[{"acknowledgement":"HYCON2; EC; European Commission\r\n","oa_version":"None","abstract":[{"lang":"eng","text":"Continuous-time Markov chains are commonly used in practice for modeling biochemical reaction networks in which the inherent randomness of themolecular interactions cannot be ignored. This has motivated recent research effort into methods for parameter inference and experiment design for such models. The major difficulty is that such methods usually require one to iteratively solve the chemical master equation that governs the time evolution of the probability distribution of the system. This, however, is rarely possible, and even approximation techniques remain limited to relatively small and simple systems. An alternative explored in this article is to base methods on only some low-order moments of the entire probability distribution. We summarize the theory behind such moment-based methods for parameter inference and experiment design and provide new case studies where we investigate their performance."}],"intvolume":" 25","month":"02","scopus_import":1,"publisher":"ACM","quality_controlled":"1","publication":"ACM Transactions on Modeling and Computer Simulation","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2015","date_created":"2018-12-11T11:54:25Z","date_published":"2015-02-01T00:00:00Z","issue":"2","doi":"10.1145/2688906","volume":25,"article_number":"8","_id":"1861","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:41Z","citation":{"apa":"Ruess, J., & Lygeros, J. (2015). Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. ACM. https://doi.org/10.1145/2688906","ama":"Ruess J, Lygeros J. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 2015;25(2). doi:10.1145/2688906","short":"J. Ruess, J. Lygeros, ACM Transactions on Modeling and Computer Simulation 25 (2015).","ieee":"J. Ruess and J. Lygeros, “Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks,” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2. ACM, 2015.","mla":"Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2, 8, ACM, 2015, doi:10.1145/2688906.","ista":"Ruess J, Lygeros J. 2015. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 25(2), 8.","chicago":"Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” ACM Transactions on Modeling and Computer Simulation. ACM, 2015. https://doi.org/10.1145/2688906."},"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"title":"Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks","author":[{"last_name":"Ruess","orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob"},{"last_name":"Lygeros","full_name":"Lygeros, John","first_name":"John"}],"publist_id":"5238"},{"language":[{"iso":"eng"}],"publication":"Communications of the ACM","day":"28","year":"2015","publication_status":"published","date_created":"2018-12-11T11:54:26Z","doi":"10.1145/2701001","date_published":"2015-01-28T00:00:00Z","volume":58,"issue":"2","page":"86-86","oa_version":"None","intvolume":" 58","month":"01","scopus_import":1,"publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Henzinger, Thomas A, and Jean Raskin. “The Equivalence Problem for Finite Automata: Technical Perspective.” Communications of the ACM. ACM, 2015. https://doi.org/10.1145/2701001.","ista":"Henzinger TA, Raskin J. 2015. The equivalence problem for finite automata: Technical perspective. Communications of the ACM. 58(2), 86–86.","mla":"Henzinger, Thomas A., and Jean Raskin. “The Equivalence Problem for Finite Automata: Technical Perspective.” Communications of the ACM, vol. 58, no. 2, ACM, 2015, pp. 86–86, doi:10.1145/2701001.","ama":"Henzinger TA, Raskin J. The equivalence problem for finite automata: Technical perspective. Communications of the ACM. 2015;58(2):86-86. doi:10.1145/2701001","apa":"Henzinger, T. A., & Raskin, J. (2015). The equivalence problem for finite automata: Technical perspective. Communications of the ACM. ACM. https://doi.org/10.1145/2701001","short":"T.A. Henzinger, J. Raskin, Communications of the ACM 58 (2015) 86–86.","ieee":"T. A. Henzinger and J. Raskin, “The equivalence problem for finite automata: Technical perspective,” Communications of the ACM, vol. 58, no. 2. ACM, pp. 86–86, 2015."},"date_updated":"2021-01-12T06:53:43Z","title":"The equivalence problem for finite automata: Technical perspective","department":[{"_id":"ToHe"}],"publist_id":"5232","author":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Jean","full_name":"Raskin, Jean","last_name":"Raskin"}],"_id":"1866","status":"public","type":"journal_article"},{"author":[{"first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","last_name":"Grones","full_name":"Grones, Peter"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5225","title":"Auxin transporters and binding proteins at a glance","citation":{"mla":"Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at a Glance.” Journal of Cell Science, vol. 128, no. 1, Company of Biologists, 2015, pp. 1–7, doi:10.1242/jcs.159418.","ama":"Grones P, Friml J. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 2015;128(1):1-7. doi:10.1242/jcs.159418","apa":"Grones, P., & Friml, J. (2015). Auxin transporters and binding proteins at a glance. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.159418","ieee":"P. Grones and J. Friml, “Auxin transporters and binding proteins at a glance,” Journal of Cell Science, vol. 128, no. 1. Company of Biologists, pp. 1–7, 2015.","short":"P. Grones, J. Friml, Journal of Cell Science 128 (2015) 1–7.","chicago":"Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at a Glance.” Journal of Cell Science. Company of Biologists, 2015. https://doi.org/10.1242/jcs.159418.","ista":"Grones P, Friml J. 2015. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 128(1), 1–7."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1 - 7","date_created":"2018-12-11T11:54:28Z","date_published":"2015-01-01T00:00:00Z","doi":"10.1242/jcs.159418","year":"2015","has_accepted_license":"1","publication":"Journal of Cell Science","day":"01","oa":1,"publisher":"Company of Biologists","quality_controlled":"1","acknowledgement":"This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP]; European Social Fund [grant number CZ.1.07/2.3.00/20.0043] and the Czech Science Foundation GAČR [grant number GA13-40637S]","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:53:45Z","ddc":["570"],"type":"journal_article","pubrep_id":"563","status":"public","_id":"1871","issue":"1","volume":128,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:11:00Z","file_name":"IST-2016-563-v1+1_1.full.pdf","date_updated":"2020-07-14T12:45:19Z","file_size":1688844,"creator":"system","checksum":"24c779f4cd9d549ca6833e26f486be27","file_id":"4852","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"scopus_import":1,"intvolume":" 128","month":"01","abstract":[{"lang":"eng","text":"The plant hormone auxin is a key regulator of plant growth and development. Differences in auxin distribution within tissues are mediated by the polar auxin transport machinery, and cellular auxin responses occur depending on changes in cellular auxin levels. Multiple receptor systems at the cell surface and in the interior operate to sense and interpret fluctuations in auxin distribution that occur during plant development. Until now, three proteins or protein complexes that can bind auxin have been identified. SCFTIR1 [a SKP1-cullin-1-F-box complex that contains transport inhibitor response 1 (TIR1) as the F-box protein] and S-phase-kinaseassociated protein 2 (SKP2) localize to the nucleus, whereas auxinbinding protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and cell surface. In this Cell Science at a Glance article, we summarize recent discoveries in the field of auxin transport and signaling that have led to the identification of new components of these pathways, as well as their mutual interaction."