[{"year":"2016","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","oa":1,"publication_identifier":{"isbn":["9780262339360"]},"title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","article_processing_charge":"No","date_updated":"2021-01-12T08:16:53Z","_id":"8094","conference":{"end_date":"2016-07-08","start_date":"2016-07-04","name":"ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems","location":"Cancun, Mexico"},"day":"01","date_published":"2016-09-01T00:00:00Z","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius","full_name":"Martius, Georg S","first_name":"Georg S"},{"last_name":"Hostettler","full_name":"Hostettler, Rafael","first_name":"Rafael"},{"last_name":"Knoll","full_name":"Knoll, Alois","first_name":"Alois"},{"last_name":"Der","first_name":"Ralf","full_name":"Der, Ralf"}],"doi":"10.7551/978-0-262-33936-0-ch029","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_created":"2020-07-05T22:00:47Z","volume":28,"intvolume":"        28","month":"09","page":"142-143","ec_funded":1,"ddc":["610"],"type":"conference","abstract":[{"text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publisher":"MIT Press","scopus_import":1,"file_date_updated":"2020-07-14T12:48:09Z","publication":"Proceedings of the Artificial Life Conference 2016","file":[{"file_id":"8096","creator":"cziletti","access_level":"open_access","checksum":"cff63e7a4b8ac466ba51a9c84153a940","content_type":"application/pdf","file_name":"2016_ProcALIFE_Martius.pdf","date_updated":"2020-07-14T12:48:09Z","file_size":678670,"date_created":"2020-07-06T12:59:09Z","relation":"main_file"}],"quality_controlled":"1","citation":{"ama":"Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: <i>Proceedings of the Artificial Life Conference 2016</i>. Vol 28. MIT Press; 2016:142-143. doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>","chicago":"Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In <i>Proceedings of the Artificial Life Conference 2016</i>, 28:142–43. MIT Press, 2016. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>.","apa":"Martius, G. S., Hostettler, R., Knoll, A., &#38; Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In <i>Proceedings of the Artificial Life Conference 2016</i> (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>","ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in <i>Proceedings of the Artificial Life Conference 2016</i>, Cancun, Mexico, 2016, vol. 28, pp. 142–143.","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. Proceedings of the Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial Life Conference 2016, MIT Press, 2016, pp. 142–143.","mla":"Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” <i>Proceedings of the Artificial Life Conference 2016</i>, vol. 28, MIT Press, 2016, pp. 142–43, doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>."},"publication_status":"published"},{"publication":"bioRxiv","date_published":"2016-07-29T00:00:00Z","publisher":"Cold Spring Harbor Laboratory","day":"29","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The stimulus selectivity of synaptic currents in cortical neurons often shows a co-tuning of excitation and inhibition, but the mechanisms that underlie the emergence and plasticity of this co-tuning are not fully understood. Using a computational model, we show that an interaction of excitatory and inhibitory synaptic plasticity reproduces both the developmental and – when combined with a disinhibitory gate – the adult plasticity of excitatory and inhibitory receptive fields in auditory cortex. The co-tuning arises from inhibitory plasticity that balances excitation and inhibition, while excitatory stimulus selectivity can result from two different mechanisms. Inhibitory inputs with a broad stimulus tuning introduce a sliding threshold as in Bienenstock-Cooper-Munro rules, introducing an excitatory stimulus selectivity at the cost of a broader inhibitory receptive field. Alternatively, input asymmetries can be amplified by synaptic competition. The latter leaves any receptive field plasticity transient, a prediction we verify in recordings in auditory cortex."