[{"page":"79 - 91","isi":1,"publist_id":"7768","type":"book_chapter","article_processing_charge":"No","fulldoi":"https://doi.org/10.1016/bs.mcb.2018.07.004","oa_version":"None","language":[{"iso":"eng"}],"_id":"153","day":"27","doi":"10.1016/bs.mcb.2018.07.004","citation":{"apa":"Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., &#38; Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In <i>Methods in Cell Biology</i> (Vol. 147, pp. 79–91). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>","ieee":"J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered ‘pillar forests’ to study cell migration in complex but controlled 3D environments,” in <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91.","mla":"Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>.","short":"J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91.","ama":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: <i>Methods in Cell Biology</i>. Vol 147. Academic Press; 2018:79-91. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>","ista":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. vol. 147, 79–91.","chicago":"Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” In <i>Methods in Cell Biology</i>, 147:79–91. Academic Press, 2018. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","publication_identifier":{"issn":["0091-679X"]},"publication_status":"published","external_id":{"pmid":["30165964"],"isi":["000452412300006"]},"publisher":"Academic Press","author":[{"last_name":"Renkawitz","full_name":"Renkawitz, Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg","orcid":"0000-0003-2856-3369"},{"last_name":"Reversat","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","first_name":"Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Leithner","full_name":"Leithner, Alexander F","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X"},{"last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"abstract":[{"lang":"eng","text":"Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters."}],"quality_controlled":"1","status":"public","scopus_import":"1","pmid":1,"intvolume":"       147","publication":"Methods in Cell Biology","year":"2018","volume":147,"date_updated":"2025-07-10T11:51:09Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"date_created":"2018-12-11T11:44:54Z","date_published":"2018-07-27T00:00:00Z","month":"07"},{"date_updated":"2023-09-18T08:12:24Z","editor":[{"last_name":"Andrews","first_name":"D L","full_name":"Andrews, D L"},{"last_name":"Ostendorf","first_name":"A","full_name":"Ostendorf, A"},{"first_name":"A J","full_name":"Bain, A J","last_name":"Bain"},{"last_name":"Nunzi","first_name":"J M","full_name":"Nunzi, J M"}],"department":[{"_id":"JoFi"}],"date_created":"2018-12-11T11:44:55Z","date_published":"2018-05-04T00:00:00Z","month":"05","alternative_title":["Proceedings of SPIE"],"publisher":"SPIE","author":[{"full_name":"Xuereb, André","first_name":"André","last_name":"Xuereb"},{"last_name":"Aquilina","first_name":"Matteo","full_name":"Aquilina, Matteo"},{"last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir"}],"oa":1,"abstract":[{"text":"There is currently significant interest in operating devices in the quantum regime, where their behaviour cannot be explained through classical mechanics. Quantum states, including entangled states, are fragile and easily disturbed by excessive thermal noise. Here we address the question of whether it is possible to create non-reciprocal devices that encourage the flow of thermal noise towards or away from a particular quantum device in a network. Our work makes use of the cascaded systems formalism to answer this question in the affirmative, showing how a three-port device can be used as an effective thermal transistor, and illustrates how this formalism maps onto an experimentally-realisable optomechanical system. Our results pave the way to more resilient quantum devices and to the use of thermal noise as a resource.","lang":"eng"}],"status":"public","quality_controlled":"1","scopus_import":"1","intvolume":"     10672","volume":10672,"year":"2018","conference":{"start_date":"2018-04-22","end_date":"2018-04-26","name":"SPIE: The international society for optical engineering","location":"Strasbourg, France"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.01000"}],"citation":{"apa":"Xuereb, A., Aquilina, M., &#38; Barzanjeh, S. (2018). Routing thermal noise through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, &#38; J. M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society for optical engineering, Strasbourg, France: SPIE. <a href=\"https://doi.org/10.1117/12.2309928\">https://doi.org/10.1117/12.2309928</a>","ama":"Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks. In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:<a href=\"https://doi.org/10.1117/12.2309928\">10.1117/12.2309928</a>","short":"A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018.","ieee":"A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through quantum networks,” presented at the SPIE: The international society for optical engineering, Strasbourg, France, 2018, vol. 10672.","mla":"Xuereb, André, et al. <i>Routing Thermal Noise through Quantum Networks</i>. Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:<a href=\"https://doi.org/10.1117/12.2309928\">10.1117/12.2309928</a>.","chicago":"Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain, and J M Nunzi, Vol. 10672. SPIE, 2018. <a href=\"https://doi.org/10.1117/12.2309928\">https://doi.org/10.1117/12.2309928</a>.","ista":"Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum networks. SPIE: The international society for optical engineering, Proceedings of SPIE, vol. 10672, 106721N."},"article_number":"106721N","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Routing thermal noise through quantum networks","publication_status":"published","external_id":{"arxiv":["1806.01000"],"isi":["000453298500019"]},"isi":1,"arxiv":1,"publist_id":"7766","type":"conference","article_processing_charge":"No","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1117/12.2309928","oa_version":"Preprint","_id":"155","day":"04","doi":"10.1117/12.2309928"},{"month":"07","date_published":"2018-07-12T00:00:00Z","department":[{"_id":"ToHe"}],"date_created":"2018-12-11T11:44:55Z","file":[{"relation":"main_file","content_type":"application/pdf","file_id":"8637","file_size":485576,"creator":"dernst","date_updated":"2020-10-09T06:22:41Z","access_level":"open_access","file_name":"2018_LNCS_Ferrere.pdf","date_created":"2020-10-09T06:22:41Z","success":1,"checksum":"a045c213c42c445f1889326f8db82a0a"}],"date_updated":"2025-07-10T11:51:10Z","year":"2018","volume":10951,"scopus_import":"1","status":"public","ddc":["000"],"quality_controlled":"1","intvolume":"     10951","file_date_updated":"2020-10-09T06:22:41Z","oa":1,"author":[{"last_name":"Ferrere","full_name":"Ferrere, Thomas","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143"}],"abstract":[{"text":"Imprecision in timing can sometimes be beneficial: Metric interval temporal logic (MITL), disabling the expression of punctuality constraints, was shown to translate to timed automata, yielding an elementary decision procedure. We show how this principle extends to other forms of dense-time specification using regular expressions. By providing a clean, automaton-based formal framework for non-punctual languages, we are able to recover and extend several results in timed systems. Metric interval regular expressions (MIRE) are introduced, providing regular expressions with non-singular duration constraints. We obtain that MIRE are expressively complete relative to a class of one-clock timed automata, which can be determinized using additional clocks. Metric interval dynamic logic (MIDL) is then defined using MIRE as temporal modalities. We show that MIDL generalizes known extensions of MITL, while translating to timed automata at comparable cost.","lang":"eng"}],"alternative_title":["LNCS"],"publisher":"Springer","title":"The compound interest in relaxing punctuality","external_id":{"isi":["000489765800009"]},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"location":"Oxford, UK","name":"FM: Formal Methods","end_date":"2018-07-17","start_date":"2018-07-15"},"citation":{"apa":"Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951, pp. 147–164). Presented at the FM: Formal Methods, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">https://doi.org/10.1007/978-3-319-95582-7_9</a>","ama":"Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer; 2018:147-164. doi:<a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">10.1007/978-3-319-95582-7_9</a>","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","mla":"Ferrere, Thomas. <i>The Compound Interest in Relaxing Punctuality</i>. Vol. 10951, Springer, 2018, pp. 147–64, doi:<a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">10.1007/978-3-319-95582-7_9</a>.","ieee":"T. Ferrere, “The compound interest in relaxing punctuality,” presented at the FM: Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164.","chicago":"Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">https://doi.org/10.1007/978-3-319-95582-7_9</a>.","ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: Formal Methods, LNCS, vol. 10951, 147–164."