[{"acknowledgement":"I would like to thank my supervisor, Christoph Lampert, for guidance throughout my studies and for patience in transforming me into a scientist, and my thesis committee, Chris Wojtan and Horst Bischof, for their help and advice. \r\n\r\nI would like to thank Elisabeth Hacker who perfectly assisted all my administrative needs and was always nice and friendly to me, and the campus team for making the IST Austria campus my second home. \r\nI was honored to collaborate with brilliant researchers and to learn from their experience. Undoubtedly, I learned most of all from Novi Quadrianto: brainstorming our projects and getting exciting results was the most enjoyable part of my work – thank you! I am also grateful to David Knowles, Zoubin Ghahramani, Daniel Hernández-Lobato, Kristian Kersting and Anastasia Pentina for the fantastic projects we worked on together, and to Kristen Grauman and Adriana Kovashka for the exceptional experience working with user studies. I would like to thank my colleagues at IST Austria and my office mates who shared their happy moods, scientific breakthroughs and thought-provoking conversations with me: Chao, Filip, Rustem, Asya, Sameh, Alex, Vlad, Mayu, Neel, Csaba, Thomas, Vladimir, Cristina, Alex Z., Avro, Amelie and Emilie, Andreas H. and Andreas E., Chris, Lena, Michael, Ali and Ipek, Vera, Igor, Katia. Special thanks to Morten for the countless games of table soccer we played together and the tournaments we teamed up for: we will definitely win next time:) A very warm hug to Asya for always being so inspiring and supportive to me, and for helping me to increase the proportion of female computer scientists in our group. ","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2015","has_accepted_license":"1","day":"01","page":"144","date_created":"2018-12-11T11:51:48Z","doi":"10.15479/at:ista:1401","date_published":"2015-04-01T00:00:00Z","citation":{"ama":"Sharmanska V. Learning with attributes for object recognition: Parametric and non-parametrics views. 2015. doi:10.15479/at:ista:1401","apa":"Sharmanska, V. (2015). Learning with attributes for object recognition: Parametric and non-parametrics views. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:1401","short":"V. Sharmanska, Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views, Institute of Science and Technology Austria, 2015.","ieee":"V. Sharmanska, “Learning with attributes for object recognition: Parametric and non-parametrics views,” Institute of Science and Technology Austria, 2015.","mla":"Sharmanska, Viktoriia. Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views. Institute of Science and Technology Austria, 2015, doi:10.15479/at:ista:1401.","ista":"Sharmanska V. 2015. Learning with attributes for object recognition: Parametric and non-parametrics views. Institute of Science and Technology Austria.","chicago":"Sharmanska, Viktoriia. “Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views.” Institute of Science and Technology Austria, 2015. https://doi.org/10.15479/at:ista:1401."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","publist_id":"5806","author":[{"orcid":"0000-0003-0192-9308","full_name":"Sharmanska, Viktoriia","last_name":"Sharmanska","first_name":"Viktoriia","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87"}],"title":"Learning with attributes for object recognition: Parametric and non-parametrics views","abstract":[{"lang":"eng","text":"The human ability to recognize objects in complex scenes has driven research in the computer vision field over couple of decades. This thesis focuses on the object recognition task in images. That is, given the image, we want the computer system to be able to predict the class of the object that appears in the image. A recent successful attempt to bridge semantic understanding of the image perceived by humans and by computers uses attribute-based models. Attributes are semantic properties of the objects shared across different categories, which humans and computers can decide on. To explore the attribute-based models we take a statistical machine learning approach, and address two key learning challenges in view of object recognition task: learning augmented attributes as mid-level discriminative feature representation, and learning with attributes as privileged information. Our main contributions are parametric and non-parametric models and algorithms to solve these frameworks. In the parametric approach, we explore an autoencoder model combined with the large margin nearest neighbor principle for mid-level feature learning, and linear support vector machines for learning with privileged information. In the non-parametric approach, we propose a supervised Indian Buffet Process for automatic augmentation of semantic attributes, and explore the Gaussian Processes classification framework for learning with privileged information. A thorough experimental analysis shows the effectiveness of the proposed models in both parametric and non-parametric views."}],"oa_version":"Published Version","main_file_link":[{"url":"http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf"}],"alternative_title":["ISTA Thesis"],"month":"04","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2021-02-22T11:33:17Z","file_size":7964342,"date_created":"2021-02-22T11:33:17Z","file_name":"2015_Thesis_Sharmanska.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"3605b402bb6934e09ae4cf672c84baf7","file_id":"9177","success":1},{"date_updated":"2021-11-17T13:47:24Z","file_size":7372241,"creator":"cchlebak","date_created":"2021-11-16T14:40:45Z","file_name":"2015_Thesis_Sharmanska_pdfa.pdf","content_type":"application/pdf","access_level":"closed","relation":"main_file","file_id":"10297","checksum":"e37593b3ee75bf3180629df2d6ca8f4e"}],"_id":"1401","type":"dissertation","status":"public","date_updated":"2023-09-07T11:40:11Z","supervisor":[{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"ddc":["000"],"department":[{"_id":"ChLa"},{"_id":"GradSch"}],"file_date_updated":"2021-11-17T13:47:24Z"},{"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"citation":{"mla":"Reiter, Johannes, et al. “Biological Auctions with Multiple Rewards.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1812, Royal Society, 2015, doi:10.1098/rspb.2015.1041.","apa":"Reiter, J., Kanodia, A., Gupta, R., Nowak, M., & Chatterjee, K. (2015). Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society. https://doi.org/10.1098/rspb.2015.1041","ama":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. 2015;282(1812). doi:10.1098/rspb.2015.1041","short":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, K. Chatterjee, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015).","ieee":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, and K. Chatterjee, “Biological auctions with multiple rewards,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1812. Royal Society, 2015.","chicago":"Reiter, Johannes, Ayush Kanodia, Raghav Gupta, Martin Nowak, and Krishnendu Chatterjee. “Biological Auctions with Multiple Rewards.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, 2015. https://doi.org/10.1098/rspb.2015.1041.","ista":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. 2015. Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1812)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["26180069"]},"article_processing_charge":"No","author":[{"last_name":"Reiter","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"},{"first_name":"Ayush","full_name":"Kanodia, Ayush","last_name":"Kanodia"},{"first_name":"Raghav","last_name":"Gupta","full_name":"Gupta, Raghav"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5425","title":"Biological auctions with multiple rewards","acknowledgement":"This work was supported by grants from the John Templeton Foundation, ERC Start Grant (279307: Graph Games), FWF NFN Grant (No S11407N23 RiSE/SHiNE), FWF Grant (No P23499N23) and a Microsoft faculty fellows award.","oa":1,"publisher":"Royal Society","quality_controlled":"1","year":"2015","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","day":"15","date_created":"2018-12-11T11:53:35Z","date_published":"2015-07-15T00:00:00Z","doi":"10.1098/rspb.2015.1041","_id":"1709","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-07T11:40:43Z","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards."}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528522/","open_access":"1"}],"scopus_import":1,"intvolume":" 282","month":"07","publication_status":"published","language":[{"iso":"eng"}],"volume":282,"issue":"1812","related_material":{"record":[{"status":"public","id":"1400","relation":"dissertation_contains"}]}},{"department":[{"_id":"KrCh"}],"title":"The subclonal evolution of cancer","article_processing_charge":"No","author":[{"last_name":"Reiter","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"}],"publist_id":"5807","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T11:40:44Z","citation":{"mla":"Reiter, Johannes. The Subclonal Evolution of Cancer. Institute of Science and Technology Austria, 2015.","short":"J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology Austria, 2015.","ieee":"J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology Austria, 2015.","ama":"Reiter J. The subclonal evolution of cancer. 2015.","apa":"Reiter, J. (2015). The subclonal evolution of cancer. Institute of Science and Technology Austria.","chicago":"Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science and Technology Austria, 2015.","ista":"Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and Technology Austria."},"supervisor":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}],"status":"public","type":"dissertation","_id":"1400","date_created":"2018-12-11T11:51:48Z","date_published":"2015-04-01T00:00:00Z","related_material":{"record":[{"status":"public","id":"1709","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"2000"},{"status":"public","id":"2247","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"2816"},{"relation":"part_of_dissertation","status":"public","id":"2858"},{"relation":"part_of_dissertation","status":"public","id":"3157"},{"relation":"part_of_dissertation","id":"3260","status":"public"}]},"page":"183","language":[{"iso":"eng"}],"day":"01","year":"2015","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"04","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"oa_version":"None","abstract":[{"text":"Cancer results from an uncontrolled growth of abnormal cells. Sequentially accumulated genetic and epigenetic alterations decrease cell death and increase cell replication. We used mathematical models to quantify the effect of driver gene mutations. The recently developed targeted therapies can lead to dramatic regressions. However, in solid cancers, clinical responses are often short-lived because resistant cancer cells evolve. We estimated that approximately 50 different mutations can confer resistance to a typical targeted therapeutic agent. We find that resistant cells are likely to be present in expanded subclones before the start of the treatment. The dominant strategy to prevent the evolution of resistance is combination therapy. Our analytical results suggest that in most patients, dual therapy, but not monotherapy, can result in long-term disease control. However, long-term control can only occur if there are no possible mutations in the genome that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous therapy with two drugs is much more likely to result in long-term disease control than sequential therapy with the same drugs. To improve our understanding of the underlying subclonal evolution we reconstruct the evolutionary history of a patient's cancer from next-generation sequencing data of spatially-distinct DNA samples. Using a quantitative measure of genetic relatedness, we found that pancreatic cancers and their metastases demonstrated a higher level of relatedness than that expected for any two cells randomly taken from a normal tissue. This minimal amount of genetic divergence among advanced lesions indicates that genetic heterogeneity, when quantitatively defined, is not a fundamental feature of the natural history of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics finds evidence for seeding patterns of metastases and can directly be used to discover rules governing the evolution of solid malignancies to transform cancer into a more predictable disease.","lang":"eng"}]},{"language":[{"iso":"eng"}],"publication":"Journal of Complexity","day":"01","publication_status":"published","year":"2015","date_created":"2018-12-11T11:54:02Z","volume":31,"related_material":{"record":[{"relation":"dissertation_contains","id":"1399","status":"public"}]},"date_published":"2015-12-01T00:00:00Z","issue":"6","doi":"10.1016/j.jco.2015.06.002","page":"773 - 797","acknowledgement":"F.P. is supported by the Graduate School of IST Austria, A.M.S is supported by the Centre for Stochastic Geometry and Advanced Bioimaging funded by a grant from the Villum Foundation.","oa_version":"None","abstract":[{"text":"Motivated by recent ideas of Harman (Unif. Distrib. Theory, 2010) we develop a new concept of variation of multivariate functions on a compact Hausdorff space with respect to a collection D of subsets. We prove a general version of the Koksma-Hlawka theorem that holds for this notion of variation and discrepancy with respect to D. As special cases, we obtain Koksma-Hlawka inequalities for classical notions, such as extreme or isotropic discrepancy. For extreme discrepancy, our result coincides with the usual Koksma-Hlawka theorem. We show that the space of functions of bounded D-variation contains important discontinuous functions and is closed under natural algebraic operations. Finally, we illustrate the results on concrete integration problems from integral geometry and stereology.","lang":"eng"}],"intvolume":" 31","month":"12","quality_controlled":"1","publisher":"Academic Press","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” Journal of Complexity, vol. 31, no. 6, Academic Press, 2015, pp. 773–97, doi:10.1016/j.jco.2015.06.002.","ama":"Pausinger F, Svane A. A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. 2015;31(6):773-797. doi:10.1016/j.jco.2015.06.002","apa":"Pausinger, F., & Svane, A. (2015). A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. Academic Press. https://doi.org/10.1016/j.jco.2015.06.002","ieee":"F. Pausinger and A. Svane, “A Koksma-Hlawka inequality for general discrepancy systems,” Journal of Complexity, vol. 31, no. 6. Academic Press, pp. 773–797, 2015.","short":"F. Pausinger, A. Svane, Journal of Complexity 31 (2015) 773–797.","chicago":"Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” Journal of Complexity. Academic Press, 2015. https://doi.org/10.1016/j.jco.2015.06.002.","ista":"Pausinger F, Svane A. 2015. A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. 31(6), 773–797."},"date_updated":"2023-09-07T11:41:25Z","title":"A Koksma-Hlawka inequality for general discrepancy systems","department":[{"_id":"HeEd"}],"publist_id":"5320","author":[{"id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pausinger","full_name":"Pausinger, Florian","orcid":"0000-0002-8379-3768"},{"first_name":"Anne","full_name":"Svane, Anne","last_name":"Svane"}],"_id":"1792","status":"public","type":"journal_article"},{"publication_status":"published","year":"2015","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"day":"01","page":"144","date_created":"2018-12-11T11:51:48Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1662"},{"status":"public","id":"1792","relation":"part_of_dissertation"},{"id":"2255","status":"public","relation":"part_of_dissertation"}]},"date_published":"2015-06-01T00:00:00Z","abstract":[{"text":"This thesis is concerned with the computation and approximation of intrinsic volumes. Given a smooth body M and a certain digital approximation of it, we develop algorithms to approximate various intrinsic volumes of M using only measurements taken from its digital approximations. The crucial idea behind our novel algorithms is to link the recent theory of persistent homology to the theory of intrinsic volumes via the Crofton formula from integral geometry and, in particular, via Euler characteristic computations. Our main contributions are a multigrid convergent digital algorithm to compute the first intrinsic volume of a solid body in R^n as well as an appropriate integration pipeline to approximate integral-geometric integrals defined over the Grassmannian manifold.","lang":"eng"}],"oa_version":"None","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"month":"06","citation":{"ieee":"F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science and Technology Austria, 2015.","short":"F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science and Technology Austria, 2015.","ama":"Pausinger F. On the approximation of intrinsic volumes. 2015.","apa":"Pausinger, F. (2015). On the approximation of intrinsic volumes. Institute of Science and Technology Austria.","mla":"Pausinger, Florian. On the Approximation of Intrinsic Volumes. Institute of Science and Technology Austria, 2015.","ista":"Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of Science and Technology Austria.","chicago":"Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute of Science and Technology Austria, 2015."},"date_updated":"2023-09-07T11:41:25Z","supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"first_name":"Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","last_name":"Pausinger","orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian"}],"publist_id":"5808","department":[{"_id":"HeEd"}],"title":"On the approximation of intrinsic volumes","_id":"1399","type":"dissertation","status":"public"},{"date_updated":"2023-09-07T11:53:49Z","ddc":["576"],"department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:10Z","_id":"1666","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"463","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"4657","checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf","date_created":"2018-12-12T10:07:58Z","creator":"system","file_size":2580778,"date_updated":"2020-07-14T12:45:10Z"}],"ec_funded":1,"issue":"11","volume":11,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9712"},{"relation":"dissertation_contains","status":"public","id":"1131"}]},"abstract":[{"text":"Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 11","month":"11","citation":{"ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639","apa":"Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758","last_name":"Tugrul"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5483","title":"Dynamics of transcription factor binding site evolution","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"year":"2015","has_accepted_license":"1","publication":"PLoS Genetics","day":"06","date_created":"2018-12-11T11:53:21Z","date_published":"2015-11-06T00:00:00Z","doi":"10.1371/journal.pgen.1005639","oa":1,"quality_controlled":"1","publisher":"Public Library of Science"},{"oa_version":"Submitted Version","abstract":[{"text":"We extend the theory of input-output conformance with operators for merge and quotient. The former is useful when testing against multiple requirements or views. The latter can be used to generate tests for patches of an already tested system. Both operators can combine systems with different action alphabets, which is usually the case when constructing complex systems and specifications from parts, for instance different views as well as newly defined functionality of a~previous version of the system.","lang":"eng"}],"month":"05","scopus_import":1,"alternative_title":["Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering "],"file":[{"checksum":"c6ce681035c163a158751f240cb7d389","file_id":"5303","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-625-v1+1_conf-cbse-BenesDHKN15.pdf","date_created":"2018-12-12T10:17:46Z","creator":"system","file_size":467561,"date_updated":"2020-07-14T12:44:59Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-4503-3471-6"]},"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1155"}]},"ec_funded":1,"_id":"1502","status":"public","pubrep_id":"625","type":"conference","conference":{"location":"Montreal, QC, Canada","end_date":"2015-05-08","start_date":"2015-05-04","name":"CBSE: Component-Based Software Engineering "},"ddc":["000"],"date_updated":"2023-09-07T11:58:33Z","file_date_updated":"2020-07-14T12:44:59Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23(RiSE) and Z211-N23 (Wittgestein Award), by People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 291734, and by the ARTEMIS JU under grant agreement 295373 (nSafeCer). Jan Křetínský has been partially supported by the Czech Science Foundation, grant No. P202/12/G061. Nikola Beneš has been supported by the\r\nMEYS project No. CZ.1.07/2.3.00/30.0009 Employment of Newly Graduated Doctors of Science for Scientific Excellence.","quality_controlled":"1","publisher":"ACM","oa":1,"day":"01","has_accepted_license":"1","year":"2015","doi":"10.1145/2737166.2737175","date_published":"2015-05-01T00:00:00Z","date_created":"2018-12-11T11:52:24Z","page":"101 - 110","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Beneš, Nikola, Przemyslaw Daca, Thomas A Henzinger, Jan Kretinsky, and Dejan Nickovic. “Complete Composition Operators for IOCO-Testing Theory,” 101–10. ACM, 2015. https://doi.org/10.1145/2737166.2737175.","ista":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. 