}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_created":"2020-07-16T12:26:55Z","publication_status":"published","citation":{"short":"C. Clopath, T.P. Vogels, R.C. Froemke, H. Sprekeler, BioRxiv (2016).","mla":"Clopath, Claudia, et al. “Receptive Field Formation by Interacting Excitatory and Inhibitory Synaptic Plasticity.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2016.","ista":"Clopath C, Vogels TP, Froemke RC, Sprekeler H. 2016. Receptive field formation by interacting excitatory and inhibitory synaptic plasticity. bioRxiv, .","ieee":"C. Clopath, T. P. Vogels, R. C. Froemke, and H. Sprekeler, “Receptive field formation by interacting excitatory and inhibitory synaptic plasticity,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2016.","apa":"Clopath, C., Vogels, T. P., Froemke, R. C., &#38; Sprekeler, H. (2016). Receptive field formation by interacting excitatory and inhibitory synaptic plasticity. <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","chicago":"Clopath, Claudia, Tim P Vogels, Robert C. Froemke, and Henning Sprekeler. “Receptive Field Formation by Interacting Excitatory and Inhibitory Synaptic Plasticity.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2016.","ama":"Clopath C, Vogels TP, Froemke RC, Sprekeler H. Receptive field formation by interacting excitatory and inhibitory synaptic plasticity. <i>bioRxiv</i>. 2016."},"extern":"1","author":[{"first_name":"Claudia","full_name":"Clopath, Claudia","last_name":"Clopath"},{"orcid":"0000-0003-3295-6181","first_name":"Tim P","full_name":"Vogels, Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"full_name":"Froemke, Robert C.","first_name":"Robert C.","last_name":"Froemke"},{"last_name":"Sprekeler","full_name":"Sprekeler, Henning","first_name":"Henning"}],"status":"public","oa_version":"Preprint","oa":1,"page":"43","month":"07","year":"2016","type":"preprint","_id":"8128","date_updated":"2021-01-12T08:17:02Z","article_processing_charge":"No","title":"Receptive field formation by interacting excitatory and inhibitory synaptic plasticity","main_file_link":[{"url":"https://doi.org/10.1101/066589 ","open_access":"1"}]},{"month":"05","intvolume":"        90","acknowledgement":"Work in the laboratory of John A. G. Briggs was funded by Deutsche\nForschungsgemeinschaft (DFG) (BR 3635/2-1). This work, including the\nefforts of Tomas Ruml, was funded by the Grant Agency of the Czech\nRepublic (14-15326S) and the Czech Ministry of Education (NPU I sus-\ntainability projects LO1302 and LO1304).","year":"2016","issue":"9","page":"4593 - 4603","title":"Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging","date_updated":"2021-01-12T08:17:03Z","type":"journal_article","_id":"813","publist_id":"6835","abstract":[{"lang":"eng","text":"The Gag polyprotein of retroviruses drives immature virus assembly by forming hexameric protein lattices. The assembly is primarily mediated by protein-protein interactions between capsid (CA) domains and by interactions between nucleocapsid (NC) domains and RNA. Specific interactions between NC and the viral RNA are required for genome packaging. Previously reported cryoelectron microscopy analysis of immature Mason-Pfizer monkey virus (M-PMV) particles suggested that a basic region (residues RKK) in CA may serve as an additional binding site for nucleic acids. Here, we have introduced mutations into the RKK region in both bacterial and proviral M-PMV vectors and have assessed their impact on M-PMV assembly, structure, RNA binding, budding/release, nuclear trafficking, and infectivity using in vitro and in vivo systems. Our data indicate that the RKK region binds and structures nucleic acid that serves to promote virus particle assembly in the cytoplasm. Moreover, the RKK region appears to be important for recruitment of viral genomic RNA into Gag particles, and this function could be linked to changes in nuclear trafficking. Together these observations suggest that in M-PMV, direct interactions between CA and nucleic acid play important functions in the late stages of the viral life cycle."