[{"publist_id":"5289","date_created":"2018-12-11T11:54:10Z","date_updated":"2021-01-12T06:53:23Z","volume":521,"author":[{"full_name":"Porazinski, Sean","last_name":"Porazinski","first_name":"Sean"},{"full_name":"Wang, Huijia","last_name":"Wang","first_name":"Huijia"},{"first_name":"Yoichi","last_name":"Asaoka","full_name":"Asaoka, Yoichi"},{"full_name":"Behrndt, Martin","last_name":"Behrndt","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tatsuo","last_name":"Miyamoto","full_name":"Miyamoto, Tatsuo"},{"last_name":"Morita","first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi"},{"first_name":"Shoji","last_name":"Hata","full_name":"Hata, Shoji"},{"first_name":"Takashi","last_name":"Sasaki","full_name":"Sasaki, Takashi"},{"full_name":"Krens, Gabriel","first_name":"Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996"},{"last_name":"Osada","first_name":"Yumi","full_name":"Osada, Yumi"},{"full_name":"Asaka, Satoshi","last_name":"Asaka","first_name":"Satoshi"},{"full_name":"Momoi, Akihiro","last_name":"Momoi","first_name":"Akihiro"},{"full_name":"Linton, Sarah","first_name":"Sarah","last_name":"Linton"},{"full_name":"Miesfeld, Joel","first_name":"Joel","last_name":"Miesfeld"},{"last_name":"Link","first_name":"Brian","full_name":"Link, Brian"},{"full_name":"Senga, Takeshi","last_name":"Senga","first_name":"Takeshi"},{"first_name":"Atahualpa","last_name":"Castillo Morales","full_name":"Castillo Morales, Atahualpa"},{"last_name":"Urrutia","first_name":"Araxi","full_name":"Urrutia, Araxi"},{"full_name":"Shimizu, Nobuyoshi","first_name":"Nobuyoshi","last_name":"Shimizu"},{"last_name":"Nagase","first_name":"Hideaki","full_name":"Nagase, Hideaki"},{"full_name":"Matsuura, Shinya","first_name":"Shinya","last_name":"Matsuura"},{"last_name":"Bagby","first_name":"Stefan","full_name":"Bagby, Stefan"},{"full_name":"Kondoh, Hisato","first_name":"Hisato","last_name":"Kondoh"},{"full_name":"Nishina, Hiroshi","first_name":"Hiroshi","last_name":"Nishina"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Furutani Seiki","first_name":"Makoto","full_name":"Furutani Seiki, Makoto"}],"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Nature Publishing Group","year":"2015","pmid":1,"month":"03","language":[{"iso":"eng"}],"doi":"10.1038/nature14215","quality_controlled":"1","external_id":{"pmid":["25778702"]},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/"}],"oa":1,"abstract":[{"text":"Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. ","lang":"eng"}],"issue":"7551","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"YAP is essential for tissue tension to ensure vertebrate 3D body shape","intvolume":" 521","_id":"1817","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","day":"16","scopus_import":1,"date_published":"2015-03-16T00:00:00Z","page":"217 - 221","publication":"Nature","citation":{"ista":"Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki T, Krens G, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld J, Link B, Senga T, Castillo Morales A, Urrutia A, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh H, Nishina H, Heisenberg C-PJ, Furutani Seiki M. 2015. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 521(7551), 217–221.","apa":"Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H., … Furutani Seiki, M. (2015). YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. Nature Publishing Group. https://doi.org/10.1038/nature14215","ieee":"S. Porazinski et al., “YAP is essential for tissue tension to ensure vertebrate 3D body shape,” Nature, vol. 521, no. 7551. Nature Publishing Group, pp. 217–221, 2015.","ama":"Porazinski S, Wang H, Asaoka Y, et al. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 2015;521(7551):217-221. doi:10.1038/nature14215","chicago":"Porazinski, Sean, Huijia Wang, Yoichi Asaoka, Martin Behrndt, Tatsuo Miyamoto, Hitoshi Morita, Shoji Hata, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature14215.","mla":"Porazinski, Sean, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” Nature, vol. 521, no. 7551, Nature Publishing Group, 2015, pp. 217–21, doi:10.1038/nature14215.","short":"S. Porazinski, H. Wang, Y. Asaoka, M. Behrndt, T. Miyamoto, H. Morita, S. Hata, T. Sasaki, G. Krens, Y. Osada, S. Asaka, A. Momoi, S. Linton, J. Miesfeld, B. Link, T. Senga, A. Castillo Morales, A. Urrutia, N. Shimizu, H. Nagase, S. Matsuura, S. Bagby, H. Kondoh, H. Nishina, C.-P.J. Heisenberg, M. Furutani Seiki, Nature 521 (2015) 217–221."}},{"month":"06","conference":{"start_date":"2015-01-25","location":"Austin, TX, USA","end_date":"2015-01-30","name":"IAAI: Innovative Applications of Artificial Intelligence"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["1411.3880"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1411.3880"}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"quality_controlled":"1","publist_id":"5286","ec_funded":1,"related_material":{"record":[{"status":"public","relation":"later_version","id":"1529"}]},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","first_name":"Martin"},{"first_name":"Raghav","last_name":"Gupta","full_name":"Gupta, Raghav"},{"last_name":"Kanodia","first_name":"Ayush","full_name":"Kanodia, Ayush"}],"volume":5,"date_updated":"2023-02-23T10:02:57Z","date_created":"2018-12-11T11:54:11Z","year":"2015","acknowledgement":" The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","department":[{"_id":"KrCh"}],"publisher":"AAAI Press","publication_status":"published","day":"01","scopus_import":1,"date_published":"2015-06-01T00:00:00Z","citation":{"ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. In: Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . Vol 5. AAAI Press; 2015:3496-3502.","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Optimal cost almost-sure reachability in POMDPs. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . IAAI: Innovative Applications of Artificial Intelligence, Artifical Intelligence, vol. 5, 3496–3502.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” in Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , Austin, TX, USA, 2015, vol. 5, pp. 3496–3502.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2015). Optimal cost almost-sure reachability in POMDPs. In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3496–3502). Austin, TX, USA: AAAI Press.","mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , vol. 5, AAAI Press, 2015, pp. 3496–502.","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , AAAI Press, 2015, pp. 3496–3502.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , 5:3496–3502. AAAI Press, 2015."},"publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ","page":"3496-3502","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst- case running time of our algorithm is double exponential, we present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples."}],"type":"conference","alternative_title":["Artifical Intelligence"],"oa_version":"Preprint","_id":"1820","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 5","status":"public","title":"Optimal cost almost-sure reachability in POMDPs"},{"project":[{"grant_number":"P 24352-N23","_id":"25357BD2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images"},{"grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/2714572","month":"04","publisher":"ACM","department":[{"_id":"ChWo"}],"publication_status":"published","year":"2015","volume":34,"date_created":"2018-12-11T11:54:09Z","date_updated":"2023-02-23T10:15:40Z","author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","last_name":"Jeschke","first_name":"Stefan","full_name":"Jeschke, Stefan"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J"}],"article_number":"27","publist_id":"5292","ec_funded":1,"file_date_updated":"2020-07-14T12:45:17Z","citation":{"ama":"Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 2015;34(3). doi:10.1145/2714572","apa":"Jeschke, S., & Wojtan, C. (2015). Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2714572","ieee":"S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,” ACM Transactions on Graphics, vol. 34, no. 3. ACM, 2015.","ista":"Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 34(3), 27.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015).","mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” ACM Transactions on Graphics, vol. 34, no. 3, 27, ACM, 2015, doi:10.1145/2714572.","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” ACM Transactions on Graphics. ACM, 2015. https://doi.org/10.1145/2714572."},"publication":"ACM Transactions on Graphics","date_published":"2015-04-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","intvolume":" 34","ddc":["000"],"title":"Water wave animation via wavefront parameter interpolation","status":"public","_id":"1814","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:12:15Z","checksum":"67c9f4fa370def68cdf31299e48bc91f","file_id":"4933","relation":"main_file","creator":"system","file_size":23712153,"content_type":"application/pdf","file_name":"IST-2016-575-v1+1_wavefront_preprint.pdf","access_level":"open_access"}],"pubrep_id":"575","type":"journal_article","issue":"3","abstract":[{"text":"We present an efficient wavefront tracking algorithm for animating bodies of water that interact with their environment. Our contributions include: a novel wavefront tracking technique that enables dispersion, refraction, reflection, and diffraction in the same simulation; a unique multivalued function interpolation method that enables our simulations to elegantly sidestep the Nyquist limit; a dispersion approximation for efficiently amplifying the number of simulated waves by several orders of magnitude; and additional extensions that allow for time-dependent effects and interactive artistic editing of the resulting animation. Our contributions combine to give us multitudes more wave details than similar algorithms, while maintaining high frame rates and allowing close camera zooms.","lang":"eng"}]},{"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/","open_access":"1"}],"external_id":{"pmid":["25941385"]},"oa":1,"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","doi":"10.1073/pnas.1421515112","language":[{"iso":"eng"}],"month":"05","pmid":1,"year":"2015","publisher":"National Academy of Sciences","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"full_name":"Polechova, Jitka","last_name":"Polechova","first_name":"Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"volume":112,"date_updated":"2021-01-12T06:53:24Z","date_created":"2018-12-11T11:54:11Z","publist_id":"5288","ec_funded":1,"citation":{"chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1421515112.","mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” PNAS, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:10.1073/pnas.1421515112.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” PNAS, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","apa":"Polechova, J., & Barton, N. H. (2015). Limits to adaptation along environmental gradients. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1421515112","ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. PNAS. 2015;112(20):6401-6406. doi:10.1073/pnas.1421515112"},"publication":"PNAS","page":"6401 - 6406","date_published":"2015-05-19T00:00:00Z","scopus_import":1,"day":"19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1818","intvolume":" 112","status":"public","title":"Limits to adaptation along environmental gradients","oa_version":"Submitted Version","type":"journal_article","issue":"20","abstract":[{"lang":"eng","text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, "swamping" by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible."}]},{"date_published":"2015-08-03T00:00:00Z","publication":"Molecular Plant","citation":{"ista":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. 2015. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 8(8), 1175–1187.","apa":"Zwiewka, M., Nodzyński, T., Robert, S., Vanneste, S., & Friml, J. (2015). Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2015.03.007","ieee":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, and J. Friml, “Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana,” Molecular Plant, vol. 8, no. 8. Elsevier, pp. 1175–1187, 2015.","ama":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 2015;8(8):1175-1187. doi:10.1016/j.molp.2015.03.007","chicago":"Zwiewka, Marta, Tomasz Nodzyński, Stéphanie Robert, Steffen Vanneste, and Jiří Friml. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant. Elsevier, 2015. https://doi.org/10.1016/j.molp.2015.03.007.","mla":"Zwiewka, Marta, et al. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant, vol. 8, no. 8, Elsevier, 2015, pp. 1175–87, doi:10.1016/j.molp.2015.03.007.","short":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant 8 (2015) 1175–1187."},"page":"1175 - 1187","day":"03","scopus_import":1,"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1819","title":"Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana","status":"public","intvolume":" 8","abstract":[{"text":"The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity.","lang":"eng"}],"issue":"8","type":"journal_article","doi":"10.1016/j.molp.2015.03.007","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"month":"08","author":[{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"last_name":"Nodzyński","first_name":"Tomasz","full_name":"Nodzyński, Tomasz"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"first_name":"Jiřĺ","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiřĺ"}],"date_created":"2018-12-11T11:54:11Z","date_updated":"2021-01-12T06:53:24Z","volume":8,"year":"2015","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to J.F.; project Postdoc I. (CZ.1.07/2.3.00/30.0009) co-financed by the European Social Fund and the state budget of the Czech Republic to M.Z. and T.N..","publication_status":"published","publisher":"Elsevier","department":[{"_id":"JiFr"}],"ec_funded":1,"publist_id":"5287"},{"month":"04","doi":"10.15252/msb.20156098","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"},{"grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth"},{"name":"Optimality principles in responses to antibiotics","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507"}],"quality_controlled":"1","ec_funded":1,"publist_id":"5283","file_date_updated":"2020-07-14T12:45:17Z","article_number":"807","author":[{"id":"424D78A0-F248-11E8-B48F-1D18A9856A87","last_name":"Chevereau","first_name":"Guillaume","full_name":"Chevereau, Guillaume"},{"full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"volume":11,"date_created":"2018-12-11T11:54:12Z","date_updated":"2021-01-12T06:53:26Z","year":"2015","department":[{"_id":"ToBo"}],"publisher":"Nature Publishing Group","publication_status":"published","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2015-04-01T00:00:00Z","citation":{"mla":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” Molecular Systems Biology, vol. 11, no. 4, 807, Nature Publishing Group, 2015, doi:10.15252/msb.20156098.","short":"G. Chevereau, M.T. Bollenbach, Molecular Systems Biology 11 (2015).","chicago":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” Molecular Systems Biology. Nature Publishing Group, 2015. https://doi.org/10.15252/msb.20156098.","ama":"Chevereau G, Bollenbach MT. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 2015;11(4). doi:10.15252/msb.20156098","ista":"Chevereau G, Bollenbach MT. 2015. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 11(4), 807.","apa":"Chevereau, G., & Bollenbach, M. T. (2015). Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.15252/msb.20156098","ieee":"G. Chevereau and M. T. Bollenbach, “Systematic discovery of drug interaction mechanisms,” Molecular Systems Biology, vol. 11, no. 4. Nature Publishing Group, 2015."},"publication":"Molecular Systems Biology","issue":"4","abstract":[{"text":"Abstract Drug combinations are increasingly important in disease treatments, for combating drug resistance, and for elucidating fundamental relationships in cell physiology. When drugs are combined, their individual effects on cells may be amplified or weakened. Such drug interactions are crucial for treatment efficacy, but their underlying mechanisms remain largely unknown. To uncover the causes of drug interactions, we developed a systematic approach based on precise quantification of the individual and joint effects of antibiotics on growth of genome-wide Escherichia coli gene deletion strains. We found that drug interactions between antibiotics representing the main modes of action are highly robust to genetic perturbation. This robustness is encapsulated in a general principle of bacterial growth, which enables the quantitative prediction of mutant growth rates under drug combinations. Rare violations of this principle exposed recurring cellular functions controlling drug interactions. In particular, we found that polysaccharide and ATP synthesis control multiple drug interactions with previously unexplained mechanisms, and small molecule adjuvants targeting these functions synthetically reshape drug interactions in predictable ways. These results provide a new conceptual framework for the design of multidrug combinations and suggest that there are universal mechanisms at the heart of most drug interactions. Synopsis A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways. Drug interactions between antibiotics are highly robust to genetic perturbations. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions. Diverse drug interactions are controlled by recurring cellular functions, including LPS synthesis and ATP synthesis. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways.","lang":"eng"}],"type":"journal_article","pubrep_id":"395","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:14:34Z","checksum":"4289b518fbe2166682fb1a1ef9b405f3","relation":"main_file","file_id":"5087","content_type":"application/pdf","file_size":1273573,"creator":"system","file_name":"IST-2015-395-v1+1_807.full.pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1823","intvolume":" 11","title":"Systematic discovery of drug interaction mechanisms","ddc":["570"],"status":"public"},{"publication":"Nature Communications","citation":{"chicago":"Knebel, Johannes, Markus Weber, Torben H Krüger, and Erwin Frey. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms7977.","short":"J. Knebel, M. Weber, T.H. Krüger, E. Frey, Nature Communications 6 (2015).","mla":"Knebel, Johannes, et al. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” Nature Communications, vol. 6, 6977, Nature Publishing Group, 2015, doi:10.1038/ncomms7977.","ieee":"J. Knebel, M. Weber, T. H. Krüger, and E. Frey, “Evolutionary games of condensates in coupled birth-death processes,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","apa":"Knebel, J., Weber, M., Krüger, T. H., & Frey, E. (2015). Evolutionary games of condensates in coupled birth-death processes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms7977","ista":"Knebel J, Weber M, Krüger TH, Frey E. 2015. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 6, 6977.","ama":"Knebel J, Weber M, Krüger TH, Frey E. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 2015;6. doi:10.1038/ncomms7977"},"date_published":"2015-04-24T00:00:00Z","scopus_import":1,"day":"24","has_accepted_license":"1","status":"public","title":"Evolutionary games of condensates in coupled birth-death processes","ddc":["530"],"intvolume":" 6","_id":"1824","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"IST-2016-451-v1+1_ncomms7977.pdf","access_level":"open_access","creator":"system","file_size":1151501,"content_type":"application/pdf","file_id":"5245","relation":"main_file","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:16:54Z","checksum":"c4cffb5c8b245e658a34eac71a03e7cc"}],"pubrep_id":"451","type":"journal_article","abstract":[{"lang":"eng","text":"Condensation phenomena arise through a collective behaviour of particles. They are observed in both classical and quantum systems, ranging from the formation of traffic jams in mass transport models to the macroscopic occupation of the energetic ground state in ultra-cold bosonic gases (Bose-Einstein condensation). Recently, it has been shown that a driven and dissipative system of bosons may form multiple condensates. Which states become the condensates has, however, remained elusive thus far. The dynamics of this condensation are described by coupled birth-death processes, which also occur in evolutionary game theory. Here we apply concepts from evolutionary game theory to explain the formation of multiple condensates in such driven-dissipative bosonic systems. We show that the vanishing of relative entropy production determines their selection. The condensation proceeds exponentially fast, but the system never comes to rest. Instead, the occupation numbers of condensates may oscillate, as we demonstrate for a rock-paper-scissors game of condensates."}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1038/ncomms7977","month":"04","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"LaEr"}],"year":"2015","date_created":"2018-12-11T11:54:13Z","date_updated":"2021-01-12T06:53:26Z","volume":6,"author":[{"full_name":"Knebel, Johannes","first_name":"Johannes","last_name":"Knebel"},{"full_name":"Weber, Markus","first_name":"Markus","last_name":"Weber"},{"full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","first_name":"Torben H"},{"full_name":"Frey, Erwin","last_name":"Frey","first_name":"Erwin"}],"article_number":"6977","file_date_updated":"2020-07-14T12:45:17Z","publist_id":"5282"},{"publist_id":"5272","article_number":"20140116","author":[{"last_name":"Kappeler","first_name":"Peter","full_name":"Kappeler, Peter"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nunn, Charles","last_name":"Nunn","first_name":"Charles"}],"date_created":"2018-12-11T11:54:15Z","date_updated":"2021-01-12T06:53:29Z","volume":370,"acknowledgement":"We thank the German Research Foundation (DFG), the Ministry of Science and Culture of Lower-Saxony (MWK Hannover) and the German Primate Centre (DPZ) for their support of the 9. Göttinger Freilandtage in 2013, a conference at which most contributions to this issue were first presented, the referees of the contributions to this issue for their constructive comments, Meggan Craft for comments, and Helen Eaton for her support in producing this theme issue.","year":"2015","pmid":1,"publication_status":"published","publisher":"Royal Society","department":[{"_id":"SyCr"}],"month":"05","doi":"10.1098/rstb.2014.0116","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410382/","open_access":"1"}],"oa":1,"external_id":{"pmid":["25870402"]},"quality_controlled":"1","abstract":[{"lang":"eng","text":"This paper introduces a theme issue presenting the latest developments in research on the impacts of sociality on health and fitness. The articles that follow cover research on societies ranging from insects to humans. Variation in measures of fitness (i.e. survival and reproduction) has been linked to various aspects of sociality in humans and animals alike, and variability in individual health and condition has been recognized as a key mediator of these relationships. Viewed from a broad evolutionary perspective, the evolutionary transitions from a solitary lifestyle to group living have resulted in several new health-related costs and benefits of sociality. Social transmission of parasites within groups represents a major cost of group living, but some behavioural mechanisms, such as grooming, have evolved repeatedly to reduce this cost. Group living also has created novel costs in terms of altered susceptibility to infectious and non-infectious disease as a result of the unavoidable physiological consequences of social competition and integration, which are partly alleviated by social buffering in some vertebrates. Here, we define the relevant aspects of sociality, summarize their health-related costs and benefits, and discuss possible fitness measures in different study systems. Given the pervasive effects of social factors on health and fitness, we propose a synthesis of existing conceptual approaches in disease ecology, ecological immunology and behavioural neurosciences by adding sociality as a key factor, with the goal to generate a broader framework for organismal integration of health-related research."}],"issue":"1669","type":"journal_article","oa_version":"Submitted Version","_id":"1831","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies","intvolume":" 370","day":"01","scopus_import":1,"date_published":"2015-05-01T00:00:00Z","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","citation":{"ama":"Kappeler P, Cremer S, Nunn C. Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0116","ieee":"P. Kappeler, S. Cremer, and C. Nunn, “Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669. Royal Society, 2015.","apa":"Kappeler, P., Cremer, S., & Nunn, C. (2015). Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2014.0116","ista":"Kappeler P, Cremer S, Nunn C. 2015. Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669), 20140116.","short":"P. Kappeler, S. Cremer, C. Nunn, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015).","mla":"Kappeler, Peter, et al. “Sociality and Health: Impacts of Sociality on Disease Susceptibility and Transmission in Animal and Human Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669, 20140116, Royal Society, 2015, doi:10.1098/rstb.2014.0116.","chicago":"Kappeler, Peter, Sylvia Cremer, and Charles Nunn. “Sociality and Health: Impacts of Sociality on Disease Susceptibility and Transmission in Animal and Human Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2015. https://doi.org/10.1098/rstb.2014.0116."}},{"citation":{"ama":"Akopyan A, Pirogov S, Rybko A. Invariant measures of genetic recombination process. Journal of Statistical Physics. 2015;160(1):163-167. doi:10.1007/s10955-015-1238-5","apa":"Akopyan, A., Pirogov, S., & Rybko, A. (2015). Invariant measures of genetic recombination process. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-015-1238-5","ieee":"A. Akopyan, S. Pirogov, and A. Rybko, “Invariant measures of genetic recombination process,” Journal of Statistical Physics, vol. 160, no. 1. Springer, pp. 163–167, 2015.","ista":"Akopyan A, Pirogov S, Rybko A. 2015. Invariant measures of genetic recombination process. Journal of Statistical Physics. 160(1), 163–167.","short":"A. Akopyan, S. Pirogov, A. Rybko, Journal of Statistical Physics 160 (2015) 163–167.","mla":"Akopyan, Arseniy, et al. “Invariant Measures of Genetic Recombination Process.” Journal of Statistical Physics, vol. 160, no. 1, Springer, 2015, pp. 163–67, doi:10.1007/s10955-015-1238-5.","chicago":"Akopyan, Arseniy, Sergey Pirogov, and Aleksandr Rybko. “Invariant Measures of Genetic Recombination Process.” Journal of Statistical Physics. Springer, 2015. https://doi.org/10.1007/s10955-015-1238-5."},"publication":"Journal of Statistical Physics","page":"163 - 167","date_published":"2015-07-01T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"01","_id":"1828","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 160","status":"public","title":"Invariant measures of genetic recombination process","oa_version":"Preprint","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We construct a non-linear Markov process connected with a biological model of a bacterial genome recombination. The description of invariant measures of this process gives us the solution of one problem in elementary probability theory."}],"main_file_link":[{"open_access":"1","url":"arxiv.org/abs/1406.5313"}],"oa":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","doi":"10.1007/s10955-015-1238-5","language":[{"iso":"eng"}],"month":"07","year":"2015","publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","author":[{"first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"first_name":"Sergey","last_name":"Pirogov","full_name":"Pirogov, Sergey"},{"full_name":"Rybko, Aleksandr","last_name":"Rybko","first_name":"Aleksandr"}],"volume":160,"date_updated":"2021-01-12T06:53:28Z","date_created":"2018-12-11T11:54:14Z","ec_funded":1,"publist_id":"5276"},{"year":"2015","publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","author":[{"full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","last_name":"Cerny"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"last_name":"Kovács","first_name":"Laura","full_name":"Kovács, Laura"},{"full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","last_name":"Radhakrishna"},{"full_name":"Zwirchmayr, Jakob","first_name":"Jakob","last_name":"Zwirchmayr"}],"volume":9032,"date_updated":"2020-08-11T10:09:32Z","date_created":"2018-12-11T11:54:16Z","publist_id":"5266","ec_funded":1,"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","doi":"10.1007/978-3-662-46669-8_5","conference":{"location":"London, United Kingdom","start_date":"2015-04-11","end_date":"2015-04-18","name":"ESOP: European Symposium on Programming"},"language":[{"iso":"eng"}],"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1836","intvolume":" 9032","title":"Segment abstraction for worst-case execution time analysis","status":"public","oa_version":"None","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"In the standard framework for worst-case execution time (WCET) analysis of programs, the main data structure is a single instance of integer linear programming (ILP) that represents the whole program. The instance of this NP-hard problem must be solved to find an estimate forWCET, and it must be refined if the estimate is not tight.We propose a new framework for WCET analysis, based on abstract segment trees (ASTs) as the main data structure. The ASTs have two advantages. First, they allow computing WCET by solving a number of independent small ILP instances. Second, ASTs store more expressive constraints, thus enabling a more efficient and precise refinement procedure. In order to realize our framework algorithmically, we develop an algorithm for WCET estimation on ASTs, and we develop an interpolation-based counterexample-guided refinement scheme for ASTs. Furthermore, we extend our framework to obtain parametric estimates of WCET. We experimentally evaluate our approach on a set of examples from WCET benchmark suites and linear-algebra packages. We show that our analysis, with comparable effort, provides WCET estimates that in many cases significantly improve those computed by existing tools.","lang":"eng"}],"citation":{"chicago":"Cerny, Pavol, Thomas A Henzinger, Laura Kovács, Arjun Radhakrishna, and Jakob Zwirchmayr. “Segment Abstraction for Worst-Case Execution Time Analysis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46669-8_5.","short":"P. Cerny, T.A. Henzinger, L. Kovács, A. Radhakrishna, J. Zwirchmayr, 9032 (2015) 105–131.","mla":"Cerny, Pavol, et al. Segment Abstraction for Worst-Case Execution Time Analysis. Vol. 9032, Springer, 2015, pp. 105–31, doi:10.1007/978-3-662-46669-8_5.","ieee":"P. Cerny, T. A. Henzinger, L. Kovács, A. Radhakrishna, and J. Zwirchmayr, “Segment abstraction for worst-case execution time analysis,” vol. 9032. Springer, pp. 105–131, 2015.","apa":"Cerny, P., Henzinger, T. A., Kovács, L., Radhakrishna, A., & Zwirchmayr, J. (2015). Segment abstraction for worst-case execution time analysis. Presented at the ESOP: European Symposium on Programming, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46669-8_5","ista":"Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. 2015. Segment abstraction for worst-case execution time analysis. 9032, 105–131.","ama":"Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. Segment abstraction for worst-case execution time analysis. 2015;9032:105-131. doi:10.1007/978-3-662-46669-8_5"},"page":"105 - 131","date_published":"2015-04-01T00:00:00Z","scopus_import":1,"series_title":"Lecture Notes in Computer Science","day":"01"},{"page":"517 - 532","citation":{"apa":"Bloem, R., Chatterjee, K., Jacobs, S., & Könighofer, R. (2015). Assume-guarantee synthesis for concurrent reactive programs with partial information (Vol. 9035, pp. 517–532). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_50","ieee":"R. Bloem, K. Chatterjee, S. Jacobs, and R. Könighofer, “Assume-guarantee synthesis for concurrent reactive programs with partial information,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom, 2015, vol. 9035, pp. 517–532.","ista":"Bloem R, Chatterjee K, Jacobs S, Könighofer R. 2015. Assume-guarantee synthesis for concurrent reactive programs with partial information. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 9035, 517–532.","ama":"Bloem R, Chatterjee K, Jacobs S, Könighofer R. Assume-guarantee synthesis for concurrent reactive programs with partial information. In: Vol 9035. Springer; 2015:517-532. doi:10.1007/978-3-662-46681-0_50","chicago":"Bloem, Roderick, Krishnendu Chatterjee, Swen Jacobs, and Robert Könighofer. “Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information,” 9035:517–32. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_50.","short":"R. Bloem, K. Chatterjee, S. Jacobs, R. Könighofer, in:, Springer, 2015, pp. 517–532.","mla":"Bloem, Roderick, et al. Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information. Vol. 9035, Springer, 2015, pp. 517–32, doi:10.1007/978-3-662-46681-0_50."