2015. Complete composition operators for IOCO-testing theory. CBSE: Component-Based Software Engineering , Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering , , 101–110.","mla":"Beneš, Nikola, et al. Complete Composition Operators for IOCO-Testing Theory. ACM, 2015, pp. 101–10, doi:10.1145/2737166.2737175.","ieee":"N. Beneš, P. Daca, T. A. Henzinger, J. Kretinsky, and D. Nickovic, “Complete composition operators for IOCO-testing theory,” presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada, 2015, pp. 101–110.","short":"N. Beneš, P. Daca, T.A. Henzinger, J. Kretinsky, D. Nickovic, in:, ACM, 2015, pp. 101–110.","ama":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. Complete composition operators for IOCO-testing theory. In: ACM; 2015:101-110. doi:10.1145/2737166.2737175","apa":"Beneš, N., Daca, P., Henzinger, T. A., Kretinsky, J., & Nickovic, D. (2015). Complete composition operators for IOCO-testing theory (pp. 101–110). Presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada: ACM. https://doi.org/10.1145/2737166.2737175"},"title":"Complete composition operators for IOCO-testing theory","author":[{"full_name":"Beneš, Nikola","last_name":"Beneš","first_name":"Nikola"},{"id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw","full_name":"Daca, Przemyslaw","last_name":"Daca"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan"}],"publist_id":"5676"},{"intvolume":" 47","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1405.0835","open_access":"1"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph algorithms with quadratic complexity to compute the simulation relation. We present an automated technique for assume-guarantee style reasoning for compositional analysis of two-player games by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We show a tight link between two-player games and MDPs, and as a consequence the results for games are lifted to MDPs with qualitative properties. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. ","lang":"eng"}],"ec_funded":1,"volume":47,"related_material":{"record":[{"status":"public","id":"1155","relation":"dissertation_contains"}]},"issue":"2","language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"1501","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-09-07T11:58:33Z","oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No. P23499- N23, FWF NFN Grant No. S11407-N23, FWF Grant S11403-N23 (RiSE), and FWF Grant Z211-N23 (Wittgenstein Award), ERC Start Grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling).","date_created":"2018-12-11T11:52:23Z","date_published":"2015-10-01T00:00:00Z","doi":"10.1007/s10703-015-0235-2","page":"230 - 264","publication":"Formal Methods in System Design","day":"01","year":"2015","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"title":"CEGAR for compositional analysis of qualitative properties in Markov decision processes","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"last_name":"Daca","full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw"}],"publist_id":"5677","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Chmelik M, Daca P. 2015. CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. 47(2), 230–264.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” Formal Methods in System Design. Springer, 2015. https://doi.org/10.1007/s10703-015-0235-2.","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. 2015;47(2):230-264. doi:10.1007/s10703-015-0235-2","apa":"Chatterjee, K., Chmelik, M., & Daca, P. (2015). CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-015-0235-2","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for compositional analysis of qualitative properties in Markov decision processes,” Formal Methods in System Design, vol. 47, no. 2. Springer, pp. 230–264, 2015.","short":"K. Chatterjee, M. Chmelik, P. Daca, Formal Methods in System Design 47 (2015) 230–264.","mla":"Chatterjee, Krishnendu, et al. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” Formal Methods in System Design, vol. 47, no. 2, Springer, 2015, pp. 230–64, doi:10.1007/s10703-015-0235-2."}},{"language":[{"iso":"eng"}],"publication_status":"published","volume":50,"issue":"1","related_material":{"record":[{"status":"public","id":"821","relation":"dissertation_contains"}]},"ec_funded":1,"oa_version":"Preprint","abstract":[{"text":"Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, etc. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring, and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, etc. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in a very important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect that we consider is that the control flow graphs for most programs have constant treewidth. Our main contributions are simple and implementable algorithms that supportmultiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing, but can answer subsequent queries significantly faster as compared to the current best-known solutions for several important problems, such as interprocedural reachability and shortest path. We provide a prototype implementation for interprocedural reachability and intraprocedural shortest path that gives a significant speed-up on several benchmarks.","lang":"eng"}],"month":"01","intvolume":" 50","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1410.7724","open_access":"1"}],"date_updated":"2023-09-07T12:01:58Z","department":[{"_id":"KrCh"}],"_id":"1602","status":"public","type":"journal_article","conference":{"name":"SIGPLAN: Symposium on Principles of Programming Languages","location":"Mumbai, India","end_date":"2015-01-17","start_date":"2015-01-15"},"day":"01","publication":"ACM SIGPLAN Notices","year":"2015","date_published":"2015-01-01T00:00:00Z","doi":"10.1145/2676726.2676979","date_created":"2018-12-11T11:52:58Z","page":"97 - 109","acknowledgement":"We thank anonymous reviewers for helpful comments to improve the presentation of the paper.","quality_controlled":"1","publisher":"ACM","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. 2015;50(1):97-109. doi:10.1145/2676726.2676979","apa":"Chatterjee, K., Ibsen-Jensen, R., Pavlogiannis, A., & Goyal, P. (2015). Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. Mumbai, India: ACM. https://doi.org/10.1145/2676726.2676979","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, P. Goyal, ACM SIGPLAN Notices 50 (2015) 97–109.","ieee":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, and P. Goyal, “Faster algorithms for algebraic path properties in recursive state machines with constant treewidth,” ACM SIGPLAN Notices, vol. 50, no. 1. ACM, pp. 97–109, 2015.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Algebraic Path Properties in Recursive State Machines with Constant Treewidth.” ACM SIGPLAN Notices, vol. 50, no. 1, ACM, 2015, pp. 97–109, doi:10.1145/2676726.2676979.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. 2015. Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. 50(1), 97–109.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Andreas Pavlogiannis, and Prateesh Goyal. “Faster Algorithms for Algebraic Path Properties in Recursive State Machines with Constant Treewidth.” ACM SIGPLAN Notices. ACM, 2015. https://doi.org/10.1145/2676726.2676979."},"title":"Faster algorithms for algebraic path properties in recursive state machines with constant treewidth","publist_id":"5565","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"full_name":"Goyal, Prateesh","last_name":"Goyal","first_name":"Prateesh"}],"external_id":{"arxiv":["1410.7724"]},"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}]},{"oa_version":"None","abstract":[{"lang":"eng","text":"We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs."}],"intvolume":" 50","month":"01","scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-1-4503-3300-9"]},"ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5445"},{"id":"821","status":"public","relation":"dissertation_contains"}]},"issue":"1","volume":50,"_id":"1604","pubrep_id":"523","status":"public","conference":{"name":"SIGPLAN: Symposium on Principles of Programming Languages","start_date":"2015-01-15","end_date":"2015-01-17","location":"Mumbai, India"},"type":"journal_article","date_updated":"2023-09-07T12:01:59Z","department":[{"_id":"KrCh"}],"quality_controlled":"1","publisher":"ACM","publication":"Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT ","day":"01","year":"2015","date_created":"2018-12-11T11:52:59Z","date_published":"2015-01-01T00:00:00Z","doi":"10.1145/2676726.2676968","page":"539 - 551","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, et al. “Quantitative Interprocedural Analysis.” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50, no. 1, ACM, 2015, pp. 539–51, doi:10.1145/2676726.2676968.","apa":"Chatterjee, K., Pavlogiannis, A., & Velner, Y. (2015). Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . Mumbai, India: ACM. https://doi.org/10.1145/2676726.2676968","ama":"Chatterjee K, Pavlogiannis A, Velner Y. Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 2015;50(1):539-551. doi:10.1145/2676726.2676968","ieee":"K. Chatterjee, A. Pavlogiannis, and Y. Velner, “Quantitative interprocedural analysis,” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50, no. 1. ACM, pp. 539–551, 2015.","short":"K. Chatterjee, A. Pavlogiannis, Y. Velner, Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT 50 (2015) 539–551.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. “Quantitative Interprocedural Analysis.” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . ACM, 2015. https://doi.org/10.1145/2676726.2676968.","ista":"Chatterjee K, Pavlogiannis A, Velner Y. 2015. Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 50(1), 539–551."},"title":"Quantitative interprocedural analysis","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"last_name":"Velner","full_name":"Velner, Yaron","first_name":"Yaron"}],"publist_id":"5563"},{"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","publisher":"Springer","quality_controlled":"1","oa":1,"day":"16","year":"2015","doi":"10.1007/978-3-319-21690-4_9","date_published":"2015-07-16T00:00:00Z","date_created":"2018-12-11T11:52:59Z","page":"140 - 157","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. Vol. 9206, Springer, 2015, pp. 140–57, doi:10.1007/978-3-319-21690-4_9.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative verification in constant treewidth graphs. In: Vol 9206. Springer; 2015:140-157. doi:10.1007/978-3-319-21690-4_9","apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms for quantitative verification in constant treewidth graphs (Vol. 9206, pp. 140–157). Presented at the CAV: Computer Aided Verification, San Francisco, CA, USA: Springer. https://doi.org/10.1007/978-3-319-21690-4_9","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Springer, 2015, pp. 140–157.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for quantitative verification in constant treewidth graphs,” presented at the CAV: Computer Aided Verification, San Francisco, CA, USA, 2015, vol. 9206, pp. 140–157.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs,” 9206:140–57. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_9.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs. CAV: Computer Aided Verification, LNCS, vol. 9206, 140–157."},"title":"Faster algorithms for quantitative verification in constant treewidth graphs","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"}],"publist_id":"5560","oa_version":"Preprint","abstract":[{"text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff property, the ratio property, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let n denote the number of nodes of a graph, m the number of edges (for constant treewidth graphs m=O(n)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a multiplicative factor of ϵ in time O(n⋅log(n/ϵ)) and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time O(n⋅log(|a⋅b|))=O(n⋅log(n⋅W)), when the output is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)). Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O(n2⋅m) time and the associated decision problem can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅log(n⋅W)) bound. We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks.","lang":"eng"}],"month":"07","intvolume":" 9206","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"url":"http://arxiv.org/abs/1504.07384","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"5430","relation":"earlier_version"},{"relation":"earlier_version","id":"5437","status":"public"},{"relation":"dissertation_contains","status":"public","id":"821"}]},"volume":9206,"ec_funded":1,"_id":"1607","status":"public","type":"conference","conference":{"start_date":"2015-07-18","end_date":"2015-07-24","location":"San Francisco, CA, USA","name":"CAV: Computer Aided Verification"},"date_updated":"2023-09-07T12:01:59Z","department":[{"_id":"KrCh"}]},{"page":"118 - 127","date_created":"2018-12-11T11:53:37Z","doi":"10.1109/RTSS.2014.9","date_published":"2015-01-15T00:00:00Z","year":"2015","publication":"Real-Time Systems Symposium","day":"15","quality_controlled":"1","publisher":"IEEE","article_processing_charge":"No","publist_id":"5417","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"first_name":"Alexander","last_name":"Kößler","full_name":"Kößler, Alexander"},{"full_name":"Schmid, Ulrich","last_name":"Schmid","first_name":"Ulrich"}],"title":"A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks","citation":{"ista":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2015. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. Real-Time Systems Symposium. RTSS: Real-Time Systems Symposium vol. 2015, 118–127.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich Schmid. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” In Real-Time Systems Symposium, 2015:118–27. IEEE, 2015. https://doi.org/10.1109/RTSS.2014.9.","apa":"Chatterjee, K., Pavlogiannis, A., Kößler, A., & Schmid, U. (2015). A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In Real-Time Systems Symposium (Vol. 2015, pp. 118–127). Rome, Italy: IEEE. https://doi.org/10.1109/RTSS.2014.9","ama":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In: Real-Time Systems Symposium. Vol 2015. IEEE; 2015:118-127. doi:10.1109/RTSS.2014.9","short":"K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, in:, Real-Time Systems Symposium, IEEE, 2015, pp. 118–127.","ieee":"K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks,” in Real-Time Systems Symposium, Rome, Italy, 2015, vol. 2015, no. January, pp. 118–127.","mla":"Chatterjee, Krishnendu, et al. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” Real-Time Systems Symposium, vol. 2015, no. January, IEEE, 2015, pp. 118–27, doi:10.1109/RTSS.2014.9."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"earlier_version","id":"5423","status":"public"},{"relation":"dissertation_contains","status":"public","id":"821"}]},"volume":2015,"issue":"January","publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"intvolume":" 2015","month":"01","abstract":[{"lang":"eng","text":"We present a flexible framework for the automated competitive analysis of on-line scheduling algorithms for firm-deadline real-time tasks based on multi-objective graphs: Given a task set and an on-line scheduling algorithm specified as a labeled transition system, along with some optional safety, liveness, and/or limit-average constraints for the adversary, we automatically compute the competitive ratio of the algorithm w.r.t. A clairvoyant scheduler. We demonstrate the flexibility and power of our approach by comparing the competitive ratio of several on-line algorithms, including Dover, that have been proposed in the past, for various task sets. Our experimental results reveal that none of these algorithms is universally optimal, in the sense that there are task sets where other schedulers provide better performance. Our framework is hence a very useful design tool for selecting optimal algorithms for a given application."}],"oa_version":"None","department":[{"_id":"KrCh"}],"date_updated":"2023-09-07T12:01:59Z","conference":{"end_date":"2014-12-05","location":"Rome, Italy","start_date":"2014-12-02","name":"RTSS: Real-Time Systems Symposium"},"type":"conference","status":"public","_id":"1714"},{"project":[{"call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"}],"article_number":"151","title":"High-resolution brittle fracture simulation with boundary elements","publist_id":"5522","author":[{"id":"357A6A66-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Hahn","full_name":"Hahn, David"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Hahn D, Wojtan C. 2015. High-resolution brittle fracture simulation with boundary elements. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 151.","chicago":"Hahn, David, and Chris Wojtan. “High-Resolution Brittle Fracture Simulation with Boundary Elements,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766896.","ieee":"D. Hahn and C. Wojtan, “High-resolution brittle fracture simulation with boundary elements,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","short":"D. Hahn, C. Wojtan, in:, ACM, 2015.","ama":"Hahn D, Wojtan C. High-resolution brittle fracture simulation with boundary elements. In: Vol 34. ACM; 2015. doi:10.1145/2766896","apa":"Hahn, D., & Wojtan, C. (2015). High-resolution brittle fracture simulation with boundary elements (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766896","mla":"Hahn, David, and Chris Wojtan. High-Resolution Brittle Fracture Simulation with Boundary Elements. Vol. 34, no. 4, 151, ACM, 2015, doi:10.1145/2766896."},"publisher":"ACM","quality_controlled":"1","oa":1,"doi":"10.1145/2766896","date_published":"2015-07-27T00:00:00Z","date_created":"2018-12-11T11:53:09Z","day":"27","has_accepted_license":"1","year":"2015","status":"public","pubrep_id":"609","type":"conference","conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","end_date":"2015-08-13","location":"Los Angeles, CA, United States","start_date":"2015-08-09"},"_id":"1633","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:45:07Z","ddc":["000"],"date_updated":"2023-09-07T12:02:56Z","month":"07","intvolume":" 34","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We present a method for simulating brittle fracture under the assumptions of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture surfaces. The computational cost of the BEM is alleviated by using a low-resolution mesh and interpolating the resulting stress intensity factors when propagating the high-resolution crack-front.\r\n\r\nOur system produces physics-based fracture surfaces with high spatial and temporal resolution, taking spatial variation of material toughness and/or strength into account. It also allows for crack initiation to be handled separately from crack propagation, which is not only more reasonable from a physics perspective, but can also be used to control the simulation.\r\n\r\nSeparating the resolution of the crack-front from the resolution of the computational mesh increases the efficiency and therefore the amount of visual detail on the resulting fracture surfaces. The BEM also allows us to re-use previously computed blocks of the system matrix."}],"volume":34,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"839"}]},"issue":"4","ec_funded":1,"file":[{"checksum":"955aee971983f6b6152bcc1c9b4a7c20","file_id":"5131","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2016-609-v1+1_FractureBEM.pdf","date_created":"2018-12-12T10:15:13Z","file_size":20154270,"date_updated":"2020-07-14T12:45:07Z","creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"project":[{"_id":"2529486C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","grant_number":"T 560-B17"},{"name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","grant_number":"I 812-B12","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Cortical contractility triggers a stochastic switch to fast amoeboid cell motility","author":[{"orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","last_name":"Ruprecht","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wieser","orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"first_name":"Andrew","last_name":"Callan Jones","full_name":"Callan Jones, Andrew"},{"last_name":"Smutny","orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"},{"first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","last_name":"Morita","full_name":"Morita, Hitoshi"},{"full_name":"Sako, Keisuke","orcid":"0000-0002-6453-8075","last_name":"Sako","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke"},{"last_name":"Barone","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa"},{"first_name":"Monika","full_name":"Ritsch Marte, Monika","last_name":"Ritsch Marte"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"last_name":"Voituriez","full_name":"Voituriez, Raphaël","first_name":"Raphaël"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"publist_id":"5634","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ruprecht, Verena, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” Cell, vol. 160, no. 4, Cell Press, 2015, pp. 673–85, doi:10.1016/j.cell.2015.01.008.","ama":"Ruprecht V, Wieser S, Callan Jones A, et al. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 2015;160(4):673-685. doi:10.1016/j.cell.2015.01.008","apa":"Ruprecht, V., Wieser, S., Callan Jones, A., Smutny, M., Morita, H., Sako, K., … Heisenberg, C.-P. J. (2015). Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.01.008","ieee":"V. Ruprecht et al., “Cortical contractility triggers a stochastic switch to fast amoeboid cell motility,” Cell, vol. 160, no. 4. Cell Press, pp. 673–685, 2015.","short":"V. Ruprecht, S. Wieser, A. Callan Jones, M. Smutny, H. Morita, K. Sako, V. Barone, M. Ritsch Marte, M.K. Sixt, R. Voituriez, C.-P.J. Heisenberg, Cell 160 (2015) 673–685.","chicago":"Ruprecht, Verena, Stefan Wieser, Andrew Callan Jones, Michael Smutny, Hitoshi Morita, Keisuke Sako, Vanessa Barone, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.01.008.","ista":"Ruprecht V, Wieser S, Callan Jones A, Smutny M, Morita H, Sako K, Barone V, Ritsch Marte M, Sixt MK, Voituriez R, Heisenberg C-PJ. 2015. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 160(4), 673–685."},"quality_controlled":"1","publisher":"Cell Press","oa":1,"acknowledgement":"We would like to thank R. Hausschild and E. Papusheva for technical assistance and the service facilities at the IST Austria for continuous support. The caRhoA plasmid was a kind gift of T. Kudoh and A. Takesono. We thank M. Piel and E. Paluch for exchanging unpublished data. ","doi":"10.1016/j.cell.2015.01.008","date_published":"2015-02-12T00:00:00Z","date_created":"2018-12-11T11:52:35Z","page":"673 - 685","day":"12","publication":"Cell","has_accepted_license":"1","year":"2015","status":"public","pubrep_id":"484","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1537","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:45:01Z","ddc":["570"],"date_updated":"2023-09-07T12:05:08Z","month":"02","intvolume":" 160","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"3D amoeboid cell migration is central to many developmental and disease-related processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid cell migration mode in early zebrafish embryos, termed stable-bleb migration. Stable-bleb cells display an invariant polarized balloon-like shape with exceptional migration speed and persistence. Progenitor cells can be reversibly transformed into stable-bleb cells irrespective of their primary fate and motile characteristics by increasing myosin II activity through biochemical or mechanical stimuli. Using a combination of theory and experiments, we show that, in stable-bleb cells, cortical contractility fluctuations trigger a stochastic switch into amoeboid motility, and a positive feedback between cortical flows and gradients in contractility maintains stable-bleb cell polarization. We further show that rearward cortical flows drive stable-bleb cell migration in various adhesive and non-adhesive environments, unraveling a highly versatile amoeboid migration phenotype.","lang":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"related_material":{"record":[{"status":"public","id":"961","relation":"dissertation_contains"}]},"volume":160,"issue":"4","file":[{"date_created":"2018-12-12T10:13:21Z","file_name":"IST-2016-484-v1+1_1-s2.0-S0092867415000094-main.pdf","date_updated":"2020-07-14T12:45:01Z","file_size":4362653,"creator":"system","file_id":"5003","checksum":"228d3edf40627d897b3875088a0ac51f","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"language":[{"iso":"eng"}],"publication_status":"published","volume":27,"issue":"1","related_material":{"record":[{"status":"public","id":"938","relation":"dissertation_contains"}]},"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Auxin participates in a multitude of developmental processes, as well as responses to environmental cues. Compared with other plant hormones, auxin exhibits a unique property, as it undergoes directional, cell-to-cell transport facilitated by plasma membrane-localized transport proteins. Among them, a prominent role has been ascribed to the PIN family of auxin efflux facilitators. PIN proteins direct polar auxin transport on account of their asymmetric subcellular localizations. In this review, we provide an overview of the multiple developmental roles of PIN proteins, including the atypical endoplasmic reticulum-localized members of the family, and look at the family from an evolutionary perspective. Next, we cover the cell biological and molecular aspects of PIN function, in particular the establishment of their polar subcellular localization. Hormonal and environmental inputs into the regulation of PIN action are summarized as well."}],"intvolume":" 27","month":"01","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330589/","open_access":"1"}],"scopus_import":1,"date_updated":"2023-09-07T12:06:09Z","department":[{"_id":"JiFr"}],"_id":"1591","status":"public","type":"journal_article","publication":"Plant Cell","day":"20","year":"2015","date_created":"2018-12-11T11:52:54Z","doi":"10.1105/tpc.114.134874","date_published":"2015-01-20T00:00:00Z","page":"20 - 32","oa":1,"quality_controlled":"1","publisher":"American Society of Plant Biologists","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Adamowski M, Friml J. 2015. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 27(1), 20–32.","chicago":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell. American Society of Plant Biologists, 2015. https://doi.org/10.1105/tpc.114.134874.","apa":"Adamowski, M., & Friml, J. (2015). PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.134874","ama":"Adamowski M, Friml J. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 2015;27(1):20-32. doi:10.1105/tpc.114.134874","ieee":"M. Adamowski and J. Friml, “PIN-dependent auxin transport: Action, regulation, and evolution,” Plant Cell, vol. 27, no. 1. American Society of Plant Biologists, pp. 20–32, 2015.","short":"M. Adamowski, J. Friml, Plant Cell 27 (2015) 20–32.","mla":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 20–32, doi:10.1105/tpc.114.134874."},"title":"PIN-dependent auxin transport: Action, regulation, and evolution","external_id":{"pmid":["25604445"]},"publist_id":"5580","author":[{"last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}]},{"oa":1,"publisher":"American Institute of Physics","quality_controlled":"1","year":"2015","publication":"Journal of Mathematical Physics","day":"09","date_created":"2018-12-11T11:53:25Z","doi":"10.1063/1.4932606","date_published":"2015-10-09T00:00:00Z","article_number":"103301","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Alt J. 2015. The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. 56(10), 103301.","chicago":"Alt, Johannes. “The Local Semicircle Law for Random Matrices with a Fourfold Symmetry.” Journal of Mathematical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4932606.","ama":"Alt J. The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. 2015;56(10). doi:10.1063/1.4932606","apa":"Alt, J. (2015). The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4932606","ieee":"J. Alt, “The local semicircle law for random matrices with a fourfold symmetry,” Journal of Mathematical Physics, vol. 56, no. 10. American Institute of Physics, 2015.","short":"J. Alt, Journal of Mathematical Physics 56 (2015).","mla":"Alt, Johannes. “The Local Semicircle Law for Random Matrices with a Fourfold Symmetry.” Journal of Mathematical Physics, vol. 56, no. 10, 103301, American Institute of Physics, 2015, doi:10.1063/1.4932606."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Alt, Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"}],"publist_id":"5472","title":"The local semicircle law for random matrices with a fourfold symmetry","abstract":[{"text":"We consider real symmetric and complex Hermitian random matrices with the additional symmetry hxy = hN-y,N-x. The matrix elements are independent (up to the fourfold symmetry) and not necessarily identically distributed. This ensemble naturally arises as the Fourier transform of a Gaussian orthogonal ensemble. Italso occurs as the flip matrix model - an approximation of the two-dimensional Anderson model at small disorder. We show that the density of states converges to the Wigner semicircle law despite the new symmetry type. We also prove the local version of the semicircle law on the optimal scale.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1506.04683"}],"scopus_import":1,"intvolume":" 56","month":"10","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":56,"related_material":{"record":[{"id":"149","status":"public","relation":"dissertation_contains"}]},"issue":"10","_id":"1677","type":"journal_article","status":"public","date_updated":"2023-09-07T12:38:08Z","department":[{"_id":"LaEr"}]},{"title":"Light-assisted small-molecule screening against protein kinases","author":[{"first_name":"Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro"},{"full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","last_name":"Gschaider-Reichhart","first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Markus","full_name":"Muellner, Markus","last_name":"Muellner"},{"id":"30845DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","full_name":"Nowak, Matthias","last_name":"Nowak"},{"full_name":"Nijman, Sebastian","last_name":"Nijman","first_name":"Sebastian"},{"first_name":"Michael","last_name":"Grusch","full_name":"Grusch, Michael"},{"last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5471","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Inglés Prieto Á, Gschaider-Reichhart E, Muellner M, Nowak M, Nijman S, Grusch M, Janovjak HL. 2015. Light-assisted small-molecule screening against protein kinases. Nature Chemical Biology. 11(12), 952–954.","chicago":"Inglés Prieto, Álvaro, Eva Gschaider-Reichhart, Markus Muellner, Matthias Nowak, Sebastian Nijman, Michael Grusch, and Harald L Janovjak. “Light-Assisted Small-Molecule Screening against Protein Kinases.” Nature Chemical Biology. Nature Publishing Group, 2015. https://doi.org/10.1038/nchembio.1933.","ama":"Inglés Prieto Á, Gschaider-Reichhart E, Muellner M, et al. Light-assisted small-molecule screening against protein kinases. Nature Chemical Biology. 2015;11(12):952-954. doi:10.1038/nchembio.1933","apa":"Inglés Prieto, Á., Gschaider-Reichhart, E., Muellner, M., Nowak, M., Nijman, S., Grusch, M., & Janovjak, H. L. (2015). Light-assisted small-molecule screening against protein kinases. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.1933","ieee":"Á. Inglés Prieto et al., “Light-assisted small-molecule screening against protein kinases,” Nature Chemical Biology, vol. 11, no. 12. Nature Publishing Group, pp. 952–954, 2015.","short":"Á. Inglés Prieto, E. Gschaider-Reichhart, M. Muellner, M. Nowak, S. Nijman, M. Grusch, H.L. Janovjak, Nature Chemical Biology 11 (2015) 952–954.","mla":"Inglés Prieto, Álvaro, et al. “Light-Assisted Small-Molecule Screening against Protein Kinases.” Nature Chemical Biology, vol. 11, no. 12, Nature Publishing Group, 2015, pp. 952–54, doi:10.1038/nchembio.1933."},"project":[{"call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_created":"2018-12-11T11:53:25Z","date_published":"2015-10-12T00:00:00Z","doi":"10.1038/nchembio.1933","page":"952 - 954","publication":"Nature Chemical Biology","day":"12","year":"2015","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"This work was supported by grants from the European Union Seventh Framework Programme (CIG-303564 to H.J. and ERC-StG-311166 to S.M.B.N.), the Human Frontier Science Program (RGY0084_2012 to H.J.) and the Herzfelder Foundation (to M.G.). A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W 1232) and a FemTech fellowship (3580812 Austrian Research Promotion Agency).","department":[{"_id":"HaJa"},{"_id":"LifeSc"}],"file_date_updated":"2020-07-14T12:45:12Z","ddc":["571"],"date_updated":"2023-09-07T12:49:09Z","pubrep_id":"837","status":"public","type":"journal_article","_id":"1678","ec_funded":1,"issue":"12","related_material":{"record":[{"relation":"dissertation_contains","id":"418","status":"public"}]},"volume":11,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2017-837-v1+1_ingles-prieto.pdf","date_created":"2018-12-12T10:10:51Z","file_size":1308364,"date_updated":"2020-07-14T12:45:12Z","creator":"system","checksum":"e9fb251dfcb7cd209b83f17867e61321","file_id":"4842","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","intvolume":" 11","month":"10","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"High-throughput live-cell screens are intricate elements of systems biology studies and drug discovery pipelines. Here, we demonstrate an optogenetics-assisted method that avoids the need for chemical activators and reporters, reduces the number of operational steps and increases information content in a cell-based small-molecule screen against human protein kinases, including an orphan receptor tyrosine kinase. This blueprint for all-optical screening can be adapted to many drug targets and cellular processes.","lang":"eng"}]},{"citation":{"chicago":"Cepeda Humerez, Sarah A, Georg Rieckh, and Gašper Tkačik. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.115.248101.","ista":"Cepeda Humerez SA, Rieckh G, Tkačik G. 2015. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 115(24), 248101.","mla":"Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters, vol. 115, no. 24, 248101, American Physical Society, 2015, doi:10.1103/PhysRevLett.115.248101.","short":"S.A. Cepeda Humerez, G. Rieckh, G. Tkačik, Physical Review Letters 115 (2015).","ieee":"S. A. Cepeda Humerez, G. Rieckh, and G. Tkačik, “Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation,” Physical Review Letters, vol. 115, no. 24. American Physical Society, 2015.","ama":"Cepeda Humerez SA, Rieckh G, Tkačik G. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 2015;115(24). doi:10.1103/PhysRevLett.115.248101","apa":"Cepeda Humerez, S. A., Rieckh, G., & Tkačik, G. (2015). Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.115.248101"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A"},{"first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","last_name":"Rieckh","full_name":"Rieckh, Georg"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"publist_id":"5595","title":"Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation","article_number":"248101","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"year":"2015","publication":"Physical Review Letters","day":"08","date_created":"2018-12-11T11:52:49Z","doi":"10.1103/PhysRevLett.115.248101","date_published":"2015-12-08T00:00:00Z","oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_updated":"2023-09-07T12:55:21Z","department":[{"_id":"GaTk"}],"_id":"1576","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6473"}]},"volume":115,"issue":"24","abstract":[{"text":"Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect regulatory crosstalk: the possibility that noncognate TFs could initiate transcription, with potentially disastrous effects for the cell. Here, we estimate the importance of crosstalk, suggest that its avoidance strongly constrains equilibrium models of TF binding, and propose an alternative nonequilibrium scheme that implements kinetic proofreading to suppress erroneous initiation. This proposal is consistent with the observed covalent modifications of the transcriptional apparatus and predicts increased noise in gene expression as a trade-off for improved specificity. Using information theory, we quantify this trade-off to find when optimal proofreading architectures are favored over their equilibrium counterparts. Such architectures exhibit significant super-Poisson noise at low expression in steady state.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.05716"}],"scopus_import":1,"intvolume":" 115","month":"12"},{"language":[{"iso":"eng"}],"publication":"arXiv","day":"15","publication_status":"submitted","year":"2015","date_created":"2020-07-30T10:45:19Z","date_published":"2015-11-15T00:00:00Z","related_material":{"record":[{"id":"9308","status":"public","relation":"later_version"},{"relation":"later_version","id":"10220","status":"public"},{"relation":"dissertation_contains","status":"public","id":"8156"}]},"acknowledgement":"We would like to thank A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful discussions.","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study conditions under which a finite simplicial complex $K$ can be mapped to $\\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding is a map $f: K\\to \\mathbb R^d$ such that the images of any $r$\r\npairwise disjoint simplices of $K$ do not have a common point. We show that if $r$ is not a prime power and $d\\geq 2r+1$, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost $r$-embedding of\r\nthe $(d+1)(r-1)$-simplex in $\\mathbb R^d$. This improves on previous constructions of counterexamples (for $d\\geq 3r$) based on a series of papers by M. \\\"Ozaydin, M. Gromov, P. Blagojevi\\'c, F. Frick, G. Ziegler, and the second and fourth present authors. The counterexamples are obtained by proving the following algebraic criterion in codimension 2: If $r\\ge3$ and if $K$ is a finite $2(r-1)$-complex then there exists an almost $r$-embedding $K\\to \\mathbb R^{2r}$ if and only if there exists a general position PL map $f:K\\to \\mathbb R^{2r}$ such that the algebraic intersection number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero. This result can be restated in terms of cohomological obstructions or equivariant maps, and extends an analogous codimension 3 criterion by the second and fourth authors. As another application we classify ornaments $f:S^3 \\sqcup S^3\\sqcup S^3\\to \\mathbb R^5$ up to ornament\r\nconcordance. It follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample."}],"month":"11","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1511.03501","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-07T13:12:17Z","citation":{"ista":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv, 1511.03501.","chicago":"Avvakumov, Sergey, Isaac Mabillard, A. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, n.d.","short":"S. Avvakumov, I. Mabillard, A. Skopenkov, U. Wagner, ArXiv (n.d.).","ieee":"S. Avvakumov, I. Mabillard, A. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections, III. Codimension 2,” arXiv. .","ama":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv.","apa":"Avvakumov, S., Mabillard, I., Skopenkov, A., & Wagner, U. (n.d.). Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv.","mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, 1511.03501."},"title":"Eliminating higher-multiplicity intersections, III. Codimension 2","department":[{"_id":"UlWa"}],"external_id":{"arxiv":["1511.03501"]},"article_processing_charge":"No","author":[{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey","last_name":"Avvakumov","full_name":"Avvakumov, Sergey"},{"full_name":"Mabillard, Isaac","last_name":"Mabillard","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac"},{"full_name":"Skopenkov, A.","last_name":"Skopenkov","first_name":"A."},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"article_number":"1511.03501","_id":"8183","status":"public","type":"preprint"},{"_id":"5441","type":"technical_report","pubrep_id":"340","status":"public","citation":{"ista":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. 2015. Algorithms for algebraic path properties in concurrent systems of constant treewidth components, IST Austria, 24p.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-340-v1-1.","ieee":"K. Chatterjee, R. Ibsen-Jensen, A. K. Goharshady, and A. Pavlogiannis, Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria, 2015.","short":"K. Chatterjee, R. Ibsen-Jensen, A.K. Goharshady, A. Pavlogiannis, Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components, IST Austria, 2015.","apa":"Chatterjee, K., Ibsen-Jensen, R., Goharshady, A. K., & Pavlogiannis, A. (2015). Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria. https://doi.org/10.15479/AT:IST-2015-340-v1-1","ama":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria; 2015. doi:10.15479/AT:IST-2015-340-v1-1","mla":"Chatterjee, Krishnendu, et al. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015, doi:10.15479/AT:IST-2015-340-v1-1."