[{"external_id":{"arxiv":["1001.1206"]},"article_processing_charge":"No","abstract":[{"text":"Particles in a perfect lattice potential perform Bloch oscillations when subject to a constant force, leading to localization and preventing conductivity. For a weakly interacting Bose-Einstein condensate of Cs atoms, we observe giant center-of-mass oscillations in position space with a displacement across hundreds of lattice sites when we add a periodic modulation to the force near the Bloch frequency. We study the dependence of these &quot;super&quot; Bloch oscillations on lattice depth, modulation amplitude, and modulation frequency and show that they provide a means to induce linear transport in a dissipation-free lattice.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"year":"2010","author":[{"first_name":"Elmar","last_name":"Haller","full_name":"Haller, Elmar"},{"full_name":"Hart, Russell","last_name":"Hart","first_name":"Russell"},{"first_name":"Manfred","full_name":"Mark, Manfred","last_name":"Mark"},{"orcid":"0000-0001-8559-3973","last_name":"Danzl","full_name":"Danzl, Johann G","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lukas","last_name":"Reichsöllner","full_name":"Reichsöllner, Lukas"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"}],"oa_version":"Preprint","status":"public","arxiv":1,"type":"journal_article","publication_status":"published","publisher":"American Physical Society","date_published":"2010-05-21T00:00:00Z","title":"Inducing transport in a dissipation-free lattice with super bloch oscillations","day":"21","publication":"Physical Review Letters","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1001.1206"}],"volume":104,"doi":"10.1103/PhysRevLett.104.200403","issue":"20","_id":"1047","extern":"1","month":"05","acknowledgement":"We thank A. R. Kolovsky, A. Zenesini, and A. Wacker for discussions and R. Grimm for generous support. We acknowledge funding by the Austrian Ministry of Science and Research and the Austrian Science Fund and by the European Union within the framework of the EuroQUASAR collective research project QuDeGPM. R. H. is supported by a Marie Curie Action within FP7.","citation":{"ama":"Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Nägerl H. Inducing transport in a dissipation-free lattice with super bloch oscillations. <i>Physical Review Letters</i>. 2010;104(20). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.200403\">10.1103/PhysRevLett.104.200403</a>","apa":"Haller, E., Hart, R., Mark, M., Danzl, J. G., Reichsöllner, L., &#38; Nägerl, H. (2010). Inducing transport in a dissipation-free lattice with super bloch oscillations. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.104.200403\">https://doi.org/10.1103/PhysRevLett.104.200403</a>","ista":"Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Nägerl H. 2010. Inducing transport in a dissipation-free lattice with super bloch oscillations. Physical Review Letters. 104(20).","chicago":"Haller, Elmar, Russell Hart, Manfred Mark, Johann G Danzl, Lukas Reichsöllner, and Hanns Nägerl. “Inducing Transport in a Dissipation-Free Lattice with Super Bloch Oscillations.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/PhysRevLett.104.200403\">https://doi.org/10.1103/PhysRevLett.104.200403</a>.","mla":"Haller, Elmar, et al. “Inducing Transport in a Dissipation-Free Lattice with Super Bloch Oscillations.” <i>Physical Review Letters</i>, vol. 104, no. 20, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.200403\">10.1103/PhysRevLett.104.200403</a>.","short":"E. Haller, R. Hart, M. Mark, J.G. Danzl, L. Reichsöllner, H. Nägerl, Physical Review Letters 104 (2010).","ieee":"E. Haller, R. Hart, M. Mark, J. G. Danzl, L. Reichsöllner, and H. Nägerl, “Inducing transport in a dissipation-free lattice with super bloch oscillations,” <i>Physical Review Letters</i>, vol. 104, no. 20. American Physical Society, 2010."},"date_created":"2018-12-11T11:49:52Z","date_updated":"2021-01-12T06:47:54Z","publist_id":"6343","intvolume":"       104"},{"oa":1,"language":[{"iso":"eng"}],"external_id":{"arxiv":["1004.3168"]},"abstract":[{"text":"Quantum many-body systems can have phase transitions even at zero temperature; fluctuations arising from Heisenbergĝ€™s uncertainty principle, as opposed to thermal effects, drive the system from one phase to another. Typically, during the transition the relative strength of two competing terms in the systemĝ€™s Hamiltonian changes across a finite critical value. A well-known example is the Mottĝ€&quot; Hubbard quantum phase transition from a superfluid to an insulating phase, which has been observed for weakly interacting bosonic atomic gases. However, for strongly interacting quantum systems confined to lower-dimensional geometry, a novel type of quantum phase transition may be induced and driven by an arbitrarily weak perturbation to the Hamiltonian. Here we observe such an effectĝ€&quot;the sineĝ€&quot;Gordon quantum phase transition from a superfluid Luttinger liquid to a Mott insulatorĝ€ &quot;in a one-dimensional quantum gas of bosonic caesium atoms with tunable interactions. For sufficiently strong interactions, the transition is induced by adding an arbitrarily weak optical lattice commensurate with the atomic granularity, which leads to immediate pinning of the atoms. We map out the phase diagram and find that our measurements in the strongly interacting regime agree well with a quantum field description based on the exactly solvable sineĝ€&quot;Gordon model. We trace the phase boundary all the way to the weakly interacting regime, where we find good agreement with the predictions of the one-dimensional Boseĝ€&quot;Hubbard model. Our results open up the experimental study of quantum phase transitions, criticality and transport phenomena beyond Hubbard-type models in the context of ultracold gases.","lang":"eng"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"597 - 600","author":[{"last_name":"Haller","full_name":"Haller, Elmar","first_name":"Elmar"},{"last_name":"Hart","full_name":"Hart, Russell","first_name":"Russell"},{"last_name":"Mark","full_name":"Mark, Manfred","first_name":"Manfred"},{"orcid":"0000-0001-8559-3973","last_name":"Danzl","full_name":"Danzl, Johann G","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lukas","full_name":"Reichsöllner, Lukas","last_name":"Reichsöllner"},{"last_name":"Gustavsson","full_name":"Gustavsson, Mattias","first_name":"Mattias"},{"first_name":"Marcello","last_name":"Dalmonte","full_name":"Dalmonte, Marcello"},{"last_name":"Pupillo","full_name":"Pupillo, Guido","first_name":"Guido"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"}],"oa_version":"Preprint","status":"public","year":"2010","date_published":"2010-07-29T00:00:00Z","title":"Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons","day":"29","publication":"Nature","arxiv":1,"type":"journal_article","publication_status":"published","publisher":"Nature Publishing Group","month":"07","acknowledgement":"We thank W. Zwerger for discussions. We are indebted to R. Grimm for generous support. We gratefully acknowledge funding by the Austrian Ministry of Science and Research (Bundesministerium für Wissenschaft und Forschung) and the Austrian Science Fund (Fonds zur Förderung der wissenschaftlichen Forschung) in the form of a START prize grant, and by the European Union through the STREP FP7-ICT-2007-C project NAME-QUAM (Nanodesigning of Atomic and Molecular Quantum Matter) and within the framework of the EuroQUASAR collective research project QuDeGPM. R.H. is supported by a Marie Curie International Incoming Fellowship within the 7th European Community Framework Programme.","citation":{"chicago":"Haller, Elmar, Russell Hart, Manfred Mark, Johann G Danzl, Lukas Reichsöllner, Mattias Gustavsson, Marcello Dalmonte, Guido Pupillo, and Hanns Nägerl. “Pinning Quantum Phase Transition for a Luttinger Liquid of Strongly Interacting Bosons.” <i>Nature</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nature09259\">https://doi.org/10.1038/nature09259</a>.","ieee":"E. Haller <i>et al.</i>, “Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons,” <i>Nature</i>, vol. 466, no. 7306. Nature Publishing Group, pp. 597–600, 2010.","short":"E. Haller, R. Hart, M. Mark, J.G. Danzl, L. Reichsöllner, M. Gustavsson, M. Dalmonte, G. Pupillo, H. Nägerl, Nature 466 (2010) 597–600.","mla":"Haller, Elmar, et al. “Pinning Quantum Phase Transition for a Luttinger Liquid of Strongly Interacting Bosons.” <i>Nature</i>, vol. 466, no. 7306, Nature Publishing Group, 2010, pp. 597–600, doi:<a href=\"https://doi.org/10.1038/nature09259\">10.1038/nature09259</a>.","apa":"Haller, E., Hart, R., Mark, M., Danzl, J. G., Reichsöllner, L., Gustavsson, M., … Nägerl, H. (2010). Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09259\">https://doi.org/10.1038/nature09259</a>","ama":"Haller E, Hart R, Mark M, et al. Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons. <i>Nature</i>. 2010;466(7306):597-600. doi:<a href=\"https://doi.org/10.1038/nature09259\">10.1038/nature09259</a>","ista":"Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Gustavsson M, Dalmonte M, Pupillo G, Nägerl H. 2010. Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons. Nature. 466(7306), 597–600."