},"date_published":"2015-01-01T00:00:00Z","scopus_import":1,"day":"01","intvolume":" 9035","title":"Assume-guarantee synthesis for concurrent reactive programs with partial information","status":"public","_id":"1838","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Synthesis of program parts is particularly useful for concurrent systems. However, most approaches do not support common design tasks, like modifying a single process without having to re-synthesize or verify the whole system. Assume-guarantee synthesis (AGS) provides robustness against modifications of system parts, but thus far has been limited to the perfect information setting. This means that local variables cannot be hidden from other processes, which renders synthesis results cumbersome or even impossible to realize.We resolve this shortcoming by defining AGS under partial information. We analyze the complexity and decidability in different settings, showing that the problem has a high worstcase complexity and is undecidable in many interesting cases. Based on these observations, we present a pragmatic algorithm based on bounded synthesis, and demonstrate its practical applicability on several examples."}],"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"main_file_link":[{"url":"http://arxiv.org/abs/1411.4604","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-46681-0_50","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2015-04-18","location":"London, United Kingdom","start_date":"2015-04-11"},"month":"01","department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","year":"2015","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through the research network RiSE (S11406-N23, S11407-N23) and grant nr. P23499-N23, by the European Commission through an ERC Start grant (279307: Graph Games) and project STANCE (317753), as well as by the German Research Foundation (DFG) through SFB/TR 14 AVACS and project ASDPS(JA 2357/2-1).","volume":9035,"date_updated":"2021-01-12T06:53:32Z","date_created":"2018-12-11T11:54:17Z","author":[{"last_name":"Bloem","first_name":"Roderick","full_name":"Bloem, Roderick"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Jacobs","first_name":"Swen","full_name":"Jacobs, Swen"},{"first_name":"Robert","last_name":"Könighofer","full_name":"Könighofer, Robert"}],"publist_id":"5264","ec_funded":1},{"volume":9035,"date_created":"2018-12-11T11:54:18Z","date_updated":"2020-01-21T13:18:52Z","author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Forejt, Vojtěch","last_name":"Forejt","first_name":"Vojtěch"},{"last_name":"Kučera","first_name":"Antonín","full_name":"Kučera, Antonín"}],"publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2015","publist_id":"5263","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-46681-0_12","conference":{"location":"London, United Kingdom","start_date":"2015-04-11","end_date":"2015-04-18","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.03093"}],"oa":1,"month":"01","oa_version":"Preprint","intvolume":" 9035","status":"public","title":"Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives","_id":"1839","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We present MultiGain, a tool to synthesize strategies for Markov decision processes (MDPs) with multiple mean-payoff objectives. Our models are described in PRISM, and our tool uses the existing interface and simulator of PRISM. Our tool extends PRISM by adding novel algorithms for multiple mean-payoff objectives, and also provides features such as (i) generating strategies and exploring them for simulation, and checking them with respect to other properties; and (ii) generating an approximate Pareto curve for two mean-payoff objectives. In addition, we present a new practical algorithm for the analysis of MDPs with multiple mean-payoff objectives under memoryless strategies.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2015-01-01T00:00:00Z","page":"181 - 187","citation":{"apa":"Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2015). Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_12","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives,” vol. 9035. Springer, pp. 181–187, 2015.","ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2015. Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. 9035, 181–187.","ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. 2015;9035:181-187. doi:10.1007/978-3-662-46681-0_12","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_12.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, 9035 (2015) 181–187.","mla":"Brázdil, Tomáš, et al. Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives. Vol. 9035, Springer, 2015, pp. 181–87, doi:10.1007/978-3-662-46681-0_12."},"day":"01","series_title":"Lecture Notes in Computer Science"},{"oa_version":"Preprint","title":"Subcritical versus supercritical transition to turbulence in curved pipes","status":"public","intvolume":" 770","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1837","abstract":[{"text":"Transition to turbulence in straight pipes occurs in spite of the linear stability of the laminar Hagen-Poiseuille flow if both the amplitude of flow perturbations and the Reynolds number Re exceed a minimum threshold (subcritical transition). As the pipe curvature increases, centrifugal effects become important, modifying the basic flow as well as the most unstable linear modes. If the curvature (tube-to-coiling diameter d/D) is sufficiently large, a Hopf bifurcation (supercritical instability) is encountered before turbulence can be excited (subcritical instability). We trace the instability thresholds in the Re - d/D parameter space in the range 0.01 ≤ d/D\\ ≤ 0.1 by means of laser-Doppler velocimetry and determine the point where the subcritical and supercritical instabilities meet. Two different experimental set-ups are used: a closed system where the pipe forms an axisymmetric torus and an open system employing a helical pipe. Implications for the measurement of friction factors in curved pipes are discussed.","lang":"eng"}],"issue":"5","type":"journal_article","date_published":"2015-04-08T00:00:00Z","article_type":"original","publication":"Journal of Fluid Mechanics","citation":{"chicago":"Kühnen, Jakob, P Braunshier, M Schwegel, Hendrik Kuhlmann, and Björn Hof. “Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” Journal of Fluid Mechanics. Cambridge University Press, 2015. https://doi.org/10.1017/jfm.2015.184.","mla":"Kühnen, Jakob, et al. “Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” Journal of Fluid Mechanics, vol. 770, no. 5, R3, Cambridge University Press, 2015, doi:10.1017/jfm.2015.184.","short":"J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, B. Hof, Journal of Fluid Mechanics 770 (2015).","ista":"Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. 2015. Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. 770(5), R3.","apa":"Kühnen, J., Braunshier, P., Schwegel, M., Kuhlmann, H., & Hof, B. (2015). Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2015.184","ieee":"J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, and B. Hof, “Subcritical versus supercritical transition to turbulence in curved pipes,” Journal of Fluid Mechanics, vol. 770, no. 5. Cambridge University Press, 2015.","ama":"Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. 2015;770(5). doi:10.1017/jfm.2015.184"},"day":"08","article_processing_charge":"No","scopus_import":1,"date_created":"2018-12-11T11:54:17Z","date_updated":"2021-01-12T06:53:31Z","volume":770,"author":[{"full_name":"Kühnen, Jakob","orcid":"0000-0003-4312-0179","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","last_name":"Kühnen","first_name":"Jakob"},{"full_name":"Braunshier, P","first_name":"P","last_name":"Braunshier"},{"first_name":"M","last_name":"Schwegel","full_name":"Schwegel, M"},{"full_name":"Kuhlmann, Hendrik","last_name":"Kuhlmann","first_name":"Hendrik"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Cambridge University Press","year":"2015","publist_id":"5265","ec_funded":1,"article_number":"R3","language":[{"iso":"eng"}],"doi":"10.1017/jfm.2015.184","quality_controlled":"1","project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589"}],"external_id":{"arxiv":["1508.06559"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.06559"}],"oa":1,"month":"04"},{"intvolume":" 137","title":"FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1848","oa_version":"Submitted Version","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"The ability to escape apoptosis is a hallmark of cancer-initiating cells and a key factor of resistance to oncolytic therapy. Here, we identify FAM96A as a ubiquitous, evolutionarily conserved apoptosome-activating protein and investigate its potential pro-apoptotic tumor suppressor function in gastrointestinal stromal tumors (GISTs). Interaction between FAM96A and apoptotic peptidase activating factor 1 (APAF1) was identified in yeast two-hybrid screen and further studied by deletion mutants, glutathione-S-transferase pull-down, co-immunoprecipitation and immunofluorescence. Effects of FAM96A overexpression and knock-down on apoptosis sensitivity were examined in cancer cells and zebrafish embryos. Expression of FAM96A in GISTs and histogenetically related cells including interstitial cells of Cajal (ICCs), “fibroblast-like cells” (FLCs) and ICC stem cells (ICC-SCs) was investigated by Northern blotting, reverse transcription—polymerase chain reaction, immunohistochemistry and Western immunoblotting. Tumorigenicity of GIST cells and transformed murine ICC-SCs stably transduced to re-express FAM96A was studied by xeno- and allografting into immunocompromised mice. FAM96A was found to bind APAF1 and to enhance the induction of mitochondrial apoptosis. FAM96A protein or mRNA was dramatically reduced or lost in 106 of 108 GIST samples representing three independent patient cohorts. Whereas ICCs, ICC-SCs and FLCs, the presumed normal counterparts of GIST, were found to robustly express FAM96A protein and mRNA, FAM96A expression was much reduced in tumorigenic ICC-SCs. Re-expression of FAM96A in GIST cells and transformed ICC-SCs increased apoptosis sensitivity and diminished tumorigenicity. Our data suggest FAM96A is a novel pro-apoptotic tumor suppressor that is lost during GIST tumorigenesis."}],"page":"1318 - 1329","article_type":"original","citation":{"ista":"Schwamb B, Pick R, Fernández S, Völp K, Heering J, Dötsch V, Bösser S, Jung J, Beinoravičiute Kellner R, Wesely J, Zörnig I, Hammerschmidt M, Nowak M, Penzel R, Zatloukal K, Joos S, Rieker R, Agaimy A, Söder S, Reid Lombardo K, Kendrick M, Bardsley M, Hayashi Y, Asuzu D, Syed S, Ördög T, Zörnig M. 2015. FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. 137(6), 1318–1329.","apa":"Schwamb, B., Pick, R., Fernández, S., Völp, K., Heering, J., Dötsch, V., … Zörnig, M. (2015). FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. Wiley. https://doi.org/10.1002/ijc.29498","ieee":"B. Schwamb et al., “FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors,” International Journal of Cancer, vol. 137, no. 6. Wiley, pp. 1318–1329, 2015.","ama":"Schwamb B, Pick R, Fernández S, et al. FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. 2015;137(6):1318-1329. doi:10.1002/ijc.29498","chicago":"Schwamb, Bettina, Robert Pick, Sara Fernández, Kirsten Völp, Jan Heering, Volker Dötsch, Susanne Bösser, et al. “FAM96A Is a Novel Pro-Apoptotic Tumor Suppressor in Gastrointestinal Stromal Tumors.” International Journal of Cancer. Wiley, 2015. https://doi.org/10.1002/ijc.29498.","mla":"Schwamb, Bettina, et al. “FAM96A Is a Novel Pro-Apoptotic Tumor Suppressor in Gastrointestinal Stromal Tumors.” International Journal of Cancer, vol. 137, no. 6, Wiley, 2015, pp. 1318–29, doi:10.1002/ijc.29498.","short":"B. Schwamb, R. Pick, S. Fernández, K. Völp, J. Heering, V. Dötsch, S. Bösser, J. Jung, R. Beinoravičiute Kellner, J. Wesely, I. Zörnig, M. Hammerschmidt, M. Nowak, R. Penzel, K. Zatloukal, S. Joos, R. Rieker, A. Agaimy, S. Söder, K. Reid Lombardo, M. Kendrick, M. Bardsley, Y. Hayashi, D. Asuzu, S. Syed, T. Ördög, M. Zörnig, International Journal of Cancer 137 (2015) 1318–1329."},"publication":"International Journal of Cancer","date_published":"2015-09-01T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"01","department":[{"_id":"LifeSc"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2015","volume":137,"date_updated":"2021-01-12T06:53:36Z","date_created":"2018-12-11T11:54:20Z","author":[{"first_name":"Bettina","last_name":"Schwamb","full_name":"Schwamb, Bettina"},{"full_name":"Pick, Robert","last_name":"Pick","first_name":"Robert"},{"last_name":"Fernández","first_name":"Sara","full_name":"Fernández, Sara"},{"full_name":"Völp, Kirsten","first_name":"Kirsten","last_name":"Völp"},{"full_name":"Heering, Jan","first_name":"Jan","last_name":"Heering"},{"full_name":"Dötsch, Volker","first_name":"Volker","last_name":"Dötsch"},{"full_name":"Bösser, Susanne","first_name":"Susanne","last_name":"Bösser"},{"full_name":"Jung, Jennifer","last_name":"Jung","first_name":"Jennifer"},{"first_name":"Rasa","last_name":"Beinoravičiute Kellner","full_name":"Beinoravičiute Kellner, Rasa"},{"first_name":"Josephine","last_name":"Wesely","full_name":"Wesely, Josephine"},{"full_name":"Zörnig, Inka","last_name":"Zörnig","first_name":"Inka"},{"full_name":"Hammerschmidt, Matthias","first_name":"Matthias","last_name":"Hammerschmidt"},{"full_name":"Nowak, Matthias","id":"30845DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Nowak"},{"full_name":"Penzel, Roland","last_name":"Penzel","first_name":"Roland"},{"full_name":"Zatloukal, Kurt","first_name":"Kurt","last_name":"Zatloukal"},{"full_name":"Joos, Stefan","first_name":"Stefan","last_name":"Joos"},{"last_name":"Rieker","first_name":"Ralf","full_name":"Rieker, Ralf"},{"full_name":"Agaimy, Abbas","last_name":"Agaimy","first_name":"Abbas"},{"first_name":"Stephan","last_name":"Söder","full_name":"Söder, Stephan"},{"full_name":"Reid Lombardo, Kmarie","first_name":"Kmarie","last_name":"Reid Lombardo"},{"full_name":"Kendrick, Michael","last_name":"Kendrick","first_name":"Michael"},{"first_name":"Michael","last_name":"Bardsley","full_name":"Bardsley, Michael"},{"first_name":"Yujiro","last_name":"Hayashi","full_name":"Hayashi, Yujiro"},{"full_name":"Asuzu, David","first_name":"David","last_name":"Asuzu"},{"full_name":"Syed, Sabriya","last_name":"Syed","first_name":"Sabriya"},{"full_name":"Ördög, Tamás","first_name":"Tamás","last_name":"Ördög"},{"first_name":"Martin","last_name":"Zörnig","full_name":"Zörnig, Martin"}],"publist_id":"5253","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497860/","open_access":"1"}],"external_id":{"pmid":["25716227"]},"language":[{"iso":"eng"}],"doi":"10.1002/ijc.29498","month":"09"},{"oa":1,"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"quality_controlled":"1","doi":"10.1007/s00236-015-0215-4","language":[{"iso":"eng"}],"month":"04","year":"2015","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","author":[{"full_name":"Beneš, Nikola","first_name":"Nikola","last_name":"Beneš"},{"last_name":"Kretinsky","first_name":"Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan"},{"first_name":"Kim","last_name":"Larsen","full_name":"Larsen, Kim"},{"full_name":"Möller, Mikael","first_name":"Mikael","last_name":"Möller"},{"first_name":"Salomon","last_name":"Sickert","full_name":"Sickert, Salomon"},{"first_name":"Jiří","last_name":"Srba","full_name":"Srba, Jiří"}],"volume":52,"date_created":"2018-12-11T11:54:20Z","date_updated":"2021-01-12T06:53:35Z","ec_funded":1,"publist_id":"5255","file_date_updated":"2020-07-14T12:45:19Z","citation":{"ieee":"N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, and J. Srba, “Refinement checking on parametric modal transition systems,” Acta Informatica, vol. 52, no. 2–3. Springer, pp. 269–297, 2015.","apa":"Beneš, N., Kretinsky, J., Larsen, K., Möller, M., Sickert, S., & Srba, J. (2015). Refinement checking on parametric modal transition systems. Acta Informatica. Springer. https://doi.org/10.1007/s00236-015-0215-4","ista":"Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. 2015. Refinement checking on parametric modal transition systems. Acta Informatica. 52(2–3), 269–297.","ama":"Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. Refinement checking on parametric modal transition systems. Acta Informatica. 2015;52(2-3):269-297. doi:10.1007/s00236-015-0215-4","chicago":"Beneš, Nikola, Jan Kretinsky, Kim Larsen, Mikael Möller, Salomon Sickert, and Jiří Srba. “Refinement Checking on Parametric Modal Transition Systems.” Acta Informatica. Springer, 2015. https://doi.org/10.1007/s00236-015-0215-4.","short":"N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, J. Srba, Acta Informatica 52 (2015) 269–297.","mla":"Beneš, Nikola, et al. “Refinement Checking on Parametric Modal Transition Systems.” Acta Informatica, vol. 52, no. 2–3, Springer, 2015, pp. 269–97, doi:10.1007/s00236-015-0215-4."