsuhiro, et al. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One, vol. 9, no. 9, e107099, Public Library of Science, 2014, doi:10.1371/journal.pone.0107099.","short":"M. Edamura, G. Murakami, H. Meng, M. Itakura, R. Shigemoto, A. Fukuda, D. Nakahara, PLoS One 9 (2014).","ieee":"M. Edamura et al., “Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014.","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. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0107099","apa":"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. Public Library of Science. https://doi.org/10.1371/journal.pone.0107099","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.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0107099.","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."},"title":"Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice","publist_id":"5200","author":[{"first_name":"Mitsuhiro","last_name":"Edamura","full_name":"Edamura, Mitsuhiro"},{"full_name":"Murakami, Gen","last_name":"Murakami","first_name":"Gen"},{"full_name":"Meng, Hongrui","last_name":"Meng","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"},{"full_name":"Fukuda, Atsuo","last_name":"Fukuda","first_name":"Atsuo"},{"full_name":"Nakahara, Daiichiro","last_name":"Nakahara","first_name":"Daiichiro"}],"article_number":"e107099","publication":"PLoS One","day":"30","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:54:35Z","date_published":"2014-09-30T00:00:00Z","doi":"10.1371/journal.pone.0107099","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,"publisher":"Public Library of Science","ddc":["570"],"date_updated":"2021-01-12T06:53:54Z","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:45:20Z","_id":"1895","pubrep_id":"439","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:20Z","file_size":6262085,"date_created":"2018-12-12T10:09:01Z","file_name":"IST-2016-439-v1+1_journal.pone.0107099.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"1f3be936be93114596d61ba44cacee69","file_id":"4724"}],"publication_status":"published","issue":"9","volume":9,"oa_version":"Published Version","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"}],"intvolume":" 9","month":"09","scopus_import":1},{"year":"2014","publication":"PNAS","day":"18","page":"2818 - 2823","date_created":"2018-12-11T11:54:34Z","date_published":"2014-02-18T00:00:00Z","doi":"10.1073/pnas.1324264111","acknowledgement":"This work was supported by grants from the Research Foundation-Flanders (Odysseus).","oa":1,"publisher":"National Academy of Sciences","citation":{"mla":"Marhavá, Petra, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS, vol. 111, no. 7, National Academy of Sciences, 2014, pp. 2818–23, doi:10.1073/pnas.1324264111.","ieee":"P. Marhavá et al., “SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis,” PNAS, 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. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1324264111","ama":"Marhavá P, Hirsch S, Feraru E, et al. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 2014;111(7):2818-2823. doi:10.1073/pnas.1324264111","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.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1324264111.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87","last_name":"Nováková","full_name":"Nováková, Petra"},{"first_name":"Sibylle","last_name":"Hirsch","full_name":"Hirsch, Sibylle"},{"first_name":"Elena","full_name":"Feraru, Elena","last_name":"Feraru"},{"first_name":"Ricardo","last_name":"Tejos","full_name":"Tejos, Ricardo"},{"last_name":"Van Wijk","full_name":"Van Wijk, Ringo","first_name":"Ringo"},{"first_name":"Tom","last_name":"Viaene","full_name":"Viaene, Tom"},{"first_name":"Mareike","last_name":"Heilmann","full_name":"Heilmann, Mareike"},{"last_name":"Lerche","full_name":"Lerche, Jennifer","first_name":"Jennifer"},{"last_name":"De Rycke","full_name":"De Rycke, Riet","first_name":"Riet"},{"last_name":"Feraru","full_name":"Feraru, Mugurel","first_name":"Mugurel"},{"last_name":"Grones","full_name":"Grones, Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"full_name":"Van Montagu, Marc","last_name":"Van Montagu","first_name":"Marc"},{"first_name":"Ingo","last_name":"Heilmann","full_name":"Heilmann, Ingo"},{"full_name":"Munnik, Teun","last_name":"Munnik","first_name":"Teun"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5202","title":"SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":111,"issue":"7","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"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932866/"}],"scopus_import":1,"intvolume":" 111","month":"02","date_updated":"2021-01-12T06:53:53Z","department":[{"_id":"JiFr"}],"_id":"1893","type":"journal_article","status":"public"},{"_id":"1896","status":"public","type":"journal_article","date_updated":"2022-08-01T10:50:10Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"oa_version":"Submitted Version","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"}],"month":"03","intvolume":" 89","scopus_import":"1","main_file_link":[{"url":"http://arxiv.org/abs/1402.0430","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":89,"article_number":"032701","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.032701.","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.","mla":"Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701.","apa":"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. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.032701","ama":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701","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,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014."},"title":"Mathematical model of alternative mechanism of telomere length maintenance","author":[{"first_name":"Richard","last_name":"Kollár","full_name":"Kollár, Richard"},{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína","orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína","last_name":"Bod'ová"},{"first_name":"Jozef","full_name":"Nosek, Jozef","last_name":"Nosek"},{"full_name":"Tomáška, Ľubomír","last_name":"Tomáška","first_name":"Ľubomír"}],"publist_id":"5198","article_processing_charge":"No","acknowledgement":"The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.).","publisher":"American Institute of Physics","oa":1,"day":"04","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","year":"2014","doi":"10.1103/PhysRevE.89.032701","date_published":"2014-03-04T00:00:00Z","date_created":"2018-12-11T11:54:35Z"},{"volume":26,"date_published":"2014-07-01T00:00:00Z","issue":"7","doi":"10.1105/tpc.114.125880","date_created":"2018-12-11T11:54:36Z","page":"3062 - 3076","day":"01","language":[{"iso":"eng"}],"publication":"Plant Cell","year":"2014","publication_status":"published","month":"07","intvolume":" 26","scopus_import":1,"publisher":"American Society of Plant Biologists","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145132/"}],"oa_version":"Submitted Version","acknowledgement":"This work was supported by the Odysseus Program of the Research Foundation-Flanders (J.F.).","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"JiFr"}],"title":"Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis","author":[{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"first_name":"Marisa","full_name":"Otegui, Marisa","last_name":"Otegui"},{"full_name":"Kutsuna, Natsumaro","last_name":"Kutsuna","first_name":"Natsumaro"},{"first_name":"Riet","last_name":"De Rycke","full_name":"De Rycke, Riet"},{"first_name":"Tomoko","last_name":"Dainobu","full_name":"Dainobu, Tomoko"},{"first_name":"Michael","last_name":"Karampelias","full_name":"Karampelias, Michael"},{"full_name":"Fujimoto, Masaru","last_name":"Fujimoto","first_name":"Masaru"},{"first_name":"Elena","full_name":"Feraru, Elena","last_name":"Feraru"},{"first_name":"Daisuke","last_name":"Miki","full_name":"Miki, Daisuke"},{"first_name":"Hiroo","full_name":"Fukuda, Hiroo","last_name":"Fukuda"},{"first_name":"Akihiko","last_name":"Nakano","full_name":"Nakano, Akihiko"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"publist_id":"5199","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:55Z","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. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.125880","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. Plant Cell. 2014;26(7):3062-3076. doi:10.1105/tpc.114.125880","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 et al., “Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis,” Plant Cell, vol. 26, no. 7. American Society of Plant Biologists, pp. 3062–3076, 2014.","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.” Plant Cell, vol. 26, no. 7, American Society of Plant Biologists, 2014, pp. 3062–76, doi:10.1105/tpc.114.125880.","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.","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.” Plant Cell. American Society of Plant Biologists, 2014. https://doi.org/10.1105/tpc.114.125880."},"status":"public","type":"journal_article","_id":"1897"},{"department":[{"_id":"SiHi"}],"date_updated":"2021-01-12T06:53:55Z","status":"public","type":"journal_article","article_type":"original","_id":"1899","volume":16,"issue":"8","language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 16","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159251/"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","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."}],"title":"Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN","author":[{"first_name":"Scott","last_name":"Williams","full_name":"Williams, Scott"},{"last_name":"Ratliff","full_name":"Ratliff, Lyndsay","first_name":"Lyndsay"},{"last_name":"Postiglione","full_name":"Postiglione, Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87","first_name":"Maria P"},{"first_name":"Juergen","last_name":"Knoblich","full_name":"Knoblich, Juergen"},{"first_name":"Elaine","last_name":"Fuchs","full_name":"Fuchs, Elaine"}],"publist_id":"5196","external_id":{"pmid":["25016959"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb3001.","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.” Nature Cell Biology, vol. 16, no. 8, Nature Publishing Group, 2014, pp. 758–69, doi:10.1038/ncb3001.","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,” Nature Cell Biology, vol. 16, no. 8. Nature Publishing Group, pp. 758–769, 2014.","short":"S. Williams, L. Ratliff, M.P. Postiglione, J. Knoblich, E. Fuchs, Nature Cell Biology 16 (2014) 758–769.","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. Nature Cell Biology. 