}],"date_published":"2016-05-01T00:00:00Z","publication":"Journal of Virology","day":"01","publisher":"ASM","quality_controlled":0,"author":[{"last_name":"Füzik","full_name":"Füzik, Tibor","first_name":"Tibor"},{"last_name":"Píchalová","first_name":"Růžena","full_name":" Píchalová, Růžena"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian","full_name":"Florian Schur","orcid":"0000-0003-4790-8078"},{"full_name":"Strohalmová, Karolína","first_name":"Karolína","last_name":"Strohalmová"},{"full_name":"Křížová, Ivana","first_name":"Ivana","last_name":"Křížová"},{"full_name":"Hadravová, Romana","first_name":"Romana","last_name":"Hadravová"},{"last_name":"Rumlová","first_name":"Michaela","full_name":"Rumlová, Michaela"},{"last_name":"Briggs","first_name":"John","full_name":"Briggs, John A"},{"last_name":"Ulbrich","first_name":"Pavel","full_name":"Ulbrich, Pavel"},{"last_name":"Ruml","full_name":"Ruml, Tomáš","first_name":"Tomáš"}],"status":"public","extern":1,"citation":{"chicago":"Füzik, Tibor, Růžena Píchalová, Florian KM Schur, Karolína Strohalmová, Ivana Křížová, Romana Hadravová, Michaela Rumlová, John Briggs, Pavel Ulbrich, and Tomáš Ruml. “Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA Promotes Virus Assembly and Genome Packaging.” <i>Journal of Virology</i>. ASM, 2016. <a href=\"https://doi.org/10.1128/JVI.03197-15\">https://doi.org/10.1128/JVI.03197-15</a>.","apa":"Füzik, T., Píchalová, R., Schur, F. K., Strohalmová, K., Křížová, I., Hadravová, R., … Ruml, T. (2016). Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging. <i>Journal of Virology</i>. ASM. <a href=\"https://doi.org/10.1128/JVI.03197-15\">https://doi.org/10.1128/JVI.03197-15</a>","ama":"Füzik T, Píchalová R, Schur FK, et al. Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging. <i>Journal of Virology</i>. 2016;90(9):4593-4603. doi:<a href=\"https://doi.org/10.1128/JVI.03197-15\">10.1128/JVI.03197-15</a>","mla":"Füzik, Tibor, et al. “Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA Promotes Virus Assembly and Genome Packaging.” <i>Journal of Virology</i>, vol. 90, no. 9, ASM, 2016, pp. 4593–603, doi:<a href=\"https://doi.org/10.1128/JVI.03197-15\">10.1128/JVI.03197-15</a>.","short":"T. Füzik, R. Píchalová, F.K. Schur, K. Strohalmová, I. Křížová, R. Hadravová, M. Rumlová, J. Briggs, P. Ulbrich, T. Ruml, Journal of Virology 90 (2016) 4593–4603.","ieee":"T. Füzik <i>et al.</i>, “Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging,” <i>Journal of Virology</i>, vol. 90, no. 9. ASM, pp. 4593–4603, 2016.","ista":"Füzik T, Píchalová R, Schur FK, Strohalmová K, Křížová I, Hadravová R, Rumlová M, Briggs J, Ulbrich P, Ruml T. 2016. Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly and genome packaging. Journal of Virology. 90(9), 4593–4603."},"publication_status":"published","date_created":"2018-12-11T11:48:38Z","volume":90,"doi":"10.1128/JVI.03197-15"},{"publist_id":"6834","abstract":[{"lang":"eng","text":"Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity. The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator of assembly and maturation and is the target of MIs.We applied optimized cryo-electron tomography and subtomogram averaging to resolve this region within assembled immature HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure reveals a network of intra- And intermolecular interactions mediating immature HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible to protease.We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure, and MI resistance develops by destabilizing CA-SP1."