}],"oa_version":"Submitted Version"},{"publication_status":"published","year":"2015","day":"01","language":[{"iso":"eng"}],"publication":"Hippocampus","page":"838 - 857","volume":25,"doi":"10.1002/hipo.22407","issue":"7","date_published":"2015-07-01T00:00:00Z","date_created":"2018-12-11T11:54:29Z","abstract":[{"text":"The hippocampal region, comprising the hippocampal formation and the parahippocampal region, has been one of the most intensively studied parts of the brain for decades. Better understanding of its functional diversity and complexity has led to an increased demand for specificity in experimental procedures and manipulations. In view of the complex 3D structure of the hippocampal region, precisely positioned experimental approaches require a fine-grained architectural description that is available and readable to experimentalists lacking detailed anatomical experience. In this paper, we provide the first cyto- and chemoarchitectural description of the hippocampal formation and parahippocampal region in the rat at high resolution and in the three standard sectional planes: coronal, horizontal and sagittal. The atlas uses a series of adjacent sections stained for neurons and for a number of chemical marker substances, particularly parvalbumin and calbindin. All the borders defined in one plane have been cross-checked against their counterparts in the other two planes. The entire dataset will be made available as a web-based interactive application through the Rodent Brain WorkBench (http://www.rbwb.org) which, together with this paper, provides a unique atlas resource.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","scopus_import":1,"publisher":"Wiley","month":"07","intvolume":" 25","date_updated":"2021-01-12T06:53:46Z","citation":{"ista":"Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. 2015. A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. 25(7), 838–857.","chicago":"Boccara, Charlotte N., Lisa Kjønigsen, Ingvild Hammer, Jan Bjaalie, Trygve Leergaard, and Menno Witter. “A Three-Plane Architectonic Atlas of the Rat Hippocampal Region.” Hippocampus. Wiley, 2015. https://doi.org/10.1002/hipo.22407.","ieee":"C. N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, and M. Witter, “A three-plane architectonic atlas of the rat hippocampal region,” Hippocampus, vol. 25, no. 7. Wiley, pp. 838–857, 2015.","short":"C.N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, M. Witter, Hippocampus 25 (2015) 838–857.","apa":"Boccara, C. N., Kjønigsen, L., Hammer, I., Bjaalie, J., Leergaard, T., & Witter, M. (2015). A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. Wiley. https://doi.org/10.1002/hipo.22407","ama":"Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. 2015;25(7):838-857. doi:10.1002/hipo.22407","mla":"Boccara, Charlotte N., et al. “A Three-Plane Architectonic Atlas of the Rat Hippocampal Region.” Hippocampus, vol. 25, no. 7, Wiley, 2015, pp. 838–57, doi:10.1002/hipo.22407."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Charlotte","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","full_name":"Boccara, Charlotte","orcid":"0000-0001-7237-5109","last_name":"Boccara"},{"first_name":"Lisa","last_name":"Kjønigsen","full_name":"Kjønigsen, Lisa"},{"first_name":"Ingvild","full_name":"Hammer, Ingvild","last_name":"Hammer"},{"last_name":"Bjaalie","full_name":"Bjaalie, Jan","first_name":"Jan"},{"last_name":"Leergaard","full_name":"Leergaard, Trygve","first_name":"Trygve"},{"first_name":"Menno","full_name":"Witter, Menno","last_name":"Witter"}],"publist_id":"5222","department":[{"_id":"JoCs"}],"title":"A three-plane architectonic atlas of the rat hippocampal region","_id":"1874","type":"journal_article","status":"public"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” Artificial Intelligence, vol. 221, Elsevier, 2015, pp. 46–72, doi:10.1016/j.artint.2014.12.009.","short":"K. Chatterjee, M. Chmelik, Artificial Intelligence 221 (2015) 46–72.","ieee":"K. Chatterjee and M. Chmelik, “POMDPs under probabilistic semantics,” Artificial Intelligence, vol. 221. Elsevier, pp. 46–72, 2015.","ama":"Chatterjee K, Chmelik M. POMDPs under probabilistic semantics. Artificial Intelligence. 2015;221:46-72. doi:10.1016/j.artint.2014.12.009","apa":"Chatterjee, K., & Chmelik, M. (2015). POMDPs under probabilistic semantics. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2014.12.009","chicago":"Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” Artificial Intelligence. Elsevier, 2015. https://doi.org/10.1016/j.artint.2014.12.009.","ista":"Chatterjee K, Chmelik M. 2015. POMDPs under probabilistic semantics. Artificial Intelligence. 221, 46–72."},"date_updated":"2021-01-12T06:53:46Z","title":"POMDPs under probabilistic semantics","department":[{"_id":"KrCh"}],"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin","last_name":"Chmelik"}],"publist_id":"5224","external_id":{"arxiv":["1408.2058"]},"_id":"1873","status":"public","type":"journal_article","day":"01","publication":"Artificial Intelligence","language":[{"iso":"eng"}],"publication_status":"published","year":"2015","doi":"10.1016/j.artint.2014.12.009","date_published":"2015-04-01T00:00:00Z","volume":221,"date_created":"2018-12-11T11:54:28Z","page":"46 - 72","oa_version":"Preprint","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with limit-average payoff, where a reward value in the interval [0,1] is associated with every transition, and the payoff of an infinite path is the long-run average of the rewards. We consider two types of path constraints: (i) a quantitative constraint defines the set of paths where the payoff is at least a given threshold λ1ε(0,1]; and (ii) a qualitative constraint which is a special case of the quantitative constraint with λ1=1. We consider the computation of the almost-sure winning set, where the controller needs to ensure that the path constraint is satisfied with probability 1. Our main results for qualitative path constraints are as follows: (i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory controller is undecidable. For quantitative path constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We also present a prototype implementation of our EXPTIME algorithm and experimental results on several examples.","lang":"eng"}],"month":"04","intvolume":" 221","quality_controlled":"1","scopus_import":1,"publisher":"Elsevier","main_file_link":[{"url":"https://arxiv.org/abs/1408.2058","open_access":"1"}],"oa":1},{"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":"459","status":"public","_id":"1879","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:53:48Z","ddc":["570"],"scopus_import":1,"intvolume":" 259","month":"08","abstract":[{"text":"When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions.","lang":"eng"}],"oa_version":"Published