2014;16(8):758-769. doi:10.1038/ncb3001","apa":"Williams, S., Ratliff, L., Postiglione, M. P., Knoblich, J., & Fuchs, E. (2014). Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3001"},"date_published":"2014-07-13T00:00:00Z","doi":"10.1038/ncb3001","date_created":"2018-12-11T11:54:36Z","page":"758 - 769","day":"13","publication":"Nature Cell Biology","year":"2014","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1},{"_id":"1898","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:55Z","citation":{"mla":"Ritzau Jost, Andreas, et al. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” Neuron, vol. 84, no. 1, Elsevier, 2014, pp. 152–63, doi:10.1016/j.neuron.2014.08.036.","ama":"Ritzau Jost A, Delvendahl I, Rings A, et al. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 2014;84(1):152-163. doi:10.1016/j.neuron.2014.08.036","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. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.08.036","ieee":"A. Ritzau Jost et al., “Ultrafast action potentials mediate kilohertz signaling at a central synapse,” Neuron, 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.","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.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.08.036.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5197","author":[{"last_name":"Ritzau Jost","full_name":"Ritzau Jost, Andreas","first_name":"Andreas"},{"first_name":"Igor","last_name":"Delvendahl","full_name":"Delvendahl, Igor"},{"last_name":"Rings","full_name":"Rings, Annika","first_name":"Annika"},{"first_name":"Niklas","full_name":"Byczkowicz, Niklas","last_name":"Byczkowicz"},{"last_name":"Harada","orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Harumi"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hirrlinger","full_name":"Hirrlinger, Johannes","first_name":"Johannes"},{"first_name":"Jens","full_name":"Eilers, Jens","last_name":"Eilers"},{"last_name":"Hallermann","full_name":"Hallermann, Stefan","first_name":"Stefan"}],"department":[{"_id":"RySh"}],"title":"Ultrafast action potentials mediate kilohertz signaling at a central synapse","abstract":[{"lang":"eng","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."}],"oa_version":"None","publisher":"Elsevier","quality_controlled":"1","scopus_import":1,"month":"10","intvolume":" 84","publication_status":"published","year":"2014","day":"01","language":[{"iso":"eng"}],"publication":"Neuron","page":"152 - 163","volume":84,"date_published":"2014-10-01T00:00:00Z","doi":"10.1016/j.neuron.2014.08.036","issue":"1","date_created":"2018-12-11T11:54:36Z"},{"pubrep_id":"573","status":"public","type":"journal_article","_id":"1906","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:45:20Z","ddc":["000"],"date_updated":"2021-01-12T06:53:59Z","intvolume":" 20","month":"09","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"In this paper, we introduce a novel scene representation for the visualization of large-scale point clouds accompanied by a set of high-resolution photographs. Many real-world applications deal with very densely sampled point-cloud data, which are augmented with photographs that often reveal lighting variations and inaccuracies in registration. Consequently, the high-quality representation of the captured data, i.e., both point clouds and photographs together, is a challenging and time-consuming task. We propose a two-phase approach, in which the first (preprocessing) phase generates multiple overlapping surface patches and handles the problem of seamless texture generation locally for each patch. The second phase stitches these patches at render-time to produce a high-quality visualization of the data. As a result of the proposed localization of the global texturing problem, our algorithm is more than an order of magnitude faster than equivalent mesh-based texturing techniques. Furthermore, since our preprocessing phase requires only a minor fraction of the whole data set at once, we provide maximum flexibility when dealing with growing data sets."}],"issue":"9","volume":20,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5297","checksum":"5bf58942d2eb20adf03c7f9ea2e68124","file_size":13594598,"date_updated":"2020-07-14T12:45:20Z","creator":"system","file_name":"IST-2016-573-v1+1_arikan-2014-pcvis-draft.pdf","date_created":"2018-12-12T10:17:41Z"}],"publication_status":"published","project":[{"_id":"25357BD2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 24352-N23","name":"Deep Pictures: Creating Visual and Haptic Vector Images"}],"title":"Large-scale point-cloud visualization through localized textured surface reconstruction","publist_id":"5189","author":[{"last_name":"Arikan","full_name":"Arikan, Murat","first_name":"Murat"},{"last_name":"Preiner","full_name":"Preiner, Reinhold","first_name":"Reinhold"},{"full_name":"Scheiblauer, Claus","last_name":"Scheiblauer","first_name":"Claus"},{"full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","full_name":"Wimmer, Michael","last_name":"Wimmer"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, and M. Wimmer, “Large-scale point-cloud visualization through localized textured surface reconstruction,” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 9. IEEE, pp. 1280–1292, 2014.","short":"M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, M. Wimmer, IEEE Transactions on Visualization and Computer Graphics 20 (2014) 1280–1292.","apa":"Arikan, M., Preiner, R., Scheiblauer, C., Jeschke, S., & Wimmer, M. (2014). Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2014.2312011","ama":"Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 2014;20(9):1280-1292. doi:10.1109/TVCG.2014.2312011","mla":"Arikan, Murat, et al. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 9, IEEE, 2014, pp. 1280–92, doi:10.1109/TVCG.2014.2312011.","ista":"Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. 2014. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 20(9), 1280–1292.","chicago":"Arikan, Murat, Reinhold Preiner, Claus Scheiblauer, Stefan Jeschke, and Michael Wimmer. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2312011."},"oa":1,"publisher":"IEEE","acknowledgement":"This research was supported by the Austrian Research Promotion Agency (FFG) project REPLICATE (no. 835948), the EU FP7 project HARVEST4D (no. 323567).","date_created":"2018-12-11T11:54:39Z","doi":"10.1109/TVCG.2014.2312011","date_published":"2014-09-09T00:00:00Z","page":"1280 - 1292","publication":"IEEE Transactions on Visualization and Computer Graphics","day":"09","year":"2014","has_accepted_license":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Tobler, Michael, Martin Plath, Rüdiger Riesch, Ingo Schlupp, Anna V Grasse, Gopi Munimanda, C Setzer, Dustin Penn, and Yoshan Moodley. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary Biology. Wiley, 2014. https://doi.org/10.1111/jeb.12370.","ista":"Tobler M, Plath M, Riesch R, Schlupp I, Grasse AV, Munimanda G, Setzer C, Penn D, Moodley Y. 2014. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 27(5), 960–974.","mla":"Tobler, Michael, et al. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary Biology, vol. 27, no. 5, Wiley, 2014, pp. 960–74, doi:10.1111/jeb.12370.","apa":"Tobler, M., Plath, M., Riesch, R., Schlupp, I., Grasse, A. V., Munimanda, G., … Moodley, Y. (2014). Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.12370","ama":"Tobler M, Plath M, Riesch R, et al. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 2014;27(5):960-974. doi:10.1111/jeb.12370","short":"M. Tobler, M. Plath, R. Riesch, I. Schlupp, A.V. Grasse, G. Munimanda, C. Setzer, D. Penn, Y. Moodley, Journal of Evolutionary Biology 27 (2014) 960–974.","ieee":"M. Tobler et al., “Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations,” Journal of Evolutionary Biology, vol. 27, no. 5. Wiley, pp. 960–974, 2014."},"title":"Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations","author":[{"full_name":"Tobler, Michael","last_name":"Tobler","first_name":"Michael"},{"first_name":"Martin","last_name":"Plath","full_name":"Plath, Martin"},{"first_name":"Rüdiger","last_name":"Riesch","full_name":"Riesch, Rüdiger"},{"first_name":"Ingo","full_name":"Schlupp, Ingo","last_name":"Schlupp"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V"},{"full_name":"Munimanda, Gopi","last_name":"Munimanda","first_name":"Gopi"},{"first_name":"C","full_name":"Setzer, C","last_name":"Setzer"},{"first_name":"Dustin","last_name":"Penn","full_name":"Penn, Dustin"},{"first_name":"Yoshan","last_name":"Moodley","full_name":"Moodley, Yoshan"}],"publist_id":"5190","external_id":{"pmid":["24725091"]},"article_processing_charge":"No","day":"12","publication":"Journal of Evolutionary Biology","year":"2014","doi":"10.1111/jeb.12370","date_published":"2014-04-12T00:00:00Z","date_created":"2018-12-11T11:54:38Z","page":"960 - 974","acknowledgement":"This study was funded by grants from the National Science Foundation (NSF) to MT (IOS-1121832) and IS (DEB-0743406) and from the German Science Foundation (DFG; PL 470/1-2) and ‘LOEWE − Landesoffensive zur Entwicklung wissenschaftlich-ökonomischer Exzellenz’ of Hesse's Ministry of Higher Education, Research, and the Arts, to MP.","quality_controlled":"1","publisher":"Wiley","date_updated":"2022-06-07T09:22:20Z","department":[{"_id":"SyCr"}],"_id":"1905","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"publication_status":"published","volume":27,"issue":"5","pmid":1,"oa_version":"None","abstract":[{"text":"The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution).","lang":"eng"}],"month":"04","intvolume":" 27","scopus_import":"1"},{"date_updated":"2022-06-07T11:08:13Z","department":[{"_id":"JoBo"}],"_id":"1902","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"publication_status":"published","volume":31,"issue":"1","oa_version":"None","pmid":1,"abstract":[{"text":"In the 1960s-1980s, determination of bacterial growth rates was an important tool in microbial genetics, biochemistry, molecular biology, and microbial physiology. The exciting technical developments of the 1990s and the 2000s eclipsed that tool; as a result, many investigators today lack experience with growth rate measurements. Recently, investigators in a number of areas have started to use measurements of bacterial growth rates for a variety of purposes. Those measurements have been greatly facilitated by the availability of microwell plate readers that permit the simultaneous measurements on up to 384 different cultures. Only the exponential (logarithmic) portions of the resulting growth curves are useful for determining growth rates, and manual determination of that portion and calculation of growth rates can be tedious for high-throughput purposes. Here, we introduce the program GrowthRates that uses plate reader output files to automatically determine the exponential portion of the curve and to automatically calculate the growth rate, the maximum culture density, and the duration of the growth lag phase. GrowthRates is freely available for Macintosh, Windows, and Linux.We discuss the effects of culture volume, the classical bacterial growth curve, and the differences between determinations in rich media and minimal (mineral salts) media. This protocol covers calibration of the plate reader, growth of culture inocula for both rich and minimal media, and experimental setup. As a guide to reliability, we report typical day-to-day variation in growth rates and variation within experiments with respect to position of wells within the plates.","lang":"eng"}],"month":"01","intvolume":" 31","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Hall, B., Acar, H., Nandipati, A., & Barlow, M. (2014). Growth rates made easy. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst187","ama":"Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. Molecular Biology and Evolution. 2014;31(1):232-238. doi:10.1093/molbev/mst187","ieee":"B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” Molecular Biology and Evolution, vol. 31, no. 1. Oxford University Press, pp. 232–238, 2014.","short":"B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution 31 (2014) 232–238.","mla":"Hall, Barry, et al. “Growth Rates Made Easy.” Molecular Biology and Evolution, vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:10.1093/molbev/mst187.","ista":"Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular Biology and Evolution. 31(1), 232–238.","chicago":"Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates Made Easy.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/mst187."},"title":"Growth rates made easy","author":[{"full_name":"Hall, Barry","last_name":"Hall","first_name":"Barry"},{"full_name":"Acar, Hande","orcid":"0000-0003-1986-9753","last_name":"Acar","first_name":"Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna","full_name":"Nandipati, Anna","last_name":"Nandipati"},{"first_name":"Miriam","last_name":"Barlow","full_name":"Barlow, Miriam"}],"publist_id":"5193","article_processing_charge":"No","external_id":{"pmid":["24170494"]},"day":"01","publication":"Molecular Biology and Evolution","year":"2014","date_published":"2014-01-01T00:00:00Z","doi":"10.1093/molbev/mst187","date_created":"2018-12-11T11:54:37Z","page":"232 - 238","publisher":"Oxford University Press","quality_controlled":"1"},{"page":"277 - 289","date_created":"2018-12-11T11:54:37Z","doi":"10.1093/mp/sst118","date_published":"2014-02-01T00:00:00Z","volume":7,"issue":"2","year":"2014","publication_status":"published","language":[{"iso":"eng"}],"publication":"Molecular Plant","day":"01","publisher":"Oxford University Press","scopus_import":1,"intvolume":" 7","month":"02","abstract":[{"lang":"eng","text":"In plants, the patterning of stem cell-enriched meristems requires a graded auxin response maximum that emerges from the concerted action of polar auxin transport, auxin biosynthesis, auxin metabolism, and cellular auxin response machinery. However, mechanisms underlying this auxin response maximum-mediated root stem cell maintenance are not fully understood. Here, we present unexpected evidence that WUSCHEL-RELATED HOMEOBOX 5 (WOX5) transcription factor modulates expression of auxin biosynthetic genes in the quiescent center (QC) of the root and thus provides a robust mechanism for the maintenance of auxin response maximum in the root tip. This WOX5 action is balanced through the activity of indole-3-acetic acid 17 (IAA17) auxin response repressor. Our combined genetic, cell biology, and computational modeling studies revealed a previously uncharacterized feedback loop linking WOX5-mediated auxin production to IAA17-dependent repression of auxin responses. This WOX5-IAA17 feedback circuit further assures the maintenance of auxin response maximum in the root tip and thereby contributes to the maintenance of distal stem cell (DSC) populations. Our experimental studies and in silico computer simulations both demonstrate that the WOX5-IAA17 feedback circuit is essential for the maintenance of auxin gradient in the root tip and the auxin-mediated root DSC differentiation."}],"acknowledgement":"This work was supported by funding from the projects CZ.1.07/2.3.00/20.0043 and CZ.1.05/1.1.00/02.0068 (to CEITEC, Central European Institute of Technology) and the Odysseus program of the Research Foundation-Flanders to J.F\r\n","oa_version":"None","publist_id":"5194","author":[{"first_name":"Huiyu","full_name":"Tian, Huiyu","last_name":"Tian"},{"first_name":"Krzysztof T","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T"},{"first_name":"Tiantian","full_name":"Niu, Tiantian","last_name":"Niu"},{"last_name":"Li","full_name":"Li, Hongjiang","first_name":"Hongjiang"},{"first_name":"Qianqian","full_name":"Yu, Qianqian","last_name":"Yu"},{"first_name":"Stephan","full_name":"Pollmann, Stephan","last_name":"Pollmann"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"last_name":"Govaerts","full_name":"Govaerts, Willy","first_name":"Willy"},{"last_name":"Rolčík","full_name":"Rolčík, Jakub","first_name":"Jakub"},{"first_name":"Markus","full_name":"Geisler, Markus","last_name":"Geisler"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"full_name":"Ding, Zhaojun","last_name":"Ding","first_name":"Zhaojun"}],"department":[{"_id":"JiFr"}],"title":"WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis","date_updated":"2021-01-12T06:53:57Z","citation":{"chicago":"Tian, Huiyu, Krzysztof T Wabnik, Tiantian Niu, Hongjiang Li, Qianqian Yu, Stephan Pollmann, Steffen Vanneste, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular Plant. Oxford University Press, 2014. https://doi.org/10.1093/mp/sst118.","ista":"Tian H, Wabnik KT, Niu T, Li H, Yu Q, Pollmann S, Vanneste S, Govaerts W, Rolčík J, Geisler M, Friml J, Ding Z. 2014. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 7(2), 277–289.","mla":"Tian, Huiyu, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular Plant, vol. 7, no. 2, Oxford University Press, 2014, pp. 277–89, doi:10.1093/mp/sst118.","short":"H. Tian, K.T. Wabnik, T. Niu, H. Li, Q. Yu, S. Pollmann, S. Vanneste, W. Govaerts, J. Rolčík, M. Geisler, J. Friml, Z. Ding, Molecular Plant 7 (2014) 277–289.","ieee":"H. Tian et al., “WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis,” Molecular Plant, vol. 7, no. 2. Oxford University Press, pp. 277–289, 2014.","ama":"Tian H, Wabnik KT, Niu T, et al. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 2014;7(2):277-289. doi:10.1093/mp/sst118","apa":"Tian, H., Wabnik, K. T., Niu, T., Li, H., Yu, Q., Pollmann, S., … Ding, Z. (2014). WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. Oxford University Press. https://doi.org/10.1093/mp/sst118"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1901"},{"project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Frank R, Lewin M, Lieb É, Seiringer R. 2014. Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. 16(7), 1507–1526.","chicago":"Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “Strichartz Inequality for Orthonormal Functions.” Journal of the European Mathematical Society. European Mathematical Society, 2014. https://doi.org/10.4171/JEMS/467.","ieee":"R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “Strichartz inequality for orthonormal functions,” Journal of the European Mathematical Society, vol. 16, no. 7. European Mathematical Society, pp. 1507–1526, 2014.","short":"R. Frank, M. Lewin, É. Lieb, R. Seiringer, Journal of the European Mathematical Society 16 (2014) 1507–1526.","apa":"Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2014). Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/467","ama":"Frank R, Lewin M, Lieb É, Seiringer R. Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. 2014;16(7):1507-1526. doi:10.4171/JEMS/467","mla":"Frank, Rupert, et al. “Strichartz Inequality for Orthonormal Functions.” Journal of the European Mathematical Society, vol. 16, no. 7, European Mathematical Society, 2014, pp. 1507–26, doi:10.4171/JEMS/467."},"title":"Strichartz inequality for orthonormal functions","author":[{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert"},{"first_name":"Mathieu","last_name":"Lewin","full_name":"Lewin, Mathieu"},{"first_name":"Élliott","last_name":"Lieb","full_name":"Lieb, Élliott"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"publist_id":"5191","publisher":"European Mathematical Society","quality_controlled":"1","oa":1,"day":"23","publication":"Journal of the European Mathematical Society","year":"2014","doi":"10.4171/JEMS/467","date_published":"2014-08-23T00:00:00Z","date_created":"2018-12-11T11:54:38Z","page":"1507 - 1526","_id":"1904","status":"public","type":"journal_article","date_updated":"2021-01-12T06:53:58Z","department":[{"_id":"RoSe"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We prove a Strichartz inequality for a system of orthonormal functions, with an optimal behavior of the constant in the limit of a large number of functions. The estimate generalizes the usual Strichartz inequality, in the same fashion as the Lieb-Thirring inequality generalizes the Sobolev inequality. As an application, we consider the Schrödinger equation with a time-dependent potential and we show the existence of the wave operator in Schatten spaces."}],"month":"08","intvolume":" 16","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1306.1309","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"7","volume":16},{"type":"journal_article","status":"public","_id":"1900","publist_id":"5195","author":[{"first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","full_name":"Behrndt, Martin"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"department":[{"_id":"CaHe"}],"title":"Lateral junction dynamics lead the way out","date_updated":"2021-01-12T06:53:56Z","citation":{"ama":"Behrndt M, Heisenberg C-PJ. Lateral junction dynamics lead the way out. Nature Cell Biology. 2014;16(2):127-129. doi:10.1038/ncb2913","apa":"Behrndt, M., & Heisenberg, C.-P. J. (2014). Lateral junction dynamics lead the way out. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2913","short":"M. Behrndt, C.-P.J. Heisenberg, Nature Cell Biology 16 (2014) 127–129.","ieee":"M. Behrndt and C.