},"day":"12","_id":"156","oa_version":"Submitted Version","fulldoi":"https://doi.org/10.1007/978-3-319-95582-7_9","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-95582-7_9","article_processing_charge":"No","type":"conference","project":[{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"publist_id":"7765","has_accepted_license":"1","page":"147 - 164","isi":1},{"citation":{"mla":"Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>, vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:<a href=\"https://doi.org/10.1038/s41586-018-0277-x\">10.1038/s41586-018-0277-x</a>.","ieee":"C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation in stochastic games,” <i>Nature</i>, vol. 559, no. 7713. Nature Publishing Group, pp. 246–249, 2018.","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249.","ama":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic games. <i>Nature</i>. 2018;559(7713):246-249. doi:<a href=\"https://doi.org/10.1038/s41586-018-0277-x\">10.1038/s41586-018-0277-x</a>","apa":"Hilbe, C., Šimsa, Š., Chatterjee, K., &#38; Nowak, M. (2018). Evolution of cooperation in stochastic games. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0277-x\">https://doi.org/10.1038/s41586-018-0277-x</a>","ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249.","chicago":"Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0277-x\">https://doi.org/10.1038/s41586-018-0277-x</a>."},"publication_status":"published","external_id":{"isi":["000438240900054"]},"title":"Evolution of cooperation in stochastic games","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","publist_id":"7764","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","issue":"7713","related_material":{"link":[{"url":"https://ist.ac.at/en/news/engineering-cooperation/","description":"News on IST Homepage","relation":"press_release"}]},"isi":1,"page":"246 - 249","doi":"10.1038/s41586-018-0277-x","oa_version":"Submitted Version","fulldoi":"https://doi.org/10.1038/s41586-018-0277-x","language":[{"iso":"eng"}],"day":"04","_id":"157","article_processing_charge":"No","acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","date_created":"2018-12-11T11:44:56Z","ec_funded":1,"department":[{"_id":"KrCh"}],"date_updated":"2025-04-15T06:30:08Z","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2020-07-14T12:45:02Z","checksum":"011ab905cf9a410bc2b96f15174d654d","file_name":"2018_Nature_Hilbe.pdf","date_created":"2019-11-19T08:09:57Z","content_type":"application/pdf","relation":"main_file","file_size":2834442,"file_id":"7049"}],"month":"07","date_published":"2018-07-04T00:00:00Z","abstract":[{"text":"Social dilemmas occur when incentives for individuals are misaligned with group interests 1-7 . According to the 'tragedy of the commons', these misalignments can lead to overexploitation and collapse of public resources. The resulting behaviours can be analysed with the tools of game theory 8 . The theory of direct reciprocity 9-15 suggests that repeated interactions can alleviate such dilemmas, but previous work has assumed that the public resource remains constant over time. Here we introduce the idea that the public resource is instead changeable and depends on the strategic choices of individuals. An intuitive scenario is that cooperation increases the public resource, whereas defection decreases it. Thus, cooperation allows the possibility of playing a more valuable game with higher payoffs, whereas defection leads to a less valuable game. We analyse this idea using the theory of stochastic games 16-19 and evolutionary game theory. We find that the dependence of the public resource on previous interactions can greatly enhance the propensity for cooperation. For these results, the interaction between reciprocity and payoff feedback is crucial: neither repeated interactions in a constant environment nor single interactions in a changing environment yield similar cooperation rates. Our framework shows which feedbacks between exploitation and environment - either naturally occurring or designed - help to overcome social dilemmas.","lang":"eng"}],"author":[{"orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hilbe, Christian","last_name":"Hilbe"},{"first_name":"Štepán","full_name":"Šimsa, Štepán","last_name":"Šimsa"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"file_date_updated":"2020-07-14T12:45:02Z","oa":1,"publisher":"Nature Publishing Group","publication":"Nature","volume":559,"year":"2018","intvolume":"       559","ddc":["000"],"status":"public","quality_controlled":"1","scopus_import":"1"},{"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211"}],"citation":{"chicago":"Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0204-z\">https://doi.org/10.1038/s41477-018-0204-z</a>.","ista":"Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553.","short":"H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J. Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018) 548–553.","ama":"Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. <i>Nature Plants</i>. 2018;4(8):548-553. doi:<a href=\"https://doi.org/10.1038/s41477-018-0204-z\">10.1038/s41477-018-0204-z</a>","ieee":"H. Robert <i>et al.</i>, “Maternal auxin supply contributes to early embryo patterning in Arabidopsis,” <i>Nature Plants</i>, vol. 4, no. 8. Nature Publishing Group, pp. 548–553, 2018.","mla":"Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” <i>Nature Plants</i>, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 548–53, doi:<a href=\"https://doi.org/10.1038/s41477-018-0204-z\">10.1038/s41477-018-0204-z</a>.","apa":"Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O., … Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning in Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0204-z\">https://doi.org/10.1038/s41477-018-0204-z</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","publication_status":"published","external_id":{"isi":["000443861300011"],"pmid":["30013211"]},"page":"548 - 553","issue":"8","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/"}]},"isi":1,"project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"publist_id":"7763","type":"journal_article","article_processing_charge":"No","oa_version":"Submitted Version","fulldoi":"https://doi.org/10.1038/s41477-018-0204-z","language":[{"iso":"eng"}],"_id":"158","day":"16","doi":"10.1038/s41477-018-0204-z","date_updated":"2025-04-15T07:48:03Z","department":[{"_id":"JiFr"}],"date_created":"2018-12-11T11:44:56Z","acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","ec_funded":1,"date_published":"2018-07-16T00:00:00Z","month":"07","publisher":"Nature Publishing Group","author":[{"last_name":"Robert","full_name":"Robert, Hélène","first_name":"Hélène"},{"first_name":"Chulmin","full_name":"Park, Chulmin","last_name":"Park"},{"last_name":"Gutièrrez","full_name":"Gutièrrez, Carla","first_name":"Carla"},{"last_name":"Wójcikowska","full_name":"Wójcikowska, Barbara","first_name":"Barbara"},{"last_name":"Pěnčík","full_name":"Pěnčík, Aleš","first_name":"Aleš"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"last_name":"Chen","first_name":"Junyi","full_name":"Chen, Junyi"},{"last_name":"Grunewald","full_name":"Grunewald, Wim","first_name":"Wim"},{"first_name":"Thomas","full_name":"Dresselhaus, Thomas","last_name":"Dresselhaus"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Laux, Thomas","first_name":"Thomas","last_name":"Laux"}],"oa":1,"abstract":[{"lang":"eng","text":"The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified3,4, only a few maternal mutations have been described to affect embryo development in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor8–10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development."