Version","issue":"2","volume":259,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-459-v1+1_KREMER_et_al-2015-Journal_of_Microscopy.pdf","date_created":"2018-12-12T10:11:19Z","creator":"system","file_size":2899898,"date_updated":"2020-07-14T12:45:19Z","file_id":"4872","checksum":"3649c5372d1644062d728ea9287e367f","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publist_id":"5218","author":[{"first_name":"A","full_name":"Kremer, A","last_name":"Kremer"},{"first_name":"Stefaan","full_name":"Lippens, Stefaan","last_name":"Lippens"},{"last_name":"Bartunkova","full_name":"Bartunkova, Sonia","first_name":"Sonia"},{"first_name":"Bob","full_name":"Asselbergh, Bob","last_name":"Asselbergh"},{"first_name":"Cendric","full_name":"Blanpain, Cendric","last_name":"Blanpain"},{"first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699"},{"first_name":"A","full_name":"Goossens, A","last_name":"Goossens"},{"full_name":"Holt, Matthew","last_name":"Holt","first_name":"Matthew"},{"last_name":"Janssens","full_name":"Janssens, Sophie","first_name":"Sophie"},{"first_name":"Michiel","full_name":"Krols, Michiel","last_name":"Krols"},{"full_name":"Larsimont, Jean","last_name":"Larsimont","first_name":"Jean"},{"first_name":"Conor","last_name":"Mc Guire","full_name":"Mc Guire, Conor"},{"last_name":"Nowack","full_name":"Nowack, Moritz","first_name":"Moritz"},{"full_name":"Saelens, Xavier","last_name":"Saelens","first_name":"Xavier"},{"full_name":"Schertel, Andreas","last_name":"Schertel","first_name":"Andreas"},{"first_name":"B","last_name":"Schepens","full_name":"Schepens, B"},{"first_name":"M","full_name":"Slezak, M","last_name":"Slezak"},{"full_name":"Timmerman, Vincent","last_name":"Timmerman","first_name":"Vincent"},{"first_name":"Clara","last_name":"Theunis","full_name":"Theunis, Clara"},{"first_name":"Ronald","full_name":"Van Brempt, Ronald","last_name":"Van Brempt"},{"first_name":"Y","last_name":"Visser","full_name":"Visser, Y"},{"first_name":"Christophe","full_name":"Guérin, Christophe","last_name":"Guérin"}],"title":"Developing 3D SEM in a broad biological context","citation":{"chicago":"Kremer, A, Stefaan Lippens, Sonia Bartunkova, Bob Asselbergh, Cendric Blanpain, Matyas Fendrych, A Goossens, et al. “Developing 3D SEM in a Broad Biological Context.” Journal of Microscopy. Wiley-Blackwell, 2015. https://doi.org/10.1111/jmi.12211.","ista":"Kremer A, Lippens S, Bartunkova S, Asselbergh B, Blanpain C, Fendrych M, Goossens A, Holt M, Janssens S, Krols M, Larsimont J, Mc Guire C, Nowack M, Saelens X, Schertel A, Schepens B, Slezak M, Timmerman V, Theunis C, Van Brempt R, Visser Y, Guérin C. 2015. Developing 3D SEM in a broad biological context. Journal of Microscopy. 259(2), 80–96.","mla":"Kremer, A., et al. “Developing 3D SEM in a Broad Biological Context.” Journal of Microscopy, vol. 259, no. 2, Wiley-Blackwell, 2015, pp. 80–96, doi:10.1111/jmi.12211.","ieee":"A. Kremer et al., “Developing 3D SEM in a broad biological context,” Journal of Microscopy, vol. 259, no. 2. Wiley-Blackwell, pp. 80–96, 2015.","short":"A. Kremer, S. Lippens, S. Bartunkova, B. Asselbergh, C. Blanpain, M. Fendrych, A. Goossens, M. Holt, S. Janssens, M. Krols, J. Larsimont, C. Mc Guire, M. Nowack, X. Saelens, A. Schertel, B. Schepens, M. Slezak, V. Timmerman, C. Theunis, R. Van Brempt, Y. Visser, C. Guérin, Journal of Microscopy 259 (2015) 80–96.","apa":"Kremer, A., Lippens, S., Bartunkova, S., Asselbergh, B., Blanpain, C., Fendrych, M., … Guérin, C. (2015). Developing 3D SEM in a broad biological context. Journal of Microscopy. Wiley-Blackwell. https://doi.org/10.1111/jmi.12211","ama":"Kremer A, Lippens S, Bartunkova S, et al. Developing 3D SEM in a broad biological context. Journal of Microscopy. 2015;259(2):80-96. doi:10.1111/jmi.12211"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","acknowledgement":"The Zeiss Merlin with Gatan 3View2XP and Zeiss Auriga were acquired through a CLEM grant from Minister Ingrid Lieten to the VIB Bio-Imaging-Core. Michiel Krols and Saskia Lippens are the recipients of a fellowship from the FWO (Fonds Wetenschappelijk Onderzoek) of Flanders.","page":"80 - 96","date_created":"2018-12-11T11:54:30Z","date_published":"2015-08-01T00:00:00Z","doi":"10.1111/jmi.12211","year":"2015","has_accepted_license":"1","publication":"Journal of Microscopy","day":"01"},{"_id":"1880","status":"public","pubrep_id":"447","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)"},"ddc":["530"],"date_updated":"2021-01-12T06:53:48Z","file_date_updated":"2020-07-14T12:45:20Z","department":[{"_id":"RoSe"}],"oa_version":"Published Version","abstract":[{"text":"We investigate the relation between Bose-Einstein condensation (BEC) and superfluidity in the ground state of a one-dimensional model of interacting bosons in a strong random potential. We prove rigorously that in a certain parameter regime the superfluid fraction can be arbitrarily small while complete BEC prevails. In another regime there is both complete BEC and complete superfluidity, despite the strong disorder","lang":"eng"}],"month":"01","intvolume":" 17","scopus_import":1,"file":[{"creator":"system","file_size":768108,"date_updated":"2020-07-14T12:45:20Z","file_name":"IST-2016-447-v1+1_document_1_.pdf","date_created":"2018-12-12T10:12:44Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4963","checksum":"38fdf2b5ac30445e26a5d613abd84b16"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":17,"article_number":"013022","project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Könenberg, Martin, et al. “Superfluid Behavior of a Bose-Einstein Condensate in a Random Potential.” New Journal of Physics, vol. 17, 013022, IOP Publishing Ltd., 2015, doi:10.1088/1367-2630/17/1/013022.","ama":"Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. 2015;17. doi:10.1088/1367-2630/17/1/013022","apa":"Könenberg, M., Moser, T., Seiringer, R., & Yngvason, J. (2015). Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/17/1/013022","ieee":"M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluid behavior of a Bose-Einstein condensate in a random potential,” New Journal of Physics, vol. 17. IOP Publishing Ltd., 2015.","short":"M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, New Journal of Physics 17 (2015).","chicago":"Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason. “Superfluid Behavior of a Bose-Einstein Condensate in a Random Potential.” New Journal of Physics. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1367-2630/17/1/013022.","ista":"Könenberg M, Moser T, Seiringer R, Yngvason J. 2015. Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. 17, 013022."