-P. J. Heisenberg, “Lateral junction dynamics lead the way out,” Nature Cell Biology, vol. 16, no. 2. Nature Publishing Group, pp. 127–129, 2014.","mla":"Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Lateral Junction Dynamics Lead the Way Out.” Nature Cell Biology, vol. 16, no. 2, Nature Publishing Group, 2014, pp. 127–29, doi:10.1038/ncb2913.","ista":"Behrndt M, Heisenberg C-PJ. 2014. Lateral junction dynamics lead the way out. Nature Cell Biology. 16(2), 127–129.","chicago":"Behrndt, Martin, and Carl-Philipp J Heisenberg. “Lateral Junction Dynamics Lead the Way Out.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb2913."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","scopus_import":1,"publisher":"Nature Publishing Group","month":"01","intvolume":" 16","abstract":[{"text":"Epithelial cell layers need to be tightly regulated to maintain their integrity and correct function. Cell integration into epithelial sheets is now shown to depend on the N-WASP-regulated stabilization of cortical F-actin, which generates distinct patterns of apical-lateral contractility at E-cadherin-based cell-cell junctions.","lang":"eng"}],"oa_version":"None","page":"127 - 129","issue":"2","date_published":"2014-01-31T00:00:00Z","doi":"10.1038/ncb2913","volume":16,"date_created":"2018-12-11T11:54:37Z","publication_status":"published","year":"2014","day":"31","publication":"Nature Cell Biology","language":[{"iso":"eng"}]},{"title":"The fitness costs of adaptation via phenotypic plasticity and maternal effects","publist_id":"5186","author":[{"first_name":"Thomas","full_name":"Ezard, Thomas","last_name":"Ezard"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan","full_name":"Prizak, Roshan","last_name":"Prizak"},{"first_name":"Rebecca","full_name":"Hoyle, Rebecca","last_name":"Hoyle"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:10.1111/1365-2435.12207.","short":"T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.","ieee":"T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell, pp. 693–701, 2014.","ama":"Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701. doi:10.1111/1365-2435.12207","apa":"Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell. https://doi.org/10.1111/1365-2435.12207","chicago":"Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207.","ista":"Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701."},"date_created":"2018-12-11T11:54:40Z","date_published":"2014-06-01T00:00:00Z","doi":"10.1111/1365-2435.12207","page":"693 - 701","publication":"Functional Ecology","day":"01","year":"2014","has_accepted_license":"1","oa":1,"publisher":"Wiley-Blackwell","acknowledgement":"Engineering and Physical Sciences Research Council. Grant Number: EP/H031928/1","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:20Z","ddc":["570"],"date_updated":"2021-01-12T06:54:00Z","pubrep_id":"419","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1909","issue":"3","volume":28,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5167","checksum":"3cbe8623174709a8ceec2103246f8fe0","date_updated":"2020-07-14T12:45:20Z","file_size":536154,"creator":"system","date_created":"2018-12-12T10:15:45Z","file_name":"IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf"}],"publication_status":"published","intvolume":" 28","month":"06","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Summary: Phenotypes are often environmentally dependent, which requires organisms to track environmental change. The challenge for organisms is to construct phenotypes using the most accurate environmental cue. Here, we use a quantitative genetic model of adaptation by additive genetic variance, within- and transgenerational plasticity via linear reaction norms and indirect genetic effects respectively. We show how the relative influence on the eventual phenotype of these components depends on the predictability of environmental change (fast or slow, sinusoidal or stochastic) and the developmental lag τ between when the environment is perceived and when selection acts. We then decompose expected mean fitness into three components (variance load, adaptation and fluctuation load) to study the fitness costs of within- and transgenerational plasticity. A strongly negative maternal effect coefficient m minimizes the variance load, but a strongly positive m minimises the fluctuation load. The adaptation term is maximized closer to zero, with positive or negative m preferred under different environmental scenarios. Phenotypic plasticity is higher when τ is shorter and when the environment changes frequently between seasonal extremes. Expected mean population fitness is highest away from highest observed levels of phenotypic plasticity. Within- and transgenerational plasticity act in concert to deliver well-adapted phenotypes, which emphasizes the need to study both simultaneously when investigating phenotypic evolution.","lang":"eng"}]},{"scopus_import":1,"publisher":"Wiley-Blackwell","intvolume":" 44","month":"02","abstract":[{"lang":"eng","text":"angerhans cells (LCs) are a unique subset of dendritic cells (DCs) that express epithelial adhesion molecules, allowing them to form contacts with epithelial cells and reside in epidermal/epithelial tissues. The dynamic regulation of epithelial adhesion plays a decisive role in the life cycle of LCs. It controls whether LCs remain immature and sessile within the epidermis or mature and egress to initiate immune responses. So far, the molecular machinery regulating epithelial adhesion molecules during LC maturation remains elusive. Here, we generated pure populations of immature human LCs in vitro to systematically probe for gene-expression changes during LC maturation. LCs down-regulate a set of epithelial genes including E-cadherin, while they upregulate the mesenchymal marker N-cadherin known to facilitate cell migration. In addition, N-cadherin is constitutively expressed by monocyte-derived DCs known to exhibit characteristics of both inflammatory-type and interstitial/dermal DCs. Moreover, the transcription factors ZEB1 and ZEB2 (ZEB is zinc-finger E-box-binding homeobox) are upregulated in migratory LCs. ZEB1 and ZEB2 have been shown to induce epithelial-to-mesenchymal transition (EMT) and invasive behavior in cancer cells undergoing metastasis. Our results provide the first hint that the molecular EMT machinery might facilitate LC mobilization. Moreover, our study suggests that N-cadherin plays a role during DC migration."}],"acknowledgement":"FWF. Grant Number: P22058-B20","oa_version":"None","page":"553 - 560","date_created":"2018-12-11T11:54:40Z","volume":44,"date_published":"2014-02-01T00:00:00Z","doi":"10.1002/eji.201343681","issue":"2","year":"2014","publication_status":"published","publication":"European Journal of Immunology","language":[{"iso":"eng"}],"day":"01","type":"journal_article","status":"public","_id":"1910","author":[{"first_name":"Sabine","last_name":"Konradi","full_name":"Konradi, Sabine"},{"first_name":"Nighat","full_name":"Yasmin, Nighat","last_name":"Yasmin"},{"first_name":"Denise","last_name":"Haslwanter","full_name":"Haslwanter, Denise"},{"first_name":"Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","last_name":"Weber","full_name":"Weber, Michele"},{"last_name":"Gesslbauer","full_name":"Gesslbauer, Bernd","first_name":"Bernd"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Strobl, Herbert","last_name":"Strobl","first_name":"Herbert"}],"publist_id":"5185","title":"Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2","department":[{"_id":"MiSi"}],"citation":{"ama":"Konradi S, Yasmin N, Haslwanter D, et al. Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. 2014;44(2):553-560. doi:10.1002/eji.201343681","apa":"Konradi, S., Yasmin, N., Haslwanter, D., Weber, M., Gesslbauer, B., Sixt, M. K., & Strobl, H. (2014). Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. Wiley-Blackwell. https://doi.org/10.1002/eji.201343681","ieee":"S. Konradi et al., “Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2,” European Journal of Immunology, vol. 44, no. 2. Wiley-Blackwell, pp. 553–560, 2014.","short":"S. Konradi, N. Yasmin, D. Haslwanter, M. Weber, B. Gesslbauer, M.K. Sixt, H. Strobl, European Journal of Immunology 44 (2014) 553–560.","mla":"Konradi, Sabine, et al. “Langerhans Cell Maturation Is Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition ZEB1/2.” European Journal of Immunology, vol. 44, no. 2, Wiley-Blackwell, 2014, pp. 553–60, doi:10.1002/eji.201343681.","ista":"Konradi S, Yasmin N, Haslwanter D, Weber M, Gesslbauer B, Sixt MK, Strobl H. 2014. Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. 44(2), 553–560.","chicago":"Konradi, Sabine, Nighat Yasmin, Denise Haslwanter, Michele Weber, Bernd Gesslbauer, Michael K Sixt, and Herbert Strobl. “Langerhans Cell Maturation Is Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition ZEB1/2.” European Journal of Immunology. Wiley-Blackwell, 2014. https://doi.org/10.1002/eji.201343681."},"date_updated":"2021-01-12T06:54:01Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"lang":"eng","text":"Most cryptographic security proofs require showing that two systems are indistinguishable. A central tool in such proofs is that of a game, where winning the game means provoking a certain condition, and it is shown that the two systems considered cannot be distinguished unless this condition is provoked. Upper bounding the probability of winning such a game, i.e., provoking this condition, for an arbitrary strategy is usually hard, except in the special case where the best strategy for winning such a game is known to be non-adaptive. A sufficient criterion for ensuring the optimality of non-adaptive strategies is that of conditional equivalence to a system, a notion introduced in [1]. In this paper, we show that this criterion is not necessary to ensure the optimality of non-adaptive strategies by giving two results of independent interest: 1) the optimality of non-adaptive strategies is not preserved under parallel composition; 2) in contrast, conditional equivalence is preserved under parallel composition."