}],"date_published":"2016-07-29T00:00:00Z","publication":"Science","day":"29","publisher":"American Association for the Advancement of Science","status":"public","quality_controlled":0,"author":[{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian","full_name":"Florian Schur"},{"last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Martin Obr","first_name":"Martin"},{"last_name":"Hagen","full_name":"Hagen, Wim J","first_name":"Wim"},{"last_name":"Wan","full_name":"Wan, William","first_name":"William"},{"last_name":"Jakobi","full_name":"Jakobi, Arjen J","first_name":"Arjen"},{"first_name":"Joanna","full_name":"Kirkpatrick, Joanna M","last_name":"Kirkpatrick"},{"first_name":"Carsten","full_name":"Sachse, Carsten","last_name":"Sachse"},{"first_name":"Hans","full_name":"Kraüsslich, Hans Georg","last_name":"Kraüsslich"},{"first_name":"John","full_name":"Briggs, John A","last_name":"Briggs"}],"extern":1,"citation":{"apa":"Schur, F. K., Obr, M., Hagen, W., Wan, W., Jakobi, A., Kirkpatrick, J., … Briggs, J. (2016). An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaf9620\">https://doi.org/10.1126/science.aaf9620</a>","chicago":"Schur, Florian KM, Martin Obr, Wim Hagen, William Wan, Arjen Jakobi, Joanna Kirkpatrick, Carsten Sachse, Hans Kraüsslich, and John Briggs. “An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation.” <i>Science</i>. American Association for the Advancement of Science, 2016. <a href=\"https://doi.org/10.1126/science.aaf9620\">https://doi.org/10.1126/science.aaf9620</a>.","ama":"Schur FK, Obr M, Hagen W, et al. An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. <i>Science</i>. 2016;353(6298):506-508. doi:<a href=\"https://doi.org/10.1126/science.aaf9620\">10.1126/science.aaf9620</a>","short":"F.K. Schur, M. Obr, W. Hagen, W. Wan, A. Jakobi, J. Kirkpatrick, C. Sachse, H. Kraüsslich, J. Briggs, Science 353 (2016) 506–508.","mla":"Schur, Florian KM, et al. “An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation.” <i>Science</i>, vol. 353, no. 6298, American Association for the Advancement of Science, 2016, pp. 506–08, doi:<a href=\"https://doi.org/10.1126/science.aaf9620\">10.1126/science.aaf9620</a>.","ista":"Schur FK, Obr M, Hagen W, Wan W, Jakobi A, Kirkpatrick J, Sachse C, Kraüsslich H, Briggs J. 2016. An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. Science. 353(6298), 506–508.","ieee":"F. K. Schur <i>et al.</i>, “An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation,” <i>Science</i>, vol. 353, no. 6298. American Association for the Advancement of Science, pp. 506–508, 2016."},"publication_status":"published","date_created":"2018-12-11T11:48:39Z","volume":353,"doi":"10.1126/science.aaf9620","month":"07","acknowledgement":"The authors thank B. Glass for preparation of the immature HIV-1 (D25A) sample; J. Plitzko and D. Tegunov for providing the K2Align software; and S. Mattei, N. Hoffman, F. Thommen, A. Sonnen, and S. Dodonova for technical assistance and/or discussion. This study was supported by Deutsche Forschungsgemeinschaft grants BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1 (to H.-G.K.). The Briggs laboratory acknowledges financial support from the European Molecular Biology Laboratory (EMBL) and from the Chica und Heinz Schaller Stiftung. W.W. was supported by a European Molecular Biology Organization Long-Term Fellowship (ALTF 748-2014). A.J.J. acknowledges support by the EMBL Interdisciplinary Postdoc Program under the Marie Curie Action COFUND (PCOFUND-GA-2008-229597) and by the Joachim Herz Stiftung. This study was technically supported by the EMBL information technology services unit and the EMBL Proteomics Core Facility. F.K.M.S., M.O., H.-G.K., and J.A.G.B. designed the experiments, with J.M.K. assisting in the design of those involving mass spectrometry. F.K.M.S. and M.O. prepared samples. W.J.H.H. implemented tomography acquisition schemes. F.K.M.S. and W.J.H.H. acquired the data. F.K.M.S. and W.W. processed images. F.K.M.S., A.J.J., and C.S. refined the model. F.K.M.S., M.O., and J.A.G.B. analyzed the data. F.K.M.S. and J.A.G.B. wrote the manuscript with support from all authors. Representative tomograms and the final electron microscopy structures have been deposited in the Electron Microscopy Data Bank with accession numbers EMD-4015, EMD-4016, EMD-4017, EMD-4018, EMD-4019, and EMD-4020. The refined HIV-1 CA-SP1 model has been deposited in the Protein Data Bank with accession number 5L93.","intvolume":"       353","year":"2016","issue":"6298","page":"506 - 