},"title":"Superfluid behavior of a Bose-Einstein condensate in a random potential","author":[{"full_name":"Könenberg, Martin","last_name":"Könenberg","first_name":"Martin"},{"full_name":"Moser, Thomas","last_name":"Moser","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"},{"first_name":"Jakob","last_name":"Yngvason","full_name":"Yngvason, Jakob"}],"publist_id":"5214","acknowledgement":"Support from the Natural Sciences and Engineering Research Council of Canada NSERC (MK and RS) and from the Austrian Science Fund FWF (JY, under project P 22929-N16) is gratefully acknowledged","quality_controlled":"1","publisher":"IOP Publishing Ltd.","oa":1,"day":"15","publication":"New Journal of Physics","has_accepted_license":"1","year":"2015","date_published":"2015-01-15T00:00:00Z","doi":"10.1088/1367-2630/17/1/013022","date_created":"2018-12-11T11:54:30Z"},{"title":"Compositionality for quantitative specifications","author":[{"full_name":"Fahrenberg, Uli","last_name":"Fahrenberg","first_name":"Uli"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Legay","full_name":"Legay, Axel","first_name":"Axel"},{"first_name":"Louis","full_name":"Traonouez, Louis","last_name":"Traonouez"}],"publist_id":"5216","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Fahrenberg, Uli, et al. Compositionality for Quantitative Specifications. Vol. 8997, Springer, 2015, pp. 306–24, doi:10.1007/978-3-319-15317-9_19.","short":"U. Fahrenberg, J. Kretinsky, A. Legay, L. Traonouez, in:, Springer, 2015, pp. 306–324.","ieee":"U. Fahrenberg, J. Kretinsky, A. Legay, and L. Traonouez, “Compositionality for quantitative specifications,” presented at the FACS: Formal Aspects of Component Software, Bertinoro, Italy, 2015, vol. 8997, pp. 306–324.","ama":"Fahrenberg U, Kretinsky J, Legay A, Traonouez L. Compositionality for quantitative specifications. In: Vol 8997. Springer; 2015:306-324. doi:10.1007/978-3-319-15317-9_19","apa":"Fahrenberg, U., Kretinsky, J., Legay, A., & Traonouez, L. (2015). Compositionality for quantitative specifications (Vol. 8997, pp. 306–324). Presented at the FACS: Formal Aspects of Component Software, Bertinoro, Italy: Springer. https://doi.org/10.1007/978-3-319-15317-9_19","chicago":"Fahrenberg, Uli, Jan Kretinsky, Axel Legay, and Louis Traonouez. “Compositionality for Quantitative Specifications,” 8997:306–24. Springer, 2015. https://doi.org/10.1007/978-3-319-15317-9_19.","ista":"Fahrenberg U, Kretinsky J, Legay A, Traonouez L. 2015. Compositionality for quantitative specifications. FACS: Formal Aspects of Component Software, LNCS, vol. 8997, 306–324."},"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_created":"2018-12-11T11:54:31Z","date_published":"2015-01-30T00:00:00Z","doi":"10.1007/978-3-319-15317-9_19","page":"306 - 324","day":"30","year":"2015","oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) project S11402-N23 (RiSE), and by the Czech Science Foundation, grant No. P202/12/G061.","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"date_updated":"2021-01-12T06:53:49Z","status":"public","conference":{"name":"FACS: Formal Aspects of Component Software","location":"Bertinoro, Italy","end_date":"2014-09-12","start_date":"2014-09-10"},"type":"conference","_id":"1882","ec_funded":1,"volume":8997,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 8997","month":"01","main_file_link":[{"url":"http://arxiv.org/abs/1408.1256","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"We provide a framework for compositional and iterative design and verification of systems with quantitative information, such as rewards, time or energy. It is based on disjunctive modal transition systems where we allow actions to bear various types of quantitative information. Throughout the design process the actions can be further refined and the information made more precise. We show how to compute the results of standard operations on the systems, including the quotient (residual), which has not been previously considered for quantitative non-deterministic systems. Our quantitative framework has close connections to the modal nu-calculus and is compositional with respect to general notions of distances between systems and the standard operations.","lang":"eng"}]},{"citation":{"ieee":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm, “Anomalous scaling in an age-dependent branching model,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2. American Institute of Physics, 2015.","short":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","apa":"Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., & Klemm, K. (2015). Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.022803","ama":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2015;91(2). doi:10.1103/PhysRevE.91.022803","mla":"Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2, 022803, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.022803.","ista":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. 2015. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(2), 022803.","chicago":"Keller-Schmidt, Stephanie, Murat Tugrul, Víctor Eguíluz, Emilio Hernandez Garcia, and Konstantin Klemm. “Anomalous Scaling in an Age-Dependent Branching Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.022803."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1012.3298"]},"article_processing_charge":"No","author":[{"first_name":"Stephanie","last_name":"Keller-Schmidt","full_name":"Keller-Schmidt, Stephanie"},{"orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat","last_name":"Tugrul","first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Eguíluz, Víctor","last_name":"Eguíluz","first_name":"Víctor"},{"first_name":"Emilio","full_name":"Hernandez Garcia, Emilio","last_name":"Hernandez Garcia"},{"full_name":"Klemm, Konstantin","last_name":"Klemm","first_name":"Konstantin"}],"publist_id":"5213","title":"Anomalous scaling in an age-dependent branching model","article_number":"022803","year":"2015","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","day":"02","date_created":"2018-12-11T11:54:31Z","date_published":"2015-02-02T00:00:00Z","doi":"10.1103/PhysRevE.91.022803","oa":1,"quality_controlled":"1","publisher":"American Institute of Physics","date_updated":"2021-01-12T06:53:49Z","department":[{"_id":"NiBa"}],"_id":"1883","article_type":"original","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"issue":"2","volume":91,"abstract":[{"text":"We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ-α. Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)2. This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point.\r\n","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1012.3298","open_access":"1"}],"scopus_import":1,"intvolume":" 91","month":"02"},{"oa_version":"None","abstract":[{"lang":"eng","text":"Petrocoptis is a small genus of chasmophytic plants endemic to the Iberian Peninsula, with some localized populations in the French Pyrenees. Within the genus, a dozen species have been recognized based on morphological diversity, most of them with limited distribution area, in small populations and frequently with potential threats to their survival. To date, however, a molecular evaluation of the current systematic treatments has not been carried out. The aim of the present study is to infer phylogenetic relationships among its subordinate taxa by using plastidial rps16 intron and nuclear internal transcribed spacer (ITS) DNA sequences; and evaluate the phylogenetic placement of the genus Petrocoptis within the family Caryophyllaceae. The monophyly of Petrocoptis is supported by both ITS and rps16 intron sequence analyses. Furthermore, time estimates using BEAST analyses indicate a Middle to Late Miocene diversification (10.59 Myr, 6.44–15.26 Myr highest posterior densities [HPD], for ITS; 14.30 Myr, 8.61–21.00 Myr HPD, for rps16 intron)."}],"month":"01","intvolume":" 128","quality_controlled":"1","scopus_import":1,"publisher":"Springer","day":"24","publication":"Journal of Plant Research","language":[{"iso":"eng"}],"year":"2015","publication_status":"published","issue":"2","doi":"10.1007/s10265-014-0691-6","volume":128,"date_published":"2015-01-24T00:00:00Z","date_created":"2018-12-11T11:54:30Z","page":"223 - 238","_id":"1878","status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:47Z","citation":{"short":"E. Cires Rodriguez, J. Prieto, Journal of Plant Research 128 (2015) 223–238.","ieee":"E. Cires Rodriguez and J. Prieto, “Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula,” Journal of Plant Research, vol. 128, no. 2. Springer, pp. 223–238, 2015.","ama":"Cires Rodriguez E, Prieto J. Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. 2015;128(2):223-238. doi:10.1007/s10265-014-0691-6","apa":"Cires Rodriguez, E., & Prieto, J. (2015). Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. Springer. https://doi.org/10.1007/s10265-014-0691-6","mla":"Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships of Petrocoptis A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the Iberian Peninsula.” Journal of Plant Research, vol. 128, no. 2, Springer, 2015, pp. 223–38, doi:10.1007/s10265-014-0691-6.","ista":"Cires Rodriguez E, Prieto J. 2015. Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. 128(2), 223–238.","chicago":"Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships of Petrocoptis A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the Iberian Peninsula.” Journal of Plant Research. Springer, 2015. https://doi.org/10.1007/s10265-014-0691-6."},"department":[{"_id":"JiFr"}],"title":"Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula","publist_id":"5217","author":[{"last_name":"Cires Rodriguez","full_name":"Cires Rodriguez, Eduardo","first_name":"Eduardo","id":"2AD56A7A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"José","full_name":"Prieto, José","last_name":"Prieto"}]},{"department":[{"_id":"GaTk"}],"title":"Positional information, positional error, and readout precision in morphogenesis: A mathematical framework","author":[{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"},{"first_name":"Julien","full_name":"Dubuis, Julien","last_name":"Dubuis"},{"first_name":"Mariela","last_name":"Petkova","full_name":"Petkova, Mariela"},{"first_name":"Thomas","full_name":"Gregor, Thomas","last_name":"Gregor"}],"publist_id":"5210","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Tkačik, Gašper, Julien Dubuis, Mariela Petkova, and Thomas Gregor. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics. Genetics Society of America, 2015. https://doi.org/10.1534/genetics.114.171850.","ista":"Tkačik G, Dubuis J, Petkova M, Gregor T. 2015. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 199(1), 39–59.","mla":"Tkačik, Gašper, et al. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics, vol. 199, no. 1, Genetics Society of America, 2015, pp. 39–59, doi:10.1534/genetics.114.171850.","ieee":"G. Tkačik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information, positional error, and readout precision in morphogenesis: A mathematical framework,” Genetics, vol. 199, no. 1. Genetics Society of America, pp. 39–59, 2015.","short":"G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.","ama":"Tkačik G, Dubuis J, Petkova M, Gregor T. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 2015;199(1):39-59. doi:10.1534/genetics.114.171850","apa":"Tkačik, G., Dubuis, J., Petkova, M., & Gregor, T. (2015). Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.114.171850"},"date_updated":"2021-01-12T06:53:50Z","status":"public","type":"journal_article","_id":"1885","date_created":"2018-12-11T11:54:32Z","date_published":"2015-01-01T00:00:00Z","volume":199,"issue":"1","doi":"10.1534/genetics.114.171850","page":"39 - 59","language":[{"iso":"eng"}],"publication":"Genetics","day":"01","publication_status":"published","year":"2015","intvolume":" 199","month":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.5599"}],"oa":1,"scopus_import":1,"quality_controlled":"1","publisher":"Genetics Society of America","oa_version":"Preprint","abstract":[{"text":"The concept of positional information is central to our understanding of how cells determine their location in a multicellular structure and thereby their developmental fates. Nevertheless, positional information has neither been defined mathematically nor quantified in a principled way. Here we provide an information-theoretic definition in the context of developmental gene expression patterns and examine the features of expression patterns that affect positional information quantitatively. We connect positional information with the concept of positional error and develop tools to directly measure information and error from experimental data. We illustrate our framework for the case of gap gene expression patterns in the early Drosophila embryo and show how information that is distributed among only four genes is sufficient to determine developmental fates with nearly single-cell resolution. Our approach can be generalized to a variety of different model systems; procedures and examples are discussed in detail. ","lang":"eng"}]},{"language":[{"iso":"eng"}],"publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","day":"15","publication_status":"published","year":"2015","date_created":"2018-12-11T11:54:49Z","volume":91,"date_published":"2015-06-15T00:00:00Z","issue":"6","doi":"10.1103/PhysRevE.91.062710","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the "input") by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively new regulatory strategy emerges where individual cells respond to the input in a nearly step-like fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models."}],"intvolume":" 91","month":"06","main_file_link":[{"url":"http://arxiv.org/abs/1501.04015","open_access":"1"}],"oa":1,"scopus_import":1,"publisher":"American Institute of Physics","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","ieee":"T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6. American Institute of Physics, 2015.","apa":"Sokolowski, T. R., & Tkačik, G. (2015). Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.062710","ama":"Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2015;91(6). doi:10.1103/PhysRevE.91.062710","mla":"Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6, 062710, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.062710.","ista":"Sokolowski TR, Tkačik G. 2015. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(6), 062710.","chicago":"Sokolowski, Thomas R, and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.062710."},"date_updated":"2021-01-12T06:54:13Z","department":[{"_id":"GaTk"}],"title":"Optimizing information flow in small genetic networks. IV. Spatial coupling","author":[{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R","last_name":"Sokolowski","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5145","article_number":"062710","_id":"1940","status":"public","type":"journal_article"},{"type":"journal_article","status":"public","_id":"1938","publist_id":"5152","author":[{"last_name":"Pausinger","orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian","first_name":"Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Steinerberger","full_name":"Steinerberger, Stefan","first_name":"Stefan"}],"department":[{"_id":"HeEd"}],"title":"On the distribution of local extrema in quantum chaos","date_updated":"2021-01-12T06:54:12Z","citation":{"chicago":"Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local Extrema in Quantum Chaos.” Physics Letters, Section A. Elsevier, 2015. https://doi.org/10.1016/j.physleta.2014.12.010.","ista":"Pausinger F, Steinerberger S. 2015. On the distribution of local extrema in quantum chaos. Physics Letters, Section A. 379(6), 535–541.","mla":"Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local Extrema in Quantum Chaos.” Physics Letters, Section A, vol. 379, no. 6, Elsevier, 2015, pp. 535–41, doi:10.1016/j.physleta.2014.12.010.","ama":"Pausinger