}],"oa_version":"Submitted Version","quality_controlled":"1","scopus_import":1,"publisher":"IEEE","main_file_link":[{"url":"https://eprint.iacr.org/2014/299","open_access":"1"}],"oa":1,"month":"01","year":"2014","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"IEEE International Symposium on Information Theory","doi":"10.1109/ISIT.2014.6875125","date_published":"2014-01-01T00:00:00Z","date_created":"2018-12-11T11:54:39Z","_id":"1907","article_number":"6875125","type":"conference","conference":{"end_date":"2014-07-04","location":"Honolulu, USA","start_date":"2014-06-29","name":"IEEE International Symposium on Information Theory Proceedings"},"status":"public","citation":{"apa":"Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2014). Optimality of non-adaptive strategies: The case of parallel games. In IEEE International Symposium on Information Theory. Honolulu, USA: IEEE. https://doi.org/10.1109/ISIT.2014.6875125","ama":"Demay G, Gazi P, Maurer U, Tackmann B. Optimality of non-adaptive strategies: The case of parallel games. In: IEEE International Symposium on Information Theory. IEEE; 2014. doi:10.1109/ISIT.2014.6875125","ieee":"G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Optimality of non-adaptive strategies: The case of parallel games,” in IEEE International Symposium on Information Theory, Honolulu, USA, 2014.","short":"G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, IEEE International Symposium on Information Theory, IEEE, 2014.","mla":"Demay, Grégory, et al. “Optimality of Non-Adaptive Strategies: The Case of Parallel Games.” IEEE International Symposium on Information Theory, 6875125, IEEE, 2014, doi:10.1109/ISIT.2014.6875125.","ista":"Demay G, Gazi P, Maurer U, Tackmann B. 2014. Optimality of non-adaptive strategies: The case of parallel games. IEEE International Symposium on Information Theory. IEEE International Symposium on Information Theory Proceedings, 6875125.","chicago":"Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Optimality of Non-Adaptive Strategies: The Case of Parallel Games.” In IEEE International Symposium on Information Theory. IEEE, 2014. https://doi.org/10.1109/ISIT.2014.6875125."},"date_updated":"2021-01-12T06:53:59Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Demay, Grégory","last_name":"Demay","first_name":"Grégory"},{"id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Gazi, Peter","last_name":"Gazi"},{"last_name":"Maurer","full_name":"Maurer, Ueli","first_name":"Ueli"},{"first_name":"Björn","last_name":"Tackmann","full_name":"Tackmann, Björn"}],"publist_id":"5188","title":"Optimality of non-adaptive strategies: The case of parallel games","department":[{"_id":"KrPi"}]},{"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":196,"issue":"4","abstract":[{"lang":"eng","text":"In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can bring together beneficial alleles from different backgrounds, but tightly linked alleles may still greatly interfere with each other. We show for well-mixed populations that when this interference is strong, the genome can be seen as consisting of many effectively asexual stretches linked together. The rate at which beneficial alleles fix is thus roughly proportional to the rate of recombination and depends only logarithmically on the mutation supply and the strength of selection. Our scaling arguments also allow us to predict, with reasonable accuracy, the fitness distribution of fixed mutations when the mutational effect sizes are broad. We focus on the regime in which crossovers occur more frequently than beneficial mutations, as is likely to be the case for many natural populations."}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.0737"}],"scopus_import":1,"intvolume":" 196","month":"04","date_updated":"2021-01-12T06:53:59Z","department":[{"_id":"NiBa"}],"_id":"1908","type":"journal_article","status":"public","year":"2014","publication":"Genetics","day":"01","page":"1167 - 1183","date_created":"2018-12-11T11:54:39Z","date_published":"2014-04-01T00:00:00Z","doi":"10.1534/genetics.113.160705","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","citation":{"mla":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics, vol. 196, no. 4, Genetics Society of America, 2014, pp. 1167–83, doi:10.1534/genetics.113.160705.","short":"D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183.","ieee":"D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations with linear chromosomes,” Genetics, vol. 196, no. 4. Genetics Society of America, pp. 1167–1183, 2014.","ama":"Weissman D, Hallatschek O. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 2014;196(4):1167-1183. doi:10.1534/genetics.113.160705","apa":"Weissman, D., & Hallatschek, O. (2014). The rate of adaptation in large sexual populations with linear chromosomes. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.160705","chicago":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics. Genetics Society of America, 2014. https://doi.org/10.1534/genetics.113.160705.","ista":"Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 196(4), 1167–1183."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","last_name":"Weissman","full_name":"Weissman, Daniel"},{"first_name":"Oskar","last_name":"Hallatschek","full_name":"Hallatschek, Oskar"}],"publist_id":"5187","title":"The rate of adaptation in large sexual populations with linear chromosomes","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}]},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:01Z","citation":{"short":"A. Engström, P. Noren, Discrete & Computational Geometry 51 (2014) 207–220.","ieee":"A. Engström and P. Noren, “Tverberg’s Theorem and Graph Coloring,” Discrete & Computational Geometry, vol. 51, no. 1. Springer, pp. 207–220, 2014.","apa":"Engström, A., & Noren, P. (2014). Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-013-9556-3","ama":"Engström A, Noren P. Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. 2014;51(1):207-220. doi:10.1007/s00454-013-9556-3","mla":"Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.” Discrete & Computational Geometry, vol. 51, no. 1, Springer, 2014, pp. 207–20, doi:10.1007/s00454-013-9556-3.","ista":"Engström A, Noren P. 2014. Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. 51(1), 207–220.","chicago":"Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-013-9556-3."},"department":[{"_id":"CaUh"}],"title":"Tverberg's Theorem and Graph Coloring","author":[{"full_name":"Engström, Alexander","last_name":"Engström","first_name":"Alexander"},{"first_name":"Patrik","id":"46870C74-F248-11E8-B48F-1D18A9856A87","last_name":"Noren","full_name":"Noren, Patrik"}],"publist_id":"5183","_id":"1911","status":"public","type":"journal_article","publication":"Discrete & Computational Geometry","language":[{"iso":"eng"}],"day":"01","year":"2014","publication_status":"published","date_created":"2018-12-11T11:54:40Z","volume":51,"doi":"10.1007/s00454-013-9556-3","issue":"1","date_published":"2014-01-01T00:00:00Z","page":"207 - 220","acknowledgement":"Patrik Norén gratefully acknowledges support from the Wallenberg foundation","oa_version":"None","abstract":[{"text":"The topological Tverberg theorem has been generalized in several directions by setting extra restrictions on the Tverberg partitions. Restricted Tverberg partitions, defined by the idea that certain points cannot be in the same part, are encoded with graphs. When two points are adjacent in the graph, they are not in the same part. If the restrictions are too harsh, then the topological Tverberg theorem fails. The colored Tverberg theorem corresponds to graphs constructed as disjoint unions of small complete graphs. Hell studied the case of paths and cycles. In graph theory these partitions are usually viewed as graph colorings. As explored by Aharoni, Haxell, Meshulam and others there are fundamental connections between several notions of graph colorings and topological combinatorics. For ordinary graph colorings it is enough to require that the number of colors q satisfy q>Δ, where Δ is the maximal degree of the graph. It was proven by the first author using equivariant topology that if q>Δ 2 then the topological Tverberg theorem still works. It is conjectured that q>KΔ is also enough for some constant K, and in this paper we prove a fixed-parameter version of that conjecture. The required topological connectivity results are proven with shellability, which also strengthens some previous partial results where the topological connectivity was proven with the nerve lemma.","lang":"eng"}],"intvolume":" 51","month":"01","publisher":"Springer","scopus_import":1},{"issue":"6170","volume":343,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157572/","open_access":"1"}],"month":"01","intvolume":" 343","abstract":[{"lang":"eng","text":"Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases characterized by progressive age-dependent loss of corticospinal motor tract function. Although the genetic basis is partly understood, only a fraction of cases can receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome sequencing in combination with network analysis, we identified 18 previously unknown putative HSP genes and validated nearly all of these genes functionally or genetically. The pathways highlighted by these mutations link HSP to cellular transport, nucleotide metabolism, and synapse and axon development. Network analysis revealed a host of further candidate genes, of which three were mutated in our cohort. Our analysis links HSP to other neurodegenerative disorders and can facilitate gene discovery and mechanistic understanding of disease."