508","title":"An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation","date_updated":"2021-01-12T08:17:12Z","type":"journal_article","_id":"816"},{"scopus_import":1,"file":[{"checksum":"7659296174fa75f5f0364f31f46f4bcf","content_type":"application/pdf","access_level":"open_access","creator":"system","file_id":"5012","relation":"main_file","date_created":"2018-12-12T10:13:29Z","file_size":483258,"date_updated":"2020-07-14T12:44:56Z","file_name":"IST-2017-766-v1+1_678.pdf"}],"file_date_updated":"2020-07-14T12:44:56Z","publication":"Computational Complexity","publisher":"Springer","department":[{"_id":"KrPi"}],"publist_id":"5715","language":[{"iso":"eng"}],"abstract":[{"text":"Most entropy notions H(.) like Shannon or min-entropy satisfy a chain rule stating that for random variables X,Z, and A we have H(X|Z,A)≥H(X|Z)−|A|. That is, by conditioning on A the entropy of X can decrease by at most the bitlength |A| of A. Such chain rules are known to hold for some computational entropy notions like Yao’s and unpredictability-entropy. For HILL entropy, the computational analogue of min-entropy, the chain rule is of special interest and has found many applications, including leakage-resilient cryptography, deterministic encryption, and memory delegation. These applications rely on restricted special cases of the chain rule. Whether the chain rule for conditional HILL entropy holds in general was an open problem for which we give a strong negative answer: we construct joint distributions (X,Z,A), where A is a distribution over a single bit, such that the HILL entropy H HILL (X|Z) is large but H HILL (X|Z,A) is basically zero.\r\n\r\nOur counterexample just makes the minimal assumption that NP⊈P/poly. Under the stronger assumption that injective one-way function exist, we can make all the distributions efficiently samplable.\r\n\r\nFinally, we show that some more sophisticated cryptographic objects like lossy functions can be used to sample a distribution constituting a counterexample to the chain rule making only a single invocation to the underlying object.","lang":"eng"}],"publication_status":"published","quality_controlled":"1","citation":{"chicago":"Krenn, Stephan, Krzysztof Z Pietrzak, Akshay Wadia, and Daniel Wichs. “A Counterexample to the Chain Rule for Conditional HILL Entropy.” <i>Computational Complexity</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00037-015-0120-9\">https://doi.org/10.1007/s00037-015-0120-9</a>.","apa":"Krenn, S., Pietrzak, K. Z., Wadia, A., &#38; Wichs, D. (2016). A counterexample to the chain rule for conditional HILL entropy. <i>Computational Complexity</i>. Springer. <a href=\"https://doi.org/10.1007/s00037-015-0120-9\">https://doi.org/10.1007/s00037-015-0120-9</a>","ama":"Krenn S, Pietrzak KZ, Wadia A, Wichs D. A counterexample to the chain rule for conditional HILL entropy. <i>Computational Complexity</i>. 2016;25(3):567-605. doi:<a href=\"https://doi.org/10.1007/s00037-015-0120-9\">10.1007/s00037-015-0120-9</a>","mla":"Krenn, Stephan, et al. “A Counterexample to the Chain Rule for Conditional HILL Entropy.” <i>Computational Complexity</i>, vol. 25, no. 3, Springer, 2016, pp. 567–605, doi:<a href=\"https://doi.org/10.1007/s00037-015-0120-9\">10.1007/s00037-015-0120-9</a>.","short":"S. Krenn, K.Z. Pietrzak, A. Wadia, D. Wichs, Computational Complexity 25 (2016) 567–605.","ista":"Krenn S, Pietrzak KZ, Wadia A, Wichs D. 2016. A counterexample to the chain rule for conditional HILL entropy. Computational Complexity. 25(3), 567–605.","ieee":"S. Krenn, K. Z. Pietrzak, A. Wadia, and D. Wichs, “A counterexample to the chain rule for conditional HILL entropy,” <i>Computational Complexity</i>, vol. 25, no. 3. Springer, pp. 567–605, 2016."},"issue":"3","page":"567 - 605","ec_funded":1,"month":"09","pubrep_id":"766","intvolume":"        25","ddc":["004"],"type":"journal_article","date_published":"2016-09-01T00:00:00Z","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:52:16Z","volume":25,"doi":"10.1007/s00037-015-0120-9","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","last_name":"Krenn","full_name":"Krenn, Stephan","first_name":"Stephan","orcid":"0000-0003-2835-9093"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"},{"last_name":"Wadia","first_name":"Akshay","full_name":"Wadia, Akshay"},{"first_name":"Daniel","full_name":"Wichs, Daniel","last_name":"Wichs"}],"oa_version":"Submitted Version","oa":1,"has_accepted_license":"1","year":"2016","project":[{"grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"This work was partly funded by the European Research Council under ERC Starting Grant 259668-PSPC and ERC Advanced Grant 321310-PERCY.