},"date_updated":"2023-09-19T14:36:19Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir","full_name":"Goharshady, Amir","orcid":"0000-0003-1702-6584","last_name":"Goharshady"},{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"}],"file_date_updated":"2020-07-14T12:46:56Z","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks."}],"oa_version":"Published Version","oa":1,"publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"month":"07","year":"2015","publication_status":"published","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"day":"11","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5531","checksum":"df383dc62c94d7b2ea639aba088a76c6","creator":"system","file_size":861396,"date_updated":"2020-07-14T12:46:56Z","file_name":"IST-2015-340-v1+1_main.pdf","date_created":"2018-12-12T11:54:09Z"}],"page":"24","date_created":"2018-12-12T11:39:21Z","doi":"10.15479/AT:IST-2015-340-v1-1","date_published":"2015-07-11T00:00:00Z","related_material":{"record":[{"relation":"later_version","id":"1437","status":"public"},{"id":"5442","status":"public","relation":"earlier_version"},{"relation":"later_version","status":"public","id":"6009"}]}},{"year":"2015","publication_status":"published","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T11:53:37Z","file_name":"IST-2015-343-v2+1_main.pdf","date_updated":"2020-07-14T12:46:57Z","file_size":658747,"creator":"system","checksum":"98fd936102f3e057fc321ef6d316001d","file_id":"5498","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"checksum":"b31d09b1241b59c75e1f42dadf09d258","file_id":"6316","relation":"main_file","access_level":"closed","content_type":"text/plain","file_name":"IST-2015-343-v2+2_anonymous.txt","date_created":"2019-04-16T12:36:08Z","creator":"dernst","file_size":139,"date_updated":"2020-07-14T12:46:57Z"}],"day":"14","page":"22","date_created":"2018-12-12T11:39:21Z","related_material":{"record":[{"status":"public","id":"1437","relation":"later_version"},{"relation":"later_version","id":"5441","status":"public"},{"status":"public","id":"6009","relation":"later_version"}]},"date_published":"2015-07-14T00:00:00Z","abstract":[{"lang":"eng","text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural properties that arise in program analysis.\r\nWe consider that each component of the concurrent system is a graph with constant treewidth, and it is known that the controlflow graphs of most programs have constant treewidth. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis problems (e.g., alias analysis). The study of multiple queries allows us to consider the tradeoff between the resource usage of the \\emph{one-time} preprocessing and for \\emph{each individual} query. The traditional approaches construct the product graph of all components and apply the best-known graph algorithm on the product. In the traditional approach, even the answer to a single query requires the transitive closure computation (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time.\r\n\r\nOur main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, \r\neach subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results that show that the worst-case running times of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (such as improving \r\nthe worst-case bounds for the shortest path problem in general graphs whose current best-known bound has not been improved in five decades). Finally, we provide a prototype implementation of our algorithms which significantly outperforms the existing algorithmic methods on several benchmarks."}],"oa_version":"Published Version","oa":1,"publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"scopus_import":1,"month":"07","citation":{"ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2015. Algorithms for algebraic path properties in concurrent systems of constant treewidth components, IST Austria, 22p.","chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components, IST Austria, 2015.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria, 2015.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, & Anonymous, 4. (2015). Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria; 2015.","mla":"Anonymous, 1, et al. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015."},"date_updated":"2023-09-19T14:36:19Z","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Anonymous, 1","last_name":"Anonymous","first_name":"1"},{"first_name":"2","last_name":"Anonymous","full_name":"Anonymous, 2"},{"first_name":"3","full_name":"Anonymous, 3","last_name":"Anonymous"},{"last_name":"Anonymous","full_name":"Anonymous, 4","first_name":"4"}],"title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","file_date_updated":"2020-07-14T12:46:57Z","_id":"5442","type":"technical_report","pubrep_id":"344","status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2015. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 259–268.","chicago":"Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, 259–68. ACM, 2015. https://doi.org/10.1145/2728606.2728608.","ieee":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta, “Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games,” in Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, Seattle, WA, United States, 2015, pp. 259–268.","short":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 259–268.","ama":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. In: Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. ACM; 2015:259-268. doi:10.1145/2728606.2728608","apa":"Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., & Belta, C. (2015). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control (pp. 259–268). Seattle, WA, United States: ACM. https://doi.org/10.1145/2728606.2728608","mla":"Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 259–68, doi:10.1145/2728606.2728608."},"date_updated":"2023-09-20T09:43:09Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"title":"Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games","publist_id":"5456","author":[{"full_name":"Svoreňová, Mária","last_name":"Svoreňová","first_name":"Mária"},{"last_name":"Kretinsky","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"last_name":"Chmelik","full_name":"Chmelik, Martin","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Cěrná, Ivana","last_name":"Cěrná","first_name":"Ivana"},{"first_name":"Cǎlin","full_name":"Belta, Cǎlin","last_name":"Belta"}],"_id":"1689","status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"}],"type":"conference","conference":{"name":"HSCC: Hybrid Systems - Computation and Control","location":"Seattle, WA, United States","end_date":"2015-04-16","start_date":"2015-04-14"},"day":"14","language":[{"iso":"eng"}],"publication":"Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control","publication_status":"published","year":"2015","related_material":{"record":[{"relation":"later_version","id":"1407","status":"public"}]},"doi":"10.1145/2728606.2728608","date_published":"2015-04-14T00:00:00Z","ec_funded":1,"date_created":"2018-12-11T11:53:29Z","page":"259 - 268","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. We demonstrate our approach on an illustrative case study."}],"month":"04","publisher":"ACM","scopus_import":1,"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.5387"}]},{"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"local","checksum":"6ff58ac220e2f20cb001ba35d4924495","file_id":"4715","file_size":481922,"date_updated":"2020-07-14T12:45:13Z","creator":"system","file_name":"IST-2015-336-v1+1_long_version.pdf","date_created":"2018-12-12T10:08:53Z"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"1130","relation":"dissertation_contains"},{"status":"public","id":"1338","relation":"later_version"}]},"volume":9207,"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"text":"We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of such sequences produced under a non-preemptive scheduler. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and rules for inserting synchronization. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient, and, since it does not require explicit specifications, is more practical than the conventional approach based on user-provided assertions.","lang":"eng"}],"month":"07","intvolume":" 9207","scopus_import":1,"alternative_title":["LNCS"],"ddc":["000"],"date_updated":"2023-09-20T11:13:50Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:13Z","series_title":"Lecture Notes in Computer Science","_id":"1729","status":"public","pubrep_id":"336","type":"conference","conference":{"name":"CAV: Computer Aided Verification","end_date":"2015-07-24","location":"San Francisco, CA, United States","start_date":"2015-07-18"},"day":"01","has_accepted_license":"1","year":"2015","doi":"10.1007/978-3-319-21668-3_11","date_published":"2015-07-01T00:00:00Z","date_created":"2018-12-11T11:53:42Z","page":"180 - 197","quality_controlled":"1","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2015. From non-preemptive to preemptive scheduling using synchronization synthesis. 9207, 180–197.","chicago":"Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-21668-3_11.","short":"P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, 9207 (2015) 180–197.","ieee":"P. Cerny et al., “From non-preemptive to preemptive scheduling using synchronization synthesis,” vol. 9207. Springer, pp. 180–197, 2015.","ama":"Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. 2015;9207:180-197. doi:10.1007/978-3-319-21668-3_11","apa":"Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., & Tarrach, T. (2015). From non-preemptive to preemptive scheduling using synchronization synthesis. Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21668-3_11","mla":"Cerny, Pavol, et al. From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis. Vol. 9207, Springer, 2015, pp. 180–97, doi:10.1007/978-3-319-21668-3_11."},"title":"From non-preemptive to preemptive scheduling using synchronization synthesis","publist_id":"5398","author":[{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","last_name":"Cerny","full_name":"Cerny, Pavol"},{"first_name":"Edmund","last_name":"Clarke","full_name":"Clarke, Edmund"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun"},{"last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid","first_name":"Leonid"},{"full_name":"Samanta, Roopsha","last_name":"Samanta","first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87"},{"id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","first_name":"Thorsten","orcid":"0000-0003-4409-8487","full_name":"Tarrach, Thorsten","last_name":"Tarrach"}],"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2 148797.\r\n","doi":"10.1007/978-3-662-46681-0_47","date_published":"2015-04-01T00:00:00Z","date_created":"2018-12-11T11:54:16Z","page":"469 - 483","day":"01","year":"2015","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Model checking gene regulatory networks","publist_id":"5267","author":[{"first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","last_name":"Giacobbe","orcid":"0000-0001-8180-0904","full_name":"Giacobbe, Mirco"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"},{"full_name":"Gupta, Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_47.","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483.","mla":"Giacobbe, Mirco, et al. Model Checking Gene Regulatory Networks. Vol. 9035, Springer, 2015, pp. 469–83, doi:10.1007/978-3-662-46681-0_47.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483.","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:10.1007/978-3-662-46681-0_47","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2015). Model checking gene regulatory networks. 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_47"},"month":"04","intvolume":" 9035","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1410.7704","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs –an important problem of interest in evolutionary biology– more efficiently than the classical simulation method. We specify the property in linear temporal logics. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights."}],"related_material":{"record":[{"relation":"later_version","id":"1351","status":"public"}]},"volume":9035,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"conference","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"London, United Kingdom","end_date":"2015-04-18","start_date":"2015-04-11"},"series_title":"Lecture Notes in Computer Science","_id":"1835","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"date_updated":"2023-09-20T11:06:03Z"},{"title":"Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene","publist_id":"5668","author":[{"last_name":"Michalko","full_name":"Michalko, Jaroslav","first_name":"Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dravecka, Marta","orcid":"0000-0002-2519-8004","last_name":"Dravecka","first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. 2015. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 4.","chicago":"Michalko, Jaroslav, Marta Lukacisinova, Mark Tobias Bollenbach, and Jiří Friml. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research . F1000 Research, 2015. https://doi.org/10.12688/f1000research.7143.1.","ieee":"J. Michalko, M. Lukacisinova, M. T. Bollenbach, and J. Friml, “Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene,” F1000 Research , vol. 4. F1000 Research, 2015.","short":"J. Michalko, M. Lukacisinova, M.T. Bollenbach, J. Friml, F1000 Research 4 (2015).","apa":"Michalko, J., Lukacisinova, M., Bollenbach, M. T., & Friml, J. (2015). Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . F1000 Research. https://doi.org/10.12688/f1000research.7143.1","ama":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 2015;4. doi:10.12688/f1000research.7143.1","mla":"Michalko, Jaroslav, et al. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research , vol. 4, F1000 Research, 2015, doi:10.12688/f1000research.7143.1."},"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"date_published":"2015-10-01T00:00:00Z","doi":"10.12688/f1000research.7143.1","date_created":"2018-12-11T11:52:26Z","day":"01","publication":"F1000 Research ","has_accepted_license":"1","year":"2015","quality_controlled":"1","publisher":"F1000 Research","oa":1,"acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP to JF). JM internship was supported by the grant “Action Austria – Slovakia”.\r\nData associated with the article are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication). \r\n\r\nData availability: \r\nF1000Research: Dataset 1. Dataset 1, 10.5256/f1000research.7143.d104552\r\n\r\nF1000Research: Dataset 2. Dataset 2, 10.5256/f1000research.7143.d104553\r\n\r\nF1000Research: Dataset 3. Dataset 3, 10.5256/f1000research.7143.d104554","file_date_updated":"2020-07-14T12:44:59Z","department":[{"_id":"JiFr"},{"_id":"ToBo"}],"ddc":["570"],"date_updated":"2023-10-10T14:10:24Z","status":"public","pubrep_id":"497","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1509","volume":4,"ec_funded":1,"file":[{"date_created":"2018-12-12T10:16:12Z","file_name":"IST-2016-497-v1+1_10.12688_f1000research.7143.1_20151102.pdf","date_updated":"2020-07-14T12:44:59Z","file_size":4414248,"creator":"system","checksum":"8beae5cbe988e1060265ae7de2ee8306","file_id":"5198","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 4","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"The Auxin Binding Protein1 (ABP1) has been identified based on its ability to bind auxin with high affinity and studied for a long time as a prime candidate for the extracellular auxin receptor responsible for mediating in particular the fast non-transcriptional auxin responses. However, the contradiction between the embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the biological importance of ABP1 and relevance of the previous genetic studies. Here we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore, the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the BSM locus by the T-DNA insertions. This clarifies the controversy of different phenotypes among published abp1 knock-out alleles and asks for reflections on the developmental role of ABP1.","lang":"eng"}]},{"citation":{"ieee":"T. Priklopil and K. Chatterjee, “Evolution of decisions in population games with sequentially searching individuals,” Games, vol. 6, no. 4. MDPI, pp. 413–437, 2015.","short":"T. Priklopil, K. Chatterjee, Games 6 (2015) 413–437.","apa":"Priklopil, T., & Chatterjee, K. (2015). Evolution of decisions in population games with sequentially searching individuals. Games. MDPI. https://doi.org/10.3390/g6040413","ama":"Priklopil T, Chatterjee K. Evolution of decisions in population games with sequentially searching individuals. Games. 2015;6(4):413-437. doi:10.3390/g6040413","mla":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games, vol. 6, no. 4, MDPI, 2015, pp. 413–37, doi:10.3390/g6040413.","ista":"Priklopil T, Chatterjee K. 2015. Evolution of decisions in population games with sequentially searching individuals. Games. 6(4), 413–437.","chicago":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games. MDPI, 2015. https://doi.org/10.3390/g6040413."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas","full_name":"Priklopil, Tadeas","last_name":"Priklopil"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}],"publist_id":"5467","article_processing_charge":"No","title":"Evolution of decisions in population games with sequentially searching individuals","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","year":"2015","day":"29","publication":"Games","page":"413 - 437","date_published":"2015-09-29T00:00:00Z","doi":"10.3390/g6040413","date_created":"2018-12-11T11:53:26Z","quality_controlled":"1","publisher":"MDPI","oa":1,"date_updated":"2023-10-17T11:42:52Z","ddc":["000"],"department":[{"_id":"NiBa"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:12Z","_id":"1681","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"448","publication_identifier":{"eissn":["2073-4336"]},"publication_status":"published","file":[{"file_size":518832,"date_updated":"2020-07-14T12:45:12Z","creator":"system","file_name":"IST-2016-448-v1+1_games-06-00413.pdf","date_created":"2018-12-12T10:12:41Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4959","checksum":"912e1acbaf201100f447a43e4d5958bd"}],"language":[{"iso":"eng"}],"volume":6,"issue":"4","ec_funded":1,"abstract":[{"lang":"eng","text":"In many social situations, individuals endeavor to find the single best possible partner, but are constrained to evaluate the candidates in sequence. Examples include the search for mates, economic partnerships, or any other long-term ties where the choice to interact involves two parties. Surprisingly, however, previous theoretical work on mutual choice problems focuses on finding equilibrium solutions, while ignoring the evolutionary dynamics of decisions. Empirically, this may be of high importance, as some equilibrium solutions can never be reached unless the population undergoes radical changes and a sufficient number of individuals change their decisions simultaneously. To address this question, we apply a mutual choice sequential search problem in an evolutionary game-theoretical model that allows one to find solutions that are favored by evolution. As an example, we study the influence of sequential search on the evolutionary dynamics of cooperation. For this, we focus on the classic snowdrift game and the prisoner’s dilemma game."}],"oa_version":"Published Version","scopus_import":"1","month":"09","intvolume":" 6"},{"oa_version":"Published Version","abstract":[{"text":"Quantifying behaviors of robots which were generated autonomously from task-independent objective functions is an important prerequisite for objective comparisons of algorithms and movements of animals. The temporal sequence of such a behavior can be considered as a time series and hence complexity measures developed for time series are natural candidates for its quantification. The predictive information and the excess entropy are such complexity measures. They measure the amount of information the past contains about the future and thus quantify the nonrandom structure in the temporal sequence. However, when using these measures for systems with continuous states one has to deal with the fact that their values will depend on the resolution with which the systems states are observed. For deterministic systems both measures will diverge with increasing resolution. We therefore propose a new decomposition of the excess entropy in resolution dependent and resolution independent parts and discuss how they depend on the dimensionality of the dynamics, correlations and the noise level. For the practical estimation we propose to use estimates based on the correlation integral instead of the direct estimation of the mutual information based on next neighbor statistics because the latter allows less control of the scale dependencies. Using our algorithm we are able to show how autonomous learning generates behavior of increasing complexity with increasing learning duration.","lang":"eng"}],"month":"10","intvolume":" 17","scopus_import":"1","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4943","checksum":"945d99631a96e0315acb26dc8541dcf9","file_size":6455007,"date_updated":"2020-07-14T12:45:08Z","creator":"system","file_name":"IST-2016-464-v1+1_entropy-17-07266.pdf","date_created":"2018-12-12T10:12:25Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":17,"issue":"10","ec_funded":1,"_id":"1655","status":"public","pubrep_id":"464","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_updated":"2023-10-17T11:42:00Z","file_date_updated":"2020-07-14T12:45:08Z","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"acknowledgement":"This work was supported by the DFG priority program 1527 (Autonomous Learning) and by the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 318723 (MatheMACS) and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734.","publisher":"MDPI","quality_controlled":"1","oa":1,"day":"23","publication":"Entropy","has_accepted_license":"1","year":"2015","date_published":"2015-10-23T00:00:00Z","doi":"10.3390/e17107266","date_created":"2018-12-11T11:53:17Z","page":"7266 - 7297","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Martius, Georg S, and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” Entropy. MDPI, 2015. https://doi.org/10.3390/e17107266.","ista":"Martius GS, Olbrich E. 2015. Quantifying emergent behavior of autonomous robots. Entropy. 