}],"oa_version":"Submitted Version","pmid":1,"department":[{"_id":"GaNo"}],"date_updated":"2021-01-12T06:54:03Z","article_type":"original","type":"journal_article","status":"public","_id":"1916","page":"506 - 511","doi":"10.1126/science.1247363","date_published":"2014-01-31T00:00:00Z","date_created":"2018-12-11T11:54:42Z","year":"2014","day":"31","publication":"Science","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"acknowledgement":"Supported by the Deutsche Forschungsgemeinschaft (G.N.)","author":[{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"first_name":"Ali","last_name":"Fenstermaker","full_name":"Fenstermaker, Ali"},{"last_name":"Zaki","full_name":"Zaki, Maha","first_name":"Maha"},{"last_name":"Hofree","full_name":"Hofree, Matan","first_name":"Matan"},{"full_name":"Silhavy, Jennifer","last_name":"Silhavy","first_name":"Jennifer"},{"first_name":"Andrew","full_name":"Heiberg, Andrew","last_name":"Heiberg"},{"full_name":"Abdellateef, Mostafa","last_name":"Abdellateef","first_name":"Mostafa"},{"full_name":"Rosti, Başak","last_name":"Rosti","first_name":"Başak"},{"last_name":"Scott","full_name":"Scott, Eric","first_name":"Eric"},{"full_name":"Mansour, Lobna","last_name":"Mansour","first_name":"Lobna"},{"first_name":"Amira","full_name":"Masri, Amira","last_name":"Masri"},{"last_name":"Kayserili","full_name":"Kayserili, Hülya","first_name":"Hülya"},{"first_name":"Jumana","last_name":"Al Aama","full_name":"Al Aama, Jumana"},{"full_name":"Abdel Salam, Ghada","last_name":"Abdel Salam","first_name":"Ghada"},{"full_name":"Karminejad, Ariana","last_name":"Karminejad","first_name":"Ariana"},{"last_name":"Kara","full_name":"Kara, Majdi","first_name":"Majdi"},{"first_name":"Bülent","full_name":"Kara, Bülent","last_name":"Kara"},{"first_name":"Bita","last_name":"Bozorgmehri","full_name":"Bozorgmehri, Bita"},{"full_name":"Ben Omran, Tawfeg","last_name":"Ben Omran","first_name":"Tawfeg"},{"first_name":"Faezeh","last_name":"Mojahedi","full_name":"Mojahedi, Faezeh"},{"first_name":"Iman","full_name":"Mahmoud, Iman","last_name":"Mahmoud"},{"first_name":"Naïma","last_name":"Bouslam","full_name":"Bouslam, Naïma"},{"first_name":"Ahmed","last_name":"Bouhouche","full_name":"Bouhouche, Ahmed"},{"first_name":"Ali","last_name":"Benomar","full_name":"Benomar, Ali"},{"full_name":"Hanein, Sylvain","last_name":"Hanein","first_name":"Sylvain"},{"full_name":"Raymond, Laure","last_name":"Raymond","first_name":"Laure"},{"last_name":"Forlani","full_name":"Forlani, Sylvie","first_name":"Sylvie"},{"first_name":"Massimo","full_name":"Mascaro, Massimo","last_name":"Mascaro"},{"first_name":"Laila","full_name":"Selim, Laila","last_name":"Selim"},{"last_name":"Shehata","full_name":"Shehata, Nabil","first_name":"Nabil"},{"first_name":"Nasir","last_name":"Al Allawi","full_name":"Al Allawi, Nasir"},{"last_name":"Bindu","full_name":"Bindu, Parayil","first_name":"Parayil"},{"full_name":"Azam, Matloob","last_name":"Azam","first_name":"Matloob"},{"full_name":"Günel, Murat","last_name":"Günel","first_name":"Murat"},{"first_name":"Ahmet","full_name":"Caglayan, Ahmet","last_name":"Caglayan"},{"full_name":"Bilgüvar, Kaya","last_name":"Bilgüvar","first_name":"Kaya"},{"last_name":"Tolun","full_name":"Tolun, Aslihan","first_name":"Aslihan"},{"first_name":"Mahmoud","last_name":"Issa","full_name":"Issa, Mahmoud"},{"first_name":"Jana","last_name":"Schroth","full_name":"Schroth, Jana"},{"first_name":"Emily","last_name":"Spencer","full_name":"Spencer, Emily"},{"first_name":"Rasim","last_name":"Rosti","full_name":"Rosti, Rasim"},{"last_name":"Akizu","full_name":"Akizu, Naiara","first_name":"Naiara"},{"last_name":"Vaux","full_name":"Vaux, Keith","first_name":"Keith"},{"full_name":"Johansen, Anide","last_name":"Johansen","first_name":"Anide"},{"full_name":"Koh, Alice","last_name":"Koh","first_name":"Alice"},{"last_name":"Megahed","full_name":"Megahed, Hisham","first_name":"Hisham"},{"first_name":"Alexandra","last_name":"Dürr","full_name":"Dürr, Alexandra"},{"first_name":"Alexis","last_name":"Brice","full_name":"Brice, Alexis"},{"first_name":"Giovanni","last_name":"Stévanin","full_name":"Stévanin, Giovanni"},{"full_name":"Gabriel, Stacy","last_name":"Gabriel","first_name":"Stacy"},{"last_name":"Ideker","full_name":"Ideker, Trey","first_name":"Trey"},{"first_name":"Joseph","full_name":"Gleeson, Joseph","last_name":"Gleeson"}],"publist_id":"5178","article_processing_charge":"No","external_id":{"pmid":["24482476"]},"title":"Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders","citation":{"apa":"Novarino, G., Fenstermaker, A., Zaki, M., Hofree, M., Silhavy, J., Heiberg, A., … Gleeson, J. (2014). Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1247363","ama":"Novarino G, Fenstermaker A, Zaki M, et al. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 2014;343(6170):506-511. doi:10.1126/science.1247363","short":"G. Novarino, A. Fenstermaker, M. Zaki, M. Hofree, J. Silhavy, A. Heiberg, M. Abdellateef, B. Rosti, E. Scott, L. Mansour, A. Masri, H. Kayserili, J. Al Aama, G. Abdel Salam, A. Karminejad, M. Kara, B. Kara, B. Bozorgmehri, T. Ben Omran, F. Mojahedi, I. Mahmoud, N. Bouslam, A. Bouhouche, A. Benomar, S. Hanein, L. Raymond, S. Forlani, M. Mascaro, L. Selim, N. Shehata, N. Al Allawi, P. Bindu, M. Azam, M. Günel, A. Caglayan, K. Bilgüvar, A. Tolun, M. Issa, J. Schroth, E. Spencer, R. Rosti, N. Akizu, K. Vaux, A. Johansen, A. Koh, H. Megahed, A. Dürr, A. Brice, G. Stévanin, S. Gabriel, T. Ideker, J. Gleeson, Science 343 (2014) 506–511.","ieee":"G. Novarino et al., “Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders,” Science, vol. 343, no. 6170. American Association for the Advancement of Science, pp. 506–511, 2014.","mla":"Novarino, Gaia, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders.” Science, vol. 343, no. 6170, American Association for the Advancement of Science, 2014, pp. 506–11, doi:10.1126/science.1247363.","ista":"Novarino G, Fenstermaker A, Zaki M, Hofree M, Silhavy J, Heiberg A, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al Aama J, Abdel Salam G, Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben Omran T, Mojahedi F, Mahmoud I, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro M, Selim L, Shehata N, Al Allawi N, Bindu P, Azam M, Günel M, Caglayan A, Bilgüvar K, Tolun A, Issa M, Schroth J, Spencer E, Rosti R, Akizu N, Vaux K, Johansen A, Koh A, Megahed H, Dürr A, Brice A, Stévanin G, Gabriel S, Ideker T, Gleeson J. 2014. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 343(6170), 506–511.","chicago":"Novarino, Gaia, Ali Fenstermaker, Maha Zaki, Matan Hofree, Jennifer Silhavy, Andrew Heiberg, Mostafa Abdellateef, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1247363."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication":"Science","day":"28","year":"2014","date_created":"2018-12-11T11:54:42Z","date_published":"2014-02-28T00:00:00Z","doi":"10.1126/science.1245125","page":"1025 - 1028","acknowledgement":"Supported by the intramural research program of the National Institute of Arthritis and Musculoskeletal and Skin Diseases and by its Laboratory Animal Care and Use Section and Flow Cytometry Group, Office of Science and Technology","oa":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Xu, Tongda, et al. “Cell Surface ABP1-TMK Auxin Sensing Complex Activates ROP GTPase Signaling.” Science, vol. 343, no. 6174, American Association for the Advancement of Science, 2014, pp. 1025–28, doi:10.1126/science.1245125.","ieee":"T. Xu et al., “Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling,” Science, vol. 343, no. 6174. American Association for the Advancement of Science, pp. 1025–1028, 2014.","short":"T. Xu, N. Dai, J. Chen, S. Nagawa, M. Cao, H. Li, Z. Zhou, X. Chen, R. De Rycke, H. Rakusová, W. Wang, A. Jones, J. Friml, S. Patterson, A. Bleecker, Z. Yang, Science 343 (2014) 1025–1028.","ama":"Xu T, Dai N, Chen J, et al. Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. 2014;343(6174):1025-1028. doi:10.1126/science.1245125","apa":"Xu, T., Dai, N., Chen, J., Nagawa, S., Cao, M., Li, H., … Yang, Z. (2014). Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1245125","chicago":"Xu, Tongda, Ning Dai, Jisheng Chen, Shingo Nagawa, Min Cao, Hongjiang Li, Zimin Zhou, et al. “Cell Surface ABP1-TMK Auxin Sensing Complex Activates ROP GTPase Signaling.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1245125.","ista":"Xu T, Dai N, Chen J, Nagawa S, Cao M, Li H, Zhou Z, Chen X, De Rycke R, Rakusová H, Wang W, Jones A, Friml J, Patterson S, Bleecker A, Yang Z. 2014. Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. 343(6174), 1025–1028."},"title":"Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling","article_processing_charge":"No","external_id":{"pmid":["24578577"]},"publist_id":"5177","author":[{"last_name":"Xu","full_name":"Xu, Tongda","first_name":"Tongda"},{"last_name":"Dai","full_name":"Dai, Ning","first_name":"Ning"},{"first_name":"Jisheng","full_name":"Chen, Jisheng","last_name":"Chen"},{"full_name":"Nagawa, Shingo","last_name":"Nagawa","first_name":"Shingo"},{"last_name":"Cao","full_name":"Cao, Min","first_name":"Min"},{"id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang","full_name":"Li, Hongjiang","orcid":"0000-0001-5039-9660","last_name":"Li"},{"full_name":"Zhou, Zimin","last_name":"Zhou","first_name":"Zimin"},{"id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu","last_name":"Chen","full_name":"Chen, Xu"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"first_name":"Hana","full_name":"Rakusová, Hana","last_name":"Rakusová"},{"first_name":"Wen","last_name":"Wang","full_name":"Wang, Wen"},{"last_name":"Jones","full_name":"Jones, Alan","first_name":"Alan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Patterson","full_name":"Patterson, Sara","first_name":"Sara"},{"last_name":"Bleecker","full_name":"Bleecker, Anthony","first_name":"Anthony"},{"last_name":"Yang","full_name":"Yang, Zhenbiao","first_name":"Zhenbiao"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"6174","volume":343,"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Auxin-binding protein 1 (ABP1) was discovered nearly 40 years ago and was shown to be essential for plant development and morphogenesis, but its mode of action remains unclear. Here, we report that the plasma membrane-localized transmembrane kinase (TMK) receptor-like kinases interact with ABP1 and transduce auxin signal to activate plasma membrane-associated ROPs [Rho-like guanosine triphosphatases (GTPase) from plants], leading to changes in the cytoskeleton and the shape of leaf pavement cells in Arabidopsis. The interaction between ABP1 and TMK at the cell surface is induced by auxin and requires ABP1 sensing of auxin. These findings show that TMK proteins and ABP1 form a cell surface auxin perception complex that activates ROP signaling pathways, regulating nontranscriptional cytoplasmic responses and associated fundamental processes."}],"intvolume":" 343","month":"02","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166562/","open_access":"1"}],"scopus_import":1,"date_updated":"2021-01-12T06:54:03Z","department":[{"_id":"JiFr"}],"_id":"1917","status":"public","article_type":"original","type":"journal_article"},{"title":"Distinct cerebellar engrams in short-term and long-term motor learning","department":[{"_id":"RySh"}],"publist_id":"5174","author":[{"first_name":"Wen","last_name":"Wang","full_name":"Wang, Wen"},{"last_name":"Nakadate","full_name":"Nakadate, Kazuhiko","first_name":"Kazuhiko"},{"first_name":"Miwako","full_name":"Masugi Tokita, Miwako","last_name":"Masugi Tokita"},{"first_name":"Fumihiro","last_name":"Shutoh","full_name":"Shutoh, Fumihiro"},{"first_name":"Wajeeha","full_name":"Aziz, Wajeeha","last_name":"Aziz"},{"full_name":"Tarusawa, Etsuko","last_name":"Tarusawa","first_name":"Etsuko"},{"first_name":"Andrea","full_name":"Lörincz, Andrea","last_name":"Lörincz"},{"full_name":"Molnár, Elek","last_name":"Molnár","first_name":"Elek"},{"full_name":"Kesaf, Sebnem","last_name":"Kesaf","first_name":"Sebnem","id":"401AB46C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yunqing","last_name":"Li","full_name":"Li, Yunqing"},{"last_name":"Fukazawa","full_name":"Fukazawa, Yugo","first_name":"Yugo"},{"first_name":"Soichi","full_name":"Nagao, Soichi","last_name":"Nagao"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:05Z","citation":{"chicago":"Wang, Wen, Kazuhiko Nakadate, Miwako Masugi Tokita, Fumihiro Shutoh, Wajeeha Aziz, Etsuko Tarusawa, Andrea Lörincz, et al. “Distinct Cerebellar Engrams in Short-Term and Long-Term Motor Learning.