[{"has_accepted_license":"1","year":"2019","author":[{"full_name":"Mócsai, Réka","last_name":"Mócsai","first_name":"Réka"},{"full_name":"Figl, Rudolf","last_name":"Figl","first_name":"Rudolf"},{"full_name":"Troschl, Clemens","first_name":"Clemens","last_name":"Troschl"},{"first_name":"Richard","last_name":"Strasser","full_name":"Strasser, Richard"},{"full_name":"Svehla, Elisabeth","last_name":"Svehla","first_name":"Elisabeth"},{"last_name":"Windwarder","first_name":"Markus","full_name":"Windwarder, Markus"},{"full_name":"Thader, Andreas","first_name":"Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Altmann","first_name":"Friedrich","full_name":"Altmann, Friedrich"}],"date_created":"2019-02-03T22:59:13Z","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-24T14:33:16Z","scopus_import":"1","month":"01","date_published":"2019-01-23T00:00:00Z","_id":"5907","publisher":"Nature Publishing Group","citation":{"chicago":"Mócsai, Réka, Rudolf Figl, Clemens Troschl, Richard Strasser, Elisabeth Svehla, Markus Windwarder, Andreas Thader, and Friedrich Altmann. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” <i>Scientific Reports</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41598-018-36884-1\">https://doi.org/10.1038/s41598-018-36884-1</a>.","ama":"Mócsai R, Figl R, Troschl C, et al. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. <i>Scientific Reports</i>. 2019;9(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-36884-1\">10.1038/s41598-018-36884-1</a>","short":"R. Mócsai, R. Figl, C. Troschl, R. Strasser, E. Svehla, M. Windwarder, A. Thader, F. Altmann, Scientific Reports 9 (2019).","apa":"Mócsai, R., Figl, R., Troschl, C., Strasser, R., Svehla, E., Windwarder, M., … Altmann, F. (2019). N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-36884-1\">https://doi.org/10.1038/s41598-018-36884-1</a>","mla":"Mócsai, Réka, et al. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” <i>Scientific Reports</i>, vol. 9, no. 1, 331, Nature Publishing Group, 2019, doi:<a href=\"https://doi.org/10.1038/s41598-018-36884-1\">10.1038/s41598-018-36884-1</a>.","ieee":"R. Mócsai <i>et al.</i>, “N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated,” <i>Scientific Reports</i>, vol. 9, no. 1. Nature Publishing Group, 2019.","ista":"Mócsai R, Figl R, Troschl C, Strasser R, Svehla E, Windwarder M, Thader A, Altmann F. 2019. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 9(1), 331."},"file_date_updated":"2020-07-14T12:47:13Z","abstract":[{"lang":"eng","text":"Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It’s possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins."}],"department":[{"_id":"FlSc"}],"article_processing_charge":"No","isi":1,"issue":"1","type":"journal_article","day":"23","volume":9,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_number":"331","oa_version":"Published Version","status":"public","publication":"Scientific Reports","external_id":{"isi":["000456392400012"]},"ddc":["580"],"quality_controlled":"1","title":"N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated","oa":1,"doi":"10.1038/s41598-018-36884-1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:13Z","file_name":"2019_ScientificReports_Mocsai.pdf","checksum":"4129c7d7663d1f8a1edf8c4232372f66","access_level":"open_access","relation":"main_file","date_created":"2019-02-05T13:10:02Z","file_id":"5923","file_size":2124292,"content_type":"application/pdf"}],"intvolume":"         9"},{"date_updated":"2023-08-24T14:31:09Z","scopus_import":"1","month":"01","date_published":"2019-01-22T00:00:00Z","_id":"5908","publisher":"National Academy of Sciences","abstract":[{"lang":"eng","text":"The interorganelle communication mediated by membrane contact sites (MCSs) is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular exchange of information between organelles and allow them to coordinate responses to changing cellular environments. In plants, the importance of MCS components in the responses to environmental stress has been widely established, but the molecular mechanisms regulating interorganelle connectivity during stress still remain opaque. In this report, we use the model plant Arabidopsis thaliana to show that ionic stress increases endoplasmic reticulum (ER)–plasma membrane (PM) connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched ER–PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton in the regulation of S-EPCS dynamics and ER–PM connectivity, and we identify the accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the PM as a molecular signal associated with the ER–PM connectivity changes. Our study highlights the functional conservation of EPCS components and PM phosphoinositides as modulators of ER–PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal regulation of ER–PM connectivity in plants."}],"citation":{"ista":"Lee E, Vanneste S, Pérez-Sancho J, Benitez-Fuente F, Strelau M, Macho AP, Botella MA, Friml J, Rosado A. 2019. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 116(4), 1420–1429.","ieee":"E. Lee <i>et al.</i>, “Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 116, no. 4. National Academy of Sciences, pp. 1420–1429, 2019.","apa":"Lee, E., Vanneste, S., Pérez-Sancho, J., Benitez-Fuente, F., Strelau, M., Macho, A. P., … Rosado, A. (2019). Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1818099116\">https://doi.org/10.1073/pnas.1818099116</a>","mla":"Lee, Eunkyoung, et al. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1420–29, doi:<a href=\"https://doi.org/10.1073/pnas.1818099116\">10.1073/pnas.1818099116</a>.","chicago":"Lee, Eunkyoung, Steffen Vanneste, Jessica Pérez-Sancho, Francisco Benitez-Fuente, Matthew Strelau, Alberto P. Macho, Miguel A. Botella, Jiří Friml, and Abel Rosado. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1818099116\">https://doi.org/10.1073/pnas.1818099116</a>.","short":"E. Lee, S. Vanneste, J. Pérez-Sancho, F. Benitez-Fuente, M. Strelau, A.P. Macho, M.A. Botella, J. Friml, A. Rosado, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 1420–1429.","ama":"Lee E, Vanneste S, Pérez-Sancho J, et al. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2019;116(4):1420-1429. doi:<a href=\"https://doi.org/10.1073/pnas.1818099116\">10.1073/pnas.1818099116</a>"},"pmid":1,"year":"2019","author":[{"full_name":"Lee, Eunkyoung","last_name":"Lee","first_name":"Eunkyoung"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"first_name":"Jessica","last_name":"Pérez-Sancho","full_name":"Pérez-Sancho, Jessica"},{"last_name":"Benitez-Fuente","first_name":"Francisco","full_name":"Benitez-Fuente, Francisco"},{"first_name":"Matthew","last_name":"Strelau","full_name":"Strelau, Matthew"},{"first_name":"Alberto P.","last_name":"Macho","full_name":"Macho, Alberto P."},{"first_name":"Miguel A.","last_name":"Botella","full_name":"Botella, Miguel A."},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Rosado, Abel","last_name":"Rosado","first_name":"Abel"}],"publication_status":"published","date_created":"2019-02-03T22:59:14Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication":"Proceedings of the National Academy of Sciences of the United States of America","external_id":{"pmid":["30610176"],"isi":["000456336100050"]},"quality_controlled":"1","title":"Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis","oa":1,"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1818099116","open_access":"1"}],"page":"1420-1429","doi":"10.1073/pnas.1818099116","language":[{"iso":"eng"}],"intvolume":"       116","department":[{"_id":"JiFr"}],"issue":"4","isi":1,"article_processing_charge":"No","type":"journal_article","day":"22","volume":116,"oa_version":"Published Version","article_type":"original"},{"abstract":[{"lang":"eng","text":"Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved."}],"citation":{"short":"R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248.","ama":"Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. <i>Trends in Ecology and Evolution</i>. 2019;34(3):239-248. doi:<a href=\"https://doi.org/10.1016/j.tree.2018.12.005\">10.1016/j.tree.2018.12.005</a>","chicago":"Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving Inversions.” <i>Trends in Ecology and Evolution</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.tree.2018.12.005\">https://doi.org/10.1016/j.tree.2018.12.005</a>.","mla":"Faria, Rui, et al. “Evolving Inversions.” <i>Trends in Ecology and Evolution</i>, vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:<a href=\"https://doi.org/10.1016/j.tree.2018.12.005\">10.1016/j.tree.2018.12.005</a>.","apa":"Faria, R., Johannesson, K., Butlin, R. K., &#38; Westram, A. M. (2019). Evolving inversions. <i>Trends in Ecology and Evolution</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tree.2018.12.005\">https://doi.org/10.1016/j.tree.2018.12.005</a>","ieee":"R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,” <i>Trends in Ecology and Evolution</i>, vol. 34, no. 3. Elsevier, pp. 239–248, 2019.","ista":"Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 239–248."