}],"quality_controlled":"1","status":"public","scopus_import":"1","pmid":1,"intvolume":"         4","publication":"Nature Plants","volume":4,"year":"2018"},{"doi":"10.1038/s41589-018-0090-8","day":"16","_id":"159","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1038/s41589-018-0090-8","oa_version":"Submitted Version","article_processing_charge":"No","type":"journal_article","publist_id":"7762","has_accepted_license":"1","isi":1,"issue":"8","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41589-021-00744-3"}]},"article_type":"original","page":"764 - 767","external_id":{"isi":["000438970200010"]},"publication_status":"published","title":"Optical control of L-type Ca2+ channels using a diltiazem photoswitch","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 14(8), 764–767.","chicago":"Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41589-018-0090-8\">https://doi.org/10.1038/s41589-018-0090-8</a>.","apa":"Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N., … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem photoswitch. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41589-018-0090-8\">https://doi.org/10.1038/s41589-018-0090-8</a>","ieee":"T. Fehrentz <i>et al.</i>, “Optical control of L-type Ca2+ channels using a diltiazem photoswitch,” <i>Nature Chemical Biology</i>, vol. 14, no. 8. Nature Publishing Group, pp. 764–767, 2018.","mla":"Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” <i>Nature Chemical Biology</i>, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 764–67, doi:<a href=\"https://doi.org/10.1038/s41589-018-0090-8\">10.1038/s41589-018-0090-8</a>.","ama":"Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. <i>Nature Chemical Biology</i>. 2018;14(8):764-767. doi:<a href=\"https://doi.org/10.1038/s41589-018-0090-8\">10.1038/s41589-018-0090-8</a>","short":"T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D. Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N. Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767."},"year":"2018","volume":14,"publication":"Nature Chemical Biology","intvolume":"        14","scopus_import":"1","ddc":["570"],"quality_controlled":"1","status":"public","abstract":[{"lang":"eng","text":"L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control."}],"oa":1,"file_date_updated":"2020-07-14T12:45:03Z","author":[{"last_name":"Fehrentz","full_name":"Fehrentz, Timm","first_name":"Timm"},{"first_name":"Florian","full_name":"Huber, Florian","last_name":"Huber"},{"full_name":"Hartrampf, Nina","first_name":"Nina","last_name":"Hartrampf"},{"first_name":"Tobias","full_name":"Bruegmann, Tobias","last_name":"Bruegmann"},{"last_name":"Frank","first_name":"James","full_name":"Frank, James"},{"full_name":"Fine, Nicholas","first_name":"Nicholas","last_name":"Fine"},{"first_name":"Daniela","full_name":"Malan, Daniela","last_name":"Malan"},{"last_name":"Danzl","full_name":"Danzl, Johann G","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"},{"full_name":"Tikhonov, Denis","first_name":"Denis","last_name":"Tikhonov"},{"last_name":"Sumser","full_name":"Sumser, Maritn","first_name":"Maritn"},{"last_name":"Sasse","full_name":"Sasse, Philipp","first_name":"Philipp"},{"full_name":"Hodson, David","first_name":"David","last_name":"Hodson"},{"last_name":"Zhorov","first_name":"Boris","full_name":"Zhorov, Boris"},{"first_name":"Nikolaj","full_name":"Klocker, Nikolaj","last_name":"Klocker"},{"last_name":"Trauner","first_name":"Dirk","full_name":"Trauner, Dirk"}],"publisher":"Nature Publishing Group","month":"07","date_published":"2018-07-16T00:00:00Z","date_created":"2018-12-11T11:44:56Z","department":[{"_id":"JoDa"}],"date_updated":"2023-09-13T09:36:35Z","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2020-07-14T12:45:03Z","checksum":"d42935094ec845f54a0688bf12986d62","date_created":"2020-05-14T12:14:09Z","file_name":"2018_NatureChemicalBiology_Fehrentz.pdf","relation":"main_file","content_type":"application/pdf","file_size":6321000,"file_id":"7832"}]},{"type":"journal_article","pubrep_id":"1062","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"has_accepted_license":"1","publist_id":"8039","isi":1,"issue":"10","article_type":"original","doi":"10.1103/PhysRevFluids.3.103303","_id":"16","day":"16","fulldoi":"https://doi.org/10.1103/PhysRevFluids.3.103303","oa_version":"Submitted Version","language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"apa":"Varshney, A., &#38; Steinberg, V. (2018). Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">https://doi.org/10.1103/PhysRevFluids.3.103303</a>","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","ama":"Varshney A, Steinberg V. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. <i>Physical Review Fluids</i>. 2018;3(10). doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">10.1103/PhysRevFluids.3.103303</a>","ieee":"A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification in a creeping viscoelastic flow,” <i>Physical Review Fluids</i>, vol. 3, no. 10. American Physical Society, 2018.","mla":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” <i>Physical Review Fluids</i>, vol. 3, no. 10, 103303, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">10.1103/PhysRevFluids.3.103303</a>.","chicago":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">https://doi.org/10.1103/PhysRevFluids.3.103303</a>.","ista":"Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303."},"external_id":{"isi":["000447469200001"]},"publication_status":"published","title":"Mixing layer instability and vorticity amplification in a creeping viscoelastic flow","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"103303","abstract":[{"text":"We report quantitative evidence of mixing-layer elastic instability in a viscoelastic fluid flow between two widely spaced obstacles hindering a channel flow at Re 1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed in the region between the obstacles. The mixing-layer instability arises in the vicinity of an inflection point on the shear velocity profile with a steep variation in the elastic stress. The instability results in an intermittent appearance of small vortices in the mixing layers and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime. The latter is characterized through scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore, the observations reported provide improved understanding of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1 and oppose the current view of suppression of vorticity solely by polymer additives.