},"date_updated":"2021-01-12T06:47:54Z","date_created":"2018-12-11T11:49:52Z","publist_id":"6341","intvolume":"       466","volume":466,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1004.3168"}],"doi":"10.1038/nature09259","issue":"7306","extern":"1","_id":"1049"},{"article_type":"original","month":"10","citation":{"chicago":"Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>.","ieee":"A. Zemach <i>et al.</i>, “Local DNA hypomethylation activates genes in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43. National Academy of Sciences, pp. 18729–18734, 2010.","short":"A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D. Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.","mla":"Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43, National Academy of Sciences, 2010, pp. 18729–34, doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>.","apa":"Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M. D., &#38; Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>","ama":"Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2010;107(43):18729-18734. doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>","ista":"Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D. 2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 107(43), 18729–18734."},"date_updated":"2021-12-14T08:40:02Z","date_created":"2021-06-07T09:31:01Z","department":[{"_id":"DaZi"}],"intvolume":"       107","volume":107,"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1009695107","open_access":"1"}],"doi":"10.1073/pnas.1009695107","issue":"43","_id":"9485","extern":"1","date_published":"2010-10-26T00:00:00Z","title":"Local DNA hypomethylation activates genes in rice endosperm","day":"26","publication":"Proceedings of the National Academy of Sciences","publication_status":"published","scopus_import":"1","type":"journal_article","quality_controlled":"1","publisher":"National Academy of Sciences","page":"18729-18734","author":[{"first_name":"Assaf","last_name":"Zemach","full_name":"Zemach, Assaf"},{"first_name":"M. Yvonne","full_name":"Kim, M. Yvonne","last_name":"Kim"},{"first_name":"Pedro","full_name":"Silva, Pedro","last_name":"Silva"},{"last_name":"Rodrigues","full_name":"Rodrigues, Jessica A.","first_name":"Jessica A."},{"last_name":"Dotson","full_name":"Dotson, Bradley","first_name":"Bradley"},{"last_name":"Brooks","full_name":"Brooks, Matthew D.","first_name":"Matthew D."},{"last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"}],"oa_version":"Published Version","status":"public","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"year":"2010","oa":1,"pmid":1,"language":[{"iso":"eng"}],"external_id":{"pmid":["20937895"]},"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"day":"14","title":"Evolution of eukaryotic DNA methylation and the pursuit of safer sex","date_published":"2010-09-14T00:00:00Z","publication":"Current Biology","quality_controlled":"1","scopus_import":"1","type":"journal_article","publication_status":"published","publisher":"Elsevier","article_type":"review","month":"09","citation":{"mla":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>, vol. 20, no. 17, Elsevier, 2010, pp. R780–85, doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>.","short":"A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.","ieee":"A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the pursuit of safer sex,” <i>Current Biology</i>, vol. 20, no. 17. Elsevier, pp. R780–R785, 2010.","chicago":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>.","ista":"Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 20(17), R780–R785.","ama":"Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. 2010;20(17):R780-R785. doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>","apa":"Zemach, A., &#38; Zilberman, D. (2010). Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>"},"department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:52:34Z","date_created":"2021-06-07T09:45:27Z","intvolume":"        20","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2010.07.007","open_access":"1"}],"volume":20,"doi":"10.1016/j.cub.2010.07.007","issue":"17","extern":"1","_id":"9489","oa":1,"pmid":1,"language":[{"iso":"eng"}],"external_id":{"pmid":["20833323"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Cytosine methylation is an ancient process with conserved enzymology but diverse biological functions that include defense against transposable elements and regulation of gene expression. Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries.","lang":"eng"}],"article_processing_charge":"No","author":[{"last_name":"Zemach","full_name":"Zemach, Assaf","first_name":"Assaf"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel"}],"page":"R780-R785","oa_version":"Published Version","status":"public","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"year":"2010"},{"type":"conference","publication_status":"published","quality_controlled":0,"abstract":[{"text":"These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We take a physicist's approach of looking for simple phenomenological descriptions that can address the questions of biological function without necessarily modeling all (mostly unknown) microscopic details; the example that is developed throughout the notes is transcriptional regulation in genetic regulatory networks. We present tools from information theory and statistical physics that can be used to analyze noisy nonlinear biological networks, and build generative and predictive models of regulatory processes.","lang":"eng"}],"publisher":"Elsevier","title":"Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics","date_published":"2010-06-22T00:00:00Z","day":"22","oa":1,"extern":1,"_id":"3430","year":"2010","conference":{"name":"Summer School on Quantitative Evolutionary and Comparative Genomics"},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/pdf/1006.4291"}],"date_updated":"2021-01-12T07:43:25Z","date_created":"2018-12-11T12:03:17Z","publist_id":"2970","status":"public","month":"06","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Gasper Tkacik","last_name":"Tkacik"}],"citation":{"chicago":"Tkačik, Gašper. “Lecture Notes for 2010 Summer School on Quantitative Evolutionary and Comparative Genomics.” Elsevier, 2010.","ieee":"G. Tkačik, “Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics,” presented at the Summer School on Quantitative Evolutionary and Comparative Genomics, 2010.","mla":"Tkačik, Gašper. <i>Lecture Notes for 2010 Summer School on Quantitative Evolutionary and Comparative Genomics</i>. Elsevier, 2010.","short":"G. Tkačik, in:, Elsevier, 2010.","apa":"Tkačik, G. (2010). Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. Presented at the Summer School on Quantitative Evolutionary and Comparative Genomics, Elsevier.","ama":"Tkačik G. Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. In: Elsevier; 2010.","ista":"Tkačik G. 2010. Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. Summer School on Quantitative Evolutionary and Comparative Genomics."}},{"oa":1,"publication":"Journal of Neuroscience","language":[{"iso":"eng"}],"date_published":"2010-04-21T00:00:00Z","title":"High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro","day":"21","abstract":[{"lang":"eng","text":"How seizures start is a major question in epilepsy research. Preictal EEG changes occur in both human patients and animal models, but their underlying mechanisms and relationship with seizure initiation remain unknown. Here we demonstrate the existence, in the hippocampal CA1 region, of a preictal state characterized by the progressive and global increase in neuronal activity associated with a widespread buildup of low-amplitude high-frequency activity (HFA) (&gt; 100 Hz) and reduction in system complexity. HFA is generated by the firing of neurons, mainly pyramidal cells, at much lower frequencies. Individual cycles of HFA are generated by the near-synchronous (within similar to 5 ms) firing of small numbers of pyramidal cells. The presence of HFA in the low-calcium model implicates nonsynaptic synchronization; the presence of very similar HFA in the high-potassium model shows that it does not depend on an absence of synaptic transmission. Immediately before seizure onset, CA1 is in a state of high sensitivity in which weak depolarizing or synchronizing perturbations can trigger seizures. Transition to seizure is characterized by a rapid expansion and fusion of the neuronal populations responsible for HFA, associated with a progressive slowing of HFA, leading to a single, massive, hypersynchronous cluster generating the high-amplitude low-frequency activity of the seizure."}],"publisher":"Society for Neuroscience","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","quality_controlled":"1","publication_status":"published","citation":{"ista":"Jiruska P, Csicsvari JL, Powell A, Fox J, Chang W, Vreugdenhil M, Li X, Palus M, Bujan A, Dearden R, Jefferys J. 2010. High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro. Journal of Neuroscience. 30(16), 5690–5701.","ama":"Jiruska P, Csicsvari JL, Powell A, et al. High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro. <i>Journal of Neuroscience</i>. 2010;30(16):5690-5701. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0535-10.2010\">10.1523/JNEUROSCI.0535-10.2010</a>","apa":"Jiruska, P., Csicsvari, J. L., Powell, A., Fox, J., Chang, W., Vreugdenhil, M., … Jefferys, J. (2010). High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0535-10.2010\">https://doi.org/10.1523/JNEUROSCI.0535-10.2010</a>","short":"P. Jiruska, J.L. Csicsvari, A. Powell, J. Fox, W. Chang, M. Vreugdenhil, X. Li, M. Palus, A. Bujan, R. Dearden, J. Jefferys, Journal of Neuroscience 30 (2010) 5690–5701.","mla":"Jiruska, Premysl, et al. “High-Frequency Network Activity, Global Increase in Neuronal Activity, and Synchrony Expansion Precede Epileptic Seizures in Vitro.” <i>Journal of Neuroscience</i>, vol. 30, no. 16, Society for Neuroscience, 2010, pp. 5690–701, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0535-10.2010\">10.1523/JNEUROSCI.0535-10.2010</a>.","ieee":"P. Jiruska <i>et al.</i>, “High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro,” <i>Journal of Neuroscience</i>, vol. 30, no. 16. Society for Neuroscience, pp. 5690–5701, 2010.","chicago":"Jiruska, Premysl, Jozsef L Csicsvari, Andrew Powell, John Fox, Wei Chang, Martin Vreugdenhil, Xiaoli Li, et al. “High-Frequency Network Activity, Global Increase in Neuronal Activity, and Synchrony Expansion Precede Epileptic Seizures in Vitro.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2010. <a href=\"https://doi.org/10.1523/JNEUROSCI.0535-10.2010\">https://doi.org/10.1523/JNEUROSCI.0535-10.2010</a>."},"page":"5690 - 5701","month":"04","author":[{"full_name":"Jiruska, Premysl","last_name":"Jiruska","first_name":"Premysl"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"},{"last_name":"Powell","full_name":"Powell, Andrew","first_name":"Andrew"},{"first_name":"John","full_name":"Fox, John","last_name":"Fox"},{"full_name":"Chang, Wei","last_name":"Chang","first_name":"Wei"},{"full_name":"Vreugdenhil, Martin","last_name":"Vreugdenhil","first_name":"Martin"},{"full_name":"Li, Xiaoli","last_name":"Li","first_name":"Xiaoli"},{"last_name":"Palus","full_name":"Palus, Milan","first_name":"Milan"},{"last_name":"Bujan","full_name":"Bujan, Alejandro","first_name":"Alejandro"},{"full_name":"Dearden, Richard","last_name":"Dearden","first_name":"Richard"},{"first_name":"John","full_name":"Jefferys, John","last_name":"Jefferys"}],"status":"public","intvolume":"        30","date_created":"2018-12-11T12:03:51Z","date_updated":"2021-01-12T07:44:10Z","oa_version":"None","publist_id":"2848","doi":"10.1523/JNEUROSCI.0535-10.2010","main_file_link":[{"open_access":"1","url":"http://www.jneurosci.org/content/30/16/5690"}],"volume":30,"year":"2010","_id":"3538","extern":"1","issue":"16"},{"type":"conference","scopus_import":1,"quality_controlled":"1","publication_status":"published","publisher":"Open Publishing Association","arxiv":1,"has_accepted_license":"1","alternative_title":["EPTCS"],"day":"30","title":"Lumpability abstractions of rule-based systems","date_published":"2010-10-30T00:00:00Z","conference":{"location":"Jena, Germany","start_date":"2010-08-23","name":"MECBIC: Membrane Computing and Biologically Inspired Process Calculi","end_date":"2010-08-23"},"_id":"3719","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:46:14Z","date_created":"2019-01-31T12:09:09Z","relation":"main_file","access_level":"open_access","file_id":"5904","checksum":"eaaba991a86fff37606b0eb5196878e8","file_name":"Lumpability_abstractions_of_rule-based_systems.pdf","file_size":907155,"creator":"kschuh"}],"volume":40,"department":[{"_id":"ToHe"},{"_id":"CaGu"}],"publist_id":"2511","date_updated":"2023-02-23T11:15:19Z","date_created":"2018-12-11T12:04:47Z","intvolume":"        40","month":"10","citation":{"ista":"Feret J, Henzinger TA, Koeppl H, Petrov T. 2010. Lumpability abstractions of rule-based systems. MECBIC: Membrane Computing and Biologically Inspired Process Calculi, EPTCS, vol. 40, 142–161.","ama":"Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule-based systems. In: Vol 40. Open Publishing Association; 2010:142-161.","apa":"Feret, J., Henzinger, T. A., Koeppl, H., &#38; Petrov, T. (2010). Lumpability abstractions of rule-based systems (Vol. 40, pp. 142–161). Presented at the MECBIC: Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany: Open Publishing Association.","mla":"Feret, Jérôme, et al. <i>Lumpability Abstractions of Rule-Based Systems</i>. Vol. 40, Open Publishing Association, 2010, pp. 142–61.","short":"J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association, 2010, pp. 142–161.","ieee":"J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions of rule-based systems,” presented at the MECBIC: Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany, 2010, vol. 40, pp. 142–161.","chicago":"Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability Abstractions of Rule-Based Systems,” 40:142–61. Open Publishing Association, 2010."},"acknowledgement":"Jérôme Feret’s contribution was partially supported by the ABSTRACTCELL ANR-Chair of Excellence. Heinz Koeppl acknowledges the support from the Swiss National Science Foundation, grant no. 200020-117975/1. Tatjana Petrov acknowledges the support from SystemsX.ch, the Swiss Initiative in Systems Biology.","external_id":{"arxiv":["1011.0496"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a math- ematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the com- binatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:14Z","language":[{"iso":"eng"}],"ddc":["570"],"oa":1,"year":"2010","oa_version":"Submitted Version","status":"public","author":[{"first_name":"Jérôme","full_name":"Feret, Jérôme","last_name":"Feret"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"first_name":"Heinz","full_name":"Koeppl, Heinz","last_name":"Koeppl"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","last_name":"Petrov","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905"}],"page":"142-161","related_material":{"record":[{"status":"public","relation":"later_version","id":"3168"}]}},{"publication_status":"published","type":"preprint","quality_controlled":0,"abstract":[{"lang":"eng","text":"These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We take a physicist's approach of looking for simple phenomenological descriptions that can address the questions of biological function without necessarily modeling all (mostly unknown) microscopic details; the example that is developed throughout the notes is transcriptional regulation in genetic regulatory networks. We present tools from information theory and statistical physics that can be used to analyze noisy nonlinear biological networks, and build generative and predictive models of regulatory processes."}],"publisher":"ArXiv","oa":1,"title":"From statistical mechanics to information theory: understanding biophysical information-processing systems","date_published":"2010-06-22T00:00:00Z","day":"22","publication":"ArXiv","main_file_link":[{"url":"http://arxiv.org/abs/1006.4291v1","open_access":"1"}],"volume":"q-bio.MN","_id":"3743","extern":1,"year":"2010","month":"06","page":"1 - 52","author":[{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Gasper Tkacik","last_name":"Tkacik"}],"citation":{"ieee":"G. Tkačik, “From statistical mechanics to information theory: understanding biophysical information-processing systems,” <i>ArXiv</i>, vol. q-MN. ArXiv, pp. 1–52, 2010.","mla":"Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” <i>ArXiv</i>, vol. q-MN, ArXiv, 2010, pp. 1–52.","short":"G. Tkačik, ArXiv q-MN (2010) 1–52.","chicago":"Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” <i>ArXiv</i>. ArXiv, 2010.","ista":"Tkačik G. 2010. From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv, q-MN, 1–52, .","apa":"Tkačik, G. (2010). From statistical mechanics to information theory: understanding biophysical information-processing systems. <i>ArXiv</i>. ArXiv.","ama":"Tkačik G. From statistical mechanics to information theory: understanding biophysical information-processing systems. <i>ArXiv</i>. 2010;q-MN:1-52."},"date_updated":"2021-01-12T07:51:53Z","date_created":"2018-12-11T12:04:55Z","publist_id":"2487","status":"public"},{"quality_controlled":0,"type":"journal_article","publication_status":"published","publisher":"Nature Publishing Group","abstract":[{"text":"The chemotaxis signalling network in Escherichia coli that controls the locomotion of bacteria is a classic model system for signal transduction1, 2. This pathway modulates the behaviour of flagellar motors to propel bacteria towards sources of chemical attractants. Although this system relaxes to a steady state in response to environmental changes, the signalling events within the chemotaxis network are noisy and cause large temporal variations of the motor behaviour even in the absence of stimulus3. That the same signalling network governs both behavioural variability and cellular response raises the question of whether these two traits are independent. Here, we experimentally establish a fluctuation–response relationship in the chemotaxis system of living bacteria. Using this relationship, we demonstrate the possibility of inferring the cellular response from the behavioural variability measured before stimulus. In monitoring the pre- and post-stimulus switching behaviour of individual bacterial motors, we found that variability scales linearly with the response time for different functioning states of the cell. This study highlights that the fundamental relationship