F, Steinerberger S. On the distribution of local extrema in quantum chaos. Physics Letters, Section A. 2015;379(6):535-541. doi:10.1016/j.physleta.2014.12.010","apa":"Pausinger, F., & Steinerberger, S. (2015). On the distribution of local extrema in quantum chaos. Physics Letters, Section A. Elsevier. https://doi.org/10.1016/j.physleta.2014.12.010","short":"F. Pausinger, S. Steinerberger, Physics Letters, Section A 379 (2015) 535–541.","ieee":"F. Pausinger and S. Steinerberger, “On the distribution of local extrema in quantum chaos,” Physics Letters, Section A, vol. 379, no. 6. Elsevier, pp. 535–541, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publisher":"Elsevier","quality_controlled":"1","month":"03","intvolume":" 379","abstract":[{"text":"We numerically investigate the distribution of extrema of 'chaotic' Laplacian eigenfunctions on two-dimensional manifolds. Our contribution is two-fold: (a) we count extrema on grid graphs with a small number of randomly added edges and show the behavior to coincide with the 1957 prediction of Longuet-Higgins for the continuous case and (b) we compute the regularity of their spatial distribution using discrepancy, which is a classical measure from the theory of Monte Carlo integration. The first part suggests that grid graphs with randomly added edges should behave like two-dimensional surfaces with ergodic geodesic flow; in the second part we show that the extrema are more regularly distributed in space than the grid Z2.","lang":"eng"}],"oa_version":"None","acknowledgement":"F.P. was supported by the Graduate School of IST Austria. S.S. was partially supported by CRC1060 of the DFG\r\nThe authors thank Olga Symonova and Michael Kerber for sharing their implementation of the persistence algorithm. ","page":"535 - 541","date_published":"2015-03-06T00:00:00Z","volume":379,"issue":"6","doi":"10.1016/j.physleta.2014.12.010","date_created":"2018-12-11T11:54:49Z","publication_status":"published","year":"2015","day":"06","language":[{"iso":"eng"}],"publication":"Physics Letters, Section A"},{"acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); the Agency for Innovation by Science and Technology (IWT) (predoctoral fellowship to H.R.); and the People Programme (Marie Curie Actions) of the European Union","oa_version":"None","intvolume":" 23","month":"02","publisher":"Elsevier","quality_controlled":"1","scopus_import":1,"publication":"Current Opinion in Plant Biology","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2015","ec_funded":1,"date_created":"2018-12-11T11:54:51Z","doi":"10.1016/j.pbi.2014.12.002","volume":23,"issue":"2","date_published":"2015-02-01T00:00:00Z","page":"116 - 123","_id":"1944","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"H. Rakusová, M. Fendrych, and J. Friml, “Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants,” Current Opinion in Plant Biology, vol. 23, no. 2. Elsevier, pp. 116–123, 2015.","short":"H. Rakusová, M. Fendrych, J. Friml, Current Opinion in Plant Biology 23 (2015) 116–123.","apa":"Rakusová, H., Fendrych, M., & Friml, J. (2015). Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2014.12.002","ama":"Rakusová H, Fendrych M, Friml J. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. 2015;23(2):116-123. doi:10.1016/j.pbi.2014.12.002","mla":"Rakusová, Hana, et al. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” Current Opinion in Plant Biology, vol. 23, no. 2, Elsevier, 2015, pp. 116–23, doi:10.1016/j.pbi.2014.12.002.","ista":"Rakusová H, Fendrych M, Friml J. 2015. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. 23(2), 116–123.","chicago":"Rakusová, Hana, Matyas Fendrych, and Jiří Friml. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” Current Opinion in Plant Biology. Elsevier, 2015. https://doi.org/10.1016/j.pbi.2014.12.002."},"date_updated":"2021-01-12T06:54:15Z","title":"Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants","department":[{"_id":"JiFr"}],"author":[{"last_name":"Rakusová","full_name":"Rakusová, Hana","first_name":"Hana"},{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"}],"publist_id":"5140"},{"title":"Succinct representation of concurrent trace sets","author":[{"first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","full_name":"Gupta, Ashutosh"},{"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":"Radhakrishna","full_name":"Radhakrishna, Arjun","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Samanta","full_name":"Samanta, Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","first_name":"Roopsha"},{"first_name":"Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","full_name":"Tarrach, Thorsten","orcid":"0000-0003-4409-8487","last_name":"Tarrach"}],"publist_id":"5091","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta, and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44. ACM, 2015. https://doi.org/10.1145/2676726.2677008.","ista":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct representation of concurrent trace sets. POPL: Principles of Programming Languages, 433–444.","mla":"Gupta, Ashutosh, et al. Succinct Representation of Concurrent Trace Sets. ACM, 2015, pp. 433–44, doi:10.1145/2676726.2677008.","ieee":"A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct representation of concurrent trace sets,” presented at the POPL: Principles of Programming Languages, Mumbai, India, 2015, pp. 433–444.","short":"A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM, 2015, pp. 433–444.","apa":"Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., & Tarrach, T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented at the POPL: Principles of Programming Languages, Mumbai, India: ACM. https://doi.org/10.1145/2676726.2677008","ama":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation of concurrent trace sets. In: ACM; 2015:433-444. doi:10.1145/2676726.2677008"},"date_created":"2018-12-11T11:55:05Z","doi":"10.1145/2676726.2677008","date_published":"2015-01-15T00:00:00Z","page":"433 - 444","day":"15","year":"2015","has_accepted_license":"1","oa":1,"publisher":"ACM","quality_controlled":"1","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:22Z","ddc":["005"],"date_updated":"2021-01-12T06:54:33Z","pubrep_id":"317","status":"public","conference":{"name":"POPL: Principles of Programming Languages","location":"Mumbai, India","end_date":"2015-01-17","start_date":"2015-01-15"},"type":"conference","_id":"1992","language":[{"iso":"eng"}],"file":[{"file_id":"5314","checksum":"f0d4395b600f410a191256ac0b73af32","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:17:56Z","file_name":"IST-2015-317-v1+1_author_version.pdf","date_updated":"2020-07-14T12:45:22Z","file_size":399462,"creator":"system"}],"publication_status":"published","publication_identifier":{"isbn":["978-1-4503-3300-9"]},"month":"01","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We present a method and a tool for generating succinct representations of sets of concurrent traces. We focus on trace sets that contain all correct or all incorrect permutations of events from a given trace. We represent trace sets as HB-Formulas that are Boolean combinations of happens-before constraints between events. To generate a representation of incorrect interleavings, our method iteratively explores interleavings that violate the specification and gathers generalizations of the discovered interleavings into an HB-Formula; its complement yields a representation of correct interleavings.