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:04Z","oa":1,"author":[{"last_name":"Varshney","full_name":"Varshney, Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul","orcid":"0000-0002-3072-5999"},{"full_name":"Steinberg, Victor","first_name":"Victor","last_name":"Steinberg"}],"publisher":"American Physical Society","volume":3,"year":"2018","publication":"Physical Review Fluids","intvolume":"         3","scopus_import":"1","status":"public","ddc":["532"],"quality_controlled":"1","ec_funded":1,"date_created":"2018-12-11T11:44:10Z","acknowledgement":"This work was partially supported by the Israel Science Foundation (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No. 2016145).","department":[{"_id":"BjHo"}],"date_updated":"2025-04-14T07:44:02Z","file":[{"file_size":1838431,"file_id":"5043","content_type":"application/pdf","relation":"main_file","checksum":"7fc0a2322214d1c04debef36d5bf2e8a","file_name":"IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf","date_created":"2018-12-12T10:13:56Z","creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:45:04Z"}],"month":"10","date_published":"2018-10-16T00:00:00Z"},{"date_published":"2018-07-18T00:00:00Z","month":"07","license":"https://creativecommons.org/licenses/by/4.0/","date_updated":"2026-04-08T07:23:52Z","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:45:04Z","creator":"dernst","checksum":"c64fff560fe5a7532ec10626ad1c215e","file_name":"2018_LNCS_Kragl.pdf","date_created":"2018-12-17T12:52:12Z","content_type":"application/pdf","relation":"main_file","file_size":1603844,"file_id":"5705"}],"date_created":"2018-12-11T11:44:57Z","department":[{"_id":"ToHe"}],"intvolume":"     10981","quality_controlled":"1","status":"public","ddc":["000"],"scopus_import":"1","year":"2018","volume":10981,"publisher":"Springer","alternative_title":["LNCS"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs."}],"author":[{"last_name":"Kragl","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard"},{"full_name":"Qadeer, Shaz","first_name":"Shaz","last_name":"Qadeer"}],"file_date_updated":"2020-07-14T12:45:04Z","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","external_id":{"isi":["000491481600005"]},"title":"Layered Concurrent Programs","citation":{"mla":"Kragl, Bernhard, and Shaz Qadeer. <i>Layered Concurrent Programs</i>. Vol. 10981, Springer, 2018, pp. 79–102, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">10.1007/978-3-319-96145-3_5</a>.","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">10.1007/978-3-319-96145-3_5</a>","apa":"Kragl, B., &#38; Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">https://doi.org/10.1007/978-3-319-96145-3_5</a>","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.","chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">https://doi.org/10.1007/978-3-319-96145-3_5</a>."},"conference":{"start_date":"2018-07-14","end_date":"2018-07-17","name":"CAV: Computer Aided Verification","location":"Oxford, UK"},"article_processing_charge":"No","doi":"10.1007/978-3-319-96145-3_5","fulldoi":"https://doi.org/10.1007/978-3-319-96145-3_5","language":[{"iso":"eng"}],"oa_version":"Published Version","_id":"160","day":"18","related_material":{"record":[{"relation":"dissertation_contains","id":"8332","status":"public"}]},"isi":1,"page":"79 - 102","publist_id":"7761","has_accepted_license":"1","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"type":"conference"},{"article_processing_charge":"No","doi":"10.1038/s41467-018-05417-9","fulldoi":"https://doi.org/10.1038/s41467-018-05417-9","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"161","day":"30","issue":"1","related_material":{"record":[{"status":"public","id":"5587","relation":"popular_science"}]},"isi":1,"publist_id":"7760","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"has_accepted_license":"1","type":"journal_article","article_number":"2988","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","external_id":{"isi":["000440149300021"]},"title":"Statistical mechanics for metabolic networks during steady state growth","citation":{"ama":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","ieee":"D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” <i>Nature Communications</i>, vol. 9, no. 1. Springer Nature, 2018.","mla":"De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>.","apa":"De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., &#38; Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>","chicago":"De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>.","ista":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988."},"intvolume":"         9","ddc":["570"],"status":"public","quality_controlled":"1","scopus_import":"1","publication":"Nature Communications","volume":9,"year":"2018","publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells.","lang":"eng"}],"author":[{"first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","last_name":"De Martino"},{"last_name":"Mc","full_name":"Mc, Andersson Anna","first_name":"Andersson Anna"},{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"},{"last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"file_date_updated":"2020-07-14T12:45:06Z","oa":1,"date_published":"2018-07-30T00:00:00Z","month":"07","date_updated":"2025-04-15T06:50:08Z","file":[{"content_type":"application/pdf","relation":"main_file","file_id":"5728","file_size":1043205,"creator":"dernst","date_updated":"2020-07-14T12:45:06Z","access_level":"open_access","date_created":"2018-12-17T16:44:28Z","file_name":"2018_NatureComm_DeMartino.pdf","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18"}],"date_created":"2018-12-11T11:44:57Z","ec_funded":1,"department":[{"_id":"GaTk"},{"_id":"CaGu"}]},{"article_number":"e34465","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","publication_status":"published","external_id":{"isi":["000436227500001"]},"citation":{"chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.34465\">https://doi.org/10.7554/eLife.34465</a>.","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7, e34465.","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M., … Adameyko, I. (2018). Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.34465\">https://doi.org/10.7554/eLife.34465</a>","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).","ama":"Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.34465\">10.7554/eLife.34465</a>","ieee":"M. Kaucka <i>et al.</i>, “Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","mla":"Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” <i>ELife</i>, vol. 7, e34465, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.34465\">10.7554/eLife.34465</a>."},"article_processing_charge":"No","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.7554/eLife.34465","oa_version":"Published Version","_id":"162","day":"13","doi":"10.7554/eLife.34465","related_material":{"record":[{"status":"public","relation":"research_data","id":"9838"}]},"isi":1,"publist_id":"7759","has_accepted_license":"1","project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord"}],"type":"journal_article","date_published":"2018-06-13T00:00:00Z","month":"06","file":[{"file_size":9816484,"file_id":"5727","content_type":"application/pdf","relation":"main_file","checksum":"da2378cdcf6b5461dcde194e4d608343","date_created":"2018-12-17T16:41:58Z","file_name":"2018_eLife_Kaucka.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:07Z","creator":"dernst"}],"date_updated":"2025-04-14T07:27:30Z","department":[{"_id":"AnKi"}],"date_created":"2018-12-11T11:44:57Z","ec_funded":1,"ddc":["571"],"status":"public","quality_controlled":"1","scopus_import":"1","intvolume":"         7","publication":"eLife","volume":7,"year":"2018","publisher":"eLife Sciences Publications","author":[{"first_name":"Marketa","full_name":"Kaucka, Marketa","last_name":"Kaucka"},{"first_name":"Julian","full_name":"Petersen, Julian","last_name":"Petersen"},{"last_name":"Tesarova","first_name":"Marketa","full_name":"Tesarova, Marketa"},{"last_name":"Szarowska","full_name":"Szarowska, Bara","first_name":"Bara"},{"last_name":"Kastriti","first_name":"Maria","full_name":"Kastriti, Maria"},{"full_name":"Xie, Meng","first_name":"Meng","last_name":"Xie"},{"last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"},{"first_name":"Karl","full_name":"Annusver, Karl","last_name":"Annusver"},{"full_name":"Kasper, Maria","first_name":"Maria","last_name":"Kasper"},{"full_name":"Symmons, Orsolya","first_name":"Orsolya","last_name":"Symmons"},{"last_name":"Pan","full_name":"Pan, Leslie","first_name":"Leslie"},{"full_name":"Spitz, Francois","first_name":"Francois","last_name":"Spitz"},{"last_name":"Kaiser","full_name":"Kaiser, Jozef","first_name":"Jozef"},{"last_name":"Hovorakova","first_name":"Maria","full_name":"Hovorakova, Maria"},{"first_name":"Tomas","full_name":"Zikmund, Tomas","last_name":"Zikmund"},{"last_name":"Sunadome","full_name":"Sunadome, Kazunori","first_name":"Kazunori"},{"full_name":"Matise, Michael P","first_name":"Michael P","last_name":"Matise"},{"last_name":"Wang","full_name":"Wang, Hui","first_name":"Hui"},{"last_name":"Marklund","full_name":"Marklund, Ulrika","first_name":"Ulrika"},{"full_name":"Abdo, Hind","first_name":"Hind","last_name":"Abdo"},{"last_name":"Ernfors","first_name":"Patrik","full_name":"Ernfors, Patrik"},{"first_name":"Pascal","full_name":"Maire, Pascal","last_name":"Maire"},{"full_name":"Wurmser, Maud","first_name":"Maud","last_name":"Wurmser"},{"first_name":"Andrei S","full_name":"Chagin, Andrei S","last_name":"Chagin"},{"last_name":"Fried","full_name":"Fried, Kaj","first_name":"Kaj"},{"last_name":"Adameyko","first_name":"Igor","full_name":"Adameyko, Igor"}],"file_date_updated":"2020-07-14T12:45:07Z","oa":1,"abstract":[{"text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here, we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000452277700005"],"pmid":["29969056"]},"publication_status":"published","publication_identifier":{"issn":["0022-1554"]},"title":"Agitation modules: Flexible means to accelerate automated freeze substitution","citation":{"mla":"Reipert, Siegfried, et al. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” <i>Journal of Histochemistry and Cytochemistry</i>, vol. 66, no. 12, SAGE Publications, 2018, pp. 903–21, doi:<a href=\"https://doi.org/10.1369/0022155418786698\">10.1369/0022155418786698</a>.","ieee":"S. Reipert <i>et al.</i>, “Agitation modules: Flexible means to accelerate automated freeze substitution,” <i>Journal of Histochemistry and Cytochemistry</i>, vol. 66, no. 12. SAGE Publications, pp. 903–921, 2018.","ama":"Reipert S, Goldammer H, Richardson C, et al. Agitation modules: Flexible means to accelerate automated freeze substitution. <i>Journal of Histochemistry and Cytochemistry</i>. 2018;66(12):903-921. doi:<a href=\"https://doi.org/10.1369/0022155418786698\">10.1369/0022155418786698</a>","short":"S. Reipert, H. Goldammer, C. Richardson, M. Goldberg, T. Hawkins, E. Saeckl, W. Kaufmann, S. Antreich, Y. Stierhof, Journal of Histochemistry and Cytochemistry 66 (2018) 903–921.","apa":"Reipert, S., Goldammer, H., Richardson, C., Goldberg, M., Hawkins, T., Saeckl, E., … Stierhof, Y. (2018). Agitation modules: Flexible means to accelerate automated freeze substitution. <i>Journal of Histochemistry and Cytochemistry</i>. SAGE Publications. <a href=\"https://doi.org/10.1369/0022155418786698\">https://doi.org/10.1369/0022155418786698</a>","ista":"Reipert S, Goldammer H, Richardson C, Goldberg M, Hawkins T, Saeckl E, Kaufmann W, Antreich S, Stierhof Y. 2018. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 66(12), 903–921.","chicago":"Reipert, Siegfried, Helmuth Goldammer, Christine Richardson, Martin Goldberg, Timothy Hawkins, Elena Saeckl, Walter Kaufmann, Sebastian Antreich, and York Stierhof. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” <i>Journal of Histochemistry and Cytochemistry</i>. SAGE Publications, 2018. <a href=\"https://doi.org/10.1369/0022155418786698\">https://doi.org/10.1369/0022155418786698</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1369/0022155418786698"}],"article_processing_charge":"No","doi":"10.1369/0022155418786698","_id":"163","day":"01","oa_version":"Published Version","fulldoi":"https://doi.org/10.1369/0022155418786698","language":[{"iso":"eng"}],"isi":1,"issue":"12","article_type":"original","page":"903-921","type":"journal_article","date_published":"2018-12-01T00:00:00Z","month":"12","date_updated":"2026-06-18T17:50:00Z","date_created":"2018-12-11T11:44:57Z","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"intvolume":"        66","scopus_import":"1","pmid":1,"quality_controlled":"1","status":"public","ddc":["570"],"volume":66,"year":"2018","publication":"Journal of Histochemistry and Cytochemistry","publisher":"SAGE Publications","abstract":[{"lang":"eng","text":"For ultrafast fixation of biological samples to avoid artifacts, high-pressure freezing (HPF) followed by freeze substitution (FS) is preferred over chemical fixation at room temperature. After HPF, samples are maintained at low temperature during dehydration and fixation, while avoiding damaging recrystallization. This is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample agitation during FS dramatically reduces the necessary time. Then, in 2015, we (H.G. and S.R.) introduced an agitation module into the cryochamber of an automated FS unit and demonstrated that the preparation of algae could be shortened from days to a couple of hours. We argued that variability in the processing, reproducibility, and safety issues are better addressed using automated FS units. For dissemination, we started low-cost manufacturing of agitation modules for two of the most widely used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from Leica Microsystems, using three dimensional (3D)-printing of the major components. To test them, several labs independently used the modules on a wide variety of specimens that had previously been processed by manual agitation, or without agitation. We demonstrate that automated processing with sample agitation saves time, increases flexibility with respect to sample requirements and protocols, and produces data of at least as good quality as other approaches."}],"oa":1,"author":[{"full_name":"Reipert, Siegfried","first_name":"Siegfried","last_name":"Reipert"},{"first_name":"Helmuth","full_name":"Goldammer, Helmuth","last_name":"Goldammer"},{"last_name":"Richardson","first_name":"Christine","full_name":"Richardson, Christine"},{"full_name":"Goldberg, Martin","first_name":"Martin","last_name":"Goldberg"},{"last_name":"Hawkins","full_name":"Hawkins, Timothy","first_name":"Timothy"},{"full_name":"Hollergschwandtner, Elena","id":"3C054040-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Hollergschwandtner"},{"last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"full_name":"Antreich, Sebastian","first_name":"Sebastian","last_name":"Antreich"},{"last_name":"Stierhof","first_name":"York","full_name":"Stierhof, York"}]},{"department":[{"_id":"BjHo"}],"date_created":"2018-12-11T11:44:11Z","ec_funded":1,"file":[{"creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:45:12Z","checksum":"e1445be33e8165114e96246275600750","file_name":"IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf","date_created":"2018-12-12T10:10:14Z","content_type":"application/pdf","relation":"main_file","file_size":1409040,"file_id":"4800"}],"date_updated":"2025-04-14T07:43:59Z","month":"10","date_published":"2018-10-15T00:00:00Z","author":[{"full_name":"Varshney, Atul","first_name":"Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999","last_name":"Varshney"},{"last_name":"Steinberg","full_name":"Steinberg, Victor","first_name":"Victor"}],"file_date_updated":"2020-07-14T12:45:12Z","oa":1,"abstract":[{"text":"Creeping flow of polymeric fluid without inertia exhibits elastic instabilities and elastic turbulence accompanied by drag enhancement due to elastic stress produced by flow-stretched polymers. However, in inertia-dominated flow at high Re and low fluid elasticity El, a reduction in turbulent frictional drag is caused by an intricate competition between inertial and elastic stresses. Here we explore the effect of inertia on the stability of viscoelastic flow in a broad range of control parameters El and (Re,Wi). We present the stability diagram of observed flow regimes in Wi-Re coordinates and find that the instabilities' onsets show an unexpectedly nonmonotonic dependence on El. Further, three distinct regions in the diagram are identified based on El. Strikingly, for high-elasticity fluids we discover a complete relaminarization of flow at Reynolds number in the range of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive effects may be explained by a finite polymer extensibility and a suppression of vorticity at high Wi. Our results call for further theoretical and numerical development to uncover the role of inertial effect on elastic turbulence in a viscoelastic flow.","lang":"eng"}],"publisher":"American Physical Society","publication":"Physical Review Fluids","year":"2018","volume":3,"quality_controlled":"1","ddc":["532"],"status":"public","scopus_import":"1","intvolume":"         3","citation":{"apa":"Varshney, A., &#38; Steinberg, V. (2018). Drag enhancement and drag reduction in viscoelastic flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">https://doi.org/10.1103/PhysRevFluids.3.103302</a>","ama":"Varshney A, Steinberg V. Drag enhancement and drag reduction in viscoelastic flow. <i>Physical Review Fluids</i>. 