between fluctuation and response is not constrained to physical systems at thermodynamic equilibrium4 but is extensible to living cells5. Such a relationship not only implies that behavioural variability and cellular response can be coupled traits, but it also provides a general framework within which we can examine how the selection of a network design shapes this interdependence","lang":"eng"}],"oa":1,"day":"09","date_published":"2010-12-09T00:00:00Z","title":"Interdependence of behavioural variability and response to small stimuli in bacteria","publication":"Nature","volume":468,"main_file_link":[{"url":"http://europepmc.org/articles/pmc3230254","open_access":"1"}],"doi":"10.1038/nature09551","_id":"3748","extern":1,"year":"2010","author":[{"first_name":"Heungwon","last_name":"Park","full_name":"Park, Heungwon"},{"full_name":"Pontius, William","last_name":"Pontius","first_name":"William"},{"full_name":"Calin Guet","last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marko","full_name":"Marko, John F","first_name":"John"},{"last_name":"Emonet","full_name":"Emonet,Thierry","first_name":"Thierry"},{"full_name":"Cluzel,Philippe","last_name":"Cluzel","first_name":"Philippe"}],"page":"819 - 823","month":"12","citation":{"ista":"Park H, Pontius W, Guet CC, Marko J, Emonet T, Cluzel P. 2010. Interdependence of behavioural variability and response to small stimuli in bacteria. Nature. 468, 819–823.","ama":"Park H, Pontius W, Guet CC, Marko J, Emonet T, Cluzel P. Interdependence of behavioural variability and response to small stimuli in bacteria. <i>Nature</i>. 2010;468:819-823. doi:<a href=\"https://doi.org/10.1038/nature09551\">10.1038/nature09551</a>","apa":"Park, H., Pontius, W., Guet, C. C., Marko, J., Emonet, T., &#38; Cluzel, P. (2010). Interdependence of behavioural variability and response to small stimuli in bacteria. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09551\">https://doi.org/10.1038/nature09551</a>","short":"H. Park, W. Pontius, C.C. Guet, J. Marko, T. Emonet, P. Cluzel, Nature 468 (2010) 819–823.","mla":"Park, Heungwon, et al. “Interdependence of Behavioural Variability and Response to Small Stimuli in Bacteria.” <i>Nature</i>, vol. 468, Nature Publishing Group, 2010, pp. 819–23, doi:<a href=\"https://doi.org/10.1038/nature09551\">10.1038/nature09551</a>.","ieee":"H. Park, W. Pontius, C. C. Guet, J. Marko, T. Emonet, and P. Cluzel, “Interdependence of behavioural variability and response to small stimuli in bacteria,” <i>Nature</i>, vol. 468. Nature Publishing Group, pp. 819–823, 2010.","chicago":"Park, Heungwon, William Pontius, Calin C Guet, John Marko, Thierry Emonet, and Philippe Cluzel. “Interdependence of Behavioural Variability and Response to Small Stimuli in Bacteria.” <i>Nature</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nature09551\">https://doi.org/10.1038/nature09551</a>."},"publist_id":"2480","date_created":"2018-12-11T12:04:57Z","date_updated":"2021-01-12T07:51:55Z","intvolume":"       468","status":"public"},{"issue":"3","_id":"3749","year":"2010","extern":1,"main_file_link":[{"open_access":"1","url":"http://europepmc.org/articles/pmc3230253"}],"volume":62,"doi":"10.1007/s00284-010-9778-z","date_created":"2018-12-11T12:04:57Z","date_updated":"2021-01-12T07:51:55Z","publist_id":"2479","status":"public","intvolume":"        62","page":"764 - 769","month":"10","author":[{"first_name":"Heungwon","full_name":"Park, Heungwon","last_name":"Park"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Calin Guet","last_name":"Guet","orcid":"0000-0001-6220-2052"},{"full_name":"Emonet,Thierry","last_name":"Emonet","first_name":"Thierry"},{"full_name":"Cluzel,Philippe","last_name":"Cluzel","first_name":"Philippe"}],"acknowledgement":"P50 GM081892-04/GM/NIGMS NIH HHS/United States\nR01 AI059195-01A1/AI/NIAID NIH HHS/United States\nR01 AI059195-02/AI/NIAID NIH HHS/United States\nR01 AI059195-03/AI/NIAID NIH HHS/United States\nR01AI059195-03/AI/NIAID NIH HHS/United States\n\n\nPMCID: PMC3230253 ","citation":{"apa":"Park, H., Guet, C. C., Emonet, T., &#38; Cluzel, P. (2010). Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay. <i>Current Microbiology</i>. Springer. <a href=\"https://doi.org/10.1007/s00284-010-9778-z\">https://doi.org/10.1007/s00284-010-9778-z</a>","ama":"Park H, Guet CC, Emonet T, Cluzel P. Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay. <i>Current Microbiology</i>. 2010;62(3):764-769. doi:<a href=\"https://doi.org/10.1007/s00284-010-9778-z\">10.1007/s00284-010-9778-z</a>","ista":"Park H, Guet CC, Emonet T, Cluzel P. 2010. Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay. Current Microbiology. 62(3), 764–769.","chicago":"Park, Heungwon, Calin C Guet, Thierry Emonet, and Philippe Cluzel. “Fine-Tuning of Chemotactic Response in E. Coli Determined by High-Throughput Capillary Assay.” <i>Current Microbiology</i>. Springer, 2010. <a href=\"https://doi.org/10.1007/s00284-010-9778-z\">https://doi.org/10.1007/s00284-010-9778-z</a>.","ieee":"H. Park, C. C. Guet, T. Emonet, and P. Cluzel, “Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay,” <i>Current Microbiology</i>, vol. 62, no. 3. Springer, pp. 764–769, 2010.","short":"H. Park, C.C. Guet, T. Emonet, P. Cluzel, Current Microbiology 62 (2010) 764–769.","mla":"Park, Heungwon, et al. “Fine-Tuning of Chemotactic Response in E. Coli Determined by High-Throughput Capillary Assay.” <i>Current Microbiology</i>, vol. 62, no. 3, Springer, 2010, pp. 764–69, doi:<a href=\"https://doi.org/10.1007/s00284-010-9778-z\">10.1007/s00284-010-9778-z</a>."},"type":"journal_article","publication_status":"published","quality_controlled":0,"abstract":[{"lang":"eng","text":"In E. coli, chemotactic behavior exhibits perfect adaptation that is robust to changes in the intracellular concentration of the chemotactic proteins, such as CheR and CheB. However, the robustness of the perfect adaptation does not explicitly imply a robust chemotactic response. Previous studies on the robustness of the chemotactic response relied on swarming assays, which can be confounded by processes besides chemotaxis, such as cellular growth and depletion of nutrients. Here, using a high-throughput capillary assay that eliminates the effects of growth, we experimentally studied how the chemotactic response depends on the relative concentration of the chemotactic proteins. We simultaneously measured both the chemotactic response of E. coli cells to L: -aspartate and the concentrations of YFP-CheR and CheB-CFP fusion proteins. We found that the chemotactic response is fine-tuned to a specific ratio of [CheR]/[CheB] with a maximum response comparable to the chemotactic response of wild-type behavior. In contrast to adaptation in chemotaxis, that is robust and exact, capillary assays revealed that the chemotactic response in swimming bacteria is fined-tuned to wild-type level of the [CheR]/[CheB] ratio."}],"publisher":"Springer","date_published":"2010-10-23T00:00:00Z","title":"Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay","day":"23","publication":"Current Microbiology","oa":1},{"status":"public","oa_version":"Published Version","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"year":"2010","pubrep_id":"524","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"oa":1,"ddc":["570","576"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:46:15Z","article_number":"e1000987","intvolume":"         6","date_created":"2018-12-11T12:05:05Z","date_updated":"2021-01-12T07:52:05Z","publist_id":"2454","department":[{"_id":"NiBa"}],"citation":{"chicago":"Barton, Nicholas H. “Understanding Adaptation in Large Populations.” <i>PLoS Genetics</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pgen.1000987\">https://doi.org/10.1371/journal.pgen.1000987</a>.","short":"N.H. Barton, PLoS Genetics 6 (2010).","mla":"Barton, Nicholas H. “Understanding Adaptation in Large Populations.” <i>PLoS Genetics</i>, vol. 6, no. 6, e1000987, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1000987\">10.1371/journal.pgen.1000987</a>.","ieee":"N. H. Barton, “Understanding adaptation in large populations,” <i>PLoS Genetics</i>, vol. 6, no. 6. Public Library of Science, 2010.","ama":"Barton NH. Understanding adaptation in large populations. <i>PLoS Genetics</i>. 2010;6(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1000987\">10.1371/journal.pgen.1000987</a>","apa":"Barton, N. H. (2010). Understanding adaptation in large populations. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1000987\">https://doi.org/10.1371/journal.pgen.1000987</a>","ista":"Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics. 6(6), e1000987."