17(10), 7266–7297.","mla":"Martius, Georg S., and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” Entropy, vol. 17, no. 10, MDPI, 2015, pp. 7266–97, doi:10.3390/e17107266.","short":"G.S. Martius, E. Olbrich, Entropy 17 (2015) 7266–7297.","ieee":"G. S. Martius and E. Olbrich, “Quantifying emergent behavior of autonomous robots,” Entropy, vol. 17, no. 10. MDPI, pp. 7266–7297, 2015.","ama":"Martius GS, Olbrich E. Quantifying emergent behavior of autonomous robots. Entropy. 2015;17(10):7266-7297. doi:10.3390/e17107266","apa":"Martius, G. S., & Olbrich, E. (2015). Quantifying emergent behavior of autonomous robots. Entropy. MDPI. https://doi.org/10.3390/e17107266"},"title":"Quantifying emergent behavior of autonomous robots","publist_id":"5495","author":[{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","full_name":"Martius, Georg S","last_name":"Martius"},{"first_name":"Eckehard","last_name":"Olbrich","full_name":"Olbrich, Eckehard"}],"article_processing_charge":"No"},{"date_created":"2018-12-11T11:54:16Z","doi":"10.1177/1759091415575845","date_published":"2015-04-13T00:00:00Z","publication":"ASN Neuro","day":"13","year":"2015","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"SAGE Publications","title":"Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats","article_processing_charge":"No","author":[{"last_name":"Chen","full_name":"Chen, Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong"},{"first_name":"Chao","last_name":"Wang","full_name":"Wang, Chao"},{"last_name":"Zhao","full_name":"Zhao, Xuan","first_name":"Xuan"},{"last_name":"Zhou","full_name":"Zhou, Tao","first_name":"Tao"},{"first_name":"Dao","full_name":"Xu, Dao","last_name":"Xu"},{"first_name":"Zhi","last_name":"Wang","full_name":"Wang, Zhi"},{"full_name":"Wang, Ying","last_name":"Wang","first_name":"Ying"}],"publist_id":"5269","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chen, Chong, et al. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” ASN Neuro, vol. 7, no. 2, SAGE Publications, 2015, doi:10.1177/1759091415575845.","ieee":"C. Chen et al., “Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats,” ASN Neuro, vol. 7, no. 2. SAGE Publications, 2015.","short":"C. Chen, C. Wang, X. Zhao, T. Zhou, D. Xu, Z. Wang, Y. Wang, ASN Neuro 7 (2015).","apa":"Chen, C., Wang, C., Zhao, X., Zhou, T., Xu, D., Wang, Z., & Wang, Y. (2015). Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. SAGE Publications. https://doi.org/10.1177/1759091415575845","ama":"Chen C, Wang C, Zhao X, et al. Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. 2015;7(2). doi:10.1177/1759091415575845","chicago":"Chen, Chong, Chao Wang, Xuan Zhao, Tao Zhou, Dao Xu, Zhi Wang, and Ying Wang. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” ASN Neuro. SAGE Publications, 2015. https://doi.org/10.1177/1759091415575845.","ista":"Chen C, Wang C, Zhao X, Zhou T, Xu D, Wang Z, Wang Y. 2015. Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. 7(2)."},"license":"https://creativecommons.org/licenses/by/3.0/","issue":"2","volume":7,"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:18Z","file_size":1146814,"creator":"system","date_created":"2018-12-12T10:14:08Z","file_name":"IST-2016-456-v1+1_ASN_Neuro-2015-Chen-.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"53e16bd3fc2ae2c0d7de9164626c37aa","file_id":"5057"}],"publication_status":"published","intvolume":" 7","month":"04","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Huge body of evidences demonstrated that volatile anesthetics affect the hippocampal neurogenesis and neurocognitive functions, and most of them showed impairment at anesthetic dose. Here, we investigated the effect of low dose (1.8%) sevoflurane on hippocampal neurogenesis and dentate gyrus-dependent learning. Neonatal rats at postnatal day 4 to 6 (P4-6) were treated with 1.8% sevoflurane for 6 hours. Neurogenesis was quantified by bromodeoxyuridine labeling and electrophysiology recording. Four and seven weeks after treatment, the Morris water maze and contextual-fear discrimination learning tests were performed to determine the influence on spatial learning and pattern separation. A 6-hour treatment with 1.8% sevoflurane promoted hippocampal neurogenesis and increased the survival of newborn cells and the proportion of immature granular cells in the dentate gyrus of neonatal rats. Sevoflurane-treated rats performed better during the training days of the Morris water maze test and in contextual-fear discrimination learning test. These results suggest that a subanesthetic dose of sevoflurane promotes hippocampal neurogenesis in neonatal rats and facilitates their performance in dentate gyrus-dependent learning tasks.","lang":"eng"}],"department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:18Z","ddc":["570"],"date_updated":"2023-10-18T06:47:30Z","pubrep_id":"456","status":"public","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"type":"journal_article","article_type":"original","_id":"1834"},{"oa":1,"quality_controlled":"1","publisher":"Faculté des sciences de Toulouse","publication":"Annales de la faculté des sciences de Toulouse","day":"01","year":"2015","date_created":"2018-12-11T11:53:10Z","doi":"10.5802/afst.1464","date_published":"2015-01-01T00:00:00Z","page":"781 - 800","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Erbar M, Maas J, Tetali P. 2015. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de la faculté des sciences de Toulouse. 24(4), 781–800.","chicago":"Erbar, Matthias, Jan Maas, and Prasad Tetali. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” Annales de La Faculté Des Sciences de Toulouse. Faculté des sciences de Toulouse, 2015. https://doi.org/10.5802/afst.1464.","ama":"Erbar M, Maas J, Tetali P. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de la faculté des sciences de Toulouse. 2015;24(4):781-800. doi:10.5802/afst.1464","apa":"Erbar, M., Maas, J., & Tetali, P. (2015). Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de La Faculté Des Sciences de Toulouse. Faculté des sciences de Toulouse. https://doi.org/10.5802/afst.1464","ieee":"M. Erbar, J. Maas, and P. Tetali, “Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models,” Annales de la faculté des sciences de Toulouse, vol. 24, no. 4. Faculté des sciences de Toulouse, pp. 781–800, 2015.","short":"M. Erbar, J. Maas, P. Tetali, Annales de La Faculté Des Sciences de Toulouse 24 (2015) 781–800.","mla":"Erbar, Matthias, et al. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” Annales de La Faculté Des Sciences de Toulouse, vol. 24, no. 4, Faculté des sciences de Toulouse, 2015, pp. 781–800, doi:10.5802/afst.1464."},"title":"Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models","article_processing_charge":"No","external_id":{"arxiv":["1409.8605"]},"publist_id":"5520","author":[{"full_name":"Erbar, Matthias","last_name":"Erbar","first_name":"Matthias"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"full_name":"Tetali, Prasad","last_name":"Tetali","first_name":"Prasad"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We calculate a Ricci curvature lower bound for some classical examples of random walks, namely, a chain on a slice of the n-dimensional discrete cube (the so-called Bernoulli-Laplace model) and the random transposition shuffle of the symmetric group of permutations on n letters."}],"intvolume":" 24","month":"01","main_file_link":[{"url":"http://arxiv.org/abs/1409.8605","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":24,"issue":"4","_id":"1635","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-10-18T07:48:28Z","department":[{"_id":"JaMa"}]},{"external_id":{"pmid":["26028443"]},"article_processing_charge":"No","author":[{"first_name":"B","full_name":"Kick, B","last_name":"Kick"},{"last_name":"Praetorius","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M"},{"full_name":"Dietz, H","last_name":"Dietz","first_name":"H"},{"first_name":"D","full_name":"Weuster-Botz, D","last_name":"Weuster-Botz"}],"title":"Efficient production of single-stranded phage DNA as scaffolds for DNA origami","citation":{"mla":"Kick, B., et al. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” Nano Letters, vol. 15, no. 7, ACS Publications, 2015, pp. 4672–76, doi:10.1021/acs.nanolett.5b01461.","ieee":"B. Kick, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Efficient production of single-stranded phage DNA as scaffolds for DNA origami,” Nano Letters, vol. 15, no. 7. ACS Publications, pp. 4672–4676, 2015.","short":"B. Kick, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Nano Letters 15 (2015) 4672–4676.","ama":"Kick B, Praetorius FM, Dietz H, Weuster-Botz D. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 2015;15(7):4672-4676. doi:10.1021/acs.nanolett.5b01461","apa":"Kick, B., Praetorius, F. M., Dietz, H., & Weuster-Botz, D. (2015). Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. ACS Publications. https://doi.org/10.1021/acs.nanolett.5b01461","chicago":"Kick, B, Florian M Praetorius, H Dietz, and D Weuster-Botz. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” Nano Letters. ACS Publications, 2015. https://doi.org/10.1021/acs.nanolett.5b01461.","ista":"Kick B, Praetorius FM, Dietz H, Weuster-Botz D. 2015. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 15(7), 4672–4676."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"4672-4676","date_created":"2023-09-06T12:52:47Z","date_published":"2015-06-01T00:00:00Z","doi":"10.1021/acs.nanolett.5b01461","year":"2015","publication":"Nano Letters","day":"01","oa":1,"quality_controlled":"1","publisher":"ACS Publications","date_updated":"2023-11-07T11:56:32Z","extern":"1","article_type":"letter_note","type":"journal_article","status":"public","_id":"14303","issue":"7","volume":15,"publication_status":"published","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1021/acs.nanolett.5b01461","open_access":"1"}],"intvolume":" 15","month":"06","abstract":[{"text":"Scaffolded DNA origami enables the fabrication of a variety of complex nanostructures that promise utility in diverse fields of application, ranging from biosensing over advanced therapeutics to metamaterials. The broad applicability of DNA origami as a material beyond the level of proof-of-concept studies critically depends, among other factors, on the availability of large amounts of pure single-stranded scaffold DNA. Here, we present a method for the efficient production of M13 bacteriophage-derived genomic DNA using high-cell-density fermentation of Escherichia coli in stirred-tank bioreactors. We achieve phage titers of up to 1.6 × 1014 plaque-forming units per mL. Downstream processing yields up to 410 mg of high-quality single-stranded DNA per one liter reaction volume, thus upgrading DNA origami-based nanotechnology from the milligram to the gram scale.","lang":"eng"}],"pmid":1,"oa_version":"Published Version"},{"publist_id":"5564","author":[{"first_name":"Tomáš","full_name":"Brázdil, Tomáš","last_name":"Brázdil"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Chmelik, Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"id":"42BABFB4-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Fellner","full_name":"Fellner, Andreas"},{"last_name":"Kretinsky","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"title":"Counterexample explanation by learning small strategies in Markov decision processes","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Andreas Fellner, and Jan Kretinsky. “Counterexample Explanation by Learning Small Strategies in Markov Decision Processes,” 9206:158–77. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_10.","ista":"Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. 2015. Counterexample explanation by learning small strategies in Markov decision processes. CAV: Computer Aided Verification, LNCS, vol. 9206, 158–177.","mla":"Brázdil, Tomáš, et al. Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Vol. 9206, Springer, 2015, pp. 158–77, doi:10.1007/978-3-319-21690-4_10.","short":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, J. Kretinsky, in:, Springer, 2015, pp. 158–177.","ieee":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, and J. Kretinsky, “Counterexample explanation by learning small strategies in Markov decision processes,” presented at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015, vol. 9206, pp. 158–177.","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Fellner, A., & Kretinsky, J. (2015). Counterexample explanation by learning small strategies in Markov decision processes (Vol. 9206, pp. 158–177). Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21690-4_10","ama":"Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. Counterexample explanation by learning small strategies in Markov decision processes. In: Vol 9206. Springer; 2015:158-177. doi:10.1007/978-3-319-21690-4_10"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"page":"158 - 177","date_published":"2015-07-16T00:00:00Z","doi":"10.1007/978-3-319-21690-4_10","date_created":"2018-12-11T11:52:58Z","year":"2015","day":"16","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"This research was funded in part by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE) and Z211-N23 (Wittgenstein Award), European Research Council (ERC) Grant No 279307 (Graph Games), ERC Grant No 267989 (QUAREM), the Czech Science Foundation Grant No P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) REA Grant No 291734.","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2024-02-21T13:52:07Z","type":"conference","conference":{"start_date":"2015-07-18","end_date":"2015-07-24","location":"San Francisco, CA, United States","name":"CAV: Computer Aided Verification"},"status":"public","_id":"1603","volume":9206,"related_material":{"record":[{"relation":"research_paper","status":"public","id":"5549"}]},"ec_funded":1,"publication_identifier":{"eisbn":["978-3-319-21690-4"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"url":"http://arxiv.org/abs/1502.02834","open_access":"1"}],"month":"07","intvolume":" 9206","abstract":[{"text":"For deterministic systems, a counterexample to a property can simply be an error trace, whereas counterexamples in probabilistic systems are necessarily more complex. For instance, a set of erroneous traces with a sufficient cumulative probability mass can be used. Since these are too large objects to understand and manipulate, compact representations such as subchains have been considered. In the case of probabilistic systems with non-determinism, the situation is even more complex. While a subchain for a given strategy (or scheduler, resolving non-determinism) is a straightforward choice, we take a different approach. Instead, we focus on the strategy itself, and extract the most important decisions it makes, and present its succinct representation.\r\nThe key tools we employ to achieve this are (1) introducing a concept of importance of a state w.r.t. the strategy, and (2) learning using decision trees. There are three main consequent advantages of our approach. Firstly, it exploits the quantitative information on states, stressing the more important decisions. Secondly, it leads to a greater variability and degree of freedom in representing the strategies. Thirdly, the representation uses a self-explanatory data structure. In summary, our approach produces more succinct and more explainable strategies, as opposed to e.g. binary decision diagrams. Finally, our experimental results show that we can extract several rules describing the strategy even for very large systems that do not fit in memory, and based on the rules explain the erroneous behaviour.","lang":"eng"}],"oa_version":"Preprint"},{"month":"08","abstract":[{"lang":"eng","text":"This repository contains the experimental part of the CAV 2015 publication Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.\r\nWe extended the probabilistic model checker PRISM to represent strategies of Markov Decision Processes as Decision Trees.\r\nThe archive contains a java executable version of the extended tool (prism_dectree.jar) together with a few examples of the PRISM benchmark library.\r\nTo execute the program, please have a look at the README.txt, which provides instructions and further information on the archive.\r\nThe archive contains scripts that (if run often enough) reproduces the data presented in the publication."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"popular_science","id":"1603","status":"public"}]},"contributor":[{"last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","ec_funded":1,"datarep_id":"28","file":[{"checksum":"b8bcb43c0893023cda66c1b69c16ac62","file_id":"5597","content_type":"application/zip","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T13:02:31Z","file_name":"IST-2015-28-v1+2_Fellner_DataRep.zip","date_updated":"2020-07-14T12:47:00Z","file_size":49557109,"creator":"system"}],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","keyword":["Markov Decision Process","Decision Tree","Probabilistic Verification","Counterexample Explanation"],"_id":"5549","file_date_updated":"2020-07-14T12:47:00Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2024-02-21T13:52:07Z","ddc":["004"],"publisher":"Institute of Science and Technology Austria","oa":1,"doi":"10.15479/AT:ISTA:28","date_published":"2015-08-13T00:00:00Z","date_created":"2018-12-12T12:31:29Z","has_accepted_license":"1","year":"2015","day":"13","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"full_name":"Fellner, Andreas","last_name":"Fellner","first_name":"Andreas","id":"42BABFB4-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5564","article_processing_charge":"No","title":"Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes","citation":{"chicago":"Fellner, Andreas. “Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015. https://doi.org/10.15479/AT:ISTA:28.","ista":"Fellner A. 2015. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:28.","mla":"Fellner, Andreas. Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria, 2015, doi:10.15479/AT:ISTA:28.","apa":"Fellner, A. (2015). Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:28","ama":"Fellner A. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. 2015. doi:10.15479/AT:ISTA:28","ieee":"A. Fellner, “Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015.","short":"A. Fellner, (2015)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"doi":"10.4230/LIPIcs.SOCG.2015.507","date_published":"2015-01-01T00:00:00Z","date_created":"2018-12-11T11:52:27Z","page":"507 - 521","day":"01","has_accepted_license":"1","year":"2015","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"acknowledgement":"PP, ZP and MT were partially supported by the Charles University Grant GAUK 421511. ZP was\r\npartially supported by the Charles University Grant SVV-2014-260103. ZP and MT were partially\r\nsupported by the ERC Advanced Grant No. 267165 and by the project CE-ITI (GACR P202/12/G061)\r\nof the Czech Science Foundation. UW was partially supported by the Swiss National Science Foundation\r\n(grants SNSF-200020-138230 and SNSF-PP00P2-138948). Part of this work was done when XG was affiliated with INRIA Nancy Grand-Est and when MT was affiliated with Institutionen för matematik, Kungliga Tekniska Högskolan, then IST Austria.","title":"Bounding Helly numbers via Betti numbers","publist_id":"5665","author":[{"last_name":"Goaoc","full_name":"Goaoc, Xavier","first_name":"Xavier"},{"first_name":"Pavel","last_name":"Paták","full_name":"Paták, Pavel"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","last_name":"Patakova","first_name":"Zuzana"},{"orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin","last_name":"Tancer","first_name":"Martin"},{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Bounding Helly numbers via Betti numbers. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:507-521. doi:10.4230/LIPIcs.SOCG.2015.507","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2015). Bounding Helly numbers via Betti numbers (Vol. 34, pp. 507–521). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.507","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Bounding Helly numbers via Betti numbers,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 507–521.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–521.","mla":"Goaoc, Xavier, et al. Bounding Helly Numbers via Betti Numbers. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–21, doi:10.4230/LIPIcs.SOCG.2015.507.","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2015. Bounding Helly numbers via Betti numbers. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 507–521.","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Bounding Helly Numbers via Betti Numbers,” 34:507–21. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.507."},"volume":34,"related_material":{"record":[{"id":"424","status":"public","relation":"later_version"}]},"file":[{"date_created":"2018-12-12T10:10:09Z","file_name":"IST-2016-501-v1+1_46.pdf","creator":"system","date_updated":"2020-07-14T12:45:00Z","file_size":633712,"checksum":"e6881df44d87fe0c2529c9f7b2724614","file_id":"4794","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"01","intvolume":" 34","scopus_import":"1","alternative_title":["LIPIcs"],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b,d) such that the following holds. If F is a finite family of subsets of R^d such that the ith reduced Betti number (with Z_2 coefficients in singular homology) of the intersection of any proper subfamily G of F is at most b for every non-negative integer i less or equal to (d-1)/2, then F has Helly number at most h(b,d). These topological conditions are sharp: not controlling any of these first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map from C_*(K) to C_*(R^d). Both techniques are of independent interest."}],"department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:45:00Z","ddc":["510"],"date_updated":"2024-02-28T12:59:37Z","status":"public","pubrep_id":"501","type":"conference","conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2015-06-22","location":"Eindhoven, Netherlands","end_date":"2015-06-25"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1512"},{"acknowledgement":"While working on this paper the authors were supported by the Leverhulme Trust and ERC grant 306457.","publisher":"Walter de Gruyter","quality_controlled":"1","oa":1,"day":"20","publication":"Journal fur die Reine und Angewandte Mathematik","year":"2015","doi":"10.1515/crelle-2014-0122","date_published":"2015-02-20T00:00:00Z","date_created":"2018-12-11T11:45:32Z","page":"203 - 234","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Browning, Timothy D, and Sean Prendiville. “Improvements in Birch’s Theorem on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter, n.d. https://doi.org/10.1515/crelle-2014-0122.","ista":"Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many variables. Journal fur die Reine und Angewandte Mathematik. 2017(731), 203–234.","mla":"Browning, Timothy D., and Sean Prendiville. “Improvements in Birch’s Theorem on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik, vol. 2017, no. 731, Walter de Gruyter, pp. 203–34, doi:10.1515/crelle-2014-0122.","ieee":"T. D. Browning and S. Prendiville, “Improvements in Birch’s theorem on forms in many variables,” Journal fur die Reine und Angewandte Mathematik, vol. 2017, no. 731. Walter de Gruyter, pp. 203–234.","short":"T.D. Browning, S. Prendiville, Journal Fur Die Reine Und Angewandte Mathematik 2017 (n.d.) 203–234.","apa":"Browning, T. D., & Prendiville, S. (n.d.). Improvements in Birch’s theorem on forms in many variables. Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle-2014-0122","ama":"Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many variables. Journal fur die Reine und Angewandte Mathematik. 2017(731):203-234. doi:10.1515/crelle-2014-0122"},"title":"Improvements in Birch's theorem on forms in many variables","publist_id":"7631","author":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D"},{"first_name":"Sean","last_name":"Prendiville","full_name":"Prendiville, Sean"}],"article_processing_charge":"No","external_id":{"arxiv":["1402.4489"]},"oa_version":"Preprint","abstract":[{"text":"We show that a non-singular integral form of degree d is soluble non-trivially over the integers if and only if it is soluble non-trivially over the reals and the p-adic numbers, provided that the form has at least (d-\\sqrt{d}/2)2^d variables. This improves on a longstanding result of Birch.","lang":"eng"}],"month":"02","intvolume":" 2017","main_file_link":[{"url":"https://arxiv.org/abs/1402.4489","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0075-4102"]},"publication_status":"submitted","issue":"731","volume":2017,"related_material":{"record":[{"relation":"later_version","status":"public","id":"256"}]},"_id":"271","status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2024-03-05T12:09:22Z"},{"scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2013/796.pdf"}],"month":"08","intvolume":" 9216","abstract":[{"lang":"eng","text":"Proofs of work (PoW) have been suggested by Dwork and Naor (Crypto’92) as protection to a shared resource. The basic idea is to ask the service requestor to dedicate some non-trivial amount of computational work to every request. The original applications included prevention of spam and protection against denial of service attacks. More recently, PoWs have been used to prevent double spending in the Bitcoin digital currency system. In this work, we put forward an alternative concept for PoWs - so-called proofs of space (PoS), where a service requestor must dedicate a significant amount of disk space as opposed to computation. We construct secure PoS schemes in the random oracle model (with one additional mild assumption required for the proof to go through), using graphs with high “pebbling complexity” and Merkle hash-trees. We discuss some applications, including follow-up work where a decentralized digital currency scheme called Spacecoin is constructed that uses PoS (instead of wasteful PoW like in Bitcoin) to prevent double spending. The main technical contribution of this work is the construction of (directed, loop-free) graphs on N vertices with in-degree O(log logN) such that even if one places Θ(N) pebbles on the nodes of the graph, there’s a constant fraction of nodes that needs Θ(N) steps to be pebbled (where in every step one can put a pebble on a node if all its parents have a pebble)."}],"oa_version":"Preprint","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2274"}]},"volume":9216,"ec_funded":1,"publication_identifier":{"issn":["0302-9743"],"isbn":["9783662479995"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"start_date":"2015-08-16","end_date":"2015-08-20","location":"Santa Barbara, CA, United States","name":"CRYPTO: International Cryptology Conference"},"status":"public","pubrep_id":"671","_id":"1675","department":[{"_id":"VlKo"},{"_id":"KrPi"}],"date_updated":"2024-03-20T08:31:49Z","quality_controlled":"1","publisher":"Springer","oa":1,"page":"585 - 605","doi":"10.1007/978-3-662-48000-7_29","date_published":"2015-08-01T00:00:00Z","date_created":"2018-12-11T11:53:24Z","year":"2015","day":"01","publication":"35th Annual Cryptology Conference","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publist_id":"5474","author":[{"full_name":"Dziembowski, Stefan","last_name":"Dziembowski","first_name":"Stefan"},{"first_name":"Sebastian","last_name":"Faust","full_name":"Faust, Sebastian"},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"}],"article_processing_charge":"No","title":"Proofs of space","citation":{"ieee":"S. Dziembowski, S. Faust, V. Kolmogorov, and K. Z. Pietrzak, “Proofs of space,” in 35th Annual Cryptology Conference, Santa Barbara, CA, United States, 2015, vol. 9216, pp. 585–605.","short":"S. Dziembowski, S. Faust, V. Kolmogorov, K.Z. Pietrzak, in:, 35th Annual Cryptology Conference, Springer, 2015, pp. 585–605.","ama":"Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. Proofs of space. In: 35th Annual Cryptology Conference. Vol 9216. Springer; 2015:585-605. doi:10.1007/978-3-662-48000-7_29","apa":"Dziembowski, S., Faust, S., Kolmogorov, V., & Pietrzak, K. Z. (2015). Proofs of space. In 35th Annual Cryptology Conference (Vol. 9216, pp. 585–605). Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-48000-7_29","mla":"Dziembowski, Stefan, et al. “Proofs of Space.” 35th Annual Cryptology Conference, vol. 9216, Springer, 2015, pp. 585–605, doi:10.1007/978-3-662-48000-7_29.","ista":"Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. 2015. Proofs of space. 35th Annual Cryptology Conference. CRYPTO: International Cryptology Conference, LNCS, vol. 9216, 585–605.","chicago":"Dziembowski, Stefan, Sebastian Faust, Vladimir Kolmogorov, and Krzysztof Z Pietrzak. “Proofs of Space.” In 35th Annual Cryptology Conference, 9216:585–605. Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_29."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"Cancer/Testis antigen PASD1 silences the circadian clock","author":[{"first_name":"Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael","full_name":"Michael, Alicia Kathleen"},{"last_name":"Harvey","full_name":"Harvey, Stacy L.","first_name":"Stacy L."},{"full_name":"Sammons, Patrick J.","last_name":"Sammons","first_name":"Patrick J."},{"full_name":"Anderson, Amanda P.","last_name":"Anderson","first_name":"Amanda P."},{"first_name":"Hema M.","last_name":"Kopalle","full_name":"Kopalle, Hema M."},{"first_name":"Alison H.","full_name":"Banham, Alison H.","last_name":"Banham"},{"last_name":"Partch","full_name":"Partch, Carrie L.","first_name":"Carrie L."}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Michael, Alicia K., et al. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” Molecular Cell, vol. 58, no. 5, Elsevier, 2015, pp. 743–54, doi:10.1016/j.molcel.2015.03.031.","short":"A.K. Michael, S.L. Harvey, P.J. Sammons, A.P. Anderson, H.M. Kopalle, A.H. Banham, C.L. Partch, Molecular Cell 58 (2015) 743–754.","ieee":"A. K. Michael et al., “Cancer/Testis antigen PASD1 silences the circadian clock,” Molecular Cell, vol. 58, no. 5. Elsevier, pp. 743–754, 2015.","ama":"Michael AK, Harvey SL, Sammons PJ, et al. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 2015;58(5):743-754. doi:10.1016/j.molcel.2015.03.031","apa":"Michael, A. K., Harvey, S. L., Sammons, P. J., Anderson, A. P., Kopalle, H. M., Banham, A. H., & Partch, C. L. (2015). Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2015.03.031","chicago":"Michael, Alicia K., Stacy L. Harvey, Patrick J. Sammons, Amanda P. Anderson, Hema M. Kopalle, Alison H. Banham, and Carrie L. Partch. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” Molecular Cell. Elsevier, 2015. https://doi.org/10.1016/j.molcel.2015.03.031.","ista":"Michael AK, Harvey SL, Sammons PJ, Anderson AP, Kopalle HM, Banham AH, Partch CL. 2015. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 58(5), 743–754."},"quality_controlled":"1","publisher":"Elsevier","oa":1,"date_published":"2015-06-04T00:00:00Z","doi":"10.1016/j.molcel.2015.03.031","date_created":"2024-03-21T07:58:08Z","page":"743-754","day":"04","publication":"Molecular Cell","year":"2015","status":"public","keyword":["Cell Biology","Molecular Biology"],"type":"journal_article","article_type":"original","_id":"15160","extern":"1","date_updated":"2024-03-25T11:52:26Z","month":"06","intvolume":" 58","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.molcel.2015.03.031","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"The circadian clock orchestrates global changes in transcriptional regulation on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven by other bHLH-PAS transcription factors have a homologous repressor that modulates activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1. We show here that the cancer/testis antigen PASD1 fulfills this role to suppress circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1 is restricted to germline tissues in healthy individuals but can be induced in cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human cancer cells significantly increases the amplitude of transcriptional oscillations to generate more robust circadian rhythms. Our results describe a function for a germline-specific protein in regulation of the circadian clock and provide a molecular link from oncogenic transformation to suppression of circadian rhythms.","lang":"eng"}],"issue":"5","volume":58,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1097-2765"]},"publication_status":"published"},{"quality_controlled":"1","publisher":"Elsevier","doi":"10.1016/j.tibs.2015.07.006","date_published":"2015-09-01T00:00:00Z","date_created":"2024-03-21T07:57:44Z","page":"489-490","day":"01","publication":"Trends in Biochemical Sciences","year":"2015","title":"Cytosolic BMAL1 moonlights as a translation factor","author":[{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia Kathleen","last_name":"Michael","full_name":"Michael, Alicia Kathleen"},{"first_name":"Hande","last_name":"Asimgil","full_name":"Asimgil, Hande"},{"first_name":"Carrie L.","full_name":"Partch, Carrie L.","last_name":"Partch"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Michael, Alicia K., et al. “Cytosolic BMAL1 Moonlights as a Translation Factor.” Trends in Biochemical Sciences, vol. 40, no. 9, Elsevier, 2015, pp. 489–90, doi:10.1016/j.tibs.2015.07.006.","ieee":"A. K. Michael, H. Asimgil, and C. L. Partch, “Cytosolic BMAL1 moonlights as a translation factor,” Trends in Biochemical Sciences, vol. 40, no. 9. Elsevier, pp. 489–490, 2015.","short":"A.K. Michael, H. Asimgil, C.L. Partch, Trends in Biochemical Sciences 40 (2015) 489–490.","ama":"Michael AK, Asimgil H, Partch CL. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 2015;40(9):489-490. doi:10.1016/j.tibs.2015.07.006","apa":"Michael, A. K., Asimgil, H., & Partch, C. L. (2015). Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. Elsevier. https://doi.org/10.1016/j.tibs.2015.07.006","chicago":"Michael, Alicia K., Hande Asimgil, and Carrie L. Partch. “Cytosolic BMAL1 Moonlights as a Translation Factor.” Trends in Biochemical Sciences. Elsevier, 2015. https://doi.org/10.1016/j.tibs.2015.07.006.","ista":"Michael AK, Asimgil H, Partch CL. 2015. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 40(9), 489–490."},"month":"09","intvolume":" 40","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"It is widely recognized that BMAL1 is an essential subunit of the primary transcription factor that drives rhythmic circadian transcription in the nucleus. In a surprising turn, Lipton et al. now show that BMAL1 rhythmically interacts with translational machinery in the cytosol to stimulate protein synthesis in response to mTOR signaling."}],"volume":40,"issue":"9","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0968-0004"]},"publication_status":"published","status":"public","keyword":["Molecular Biology","Biochemistry"],"article_type":"original","type":"journal_article","_id":"15159","extern":"1","date_updated":"2024-03-25T11:53:58Z"},{"_id":"1619","pubrep_id":"468","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2024-03-27T23:30:28Z","department":[{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:45:07Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution."}],"intvolume":" 13","month":"11","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_size":1387760,"date_updated":"2020-07-14T12:45:07Z","creator":"system","file_name":"IST-2016-468-v1+1_journal.pbio.1002299.pdf","date_created":"2018-12-12T10:09:00Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4723","checksum":"0e82e3279f50b15c6c170c042627802b"}],"publication_status":"published","ec_funded":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9711"},{"status":"public","id":"9765","relation":"research_data"},{"relation":"dissertation_contains","id":"6263","status":"public"}]},"volume":13,"issue":"11","article_number":"e1002299","project":[{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"},{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions"},{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303507","name":"Optimality principles in responses to antibiotics"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology, vol. 13, no. 11, e1002299, Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.","ieee":"G. Chevereau et al., “Quantifying the determinants of evolutionary dynamics leading to drug resistance,” PLoS Biology, vol. 13, no. 11. Public Library of Science, 2015.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak, M.T. Bollenbach, PLoS Biology 13 (2015).","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak, E., & Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 2015;13(11). doi:10.1371/journal.pbio.1002299","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 13(11), e1002299."},"title":"Quantifying the determinants of evolutionary dynamics leading to drug resistance","author":[{"id":"424D78A0-F248-11E8-B48F-1D18A9856A87","first_name":"Guillaume","last_name":"Chevereau","full_name":"Chevereau, Guillaume"},{"first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Dravecka, Marta","orcid":"0000-0002-2519-8004","last_name":"Dravecka"},{"full_name":"Batur, Tugce","last_name":"Batur","first_name":"Tugce"},{"first_name":"Aysegul","full_name":"Guvenek, Aysegul","last_name":"Guvenek"},{"first_name":"Dilay","last_name":"Ayhan","full_name":"Ayhan, Dilay"},{"last_name":"Toprak","full_name":"Toprak, Erdal","first_name":"Erdal"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach"}],"publist_id":"5547","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","publication":"PLoS Biology","day":"18","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:53:04Z","doi":"10.1371/journal.pbio.1002299","date_published":"2015-11-18T00:00:00Z"},{"citation":{"ista":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 111(50), 17869–17874.","chicago":"Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410159111.","short":"A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National Academy of Sciences 111 (2014) 17869–17874.","ieee":"A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of nonspecific interactions in amyloid nucleation,” Proceedings of the National Academy of Sciences, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874, 2014.","ama":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 2014;111(50):17869-17874. doi:10.1073/pnas.1410159111","apa":"Šarić, A., Chebaro, Y. C., Knowles, T. P. J., & Frenkel, D. (2014). Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1410159111","mla":"Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings of the National Academy of Sciences, vol. 111, no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:10.1073/pnas.1410159111."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","external_id":{"arxiv":["1412.0897"],"pmid":["25453085"]},"author":[{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"},{"first_name":"Yassmine C.","last_name":"Chebaro","full_name":"Chebaro, Yassmine C."},{"first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J.","last_name":"Knowles"},{"last_name":"Frenkel","full_name":"Frenkel, Daan","first_name":"Daan"}],"title":"Crucial role of nonspecific interactions in amyloid nucleation","acknowledgement":"We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs, for helpful discussions. A.Š. acknowledges support from the Human Frontier Science Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology and Biological Sciences Research Council. D.F. acknowledges European Research Council Advanced Grant 227758.","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","year":"2014","publication":"Proceedings of the National Academy of Sciences","day":"01","page":"17869-17874","date_created":"2021-11-29T13:09:53Z","doi":"10.1073/pnas.1410159111","date_published":"2014-12-01T00:00:00Z","_id":"10382","article_type":"original","type":"journal_article","keyword":["multidisciplinary"],"status":"public","date_updated":"2021-11-29T13:29:05Z","extern":"1","abstract":[{"text":"Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://www.pnas.org/content/111/50/17869"}],"scopus_import":"1","intvolume":" 111","month":"12","publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"volume":111,"issue":"50"},{"oa":1,"quality_controlled":"1","publisher":"American Physical Society","publication":"Physical Review E","day":"06","year":"2014","date_created":"2021-11-29T13:10:33Z","date_published":"2014-05-06T00:00:00Z","doi":"10.1103/physreve.89.052303","article_number":"052303","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.052303.","ista":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303.","mla":"Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical Review E, vol. 89, no. 5, 052303, American Physical Society, 2014, doi:10.1103/physreve.89.052303.","ama":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 2014;89(5). doi:10.1103/physreve.89.052303","apa":"Mallory, S. A., Šarić, A., Valeriani, C., & Cacciuto, A. (2014). Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.89.052303","ieee":"S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical properties of a self-propelled colloidal fluid,” Physical Review E, vol. 89, no. 5. American Physical Society, 2014.","short":"S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014)."},"title":"Anomalous thermomechanical properties of a self-propelled colloidal fluid","article_processing_charge":"No","external_id":{"pmid":["25353796"],"arxiv":["1310.0826"]},"author":[{"full_name":"Mallory, S. A.","last_name":"Mallory","first_name":"S. A."},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Valeriani, C.","last_name":"Valeriani","first_name":"C."},{"first_name":"A.","last_name":"Cacciuto","full_name":"Cacciuto, A."}],"pmid":1,"oa_version":"Preprint","abstract":[{"text":"We use numerical simulations to compute the equation of state of a suspension of spherical self-propelled nanoparticles in two and three dimensions. We study in detail the effect of excluded volume interactions and confinement as a function of the system's temperature, concentration, and strength of the propulsion. We find a striking nonmonotonic dependence of the pressure on the temperature and provide simple scaling arguments to predict and explain the occurrence of such anomalous behavior. We explicitly show how our results have important implications for the effective forces on passive components suspended in a bath of active particles.","lang":"eng"}],"intvolume":" 89","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1310.0826"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1550-2376"],"issn":["1539-3755"]},"issue":"5","volume":89,"_id":"10383","status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2021-11-29T13:29:01Z"},{"_id":"1058","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"ista":"Jensen N, Danzl JG, Willig K, Lavoie Cardinal F, Brakemann T, Hell S, Jakobs S. 2014. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 15(4), 756–762.","chicago":"Jensen, Nickels, Johann G Danzl, Katrin Willig, Flavie Lavoie Cardinal, Tanja Brakemann, Stefan Hell, and Stefan Jakobs. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem. Wiley-Blackwell, 2014. https://doi.org/10.1002/cphc.201301034.","short":"N. Jensen, J.G. Danzl, K. Willig, F. Lavoie Cardinal, T. Brakemann, S. Hell, S. Jakobs, ChemPhysChem 15 (2014) 756–762.","ieee":"N. Jensen et al., “Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang,” ChemPhysChem, vol. 15, no. 4. Wiley-Blackwell, pp. 756–762, 2014.","apa":"Jensen, N., Danzl, J. G., Willig, K., Lavoie Cardinal, F., Brakemann, T., Hell, S., & Jakobs, S. (2014). Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. Wiley-Blackwell. https://doi.org/10.1002/cphc.201301034","ama":"Jensen N, Danzl JG, Willig K, et al. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 2014;15(4):756-762. doi:10.1002/cphc.201301034","mla":"Jensen, Nickels, et al. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem, vol. 15, no. 4, Wiley-Blackwell, 2014, pp. 756–62, doi:10.1002/cphc.201301034."},"date_updated":"2021-01-12T06:47:58Z","title":"Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang","article_processing_charge":"No","author":[{"full_name":"Jensen, Nickels","last_name":"Jensen","first_name":"Nickels"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl"},{"first_name":"Katrin","full_name":"Willig, Katrin","last_name":"Willig"},{"last_name":"Lavoie Cardinal","full_name":"Lavoie Cardinal, Flavie","first_name":"Flavie"},{"full_name":"Brakemann, Tanja","last_name":"Brakemann","first_name":"Tanja"},{"first_name":"Stefan","full_name":"Hell, Stefan","last_name":"Hell"},{"last_name":"Jakobs","full_name":"Jakobs, Stefan","first_name":"Stefan"}],"publist_id":"6332","oa_version":"None","abstract":[{"lang":"eng","text":"Diffraction-unlimited far-field super-resolution fluorescence (nanoscopy) methods typically rely on transiently transferring fluorophores between two states, whereby this transfer is usually laid out as a switch. However, depending on whether this is induced in a spatially controlled manner using a pattern of light (coordinate-targeted) or stochastically on a single-molecule basis, specific requirements on the fluorophores are imposed. Therefore, the fluorophores are usually utilized just for one class of methods only. In this study we demonstrate that the reversibly switchable fluorescent protein Dreiklang enables live-cell recordings in both spatially controlled and stochastic modes. We show that the Dreiklang chromophore entails three different light-induced switching mechanisms, namely a reversible photochemical one, off-switching by stimulated emission, and a reversible transfer to a long-lived dark state from the S1 state, all of which can be utilized to overcome the diffraction barrier. We also find that for the single-molecule- based stochastic GSDIM approach (ground-state depletion followed by individual molecule return), Dreiklang provides a larger number of on-off localization events as compared to its progenitor Citrine. Altogether, Dreiklang is a versatile probe for essentially all popular forms of live-cell fluorescence nanoscopy."}],"intvolume":" 15","month":"03","publisher":"Wiley-Blackwell","language":[{"iso":"eng"}],"publication":"ChemPhysChem","day":"17","year":"2014","publication_status":"published","date_created":"2018-12-11T11:49:55Z","date_published":"2014-03-17T00:00:00Z","issue":"4","doi":"10.1002/cphc.201301034","volume":15,"page":"756 - 762"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Hashimoto, Masakazu, et al. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” Congenital Anomalies, vol. 54, no. 1, Wiley, 2014, pp. 1–7, doi:10.1111/cga.12039.","short":"M. Hashimoto, H. Morita, N. Ueno, Congenital Anomalies 54 (2014) 1–7.","ieee":"M. Hashimoto, H. Morita, and N. Ueno, “Molecular and cellular mechanisms of development underlying congenital diseases,” Congenital Anomalies, vol. 54, no. 1. Wiley, pp. 1–7, 2014.","apa":"Hashimoto, M., Morita, H., & Ueno, N. (2014). Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. Wiley. https://doi.org/10.1111/cga.12039","ama":"Hashimoto M, Morita H, Ueno N. Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. 2014;54(1):1-7. doi:10.1111/cga.12039","chicago":"Hashimoto, Masakazu, Hitoshi Morita, and Naoto Ueno. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” Congenital Anomalies. Wiley, 2014. https://doi.org/10.1111/cga.12039.","ista":"Hashimoto M, Morita H, Ueno N. 2014. Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. 54(1), 1–7."},"title":"Molecular and cellular mechanisms of development underlying congenital diseases","external_id":{"pmid":["24666178"]},"article_processing_charge":"No","author":[{"first_name":"Masakazu","last_name":"Hashimoto","full_name":"Hashimoto, Masakazu"},{"last_name":"Morita","full_name":"Morita, Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","first_name":"Hitoshi"},{"first_name":"Naoto","last_name":"Ueno","full_name":"Ueno, Naoto"}],"acknowledgement":"The authors thank all the members of the Division of Morphogenesis, National Institute for Basic Biology, for their contributions to the research, their encouragement, and helpful discussions, particularly Dr M. Suzuki for his critical reading of the manuscript. We also thank the Model Animal Research and Spectrography and Bioimaging Facilities, NIBB Core Research Facilities, for technical support. M.H. was supported by a research fellowship from the Japan Society for the Promotion of Science (JSPS). Our work introduced in this review was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan, to N.U.","oa":1,"quality_controlled":"1","publisher":"Wiley","publication":"Congenital Anomalies","day":"01","year":"2014","date_created":"2022-03-04T08:17:25Z","date_published":"2014-02-01T00:00:00Z","doi":"10.1111/cga.12039","page":"1-7","_id":"10815","keyword":["Developmental Biology","Embryology","General Medicine","Pediatrics","Perinatology","and Child Health"],"status":"public","type":"journal_article","article_type":"original","date_updated":"2022-03-04T08:26:05Z","department":[{"_id":"CaHe"}],"oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"In the last several decades, developmental biology has clarified the molecular mechanisms of embryogenesis and organogenesis. In particular, it has demonstrated that the “tool-kit genes” essential for regulating developmental processes are not only highly conserved among species, but are also used as systems at various times and places in an organism to control distinct developmental events. Therefore, mutations in many of these tool-kit genes may cause congenital diseases involving morphological abnormalities. This link between genes and abnormal morphological phenotypes underscores the importance of understanding how cells behave and contribute to morphogenesis as a result of gene function. Recent improvements in live imaging and in quantitative analyses of cellular dynamics will advance our understanding of the cellular pathogenesis of congenital diseases associated with aberrant morphologies. In these studies, it is critical to select an appropriate model organism for the particular phenomenon of interest."}],"intvolume":" 54","month":"02","main_file_link":[{"url":"https://doi.org/10.1111/cga.12039","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0914-3505"]},"volume":54,"issue":"1"},{"edition":"1","scopus_import":"1","quality_controlled":"1","publisher":"Springer Nature","month":"04","place":"Vienna","abstract":[{"text":"Auxin is an important signaling compound in plants and vital for plant development and growth. The present book, Auxin and its Role in Plant Development, provides the reader with detailed and comprehensive insight into the functioning of the molecule on the whole and specifically in plant development. In the first part, the functioning, metabolism and signaling pathways of auxin in plants are explained, the second part depicts the specific role of auxin in plant development and the third part describes the interaction and functioning of the signaling compound upon stimuli of the environment. Each chapter is written by international experts in the respective field and designed for scientists and researchers in plant biology, plant development and cell biology to summarize the recent progress in understanding the role of auxin and suggest future perspectives for auxin research.","lang":"eng"}],"oa_version":"None","page":"444","date_created":"2022-03-03T11:52:44Z","doi":"10.1007/978-3-7091-1526-8","date_published":"2014-04-01T00:00:00Z","year":"2014","publication_status":"published","publication_identifier":{"isbn":["9783709115251"],"eisbn":["9783709115268"]},"language":[{"iso":"eng"}],"day":"01","type":"book_editor","status":"public","_id":"10811","article_processing_charge":"No","title":"Auxin and Its Role in Plant Development","department":[{"_id":"EvBe"}],"editor":[{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"}],"citation":{"ama":"Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development. 1st ed. Vienna: Springer Nature; 2014. doi:10.1007/978-3-7091-1526-8","apa":"Zažímalová, E., Petrášek, J., & Benková, E. (Eds.). (2014). Auxin and Its Role in Plant Development (1st ed.). Vienna: Springer Nature. https://doi.org/10.1007/978-3-7091-1526-8","short":"E. Zažímalová, J. Petrášek, E. Benková, eds., Auxin and Its Role in Plant Development, 1st ed., Springer Nature, Vienna, 2014.","ieee":"E. Zažímalová, J. Petrášek, and E. Benková, Eds., Auxin and Its Role in Plant Development, 1st ed. Vienna: Springer Nature, 2014.","mla":"Zažímalová, Eva, et al., editors. Auxin and Its Role in Plant Development. 1st ed., Springer Nature, 2014, doi:10.1007/978-3-7091-1526-8.","ista":"Zažímalová E, Petrášek J, Benková E eds. 2014. Auxin and Its Role in Plant Development 1st ed., Vienna: Springer Nature, 444p.","chicago":"Zažímalová, Eva, Jan Petrášek, and Eva Benková, eds. Auxin and Its Role in Plant Development. 1st ed. Vienna: Springer Nature, 2014. https://doi.org/10.1007/978-3-7091-1526-8."},"date_updated":"2022-03-04T07:38:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_created":"2022-03-18T13:01:22Z","date_published":"2014-01-30T00:00:00Z","doi":"10.1007/978-3-642-54013-4_15","page":"262-281","publication":"Verification, Model Checking, and Abstract Interpretation","day":"30","year":"2014","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"This work was supported by the Austrian Science Fund through grant P23499-N23\r\nand through the RiSE network (S11403, S11405, S11406, S11407-N23); ERC Starting Grant (279307: Graph Games); Vienna Science and Technology Fund (WWTF)\r\ngrants PROSEED, ICT12-059, and VRG11-005.","title":"Parameterized model checking of token-passing systems","article_processing_charge":"No","external_id":{"arxiv":["1311.4425"]},"author":[{"last_name":"Aminof","full_name":"Aminof, Benjamin","first_name":"Benjamin","id":"4A55BD00-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jacobs","full_name":"Jacobs, Swen","first_name":"Swen"},{"first_name":"Ayrat","last_name":"Khalimov","full_name":"Khalimov, Ayrat"},{"full_name":"Rubin, Sasha","last_name":"Rubin","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Aminof B, Jacobs S, Khalimov A, Rubin S. Parameterized model checking of token-passing systems. In: Verification, Model Checking, and Abstract Interpretation. Vol 8318. Springer Nature; 2014:262-281. doi:10.1007/978-3-642-54013-4_15","apa":"Aminof, B., Jacobs, S., Khalimov, A., & Rubin, S. (2014). Parameterized model checking of token-passing systems. In Verification, Model Checking, and Abstract Interpretation (Vol. 8318, pp. 262–281). San Diego, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_15","short":"B. Aminof, S. Jacobs, A. Khalimov, S. Rubin, in:, Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 262–281.","ieee":"B. Aminof, S. Jacobs, A. Khalimov, and S. Rubin, “Parameterized model checking of token-passing systems,” in Verification, Model Checking, and Abstract Interpretation, San Diego, CA, United States, 2014, vol. 8318, pp. 262–281.","mla":"Aminof, Benjamin, et al. “Parameterized Model Checking of Token-Passing Systems.” Verification, Model Checking, and Abstract Interpretation, vol. 8318, Springer Nature, 2014, pp. 262–81, doi:10.1007/978-3-642-54013-4_15.","ista":"Aminof B, Jacobs S, Khalimov A, Rubin S. 2014. Parameterized model checking of token-passing systems. Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 262–281.","chicago":"Aminof, Benjamin, Swen Jacobs, Ayrat Khalimov, and Sasha Rubin. “Parameterized Model Checking of Token-Passing Systems.” In Verification, Model Checking, and Abstract Interpretation, 8318:262–81. Springer Nature, 2014. https://doi.org/10.1007/978-3-642-54013-4_15."},"project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"ec_funded":1,"volume":8318,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eisbn":["9783642540134"],"isbn":["9783642540127"],"eissn":["1611-3349"],"issn":["0302-9743"]},"intvolume":" 8318","month":"01","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1311.4425"}],"scopus_import":"1","alternative_title":["LNCS"],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We revisit the parameterized model checking problem for token-passing systems and specifications in indexed CTL ∗ \\X. Emerson and Namjoshi (1995, 2003) have shown that parameterized model checking of indexed CTL ∗ \\X in uni-directional token rings can be reduced to checking rings up to some cutoff size. Clarke et al. (2004) have shown a similar result for general topologies and indexed LTL \\X, provided processes cannot choose the directions for sending or receiving the token.\r\nWe unify and substantially extend these results by systematically exploring fragments of indexed CTL ∗ \\X with respect to general topologies. For each fragment we establish whether a cutoff exists, and for some concrete topologies, such as rings, cliques and stars, we infer small cutoffs. Finally, we show that the problem becomes undecidable, and thus no cutoffs exist, if processes are allowed to choose the directions in which they send or from which they receive the token."}],"department":[{"_id":"KrCh"}],"date_updated":"2022-05-17T08:36:01Z","status":"public","conference":{"name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation","start_date":"2014-01-19","location":"San Diego, CA, United States","end_date":"2014-01-21"},"type":"conference","_id":"10884"},{"citation":{"mla":"Kasten, Jens, et al. “Toward the Extraction of Saddle Periodic Orbits.” Topological Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer et al., vol. 1, Springer, 2014, pp. 55–69, doi:10.1007/978-3-319-04099-8_4.","ieee":"J. Kasten, J. Reininghaus, W. Reich, and G. Scheuermann, “Toward the extraction of saddle periodic orbits,” in Topological Methods in Data Analysis and Visualization III , vol. 1, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Cham: Springer, 2014, pp. 55–69.","short":"J. Kasten, J. Reininghaus, W. Reich, G. Scheuermann, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III , Springer, Cham, 2014, pp. 55–69.","ama":"Kasten J, Reininghaus J, Reich W, Scheuermann G. Toward the extraction of saddle periodic orbits. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III . Vol 1. Mathematics and Visualization. Cham: Springer; 2014:55-69. doi:10.1007/978-3-319-04099-8_4","apa":"Kasten, J., Reininghaus, J., Reich, W., & Scheuermann, G. (2014). Toward the extraction of saddle periodic orbits. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III (Vol. 1, pp. 55–69). Cham: Springer. https://doi.org/10.1007/978-3-319-04099-8_4","chicago":"Kasten, Jens, Jan Reininghaus, Wieland Reich, and Gerik Scheuermann. “Toward the Extraction of Saddle Periodic Orbits.” In Topological Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 1:55–69. Mathematics and Visualization. Cham: Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_4.","ista":"Kasten J, Reininghaus J, Reich W, Scheuermann G. 2014.Toward the extraction of saddle periodic orbits. In: Topological Methods in Data Analysis and Visualization III . vol. 1, 55–69."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jens","last_name":"Kasten","full_name":"Kasten, Jens"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Reininghaus, Jan","last_name":"Reininghaus"},{"last_name":"Reich","full_name":"Reich, Wieland","first_name":"Wieland"},{"first_name":"Gerik","full_name":"Scheuermann, Gerik","last_name":"Scheuermann"}],"article_processing_charge":"No","editor":[{"last_name":"Bremer","full_name":"Bremer, Peer-Timo","first_name":"Peer-Timo"},{"full_name":"Hotz, Ingrid","last_name":"Hotz","first_name":"Ingrid"},{"first_name":"Valerio","last_name":"Pascucci","full_name":"Pascucci, Valerio"},{"last_name":"Peikert","full_name":"Peikert, Ronald","first_name":"Ronald"}],"title":"Toward the extraction of saddle periodic orbits","project":[{"call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","grant_number":"318493"}],"year":"2014","day":"19","publication":"Topological Methods in Data Analysis and Visualization III ","page":"55-69","doi":"10.1007/978-3-319-04099-8_4","date_published":"2014-03-19T00:00:00Z","date_created":"2022-03-21T07:11:23Z","acknowledgement":"First, we thank the reviewers of this paper for their ideas and critical comments. In addition, we thank Ronny Peikert and Filip Sadlo for a fruitful discussions. This research is supported by the European Commission under the TOPOSYS project FP7-ICT-318493-STREP, the European Social Fund (ESF App. No. 100098251), and the European Science Foundation under the ACAT Research Network Program.","publisher":"Springer","quality_controlled":"1","date_updated":"2022-06-21T12:01:47Z","department":[{"_id":"HeEd"}],"_id":"10893","series_title":"Mathematics and Visualization","type":"book_chapter","status":"public","publication_identifier":{"eisbn":["9783319040998"],"isbn":["9783319040981"],"eissn":["2197-666X"],"issn":["1612-3786"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":1,"ec_funded":1,"abstract":[{"text":"Saddle periodic orbits are an essential and stable part of the topological skeleton of a 3D vector field. Nevertheless, there is currently no efficient algorithm to robustly extract these features. In this chapter, we present a novel technique to extract saddle periodic orbits. Exploiting the analytic properties of such an orbit, we propose a scalar measure based on the finite-time Lyapunov exponent (FTLE) that indicates its presence. Using persistent homology, we can then extract the robust cycles of this field. These cycles thereby represent the saddle periodic orbits of the given vector field. We discuss the different existing FTLE approximation schemes regarding their applicability to this specific problem and propose an adapted version of FTLE called Normalized Velocity Separation. Finally, we evaluate our method using simple analytic vector field data.","lang":"eng"}],"oa_version":"None","scopus_import":"1","place":"Cham","month":"03","intvolume":" 1"},{"quality_controlled":"1","publisher":"Elsevier","oa":1,"doi":"10.1016/j.cell.2014.02.004","date_published":"2014-02-27T00:00:00Z","date_created":"2022-04-07T07:50:04Z","page":"868-869","day":"27","publication":"Cell","year":"2014","title":"Nuclear pores set the speed limit for mitosis","author":[{"full_name":"Buchwalter, Abigail","last_name":"Buchwalter","first_name":"Abigail"},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER"}],"article_processing_charge":"No","external_id":{"pmid":["24581486"]},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"chicago":"Buchwalter, Abigail, and Martin Hetzer. “Nuclear Pores Set the Speed Limit for Mitosis.