2018;3(10). doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">10.1103/PhysRevFluids.3.103302</a>","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","mla":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” <i>Physical Review Fluids</i>, vol. 3, no. 10, 103302, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">10.1103/PhysRevFluids.3.103302</a>.","ieee":"A. Varshney and V. Steinberg, “Drag enhancement and drag reduction in viscoelastic flow,” <i>Physical Review Fluids</i>, vol. 3, no. 10. American Physical Society, 2018.","chicago":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">https://doi.org/10.1103/PhysRevFluids.3.103302</a>.","ista":"Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 3(10), 103302."},"title":"Drag enhancement and drag reduction in viscoelastic flow","publication_status":"published","external_id":{"isi":["000447311500001"]},"article_number":"103302 ","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"publist_id":"8038","has_accepted_license":"1","pubrep_id":"1061","type":"journal_article","issue":"10","isi":1,"fulldoi":"https://doi.org/10.1103/PhysRevFluids.3.103302","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"17","day":"15","doi":"10.1103/PhysRevFluids.3.103302","article_processing_charge":"No"},{"conference":{"end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary","start_date":"2018-06-11"},"citation":{"apa":"Fulek, R., &#38; Kynčl, J. (2018). Hanani-Tutte for approximating maps of graphs (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">https://doi.org/10.4230/LIPIcs.SoCG.2018.39</a>","ama":"Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">10.4230/LIPIcs.SoCG.2018.39</a>","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Fulek, Radoslav, and Jan Kynčl. <i>Hanani-Tutte for Approximating Maps of Graphs</i>. Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">10.4230/LIPIcs.SoCG.2018.39</a>.","ieee":"R. Fulek and J. Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","chicago":"Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">https://doi.org/10.4230/LIPIcs.SoCG.2018.39</a>.","ista":"Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 39."},"title":"Hanani-Tutte for approximating maps of graphs","publication_identifier":{"isbn":["978-3-95977-066-8"]},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"39","has_accepted_license":"1","project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281"}],"publist_id":"7735","type":"conference","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.4230/LIPIcs.SoCG.2018.39","oa_version":"Published Version","_id":"185","day":"01","doi":"10.4230/LIPIcs.SoCG.2018.39","department":[{"_id":"UlWa"}],"date_created":"2018-12-11T11:45:04Z","file":[{"checksum":"f1b94f1a75b37c414a1f61d59fb2cd4c","file_name":"2018_LIPIcs_Fulek.pdf","date_created":"2018-12-17T12:33:52Z","creator":"dernst","access_level":"open_access","date_updated":"2020-07-14T12:45:19Z","file_size":718857,"file_id":"5701","content_type":"application/pdf","relation":"main_file"}],"date_updated":"2021-01-12T06:53:36Z","month":"01","date_published":"2018-01-01T00:00:00Z","author":[{"last_name":"Fulek","orcid":"0000-0001-8485-1774","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav"},{"full_name":"Kynčl, Jan","first_name":"Jan","last_name":"Kynčl"}],"oa":1,"file_date_updated":"2020-07-14T12:45:19Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"text":"We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998), and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the setting of approximating maps of graphs on 2-dimensional surfaces by embeddings. Our proof of this result is constructive and almost immediately implies an efficient algorithm for testing whether a given piecewise linear map of a graph in a surface is approximable by an embedding. More precisely, an instance of this problem consists of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact surface M given as the union of a set of pairwise disjoint discs corresponding to the clusters and a set of pairwise disjoint &quot;pipes&quot; corresponding to the bundles, connecting certain pairs of these discs. We are to decide whether G can be embedded inside M so that the vertices in every cluster are drawn in the corresponding disc, the edges in every bundle pass only through its corresponding pipe, and every edge crosses the boundary of each disc at most once.","lang":"eng"}],"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2018","volume":99,"quality_controlled":"1","status":"public","ddc":["510"],"scopus_import":1,"intvolume":"        99"},{"external_id":{"arxiv":["1803.05085"]},"publication_status":"published","title":"The ℤ2-Genus of Kuratowski minors","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">https://doi.org/10.4230/LIPIcs.SoCG.2018.40</a>.","ista":"Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14.","apa":"Fulek, R., &#38; Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol. 99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">https://doi.org/10.4230/LIPIcs.SoCG.2018.40</a>","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14.","ama":"Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">10.4230/LIPIcs.SoCG.2018.40</a>","ieee":"R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 40.1-40.14.","mla":"Fulek, Radoslav, and Jan Kynčl. <i>The ℤ2-Genus of Kuratowski Minors</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">10.4230/LIPIcs.SoCG.2018.40</a>."},"main_file_link":[{"url":"https://arxiv.org/abs/1803.05085","open_access":"1"}],"conference":{"start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary","end_date":"2018-06-14"},"doi":"10.4230/LIPIcs.SoCG.2018.40","_id":"186","day":"11","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.4230/LIPIcs.SoCG.2018.40","oa_version":"Submitted Version","article_processing_charge":"No","type":"conference","project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs"}],"publist_id":"7734","arxiv":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"11593"}]},"page":"40.1 - 40.14","month":"06","date_published":"2018-06-11T00:00:00Z","date_created":"2018-12-11T11:45:05Z","department":[{"_id":"UlWa"}],"date_updated":"2025-04-14T13:52:37Z","year":"2018","volume":99,"intvolume":"        99","scopus_import":"1","status":"public","quality_controlled":"1","abstract":[{"lang":"eng","text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces."}],"oa":1,"author":[{"last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"full_name":"Kynčl, Jan","first_name":"Jan","last_name":"Kynčl"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"]},{"date_published":"2018-06-11T00:00:00Z","month":"06","date_updated":"2026-04-08T07:01:29Z","file":[{"file_id":"5738","file_size":528018,"content_type":"application/pdf","relation":"main_file","file_name":"2018_LIPIcs_Edelsbrunner_Osang.pdf","date_created":"2018-12-18T09:27:22Z","checksum":"d8c0533ad0018eb4ed1077475eb8fc18","creator":"dernst","date_updated":"2020-07-14T12:45:19Z","access_level":"open_access"}],"date_created":"2018-12-11T11:45:05Z","acknowledgement":"This work is partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","department":[{"_id":"HeEd"}],"intvolume":"        99","scopus_import":1,"ddc":["516"],"quality_controlled":"1","status":"public","year":"2018","volume":99,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"],"abstract":[{"text":"Given a locally finite X ⊆ ℝd and a radius r ≥ 0, the k-fold cover of X and r consists of all points in ℝd that have k or more points of X within distance r. We consider two filtrations - one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k - and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in ℝd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module from Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. ","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:45:19Z","oa":1,"author":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"orcid":"0000-0002-8882-5116","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F","last_name":"Osang"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"34","publication_status":"published","title":"The multi-cover persistence of Euclidean balls","citation":{"ista":"Edelsbrunner H, Osang GF. 2018. The multi-cover persistence of Euclidean balls. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 34.","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">https://doi.org/10.4230/LIPIcs.SoCG.2018.34</a>.","ieee":"H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. <i>The Multi-Cover Persistence of Euclidean Balls</i>. Vol. 99, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">10.4230/LIPIcs.SoCG.2018.34</a>.","short":"H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ama":"Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">10.4230/LIPIcs.SoCG.2018.34</a>","apa":"Edelsbrunner, H., &#38; Osang, G. F. (2018). The multi-cover persistence of Euclidean balls (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">https://doi.org/10.4230/LIPIcs.SoCG.2018.34</a>"},"conference":{"end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary","start_date":"2018-06-11"},"doi":"10.4230/LIPIcs.SoCG.2018.34","_id":"187","day":"11","fulldoi":"https://doi.org/10.4230/LIPIcs.SoCG.2018.34","language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"later_version","id":"9317","status":"public"},{"relation":"dissertation_contains","id":"9056","status":"public"}]},"type":"conference","project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"has_accepted_license":"1","publist_id":"7732"},{"file":[{"relation":"main_file","content_type":"application/pdf","file_size":489080,"file_id":"5724","creator":"dernst","access_level":"open_access","date_updated":"2020-07-14T12:45:20Z","checksum":"7509403803b3ac1aee94bbc2ad293d21","file_name":"2018_LIPIcs_Edelsbrunner.pdf","date_created":"2018-12-17T16:31:31Z"}],"date_updated":"2021-01-12T06:53:48Z","department":[{"_id":"HeEd"}],"acknowledgement":"This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund","date_created":"2018-12-11T11:45:05Z","date_published":"2018-06-11T00:00:00Z","month":"06","alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"last_name":"Virk","first_name":"Ziga","full_name":"Virk, Ziga"},{"full_name":"Wagner, Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","first_name":"Hubert","last_name":"Wagner"}],"file_date_updated":"2020-07-14T12:45:20Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Smallest enclosing spheres of finite point sets are central to methods in topological data analysis. Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex."}],"ddc":["000"],"status":"public","quality_controlled":"1","scopus_import":1,"intvolume":"        99","volume":99,"year":"2018","conference":{"location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry","end_date":"2018-06-14","start_date":"2018-06-11"},"citation":{"apa":"Edelsbrunner, H., Virk, Z., &#38; Wagner, H. (2018). Smallest enclosing spheres and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">https://doi.org/10.4230/LIPIcs.SoCG.2018.35</a>","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13.","mla":"Edelsbrunner, Herbert, et al. <i>Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">10.4230/LIPIcs.SoCG.2018.35</a>.","short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13.","ama":"Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:35:1-35:13. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">10.4230/LIPIcs.SoCG.2018.35</a>","ista":"Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13.","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">https://doi.org/10.4230/LIPIcs.SoCG.2018.35</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Smallest enclosing spheres and Chernoff points in Bregman geometry","publication_status":"published","page":"35:1 - 35:13","project":[{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"publist_id":"7733","has_accepted_license":"1","type":"conference","oa_version":"Published Version","fulldoi":"https://doi.org/10.4230/LIPIcs.SoCG.2018.35","language":[{"iso":"eng"}],"day":"11","_id":"188","doi":"10.4230/LIPIcs.SoCG.2018.35"},{"abstract":[{"text":"Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses.","lang":"eng"}],"oa":1,"author":[{"first_name":"Adam","full_name":"Palmer, Adam","last_name":"Palmer"},{"last_name":"Chait","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kishony, Roy","first_name":"Roy","last_name":"Kishony"}],"publisher":"Oxford University Press","year":"2018","volume":35,"publication":"Molecular Biology and Evolution","intvolume":"        35","scopus_import":"1","pmid":1,"quality_controlled":"1","status":"public","date_created":"2018-12-11T11:44:11Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"date_updated":"2023-10-17T11:51:06Z","month":"08","date_published":"2018-08-28T00:00:00Z","type":"journal_article","publist_id":"8036","isi":1,"issue":"11","article_type":"original","page":"2669 - 2684","doi":"10.1093/molbev/msy163","day":"28","_id":"19","fulldoi":"https://doi.org/10.1093/molbev/msy163","language":[{"iso":"eng"}],"oa_version":"Submitted Version","article_processing_charge":"No","citation":{"apa":"Palmer, A., Chait, R. P., &#38; Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>","mla":"Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11, Oxford University Press, 2018, pp. 2669–84, doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>.","ieee":"A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","ama":"Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. 2018;35(11):2669-2684. doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>","ista":"Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684.","chicago":"Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>."},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679"}],"external_id":{"pmid":["30169679"],"isi":["000452567200006"]},"publication_status":"published","publication_identifier":{"issn":["0737-4038"]},"title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","publication_status":"published","external_id":{"isi":["000443231000002"],"pmid":["29998472"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"open_access":"1","url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824"}],"citation":{"ista":"Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 330, 254–264.","chicago":"Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles, Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>.","apa":"Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer, E., … Schal, C. (2018). Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>","mla":"Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330, Wiley, 2018, pp. 254–64, doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>.","ieee":"M. Harrison <i>et al.</i>, “Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest,” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330. Wiley, pp. 254–264, 2018.","ama":"Harrison M, Arning N, Kremer L, et al. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. 2018;330:254-264. doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>","short":"M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer, A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264."