},"publication":"Acta Informatica","page":"269 - 297","article_type":"original","date_published":"2015-04-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","article_processing_charge":"No","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1846","intvolume":" 52","ddc":["000"],"title":"Refinement checking on parametric modal transition systems","status":"public","file":[{"file_name":"2015_ActaInfo_Benes.pdf","access_level":"open_access","content_type":"application/pdf","file_size":488482,"creator":"dernst","relation":"main_file","file_id":"7854","date_created":"2020-05-15T08:57:44Z","date_updated":"2020-07-14T12:45:19Z","checksum":"fb4037ddc4fc05f33080dd3547ede350"}],"oa_version":"Submitted Version","type":"journal_article","issue":"2-3","abstract":[{"text":"Modal transition systems (MTS) is a well-studied specification formalism of reactive systems supporting a step-wise refinement methodology. Despite its many advantages, the formalism as well as its currently known extensions are incapable of expressing some practically needed aspects in the refinement process like exclusive, conditional and persistent choices. We introduce a new model called parametric modal transition systems (PMTS) together with a general modal refinement notion that overcomes many of the limitations. We investigate the computational complexity of modal and thorough refinement checking on PMTS and its subclasses and provide a direct encoding of the modal refinement problem into quantified Boolean formulae, allowing us to employ state-of-the-art QBF solvers for modal refinement checking. The experiments we report on show that the feasibility of refinement checking is more influenced by the degree of nondeterminism rather than by the syntactic restrictions on the types of formulae allowed in the description of the PMTS.","lang":"eng"}]},{"year":"2015","department":[{"_id":"PeJo"}],"publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","first_name":"David H","last_name":"Vandael"},{"id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082","first_name":"Claudia ","last_name":"Espinoza Martinez","full_name":"Espinoza Martinez, Claudia "},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"volume":85,"date_created":"2018-12-11T11:54:19Z","date_updated":"2021-10-08T09:07:34Z","publist_id":"5256","file_date_updated":"2020-07-14T12:45:19Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","doi":"10.1016/j.neuron.2015.03.006","language":[{"iso":"eng"}],"month":"03","_id":"1845","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 85","ddc":["570"],"status":"public","title":"Excitement about inhibitory presynaptic terminals","pubrep_id":"822","file":[{"date_created":"2018-12-12T10:16:07Z","date_updated":"2020-07-14T12:45:19Z","checksum":"d1808550e376a0eca2a950fda017cfa6","relation":"main_file","file_id":"5192","content_type":"application/pdf","file_size":411832,"creator":"system","file_name":"IST-2017-822-v1+1_Perspective_Fig__Final.pdf","access_level":"open_access"},{"file_id":"5193","relation":"main_file","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:16:07Z","checksum":"a279f4ae61e6c8f33d68f69a0d02097d","file_name":"IST-2017-822-v1+2_Perspective_Final2.pdf","access_level":"open_access","creator":"system","file_size":100769,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"6","abstract":[{"text":"Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression. Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression.","lang":"eng"}],"citation":{"ista":"Vandael DH, Espinoza Martinez C, Jonas PM. 2015. Excitement about inhibitory presynaptic terminals. Neuron. 85(6), 1149–1151.","ieee":"D. H. Vandael, C. Espinoza Martinez, and P. M. Jonas, “Excitement about inhibitory presynaptic terminals,” Neuron, vol. 85, no. 6. Elsevier, pp. 1149–1151, 2015.","apa":"Vandael, D. H., Espinoza Martinez, C., & Jonas, P. M. (2015). Excitement about inhibitory presynaptic terminals. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.03.006","ama":"Vandael DH, Espinoza Martinez C, Jonas PM. Excitement about inhibitory presynaptic terminals. Neuron. 2015;85(6):1149-1151. doi:10.1016/j.neuron.2015.03.006","chicago":"Vandael, David H, Claudia Espinoza Martinez, and Peter M Jonas. “Excitement about Inhibitory Presynaptic Terminals.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.03.006.","mla":"Vandael, David H., et al. “Excitement about Inhibitory Presynaptic Terminals.” Neuron, vol. 85, no. 6, Elsevier, 2015, pp. 1149–51, doi:10.1016/j.neuron.2015.03.006.","short":"D.H. Vandael, C. Espinoza Martinez, P.M. Jonas, Neuron 85 (2015) 1149–1151."},"publication":"Neuron","page":"1149 - 1151","date_published":"2015-03-18T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"18"},{"month":"04","publication_identifier":{"issn":["0018-9286"]},"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.6603"}],"language":[{"iso":"eng"}],"doi":"10.1109/TAC.2014.2364971","publist_id":"5262","publication_status":"published","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"publisher":"IEEE","acknowledgement":"This work was supported by the Austrian Research Association under Project 06/12684, by the Swiss National Science Foundation (SNSF) under Grant PP00P2 128503/1, by the SystemsX.ch (the Swiss Inititative for Systems Biology), and by a SNSF Early Postdoc.Mobility Fellowship grant P2EZP2_148797.\r\n","year":"2015","date_updated":"2021-01-12T06:53:33Z","date_created":"2018-12-11T11:54:18Z","volume":60,"author":[{"first_name":"Bernhard","last_name":"Geiger","full_name":"Geiger, Bernhard"},{"full_name":"Petrov, Tatjana","last_name":"Petrov","first_name":"Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kubin, Gernot","last_name":"Kubin","first_name":"Gernot"},{"full_name":"Koeppl, Heinz","last_name":"Koeppl","first_name":"Heinz"}],"scopus_import":1,"day":"01","page":"1010 - 1022","publication":"IEEE Transactions on Automatic Control","citation":{"ieee":"B. Geiger, T. Petrov, G. Kubin, and H. Koeppl, “Optimal Kullback-Leibler aggregation via information bottleneck,” IEEE Transactions on Automatic Control, vol. 60, no. 4. IEEE, pp. 1010–1022, 2015.","apa":"Geiger, B., Petrov, T., Kubin, G., & Koeppl, H. (2015). Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. IEEE. https://doi.org/10.1109/TAC.2014.2364971","ista":"Geiger B, Petrov T, Kubin G, Koeppl H. 2015. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 60(4), 1010–1022.","ama":"Geiger B, Petrov T, Kubin G, Koeppl H. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 2015;60(4):1010-1022. doi:10.1109/TAC.2014.2364971","chicago":"Geiger, Bernhard, Tatjana Petrov, Gernot Kubin, and Heinz Koeppl. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” IEEE Transactions on Automatic Control. IEEE, 2015. https://doi.org/10.1109/TAC.2014.2364971.","short":"B. Geiger, T. Petrov, G. Kubin, H. Koeppl, IEEE Transactions on Automatic Control 60 (2015) 1010–1022.","mla":"Geiger, Bernhard, et al. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” IEEE Transactions on Automatic Control, vol. 60, no. 4, IEEE, 2015, pp. 1010–22, doi:10.1109/TAC.2014.2364971."},"date_published":"2015-04-01T00:00:00Z","type":"journal_article","abstract":[{"text":"In this paper, we present a method for reducing a regular, discrete-time Markov chain (DTMC) to another DTMC with a given, typically much smaller number of states. The cost of reduction is defined as the Kullback-Leibler divergence rate between a projection of the original process through a partition function and a DTMC on the correspondingly partitioned state space. Finding the reduced model with minimal cost is computationally expensive, as it requires an exhaustive search among all state space partitions, and an exact evaluation of the reduction cost for each candidate partition. Our approach deals with the latter problem by minimizing an upper bound on the reduction cost instead of minimizing the exact cost. The proposed upper bound is easy to compute and it is tight if the original chain is lumpable with respect to the partition. Then, we express the problem in the form of information bottleneck optimization, and propose using the agglomerative information bottleneck algorithm for searching a suboptimal partition greedily, rather than exhaustively. The theory is illustrated with examples and one application scenario in the context of modeling bio-molecular interactions.","lang":"eng"}],"issue":"4","title":"Optimal Kullback-Leibler aggregation via information bottleneck","status":"public","intvolume":" 60","_id":"1840","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"date_published":"2015-05-01T00:00:00Z","page":"919 - 930","citation":{"chicago":"Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2015. https://doi.org/10.1109/TPAMI.2014.2363465.","mla":"Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37, no. 5, IEEE, 2015, pp. 919–30, doi:10.1109/TPAMI.2014.2363465.","short":"V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence 37 (2015) 919–930.","ista":"Kolmogorov V. 2015. A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 37(5), 919–930.","ieee":"V. Kolmogorov, “A new look at reweighted message passing,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37, no. 5. IEEE, pp. 919–930, 2015.","apa":"Kolmogorov, V. (2015). A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2014.2363465","ama":"Kolmogorov V. A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2015;37(5):919-930. doi:10.1109/TPAMI.2014.2363465"},"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","day":"01","scopus_import":1,"oa_version":"Preprint","intvolume":" 37","title":"A new look at reweighted message passing","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1841","issue":"5","abstract":[{"text":"We propose a new family of message passing techniques for MAP estimation in graphical models which we call Sequential Reweighted Message Passing (SRMP). Special cases include well-known techniques such as Min-Sum Diffusion (MSD) and a faster Sequential Tree-Reweighted Message Passing (TRW-S). Importantly, our derivation is simpler than the original derivation of TRW-S, and does not involve a decomposition into trees. This allows easy generalizations. The new family of algorithms can be viewed as a generalization of TRW-S from pairwise to higher-order graphical models. We test SRMP on several real-world problems with promising results.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1109/TPAMI.2014.2363465","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1309.5655","open_access":"1"}],"oa":1,"month":"05","volume":37,"date_created":"2018-12-11T11:54:18Z","date_updated":"2021-01-12T06:53:33Z","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"}],"publisher":"IEEE","department":[{"_id":"VlKo"}],"publication_status":"published","year":"2015","publist_id":"5261","ec_funded":1},{"_id":"1849","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The contributing authors were supported by the Ghent University Special Research Fund (to E.H.), the Interuniversity Attraction Poles Programme (IAP VI/33 and IUAP P7/29 ‘MARS’), the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), and the Research Foundation Flanders (to S.V.).","year":"2015","title":"Calcium is an organizer of cell polarity in plants","publication_status":"published","status":"public","publisher":"Elsevier","department":[{"_id":"JiFr"}],"intvolume":" 1853","author":[{"last_name":"Himschoot","first_name":"Ellie","full_name":"Himschoot, Ellie"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"last_name":"Friml","first_name":"Jiřĺ","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiřĺ"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"}],"date_updated":"2021-01-12T06:53:36Z","date_created":"2018-12-11T11:54:21Z","oa_version":"None","volume":1853,"type":"journal_article","abstract":[{"lang":"eng","text":"Cell polarity is a fundamental property of pro- and eukaryotic cells. It is necessary for coordination of cell division, cell morphogenesis and signaling processes. How polarity is generated and maintained is a complex issue governed by interconnected feed-back regulations between small GTPase signaling and membrane tension-based signaling that controls membrane trafficking, and cytoskeleton organization and dynamics. Here, we will review the potential role for calcium as a crucial signal that connects and coordinates the respective processes during polarization processes in plants. This article is part of a Special Issue entitled: 13th European Symposium on Calcium."}],"issue":"9","publist_id":"5252","publication":"Biochimica et Biophysica Acta - Molecular Cell Research","citation":{"chicago":"Himschoot, Ellie, Tom Beeckman, Jiří Friml, and Steffen Vanneste. “Calcium Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2015.02.017.","short":"E. Himschoot, T. Beeckman, J. Friml, S. Vanneste, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 2168–2172.","mla":"Himschoot, Ellie, et al. “Calcium Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 9, Elsevier, 2015, pp. 2168–72, doi:10.1016/j.bbamcr.2015.02.017.","apa":"Himschoot, E., Beeckman, T., Friml, J., & Vanneste, S. (2015). Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2015.02.017","ieee":"E. Himschoot, T. Beeckman, J. Friml, and S. Vanneste, “Calcium is an organizer of cell polarity in plants,” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 9. Elsevier, pp. 2168–2172, 2015.","ista":"Himschoot E, Beeckman T, Friml J, Vanneste S. 2015. Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(9), 2168–2172.","ama":"Himschoot E, Beeckman T, Friml J, Vanneste S. Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. 2015;1853(9):2168-2172. doi:10.1016/j.bbamcr.2015.02.017"},"quality_controlled":"1","page":"2168 - 2172","date_published":"2015-09-01T00:00:00Z","doi":"10.1016/j.bbamcr.2015.02.017","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"09"},{"scopus_import":1,"month":"03","day":"02","citation":{"ieee":"P. Grones and J. Friml, “ABP1: Finally docking,” Molecular Plant, vol. 8, no. 3. Elsevier, pp. 356–358, 2015.","apa":"Grones, P., & Friml, J. (2015). ABP1: Finally docking. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2014.12.013","ista":"Grones P, Friml J. 2015. ABP1: Finally docking. Molecular Plant. 8(3), 356–358.","ama":"Grones P, Friml J. ABP1: Finally docking. Molecular Plant. 2015;8(3):356-358. doi:10.1016/j.molp.2014.12.013","chicago":"Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant. Elsevier, 2015. https://doi.org/10.1016/j.molp.2014.12.013.","short":"P. Grones, J. Friml, Molecular Plant 8 (2015) 356–358.","mla":"Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant, vol. 8, no. 3, Elsevier, 2015, pp. 356–58, doi:10.1016/j.molp.2014.12.013."},"publication":"Molecular Plant","page":"356 - 358","quality_controlled":"1","doi":"10.1016/j.molp.2014.12.013","date_published":"2015-03-02T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","issue":"3","publist_id":"5254","_id":"1847","year":"2015","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), European Social Fund (CZ.1.07/2.3.00/20.0043), and the Czech Science Foundation GAČR (GA13-40637S).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8","publisher":"Elsevier","department":[{"_id":"JiFr"}],"title":"ABP1: Finally docking","status":"public","publication_status":"published","author":[{"first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"full_name":"Friml, Jiřĺ","first_name":"Jiřĺ","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"volume":8,"oa_version":"None","date_created":"2018-12-11T11:54:20Z","date_updated":"2021-01-12T06:53:35Z"},{"year":"2015","publication_status":"published","publisher":"Elsevier","department":[{"_id":"NiBa"},{"_id":"SyCr"}],"author":[{"full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"}],"date_created":"2018-12-11T11:54:21Z","date_updated":"2021-01-12T06:53:37Z","volume":372,"file_date_updated":"2020-07-14T12:45:19Z","ec_funded":1,"publist_id":"5251","oa":1,"quality_controlled":"1","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"}],"doi":"10.1016/j.jtbi.2015.02.018","language":[{"iso":"eng"}],"month":"05","_id":"1850","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"title":"Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates","status":"public","intvolume":" 372","pubrep_id":"329","file":[{"date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:18:07Z","checksum":"3c0dcacc900bc45cc65a453dfda4ca43","file_id":"5326","relation":"main_file","creator":"system","file_size":1546914,"content_type":"application/pdf","file_name":"IST-2015-329-v1+1_manuscript.