},"month":"06","_id":"3772","issue":"6","doi":"10.1371/journal.pgen.1000987","volume":6,"file":[{"creator":"system","file_name":"IST-2016-524-v1+1_journal.pgen.1000987.PDF","file_size":349965,"date_created":"2018-12-12T10:14:24Z","date_updated":"2020-07-14T12:46:15Z","access_level":"open_access","relation":"main_file","file_id":"5075","checksum":"5c14de2680ab483cb835096c99ee734d","content_type":"application/pdf"}],"publication":"PLoS Genetics","title":"Understanding adaptation in large populations","date_published":"2010-06-17T00:00:00Z","day":"17","publisher":"Public Library of Science","quality_controlled":"1","publication_status":"published","scopus_import":1,"type":"journal_article","has_accepted_license":"1"},{"oa":1,"pmid":1,"language":[{"iso":"eng"}],"external_id":{"pmid":["20439284"]},"abstract":[{"lang":"eng","text":"If distinct biological species are to coexist in sympatry, they must be reproductively isolated and must exploit different limiting resources. A two-niche Levene model is analysed, in which habitat preference and survival depend on underlying additive traits. The population genetics of preference and viability are equivalent. However, there is a linear trade-off between the chances of settling in either niche, whereas viabilities may be constrained arbitrarily. With a convex trade-off, a sexual population evolves a single generalist genotype, whereas with a concave trade-off, disruptive selection favours maximal variance. A pure habitat preference evolves to global linkage equilibrium if mating occurs in a single pool, but remarkably, evolves to pairwise linkage equilibrium within niches if mating is within those niches--independent of the genetics. With a concave trade-off, the population shifts sharply between a unimodal distribution with high gene flow and a bimodal distribution with strong isolation, as the underlying genetic variance increases. However, these alternative states are only simultaneously stable for a narrow parameter range. A sharp threshold is only seen if survival in the 'wrong' niche is low; otherwise, strong isolation is impossible. Gene flow from divergent demes makes speciation much easier in parapatry than in sympatry."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"1825 - 1840","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","status":"public","year":"2010","title":"What role does natural selection play in speciation?","date_published":"2010-06-12T00:00:00Z","day":"12","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","quality_controlled":"1","scopus_import":1,"type":"journal_article","publication_status":"published","publisher":"Royal Society","month":"06","acknowledgement":"The author thanks the Werner-Gren Foundation and the Royal Swedish Academy of Sciences for organizing the symposium on the ‘Origin of Species’. He also thanks Reinhard Bürger, and two anonymous referees, for their helpful comments.\r\n","citation":{"ista":"Barton NH. 2010. What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1547), 1825–1840.","ama":"Barton NH. What role does natural selection play in speciation? <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1547):1825-1840. doi:<a href=\"https://doi.org/10.1098/rstb.2010.0001\">10.1098/rstb.2010.0001</a>","apa":"Barton, N. H. (2010). What role does natural selection play in speciation? <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2010.0001\">https://doi.org/10.1098/rstb.2010.0001</a>","mla":"Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1547, Royal Society, 2010, pp. 1825–40, doi:<a href=\"https://doi.org/10.1098/rstb.2010.0001\">10.1098/rstb.2010.0001</a>.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1825–1840.","ieee":"N. H. Barton, “What role does natural selection play in speciation?,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1547. Royal Society, pp. 1825–1840, 2010.","chicago":"Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, 2010. <a href=\"https://doi.org/10.1098/rstb.2010.0001\">https://doi.org/10.1098/rstb.2010.0001</a>."},"date_updated":"2021-01-12T07:52:06Z","date_created":"2018-12-11T12:05:05Z","department":[{"_id":"NiBa"}],"publist_id":"2455","intvolume":"       365","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pubmed/20439284","open_access":"1"}],"volume":365,"doi":"10.1098/rstb.2010.0001","issue":"1547","_id":"3773"},{"date_updated":"2021-01-12T07:52:07Z","date_created":"2018-12-11T12:05:06Z","department":[{"_id":"NiBa"}],"publist_id":"2450","intvolume":"       365","month":"08","acknowledgement":"Royal Society and Wolfson Foundation for their support\r\nWe would like to thank Brian Charlesworth and Sally Otto for their helpful comments.","citation":{"mla":"Barton, Nicholas H. “Genetic Linkage and Natural Selection.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1552, Royal Society, 2010, pp. 2559–69, doi:<a href=\"https://doi.org/10.1098/rstb.2010.0106\">10.1098/rstb.2010.0106</a>.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 2559–2569.","ieee":"N. H. Barton, “Genetic linkage and natural selection,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1552. Royal Society, pp. 2559–2569, 2010.","chicago":"Barton, Nicholas H. “Genetic Linkage and Natural Selection.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, 2010. <a href=\"https://doi.org/10.1098/rstb.2010.0106\">https://doi.org/10.1098/rstb.2010.0106</a>.","ista":"Barton NH. 2010. Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1552), 2559–2569.","ama":"Barton NH. Genetic linkage and natural selection. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1552):2559-2569. doi:<a href=\"https://doi.org/10.1098/rstb.2010.0106\">10.1098/rstb.2010.0106</a>","apa":"Barton, N. H. (2010). Genetic linkage and natural selection. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2010.0106\">https://doi.org/10.1098/rstb.2010.0106</a>"},"issue":"1552","_id":"3776","volume":365,"file":[{"creator":"system","file_name":"IST-2016-555-v1+1_RS2009_revised.pdf","file_size":250255,"date_created":"2018-12-12T10:14:40Z","relation":"main_file","date_updated":"2020-07-14T12:46:15Z","access_level":"open_access","file_id":"5093","checksum":"4d8aade10db030124ab158b622e337e0","content_type":"application/pdf"}],"doi":"10.1098/rstb.2010.0106","title":"Genetic linkage and natural selection","date_published":"2010-08-27T00:00:00Z","day":"27","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","quality_controlled":"1","publication_status":"published","type":"journal_article","scopus_import":1,"publisher":"Royal Society","has_accepted_license":"1","oa_version":"Submitted Version","status":"public","page":"2559 - 2569","author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"pubrep_id":"555","year":"2010","language":[{"iso":"eng"}],"ddc":["570"],"oa":1,"abstract":[{"lang":"eng","text":"The prevalence of recombination in eukaryotes poses one of the most puzzling questions in biology. The most compelling general explanation is that recombination facilitates selection by breaking down the negative associations generated by random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of HRI owing to: deleterious mutation, balancing selection and selective sweeps on: neutral diversity, rates of adaptation and the mutation load. These effects are mediated primarily by the density of deleterious mutations and of selective sweeps. Sequence polymorphism and divergence suggest that these rates may be high enough to cause significant interference even in genomic regions of high recombination. However, neither seems able to generate enough variance in fitness to select strongly for high rates of recombination. It is plausible that spatial and temporal fluctuations in selection generate much more fitness variance, and hence selection for recombination, than can be explained by uniformly deleterious mutations or species-wide selective sweeps."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:46:15Z"},{"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","day":"27","date_published":"2010-04-27T00:00:00Z","title":"Mutation and the evolution of recombination","publisher":"Royal Society","scopus_import":1,"publication_status":"published","quality_controlled":"1","type":"journal_article","intvolume":"       365","publist_id":"2451","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:52:07Z","date_created":"2018-12-11T12:05:07Z","citation":{"ista":"Barton NH. 2010. Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1281–1294.","apa":"Barton, N. H. (2010). Mutation and the evolution of recombination. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2009.0320\">https://doi.org/10.1098/rstb.2009.0320</a>","ama":"Barton NH. Mutation and the evolution of recombination. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1544):1281-1294. doi:<a href=\"https://doi.org/10.1098/rstb.2009.0320\">10.1098/rstb.2009.0320</a>","ieee":"N. H. Barton, “Mutation and the evolution of recombination,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1544. Royal Society, pp. 1281–1294, 2010.","mla":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1544, Royal Society, 2010, pp. 1281–94, doi:<a href=\"https://doi.org/10.1098/rstb.2009.0320\">10.1098/rstb.2009.0320</a>.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1281–1294.","chicago":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, 2010. <a href=\"https://doi.org/10.1098/rstb.2009.0320\">https://doi.org/10.1098/rstb.2009.0320</a>."},"acknowledgement":"I would like to thank W. G. Hill and L. Loewe for organizing this special issue, and the Royal Society and Wolfson Foundation for their support. Also, A. Kondrashov and L. Loewe gave very helpful comments that helped improve the manuscript.","month":"04","_id":"3777","issue":"1544","doi":"10.1098/rstb.2009.0320","volume":365,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pubmed/20308104","open_access":"1"}],"language":[{"iso":"eng"}],"pmid":1,"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill-Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model."