},"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1002/jez.b.22824","oa_version":"Submitted Version","_id":"190","day":"11","doi":"10.1002/jez.b.22824","article_processing_charge":"No","publist_id":"7730","type":"journal_article","page":"254-264","article_type":"original","isi":1,"month":"07","date_published":"2018-07-11T00:00:00Z","department":[{"_id":"BeVi"}],"date_created":"2018-12-11T11:45:06Z","date_updated":"2023-09-11T13:59:54Z","publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","year":"2018","volume":330,"status":"public","quality_controlled":"1","scopus_import":"1","pmid":1,"intvolume":"       330","author":[{"full_name":"Harrison, Mark","first_name":"Mark","last_name":"Harrison"},{"first_name":"Nicolas","full_name":"Arning, Nicolas","last_name":"Arning"},{"last_name":"Kremer","first_name":"Lucas","full_name":"Kremer, Lucas"},{"full_name":"Ylla, Guillem","first_name":"Guillem","last_name":"Ylla"},{"last_name":"Belles","full_name":"Belles, Xavier","first_name":"Xavier"},{"last_name":"Bornberg Bauer","full_name":"Bornberg Bauer, Erich","first_name":"Erich"},{"last_name":"Huylmans","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K"},{"last_name":"Jongepier","first_name":"Evelien","full_name":"Jongepier, Evelien"},{"last_name":"Puilachs","full_name":"Puilachs, Maria","first_name":"Maria"},{"full_name":"Richards, Stephen","first_name":"Stephen","last_name":"Richards"},{"full_name":"Schal, Coby","first_name":"Coby","last_name":"Schal"}],"oa":1,"abstract":[{"text":"The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control.","lang":"eng"}],"publisher":"Wiley"},{"article_processing_charge":"No","oa_version":"Submitted Version","fulldoi":"https://doi.org/10.1038/s41477-018-0190-1","language":[{"iso":"eng"}],"day":"25","_id":"192","doi":"10.1038/s41477-018-0190-1","page":"453 - 459","article_type":"original","issue":"7","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/"}]},"isi":1,"publist_id":"7728","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","publication_status":"published","external_id":{"isi":["000443221200017"],"pmid":["29942048"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048"}],"citation":{"apa":"Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-018-0190-1\">https://doi.org/10.1038/s41477-018-0190-1</a>","short":"M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.","ama":"Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. <i>Nature Plants</i>. 2018;4(7):453-459. doi:<a href=\"https://doi.org/10.1038/s41477-018-0190-1\">10.1038/s41477-018-0190-1</a>","ieee":"M. Fendrych <i>et al.</i>, “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” <i>Nature Plants</i>, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018.","mla":"Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” <i>Nature Plants</i>, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:<a href=\"https://doi.org/10.1038/s41477-018-0190-1\">10.1038/s41477-018-0190-1</a>.","chicago":"Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” <i>Nature Plants</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0190-1\">https://doi.org/10.1038/s41477-018-0190-1</a>.","ista":"Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459."},"status":"public","quality_controlled":"1","scopus_import":"1","pmid":1,"intvolume":"         4","publication":"Nature Plants","volume":4,"year":"2018","publisher":"Springer Nature","author":[{"id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych"},{"last_name":"Akhmanova","first_name":"Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1522-3162","full_name":"Akhmanova, Maria"},{"last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"last_name":"Glanc","full_name":"Glanc, Matous","first_name":"Matous"},{"full_name":"Hagihara, Shinya","first_name":"Shinya","last_name":"Hagihara"},{"last_name":"Takahashi","full_name":"Takahashi, Koji","first_name":"Koji"},{"full_name":"Uchida, Naoyuki","first_name":"Naoyuki","last_name":"Uchida"},{"first_name":"Keiko U","full_name":"Torii, Keiko U","last_name":"Torii"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml"}],"oa":1,"abstract":[{"lang":"eng","text":"The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway."}],"date_published":"2018-06-25T00:00:00Z","month":"06","date_updated":"2023-09-15T12:11:03Z","department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"date_created":"2018-12-11T11:45:07Z"},{"publisher":"ACM","oa":1,"author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","full_name":"Alwen, Joel F","last_name":"Alwen"},{"last_name":"Gazi","full_name":"Gazi, Peter","first_name":"Peter"},{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg"},{"first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen","last_name":"Klein"},{"last_name":"Osang","full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","orcid":"0000-0002-8882-5116"},{"orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"},{"last_name":"Reyzin","first_name":"Lenoid","full_name":"Reyzin, Lenoid"},{"full_name":"Rolinek, Michal","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","last_name":"Rolinek"},{"last_name":"Rybar","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Rybar, Michal"}],"abstract":[{"text":"We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki'16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block'16] for analyzing the hardware costs of an iMHF.","lang":"eng"}],"scopus_import":"1","status":"public","quality_controlled":"1","year":"2018","publication":"Proceedings of the 2018 on Asia Conference on Computer and Communication Security","date_updated":"2024-11-04T13:52:29Z","department":[{"_id":"KrPi"},{"_id":"HeEd"},{"_id":"VlKo"}],"ec_funded":1,"date_created":"2018-12-11T11:45:07Z","acknowledgement":"Leonid Reyzin was supported in part by IST Austria and by US NSF grants 1012910, 1012798, and 1422965; this research was performed while he was visiting IST Austria.","date_published":"2018-06-01T00:00:00Z","month":"06","page":"51 - 65","isi":1,"type":"conference","publist_id":"7723","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"},{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","day":"01","_id":"193","fulldoi":"https://doi.org/10.1145/3196494.3196534","language":[{"iso":"eng"}],"oa_version":"Submitted Version","doi":"10.1145/3196494.3196534","main_file_link":[{"url":"https://eprint.iacr.org/2016/783","open_access":"1"}],"conference":{"location":"Incheon, Republic of Korea","name":"ASIACCS: Asia Conference on Computer and Communications Security ","end_date":"2018-06-08","start_date":"2018-06-04"},"citation":{"apa":"Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak, K. Z., … Rybar, M. (2018). On the memory hardness of data independent password hashing functions. In <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i> (pp. 51–65). Incheon, Republic of Korea: ACM. <a href=\"https://doi.org/10.1145/3196494.3196534\">https://doi.org/10.1145/3196494.3196534</a>","ieee":"J. F. Alwen <i>et al.</i>, “On the memory hardness of data independent password hashing functions,” in <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, Incheon, Republic of Korea, 2018, pp. 51–65.","mla":"Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password Hashing Functions.” <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, ACM, 2018, pp. 51–65, doi:<a href=\"https://doi.org/10.1145/3196494.3196534\">10.1145/3196494.3196534</a>.","short":"J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak, L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65.","ama":"Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data independent password hashing functions. In: <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>. ACM; 2018:51-65. doi:<a href=\"https://doi.org/10.1145/3196494.3196534\">10.1145/3196494.3196534</a>","ista":"Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password hashing functions. Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ASIACCS: Asia Conference on Computer and Communications Security , 51–65.","chicago":"Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar. “On the Memory Hardness of Data Independent Password Hashing Functions.” In <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, 51–65. ACM, 2018. <a href=\"https://doi.org/10.1145/3196494.3196534\">https://doi.org/10.1145/3196494.3196534</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"On the memory hardness of data independent password hashing functions","external_id":{"isi":["000516620100005"]},"publication_status":"published"}]