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Entomopathogenic fungi are potent biocontrol agents that are widely used against insect pests, many of which are social insects. Nevertheless, theoretical investigations of their particular life history are scarce. We develop a model that takes into account the main distinguishing features between traditionally studied diseases and obligate killing pathogens, like the (biocontrol-relevant) insect-pathogenic fungi Metarhizium and Beauveria. First, obligate killing entomopathogenic fungi produce new infectious particles (conidiospores) only after host death and not yet on the living host. Second, the killing rates of entomopathogenic fungi depend strongly on the initial exposure dosage, thus we explicitly consider the pathogen load of individual hosts. Further, we make the model applicable not only to solitary host species, but also to group living species by incorporating social interactions between hosts, like the collective disease defences of insect societies. Our results identify the optimal killing rate for the pathogen that minimises its invasion threshold. Furthermore, we find that the rate of contact between hosts has an ambivalent effect: dense interaction networks between individuals are considered to facilitate disease outbreaks because of increased pathogen transmission. In social insects, this is compensated by their collective disease defences, i.e., social immunity. For the type of pathogens considered here, we show that even without social immunity, high contact rates between live individuals dilute the pathogen in the host colony and hence can reduce individual pathogen loads below disease-causing levels.","lang":"eng"}],"issue":"5","publication":"Journal of Theoretical Biology","citation":{"mla":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” Journal of Theoretical Biology, vol. 372, no. 5, Elsevier, 2015, pp. 54–64, doi:10.1016/j.jtbi.2015.02.018.","short":"S. Novak, S. Cremer, Journal of Theoretical Biology 372 (2015) 54–64.","chicago":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.02.018.","ama":"Novak S, Cremer S. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 2015;372(5):54-64. doi:10.1016/j.jtbi.2015.02.018","ista":"Novak S, Cremer S. 2015. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 372(5), 54–64.","ieee":"S. Novak and S. Cremer, “Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates,” Journal of Theoretical Biology, vol. 372, no. 5. Elsevier, pp. 54–64, 2015.","apa":"Novak, S., & Cremer, S. (2015). Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.02.018"},"page":"54 - 64","date_published":"2015-05-07T00:00:00Z","scopus_import":1,"day":"07","has_accepted_license":"1"},{"month":"02","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"language":[{"iso":"eng"}],"doi":"10.1111/evo.12618","quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"oa":1,"external_id":{"pmid":["25662095"]},"file_date_updated":"2020-07-14T12:45:19Z","ec_funded":1,"publist_id":"5249","date_created":"2018-12-11T11:54:21Z","date_updated":"2022-06-07T10:52:37Z","volume":69,"author":[{"full_name":"Priklopil, Tadeas","last_name":"Priklopil","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kisdi","first_name":"Eva","full_name":"Kisdi, Eva"},{"first_name":"Mats","last_name":"Gyllenberg","full_name":"Gyllenberg, Mats"}],"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"year":"2015","pmid":1,"day":"09","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2015-02-09T00:00:00Z","article_type":"original","page":"1015 - 1026","publication":"Evolution","citation":{"short":"T. Priklopil, E. Kisdi, M. Gyllenberg, Evolution 69 (2015) 1015–1026.","mla":"Priklopil, Tadeas, et al. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” Evolution, vol. 69, no. 4, Wiley, 2015, pp. 1015–26, doi:10.1111/evo.12618.","chicago":"Priklopil, Tadeas, Eva Kisdi, and Mats Gyllenberg. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12618.","ama":"Priklopil T, Kisdi E, Gyllenberg M. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. 2015;69(4):1015-1026. doi:10.1111/evo.12618","apa":"Priklopil, T., Kisdi, E., & Gyllenberg, M. (2015). Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. Wiley. https://doi.org/10.1111/evo.12618","ieee":"T. Priklopil, E. Kisdi, and M. Gyllenberg, “Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating,” Evolution, vol. 69, no. 4. Wiley, pp. 1015–1026, 2015.","ista":"Priklopil T, Kisdi E, Gyllenberg M. 2015. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. 69(4), 1015–1026."},"abstract":[{"text":"We consider mating strategies for females who search for males sequentially during a season of limited length. We show that the best strategy rejects a given male type if encountered before a time-threshold but accepts him after. For frequency-independent benefits, we obtain the optimal time-thresholds explicitly for both discrete and continuous distributions of males, and allow for mistakes being made in assessing the correct male type. When the benefits are indirect (genes for the offspring) and the population is under frequency-dependent ecological selection, the benefits depend on the mating strategy of other females as well. This case is particularly relevant to speciation models that seek to explore the stability of reproductive isolation by assortative mating under frequency-dependent ecological selection. We show that the indirect benefits are to be quantified by the reproductive values of couples, and describe how the evolutionarily stable time-thresholds can be found. We conclude with an example based on the Levene model, in which we analyze the evolutionarily stable assortative mating strategies and the strength of reproductive isolation provided by them.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2015_Evolution_Priklopil.pdf","file_size":967214,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7855","checksum":"1e8be0b1d7598a78cd2623d8ee8e7798","date_created":"2020-05-15T09:05:34Z","date_updated":"2020-07-14T12:45:19Z"}],"status":"public","title":"Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating","ddc":["570"],"intvolume":" 69","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1851"},{"type":"conference","ec_funded":1,"publist_id":"5240","abstract":[{"text":"Structural support vector machines (SSVMs) are amongst the best performing models for structured computer vision tasks, such as semantic image segmentation or human pose estimation. Training SSVMs, however, is computationally costly, because it requires repeated calls to a structured prediction subroutine (called \\emph{max-oracle}), which has to solve an optimization problem itself, e.g. a graph cut.\r\nIn this work, we introduce a new algorithm for SSVM training that is more efficient than earlier techniques when the max-oracle is computationally expensive, as it is frequently the case in computer vision tasks. The main idea is to (i) combine the recent stochastic Block-Coordinate Frank-Wolfe algorithm with efficient hyperplane caching, and (ii) use an automatic selection rule for deciding whether to call the exact max-oracle or to rely on an approximate one based on the cached hyperplanes.\r\nWe show experimentally that this strategy leads to faster convergence to the optimum with respect to the number of requires oracle calls, and that this translates into faster convergence with respect to the total runtime when the max-oracle is slow compared to the other steps of the algorithm. ","lang":"eng"}],"_id":"1859","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"VlKo"},{"_id":"ChLa"}],"publisher":"IEEE","title":"A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle","status":"public","publication_status":"published","author":[{"last_name":"Shah","first_name":"Neel","id":"31ABAF80-F248-11E8-B48F-1D18A9856A87","full_name":"Shah, Neel"},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"oa_version":"Preprint","date_created":"2018-12-11T11:54:24Z","date_updated":"2021-01-12T06:53:40Z","scopus_import":1,"month":"06","day":"01","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1408.6804","open_access":"1"}],"citation":{"ista":"Shah N, Kolmogorov V, Lampert C. 2015. A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle. CVPR: Computer Vision and Pattern Recognition, 2737–2745.","apa":"Shah, N., Kolmogorov, V., & Lampert, C. (2015). A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle (pp. 2737–2745). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7298890","ieee":"N. Shah, V. Kolmogorov, and C. Lampert, “A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 2737–2745.","ama":"Shah N, Kolmogorov V, Lampert C. A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle. In: IEEE; 2015:2737-2745. doi:10.1109/CVPR.2015.7298890","chicago":"Shah, Neel, Vladimir Kolmogorov, and Christoph Lampert. “A Multi-Plane Block-Coordinate Frank-Wolfe Algorithm for Training Structural SVMs with a Costly Max-Oracle,” 2737–45. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7298890.","mla":"Shah, Neel, et al. A Multi-Plane Block-Coordinate Frank-Wolfe Algorithm for Training Structural SVMs with a Costly Max-Oracle. IEEE, 2015, pp. 2737–45, doi:10.1109/CVPR.2015.7298890.","short":"N. Shah, V. Kolmogorov, C. Lampert, in:, IEEE, 2015, pp. 2737–2745."},"page":"2737 - 2745","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"},{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"quality_controlled":"1","date_published":"2015-06-01T00:00:00Z","doi":"10.1109/CVPR.2015.7298890","conference":{"end_date":"2015-06-12","start_date":"2015-06-07","location":"Boston, MA, USA","name":"CVPR: Computer Vision and Pattern Recognition"},"language":[{"iso":"eng"}]},{"scopus_import":1,"month":"06","day":"01","main_file_link":[{"open_access":"1","url":"http://www.cv-foundation.org/openaccess/content_cvpr_2015/papers/Royer_Classifier_Adaptation_at_2015_CVPR_paper.pdf"}],"citation":{"ista":"Royer A, Lampert C. 2015. Classifier adaptation at prediction time. CVPR: Computer Vision and Pattern Recognition, 1401–1409.","apa":"Royer, A., & Lampert, C. (2015). Classifier adaptation at prediction time (pp. 1401–1409). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States: IEEE. https://doi.org/10.1109/CVPR.2015.7298746","ieee":"A. Royer and C. Lampert, “Classifier adaptation at prediction time,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States, 2015, pp. 1401–1409.","ama":"Royer A, Lampert C. Classifier adaptation at prediction time. In: IEEE; 2015:1401-1409. doi:10.1109/CVPR.2015.7298746","chicago":"Royer, Amélie, and Christoph Lampert. “Classifier Adaptation at Prediction Time,” 1401–9. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7298746.","mla":"Royer, Amélie, and Christoph Lampert. Classifier Adaptation at Prediction Time. IEEE, 2015, pp. 1401–09, doi:10.1109/CVPR.2015.7298746.","short":"A. Royer, C. Lampert, in:, IEEE, 2015, pp. 1401–1409."},"oa":1,"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"page":"1401 - 1409","quality_controlled":"1","doi":"10.1109/CVPR.2015.7298746","date_published":"2015-06-01T00:00:00Z","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","start_date":"2015-06-07","location":"Boston, MA, United States","end_date":"2015-06-12"},"language":[{"iso":"eng"}],"type":"conference","ec_funded":1,"publist_id":"5239","abstract":[{"lang":"eng","text":"Classifiers for object categorization are usually evaluated by their accuracy on a set of i.i.d. test examples. This provides us with an estimate of the expected error when applying the classifiers to a single new image. In real application, however, classifiers are rarely only used for a single image and then discarded. Instead, they are applied sequentially to many images, and these are typically not i.i.d. samples from a fixed data distribution, but they carry dependencies and their class distribution varies over time. In this work, we argue that the phenomenon of correlated data at prediction time is not a nuisance, but a blessing in disguise. We describe a probabilistic method for adapting classifiers at prediction time without having to retrain them. We also introduce a framework for creating realistically distributed image sequences, which offers a way to benchmark classifier adaptation methods, such as the one we propose. Experiments on the ILSVRC2010 and ILSVRC2012 datasets show that adapting object classification systems at prediction time can significantly reduce their error rate, even with no additional human feedback."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1860","year":"2015","department":[{"_id":"ChLa"}],"publisher":"IEEE","title":"Classifier adaptation at prediction time","status":"public","publication_status":"published","author":[{"last_name":"Royer","first_name":"Amélie","full_name":"Royer, Amélie"},{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","date_updated":"2021-01-12T06:53:41Z","date_created":"2018-12-11T11:54:24Z"},{"publist_id":"5241","abstract":[{"text":"We study the problem of predicting the future, though only in the probabilistic sense of estimating a future state of a time-varying probability distribution. This is not only an interesting academic problem, but solving this extrapolation problem also has many practical application, e.g. for training classifiers that have to operate under time-varying conditions. Our main contribution is a method for predicting the next step of the time-varying distribution from a given sequence of sample sets from earlier time steps. For this we rely on two recent machine learning techniques: embedding probability distributions into a reproducing kernel Hilbert space, and learning operators by vector-valued regression. We illustrate the working principles and the practical usefulness of our method by experiments on synthetic and real data. We also highlight an exemplary application: training a classifier in a domain adaptation setting without having access to examples from the test time distribution at training time.","lang":"eng"}],"type":"conference","oa_version":"Preprint","date_created":"2018-12-11T11:54:24Z","date_updated":"2021-01-12T06:53:40Z","author":[{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"}],"publisher":"IEEE","department":[{"_id":"ChLa"}],"publication_status":"published","title":"Predicting the future behavior of a time-varying probability distribution","status":"public","_id":"1858","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","month":"10","day":"15","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1109/CVPR.2015.7298696","date_published":"2015-10-15T00:00:00Z","conference":{"end_date":"2015-06-12","start_date":"2015-06-07","location":"Boston, MA, United States","name":"CVPR: Computer Vision and Pattern Recognition"},"page":"942 - 950","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1406.5362"]},"citation":{"ista":"Lampert C. 2015. Predicting the future behavior of a time-varying probability distribution. CVPR: Computer Vision and Pattern Recognition, 942–950.","apa":"Lampert, C. (2015). Predicting the future behavior of a time-varying probability distribution (pp. 942–950). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States: IEEE. https://doi.org/10.1109/CVPR.2015.7298696","ieee":"C. Lampert, “Predicting the future behavior of a time-varying probability distribution,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States, 2015, pp. 942–950.","ama":"Lampert C. Predicting the future behavior of a time-varying probability distribution. In: IEEE; 2015:942-950. doi:10.1109/CVPR.2015.7298696","chicago":"Lampert, Christoph. “Predicting the Future Behavior of a Time-Varying Probability Distribution,” 942–50. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7298696.","mla":"Lampert, Christoph. Predicting the Future Behavior of a Time-Varying Probability Distribution. IEEE, 2015, pp. 942–50, doi:10.1109/CVPR.2015.7298696.","short":"C. Lampert, in:, IEEE, 2015, pp. 942–950."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1406.5362"}]},{"oa_version":"Preprint","date_updated":"2023-02-23T10:17:31Z","date_created":"2018-12-11T11:54:23Z","author":[{"id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","last_name":"Pentina","first_name":"Anastasia","full_name":"Pentina, Anastasia"},{"id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308","first_name":"Viktoriia","last_name":"Sharmanska","full_name":"Sharmanska, Viktoriia"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"}],"department":[{"_id":"ChLa"}],"publisher":"IEEE","title":"Curriculum learning of multiple tasks","status":"public","publication_status":"published","year":"2015","_id":"1857","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5243","abstract":[{"lang":"eng","text":"Sharing information between multiple tasks enables algorithms to achieve good generalization performance even from small amounts of training data. However, in a realistic scenario of multi-task learning not all tasks are equally related to each other, hence it could be advantageous to transfer information only between the most related tasks. In this work we propose an approach that processes multiple tasks in a sequence with sharing between subsequent tasks instead of solving all tasks jointly. Subsequently, we address the question of curriculum learning of tasks, i.e. finding the best order of tasks to be learned. Our approach is based on a generalization bound criterion for choosing the task order that optimizes the average expected classification performance over all tasks. Our experimental results show that learning multiple related tasks sequentially can be more effective than learning them jointly, the order in which tasks are being solved affects the overall performance, and that our model is able to automatically discover the favourable order of tasks. "}],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1109/CVPR.2015.7299188","date_published":"2015-06-01T00:00:00Z","conference":{"end_date":"2015-06-12","location":"Boston, MA, United States","start_date":"2015-06-07","name":"CVPR: Computer Vision and Pattern Recognition"},"page":"5492 - 5500","quality_controlled":"1","oa":1,"citation":{"ama":"Pentina A, Sharmanska V, Lampert C. Curriculum learning of multiple tasks. In: IEEE; 2015:5492-5500. doi:10.1109/CVPR.2015.7299188","ieee":"A. Pentina, V. Sharmanska, and C. Lampert, “Curriculum learning of multiple tasks,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States, 2015, pp. 5492–5500.","apa":"Pentina, A., Sharmanska, V., & Lampert, C. (2015). Curriculum learning of multiple tasks (pp. 5492–5500). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States: IEEE. https://doi.org/10.1109/CVPR.2015.7299188","ista":"Pentina A, Sharmanska V, Lampert C. 2015. Curriculum learning of multiple tasks. CVPR: Computer Vision and Pattern Recognition, 5492–5500.","short":"A. Pentina, V. Sharmanska, C. Lampert, in:, IEEE, 2015, pp. 5492–5500.","mla":"Pentina, Anastasia, et al. Curriculum Learning of Multiple Tasks. IEEE, 2015, pp. 5492–500, doi:10.1109/CVPR.2015.7299188.","chicago":"Pentina, Anastasia, Viktoriia Sharmanska, and Christoph Lampert. “Curriculum Learning of Multiple Tasks,” 5492–5500. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299188."},"main_file_link":[{"url":"http://arxiv.org/abs/1412.1353","open_access":"1"}],"day":"01","month":"06","scopus_import":1},{"day":"01","scopus_import":1,"date_published":"2015-02-01T00:00:00Z","page":"518 - 525","publication":"Electrophoresis","citation":{"chicago":"Hühner, Jens, Álvaro Inglés Prieto, Christian Neusüß, Michael Lämmerhofer, and Harald L Janovjak. “Quantification of Riboflavin, Flavin Mononucleotide, and Flavin Adenine Dinucleotide in Mammalian Model Cells by CE with LED-Induced Fluorescence Detection.” Electrophoresis. Wiley, 2015. https://doi.org/10.1002/elps.201400451.","short":"J. Hühner, Á. Inglés Prieto, C. Neusüß, M. Lämmerhofer, H.L. Janovjak, Electrophoresis 36 (2015) 518–525.","mla":"Hühner, Jens, et al. “Quantification of Riboflavin, Flavin Mononucleotide, and Flavin Adenine Dinucleotide in Mammalian Model Cells by CE with LED-Induced Fluorescence Detection.” Electrophoresis, vol. 36, no. 4, Wiley, 2015, pp. 518–25, doi:10.1002/elps.201400451.","apa":"Hühner, J., Inglés Prieto, Á., Neusüß, C., Lämmerhofer, M., & Janovjak, H. L. (2015). Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. Electrophoresis. Wiley. https://doi.org/10.1002/elps.201400451","ieee":"J. Hühner, Á. Inglés Prieto, C. Neusüß, M. Lämmerhofer, and H. L. Janovjak, “Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection,” Electrophoresis, vol. 36, no. 4. Wiley, pp. 518–525, 2015.","ista":"Hühner J, Inglés Prieto Á, Neusüß C, Lämmerhofer M, Janovjak HL. 2015. Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. Electrophoresis. 36(4), 518–525.","ama":"Hühner J, Inglés Prieto Á, Neusüß C, Lämmerhofer M, Janovjak HL. Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. Electrophoresis. 2015;36(4):518-525. doi:10.1002/elps.201400451"},"abstract":[{"text":"Cultured mammalian cells essential are model systems in basic biology research, production platforms of proteins for medical use, and testbeds in synthetic biology. Flavin cofactors, in particular flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), are critical for cellular redox reactions and sense light in naturally occurring photoreceptors and optogenetic tools. Here, we quantified flavin contents of commonly used mammalian cell lines. We first compared three procedures for extraction of free and noncovalently protein-bound flavins and verified extraction using fluorescence spectroscopy. For separation, two CE methods with different BGEs were established, and detection was performed by LED-induced fluorescence with limit of detections (LODs 0.5-3.8 nM). We found that riboflavin (RF), FMN, and FAD contents varied significantly between cell lines. RF (3.1-14 amol/cell) and FAD (2.2-17.0 amol/cell) were the predominant flavins, while FMN (0.46-3.4 amol/cell) was found at markedly lower levels. Observed flavin contents agree with those previously extracted from mammalian tissues, yet reduced forms of RF were detected that were not described previously. Quantification of flavins in mammalian cell lines will allow a better understanding of cellular redox reactions and optogenetic tools.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"None","pubrep_id":"836","title":"Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection","status":"public","intvolume":" 36","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1867","month":"02","language":[{"iso":"eng"}],"doi":"10.1002/elps.201400451","quality_controlled":"1","project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564"},{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"publist_id":"5230","date_updated":"2021-01-12T06:53:43Z","date_created":"2018-12-11T11:54:26Z","volume":36,"author":[{"first_name":"Jens","last_name":"Hühner","full_name":"Hühner, Jens"},{"first_name":"Álvaro","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro"},{"full_name":"Neusüß, Christian","first_name":"Christian","last_name":"Neusüß"},{"full_name":"Lämmerhofer, Michael","last_name":"Lämmerhofer","first_name":"Michael"},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"publication_status":"published","publisher":"Wiley","department":[{"_id":"HaJa"}],"year":"2015"},{"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"doi":"10.1242/dev.115832","language":[{"iso":"eng"}],"month":"02","year":"2015","acknowledgement":"W.G. is a post-doctoral fellow of the Research Foundation Flanders. H.S.R. is supported by Employment of Best Young Scientists for International Cooperation Empowerment [CZ.1.07/2.3.00/30.0037], co-financed by the European Social Fund and the state budget of the Czech Republic. Mi.S. was funded by the Ramón y Cajal program. This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP], project ‘CEITEC – Central European Institute of Technology’ [CZ.1.05/1.1.00/02.0068], the European Social Fund [CZ.1.07/2.3.00/20.0043] and the Czech Science Foundation GACR [GA13-40637S] to J.F. We acknowledge funding from the Biological and Biotechnological Science Research Council (BBSRC) and Engineering Physics Science Research Council (EPSRC) to R.S. and M.B","publication_status":"published","publisher":"Company of Biologists","department":[{"_id":"JiFr"}],"author":[{"last_name":"Robert","first_name":"Hélène","full_name":"Robert, Hélène"},{"first_name":"Wim","last_name":"Grunewald","full_name":"Grunewald, Wim"},{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"last_name":"Cannoot","first_name":"Bernard","full_name":"Cannoot, Bernard"},{"full_name":"Soriano, Mercedes","first_name":"Mercedes","last_name":"Soriano"},{"full_name":"Swarup, Ranjan","first_name":"Ranjan","last_name":"Swarup"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"full_name":"Bennett, Malcolm","last_name":"Bennett","first_name":"Malcolm"},{"first_name":"Kim","last_name":"Boutilier","full_name":"Boutilier, Kim"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"date_created":"2018-12-11T11:54:26Z","date_updated":"2021-01-12T06:53:43Z","volume":142,"ec_funded":1,"publist_id":"5231","publication":"Development","citation":{"chicago":"Robert, Hélène, Wim Grunewald, Michael Sauer, Bernard Cannoot, Mercedes Soriano, Ranjan Swarup, Dolf Weijers, Malcolm Bennett, Kim Boutilier, and Jiří Friml. “Plant Embryogenesis Requires AUX/LAX-Mediated Auxin Influx.” Development. Company of Biologists, 2015. https://doi.org/10.1242/dev.115832.","short":"H. Robert, W. Grunewald, M. Sauer, B. Cannoot, M. Soriano, R. Swarup, D. Weijers, M. Bennett, K. Boutilier, J. Friml, Development 142 (2015) 702–711.","mla":"Robert, Hélène, et al. “Plant Embryogenesis Requires AUX/LAX-Mediated Auxin Influx.” Development, vol. 142, no. 4, Company of Biologists, 2015, pp. 702–11, doi:10.1242/dev.115832.","apa":"Robert, H., Grunewald, W., Sauer, M., Cannoot, B., Soriano, M., Swarup, R., … Friml, J. (2015). Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. Company of Biologists. https://doi.org/10.1242/dev.115832","ieee":"H. Robert et al., “Plant embryogenesis requires AUX/LAX-mediated auxin influx,” Development, vol. 142, no. 4. Company of Biologists, pp. 702–711, 2015.","ista":"Robert H, Grunewald W, Sauer M, Cannoot B, Soriano M, Swarup R, Weijers D, Bennett M, Boutilier K, Friml J. 2015. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. 142(4), 702–711.","ama":"Robert H, Grunewald W, Sauer M, et al. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. 2015;142(4):702-711. doi:10.1242/dev.115832"},"page":"702 - 711","date_published":"2015-02-15T00:00:00Z","scopus_import":1,"day":"15","_id":"1865","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Plant embryogenesis requires AUX/LAX-mediated auxin influx","status":"public","intvolume":" 142","oa_version":"None","type":"journal_article","abstract":[{"text":"The plant hormone auxin and its directional transport are known to play a crucial role in defining the embryonic axis and subsequent development of the body plan. Although the role of PIN auxin efflux transporters has been clearly assigned during embryonic shoot and root specification, the role of the auxin influx carriers AUX1 and LIKE-AUX1 (LAX) proteins is not well established. Here, we used chemical and genetic tools on Brassica napus microspore-derived embryos and Arabidopsis thaliana zygotic embryos, and demonstrate that AUX1, LAX1 and LAX2 are required for both shoot and root pole formation, in concert with PIN efflux carriers. Furthermore, we uncovered a positive-feedback loop betweenMONOPTEROS(ARF5)-dependent auxin signalling and auxin transport. ThisMONOPTEROSdependent transcriptional regulation of auxin influx (AUX1, LAX1 and LAX2) and auxin efflux (PIN1 and PIN4) carriers by MONOPTEROS helps to maintain proper auxin transport to the root tip. These results indicate that auxin-dependent cell specification during embryo development requires balanced auxin transport involving both influx and efflux mechanisms, and that this transport is maintained by a positive transcriptional feedback on auxin signalling.","lang":"eng"}],"issue":"4"},{"language":[{"iso":"eng"}],"date_published":"2015-02-09T00:00:00Z","doi":"10.1103/PhysRevE.91.022906","quality_controlled":"1","citation":{"ama":"Park Y, Do Y, Altmeyer S, Lai Y, Lee G. Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. Physical Review E. 2015;91(2). doi:10.1103/PhysRevE.91.022906","apa":"Park, Y., Do, Y., Altmeyer, S., Lai, Y., & Lee, G. (2015). Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.91.022906","ieee":"Y. Park, Y. Do, S. Altmeyer, Y. Lai, and G. Lee, “Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances,” Physical Review E, vol. 91, no. 2. American Physical Society, 2015.","ista":"Park Y, Do Y, Altmeyer S, Lai Y, Lee G. 2015. Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. Physical Review E. 91(2), 022906.","short":"Y. Park, Y. Do, S. Altmeyer, Y. Lai, G. Lee, Physical Review E 91 (2015).","mla":"Park, Youngyong, et al. “Early Effect in Time-Dependent, High-Dimensional Nonlinear Dynamical Systems with Multiple Resonances.” Physical Review E, vol. 91, no. 2, 022906, American Physical Society, 2015, doi:10.1103/PhysRevE.91.022906.","chicago":"Park, Youngyong, Younghae Do, Sebastian Altmeyer, Yingcheng Lai, and Gyuwon Lee. “Early Effect in Time-Dependent, High-Dimensional Nonlinear Dynamical Systems with Multiple Resonances.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/PhysRevE.91.022906."},"publication":"Physical Review E","publication_identifier":{"issn":["1539-3755"]},"day":"09","month":"02","scopus_import":1,"oa_version":"None","volume":91,"date_created":"2018-12-11T11:54:27Z","date_updated":"2021-01-12T06:53:44Z","author":[{"last_name":"Park","first_name":"Youngyong","full_name":"Park, Youngyong"},{"full_name":"Do, Younghae","last_name":"Do","first_name":"Younghae"},{"first_name":"Sebastian","last_name":"Altmeyer","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5964-0203","full_name":"Altmeyer, Sebastian"},{"full_name":"Lai, Yingcheng","last_name":"Lai","first_name":"Yingcheng"},{"last_name":"Lee","first_name":"Gyuwon","full_name":"Lee, Gyuwon"}],"intvolume":" 91","department":[{"_id":"BjHo"}],"publisher":"American Physical Society","publication_status":"published","title":"Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances","status":"public","year":"2015","_id":"1868","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5229","issue":"2","abstract":[{"text":"We investigate high-dimensional nonlinear dynamical systems exhibiting multiple resonances under adiabatic parameter variations. Our motivations come from experimental considerations where time-dependent sweeping of parameters is a practical approach to probing and characterizing the bifurcations of the system. The question is whether bifurcations so detected are faithful representations of the bifurcations intrinsic to the original stationary system. Utilizing a harmonically forced, closed fluid flow system that possesses multiple resonances and solving the Navier-Stokes equation under proper boundary conditions, we uncover the phenomenon of the early effect. Specifically, as a control parameter, e.g., the driving frequency, is adiabatically increased from an initial value, resonances emerge at frequency values that are lower than those in the corresponding stationary system. The phenomenon is established by numerical characterization of physical quantities through the resonances, which include the kinetic energy and the vorticity field, and a heuristic analysis based on the concept of instantaneous frequency. A simple formula is obtained which relates the resonance points in the time-dependent and time-independent systems. Our findings suggest that, in general, any true bifurcation of a nonlinear dynamical system can be unequivocally uncovered through adiabatic parameter sweeping, in spite of a shift in the bifurcation point, which is of value to experimental studies of nonlinear dynamical systems.","lang":"eng"}],"type":"journal_article","article_number":"022906"},{"language":[{"iso":"eng"}],"doi":"10.1007/s00023-014-0333-5","project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1309.5107","open_access":"1"}],"month":"03","volume":16,"date_updated":"2021-01-12T06:53:42Z","date_created":"2018-12-11T11:54:26Z","author":[{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"Erdös, László"},{"first_name":"Antti","last_name":"Knowles","full_name":"Knowles, Antti"}],"publisher":"Springer","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2015","publist_id":"5233","ec_funded":1,"date_published":"2015-03-01T00:00:00Z","page":"709 - 799","citation":{"chicago":"Erdös, László, and Antti Knowles. “The Altshuler–Shklovskii Formulas for Random Band Matrices II: The General Case.” Annales Henri Poincare. Springer, 2015. https://doi.org/10.1007/s00023-014-0333-5.","short":"L. Erdös, A. Knowles, Annales Henri Poincare 16 (2015) 709–799.","mla":"Erdös, László, and Antti Knowles. “The Altshuler–Shklovskii Formulas for Random Band Matrices II: The General Case.” Annales Henri Poincare, vol. 16, no. 3, Springer, 2015, pp. 709–99, doi:10.1007/s00023-014-0333-5.","ieee":"L. Erdös and A. Knowles, “The Altshuler–Shklovskii formulas for random band matrices II: The general case,” Annales Henri Poincare, vol. 16, no. 3. Springer, pp. 709–799, 2015.","apa":"Erdös, L., & Knowles, A. (2015). The Altshuler–Shklovskii formulas for random band matrices II: The general case. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-014-0333-5","ista":"Erdös L, Knowles A. 2015. The Altshuler–Shklovskii formulas for random band matrices II: The general case. Annales Henri Poincare. 16(3), 709–799.","ama":"Erdös L, Knowles A. The Altshuler–Shklovskii formulas for random band matrices II: The general case. Annales Henri Poincare. 2015;16(3):709-799. doi:10.1007/s00023-014-0333-5"},"publication":"Annales Henri Poincare","day":"01","scopus_import":1,"oa_version":"Preprint","intvolume":" 16","title":"The Altshuler–Shklovskii formulas for random band matrices II: The general case","status":"public","_id":"1864","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"text":"The Altshuler–Shklovskii formulas (Altshuler and Shklovskii, BZh Eksp Teor Fiz 91:200, 1986) predict, for any disordered quantum system in the diffusive regime, a universal power law behaviour for the correlation functions of the mesoscopic eigenvalue density. In this paper and its companion (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013), we prove these formulas for random band matrices. In (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013) we introduced a diagrammatic approach and presented robust estimates on general diagrams under certain simplifying assumptions. In this paper, we remove these assumptions by giving a general estimate of the subleading diagrams. We also give a precise analysis of the leading diagrams which give rise to the Altschuler–Shklovskii power laws. Moreover, we introduce a family of general random band matrices which interpolates between real symmetric (β = 1) and complex Hermitian (β = 2) models, and track the transition for the mesoscopic density–density correlation. Finally, we address the higher-order correlation functions by proving that they behave asymptotically according to a Gaussian process whose covariance is given by the Altshuler–Shklovskii formulas.