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.02.004.","ista":"Buchwalter A, Hetzer M. 2014. Nuclear pores set the speed limit for mitosis. Cell. 156(5), 868–869.","mla":"Buchwalter, Abigail, and Martin Hetzer. “Nuclear Pores Set the Speed Limit for Mitosis.” Cell, vol. 156, no. 5, Elsevier, 2014, pp. 868–69, doi:10.1016/j.cell.2014.02.004.","ama":"Buchwalter A, Hetzer M. Nuclear pores set the speed limit for mitosis. Cell. 2014;156(5):868-869. doi:10.1016/j.cell.2014.02.004","apa":"Buchwalter, A., & Hetzer, M. (2014). Nuclear pores set the speed limit for mitosis. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.02.004","ieee":"A. Buchwalter and M. Hetzer, “Nuclear pores set the speed limit for mitosis,” Cell, vol. 156, no. 5. Elsevier, pp. 868–869, 2014.","short":"A. Buchwalter, M. Hetzer, Cell 156 (2014) 868–869."},"month":"02","intvolume":" 156","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2014.02.004"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The spindle assembly checkpoint prevents separation of sister chromatids until each kinetochore is attached to the mitotic spindle. Rodriguez-Bravo et al. report that the nuclear pore complex scaffolds spindle assembly checkpoint signaling in interphase, providing a store of inhibitory signals that limits the speed of the subsequent mitosis."}],"issue":"5","volume":156,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0092-8674"]},"publication_status":"published","status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology"],"article_type":"original","type":"journal_article","_id":"11080","extern":"1","date_updated":"2022-07-18T08:44:33Z"},{"year":"2014","day":"15","publication":"Molecular Biology of the Cell","page":"2472-2484","date_published":"2014-08-15T00:00:00Z","doi":"10.1091/mbc.e14-04-0865","date_created":"2022-04-07T07:50:24Z","publisher":"American Society for Cell Biology","quality_controlled":"1","oa":1,"citation":{"chicago":"Buchwalter, Abigail L., Yun Liang, and Martin Hetzer. “Nup50 Is Required for Cell Differentiation and Exhibits Transcription-Dependent Dynamics.” Molecular Biology of the Cell. American Society for Cell Biology, 2014. https://doi.org/10.1091/mbc.e14-04-0865.","ista":"Buchwalter AL, Liang Y, Hetzer M. 2014. Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. 25(16), 2472–2484.","mla":"Buchwalter, Abigail L., et al. “Nup50 Is Required for Cell Differentiation and Exhibits Transcription-Dependent Dynamics.” Molecular Biology of the Cell, vol. 25, no. 16, American Society for Cell Biology, 2014, pp. 2472–84, doi:10.1091/mbc.e14-04-0865.","apa":"Buchwalter, A. L., Liang, Y., & Hetzer, M. (2014). Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.e14-04-0865","ama":"Buchwalter AL, Liang Y, Hetzer M. Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. 2014;25(16):2472-2484. doi:10.1091/mbc.e14-04-0865","short":"A.L. Buchwalter, Y. Liang, M. Hetzer, Molecular Biology of the Cell 25 (2014) 2472–2484.","ieee":"A. L. Buchwalter, Y. Liang, and M. Hetzer, “Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics,” Molecular Biology of the Cell, vol. 25, no. 16. American Society for Cell Biology, pp. 2472–2484, 2014."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","author":[{"first_name":"Abigail L.","last_name":"Buchwalter","full_name":"Buchwalter, Abigail L."},{"last_name":"Liang","full_name":"Liang, Yun","first_name":"Yun"},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER"}],"article_processing_charge":"No","title":"Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics","publication_identifier":{"issn":["1059-1524","1939-4586"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":25,"issue":"16","abstract":[{"lang":"eng","text":"The nuclear pore complex (NPC) plays a critical role in gene expression by mediating import of transcription regulators into the nucleus and export of RNA transcripts to the cytoplasm. Emerging evidence suggests that in addition to mediating transport, a subset of nucleoporins (Nups) engage in transcriptional activation and elongation at genomic loci that are not associated with NPCs. The underlying mechanism and regulation of Nup mobility on and off nuclear pores remain unclear. Here we show that Nup50 is a mobile Nup with a pronounced presence both at the NPC and in the nucleoplasm that can move between these different localizations. Strikingly, the dynamic behavior of Nup50 in both locations is dependent on active transcription by RNA polymerase II and requires the N-terminal half of the protein, which contains importin α– and Nup153-binding domains. However, Nup50 dynamics are independent of importin α, Nup153, and Nup98, even though the latter two proteins also exhibit transcription-dependent mobility. Of interest, depletion of Nup50 from C2C12 myoblasts does not affect cell proliferation but inhibits differentiation into myotubes. Taken together, our results suggest a transport-independent role for Nup50 in chromatin biology that occurs away from the NPC."}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1091/mbc.e14-04-0865"}],"month":"08","intvolume":" 25","date_updated":"2022-07-18T08:45:20Z","extern":"1","_id":"11082","type":"journal_article","article_type":"original","status":"public","keyword":["Cell Biology","Molecular Biology"]},{"volume":205,"issue":"2","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1540-8140","0021-9525"]},"intvolume":" 205","month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1083/jcb.201402003"}],"scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"In eukaryotic cells the nuclear genome is enclosed by the nuclear envelope (NE). In metazoans, the NE breaks down in mitosis and it has been assumed that the physical barrier separating nucleoplasm and cytoplasm remains intact during the rest of the cell cycle and cell differentiation. However, recent studies suggest that nonmitotic NE remodeling plays a critical role in development, virus infection, laminopathies, and cancer. Although the mechanisms underlying these NE restructuring events are currently being defined, one common theme is activation of protein kinase C family members in the interphase nucleus to disrupt the nuclear lamina, demonstrating the importance of the lamina in maintaining nuclear integrity."}],"extern":"1","date_updated":"2022-07-18T08:45:09Z","keyword":["Cell Biology"],"status":"public","type":"journal_article","article_type":"review","_id":"11081","date_created":"2022-04-07T07:50:13Z","date_published":"2014-04-21T00:00:00Z","doi":"10.1083/jcb.201402003","page":"133-141","publication":"Journal of Cell Biology","day":"21","year":"2014","oa":1,"quality_controlled":"1","publisher":"Rockefeller University Press","title":"Breaching the nuclear envelope in development and disease","article_processing_charge":"No","external_id":{"pmid":["24751535"]},"author":[{"full_name":"Hatch, Emily","last_name":"Hatch","first_name":"Emily"},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER"}],"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"ista":"Hatch E, Hetzer M. 2014. Breaching the nuclear envelope in development and disease. Journal of Cell Biology. 205(2), 133–141.","chicago":"Hatch, Emily, and Martin Hetzer. “Breaching the Nuclear Envelope in Development and Disease.” Journal of Cell Biology. Rockefeller University Press, 2014. https://doi.org/10.1083/jcb.201402003.","short":"E. Hatch, M. Hetzer, Journal of Cell Biology 205 (2014) 133–141.","ieee":"E. Hatch and M. Hetzer, “Breaching the nuclear envelope in development and disease,” Journal of Cell Biology, vol. 205, no. 2. Rockefeller University Press, pp. 133–141, 2014.","apa":"Hatch, E., & Hetzer, M. (2014). Breaching the nuclear envelope in development and disease. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201402003","ama":"Hatch E, Hetzer M. Breaching the nuclear envelope in development and disease. Journal of Cell Biology. 2014;205(2):133-141. doi:10.1083/jcb.201402003","mla":"Hatch, Emily, and Martin Hetzer. “Breaching the Nuclear Envelope in Development and Disease.” Journal of Cell Biology, vol. 205, no. 2, Rockefeller University Press, 2014, pp. 133–41, doi:10.1083/jcb.201402003."}},{"article_processing_charge":"No","external_id":{"arxiv":["1402.6697"]},"author":[{"orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"first_name":"David","full_name":"Sobral, David","last_name":"Sobral"},{"first_name":"A. M.","last_name":"Swinbank","full_name":"Swinbank, A. M."},{"last_name":"Smail","full_name":"Smail, Ian","first_name":"Ian"},{"full_name":"Best, P. N.","last_name":"Best","first_name":"P. N."},{"first_name":"Jae-Woo","last_name":"Kim","full_name":"Kim, Jae-Woo"},{"first_name":"Marijn","full_name":"Franx, Marijn","last_name":"Franx"},{"first_name":"Bo","last_name":"Milvang-Jensen","full_name":"Milvang-Jensen, Bo"},{"first_name":"Johan","last_name":"Fynbo","full_name":"Fynbo, Johan"}],"title":"A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys","citation":{"ista":"Matthee JJ, Sobral D, Swinbank AM, Smail I, Best PN, Kim J-W, Franx M, Milvang-Jensen B, Fynbo J. 2014. A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. 440(3), 2375–2387.","chicago":"Matthee, Jorryt J, David Sobral, A. M. Swinbank, Ian Smail, P. N. Best, Jae-Woo Kim, Marijn Franx, Bo Milvang-Jensen, and Johan Fynbo. “A 10 Deg2 Lyman α Survey at Z=8.8 with Spectroscopic Follow-up: Strong Constraints on the Luminosity Function and Implications for Other Surveys.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2014. https://doi.org/10.1093/mnras/stu392.","ieee":"J. J. Matthee et al., “A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys,” Monthly Notices of the Royal Astronomical Society, vol. 440, no. 3. Oxford University Press, pp. 2375–2387, 2014.","short":"J.J. Matthee, D. Sobral, A.M. Swinbank, I. Smail, P.N. Best, J.-W. Kim, M. Franx, B. Milvang-Jensen, J. Fynbo, Monthly Notices of the Royal Astronomical Society 440 (2014) 2375–2387.","apa":"Matthee, J. J., Sobral, D., Swinbank, A. M., Smail, I., Best, P. N., Kim, J.-W., … Fynbo, J. (2014). A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stu392","ama":"Matthee JJ, Sobral D, Swinbank AM, et al. A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. 2014;440(3):2375-2387. doi:10.1093/mnras/stu392","mla":"Matthee, Jorryt J., et al. “A 10 Deg2 Lyman α Survey at Z=8.8 with Spectroscopic Follow-up: Strong Constraints on the Luminosity Function and Implications for Other Surveys.” Monthly Notices of the Royal Astronomical Society, vol. 440, no. 3, Oxford University Press, 2014, pp. 2375–87, doi:10.1093/mnras/stu392."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"We thank the anonymous referee for the comments and suggestions which improved both the quality and clarity of this work. DS acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a Veni fellowship. IRS acknowledges support from STFC (ST/I001573/1), a Leverhulme Fellowship, the ERC Advanced Investigator programme DUSTYGAL 321334 and a Royal Society/Wolfson Merit Award. PNB acknowledges support from the Leverhulme Trust. JWK acknowledges the support from the Creative Research Initiative Program, no. 2008- 0060544, of the National Research Foundation of Korea (NRF) funded by the Korean government (MSIP). JPUF and BMJ acknowledge support from the ERC-StG grant EGGS-278202. The Dark Cosmology Centre is funded by the Danish National Research Foundation. This work is based in part on data obtained as part of the UKIRT Infrared Deep Sky Survey. Based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and CEA/IRFU, at the Canada–France–Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de l’Univers of the Centre National de la Recherche Scientifique (CNRS) of France and the University of Hawaii. This work is based in part on data products produced at Terapix available at the Canadian Astronomy Data Centre as part of the Canada-France-Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. This work was only possible due to OPTICON/FP7 and the access that it granted to the CFHT telescope. The authors also wish to acknowledge the CFHTLS and UKIDSS surveys for their excellent legacy and complementary value – without such high-quality data sets, this research would not have been possible.","page":"2375-2387","date_created":"2022-07-14T12:33:24Z","doi":"10.1093/mnras/stu392","date_published":"2014-05-21T00:00:00Z","year":"2014","publication":"Monthly Notices of the Royal Astronomical Society","day":"21","type":"journal_article","article_type":"original","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","cosmology: observations","dark ages","reionization","first stars"],"status":"public","_id":"11583","date_updated":"2022-08-19T08:30:30Z","extern":"1","main_file_link":[{"url":"https://arxiv.org/abs/1402.6697","open_access":"1"}],"scopus_import":"1","intvolume":" 440","month":"05","abstract":[{"lang":"eng","text":"Candidate galaxies at redshifts of z ∼ 10 are now being found in extremely deep surveys, probing very small areas. As a consequence, candidates are very faint, making spectroscopic confirmation practically impossible. In order to overcome such limitations, we have undertaken the CF-HiZELS survey, which is a large-area, medium-depth near-infrared narrow-band survey targeted at z = 8.8 Lyman α (Lyα) emitters (LAEs) and covering 10 deg2 in part of the SSA22 field with the Canada–France–Hawaii Telescope (CFHT). We surveyed a comoving volume of 4.7 × 106 Mpc3 to a Lyα luminosity limit of 6.3 × 1043舁erg舁s−1. We look for Lyα candidates by applying the following criteria: (i) clear emission-line source, (ii) no optical detections (ugriz from CFHTLS), (iii) no visible detection in the optical stack (ugriz > 27), (iv) visually checked reliable NBJ and J detections and (v) J − K ≤ 0. We compute photometric redshifts and remove a significant amount of dusty lower redshift line-emitters at z ∼ 1.4 or 2.2. A total of 13 Lyα candidates were found, of which two are marked as strong candidates, but the majority have very weak constraints on their spectral energy distributions. Using follow-up observations with SINFONI/VLT, we are able to exclude the most robust candidates as LAEs. We put a strong constraint on the Lyα luminosity function at z ∼ 9 and make realistic predictions for ongoing and future surveys. Our results show that surveys for the highest redshift LAEs are susceptible of multiple contaminations and that spectroscopic follow-up is absolutely necessary."}],"oa_version":"Preprint","issue":"3","volume":440,"publication_status":"published","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"language":[{"iso":"eng"}]},{"acknowledgement":"First, we acknowledge the referee for their comments, which have improved the clarity of this paper. JPS and IRS acknowledge support from STFC (ST/I001573/1). IRS also acknowledges support from the ERC Advanced Investigator programme DUSTYGAL and a Royal Society/Wolfson Merit Award. DS acknowledges financial support from NWO through a Veni fellowship and from FCT through the award of an FCT-IF starting grant. PNB acknowledges STFC for financial support.","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","year":"2014","publication":"Monthly Notices of the Royal Astronomical Society","day":"21","page":"2695-2704","date_created":"2022-07-14T12:16:10Z","date_published":"2014-09-21T00:00:00Z","doi":"10.1093/mnras/stu1343","citation":{"chicago":"Stott, John P., David Sobral, A. M. Swinbank, Ian Smail, Richard Bower, Philip N. Best, Ray M. Sharples, James E. Geach, and Jorryt J Matthee. “A Relationship between Specific Star Formation Rate and Metallicity Gradient within z ∼ 1 Galaxies from KMOS-HiZELS.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2014. https://doi.org/10.1093/mnras/stu1343.","ista":"Stott JP, Sobral D, Swinbank AM, Smail I, Bower R, Best PN, Sharples RM, Geach JE, Matthee JJ. 2014. A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. 443(3), 2695–2704.","mla":"Stott, John P., et al. “A Relationship between Specific Star Formation Rate and Metallicity Gradient within z ∼ 1 Galaxies from KMOS-HiZELS.” Monthly Notices of the Royal Astronomical Society, vol. 443, no. 3, Oxford University Press, 2014, pp. 2695–704, doi:10.1093/mnras/stu1343.","apa":"Stott, J. P., Sobral, D., Swinbank, A. M., Smail, I., Bower, R., Best, P. N., … Matthee, J. J. (2014). A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stu1343","ama":"Stott JP, Sobral D, Swinbank AM, et al. A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. 2014;443(3):2695-2704. doi:10.1093/mnras/stu1343","short":"J.P. Stott, D. Sobral, A.M. Swinbank, I. Smail, R. Bower, P.N. Best, R.M. Sharples, J.E. Geach, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 443 (2014) 2695–2704.","ieee":"J. P. Stott et al., “A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS,” Monthly Notices of the Royal Astronomical Society, vol. 443, no. 3. Oxford University Press, pp. 2695–2704, 2014."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1407.1047"]},"author":[{"first_name":"John P.","last_name":"Stott","full_name":"Stott, John P."},{"first_name":"David","full_name":"Sobral, David","last_name":"Sobral"},{"first_name":"A. M.","full_name":"Swinbank, A. M.","last_name":"Swinbank"},{"last_name":"Smail","full_name":"Smail, Ian","first_name":"Ian"},{"first_name":"Richard","last_name":"Bower","full_name":"Bower, Richard"},{"full_name":"Best, Philip N.","last_name":"Best","first_name":"Philip N."},{"first_name":"Ray M.","last_name":"Sharples","full_name":"Sharples, Ray M."},{"first_name":"James E.","full_name":"Geach, James E.","last_name":"Geach"},{"full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"}],"title":"A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS","abstract":[{"lang":"eng","text":"We have observed a sample of typical z ∼ 1 star-forming galaxies, selected from the HiZELS survey, with the new K-band Multi-Object Spectrograph (KMOS) near-infrared, multi-integral field unit instrument on the Very Large Telescope (VLT), in order to obtain their dynamics and metallicity gradients. The majority of our galaxies have a metallicity gradient consistent with being flat or negative (i.e. higher metallicity cores than outskirts). Intriguingly, we find a trend between metallicity gradient and specific star formation rate (sSFR), such that galaxies with a high sSFR tend to have relatively metal poor centres, a result which is strengthened when combined with data sets from the literature. This result appears to explain the discrepancies reported between different high-redshift studies and varying claims for evolution. From a galaxy evolution perspective, the trend we see would mean that a galaxy's sSFR is governed by the amount of metal-poor gas that can be funnelled into its core, triggered either by merging or through efficient accretion. In fact, merging may play a significant role as it is the starburst galaxies at all epochs, which have the more positive metallicity gradients. Our results may help to explain the origin of the fundamental metallicity relation, in which galaxies at a fixed mass are observed to have lower metallicities at higher star formation rates, especially if the metallicity is measured in an aperture encompassing only the central regions of the galaxy. Finally, we note that this study demonstrates the power of KMOS as an efficient instrument for large-scale resolved galaxy surveys."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1407.1047"}],"scopus_import":"1","intvolume":" 443","month":"09","publication_status":"published","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"language":[{"iso":"eng"}],"volume":443,"issue":"3","_id":"11582","article_type":"original","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: abundances","galaxies: evolution","galaxies: kinematics and dynamics"],"status":"public","date_updated":"2022-08-19T08:27:25Z","extern":"1"}]