},"file_date_updated":"2020-07-14T12:47:13Z","publisher":"Elsevier","ec_funded":1,"date_published":"2019-03-01T00:00:00Z","_id":"5911","month":"03","date_updated":"2023-08-24T14:29:48Z","scopus_import":"1","publication_status":"published","date_created":"2019-02-03T22:59:15Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","has_accepted_license":"1","author":[{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.tree.2018.12.005","intvolume":"        34","file":[{"creator":"cziletti","date_updated":"2020-07-14T12:47:13Z","file_name":"2019_Trends_Evolution_Faria.pdf","checksum":"ef24572d6ebcc1452c067e05410cc4a2","access_level":"open_access","relation":"main_file","date_created":"2020-01-09T10:55:58Z","file_id":"7245","file_size":1946795,"content_type":"application/pdf"}],"title":"Evolving inversions","quality_controlled":"1","page":"239-248","oa":1,"ddc":["570"],"external_id":{"isi":["000459899000013"]},"publication":"Trends in Ecology and Evolution","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["01695347"]},"status":"public","article_type":"original","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"volume":34,"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_processing_charge":"No","isi":1,"issue":"3","day":"01","type":"journal_article","department":[{"_id":"NiBa"}]},{"arxiv":1,"oa_version":"Preprint","volume":863,"article_type":"original","department":[{"_id":"BjHo"}],"day":"25","type":"journal_article","article_processing_charge":"No","isi":1,"page":"386-406","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1902.07931","open_access":"1"}],"title":"Experiments on a jet in a crossflow in the low-velocity-ratio regime","quality_controlled":"1","intvolume":"       863","language":[{"iso":"eng"}],"doi":"10.1017/jfm.2018.974","status":"public","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"publication":"Journal of Fluid Mechanics","external_id":{"isi":["000526029100016"],"arxiv":["1902.07931"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","date_created":"2019-02-10T22:59:15Z","author":[{"orcid":"0000-0003-1740-7635","last_name":"Klotz","first_name":"Lukasz","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","full_name":"Klotz, Lukasz"},{"full_name":"Gumowski, Konrad","last_name":"Gumowski","first_name":"Konrad"},{"last_name":"Wesfreid","first_name":"José Eduardo","full_name":"Wesfreid, José Eduardo"}],"year":"2019","publisher":"Cambridge University Press","citation":{"ieee":"L. Klotz, K. Gumowski, and J. E. Wesfreid, “Experiments on a jet in a crossflow in the low-velocity-ratio regime,” <i>Journal of Fluid Mechanics</i>, vol. 863. Cambridge University Press, pp. 386–406, 2019.","ista":"Klotz L, Gumowski K, Wesfreid JE. 2019. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 863, 386–406.","chicago":"Klotz, Lukasz, Konrad Gumowski, and José Eduardo Wesfreid. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2019. <a href=\"https://doi.org/10.1017/jfm.2018.974\">https://doi.org/10.1017/jfm.2018.974</a>.","short":"L. Klotz, K. Gumowski, J.E. Wesfreid, Journal of Fluid Mechanics 863 (2019) 386–406.","ama":"Klotz L, Gumowski K, Wesfreid JE. Experiments on a jet in a crossflow in the low-velocity-ratio regime. <i>Journal of Fluid Mechanics</i>. 2019;863:386-406. doi:<a href=\"https://doi.org/10.1017/jfm.2018.974\">10.1017/jfm.2018.974</a>","apa":"Klotz, L., Gumowski, K., &#38; Wesfreid, J. E. (2019). Experiments on a jet in a crossflow in the low-velocity-ratio regime. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2018.974\">https://doi.org/10.1017/jfm.2018.974</a>","mla":"Klotz, Lukasz, et al. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” <i>Journal of Fluid Mechanics</i>, vol. 863, Cambridge University Press, 2019, pp. 386–406, doi:<a href=\"https://doi.org/10.1017/jfm.2018.974\">10.1017/jfm.2018.974</a>."},"abstract":[{"text":"The hairpin instability of a jet in a crossflow (JICF) for a low jet-to-crossflow velocity ratio is investigated experimentally for a velocity ratio range of R ∈ (0.14, 0.75) and crossflow Reynolds numbers ReD ∈ (260, 640). From spectral analysis we characterize the Strouhal number and amplitude of the hairpin instability as a function of R and ReD. We demonstrate that the dynamics of the hairpins is well described by the Landau model, and, hence, that the instability occurs through Hopf bifurcation, similarly to other hydrodynamical oscillators such as wake behind different bluff bodies. Using the Landau model, we determine the precise threshold values of hairpin shedding. We also study the spatial dependence of this hydrodynamical instability, which shows a global behaviour.","lang":"eng"}],"month":"03","date_updated":"2023-08-24T14:43:13Z","scopus_import":"1","_id":"5943","ec_funded":1,"date_published":"2019-03-25T00:00:00Z"},{"year":"2019","has_accepted_license":"1","author":[{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat","orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","date_created":"2019-02-10T22:59:15Z","date_published":"2019-01-15T00:00:00Z","_id":"5944","month":"01","scopus_import":"1","date_updated":"2023-08-24T14:43:41Z","citation":{"ista":"Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 9(1), 9.","ieee":"B. Corominas-Murtra, “Thermodynamics of duplication thresholds in synthetic protocell systems,” <i>Life</i>, vol. 9, no. 1. MDPI, 2019.","mla":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” <i>Life</i>, vol. 9, no. 1, 9, MDPI, 2019, doi:<a href=\"https://doi.org/10.3390/life9010009\">10.3390/life9010009</a>.","apa":"Corominas-Murtra, B. (2019). Thermodynamics of duplication thresholds in synthetic protocell systems. <i>Life</i>. MDPI. <a href=\"https://doi.org/10.3390/life9010009\">https://doi.org/10.3390/life9010009</a>","ama":"Corominas-Murtra B. Thermodynamics of duplication thresholds in synthetic protocell systems. <i>Life</i>. 2019;9(1). doi:<a href=\"https://doi.org/10.3390/life9010009\">10.3390/life9010009</a>","short":"B. Corominas-Murtra, Life 9 (2019).","chicago":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” <i>Life</i>. MDPI, 2019. <a href=\"https://doi.org/10.3390/life9010009\">https://doi.org/10.3390/life9010009</a>."},"abstract":[{"lang":"eng","text":"Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract—yet realistic—synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural—and eventually, functional—elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational, and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around ~ 10−13J , which results, in the case of duplication of all the vesicles contained in a liter of emulsion, in an amount of energy around ~ 1kJ . Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it."}],"file_date_updated":"2020-07-14T12:47:13Z","publisher":"MDPI","issue":"1","isi":1,"article_processing_charge":"No","type":"journal_article","day":"15","department":[{"_id":"EdHa"}],"volume":9,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","article_number":"9","ddc":["570"],"publication":"Life","external_id":{"isi":["000464125500001"]},"publication_identifier":{"eissn":["20751729"]},"status":"public","language":[{"iso":"eng"}],"doi":"10.3390/life9010009","intvolume":"         9","file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:13Z","checksum":"7d2322cd96ace41959909b66702d5cf4","file_name":"2019_Life_Corominas.pdf","relation":"main_file","access_level":"open_access","file_id":"5951","date_created":"2019-02-11T10:45:27Z","content_type":"application/pdf","file_size":963454}],"title":"Thermodynamics of duplication thresholds in synthetic protocell systems","quality_controlled":"1","oa":1},{"department":[{"_id":"GaTk"}],"day":"07","type":"journal_article","related_material":{"link":[{"url":"https://ist.ac.at/en/news/cells-find-their-identity-using-a-mathematically-optimal-strategy/","description":"News on IST Homepage","relation":"press_release"}]},"article_processing_charge":"No","issue":"4","isi":1,"oa_version":"Published Version","volume":176,"article_type":"original","status":"public","project":[{"name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF"}],"publication":"Cell","external_id":{"pmid":["30712870"],"isi":["000457969200015"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.01.007","open_access":"1"}],"page":"844-855.e15","quality_controlled":"1","title":"Optimal decoding of cellular identities in a genetic network","intvolume":"       176","doi":"10.1016/j.cell.2019.01.007","language":[{"iso":"eng"}],"pmid":1,"author":[{"last_name":"Petkova","first_name":"Mariela D.","full_name":"Petkova, Mariela D."},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"},{"first_name":"Eric F.","last_name":"Wieschaus","full_name":"Wieschaus, Eric F."},{"full_name":"Gregor, Thomas","last_name":"Gregor","first_name":"Thomas"}],"year":"2019","publication_status":"published","date_created":"2019-02-10T22:59:16Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-24T14:42:47Z","scopus_import":"1","month":"02","_id":"5945","date_published":"2019-02-07T00:00:00Z","publisher":"Cell Press","citation":{"ista":"Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding of cellular identities in a genetic network. Cell. 176(4), 844–855.e15.","ieee":"M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” <i>Cell</i>, vol. 176, no. 4. Cell Press, p. 844–855.e15, 2019.","apa":"Petkova, M. D., Tkačik, G., Bialek, W., Wieschaus, E. F., &#38; Gregor, T. (2019). Optimal decoding of cellular identities in a genetic network. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2019.01.007\">https://doi.org/10.1016/j.cell.2019.01.007</a>","mla":"Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.” <i>Cell</i>, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.01.007\">10.1016/j.cell.2019.01.007</a>.","chicago":"Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus, and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.” <i>Cell</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.01.007\">https://doi.org/10.1016/j.cell.2019.01.007</a>.","short":"M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15.","ama":"Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of cellular identities in a genetic network. <i>Cell</i>. 2019;176(4):844-855.e15. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.01.007\">10.1016/j.cell.2019.01.007</a>"},"abstract":[{"lang":"eng","text":"In developing organisms, spatially prescribed cell identities are thought to be determined by the expression levels of multiple genes. Quantitative tests of this idea, however, require a theoretical framework capable of exposing the rules and precision of cell specification over developmental time. We use the gap gene network in the early fly embryo as an example to show how expression levels of the four gap genes can be jointly decoded into an optimal specification of position with 1% accuracy. The decoder correctly predicts, with no free parameters, the dynamics of pair-rule expression patterns at different developmental time points and in various mutant backgrounds. Precise cellular identities are thus available at the earliest stages of development, contrasting the prevailing view of positional information being slowly refined across successive layers of the patterning network. Our results suggest that developmental enhancers closely approximate a mathematically optimal decoding strategy."}]},{"scopus_import":"1","date_updated":"2023-08-24T14:41:53Z","month":"01","date_published":"2019-01-04T00:00:00Z","_id":"5947","publisher":"ACM","citation":{"apa":"Chatterjee, B., Peri, S., Sa, M., &#38; Singhal, N. (2019). A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In <i>ACM International Conference Proceeding Series</i> (pp. 168–177). Bangalore, India: ACM. <a href=\"https://doi.org/10.1145/3288599.3288617\">https://doi.org/10.1145/3288599.3288617</a>","mla":"Chatterjee, Bapi, et al. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” <i>ACM International Conference Proceeding Series</i>, ACM, 2019, pp. 168–77, doi:<a href=\"https://doi.org/10.1145/3288599.3288617\">10.1145/3288599.3288617</a>.","chicago":"Chatterjee, Bapi, Sathya Peri, Muktikanta Sa, and Nandini Singhal. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” In <i>ACM International Conference Proceeding Series</i>, 168–77. ACM, 2019. <a href=\"https://doi.org/10.1145/3288599.3288617\">https://doi.org/10.1145/3288599.3288617</a>.","ama":"Chatterjee B, Peri S, Sa M, Singhal N. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In: <i>ACM International Conference Proceeding Series</i>. ACM; 2019:168-177. doi:<a href=\"https://doi.org/10.1145/3288599.3288617\">10.1145/3288599.3288617</a>","short":"B. Chatterjee, S. Peri, M. Sa, N. Singhal, in:, ACM International Conference Proceeding Series, ACM, 2019, pp. 168–177.","ista":"Chatterjee B, Peri S, Sa M, Singhal N. 2019. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. ACM International Conference Proceeding Series. ICDCN: Conference on Distributed Computing and Networking, 168–177.","ieee":"B. Chatterjee, S. Peri, M. Sa, and N. Singhal, “A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries,” in <i>ACM International Conference Proceeding Series</i>, Bangalore, India, 2019, pp. 168–177."},"abstract":[{"lang":"eng","text":"Graph algorithms applied in many applications, including social networks, communication networks, VLSI design, graphics, and several others, require dynamic modifications - addition and removal of vertices and/or edges - in the graph. This paper presents a novel concurrent non-blocking algorithm to implement a dynamic unbounded directed graph in a shared-memory machine. The addition and removal operations of vertices and edges are lock-free. For a finite sized graph, the lookup operations are wait-free. Most significant component of the presented algorithm is the reachability query in a concurrent graph. The reachability queries in our algorithm are obstruction-free and thus impose minimal additional synchronization cost over other operations. We prove that each of the data structure operations are linearizable. We extensively evaluate a sample C/C++ implementation of the algorithm through a number of micro-benchmarks. The experimental results show that the proposed algorithm scales well with the number of threads and on an average provides 5 to 7x performance improvement over a concurrent graph implementation using coarse-grained locking."}],"year":"2019","author":[{"first_name":"Bapi","orcid":"0000-0002-2742-4028","last_name":"Chatterjee","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Bapi"},{"first_name":"Sathya","last_name":"Peri","full_name":"Peri, Sathya"},{"first_name":"Muktikanta","last_name":"Sa","full_name":"Sa, Muktikanta"},{"full_name":"Singhal, Nandini","last_name":"Singhal","first_name":"Nandini"}],"date_created":"2019-02-10T22:59:17Z","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"isbn":["978-1-4503-6094-4 "]},"status":"public","publication":"ACM International Conference Proceeding Series","external_id":{"isi":["000484491600019"],"arxiv":["1809.00896"]},"quality_controlled":"1","title":"A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries","main_file_link":[{"url":"https://arxiv.org/abs/1809.00896","open_access":"1"}],"oa":1,"page":"168-177","doi":"10.1145/3288599.3288617","language":[{"iso":"eng"}],"department":[{"_id":"DaAl"}],"isi":1,"article_processing_charge":"No","conference":{"location":"Bangalore, India","name":"ICDCN: Conference on Distributed Computing and Networking","end_date":"2019-01-07","start_date":"2019-01-04"},"type":"conference","day":"04","oa_version":"Preprint","arxiv":1},{"date_updated":"2025-06-02T08:53:41Z","scopus_import":"1","month":"01","date_published":"2019-01-11T00:00:00Z","_id":"5948","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"We study the termination problem for nondeterministic probabilistic programs. We consider the bounded termination problem that asks whether the supremum of the expected termination time over all schedulers is bounded. First, we show that ranking supermartingales (RSMs) are both sound and complete for proving bounded termination over nondeterministic probabilistic programs. For nondeterministic probabilistic programs a previous result claimed that RSMs are not complete for bounded termination, whereas our result corrects the previous flaw and establishes completeness with a rigorous proof. Second, we present the first sound approach to establish lower bounds on expected termination time through RSMs."}],"citation":{"chicago":"Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” In <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>, 11388:468–90. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">https://doi.org/10.1007/978-3-030-11245-5_22</a>.","short":"H. Fu, K. Chatterjee, in:, International Conference on Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2019, pp. 468–490.","ama":"Fu H, Chatterjee K. Termination of nondeterministic probabilistic programs. In: <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>. Vol 11388. Springer Nature; 2019:468-490. doi:<a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">10.1007/978-3-030-11245-5_22</a>","apa":"Fu, H., &#38; Chatterjee, K. (2019). Termination of nondeterministic probabilistic programs. In <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i> (Vol. 11388, pp. 468–490). Cascais, Portugal: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">https://doi.org/10.1007/978-3-030-11245-5_22</a>","mla":"Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>, vol. 11388, Springer Nature, 2019, pp. 468–90, doi:<a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">10.1007/978-3-030-11245-5_22</a>.","ieee":"H. Fu and K. Chatterjee, “Termination of nondeterministic probabilistic programs,” in <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>, Cascais, Portugal, 2019, vol. 11388, pp. 468–490.","ista":"Fu H, Chatterjee K. 2019. Termination of nondeterministic probabilistic programs. International Conference on Verification, Model Checking, and Abstract Interpretation. VMCAI: Verification, Model Checking, and Abstract Interpretation, LNCS, vol. 11388, 468–490."},"year":"2019","author":[{"full_name":"Fu, Hongfei","first_name":"Hongfei","last_name":"Fu"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","date_created":"2019-02-10T22:59:17Z","project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"status":"public","external_id":{"isi":["000931943000022"],"arxiv":["1701.02944"]},"publication":"International Conference on Verification, Model Checking, and Abstract Interpretation","quality_controlled":"1","title":"Termination of nondeterministic probabilistic programs","main_file_link":[{"url":"https://arxiv.org/abs/1701.02944"}],"page":"468-490","doi":"10.1007/978-3-030-11245-5_22","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"intvolume":"     11388","department":[{"_id":"KrCh"}],"isi":1,"article_processing_charge":"No","conference":{"start_date":"2019-01-13","location":"Cascais, Portugal","name":"VMCAI: Verification, Model Checking, and Abstract Interpretation","end_date":"2019-01-15"},"day":"11","type":"conference","volume":11388,"arxiv":1,"oa_version":"Preprint"},{"ddc":["570"],"external_id":{"isi":["000480635400003"]},"publication":"Hippocampus","project":[{"call_identifier":"FP7","grant_number":"607616","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","name":"Inter-and intracellular signalling in schizophrenia"}],"status":"public","language":[{"iso":"eng"}],"doi":"10.1002/hipo.23076","intvolume":"        29","file":[{"date_updated":"2020-07-14T12:47:13Z","creator":"dernst","date_created":"2019-02-11T10:42:51Z","file_id":"5950","file_size":2132893,"content_type":"application/pdf","file_name":"2019_Hippocampus_Kaefer.pdf","checksum":"5e8de271ca04aef92a5de42d6aac4404","access_level":"open_access","relation":"main_file"}],"title":"Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization","quality_controlled":"1","page":"802-816","oa":1,"article_processing_charge":"Yes (via OA