\r\n","lang":"eng"}],"type":"journal_article"},{"language":[{"iso":"eng"}],"date_published":"2015-02-01T00:00:00Z","doi":"10.1145/2688906","quality_controlled":"1","citation":{"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.","short":"J. Ruess, J. Lygeros, ACM Transactions on Modeling and Computer Simulation 25 (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.","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","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.","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.","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"},"publication":"ACM Transactions on Modeling and Computer Simulation","day":"01","month":"02","scopus_import":1,"volume":25,"oa_version":"None","date_updated":"2021-01-12T06:53:41Z","date_created":"2018-12-11T11:54:25Z","author":[{"last_name":"Ruess","first_name":"Jakob","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob"},{"full_name":"Lygeros, John","last_name":"Lygeros","first_name":"John"}],"publisher":"ACM","intvolume":" 25","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"title":"Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks","status":"public","publication_status":"published","_id":"1861","acknowledgement":"HYCON2; EC; European Commission\r\n","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5238","issue":"2","abstract":[{"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.","lang":"eng"}],"type":"journal_article","article_number":"8"},{"volume":58,"oa_version":"None","date_updated":"2021-01-12T06:53:43Z","date_created":"2018-12-11T11:54:26Z","author":[{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Raskin, Jean","last_name":"Raskin","first_name":"Jean"}],"department":[{"_id":"ToHe"}],"publisher":"ACM","intvolume":" 58","publication_status":"published","title":"The equivalence problem for finite automata: Technical perspective","status":"public","year":"2015","_id":"1866","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","publist_id":"5232","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2015-01-28T00:00:00Z","doi":"10.1145/2701001","page":"86-86","citation":{"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","ista":"Henzinger TA, Raskin J. 2015. The equivalence problem for finite automata: Technical perspective. Communications of the ACM. 58(2), 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.","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","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.","short":"T.A. Henzinger, J. Raskin, Communications of the ACM 58 (2015) 86–86.","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."},"publication":"Communications of the ACM","day":"28","month":"01","scopus_import":1},{"type":"journal_article","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."}],"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1871","title":"Auxin transporters and binding proteins at a glance","ddc":["570"],"status":"public","intvolume":" 128","pubrep_id":"563","oa_version":"Submitted Version","file":[{"date_created":"2018-12-12T10:11:00Z","date_updated":"2020-07-14T12:45:19Z","checksum":"24c779f4cd9d549ca6833e26f486be27","file_id":"4852","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":1688844,"file_name":"IST-2016-563-v1+1_1.full.pdf","access_level":"open_access"}],"scopus_import":1,"day":"01","has_accepted_license":"1","publication":"Journal of Cell Science","citation":{"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.","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.","short":"P. Grones, J. Friml, Journal of Cell Science 128 (2015) 1–7.","ista":"Grones P, Friml J. 2015. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 128(1), 1–7.","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.","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"},"page":"1 - 7","date_published":"2015-01-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:19Z","publist_id":"5225","year":"2015","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]","publication_status":"published","publisher":"Company of Biologists","department":[{"_id":"JiFr"}],"author":[{"full_name":"Grones, Peter","last_name":"Grones","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"date_updated":"2021-01-12T06:53:45Z","date_created":"2018-12-11T11:54:28Z","volume":128,"month":"01","oa":1,"quality_controlled":"1","doi":"10.1242/jcs.159418","language":[{"iso":"eng"}]},{"date_published":"2015-07-01T00:00:00Z","doi":"10.1002/hipo.22407","language":[{"iso":"eng"}],"publication":"Hippocampus","citation":{"short":"C.N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, M. Witter, Hippocampus 25 (2015) 838–857.","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.","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.","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","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.","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","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."},"quality_controlled":"1","page":"838 - 857","day":"01","month":"07","scopus_import":1,"author":[{"full_name":"Boccara, Charlotte","orcid":"0000-0001-7237-5109","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","last_name":"Boccara","first_name":"Charlotte"},{"first_name":"Lisa","last_name":"Kjønigsen","full_name":"Kjønigsen, Lisa"},{"first_name":"Ingvild","last_name":"Hammer","full_name":"Hammer, Ingvild"},{"full_name":"Bjaalie, Jan","first_name":"Jan","last_name":"Bjaalie"},{"full_name":"Leergaard, Trygve","first_name":"Trygve","last_name":"Leergaard"},{"full_name":"Witter, Menno","last_name":"Witter","first_name":"Menno"}],"date_updated":"2021-01-12T06:53:46Z","date_created":"2018-12-11T11:54:29Z","oa_version":"None","volume":25,"_id":"1874","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A three-plane architectonic atlas of the rat hippocampal region","publication_status":"published","status":"public","department":[{"_id":"JoCs"}],"publisher":"Wiley","intvolume":" 25","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"}],"issue":"7","publist_id":"5222","type":"journal_article"},{"quality_controlled":"1","page":"46 - 72","publication":"Artificial Intelligence","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.","chicago":"Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” Artificial Intelligence. Elsevier, 2015. https://doi.org/10.1016/j.artint.2014.12.009.","ama":"Chatterjee K, Chmelik M. POMDPs under probabilistic semantics. Artificial Intelligence. 2015;221:46-72. doi:10.1016/j.artint.2014.12.009","ista":"Chatterjee K, Chmelik M. 2015. POMDPs under probabilistic semantics. Artificial Intelligence. 221, 46–72.","ieee":"K. Chatterjee and M. Chmelik, “POMDPs under probabilistic semantics,” Artificial Intelligence, vol. 221. Elsevier, pp. 46–72, 2015.","apa":"Chatterjee, K., & Chmelik, M. (2015). POMDPs under probabilistic semantics. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2014.12.009"},"oa":1,"external_id":{"arxiv":["1408.2058"]},"main_file_link":[{"url":"https://arxiv.org/abs/1408.2058","open_access":"1"}],"language":[{"iso":"eng"}],"date_published":"2015-04-01T00:00:00Z","doi":"10.1016/j.artint.2014.12.009","scopus_import":1,"day":"01","month":"04","status":"public","title":"POMDPs under probabilistic semantics","publication_status":"published","publisher":"Elsevier","intvolume":" 221","department":[{"_id":"KrCh"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1873","year":"2015","date_created":"2018-12-11T11:54:28Z","date_updated":"2021-01-12T06:53:46Z","volume":221,"oa_version":"Preprint","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","first_name":"Martin"}],"type":"journal_article","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"}],"publist_id":"5224"},{"publist_id":"5218","file_date_updated":"2020-07-14T12:45:19Z","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.","year":"2015","department":[{"_id":"JiFr"}],"publisher":"Wiley-Blackwell","publication_status":"published","author":[{"full_name":"Kremer, A","first_name":"A","last_name":"Kremer"},{"full_name":"Lippens, Stefaan","first_name":"Stefaan","last_name":"Lippens"},{"first_name":"Sonia","last_name":"Bartunkova","full_name":"Bartunkova, Sonia"},{"last_name":"Asselbergh","first_name":"Bob","full_name":"Asselbergh, Bob"},{"last_name":"Blanpain","first_name":"Cendric","full_name":"Blanpain, Cendric"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych","full_name":"Fendrych, Matyas"},{"last_name":"Goossens","first_name":"A","full_name":"Goossens, A"},{"full_name":"Holt, Matthew","first_name":"Matthew","last_name":"Holt"},{"full_name":"Janssens, Sophie","first_name":"Sophie","last_name":"Janssens"},{"last_name":"Krols","first_name":"Michiel","full_name":"Krols, Michiel"},{"last_name":"Larsimont","first_name":"Jean","full_name":"Larsimont, Jean"},{"first_name":"Conor","last_name":"Mc Guire","full_name":"Mc Guire, Conor"},{"full_name":"Nowack, Moritz","first_name":"Moritz","last_name":"Nowack"},{"last_name":"Saelens","first_name":"Xavier","full_name":"Saelens, Xavier"},{"full_name":"Schertel, Andreas","last_name":"Schertel","first_name":"Andreas"},{"full_name":"Schepens, B","first_name":"B","last_name":"Schepens"},{"first_name":"M","last_name":"Slezak","full_name":"Slezak, M"},{"full_name":"Timmerman, Vincent","last_name":"Timmerman","first_name":"Vincent"},{"full_name":"Theunis, Clara","first_name":"Clara","last_name":"Theunis"},{"full_name":"Van Brempt, Ronald","last_name":"Van Brempt","first_name":"Ronald"},{"full_name":"Visser, Y","first_name":"Y","last_name":"Visser"},{"last_name":"Guérin","first_name":"Christophe","full_name":"Guérin, Christophe"}],"volume":259,"date_created":"2018-12-11T11:54:30Z","date_updated":"2021-01-12T06:53:48Z","month":"08","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1111/jmi.12211","language":[{"iso":"eng"}],"type":"journal_article","issue":"2","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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1879","intvolume":" 259","title":"Developing 3D SEM in a broad biological context","status":"public","ddc":["570"],"pubrep_id":"459","oa_version":"Published Version","file":[{"file_id":"4872","relation":"main_file","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:11:19Z","checksum":"3649c5372d1644062d728ea9287e367f","file_name":"IST-2016-459-v1+1_KREMER_et_al-2015-Journal_of_Microscopy.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":2899898}],"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"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.","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.","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.","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","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.","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","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."},"publication":"Journal of Microscopy","page":"80 - 96","date_published":"2015-08-01T00:00:00Z"},{"pubrep_id":"447","file":[{"access_level":"open_access","file_name":"IST-2016-447-v1+1_document_1_.pdf","file_size":768108,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4963","checksum":"38fdf2b5ac30445e26a5d613abd84b16","date_created":"2018-12-12T10:12:44Z","date_updated":"2020-07-14T12:45:20Z"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1880","intvolume":" 17","title":"Superfluid behavior of a Bose-Einstein condensate in a random potential","status":"public","ddc":["530"],"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"}],"type":"journal_article","date_published":"2015-01-15T00:00:00Z","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.","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.","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","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.","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.","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"},"publication":"New Journal of Physics","has_accepted_license":"1","day":"15","scopus_import":1,"author":[{"full_name":"Könenberg, Martin","first_name":"Martin","last_name":"Könenberg"},{"full_name":"Moser, Thomas","first_name":"Thomas","last_name":"Moser","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"},{"full_name":"Yngvason, Jakob","last_name":"Yngvason","first_name":"Jakob"}],"volume":17,"date_created":"2018-12-11T11:54:30Z","date_updated":"2021-01-12T06:53:48Z","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","year":"2015","publisher":"IOP Publishing Ltd.","department":[{"_id":"RoSe"}],"publication_status":"published","publist_id":"5214","file_date_updated":"2020-07-14T12:45:20Z","article_number":"013022","doi":"10.1088/1367-2630/17/1/013022","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","month":"01"},{"day":"30","scopus_import":1,"date_published":"2015-01-30T00:00:00Z","citation":{"short":"U. Fahrenberg, J. Kretinsky, A. Legay, L. Traonouez, in:, Springer, 2015, pp. 306–324.","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.","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.","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","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.","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."},"page":"306 - 324","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"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"1882","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8997","title":"Compositionality for quantitative specifications","status":"public","month":"01","doi":"10.1007/978-3-319-15317-9_19","conference":{"name":"FACS: Formal Aspects of Component Software","location":"Bertinoro, Italy","start_date":"2014-09-10","end_date":"2014-09-12"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1408.1256"}],"oa":1,"project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","ec_funded":1,"publist_id":"5216","author":[{"last_name":"Fahrenberg","first_name":"Uli","full_name":"Fahrenberg, Uli"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky","full_name":"Kretinsky, Jan"},{"last_name":"Legay","first_name":"Axel","full_name":"Legay, Axel"},{"full_name":"Traonouez, Louis","last_name":"Traonouez","first_name":"Louis"}],"volume":8997,"date_updated":"2021-01-12T06:53:49Z","date_created":"2018-12-11T11:54:31Z","year":"2015","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"}],"publisher":"Springer","publication_status":"published"},{"oa_version":"Preprint","title":"Anomalous scaling in an age-dependent branching model","status":"public","intvolume":" 91","_id":"1883","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","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"}],"issue":"2","type":"journal_article","date_published":"2015-02-02T00:00:00Z","article_type":"original","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","citation":{"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","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","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.","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.","short":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","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.","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."},"day":"02","article_processing_charge":"No","scopus_import":1,"date_updated":"2021-01-12T06:53:49Z","date_created":"2018-12-11T11:54:31Z","volume":91,"author":[{"full_name":"Keller-Schmidt, Stephanie","first_name":"Stephanie","last_name":"Keller-Schmidt"},{"first_name":"Murat","last_name":"Tugrul","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat"},{"full_name":"Eguíluz, Víctor","first_name":"Víctor","last_name":"Eguíluz"},{"last_name":"Hernandez Garcia","first_name":"Emilio","full_name":"Hernandez Garcia, Emilio"},{"last_name":"Klemm","first_name":"Konstantin","full_name":"Klemm, Konstantin"}],"publication_status":"published","publisher":"American Institute of Physics","department":[{"_id":"NiBa"}],"year":"2015","publist_id":"5213","article_number":"022803","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.91.022803","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1012.3298"}],"external_id":{"arxiv":["1012.3298"]},"oa":1,"month":"02"},{"day":"24","month":"01","scopus_import":1,"date_published":"2015-01-24T00:00:00Z","doi":"10.1007/s10265-014-0691-6","language":[{"iso":"eng"}],"citation":{"short":"E. Cires Rodriguez, J. Prieto, Journal of Plant Research 128 (2015) 223–238.","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.","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.","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","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.","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."