\r\n\r\nWe claim that our trace set representations can drive diverse verification, fault localization, repair, and synthesis techniques for concurrent programs. We demonstrate this by using our tool in three case studies involving synchronization synthesis, bug summarization, and abstraction refinement based verification. In each case study, our initial experimental results have been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring missing synchronization from an HB-Formula representing correct interleavings of a given trace. The algorithm applies rules to rewrite specific patterns in the HB-Formula into locks, barriers, and wait-notify constructs. In the second case study, we use an HB-Formula representing incorrect interleavings for bug summarization. While the HB-Formula itself is a concise counterexample summary, we present additional inference rules to help identify specific concurrency bugs such as data races, define-use order violations, and two-stage access bugs. In the final case study, we present a novel predicate learning procedure that uses HB-Formulas representing abstract counterexamples to accelerate counterexample-guided abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure refines the abstraction to eliminate multiple spurious abstract counterexamples drawn from the HB-Formula."}]},{"_id":"1997","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Noren P. The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. 2015;68/Part 2(May-June):285-296. doi:10.1016/j.jsc.2014.09.014","apa":"Noren, P. (2015). The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2014.09.014","short":"P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.","ieee":"P. Noren, “The three-state toric homogeneous Markov chain model has Markov degree two,” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June. Elsevier, pp. 285–296, 2015.","mla":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June, Elsevier, 2015, pp. 285–96, doi:10.1016/j.jsc.2014.09.014.","ista":"Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296.","chicago":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” Journal of Symbolic Computation. Elsevier, 2015. https://doi.org/10.1016/j.jsc.2014.09.014."},"date_updated":"2021-01-12T06:54:35Z","title":"The three-state toric homogeneous Markov chain model has Markov degree two","department":[{"_id":"CaUh"}],"author":[{"id":"46870C74-F248-11E8-B48F-1D18A9856A87","first_name":"Patrik","full_name":"Noren, Patrik","last_name":"Noren"}],"publist_id":"5082","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We prove that the three-state toric homogeneous Markov chain model has Markov degree two. In algebraic terminology this means, that a certain class of toric ideals is generated by quadratic binomials. This was conjectured by Haws, Martin del Campo, Takemura and Yoshida, who proved that they are generated by degree six binomials."}],"month":"05","scopus_import":1,"publisher":"Elsevier","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1207.0077","open_access":"1"}],"day":"01","publication":"Journal of Symbolic Computation","language":[{"iso":"eng"}],"year":"2015","publication_status":"published","issue":"May-June","volume":"68/Part 2","doi":"10.1016/j.jsc.2014.09.014","date_published":"2015-05-01T00:00:00Z","date_created":"2018-12-11T11:55:07Z","page":"285 - 296"},{"page":"832 - 847","date_created":"2018-12-11T11:55:11Z","doi":"10.1111/sjos.12139","date_published":"2015-09-01T00:00:00Z","year":"2015","publication":"Scandinavian Journal of Statistics","day":"01","oa":1,"quality_controlled":"1","publisher":"Wiley","acknowledgement":"Part of the material presented here was contained in the PhD thesis of the first author to which the second author and Thomas Richardson were advisers. The authors wish to thank him for several comments and suggestions. We also thank the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1 uses the idea of Olga Klimova, to whom the authors are also indebted. The second author was supported in part by Grant K-106154 from the Hungarian National Scientific Research Fund (OTKA).","author":[{"first_name":"Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","last_name":"Klimova","full_name":"Klimova, Anna"},{"full_name":"Rudas, Tamás","last_name":"Rudas","first_name":"Tamás"}],"publist_id":"5068","title":"Iterative scaling in curved exponential families","citation":{"chicago":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” Scandinavian Journal of Statistics. Wiley, 2015. https://doi.org/10.1111/sjos.12139.","ista":"Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847.","mla":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” Scandinavian Journal of Statistics, vol. 42, no. 3, Wiley, 2015, pp. 832–47, doi:10.1111/sjos.12139.","apa":"Klimova, A., & Rudas, T. (2015). Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. Wiley. https://doi.org/10.1111/sjos.12139","ama":"Klimova A, Rudas T. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 2015;42(3):832-847. doi:10.1111/sjos.12139","ieee":"A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,” Scandinavian Journal of Statistics, vol. 42, no. 3. Wiley, pp. 832–847, 2015.","short":"A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","volume":42,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1307.3282","open_access":"1"}],"scopus_import":1,"intvolume":" 42","month":"09","abstract":[{"lang":"eng","text":"The paper describes a generalized iterative proportional fitting procedure that can be used for maximum likelihood estimation in a special class of the general log-linear model. The models in this class, called relational, apply to multivariate discrete sample spaces that do not necessarily have a Cartesian product structure and may not contain an overall effect. When applied to the cell probabilities, the models without the overall effect are curved exponential families and the values of the sufficient statistics are reproduced by the MLE only up to a constant of proportionality. The paper shows that Iterative Proportional Fitting, Generalized Iterative Scaling, and Improved Iterative Scaling fail to work for such models. The algorithm proposed here is based on iterated Bregman projections. As a by-product, estimates of the multiplicative parameters are also obtained. An implementation of the algorithm is available as an R-package."}],"oa_version":"Preprint","department":[{"_id":"CaUh"}],"date_updated":"2021-01-12T06:54:41Z","type":"journal_article","status":"public","_id":"2008"},{"date_updated":"2021-01-12T06:54:40Z","department":[{"_id":"CaUh"}],"_id":"2006","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":24,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The monotone secant conjecture posits a rich class of polynomial systems, all of whose solutions are real. These systems come from the Schubert calculus on flag manifolds, and the monotone secant conjecture is a compelling generalization of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko). We present some theoretical evidence for this conjecture, as well as computational evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of the phenomena we observed in our data. "}],"intvolume":" 24","month":"06","main_file_link":[{"url":"http://arxiv.org/abs/1109.3436","open_access":"1"}],"scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 24(3), 261–269.","chicago":"Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert Calculus.” Experimental Mathematics. Taylor & Francis, 2015. https://doi.org/10.1080/10586458.2014.980044.","ieee":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler, “The monotone secant conjecture in the real Schubert calculus,” Experimental Mathematics, vol. 24, no. 3. Taylor & Francis, pp. 261–269, 2015.","short":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269.","apa":"Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., & Teitler, Z. (2015). The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. Taylor & Francis. https://doi.org/10.1080/10586458.2014.980044","ama":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 2015;24(3):261-269. doi:10.1080/10586458.2014.980044","mla":"Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert Calculus.” Experimental Mathematics, vol. 24, no. 3, Taylor & Francis, 2015, pp. 261–69, doi:10.1080/10586458.2014.980044."