deal)","issue":"9","isi":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6825"}]},"type":"journal_article","day":"01","department":[{"_id":"JoCs"}],"article_type":"original","volume":29,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"date_published":"2019-09-01T00:00:00Z","_id":"5949","month":"09","date_updated":"2024-03-25T23:30:11Z","scopus_import":"1","file_date_updated":"2020-07-14T12:47:13Z","abstract":[{"lang":"eng","text":"Aberrant proteostasis of protein aggregation may lead to behavior disorders including chronic mental illnesses (CMI). Furthermore, the neuronal activity alterations that underlie CMI are not well understood. We recorded the local field potential and single-unit activity of the hippocampal CA1 region in vivo in rats transgenically overexpressing the Disrupted-in-Schizophrenia 1 (DISC1) gene (tgDISC1), modeling sporadic CMI. These tgDISC1 rats have previously been shown to exhibit DISC1 protein aggregation, disturbances in the dopaminergic system and attention-related deficits. Recordings were performed during exploration of familiar and novel open field environments and during sleep, allowing investigation of neuronal abnormalities in unconstrained behavior. Compared to controls, tgDISC1 place cells exhibited smaller place fields and decreased speed-modulation of their firing rates, demonstrating altered spatial coding and deficits in encoding location-independent sensory inputs. Oscillation analyses showed that tgDISC1 pyramidal neurons had higher theta phase locking strength during novelty, limiting their phase coding ability. However, their mean theta phases were more variable at the population level, reducing oscillatory network synchronization. Finally, tgDISC1 pyramidal neurons showed a lack of novelty-induced shift in their preferred theta and gamma firing phases, indicating deficits in coding of novel environments with oscillatory firing. By combining single cell and neuronal population analyses, we link DISC1 protein pathology with abnormal hippocampal neural coding and network synchrony, and thereby gain a more comprehensive understanding of CMI mechanisms."}],"citation":{"mla":"Käfer, Karola, et al. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” <i>Hippocampus</i>, vol. 29, no. 9, Wiley, 2019, pp. 802–16, doi:<a href=\"https://doi.org/10.1002/hipo.23076\">10.1002/hipo.23076</a>.","apa":"Käfer, K., Malagon-Vina, H., Dickerson, D., O’Neill, J., Trossbach, S. V., Korth, C., &#38; Csicsvari, J. L. (2019). Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. <i>Hippocampus</i>. Wiley. <a href=\"https://doi.org/10.1002/hipo.23076\">https://doi.org/10.1002/hipo.23076</a>","short":"K. Käfer, H. Malagon-Vina, D. Dickerson, J. O’Neill, S.V. Trossbach, C. Korth, J.L. Csicsvari, Hippocampus 29 (2019) 802–816.","ama":"Käfer K, Malagon-Vina H, Dickerson D, et al. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. <i>Hippocampus</i>. 2019;29(9):802-816. doi:<a href=\"https://doi.org/10.1002/hipo.23076\">10.1002/hipo.23076</a>","chicago":"Käfer, Karola, Hugo Malagon-Vina, Desiree Dickerson, Joseph O’Neill, Svenja V. Trossbach, Carsten Korth, and Jozsef L Csicsvari. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” <i>Hippocampus</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/hipo.23076\">https://doi.org/10.1002/hipo.23076</a>.","ista":"Käfer K, Malagon-Vina H, Dickerson D, O’Neill J, Trossbach SV, Korth C, Csicsvari JL. 2019. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. 29(9), 802–816.","ieee":"K. Käfer <i>et al.</i>, “Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization,” <i>Hippocampus</i>, vol. 29, no. 9. Wiley, pp. 802–816, 2019."},"publisher":"Wiley","year":"2019","has_accepted_license":"1","author":[{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","last_name":"Käfer","first_name":"Karola","full_name":"Käfer, Karola"},{"full_name":"Malagon-Vina, Hugo","last_name":"Malagon-Vina","first_name":"Hugo"},{"full_name":"Dickerson, Desiree","id":"444EB89E-F248-11E8-B48F-1D18A9856A87","first_name":"Desiree","last_name":"Dickerson"},{"first_name":"Joseph","last_name":"O'Neill","full_name":"O'Neill, Joseph"},{"last_name":"Trossbach","first_name":"Svenja V.","full_name":"Trossbach, Svenja V."},{"full_name":"Korth, Carsten","first_name":"Carsten","last_name":"Korth"},{"orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L"}],"date_created":"2019-02-10T22:59:18Z","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"intvolume":"        61","file":[{"file_size":556276,"content_type":"application/pdf","date_created":"2019-02-14T11:57:22Z","file_id":"5988","relation":"main_file","access_level":"open_access","checksum":"e1bff88f1d77001b53b78c485ce048d7","file_name":"2018_DiscreteGeometry_Lubiw.pdf","date_updated":"2020-07-14T12:47:14Z","creator":"dernst"}],"language":[{"iso":"eng"}],"doi":"10.1007/s00454-018-0035-8","page":"880-898","oa":1,"title":"A proof of the orbit conjecture for flipping edge-labelled triangulations","quality_controlled":"1","ddc":["000"],"publication":"Discrete & Computational Geometry","external_id":{"arxiv":["1710.02741"],"isi":["000466130000009"]},"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"status":"public","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"article_type":"original","oa_version":"Published Version","arxiv":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":61,"type":"journal_article","day":"01","isi":1,"issue":"4","article_processing_charge":"Yes (via OA deal)","related_material":{"record":[{"relation":"earlier_version","id":"683","status":"public"},{"status":"public","relation":"dissertation_contains","id":"7944"}]},"department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:47:14Z","citation":{"ista":"Lubiw A, Masárová Z, Wagner U. 2019. A proof of the orbit conjecture for flipping edge-labelled triangulations. Discrete &#38; Computational Geometry. 61(4), 880–898.","ieee":"A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for flipping edge-labelled triangulations,” <i>Discrete &#38; Computational Geometry</i>, vol. 61, no. 4. Springer Nature, pp. 880–898, 2019.","apa":"Lubiw, A., Masárová, Z., &#38; Wagner, U. (2019). A proof of the orbit conjecture for flipping edge-labelled triangulations. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-018-0035-8\">https://doi.org/10.1007/s00454-018-0035-8</a>","mla":"Lubiw, Anna, et al. “A Proof of the Orbit Conjecture for Flipping Edge-Labelled Triangulations.” <i>Discrete &#38; Computational Geometry</i>, vol. 61, no. 4, Springer Nature, 2019, pp. 880–98, doi:<a href=\"https://doi.org/10.1007/s00454-018-0035-8\">10.1007/s00454-018-0035-8</a>.","chicago":"Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture for Flipping Edge-Labelled Triangulations.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s00454-018-0035-8\">https://doi.org/10.1007/s00454-018-0035-8</a>.","ama":"Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping edge-labelled triangulations. <i>Discrete &#38; Computational Geometry</i>. 2019;61(4):880-898. doi:<a href=\"https://doi.org/10.1007/s00454-018-0035-8\">10.1007/s00454-018-0035-8</a>","short":"A. Lubiw, Z. Masárová, U. Wagner, Discrete &#38; Computational Geometry 61 (2019) 880–898."},"abstract":[{"lang":"eng","text":"Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm (with 𝑂(𝑛8) being a crude bound on the run-time) to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of 𝑂(𝑛7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture."}],"publisher":"Springer Nature","_id":"5986","date_published":"2019-06-01T00:00:00Z","month":"06","scopus_import":"1","date_updated":"2023-09-07T13:17:36Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","date_created":"2019-02-14T11:54:08Z","author":[{"first_name":"Anna","last_name":"Lubiw","full_name":"Lubiw, Anna"},{"orcid":"0000-0002-6660-1322","first_name":"Zuzana","last_name":"Masárová","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","full_name":"Masárová, Zuzana"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"year":"2019","has_accepted_license":"1"},{"department":[{"_id":"BjHo"}],"isi":1,"article_processing_charge":"No","day":"08","type":"journal_article","volume":10,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"arxiv":1,"oa_version":"Published Version","article_number":"652","article_type":"original","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"status":"public","publication_identifier":{"issn":["2041-1723"]},"ddc":["530"],"external_id":{"isi":["000458175300001"],"arxiv":["1902.03763"]},"publication":"Nature Communications","title":"Elastic alfven waves in elastic turbulence","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-08551-0","intvolume":"        10","file":[{"file_name":"2019_NatureComm_Varshney.pdf","checksum":"d3acf07eaad95ec040d8e8565fc9ac37","access_level":"open_access","relation":"main_file","file_id":"6015","date_created":"2019-02-15T07:15:00Z","file_size":1331490,"content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:47:17Z"}],"year":"2019","has_accepted_license":"1","author":[{"full_name":"Varshney, Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999","first_name":"Atul","last_name":"Varshney"},{"full_name":"Steinberg, Victor","last_name":"Steinberg","first_name":"Victor"}],"publication_status":"published","date_created":"2019-02-15T07:10:46Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"02","scopus_import":"1","date_updated":"2023-09-08T11:39:54Z","ec_funded":1,"date_published":"2019-02-08T00:00:00Z","_id":"6014","publisher":"Springer Nature","file_date_updated":"2020-07-14T12:47:17Z","abstract":[{"lang":"eng","text":"Speed of sound waves in gases and liquids are governed by the compressibility of the medium. There exists another type of non-dispersive wave where the wave speed depends on stress instead of elasticity of the medium. A well-known example is the Alfven wave, which propagates through plasma permeated by a magnetic field with the speed determined by magnetic tension. An elastic analogue of Alfven waves has been predicted in a flow of dilute polymer solution where the elastic stress of the stretching polymers determines the elastic wave speed. Here we present quantitative evidence of elastic Alfven waves in elastic turbulence of a viscoelastic creeping flow between two obstacles in channel flow. The key finding in the experimental proof is a nonlinear dependence of the elastic wave speed cel on the Weissenberg number Wi, which deviates from predictions based on a model of linear polymer elasticity."