},"publication":"Journal of Plant Research","page":"223 - 238","quality_controlled":"1","issue":"2","publist_id":"5217","abstract":[{"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).","lang":"eng"}],"type":"journal_article","author":[{"id":"2AD56A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Cires Rodriguez","first_name":"Eduardo","full_name":"Cires Rodriguez, Eduardo"},{"full_name":"Prieto, José","first_name":"José","last_name":"Prieto"}],"oa_version":"None","volume":128,"date_created":"2018-12-11T11:54:30Z","date_updated":"2021-01-12T06:53:47Z","year":"2015","_id":"1878","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 128","department":[{"_id":"JiFr"}],"publisher":"Springer","status":"public","title":"Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula","publication_status":"published"},{"type":"journal_article","abstract":[{"lang":"eng","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. "}],"issue":"1","publist_id":"5210","title":"Positional information, positional error, and readout precision in morphogenesis: A mathematical framework","status":"public","publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"GaTk"}],"intvolume":" 199","year":"2015","_id":"1885","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:54:32Z","date_updated":"2021-01-12T06:53:50Z","volume":199,"oa_version":"Preprint","author":[{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"full_name":"Dubuis, Julien","last_name":"Dubuis","first_name":"Julien"},{"last_name":"Petkova","first_name":"Mariela","full_name":"Petkova, Mariela"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"}],"scopus_import":1,"month":"01","day":"01","quality_controlled":"1","page":"39 - 59","publication":"Genetics","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.5599"}],"oa":1,"citation":{"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","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.","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.","short":"G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 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.","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."},"language":[{"iso":"eng"}],"date_published":"2015-01-01T00:00:00Z","doi":"10.1534/genetics.114.171850"},{"author":[{"first_name":"Thomas R","last_name":"Sokolowski","id":"3E999752-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R"},{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"date_updated":"2021-01-12T06:54:13Z","date_created":"2018-12-11T11:54:49Z","volume":91,"oa_version":"Preprint","_id":"1940","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Optimizing information flow in small genetic networks. IV. Spatial coupling","department":[{"_id":"GaTk"}],"publisher":"American Institute of Physics","intvolume":" 91","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."}],"publist_id":"5145","issue":"6","article_number":"062710","type":"journal_article","date_published":"2015-06-15T00:00:00Z","doi":"10.1103/PhysRevE.91.062710","language":[{"iso":"eng"}],"publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","main_file_link":[{"url":"http://arxiv.org/abs/1501.04015","open_access":"1"}],"citation":{"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.","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.","short":"T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","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.","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"},"oa":1,"quality_controlled":"1","day":"15","month":"06","scopus_import":1},{"type":"journal_article","publist_id":"5152","issue":"6","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"}],"_id":"1938","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","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. ","intvolume":" 379","publisher":"Elsevier","department":[{"_id":"HeEd"}],"status":"public","publication_status":"published","title":"On the distribution of local extrema in quantum chaos","author":[{"full_name":"Pausinger, Florian","first_name":"Florian","last_name":"Pausinger","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8379-3768"},{"first_name":"Stefan","last_name":"Steinerberger","full_name":"Steinerberger, Stefan"}],"volume":379,"oa_version":"None","date_created":"2018-12-11T11:54:49Z","date_updated":"2021-01-12T06:54:12Z","scopus_import":1,"day":"06","month":"03","citation":{"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","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.","ista":"Pausinger F, Steinerberger S. 2015. On the distribution of local extrema in quantum chaos. Physics Letters, Section A. 379(6), 535–541.","short":"F. Pausinger, S. Steinerberger, Physics Letters, Section A 379 (2015) 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.","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."},"publication":"Physics Letters, Section A","page":"535 - 541","quality_controlled":"1","doi":"10.1016/j.physleta.2014.12.010","date_published":"2015-03-06T00:00:00Z","language":[{"iso":"eng"}]},{"ec_funded":1,"issue":"2","publist_id":"5140","type":"journal_article","author":[{"full_name":"Rakusová, Hana","first_name":"Hana","last_name":"Rakusová"},{"full_name":"Fendrych, Matyas","first_name":"Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"volume":23,"oa_version":"None","date_updated":"2021-01-12T06:54:15Z","date_created":"2018-12-11T11:54:51Z","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","_id":"1944","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2015","intvolume":" 23","department":[{"_id":"JiFr"}],"publisher":"Elsevier","title":"Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants","publication_status":"published","status":"public","month":"02","day":"01","scopus_import":1,"doi":"10.1016/j.pbi.2014.12.002","date_published":"2015-02-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"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","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.","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","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.","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.","short":"H. Rakusová, M. Fendrych, J. Friml, Current Opinion in Plant Biology 23 (2015) 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."},"publication":"Current Opinion in Plant Biology","page":"116 - 123","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1"},{"type":"conference","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":"1992","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Succinct representation of concurrent trace sets","ddc":["005"],"pubrep_id":"317","file":[{"date_updated":"2020-07-14T12:45:22Z","date_created":"2018-12-12T10:17:56Z","checksum":"f0d4395b600f410a191256ac0b73af32","file_id":"5314","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":399462,"file_name":"IST-2015-317-v1+1_author_version.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","scopus_import":1,"day":"15","has_accepted_license":"1","citation":{"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.","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","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.","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","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.","short":"A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM, 2015, pp. 433–444.","mla":"Gupta, Ashutosh, et al. Succinct Representation of Concurrent Trace Sets. ACM, 2015, pp. 433–44, doi:10.1145/2676726.2677008."},"page":"433 - 444","date_published":"2015-01-15T00:00:00Z","file_date_updated":"2020-07-14T12:45:22Z","publist_id":"5091","year":"2015","publication_status":"published","publisher":"ACM","department":[{"_id":"ToHe"}],"author":[{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","first_name":"Arjun"},{"id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","last_name":"Samanta","first_name":"Roopsha","full_name":"Samanta, Roopsha"},{"first_name":"Thorsten","last_name":"Tarrach","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4409-8487","full_name":"Tarrach, Thorsten"}],"date_updated":"2021-01-12T06:54:33Z","date_created":"2018-12-11T11:55:05Z","month":"01","publication_identifier":{"isbn":["978-1-4503-3300-9"]},"oa":1,"quality_controlled":"1","conference":{"start_date":"2015-01-15","location":"Mumbai, India","end_date":"2015-01-17","name":"POPL: Principles of Programming Languages"},"doi":"10.1145/2676726.2677008","language":[{"iso":"eng"}]},{"date_published":"2015-05-01T00:00:00Z","doi":"10.1016/j.jsc.2014.09.014","language":[{"iso":"eng"}],"citation":{"short":"P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.","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.","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.","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","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.","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","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."},"main_file_link":[{"url":"http://arxiv.org/abs/1207.0077","open_access":"1"}],"oa":1,"publication":"Journal of Symbolic Computation","page":"285 - 296","quality_controlled":"1","month":"05","day":"01","scopus_import":1,"author":[{"id":"46870C74-F248-11E8-B48F-1D18A9856A87","first_name":"Patrik","last_name":"Noren","full_name":"Noren, Patrik"}],"oa_version":"Preprint","volume":"68/Part 2","date_updated":"2021-01-12T06:54:35Z","date_created":"2018-12-11T11:55:07Z","_id":"1997","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaUh"}],"publisher":"Elsevier","publication_status":"published","title":"The three-state toric homogeneous Markov chain model has Markov degree two","status":"public","publist_id":"5082","issue":"May-June","abstract":[{"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.","lang":"eng"}],"type":"journal_article"},{"issue":"3","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2008","intvolume":" 42","status":"public","title":"Iterative scaling in curved exponential families","day":"01","scopus_import":1,"date_published":"2015-09-01T00:00:00Z","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.","short":"A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 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","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.","ista":"Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847.","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"},"publication":"Scandinavian Journal of Statistics","page":"832 - 847","publist_id":"5068","author":[{"id":"31934120-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Klimova","full_name":"Klimova, Anna"},{"full_name":"Rudas, Tamás","last_name":"Rudas","first_name":"Tamás"}],"volume":42,"date_updated":"2021-01-12T06:54:41Z","date_created":"2018-12-11T11:55:11Z","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).","year":"2015","publisher":"Wiley","department":[{"_id":"CaUh"}],"publication_status":"published","month":"09","doi":"10.1111/sjos.12139","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.3282"}],"quality_controlled":"1"},{"department":[{"_id":"CaUh"}],"publisher":"Taylor & Francis","publication_status":"published","year":"2015","volume":24,"date_created":"2018-12-11T11:55:10Z","date_updated":"2021-01-12T06:54:40Z","author":[{"first_name":"Nicolas","last_name":"Hein","full_name":"Hein, Nicolas"},{"last_name":"Hillar","first_name":"Christopher","full_name":"Hillar, Christopher"},{"first_name":"Abraham","last_name":"Martin Del Campo Sanchez","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","full_name":"Martin Del Campo Sanchez, Abraham"},{"full_name":"Sottile, Frank","last_name":"Sottile","first_name":"Frank"},{"first_name":"Zach","last_name":"Teitler","full_name":"Teitler, Zach"}],"publist_id":"5070","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.3436"}],"language":[{"iso":"eng"}],"doi":"10.1080/10586458.2014.980044","month":"06","intvolume":" 24","title":"The monotone secant conjecture in the real Schubert calculus","status":"public","_id":"2006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","issue":"3","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. "}],"page":"261 - 269","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.","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","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.","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","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.","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.","short":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269."},"publication":"Experimental Mathematics","date_published":"2015-06-23T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"23"},{"type":"journal_article","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","publist_id":"5062","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2014","year":"2015","status":"public","title":"Faithfulness and learning hypergraphs from discrete distributions","publication_status":"published","department":[{"_id":"CaUh"}],"intvolume":" 87","publisher":"Elsevier","author":[{"full_name":"Klimova, Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Klimova"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","first_name":"Caroline","last_name":"Uhler","full_name":"Uhler, Caroline"},{"first_name":"Tamás","last_name":"Rudas","full_name":"Rudas, Tamás"}],"date_created":"2018-12-11T11:55:13Z","date_updated":"2021-01-12T06:54:43Z","volume":87,"oa_version":"Preprint","scopus_import":1,"day":"01","month":"07","publication":"Computational Statistics & Data Analysis","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.6617"}],"oa":1,"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.","short":"A. Klimova, C. Uhler, T. Rudas, Computational Statistics & Data Analysis 87 (2015) 57–72.","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.","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","ista":"Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. 87(7), 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","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."},"quality_controlled":"1","page":"57 - 72","doi":"10.1016/j.csda.2015.01.017","date_published":"2015-07-01T00:00:00Z","language":[{"iso":"eng"}]},{"month":"01","quality_controlled":"1","oa":1,"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"language":[{"iso":"eng"}],"doi":"10.1016/j.bbamcr.2014.10.009","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:45:25Z","publist_id":"5047","publication_status":"published","publisher":"Elsevier","department":[{"_id":"DaSi"}],"year":"2015","date_updated":"2021-01-12T06:54:48Z","date_created":"2018-12-11T11:55:17Z","volume":1853,"author":[{"full_name":"Kawada, Daiki","last_name":"Kawada","first_name":"Daiki"},{"full_name":"Kobayashi, Hiromu","first_name":"Hiromu","last_name":"Kobayashi"},{"full_name":"Tomita, Tsuyoshi","last_name":"Tomita","first_name":"Tsuyoshi"},{"full_name":"Nakata, Eisuke","first_name":"Eisuke","last_name":"Nakata"},{"full_name":"Nagano, Makoto","first_name":"Makoto","last_name":"Nagano"},{"full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Toshima, Junko","first_name":"Junko","last_name":"Toshima"},{"full_name":"Toshimaa, Jiro","first_name":"Jiro","last_name":"Toshimaa"}],"scopus_import":1,"day":"01","has_accepted_license":"1","page":"144 - 156","publication":"Biochimica et Biophysica Acta - Molecular Cell Research","citation":{"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","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.","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.","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","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.","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."},"date_published":"2015-01-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"1","status":"public","ddc":["570"],"title":"The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins","intvolume":" 1853","_id":"2025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"file_id":"4936","relation":"main_file","checksum":"5bb328edebb6a91337cadd7d63f961b7","date_updated":"2020-07-14T12:45:25Z","date_created":"2018-12-12T10:12:18Z","access_level":"open_access","file_name":"IST-2016-615-v1+1_BBAMCR.pdf","creator":"system","content_type":"application/pdf","file_size":926685}],"pubrep_id":"615"}]