\r\n","related_material":{"record":[{"id":"2940","status":"public","relation":"earlier_version"}]},"date_updated":"2023-02-23T11:05:09Z","_id":"1479","title":"A counterexample to the chain rule for conditional HILL entropy"},{"date_updated":"2021-01-12T06:51:02Z","type":"journal_article","_id":"1480","title":"Exponential varieties","main_file_link":[{"url":"http://arxiv.org/abs/1412.6185","open_access":"1"}],"issue":"1","page":"27 - 56","oa":1,"month":"01","year":"2016","intvolume":"       112","date_created":"2018-12-11T11:52:16Z","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":112,"doi":"10.1112/plms/pdv066","quality_controlled":"1","author":[{"full_name":"Michałek, Mateusz","first_name":"Mateusz","last_name":"Michałek"},{"last_name":"Sturmfels","full_name":"Sturmfels, Bernd","first_name":"Bernd"},{"last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","first_name":"Caroline"},{"last_name":"Zwiernik","full_name":"Zwiernik, Piotr","first_name":"Piotr"}],"status":"public","citation":{"ama":"Michałek M, Sturmfels B, Uhler C, Zwiernik P. Exponential varieties. <i>Proceedings of the London Mathematical Society</i>. 2016;112(1):27-56. doi:<a href=\"https://doi.org/10.1112/plms/pdv066\">10.1112/plms/pdv066</a>","apa":"Michałek, M., Sturmfels, B., Uhler, C., &#38; Zwiernik, P. (2016). Exponential varieties. <i>Proceedings of the London Mathematical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1112/plms/pdv066\">https://doi.org/10.1112/plms/pdv066</a>","chicago":"Michałek, Mateusz, Bernd Sturmfels, Caroline Uhler, and Piotr Zwiernik. “Exponential Varieties.” <i>Proceedings of the London Mathematical Society</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1112/plms/pdv066\">https://doi.org/10.1112/plms/pdv066</a>.","ista":"Michałek M, Sturmfels B, Uhler C, Zwiernik P. 2016. Exponential varieties. Proceedings of the London Mathematical Society. 112(1), 27–56.","ieee":"M. Michałek, B. Sturmfels, C. Uhler, and P. Zwiernik, “Exponential varieties,” <i>Proceedings of the London Mathematical Society</i>, vol. 112, no. 1. Oxford University Press, pp. 27–56, 2016.","short":"M. Michałek, B. Sturmfels, C. Uhler, P. Zwiernik, Proceedings of the London Mathematical Society 112 (2016) 27–56.","mla":"Michałek, Mateusz, et al. “Exponential Varieties.” <i>Proceedings of the London Mathematical Society</i>, vol. 112, no. 1, Oxford University Press, 2016, pp. 27–56, doi:<a href=\"https://doi.org/10.1112/plms/pdv066\">10.1112/plms/pdv066</a>."},"oa_version":"Preprint","date_published":"2016-01-07T00:00:00Z","scopus_import":1,"publication":"Proceedings of the London Mathematical Society","day":"07","publisher":"Oxford University Press","language":[{"iso":"eng"}],"department":[{"_id":"CaUh"}],"publist_id":"5714","abstract":[{"text":"Exponential varieties arise from exponential families in statistics. These real algebraic varieties have strong positivity and convexity properties, familiar from toric varieties and their moment maps. Among them are varieties of inverses of symmetric matrices satisfying linear constraints. This class includes Gaussian graphical models. We develop a general theory of exponential varieties. These are derived from hyperbolic polynomials and their integral representations. We compare the multidegrees and ML degrees of the gradient map for hyperbolic polynomials. ","lang":"eng"}]},{"oa":1,"has_accepted_license":"1","acknowledgement":"We thank J. Traas, B. Müller and V. Reddy for providing seed materials and Y. Deb for advice regarding the laser ablation experiments. We specially thank Thomas Laux for stimulating discussions and support in the initial phase of this