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1315541111.","ista":"Wang W, Nakadate K, Masugi Tokita M, Shutoh F, Aziz W, Tarusawa E, Lörincz A, Molnár E, Kesaf S, Li Y, Fukazawa Y, Nagao S, Shigemoto R. 2014. Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. 111(1), E188–E193.","mla":"Wang, Wen, et al. “Distinct Cerebellar Engrams in Short-Term and Long-Term Motor Learning.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. E188–93, doi:10.1073/pnas.1315541111.","apa":"Wang, W., Nakadate, K., Masugi Tokita, M., Shutoh, F., Aziz, W., Tarusawa, E., … Shigemoto, R. (2014). Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1315541111","ama":"Wang W, Nakadate K, Masugi Tokita M, et al. Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. 2014;111(1):E188-E193. doi:10.1073/pnas.1315541111","short":"W. Wang, K. Nakadate, M. Masugi Tokita, F. Shutoh, W. Aziz, E. Tarusawa, A. Lörincz, E. Molnár, S. Kesaf, Y. Li, Y. Fukazawa, S. Nagao, R. Shigemoto, PNAS 111 (2014) E188–E193.","ieee":"W. Wang et al., “Distinct cerebellar engrams in short-term and long-term motor learning,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. E188–E193, 2014."},"status":"public","type":"journal_article","_id":"1920","date_created":"2018-12-11T11:54:43Z","volume":111,"issue":"1","date_published":"2014-01-07T00:00:00Z","doi":"10.1073/pnas.1315541111","page":"E188 - E193","language":[{"iso":"eng"}],"publication":"PNAS","day":"07","publication_status":"published","year":"2014","intvolume":" 111","month":"01","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890858/","open_access":"1"}],"publisher":"National Academy of Sciences","scopus_import":1,"acknowledgement":"This work was supported by Solution-Oriented Research for Science and Technology from the Japan Science and Technology Agency; Ministry of Education, Culture, Sports, Science and Technology of Japan Grant 16300114 (to R.S.).","oa_version":"Submitted Version","abstract":[{"text":"Cerebellar motor learning is suggested to be caused by long-term plasticity of excitatory parallel fiber-Purkinje cell (PF-PC) synapses associated with changes in the number of synaptic AMPA-type glutamate receptors (AMPARs). However, whether the AMPARs decrease or increase in individual PF-PC synapses occurs in physiological motor learning and accounts for memory that lasts over days remains elusive. We combined quantitative SDS-digested freeze-fracture replica labeling for AMPAR and physical dissector electron microscopy with a simple model of cerebellar motor learning, adaptation of horizontal optokinetic response (HOKR) in mouse. After 1-h training of HOKR, short-term adaptation (STA) was accompanied with transient decrease in AMPARs by 28% in target PF-PC synapses. STA was well correlated with AMPAR decrease in individual animals and both STA and AMPAR decrease recovered to basal levels within 24 h. Surprisingly, long-termadaptation (LTA) after five consecutive daily trainings of 1-h HOKR did not alter the number of AMPARs in PF-PC synapses but caused gradual and persistent synapse elimination by 45%, with corresponding PC spine loss by the fifth training day. Furthermore, recovery of LTA after 2 wk was well correlated with increase of PF-PC synapses to the control level. Our findings indicate that the AMPARs decrease in PF-PC synapses and the elimination of these synapses are in vivo engrams in short- and long-term motor learning, respectively, showing a unique type of synaptic plasticity that may contribute to memory consolidation.","lang":"eng"}]},{"acknowledgement":"This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP], Central European Institute of Technology (CEITEC) [grant number CZ.1.05/1.1.00/02.0068], European Social Fund [grant number CZ.1.07/2.3.00/20.0043] and the Czec","publisher":"Portland Press","quality_controlled":"1","year":"2014","publication":"Biochemical Society Transactions","day":"01","page":"212 - 218","date_created":"2018-12-11T11:54:41Z","doi":"10.1042/BST20130269","date_published":"2014-02-01T00:00:00Z","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"citation":{"chicago":"Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant Cell Polarity.” Biochemical Society Transactions. Portland Press, 2014. https://doi.org/10.1042/BST20130269.","ista":"Chen X, Friml J. 2014. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. 42(1), 212–218.","mla":"Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant Cell Polarity.” Biochemical Society Transactions, vol. 42, no. 1, Portland Press, 2014, pp. 212–18, doi:10.1042/BST20130269.","ama":"Chen X, Friml J. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. 2014;42(1):212-218. doi:10.1042/BST20130269","apa":"Chen, X., & Friml, J. (2014). Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/BST20130269","short":"X. Chen, J. Friml, Biochemical Society Transactions 42 (2014) 212–218.","ieee":"X. Chen and J. Friml, “Rho-GTPase-regulated vesicle trafficking in plant cell polarity,” Biochemical Society Transactions, vol. 42, no. 1. Portland Press, pp. 212–218, 2014."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["24450654"]},"article_processing_charge":"No","author":[{"first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Xu"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publist_id":"5179","title":"Rho-GTPase-regulated vesicle trafficking in plant cell polarity","abstract":[{"lang":"eng","text":"ROPs (Rho of plants) belong to a large family of plant-specific Rho-like small GTPases that function as essential molecular switches to control diverse cellular processes including cytoskeleton organization, cell polarization, cytokinesis, cell differentiation and vesicle trafficking. Although the machineries of vesicle trafficking and cell polarity in plants have been individually well addressed, how ROPs co-ordinate those processes is still largely unclear. Recent progress has been made towards an understanding of the coordination of ROP signalling and trafficking of PIN (PINFORMED) transporters for the plant hormone auxin in both root and leaf pavement cells. PIN transporters constantly shuttle between the endosomal compartments and the polar plasma membrane domains, therefore the modulation of PIN-dependent auxin transport between cells is a main developmental output of ROP-regulated vesicle trafficking. The present review focuses on these cellular mechanisms, especially the integration of ROP-based vesicle trafficking and plant cell polarity."}],"oa_version":"None","pmid":1,"scopus_import":"1","intvolume":" 42","month":"02","publication_status":"published","publication_identifier":{"eissn":["1470-8752"],"issn":["0300-5127"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":42,"issue":"1","_id":"1915","type":"journal_article","article_type":"original","status":"public","date_updated":"2022-06-07T11:20:56Z","department":[{"_id":"JiFr"}]},{"_id":"1919","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Aziz, W., Wang, W., Kesaf, S., Mohamed, A., Fukazawa, Y., & Shigemoto, R. (2014). Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1303317110","ama":"Aziz W, Wang W, Kesaf S, Mohamed A, Fukazawa Y, Shigemoto R. Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. 2014;111(1):E194-E202. doi:10.1073/pnas.1303317110","ieee":"W. Aziz, W. Wang, S. Kesaf, A. Mohamed, Y. Fukazawa, and R. Shigemoto, “Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. E194–E202, 2014.","short":"W. Aziz, W. Wang, S. Kesaf, A. Mohamed, Y. Fukazawa, R. Shigemoto, PNAS 111 (2014) E194–E202.","mla":"Aziz, Wajeeha, et al. “Distinct Kinetics of Synaptic Structural Plasticity, Memory Formation, and Memory Decay in Massed and Spaced Learning.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. E194–202, doi:10.1073/pnas.1303317110.","ista":"Aziz W, Wang W, Kesaf S, Mohamed A, Fukazawa Y, Shigemoto R. 2014. Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. 111(1), E194–E202.","chicago":"Aziz, Wajeeha, Wen Wang, Sebnem Kesaf, Alsayed Mohamed, Yugo Fukazawa, and Ryuichi Shigemoto. “Distinct Kinetics of Synaptic Structural Plasticity, Memory Formation, and Memory Decay in Massed and Spaced Learning.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1303317110."},"date_updated":"2021-01-12T06:54:04Z","department":[{"_id":"RySh"}],"title":"Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning","publist_id":"5175","author":[{"full_name":"Aziz, Wajeeha","last_name":"Aziz","first_name":"Wajeeha"},{"full_name":"Wang, Wen","last_name":"Wang","first_name":"Wen"},{"first_name":"Sebnem","id":"401AB46C-F248-11E8-B48F-1D18A9856A87","last_name":"Kesaf","full_name":"Kesaf, Sebnem"},{"full_name":"Mohamed, Alsayed","last_name":"Mohamed","first_name":"Alsayed"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"}],"acknowledgement":"his work was supported by Solution Oriented Research for Science and Technology (R.S.), Core Research for Evolutional Science and Technology, Japan Science and Technology Agency (Y.F.), and Grants-in-Aid for Scientific Research on Priority Areas-Molecular Brain Sciences 16300114 (to R.S.) and 18022043 (to Y.F.).","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Long-lasting memories are formed when the stimulus is temporally distributed (spacing effect). However, the synaptic mechanisms underlying this robust phenomenon and the precise time course of the synaptic modifications that occur during learning remain unclear. Here we examined the adaptation of horizontal optokinetic response in mice that underwent 1 h of massed and spaced training at varying intervals. Despite similar acquisition by all training protocols, 1 h of spacing produced the highest memory retention at 24 h, which lasted for 1 mo. The distinct kinetics of memory are strongly correlated with the reduction of floccular parallel fiber-Purkinje cell synapses but not with AMPA receptor (AMPAR) number and synapse size. After the spaced training, we observed 25%, 23%, and 12% reduction in AMPAR density, synapse size, and synapse number, respectively. Four hours after the spaced training, half of the synapses and Purkinje cell spines had been eliminated, whereas AMPAR density and synapse size were recovered in remaining synapses. Surprisingly, massed training also produced long-term memory and halving of synapses; however, this occurred slowly over days, and the memory lasted for only 1 wk. This distinct kinetics of structural plasticity may serve as a basis for unique temporal profiles in the formation and decay of memory with or without intervals."