}],"external_id":{"pmid":["20308104"]},"status":"public","oa_version":"Submitted Version","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"page":"1281 - 1294","year":"2010"},{"related_material":{"record":[{"relation":"research_data","status":"public","id":"9764"}]},"author":[{"full_name":"Rosas, Ulises","last_name":"Rosas","first_name":"Ulises"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Copsey","full_name":"Copsey, Lucy","first_name":"Lucy"},{"first_name":"Pierre","full_name":"Barbier De Reuille, Pierre","last_name":"Barbier De Reuille"},{"last_name":"Coen","full_name":"Coen, Enrico","first_name":"Enrico"}],"status":"public","oa_version":"Published Version","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2010","pubrep_id":"366","oa":1,"ddc":["576"],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:15Z","article_number":"e1000429","abstract":[{"lang":"eng","text":"Crosses between closely related species give two contrasting results. One result is that species hybrids may be inferior to their parents, for example, being less fertile [1]. The other is that F1 hybrids may display superior performance (heterosis), for example with increased vigour [2]. Although various hypotheses have been proposed to account for these two aspects of hybridisation, their biological basis is still poorly understood [3]. To gain further insights into this issue, we analysed the role that variation in gene expression may play. We took a conserved trait, flower asymmetry in Antirrhinum, and determined the extent to which the underlying regulatory genes varied in expression among closely related species. We show that expression of both genes analysed, CYC and RAD, varies significantly between species because of cis-acting differences. By making a quantitative genotype-phenotype map, using a range of mutant alleles, we demonstrate that the species lie on a plateau in gene expression-morphology space, so that the variation has no detectable phenotypic effect. However, phenotypic differences can be revealed by shifting genotypes off the plateau through genetic crosses. Our results can be readily explained if genomes are free to evolve within an effectively neutral zone in gene expression space. The consequences of this drift will be negligible for individual loci, but when multiple loci across the genome are considered, we show that the variation may have significant effects on phenotype and fitness, causing a significant drift load. By considering these consequences for various gene-expression-fitness landscapes, we conclude that F1 hybrids might be expected to show increased performance with regard to conserved traits, such as basic physiology, but reduced performance with regard to others. Thus, our study provides a new way of explaining how various aspects of hybrid performance may arise through natural variation in gene activity."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This was supported by a Marie Curie grant for early stage training and the BBSRC-John Innes Centre PhD Rotation Program.\r\nWe would like to thank X. Feng and A. Hudson for assistance with introgressions and genotyping; A. Green, A. Bangham and J. Pateman for advice and assistance on shape model procedures; F. Alderson and S.Mitchell from JIC horticultural services; P.J. Wittkopp for protocols and advice on pyrosequencing; and R. Sablowski for discussions and comments.\r\n","citation":{"ista":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Cryptic variation between species and the basis of hybrid performance. PLoS Biology. 8(7), e1000429.","ama":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Cryptic variation between species and the basis of hybrid performance. <i>PLoS Biology</i>. 2010;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429\">10.1371/journal.pbio.1000429</a>","apa":"Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., &#38; Coen, E. (2010). Cryptic variation between species and the basis of hybrid performance. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000429\">https://doi.org/10.1371/journal.pbio.1000429</a>","mla":"Rosas, Ulises, et al. “Cryptic Variation between Species and the Basis of Hybrid Performance.” <i>PLoS Biology</i>, vol. 8, no. 7, e1000429, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429\">10.1371/journal.pbio.1000429</a>.","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology 8 (2010).","ieee":"U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic variation between species and the basis of hybrid performance,” <i>PLoS Biology</i>, vol. 8, no. 7. Public Library of Science, 2010.","chicago":"Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Cryptic Variation between Species and the Basis of Hybrid Performance.” <i>PLoS Biology</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pbio.1000429\">https://doi.org/10.1371/journal.pbio.1000429</a>."},"month":"07","intvolume":"         8","date_created":"2018-12-11T12:05:07Z","date_updated":"2023-02-23T14:07:34Z","department":[{"_id":"NiBa"}],"publist_id":"2448","doi":"10.1371/journal.pbio.1000429","volume":8,"file":[{"creator":"system","file_name":"IST-2015-366-v1+1_journal.pbio.1000429.pdf","file_size":1089530,"file_id":"5060","checksum":"ee1ce2fb283a6b4127544ae532d0b4a1","date_updated":"2020-07-14T12:46:15Z","access_level":"open_access","date_created":"2018-12-12T10:14:11Z","relation":"main_file","content_type":"application/pdf"}],"_id":"3779","issue":"7","publication":"PLoS Biology","date_published":"2010-07-20T00:00:00Z","title":"Cryptic variation between species and the basis of hybrid performance","day":"20","has_accepted_license":"1","publisher":"Public Library of Science","type":"journal_article","scopus_import":1,"quality_controlled":"1","publication_status":"published"},{"year":"2010","status":"public","oa_version":"Submitted Version","author":[{"last_name":"Palero","full_name":"Palero, Ferran","orcid":"0000-0002-0343-8329","first_name":"Ferran","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hall","full_name":"Hall, Sally","first_name":"Sally"},{"first_name":"Paul","full_name":"Clark, Paul","last_name":"Clark"},{"full_name":"Johnston, David","last_name":"Johnston","first_name":"David"},{"last_name":"Mackenzie Dodds","full_name":"Mackenzie Dodds, Jackie","first_name":"Jackie"},{"full_name":"Thatje, Sven","last_name":"Thatje","first_name":"Sven"}],"page":"465 - 470","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"DNA samples were extracted from ethanol and formalin-fixed decapod crustacean tissue using a new method based on Tetramethylsilane (TMS)-Chelex. It is shown that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors impede PCR success when dealing with formalin-fixed material. Instead, amplification success from formalin-fixed tissue appears to depend on the presence of unmodified DNA in the extracted sample. A staining method that facilitates the targeting of samples with a high content of unmodified DNA is provided.","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"_id":"3787","issue":"3","doi":"10.3989/scimar.2010.74n3465","main_file_link":[{"open_access":"1","url":"https://eprints.soton.ac.uk/68731/"}],"volume":74,"intvolume":"        74","publist_id":"2440","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:52:11Z","date_created":"2018-12-11T12:05:10Z","citation":{"ista":"Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. 2010. DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. 74(3), 465–470.","apa":"Palero, F., Hall, S., Clark, P., Johnston, D., Mackenzie Dodds, J., &#38; Thatje, S. (2010). DNA extraction from formalin-fixed tissue: new light from the deep sea. <i>Scientia Marina</i>. Consejo Superior de Investigaciones Científicas. <a href=\"https://doi.org/10.3989/scimar.2010.74n3465\">https://doi.org/10.3989/scimar.2010.74n3465</a>","ama":"Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. DNA extraction from formalin-fixed tissue: new light from the deep sea. <i>Scientia Marina</i>. 2010;74(3):465-470. doi:<a href=\"https://doi.org/10.3989/scimar.2010.74n3465\">10.3989/scimar.2010.74n3465</a>","ieee":"F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, and S. Thatje, “DNA extraction from formalin-fixed tissue: new light from the deep sea,” <i>Scientia Marina</i>, vol. 74, no. 3. Consejo Superior de Investigaciones Científicas, pp. 465–470, 2010.","short":"F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, S. Thatje, Scientia Marina 74 (2010) 465–470.","mla":"Palero, Ferran, et al. “DNA Extraction from Formalin-Fixed Tissue: New Light from the Deep Sea.” <i>Scientia Marina</i>, vol. 74, no. 3, Consejo Superior de Investigaciones Científicas, 2010, pp. 465–70, doi:<a href=\"https://doi.org/10.3989/scimar.2010.74n3465\">10.3989/scimar.2010.74n3465</a>.","chicago":"Palero, Ferran, Sally Hall, Paul Clark, David Johnston, Jackie Mackenzie Dodds, and Sven Thatje. “DNA Extraction from Formalin-Fixed Tissue: New Light from the Deep Sea.” <i>Scientia Marina</i>. Consejo Superior de Investigaciones Científicas, 2010. <a href=\"https://doi.org/10.3989/scimar.2010.74n3465\">https://doi.org/10.3989/scimar.2010.74n3465</a>."