}],"citation":{"chicago":"Varshney, Atul, and Victor Steinberg. “Elastic Alfven Waves in Elastic Turbulence.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-08551-0\">https://doi.org/10.1038/s41467-019-08551-0</a>.","ama":"Varshney A, Steinberg V. Elastic alfven waves in elastic turbulence. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-08551-0\">10.1038/s41467-019-08551-0</a>","short":"A. Varshney, V. Steinberg, Nature Communications 10 (2019).","apa":"Varshney, A., &#38; Steinberg, V. (2019). Elastic alfven waves in elastic turbulence. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-08551-0\">https://doi.org/10.1038/s41467-019-08551-0</a>","mla":"Varshney, Atul, and Victor Steinberg. “Elastic Alfven Waves in Elastic Turbulence.” <i>Nature Communications</i>, vol. 10, 652, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-08551-0\">10.1038/s41467-019-08551-0</a>.","ieee":"A. Varshney and V. Steinberg, “Elastic alfven waves in elastic turbulence,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019.","ista":"Varshney A, Steinberg V. 2019. Elastic alfven waves in elastic turbulence. Nature Communications. 10, 652."}},{"oa_version":"Published Version","article_number":"e2005902","license":"https://creativecommons.org/publicdomain/zero/1.0/","volume":17,"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"department":[{"_id":"NiBa"}],"day":"07","type":"journal_article","isi":1,"issue":"2","article_processing_charge":"No","related_material":{"record":[{"id":"9801","relation":"research_data","status":"public"}]},"oa":1,"title":"Genetic dissection of assortative mating behavior","quality_controlled":"1","intvolume":"        17","file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:17Z","file_name":"2019_PLOS_Merrill.pdf","checksum":"5f34001617ee729314ca520c049b1112","access_level":"open_access","relation":"main_file","date_created":"2019-02-18T14:57:24Z","file_id":"6036","file_size":2005949,"content_type":"application/pdf"}],"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2005902","status":"public","ddc":["570"],"publication":"PLoS Biology","external_id":{"isi":["000460317100001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","date_created":"2019-02-17T22:59:21Z","author":[{"full_name":"Merrill, Richard M.","first_name":"Richard M.","last_name":"Merrill"},{"full_name":"Rastas, Pasi","first_name":"Pasi","last_name":"Rastas"},{"last_name":"Martin","first_name":"Simon H.","full_name":"Martin, Simon H."},{"full_name":"Melo Hurtado, Maria C","last_name":"Melo Hurtado","first_name":"Maria C","id":"386D7308-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barker","first_name":"Sarah","full_name":"Barker, Sarah"},{"full_name":"Davey, John","first_name":"John","last_name":"Davey"},{"full_name":"Mcmillan, W. Owen","first_name":"W. Owen","last_name":"Mcmillan"},{"first_name":"Chris D.","last_name":"Jiggins","full_name":"Jiggins, Chris D."}],"year":"2019","has_accepted_license":"1","publisher":"Public Library of Science","citation":{"ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Genetic dissection of assortative mating behavior. PLoS Biology. 17(2), e2005902.","ieee":"R. M. Merrill <i>et al.</i>, “Genetic dissection of assortative mating behavior,” <i>PLoS Biology</i>, vol. 17, no. 2. Public Library of Science, 2019.","mla":"Merrill, Richard M., et al. “Genetic Dissection of Assortative Mating Behavior.” <i>PLoS Biology</i>, vol. 17, no. 2, e2005902, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005902\">10.1371/journal.pbio.2005902</a>.","apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Genetic dissection of assortative mating behavior. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005902\">https://doi.org/10.1371/journal.pbio.2005902</a>","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, PLoS Biology 17 (2019).","ama":"Merrill RM, Rastas P, Martin SH, et al. Genetic dissection of assortative mating behavior. <i>PLoS Biology</i>. 2019;17(2). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005902\">10.1371/journal.pbio.2005902</a>","chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Genetic Dissection of Assortative Mating Behavior.” <i>PLoS Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pbio.2005902\">https://doi.org/10.1371/journal.pbio.2005902</a>."},"abstract":[{"lang":"eng","text":"The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution or more generally about the genetic basis for assortative mating behaviors. Both tight physical linkage and the existence of large-effect preference loci will strengthen genetic associations between behavioral and ecological barriers, promoting the evolution of assortative mating. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of nonmimetic hybrids and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. We identify three QTLs that together explain a large proportion (approximately 60%) of the difference in preference behavior observed between the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM) from the major color pattern gene optix, and, individually, all three have a large effect on the preference phenotype. Genomic divergence between H. cydno and H. melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix color pattern locus but not the other preference QTLs. The simple genetic architecture we reveal will facilitate the evolution and maintenance of new species despite ongoing gene flow by coupling behavioral and ecological aspects of reproductive isolation."}],"file_date_updated":"2020-07-14T12:47:17Z","month":"02","scopus_import":"1","date_updated":"2023-08-24T14:46:23Z","_id":"6022","date_published":"2019-02-07T00:00:00Z"},{"status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"external_id":{"isi":["000460479600014"]},"publication":"Nature Plants","page":"160-166","oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/479113v1.abstract","open_access":"1"}],"title":"A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis","quality_controlled":"1","intvolume":"         5","language":[{"iso":"eng"}],"doi":"10.1038/s41477-019-0363-6","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"type":"journal_article","day":"08","issue":"2","article_processing_charge":"No","isi":1,"oa_version":"Submitted Version","volume":5,"month":"02","date_updated":"2023-08-24T14:46:47Z","scopus_import":"1","_id":"6023","ec_funded":1,"date_published":"2019-02-08T00:00:00Z","publisher":"Springer Nature","citation":{"apa":"Yoshida, S., Van Der Schuren, A., Van Dop, M., Van Galen, L., Saiga, S., Adibi, M., … Weijers, D. (2019). A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-019-0363-6\">https://doi.org/10.1038/s41477-019-0363-6</a>","mla":"Yoshida, Saiko, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” <i>Nature Plants</i>, vol. 5, no. 2, Springer Nature, 2019, pp. 160–66, doi:<a href=\"https://doi.org/10.1038/s41477-019-0363-6\">10.1038/s41477-019-0363-6</a>.","chicago":"Yoshida, Saiko, Alja Van Der Schuren, Maritza Van Dop, Luc Van Galen, Shunsuke Saiga, Milad Adibi, Barbara Möller, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” <i>Nature Plants</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41477-019-0363-6\">https://doi.org/10.1038/s41477-019-0363-6</a>.","ama":"Yoshida S, Van Der Schuren A, Van Dop M, et al. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. <i>Nature Plants</i>. 2019;5(2):160-166. doi:<a href=\"https://doi.org/10.1038/s41477-019-0363-6\">10.1038/s41477-019-0363-6</a>","short":"S. Yoshida, A. Van Der Schuren, M. Van Dop, L. Van Galen, S. Saiga, M. Adibi, B. Möller, C.A. Ten Hove, P. Marhavý, R. Smith, J. Friml, D. Weijers, Nature Plants 5 (2019) 160–166.","ista":"Yoshida S, Van Der Schuren A, Van Dop M, Van Galen L, Saiga S, Adibi M, Möller B, Ten Hove CA, Marhavý P, Smith R, Friml J, Weijers D. 2019. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 5(2), 160–166.","ieee":"S. Yoshida <i>et al.</i>, “A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis,” <i>Nature Plants</i>, vol. 5, no. 2. Springer Nature, pp. 160–166, 2019."},"abstract":[{"lang":"eng","text":"Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division 1–3 . In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain."}],"author":[{"full_name":"Yoshida, Saiko","first_name":"Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van Der Schuren, Alja","first_name":"Alja","last_name":"Van Der Schuren"},{"full_name":"Van Dop, Maritza","last_name":"Van Dop","first_name":"Maritza"},{"last_name":"Van Galen","first_name":"Luc","full_name":"Van Galen, Luc"},{"full_name":"Saiga, Shunsuke","first_name":"Shunsuke","last_name":"Saiga"},{"last_name":"Adibi","first_name":"Milad","full_name":"Adibi, Milad"},{"full_name":"Möller, Barbara","first_name":"Barbara","last_name":"Möller"},{"full_name":"Ten Hove, Colette A.","first_name":"Colette A.","last_name":"Ten Hove"},{"full_name":"Marhavy, Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavy","first_name":"Peter","orcid":"0000-0001-5227-5741"},{"full_name":"Smith, Richard","last_name":"Smith","first_name":"Richard"},{"full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"}],"year":"2019","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-02-17T22:59:21Z"},{"project":[{"call_identifier":"H2020","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"status":"public","ddc":["570"],"external_id":{"isi":["000458025300001"]},"publication":"eLife","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"title":"Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.42093","intvolume":"         8","file":[{"file_size":5500707,"content_type":"application/pdf","date_created":"2019-02-18T15:17:21Z","file_id":"6041","access_level":"open_access","relation":"main_file","file_name":"2019_elife_Capek.pdf","checksum":"6cb4ca6d4aa96f6f187a5983aa3e660a","date_updated":"2020-07-14T12:47:17Z","creator":"dernst"}],"department":[{"_id":"CaHe"},{"_id":"HaJa"}],"isi":1,"article_processing_charge":"No","day":"06","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":8,"oa_version":"Published Version","article_number":"e42093","month":"02","scopus_import":"1","date_updated":"2023-08-24T14:46:01Z","ec_funded":1,"date_published":"2019-02-06T00:00:00Z","_id":"6025","publisher":"eLife Sciences Publications","file_date_updated":"2020-07-14T12:47:17Z","abstract":[{"text":"Non-canonical Wnt signaling plays a central role for coordinated cell polarization and directed migration in metazoan development. While spatiotemporally restricted activation of non-canonical Wnt-signaling drives cell polarization in epithelial tissues, it remains unclear whether such instructive activity is also critical for directed mesenchymal cell migration. Here, we developed a light-activated version of the non-canonical Wnt receptor Frizzled 7 (Fz7) to analyze how restricted activation of non-canonical Wnt signaling affects directed anterior axial mesendoderm (prechordal plate, ppl) cell migration within the zebrafish gastrula. We found that Fz7 signaling is required for ppl cell protrusion formation and migration and that spatiotemporally restricted ectopic activation is capable of redirecting their migration. Finally, we show that uniform activation of Fz7 signaling in ppl cells fully rescues defective directed cell migration in fz7 mutant embryos. Together, our findings reveal that in contrast to the situation in epithelial cells, non-canonical Wnt signaling functions permissively rather than instructively in directed mesenchymal cell migration during gastrulation.","lang":"eng"}],"citation":{"mla":"Capek, Daniel, et al. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” <i>ELife</i>, vol. 8, e42093, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.42093\">10.7554/eLife.42093</a>.","apa":"Capek, D., Smutny, M., Tichy, A. M., Morri, M., Janovjak, H. L., &#38; Heisenberg, C.-P. J. (2019). Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.42093\">https://doi.org/10.7554/eLife.42093</a>","ama":"Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.42093\">10.7554/eLife.42093</a>","short":"D. Capek, M. Smutny, A.M. Tichy, M. Morri, H.L. Janovjak, C.-P.J. Heisenberg, ELife 8 (2019).","chicago":"Capek, Daniel, Michael Smutny, Alexandra Madelaine Tichy, Maurizio Morri, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.42093\">https://doi.org/10.7554/eLife.42093</a>.","ista":"Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. 2019. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. eLife. 8, e42093.","ieee":"D. Capek, M. Smutny, A. M. Tichy, M. Morri, H. L. Janovjak, and C.-P. J. Heisenberg, “Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019."},"year":"2019","has_accepted_license":"1","author":[{"first_name":"Daniel","last_name":"Capek","orcid":"0000-0001-5199-9940","id":"31C42484-F248-11E8-B48F-1D18A9856A87","full_name":"Capek, Daniel"},{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5920-9090","last_name":"Smutny","first_name":"Michael","full_name":"Smutny, Michael"},{"last_name":"Tichy","first_name":"Alexandra Madelaine","full_name":"Tichy, Alexandra Madelaine"},{"full_name":"Morri, Maurizio","first_name":"Maurizio","last_name":"Morri","id":"4863116E-F248-11E8-B48F-1D18A9856A87"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","full_name":"Janovjak, Harald L"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-02-17T22:59:22Z","publication_status":"published"},{"file":[{"creator":"kschuh","date_updated":"2020-07-14T12:47:17Z","relation":"main_file","access_level":"open_access","checksum":"09aec427eb48c0f96a1cce9ff53f013b","file_name":"2019_Wiley_Gerencser.pdf","file_size":381350,"content_type":"application/pdf","date_created":"2020-01-07T13:25:55Z","file_id":"7237"}],"intvolume":"        72","doi":"10.1002/cpa.21816","language":[{"iso":"eng"}],"oa":1,"page":"1983-2005","quality_controlled":"1","title":"A solution theory for quasilinear singular SPDEs","external_id":{"isi":["000475465000003"]},"publication":"Communications on Pure and Applied Mathematics","ddc":["500"],"status":"public","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":72,"day":"08","type":"journal_article","isi":1,"article_processing_charge":"Yes (via OA deal)","issue":"9","department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:47:17Z","abstract":[{"lang":"eng","text":"We give a construction allowing us to build local renormalized solutions to general quasilinear stochastic PDEs within the theory of regularity structures, thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking, our construction covers quasilinear variants of all classes of equations for which the general construction of [3, 4, 7] applies, including in particular one‐dimensional systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less singular and more specific case, we furthermore show that the counterterms introduced by the renormalization procedure are given by local functionals of the solution. The main feature of our construction is that it allows exploitation of a number of existing results developed for the semilinear case, so that the number of additional arguments it requires is relatively small."}],"citation":{"ista":"Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 72(9), 1983–2005.","ieee":"M. Gerencser and M. Hairer, “A solution theory for quasilinear singular SPDEs,” <i>Communications on Pure and Applied Mathematics</i>, vol. 72, no. 9. Wiley, pp. 1983–2005, 2019.","apa":"Gerencser, M., &#38; Hairer, M. (2019). A solution theory for quasilinear singular SPDEs. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21816\">https://doi.org/10.1002/cpa.21816</a>","mla":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” <i>Communications on Pure and Applied Mathematics</i>, vol. 72, no. 9, Wiley, 2019, pp. 1983–2005, doi:<a href=\"https://doi.org/10.1002/cpa.21816\">10.1002/cpa.21816</a>.","chicago":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/cpa.21816\">https://doi.org/10.1002/cpa.21816</a>.","ama":"Gerencser M, Hairer M. A solution theory for quasilinear singular SPDEs. <i>Communications on Pure and Applied Mathematics</i>. 2019;72(9):1983-2005. doi:<a href=\"https://doi.org/10.1002/cpa.21816\">10.1002/cpa.21816</a>","short":"M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72 (2019) 1983–2005."},"publisher":"Wiley","_id":"6028","date_published":"2019-02-08T00:00:00Z","scopus_import":"1","date_updated":"2023-08-24T14:44:31Z","month":"02","date_created":"2019-02-17T22:59:24Z","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Gerencser, Mate","last_name":"Gerencser","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hairer, Martin","last_name":"Hairer","first_name":"Martin"}],"has_accepted_license":"1","year":"2019"},{"abstract":[{"text":"Protein micropatterning has become an important tool for many biomedical applications as well as in academic research. Current techniques that allow to reduce the feature size of patterns below 1 μm are, however, often costly and require sophisticated equipment. We present here a straightforward and convenient method to generate highly condensed nanopatterns of proteins without the need for clean room facilities or expensive equipment. Our approach is based on nanocontact printing and allows for the fabrication of protein patterns with feature sizes of 80 nm and periodicities down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane) (X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle, different proteins at various scales were printed and the pattern quality was evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:17Z","citation":{"ieee":"M. Lindner <i>et al.</i>, “A fast and simple contact printing approach to generate 2D protein nanopatterns,” <i>Frontiers in Chemistry</i>, vol. 6. Frontiers Media S.A., 2019.","ista":"Lindner M, Tresztenyak A, Fülöp G, Jahr W, Prinz A, Prinz I, Danzl JG, Schütz GJ, Sevcsik E. 2019. A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 6, 655.","short":"M. Lindner, A. Tresztenyak, G. Fülöp, W. Jahr, A. Prinz, I. Prinz, J.G. Danzl, G.J. Schütz, E. Sevcsik, Frontiers in Chemistry 6 (2019).","ama":"Lindner M, Tresztenyak A, Fülöp G, et al. A fast and simple contact printing approach to generate 2D protein nanopatterns. <i>Frontiers in Chemistry</i>. 2019;6. doi:<a href=\"https://doi.org/10.3389/fchem.2018.00655\">10.3389/fchem.2018.00655</a>","chicago":"Lindner, Marco, Aliz Tresztenyak, Gergö Fülöp, Wiebke Jahr, Adrian Prinz, Iris Prinz, Johann G Danzl, Gerhard J. Schütz, and Eva Sevcsik. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” <i>Frontiers in Chemistry</i>. Frontiers Media S.A., 2019. <a href=\"https://doi.org/10.3389/fchem.2018.00655\">https://doi.org/10.3389/fchem.2018.00655</a>.","mla":"Lindner, Marco, et al. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” <i>Frontiers in Chemistry</i>, vol. 6, 655, Frontiers Media S.A., 2019, doi:<a href=\"https://doi.org/10.3389/fchem.2018.00655\">10.3389/fchem.2018.00655</a>.","apa":"Lindner, M., Tresztenyak, A., Fülöp, G., Jahr, W., Prinz, A., Prinz, I., … Sevcsik, E. (2019). A fast and simple contact printing approach to generate 2D protein nanopatterns. <i>Frontiers in Chemistry</i>. Frontiers Media S.A. <a href=\"https://doi.org/10.3389/fchem.2018.00655\">https://doi.org/10.3389/fchem.2018.00655</a>"},"publisher":"Frontiers Media S.A.","_id":"6029","date_published":"2019-01-24T00:00:00Z","scopus_import":"1","date_updated":"2023-08-24T14:45:38Z","month":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","date_created":"2019-02-17T22:59:24Z","author":[{"first_name":"Marco","last_name":"Lindner","full_name":"Lindner, Marco"},{"first_name":"Aliz","last_name":"Tresztenyak","full_name":"Tresztenyak, Aliz"},{"full_name":"Fülöp, Gergö","first_name":"Gergö","last_name":"Fülöp"},{"full_name":"Jahr, Wiebke","first_name":"Wiebke","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Prinz, Adrian","first_name":"Adrian","last_name":"Prinz"},{"full_name":"Prinz, Iris","first_name":"Iris","last_name":"Prinz"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G"},{"full_name":"Schütz, Gerhard J.","last_name":"Schütz","first_name":"Gerhard J."},{"last_name":"Sevcsik","first_name":"Eva","full_name":"Sevcsik, Eva"}],"has_accepted_license":"1","year":"2019","file":[{"content_type":"application/pdf","file_size":1766820,"date_created":"2019-02-18T15:10:34Z","file_id":"6039","relation":"main_file","access_level":"open_access","checksum":"7841301d7c53b56ef873791b4b6f7b24","file_name":"2019_frontiers_Lindner.pdf","date_updated":"2020-07-14T12:47:17Z","creator":"dernst"}],"intvolume":"         6","doi":"10.3389/fchem.2018.00655","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","title":"A fast and simple contact printing approach to generate 2D protein nanopatterns","external_id":{"isi":["000456718000001"]},"publication":"Frontiers in Chemistry","ddc":["540"],"status":"public","publication_identifier":{"eissn":["22962646"]},"article_number":"655","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":6,"day":"24","type":"journal_article","isi":1,"article_processing_charge":"No","department":[{"_id":"JoDa"}]},{"oa_version":"Submitted Version","arxiv":1,"volume":22,"keyword":["reachability analysis","hybrid systems","lazy computation"],"department":[{"_id":"ToHe"}],"day":"16","conference":{"location":"Montreal, QC, Canada","end_date":"2019-04-18","name":"HSCC: Hybrid Systems Computation and Control","start_date":"2019-04-16"},"type":"conference","isi":1,"article_processing_charge":"No","page":"39-44","oa":1,"title":"JuliaReach: A toolbox for set-based reachability","quality_controlled":"1","intvolume":"        22","file":[{"creator":"cschilli","date_updated":"2020-07-14T12:47:17Z","checksum":"28ed56439aea5991c3122d4730fd828f","file_name":"hscc19.pdf","relation":"main_file","access_level":"open_access","date_created":"2019-03-05T09:27:18Z","file_id":"6067","file_size":3784414,"content_type":"application/pdf"}],"language":[{"iso":"eng"}],"doi":"10.1145/3302504.3311804","publication_identifier":{"isbn":["9781450362825"]},"status":"public","project":[{"call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"ddc":["000"],"publication":"Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control","external_id":{"arxiv":["1901.10736"],"isi":["000516713900005"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-02-18T14:43:28Z","publication_status":"published","author":[{"full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","last_name":"Bogomolov","orcid":"0000-0002-0686-0365"},{"last_name":"Forets","first_name":"Marcelo","full_name":"Forets, Marcelo"},{"full_name":"Frehse, Goran","first_name":"Goran","last_name":"Frehse"},{"full_name":"Potomkin, Kostiantyn","first_name":"Kostiantyn","last_name":"Potomkin"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Schilling","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian"}],"year":"2019","has_accepted_license":"1","publisher":"ACM","citation":{"apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., &#38; Schilling, C. (2019). JuliaReach: A toolbox for set-based reachability. In <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i> (Vol. 22, pp. 39–44). Montreal, QC, Canada: ACM. <a href=\"https://doi.org/10.1145/3302504.3311804\">https://doi.org/10.1145/3302504.3311804</a>","mla":"Bogomolov, Sergiy, et al. “JuliaReach: A Toolbox for Set-Based Reachability.” <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i>, vol. 22, ACM, 2019, pp. 39–44, doi:<a href=\"https://doi.org/10.1145/3302504.3311804\">10.1145/3302504.3311804</a>.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “JuliaReach: A Toolbox for Set-Based Reachability.” In <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i>, 22:39–44. ACM, 2019. <a href=\"https://doi.org/10.1145/3302504.3311804\">https://doi.org/10.1145/3302504.3311804</a>.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 39–44.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. JuliaReach: A toolbox for set-based reachability. In: <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i>. Vol 22. ACM; 2019:39-44. doi:<a href=\"https://doi.org/10.1145/3302504.3311804\">10.1145/3302504.3311804</a>","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2019. JuliaReach: A toolbox for set-based reachability. Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control vol. 22, 39–44.","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “JuliaReach: A toolbox for set-based reachability,” in <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i>, Montreal, QC, Canada, 2019, vol. 22, pp. 39–44."},"file_date_updated":"2020-07-14T12:47:17Z","abstract":[{"text":"We present JuliaReach, a toolbox for set-based reachability analysis of dynamical systems. JuliaReach consists of two main packages: Reachability, containing implementations of reachability algorithms for continuous and hybrid systems, and LazySets, a standalone library that implements state-of-the-art algorithms for calculus with convex sets. The library offers both concrete and lazy set representations, where the latter stands for the ability to delay set computations until they are needed. The choice of the programming language Julia and the accompanying documentation of our toolbox allow researchers to easily translate set-based algorithms from mathematics to software in a platform-independent way, while achieving runtime performance that is comparable to statically compiled languages. Combining lazy operations in high dimensions and explicit computations in low dimensions, JuliaReach can be applied to solve complex, large-scale problems.","lang":"eng"}],"month":"04","date_updated":"2023-08-24T14:47:21Z","scopus_import":"1","_id":"6035","ec_funded":1,"date_published":"2019-04-16T00:00:00Z"},{"status":"public","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"}],"ddc":["000"],"publication":"25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems ","external_id":{"isi":["000681166500013"]},"page":"226-243","oa":1,"title":"Semantic fault localization and suspiciousness ranking","quality_controlled":"1","intvolume":"     11427","file":[{"date_updated":"2020-07-14T12:47:17Z","creator":"dernst","file_id":"6408","date_created":"2019-05-10T14:16:05Z","file_size":773083,"content_type":"application/pdf","checksum":"9998496f6fe202c0a19124b4209154c6","file_name":"2019_LNCS_Christakis.pdf","relation":"main_file","access_level":"open_access"}],"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-17462-0_13","department":[{"_id":"ToHe"}],"conference":{"location":"Prague, Czech Republic","end_date":"2019-04-11","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2019-04-06"},"type":"conference","day":"04","isi":1,"article_processing_charge":"No","oa_version":"Published Version","volume":11427,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"04","scopus_import":"1","date_updated":"2023-08-24T14:47:45Z","_id":"6042","ec_funded":1,"date_published":"2019-04-04T00:00:00Z","publisher":"Springer Nature","file_date_updated":"2020-07-14T12:47:17Z","abstract":[{"text":"Static program analyzers are increasingly effective in checking correctness properties of programs and reporting any errors found, often in the form of error traces. However, developers still spend a significant amount of time on debugging. This involves processing long error traces in an effort to localize a bug to a relatively small part of the program and to identify its cause. In this paper, we present a technique for automated fault localization that, given a program and an error trace, efficiently narrows down the cause of the error to a few statements. These statements are then ranked in terms of their suspiciousness. Our technique relies only on the semantics of the given program and does not require any test cases or user guidance. In experiments on a set of C benchmarks, we show that our technique is effective in quickly isolating the cause of error while out-performing other state-of-the-art fault-localization techniques.","lang":"eng"}],"citation":{"apa":"Christakis, M., Heizmann, M., Mansur, M. N., Schilling, C., &#38; Wüstholz, V. (2019). Semantic fault localization and suspiciousness ranking. In <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i> (Vol. 11427, pp. 226–243). Prague, Czech Republic: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">https://doi.org/10.1007/978-3-030-17462-0_13</a>","mla":"Christakis, Maria, et al. “Semantic Fault Localization and Suspiciousness Ranking.” <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>, vol. 11427, Springer Nature, 2019, pp. 226–43, doi:<a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">10.1007/978-3-030-17462-0_13</a>.","chicago":"Christakis, Maria, Matthias Heizmann, Muhammad Numair Mansur, Christian Schilling, and Valentin Wüstholz. “Semantic Fault Localization and Suspiciousness Ranking.” In <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>, 11427:226–43. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">https://doi.org/10.1007/978-3-030-17462-0_13</a>.","ama":"Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. Semantic fault localization and suspiciousness ranking. In: <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>. Vol 11427. Springer Nature; 2019:226-243. doi:<a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">10.1007/978-3-030-17462-0_13</a>","short":"M. Christakis, M. Heizmann, M.N. Mansur, C. Schilling, V. Wüstholz, in:, 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2019, pp. 226–243.","ista":"Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. 2019. Semantic fault localization and suspiciousness ranking. 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 11427, 226–243.","ieee":"M. Christakis, M. Heizmann, M. N. Mansur, C. Schilling, and V. Wüstholz, “Semantic fault localization and suspiciousness ranking,” in <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>, Prague, Czech Republic, 2019, vol. 11427, pp. 226–243."},"author":[{"full_name":"Christakis, Maria","last_name":"Christakis","first_name":"Maria"},{"full_name":"Heizmann, Matthias","last_name":"Heizmann","first_name":"Matthias"},{"first_name":"Muhammad Numair","last_name":"Mansur","full_name":"Mansur, Muhammad Numair"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Schilling","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian"},{"first_name":"Valentin","last_name":"Wüstholz","full_name":"Wüstholz, Valentin"}],"year":"2019","has_accepted_license":"1","date_created":"2019-02-18T16:44:06Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published"},{"month":"02","date_updated":"2023-08-24T14:49:53Z","scopus_import":"1","_id":"6046","date_published":"2019-02-14T00:00:00Z","publisher":"Embo Press","abstract":[{"lang":"eng","text":"Sudden stress often triggers diverse, temporally structured gene expression responses in microbes, but it is largely unknown how variable in time such responses are and if genes respond in the same temporal order in every single cell. Here, we quantified timing variability of individual promoters responding to sublethal antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy. We identified lower and upper bounds that put definite constraints on timing variability, which varies strongly among promoters and conditions. Timing variability can be interpreted using results from statistical kinetics, which enable us to estimate the number of rate‐limiting molecular steps underlying different responses. We found that just a few critical steps control some responses while others rely on dozens of steps. To probe connections between different stress responses, we then tracked the temporal order and response time correlations of promoter pairs in individual cells. Our results support that, when bacteria are exposed to the antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are part of the same causal chain of molecular events. In contrast, under trimethoprim, the acid stress response and the SOS response are part of different chains of events running in parallel. Our approach reveals fundamental constraints on gene expression timing and provides new insights into the molecular events that underlie the timing of stress responses."}],"citation":{"ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Temporal order and precision of complex stress responses in individual bacteria,” <i>Molecular systems biology</i>, vol. 15, no. 2. Embo Press, 2019.","ista":"Mitosch K, Rieckh G, Bollenbach MT. 2019. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 15(2), e8470.","chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” <i>Molecular Systems Biology</i>. Embo Press, 2019. <a href=\"https://doi.org/10.15252/msb.20188470\">https://doi.org/10.15252/msb.20188470</a>.","ama":"Mitosch K, Rieckh G, Bollenbach MT. Temporal order and precision of complex stress responses in individual bacteria. <i>Molecular systems biology</i>. 2019;15(2). doi:<a href=\"https://doi.org/10.15252/msb.20188470\">10.15252/msb.20188470</a>","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).","apa":"Mitosch, K., Rieckh, G., &#38; Bollenbach, M. T. (2019). Temporal order and precision of complex stress responses in individual bacteria. <i>Molecular Systems Biology</i>. Embo Press. <a href=\"https://doi.org/10.15252/msb.20188470\">https://doi.org/10.15252/msb.20188470</a>","mla":"Mitosch, Karin, et al. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” <i>Molecular Systems Biology</i>, vol. 15, no. 2, e8470, Embo Press, 2019, doi:<a href=\"https://doi.org/10.15252/msb.20188470\">10.15252/msb.20188470</a>."},"pmid":1,"author":[{"full_name":"Mitosch, Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","last_name":"Mitosch","first_name":"Karin"},{"last_name":"Rieckh","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg"},{"first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias"}],"year":"2019","date_created":"2019-02-24T22:59:18Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","status":"public","project":[{"call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013"}],"acknowledged_ssus":[{"_id":"Bio"}],"external_id":{"pmid":["30765425"],"isi":["000459628300003"]},"publication":"Molecular systems biology","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30765425","open_access":"1"}],"title":"Temporal order and precision of complex stress responses in individual bacteria","quality_controlled":"1","intvolume":"        15","language":[{"iso":"eng"}],"doi":"10.15252/msb.20188470","department":[{"_id":"GaTk"}],"type":"journal_article","day":"14","isi":1,"issue":"2","article_processing_charge":"No","oa_version":"Submitted Version","article_number":"e8470","volume":15},{"oa":1,"quality_controlled":"1","title":"Feedback-induced self-oscillations in large interacting systems subjected to phase transitions","file":[{"file_size":1804557,"content_type":"application/pdf","date_created":"2019-04-19T12:18:57Z","file_id":"6344","relation":"main_file","access_level":"open_access","checksum":"1112304ad363a6d8afaeccece36473cf","file_name":"2019_IOP_DeMartino.pdf","date_updated":"2020-07-14T12:47:17Z","creator":"kschuh"}],"intvolume":"        52","doi":"10.1088/1751-8121/aaf2dd","language":[{"iso":"eng"}],"status":"public","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000455379500001"]},"publication":"Journal of Physics A: Mathematical and Theoretical","ddc":["570"],"article_number":"045002","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":52,"department":[{"_id":"GaTk"}],"day":"07","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","issue":"4","isi":1,"publisher":"IOP Publishing","citation":{"ista":"De Martino D. 2019. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 52(4), 045002.","ieee":"D. De Martino, “Feedback-induced self-oscillations in large interacting systems subjected to phase transitions,” <i>Journal of Physics A: Mathematical and Theoretical</i>, vol. 52, no. 4. IOP Publishing, 2019.","mla":"De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” <i>Journal of Physics A: Mathematical and Theoretical</i>, vol. 52, no. 4, 045002, IOP Publishing, 2019, doi:<a href=\"https://doi.org/10.1088/1751-8121/aaf2dd\">10.1088/1751-8121/aaf2dd</a>.","apa":"De Martino, D. (2019). Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. <i>Journal of Physics A: Mathematical and Theoretical</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1751-8121/aaf2dd\">https://doi.org/10.1088/1751-8121/aaf2dd</a>","short":"D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).","ama":"De Martino D. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. <i>Journal of Physics A: Mathematical and Theoretical</i>. 2019;52(4). doi:<a href=\"https://doi.org/10.1088/1751-8121/aaf2dd\">10.1088/1751-8121/aaf2dd</a>","chicago":"De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” <i>Journal of Physics A: Mathematical and Theoretical</i>. IOP Publishing, 2019. <a href=\"https://doi.org/10.1088/1751-8121/aaf2dd\">https://doi.org/10.1088/1751-8121/aaf2dd</a>."},"file_date_updated":"2020-07-14T12:47:17Z","abstract":[{"text":"In this article it is shown that large systems with many interacting units endowing multiple phases display self-oscillations in the presence of linear feedback between the control and order parameters, where an Andronov–Hopf bifurcation takes over the phase transition. This is simply illustrated through the mean field Landau theory whose feedback dynamics turn out to be described by the Van der Pol equation and it is then validated for the fully connected Ising model following heat bath dynamics. Despite its simplicity, this theory accounts potentially for a rich range of phenomena: here it is applied to describe in a stylized way (i) excess demand-price cycles due to strong herding in a simple agent-based market model; (ii) congestion waves in queuing networks triggered by user feedback to delays in overloaded conditions; and (iii) metabolic network oscillations resulting from cell growth control in a bistable phenotypic landscape.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-08-24T14:49:23Z","month":"01","_id":"6049","date_published":"2019-01-07T00:00:00Z","ec_funded":1,"date_created":"2019-02-24T22:59:19Z","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"De Martino, Daniele","first_name":"Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","year":"2019"}]