}],"intvolume":" 111","month":"01","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890840/","open_access":"1"}],"publisher":"National Academy of Sciences","scopus_import":1,"publication":"PNAS","language":[{"iso":"eng"}],"day":"07","year":"2014","publication_status":"published","date_created":"2018-12-11T11:54:43Z","doi":"10.1073/pnas.1303317110","issue":"1","volume":111,"date_published":"2014-01-07T00:00:00Z","page":"E194 - E202"},{"_id":"1918","type":"journal_article","status":"public","date_updated":"2021-01-12T06:54:04Z","department":[{"_id":"RoSe"}],"abstract":[{"text":"As the nuclear charge Z is continuously decreased an N-electron atom undergoes a binding-unbinding transition. We investigate whether the electrons remain bound and whether the radius of the system stays finite as the critical value Zc is approached. Existence of a ground state at Zc is shown under the condition Zc < N-K, where K is the maximal number of electrons that can be removed at Zc without changing the energy.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1301.5370"}],"month":"02","intvolume":" 26","publication_status":"published","language":[{"iso":"eng"}],"volume":26,"issue":"1","article_number":"1350021","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Bellazzini J, Frank R, Lieb É, Seiringer R. 2014. Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. 26(1), 1350021.","chicago":"Bellazzini, Jacopo, Rupert Frank, Élliott Lieb, and Robert Seiringer. “Existence of Ground States for Negative Ions at the Binding Threshold.” Reviews in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X13500219.","ieee":"J. Bellazzini, R. Frank, É. Lieb, and R. Seiringer, “Existence of ground states for negative ions at the binding threshold,” Reviews in Mathematical Physics, vol. 26, no. 1. World Scientific Publishing, 2014.","short":"J. Bellazzini, R. Frank, É. Lieb, R. Seiringer, Reviews in Mathematical Physics 26 (2014).","ama":"Bellazzini J, Frank R, Lieb É, Seiringer R. Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. 2014;26(1). doi:10.1142/S0129055X13500219","apa":"Bellazzini, J., Frank, R., Lieb, É., & Seiringer, R. (2014). Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X13500219","mla":"Bellazzini, Jacopo, et al. “Existence of Ground States for Negative Ions at the Binding Threshold.” Reviews in Mathematical Physics, vol. 26, no. 1, 1350021, World Scientific Publishing, 2014, doi:10.1142/S0129055X13500219."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jacopo","full_name":"Bellazzini, Jacopo","last_name":"Bellazzini"},{"first_name":"Rupert","full_name":"Frank, Rupert","last_name":"Frank"},{"first_name":"Élliott","full_name":"Lieb, Élliott","last_name":"Lieb"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5176","title":"Existence of ground states for negative ions at the binding threshold","quality_controlled":"1","publisher":"World Scientific Publishing","oa":1,"year":"2014","day":"01","publication":"Reviews in Mathematical Physics","date_published":"2014-02-01T00:00:00Z","doi":"10.1142/S0129055X13500219","date_created":"2018-12-11T11:54:42Z"},{"publist_id":"5180","author":[{"first_name":"Michael","last_name":"Sauer","full_name":"Sauer, Michael"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"title":"Plant biology: Gatekeepers of the road to protein perdition","department":[{"_id":"JiFr"}],"citation":{"short":"M. Sauer, J. Friml, Current Biology 24 (2014) R27–R29.","ieee":"M. Sauer and J. Friml, “Plant biology: Gatekeepers of the road to protein perdition,” Current Biology, vol. 24, no. 1. Cell Press, pp. R27–R29, 2014.","ama":"Sauer M, Friml J. Plant biology: Gatekeepers of the road to protein perdition. Current Biology. 2014;24(1):R27-R29. doi:10.1016/j.cub.2013.11.019","apa":"Sauer, M., & Friml, J. (2014). Plant biology: Gatekeepers of the road to protein perdition. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.11.019","mla":"Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to Protein Perdition.” Current Biology, vol. 24, no. 1, Cell Press, 2014, pp. R27–29, doi:10.1016/j.cub.2013.11.019.","ista":"Sauer M, Friml J. 2014. Plant biology: Gatekeepers of the road to protein perdition. Current Biology. 24(1), R27–R29.","chicago":"Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to Protein Perdition.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2013.11.019."},"date_updated":"2021-01-12T06:54:02Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1914","page":"R27 - R29","volume":24,"date_published":"2014-01-06T00:00:00Z","issue":"1","doi":"10.1016/j.cub.2013.11.019","date_created":"2018-12-11T11:54:41Z","publication_status":"published","year":"2014","day":"06","publication":"Current Biology","language":[{"iso":"eng"}],"quality_controlled":"1","scopus_import":1,"publisher":"Cell Press","month":"01","intvolume":" 24","abstract":[{"lang":"eng","text":"Targeting membrane proteins for degradation requires the sequential action of ESCRT sub-complexes ESCRT-0 to ESCRT-III. Although this machinery is generally conserved among kingdoms, plants lack the essential ESCRT-0 components. A new report closes this gap by identifying a novel protein family that substitutes for ESCRT-0 function in plants."}],"oa_version":"None"},{"publisher":"IOP Publishing","oa":1,"acknowledgement":"This work was supported by EC grant Marie Curie RTN-CT-2006-035616, CARBIO 'Carbon nanotubes for biomedical applications' and Austrian FFG grant mnt-era.net 823980, 'IntelliTip'.\r\n","date_published":"2014-03-28T00:00:00Z","doi":"10.1088/0957-4484/25/12/125704","date_created":"2018-12-11T11:54:45Z","has_accepted_license":"1","year":"2014","day":"28","publication":"Nanotechnology","article_number":"125704","author":[{"full_name":"Lamprecht, Constanze","last_name":"Lamprecht","first_name":"Constanze"},{"full_name":"Plochberger, Birgit","last_name":"Plochberger","first_name":"Birgit"},{"first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena"},{"last_name":"Wieser","orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan","first_name":"Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","last_name":"Rankl","full_name":"Rankl, Christian"},{"first_name":"Elena","last_name":"Heister","full_name":"Heister, Elena"},{"full_name":"Unterauer, Barbara","last_name":"Unterauer","first_name":"Barbara"},{"first_name":"Mario","last_name":"Brameshuber","full_name":"Brameshuber, Mario"},{"first_name":"Jürgen","last_name":"Danzberger","full_name":"Danzberger, Jürgen"},{"last_name":"Lukanov","full_name":"Lukanov, Petar","first_name":"Petar"},{"last_name":"Flahaut","full_name":"Flahaut, Emmanuel","first_name":"Emmanuel"},{"last_name":"Schütz","full_name":"Schütz, Gerhard","first_name":"Gerhard"},{"first_name":"Peter","full_name":"Hinterdorfer, Peter","last_name":"Hinterdorfer"},{"full_name":"Ebner, Andreas","last_name":"Ebner","first_name":"Andreas"}],"publist_id":"5169","article_processing_charge":"No","title":"A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes","citation":{"ama":"Lamprecht C, Plochberger B, Ruprecht V, et al. A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. 2014;25(12). doi:10.1088/0957-4484/25/12/125704","apa":"Lamprecht, C., Plochberger, B., Ruprecht, V., Wieser, S., Rankl, C., Heister, E., … Ebner, A. (2014). A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. IOP Publishing. https://doi.org/10.1088/0957-4484/25/12/125704","ieee":"C. Lamprecht et al., “A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes,” Nanotechnology, vol. 25, no. 12. IOP Publishing, 2014.","short":"C. Lamprecht, B. Plochberger, V. Ruprecht, S. Wieser, C. Rankl, E. Heister, B. Unterauer, M. Brameshuber, J. Danzberger, P. Lukanov, E. Flahaut, G. Schütz, P. Hinterdorfer, A. Ebner, Nanotechnology 25 (2014).","mla":"Lamprecht, Constanze, et al. “A Single-Molecule Approach to Explore Binding Uptake and Transport of Cancer Cell Targeting Nanotubes.” Nanotechnology, vol. 25, no. 12, 125704, IOP Publishing, 2014, doi:10.1088/0957-4484/25/12/125704.","ista":"Lamprecht C, Plochberger B, Ruprecht V, Wieser S, Rankl C, Heister E, Unterauer B, Brameshuber M, Danzberger J, Lukanov P, Flahaut E, Schütz G, Hinterdorfer P, Ebner A. 2014. A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. 25(12), 125704.","chicago":"Lamprecht, Constanze, Birgit Plochberger, Verena Ruprecht, Stefan Wieser, Christian Rankl, Elena Heister, Barbara Unterauer, et al. “A Single-Molecule Approach to Explore Binding Uptake and Transport of Cancer Cell Targeting Nanotubes.” Nanotechnology. IOP Publishing, 2014. https://doi.org/10.1088/0957-4484/25/12/125704."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"month":"03","intvolume":" 25","abstract":[{"text":"In the past decade carbon nanotubes (CNTs) have been widely studied as a potential drug-delivery system, especially with functionality for cellular targeting. Yet, little is known about the actual process of docking to cell receptors and transport dynamics after internalization. Here we performed single-particle studies of folic acid (FA) mediated CNT binding to human carcinoma cells and their transport inside the cytosol. In particular, we employed molecular recognition force spectroscopy, an atomic force microscopy based method, to visualize and quantify docking of FA functionalized CNTs to FA binding receptors in terms of binding probability and binding force. We then traced individual fluorescently labeled, FA functionalized CNTs after specific uptake, and created a dynamic 'roadmap' that clearly showed trajectories of directed diffusion and areas of nanotube confinement in the cytosol. Our results demonstrate the potential of a single-molecule approach for investigation of drug-delivery vehicles and their targeting capacity.","lang":"eng"}],"oa_version":"Submitted Version","issue":"12","volume":25,"publication_status":"published","file":[{"creator":"dernst","file_size":3804152,"date_updated":"2020-07-14T12:45:21Z","file_name":"2014_Nanotechnology_Lamprecht.pdf","date_created":"2020-05-15T09:21:19Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"df4e03d225a19179e7790f6d87a12332","file_id":"7856"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"1925","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:45:21Z","date_updated":"2021-01-12T06:54:07Z","ddc":["570"]}]