},"acknowledgement":"The authors would like to thank two anonymous reviewers for their remarks, which helped to improve the manuscript. This project was supported by the Marine Biodiversity and Ecosystem Functioning Network of Excellence MarBEF (Contract no. GOCE-CT-2003-505446) of the 6th European Framework Programme(FP6), the Zoology Research Fund, Department of Zoology, NHM, London, a Research Grant from the Royal Society to S.T., and a pre-doctoral fellowship awarded by the Autonomous Government of Catalonia to F.P.(2006FIC-00082). This research received support from the SYNTHESYS Project http://www.synthesys. info/ which is financed by European Community Research Infrastructure Action under the FP6 “Structuring the European Research Area” Programme. Many thanks are due to J. Fortuño for suggesting TMS as an alternative to critical point drying, P.Crabb for helping with the UV-light photography setting and our colleagues/friends in the Whale Basement Molecular Laboratories, Department of Zoology NHM \r\n\r\n","month":"09","publisher":"Consejo Superior de Investigaciones Científicas","scopus_import":1,"publication_status":"published","quality_controlled":"1","type":"journal_article","publication":"Scientia Marina","day":"01","date_published":"2010-09-01T00:00:00Z","title":"DNA extraction from formalin-fixed tissue: new light from the deep sea"},{"date_published":"2010-11-30T00:00:00Z","title":"Control of directed cell migration in vivo by membrane-to-cortex attachment","day":"30","publication":"PLoS Biology","has_accepted_license":"1","type":"journal_article","scopus_import":1,"publication_status":"published","quality_controlled":"1","publisher":"Public Library of Science","month":"11","acknowledgement":"We would like to thank A. G. Clark, S. Grill, A. Oates, E. Raz, L. Rohde, and M. Zerial for reading earlier versions of the manuscript. We are grateful to W. Zachariae, Y. Arboleda-Estudillo, S. Schneider, P. Stockinger, D. Panhans, M. Biro, J. C. Olaya, and the BIOTEC/MPI-CBG zebrafish and imaging facilities for help and advice at various stages of this project and to J. Helenius for help with programming. This work was supported by grants from the Boehringer Ingelheim Fonds to MK, the Polish Ministry of Science and Higher Education to E. P., and the Deutsche Forschungsgemeinschaft (HE 3231/6-1 and PA 1590/1-1) to CPH and EP.\r\n","citation":{"chicago":"Diz Muñoz, Alba, Michael Krieg, Martin Bergert, Itziar Ibarlucea Benitez, Daniel Müller, Ewa Paluch, and Carl-Philipp J Heisenberg. “Control of Directed Cell Migration in Vivo by Membrane-to-Cortex Attachment.” <i>PLoS Biology</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pbio.1000544\">https://doi.org/10.1371/journal.pbio.1000544</a>.","ieee":"A. Diz Muñoz <i>et al.</i>, “Control of directed cell migration in vivo by membrane-to-cortex attachment,” <i>PLoS Biology</i>, vol. 8, no. 11. Public Library of Science, 2010.","mla":"Diz Muñoz, Alba, et al. “Control of Directed Cell Migration in Vivo by Membrane-to-Cortex Attachment.” <i>PLoS Biology</i>, vol. 8, no. 11, e1000544, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000544\">10.1371/journal.pbio.1000544</a>.","short":"A. Diz Muñoz, M. Krieg, M. Bergert, I. Ibarlucea Benitez, D. Müller, E. Paluch, C.-P.J. Heisenberg, PLoS Biology 8 (2010).","apa":"Diz Muñoz, A., Krieg, M., Bergert, M., Ibarlucea Benitez, I., Müller, D., Paluch, E., &#38; Heisenberg, C.-P. J. (2010). Control of directed cell migration in vivo by membrane-to-cortex attachment. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000544\">https://doi.org/10.1371/journal.pbio.1000544</a>","ama":"Diz Muñoz A, Krieg M, Bergert M, et al. Control of directed cell migration in vivo by membrane-to-cortex attachment. <i>PLoS Biology</i>. 2010;8(11). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000544\">10.1371/journal.pbio.1000544</a>","ista":"Diz Muñoz A, Krieg M, Bergert M, Ibarlucea Benitez I, Müller D, Paluch E, Heisenberg C-PJ. 2010. Control of directed cell migration in vivo by membrane-to-cortex attachment. PLoS Biology. 8(11), e1000544."},"date_created":"2018-12-11T12:05:11Z","date_updated":"2021-01-12T07:52:13Z","publist_id":"2437","department":[{"_id":"CaHe"}],"intvolume":"         8","volume":8,"file":[{"file_name":"IST-2015-365-v1+1_journal.pbio.1000544.pdf","file_size":799506,"creator":"system","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:46:16Z","date_created":"2018-12-12T10:08:24Z","checksum":"52d18c90ca6b02234cea5e8b399b7f46","file_id":"4685"}],"doi":"10.1371/journal.pbio.1000544","issue":"11","_id":"3790","ddc":["576"],"oa":1,"language":[{"iso":"eng"}],"article_number":"e1000544","file_date_updated":"2020-07-14T12:46:16Z","abstract":[{"text":"Cell shape and motility are primarily controlled by cellular mechanics. The attachment of the plasma membrane to the underlying actomyosin cortex has been proposed to be important for cellular processes involving membrane deformation. However, little is known about the actual function of membrane-to-cortex attachment (MCA) in cell protrusion formation and migration, in particular in the context of the developing embryo. Here, we use a multidisciplinary approach to study MCA in zebrafish mesoderm and endoderm (mesendoderm) germ layer progenitor cells, which migrate using a combination of different protrusion types, namely, lamellipodia, filopodia, and blebs, during zebrafish gastrulation. By interfering with the activity of molecules linking the cortex to the membrane and measuring resulting changes in MCA by atomic force microscopy, we show that reducing MCA in mesendoderm progenitors increases the proportion of cellular blebs and reduces the directionality of cell migration. We propose that MCA is a key parameter controlling the relative proportions of different cell protrusion types in mesendoderm progenitors, and thus is key in controlling directed migration during gastrulation.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Diz Muñoz, Alba","last_name":"Diz Muñoz","first_name":"Alba"},{"first_name":"Michael","last_name":"Krieg","full_name":"Krieg, Michael"},{"full_name":"Bergert, Martin","last_name":"Bergert","first_name":"Martin"},{"last_name":"Ibarlucea Benitez","full_name":"Ibarlucea Benitez, Itziar","first_name":"Itziar"},{"last_name":"Müller","full_name":"Müller, Daniel","first_name":"Daniel"},{"first_name":"Ewa","full_name":"Paluch, Ewa","last_name":"Paluch"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"oa_version":"Published Version","status":"public","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pubrep_id":"365","year":"2010"},{"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Recent progress in per-pixel object class labeling of natural images can be attributed to the use of multiple types of image features and sound statistical learning approaches. Within the latter, Conditional Random Fields (CRF) are prominently used for their ability to represent interactions between random variables. Despite their popularity in computer vision, parameter learning for CRFs has remained difficult, popular approaches being cross-validation and piecewise training.\r\nIn this work, we propose a simple yet expressive tree-structured CRF based on a recent hierarchical image segmentation method. Our model combines and weights multiple image features within a hierarchical representation and allows simple and efficient globally-optimal learning of ≈ 105 parameters. The tractability of our model allows us to pose and answer some of the open questions regarding parameter learning applying to CRF-based approaches. The key findings for learning CRF models are, from the obvious to the surprising, i) multiple image features always help, ii) the limiting dimension with respect to current models is the amount of training data, iii) piecewise training is competitive, iv) current methods for max-margin training fail for models with many parameters.\r\n"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:46:16Z","language":[{"iso":"eng"}],"ddc":["000"],"oa":1,"year":"2010","oa_version":"Submitted Version","status":"public","page":"98 - 111","author":[{"full_name":"Nowozin, Sebastian","last_name":"Nowozin","first_name":"Sebastian"},{"first_name":"Peter","last_name":"Gehler","full_name":"Gehler, Peter"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887"}],"type":"conference","scopus_import":1,"publication_status":"published","quality_controlled":"1","publisher":"Springer","alternative_title":["LNCS"],"has_accepted_license":"1","date_published":"2010-11-04T00:00:00Z","title":"On parameter learning in CRF-based approaches to object class image segmentation","day":"04","_id":"3793","conference":{"start_date":"2010-09-05","location":"Heraklion, Crete, Greece","name":"ECCV: European Conference on Computer Vision","end_date":"2010-09-11"},"volume":6316,"file":[{"date_created":"2020-05-19T16:27:34Z","date_updated":"2020-07-14T12:46:16Z","relation":"main_file","access_level":"open_access","file_id":"7871","checksum":"3716e10e161f7c714fd17ec193a223c3","content_type":"application/pdf","creator":"dernst","file_name":"2010_ECCV_Nowozin.pdf","file_size":4087332}],"doi":"10.1007/978-3-642-15567-3_8","date_updated":"2021-01-12T07:52:14Z","date_created":"2018-12-11T12:05:12Z","department":[{"_id":"ChLa"}],"publist_id":"2431","intvolume":"      6316","month":"11","citation":{"chicago":"Nowozin, Sebastian, Peter Gehler, and Christoph Lampert. “On Parameter Learning in CRF-Based Approaches to Object Class Image Segmentation,” 6316:98–111. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-15567-3_8\">https://doi.org/10.1007/978-3-642-15567-3_8</a>.","ieee":"S. Nowozin, P. Gehler, and C. Lampert, “On parameter learning in CRF-based approaches to object class image segmentation,” presented at the ECCV: European Conference on Computer Vision, Heraklion, Crete, Greece, 2010, vol. 6316, pp. 98–111.","mla":"Nowozin, Sebastian, et al. <i>On Parameter Learning in CRF-Based Approaches to Object Class Image Segmentation</i>. Vol. 6316, Springer, 2010, pp. 98–111, doi:<a href=\"https://doi.org/10.1007/978-3-642-15567-3_8\">10.1007/978-3-642-15567-3_8</a>.","short":"S. Nowozin, P. Gehler, C. Lampert, in:, Springer, 2010, pp. 98–111.","apa":"Nowozin, S., Gehler, P., &#38; Lampert, C. (2010). On parameter learning in CRF-based approaches to object class image segmentation (Vol. 6316, pp. 98–111). Presented at the ECCV: European Conference on Computer Vision, Heraklion, Crete, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-642-15567-3_8\">https://doi.org/10.1007/978-3-642-15567-3_8</a>","ama":"Nowozin S, Gehler P, Lampert C. On parameter learning in CRF-based approaches to object class image segmentation. In: Vol 6316. Springer; 2010:98-111. doi:<a href=\"https://doi.org/10.1007/978-3-642-15567-3_8\">10.1007/978-3-642-15567-3_8</a>","ista":"Nowozin S, Gehler P, Lampert C. 2010. On parameter learning in CRF-based approaches to object class image segmentation. ECCV: European Conference on Computer Vision, LNCS, vol. 6316, 98–111."}},{"status":"public","oa_version":"Submitted Version","author":[{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"full_name":"Morozov, Dmitriy","last_name":"Morozov","first_name":"Dmitriy"},{"last_name":"Patel","full_name":"Patel, Amit","first_name":"Amit","id":"34A254A0-F248-11E8-B48F-1D18A9856A87"}],"page":"27 - 42","year":"2010","pubrep_id":"538","language":[{"iso":"eng"}],"oa":1,"ddc":["000"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The (apparent) contour of a smooth mapping from a 2-manifold to the plane, f: M → R2 , is the set of critical values, that is, the image of the points at which the gradients of the two component functions are linearly dependent. Assuming M is compact and orientable and measuring difference with the erosion distance, we prove that the contour is stable.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:16Z","department":[{"_id":"HeEd"}],"publist_id":"2428","date_updated":"2021-01-12T07:52:15Z","date_created":"2018-12-11T12:05:13Z","citation":{"ieee":"H. Edelsbrunner, D. Morozov, and A. Patel, “The stability of the apparent contour of an orientable 2-manifold,” in <i>Topological Data Analysis and Visualization: Theory, Algorithms and Applications</i>, Springer, 2010, pp. 27–42.","short":"H. Edelsbrunner, D. Morozov, A. Patel, in:, Topological Data Analysis and Visualization: Theory, Algorithms and Applications, Springer, 2010, pp. 27–42.","mla":"Edelsbrunner, Herbert, et al. “The Stability of the Apparent Contour of an Orientable 2-Manifold.” <i>Topological Data Analysis and Visualization: Theory, Algorithms and Applications</i>, Springer, 2010, pp. 27–42, doi:<a href=\"https://doi.org/10.1007/978-3-642-15014-2_3\">10.1007/978-3-642-15014-2_3</a>.","chicago":"Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “The Stability of the Apparent Contour of an Orientable 2-Manifold.” In <i>Topological Data Analysis and Visualization: Theory, Algorithms and Applications</i>, 27–42. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-15014-2_3\">https://doi.org/10.1007/978-3-642-15014-2_3</a>.","ista":"Edelsbrunner H, Morozov D, Patel A. 2010.The stability of the apparent contour of an orientable 2-manifold. In: Topological Data Analysis and Visualization: Theory, Algorithms and Applications. Mathematics and Visualization, , 27–42.","apa":"Edelsbrunner, H., Morozov, D., &#38; Patel, A. (2010). The stability of the apparent contour of an orientable 2-manifold. In <i>Topological Data Analysis and Visualization: Theory, Algorithms and Applications</i> (pp. 27–42). Springer. <a href=\"https://doi.org/10.1007/978-3-642-15014-2_3\">https://doi.org/10.1007/978-3-642-15014-2_3</a>","ama":"Edelsbrunner H, Morozov D, Patel A. The stability of the apparent contour of an orientable 2-manifold. In: <i>Topological Data Analysis and Visualization: Theory, Algorithms and Applications</i>. Springer; 2010:27-42. doi:<a href=\"https://doi.org/10.1007/978-3-642-15014-2_3\">10.1007/978-3-642-15014-2_3</a>"},"acknowledgement":"This research is partially supported by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.","month":"12","_id":"3795","doi":"10.1007/978-3-642-15014-2_3","file":[{"date_updated":"2020-07-14T12:46:16Z","date_created":"2018-12-12T10:11:40Z","relation":"main_file","access_level":"open_access","file_id":"4896","checksum":"f03a44c3d1c3e2d4fedb3b94404f3fd5","content_type":"application/pdf","creator":"system","file_size":210710,"file_name":"IST-2016-538-v1+1_2011-B-02-ApparentContour.pdf"}],"publication":"Topological Data Analysis and Visualization: Theory, Algorithms and Applications","day":"22","date_published":"2010-12-22T00:00:00Z","title":"The stability of the apparent contour of an orientable 2-manifold","publisher":"Springer","type":"book_chapter","scopus_import":1,"publication_status":"published","quality_controlled":"1","alternative_title":["Mathematics and Visualization"],"has_accepted_license":"1"},{"_id":"3831","year":"2010","extern":1,"issue":"2","doi":"10.1073/pnas.0910716107","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818894/#!po=4.16667","open_access":"1"}],"volume":107,"intvolume":"       107","status":"public","publist_id":"2379","date_updated":"2021-01-12T07:52:31Z","date_created":"2018-12-11T12:05:24Z","citation":{"ama":"Norenberg A, Hu H, Vida I, Bartos M, Jonas PM. Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons. <i>PNAS</i>. 2010;107(2):894-899. doi:<a href=\"https://doi.org/10.1073/pnas.0910716107\">10.1073/pnas.0910716107</a>","apa":"Norenberg, A., Hu, H., Vida, I., Bartos, M., &#38; Jonas, P. M. (2010). Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0910716107\">https://doi.org/10.1073/pnas.0910716107</a>","ista":"Norenberg A, Hu H, Vida I, Bartos M, Jonas PM. 2010. Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons. PNAS. 107(2), 894–9.","chicago":"Norenberg, Anja, Hua Hu, Imre Vida, Marlene Bartos, and Peter M Jonas. “Distinct Nonuniform Cable Properties Optimize Rapid and Efficient Activation of Fast-Spiking GABAergic Interneurons.” <i>PNAS</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.0910716107\">https://doi.org/10.1073/pnas.0910716107</a>.","short":"A. Norenberg, H. Hu, I. Vida, M. Bartos, P.M. Jonas, PNAS 107 (2010) 894–9.","mla":"Norenberg, Anja, et al. “Distinct Nonuniform Cable Properties Optimize Rapid and Efficient Activation of Fast-Spiking GABAergic Interneurons.” <i>PNAS</i>, vol. 107, no. 2, National Academy of Sciences, 2010, pp. 894–99, doi:<a href=\"https://doi.org/10.1073/pnas.0910716107\">10.1073/pnas.0910716107</a>.","ieee":"A. Norenberg, H. Hu, I. Vida, M. Bartos, and P. M. Jonas, “Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons,” <i>PNAS</i>, vol. 107, no. 2. National Academy of Sciences, pp. 894–9, 2010."},"author":[{"full_name":"Norenberg, Anja","last_name":"Norenberg","first_name":"Anja"},{"first_name":"Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","last_name":"Hu","full_name":"Hua Hu"},{"last_name":"Vida","full_name":"Vida, Imre","first_name":"Imre"},{"last_name":"Bartos","full_name":"Bartos, Marlene","first_name":"Marlene"},{"full_name":"Peter Jonas","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"page":"894 - 9","month":"01","publisher":"National Academy of Sciences","abstract":[{"lang":"eng","text":"Fast-spiking, parvalbumin-expressing basket cells (BCs) play a key role in feedforward and feedback inhibition in the hippocampus. However, the dendritic mechanisms underlying rapid interneuron recruitment have remained unclear. To quantitatively address this question, we developed detailed passive cable models of BCs in the dentate gyrus based on dual somatic or somatodendritic recordings and complete morphologic reconstructions. Both specific membrane capacitance and axial resistivity were comparable to those of pyramidal neurons, but the average somatodendritic specific membrane resistance (R(m)) was substantially lower in BCs. Furthermore, R(m) was markedly nonuniform, being lowest in soma and proximal dendrites, intermediate in distal dendrites, and highest in the axon. Thus, the somatodendritic gradient of R(m) was the reverse of that in pyramidal neurons. Further computational analysis revealed that these unique cable properties accelerate the time course of synaptic potentials at the soma in response to fast inputs, while boosting the efficacy of slow distal inputs. These properties will facilitate both rapid phasic and efficient tonic activation of BCs in hippocampal microcircuits."}],"type":"journal_article","quality_controlled":0,"publication_status":"published","publication":"PNAS","day":"01","title":"Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons","date_published":"2010-01-01T00:00:00Z","oa":1}]