},"title":"The monotone secant conjecture in the real Schubert calculus","article_processing_charge":"No","author":[{"full_name":"Hein, Nicolas","last_name":"Hein","first_name":"Nicolas"},{"first_name":"Christopher","last_name":"Hillar","full_name":"Hillar, Christopher"},{"id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","first_name":"Abraham","last_name":"Martin Del Campo Sanchez","full_name":"Martin Del Campo Sanchez, Abraham"},{"first_name":"Frank","last_name":"Sottile","full_name":"Sottile, Frank"},{"first_name":"Zach","full_name":"Teitler, Zach","last_name":"Teitler"}],"publist_id":"5070","publication":"Experimental Mathematics","day":"23","year":"2015","date_created":"2018-12-11T11:55:10Z","doi":"10.1080/10586458.2014.980044","date_published":"2015-06-23T00:00:00Z","page":"261 - 269","oa":1,"quality_controlled":"1","publisher":"Taylor & Francis"},{"month":"07","intvolume":" 87","publisher":"Elsevier","quality_controlled":"1","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1404.6617","open_access":"1"}],"oa":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The concepts of faithfulness and strong-faithfulness are important for statistical learning of graphical models. Graphs are not sufficient for describing the association structure of a discrete distribution. Hypergraphs representing hierarchical log-linear models are considered instead, and the concept of parametric (strong-) faithfulness with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence of uniformly consistent parameter estimators and enables building uniformly consistent procedures for a hypergraph search. The strength of association in a discrete distribution can be quantified with various measures, leading to different concepts of strong-faithfulness. Lower and upper bounds for the proportions of distributions that do not satisfy strong-faithfulness are computed for different parameterizations and measures of association."}],"issue":"7","doi":"10.1016/j.csda.2015.01.017","volume":87,"date_published":"2015-07-01T00:00:00Z","date_created":"2018-12-11T11:55:13Z","page":"57 - 72","day":"01","language":[{"iso":"eng"}],"publication":"Computational Statistics & Data Analysis","publication_status":"published","year":"2015","status":"public","type":"journal_article","_id":"2014","department":[{"_id":"CaUh"}],"title":"Faithfulness and learning hypergraphs from discrete distributions","publist_id":"5062","author":[{"full_name":"Klimova, Anna","last_name":"Klimova","first_name":"Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Uhler","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"},{"first_name":"Tamás","last_name":"Rudas","full_name":"Rudas, Tamás"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” Computational Statistics & Data Analysis, vol. 87, no. 7, Elsevier, 2015, pp. 57–72, doi:10.1016/j.csda.2015.01.017.","ieee":"A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs from discrete distributions,” Computational Statistics & Data Analysis, vol. 87, no. 7. Elsevier, pp. 57–72, 2015.","short":"A. Klimova, C. Uhler, T. Rudas, Computational Statistics & Data Analysis 87 (2015) 57–72.","apa":"Klimova, A., Uhler, C., & Rudas, T. (2015). Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. Elsevier. https://doi.org/10.1016/j.csda.2015.01.017","ama":"Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. 2015;87(7):57-72. doi:10.1016/j.csda.2015.01.017","chicago":"Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” Computational Statistics & Data Analysis. Elsevier, 2015. https://doi.org/10.1016/j.csda.2015.01.017.","ista":"Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. 87(7), 57–72."},"date_updated":"2021-01-12T06:54:43Z"},{"oa_version":"Submitted Version","abstract":[{"text":"Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins.","lang":"eng"}],"month":"01","intvolume":" 1853","scopus_import":1,"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"5bb328edebb6a91337cadd7d63f961b7","file_id":"4936","date_updated":"2020-07-14T12:45:25Z","file_size":926685,"creator":"system","date_created":"2018-12-12T10:12:18Z","file_name":"IST-2016-615-v1+1_BBAMCR.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"1","volume":1853,"_id":"2025","status":"public","pubrep_id":"615","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"ddc":["570"],"date_updated":"2021-01-12T06:54:48Z","department":[{"_id":"DaSi"}],"file_date_updated":"2020-07-14T12:45:25Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"day":"01","publication":"Biochimica et Biophysica Acta - Molecular Cell Research","has_accepted_license":"1","year":"2015","doi":"10.1016/j.bbamcr.2014.10.009","date_published":"2015-01-01T00:00:00Z","date_created":"2018-12-11T11:55:17Z","page":"144 - 156","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:10.1016/j.bbamcr.2014.10.009.","apa":"Kawada, D., Kobayashi, H., Tomita, T., Nakata, E., Nagano, M., Siekhaus, D. E., … Toshimaa, J. (2015). The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2014.10.009","ama":"Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 2015;1853(1):144-156. doi:10.1016/j.bbamcr.2014.10.009","ieee":"D. Kawada et al., “The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins,” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 1. Elsevier, pp. 144–156, 2015.","short":"D. Kawada, H. Kobayashi, T. Tomita, E. Nakata, M. Nagano, D.E. Siekhaus, J. Toshima, J. Toshimaa, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 144–156.","chicago":"Kawada, Daiki, Hiromu Kobayashi, Tsuyoshi Tomita, Eisuke Nakata, Makoto Nagano, Daria E Siekhaus, Junko Toshima, and Jiro Toshimaa. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2014.10.009.","ista":"Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima J, Toshimaa J. 2015. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(1), 144–156."},"title":"The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins","author":[{"last_name":"Kawada","full_name":"Kawada, Daiki","first_name":"Daiki"},{"last_name":"Kobayashi","full_name":"Kobayashi, Hiromu","first_name":"Hiromu"},{"first_name":"Tsuyoshi","last_name":"Tomita","full_name":"Tomita, Tsuyoshi"},{"full_name":"Nakata, Eisuke","last_name":"Nakata","first_name":"Eisuke"},{"last_name":"Nagano","full_name":"Nagano, Makoto","first_name":"Makoto"},{"last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Junko","full_name":"Toshima, Junko","last_name":"Toshima"},{"first_name":"Jiro","last_name":"Toshimaa","full_name":"Toshimaa, Jiro"}],"publist_id":"5047"}]