project.","year":"2016","date_updated":"2021-01-12T06:51:03Z","_id":"1482","title":"Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization","date_published":"2016-02-01T00:00:00Z","day":"01","date_created":"2018-12-11T11:52:17Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":11,"doi":"10.1371/journal.pone.0147830","author":[{"first_name":"Milad","full_name":"Adibi, Milad","last_name":"Adibi"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","last_name":"Yoshida","full_name":"Yoshida, Saiko","first_name":"Saiko"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"},{"first_name":"Christian","full_name":"Fleck, Christian","last_name":"Fleck"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa_version":"Published Version","issue":"2","month":"02","pubrep_id":"521","intvolume":"        11","article_number":"e0147830","ddc":["570"],"type":"journal_article","file":[{"file_size":4297148,"date_created":"2018-12-12T10:14:16Z","file_name":"IST-2016-521-v1+1_journal.pone.0147830.PDF","date_updated":"2020-07-14T12:44:57Z","relation":"main_file","file_id":"5066","content_type":"application/pdf","checksum":"6066146e527335030f83aa5924ab72a6","creator":"system","access_level":"open_access"}],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:57Z","publication":"PLoS One","publisher":"Public Library of Science","department":[{"_id":"JiFr"}],"publist_id":"5711","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation."}],"publication_status":"published","quality_controlled":"1","citation":{"ama":"Adibi M, Yoshida S, Weijers D, Fleck C. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. <i>PLoS One</i>. 2016;11(2). doi:<a href=\"https://doi.org/10.1371/journal.pone.0147830\">10.1371/journal.pone.0147830</a>","apa":"Adibi, M., Yoshida, S., Weijers, D., &#38; Fleck, C. (2016). Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0147830\">https://doi.org/10.1371/journal.pone.0147830</a>","chicago":"Adibi, Milad, Saiko Yoshida, Dolf Weijers, and Christian Fleck. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” <i>PLoS One</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0147830\">https://doi.org/10.1371/journal.pone.0147830</a>.","ista":"Adibi M, Yoshida S, Weijers D, Fleck C. 2016. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 11(2), e0147830.","ieee":"M. Adibi, S. Yoshida, D. Weijers, and C. Fleck, “Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization,” <i>PLoS One</i>, vol. 11, no. 2. Public Library of Science, 2016.","mla":"Adibi, Milad, et al. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” <i>PLoS One</i>, vol. 11, no. 2, e0147830, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0147830\">10.1371/journal.pone.0147830</a>.","short":"M. Adibi, S. Yoshida, D. Weijers, C. Fleck, PLoS One 11 (2016)."}},{"title":"Environmental and endogenous control of cortical microtubule orientation","_id":"1484","date_updated":"2021-01-12T06:51:04Z","has_accepted_license":"1","acknowledgement":"We thank Maciek Adamowski for helpful discussions and Qiang Zhu and Israel Ausin for critical reading of the manuscript. We sincerely apologize to colleagues whose work we could not include owing to space limitations.","year":"2016","oa":1,"status":"public","author":[{"id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Xu","full_name":"Chen, Xu"},{"full_name":"Wu, Shuang","first_name":"Shuang","last_name":"Wu"},{"first_name":"Zengyu","full_name":"Liu, Zengyu","last_name":"Liu"},{"orcid":"0000-0002-8302-7596","first_name":"Jiřĺ","full_name":"Friml, Jiřĺ","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","volume":26,"date_created":"2018-12-11T11:52:17Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.tcb.2016.02.003","date_published":"2016-06-01T00:00:00Z","day":"01","type":"journal_article","ddc":["581"],"month":"06","intvolume":"        26","pubrep_id":"1002","issue":"6","page":"409 - 419","citation":{"short":"X. Chen, S. Wu, Z. Liu, J. Friml, Trends in Cell Biology 26 (2016) 409–419.","mla":"Chen, Xu, et al. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” <i>Trends in Cell Biology</i>, vol. 26, no. 6, Cell Press, 2016, pp. 409–19, doi:<a href=\"https://doi.org/10.1016/j.tcb.2016.02.003\">10.1016/j.tcb.2016.02.003</a>.","ieee":"X. Chen, S. Wu, Z. Liu, and J. Friml, “Environmental and endogenous control of cortical microtubule orientation,” <i>Trends in Cell Biology</i>, vol. 26, no. 6. Cell Press, pp. 409–419, 2016.","ista":"Chen X, Wu S, Liu Z, Friml J. 2016. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 26(6), 409–419.","apa":"Chen, X., Wu, S., Liu, Z., &#38; Friml, J. (2016). Environmental and endogenous control of cortical microtubule orientation. <i>Trends in Cell Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tcb.2016.02.003\">https://doi.org/10.1016/j.tcb.2016.02.003</a>","chicago":"Chen, Xu, Shuang Wu, Zengyu Liu, and Jiří Friml. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” <i>Trends in Cell Biology</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.tcb.2016.02.003\">https://doi.org/10.1016/j.tcb.2016.02.003</a>.","ama":"Chen X, Wu S, Liu Z, Friml J. Environmental and endogenous control of cortical microtubule orientation. <i>Trends in Cell Biology</i>. 2016;26(6):409-419. doi:<a href=\"https://doi.org/10.1016/j.tcb.2016.02.003\">10.1016/j.tcb.2016.02.003</a>"},"quality_controlled":"1","publication_status":"published","article_type":"review","department":[{"_id":"JiFr"}],"publist_id":"5704","language":[{"iso":"eng"}],"file":[{"file_id":"5155","access_level":"open_access","creator":"system","checksum":"b229e5bb4676ec3e27b7b9ea603b3a63","content_type":"application/pdf","date_updated":"2020-07-14T12:44:57Z","file_name":"IST-2018-1002-v1+1_Chen_TICB_2016_proofs.pdf","date_created":"2018-12-12T10:15:34Z","file_size":2329117,"relation":"main_file"}],"publication":"Trends in Cell Biology","file_date_updated":"2020-07-14T12:44:57Z","scopus_import":1,"publisher":"Cell Press"},{"publication_status":"published","citation":{"ama":"De Martino D. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. <i>Physical Biology</i>. 2016;13(1). doi:<a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">10.1088/1478-3975/13/1/016003</a>","chicago":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” <i>Physical Biology</i>. IOP Publishing Ltd., 2016. <a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">https://doi.org/10.1088/1478-3975/13/1/016003</a>.","apa":"De Martino, D. (2016). Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. <i>Physical Biology</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">https://doi.org/10.1088/1478-3975/13/1/016003</a>","ista":"De Martino D. 2016. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 13(1), 016003.","ieee":"D. De Martino, “Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis,” <i>Physical Biology</i>, vol. 13, no. 1. IOP Publishing Ltd., 2016.","mla":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” <i>Physical Biology</i>, vol. 13, no. 1, 016003, IOP Publishing Ltd., 2016, doi:<a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">10.1088/1478-3975/13/1/016003</a>.","short":"D. De Martino, Physical Biology 13 (2016)."},"quality_controlled":"1","scopus_import":1,"publication":"Physical Biology","publisher":"IOP Publishing Ltd.","language":[{"iso":"eng"}],"publist_id":"5702","department":[{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. Coli in stationary growth conditions from which we infer the metabolites turnover times. However the latter are inferred from net fluxes, and we argue that this approximation is not valid for enzymes working nearby thermodynamic equilibrium. We recalculate turnover times from total fluxes by performing an energy balance analysis of the network and recurring to the fluctuation theorem. We find in many cases values one of order of magnitude lower, implying a faster picture of intermediate metabolism."}],"type":"journal_article","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1505.04613"}],"issue":"1","ec_funded":1,"month":"01","article_number":"016003","intvolume":"        13","volume":13,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:52:18Z","doi":"10.1088/1478-3975/13/1/016003","author":[{"last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele"}],"status":"public","oa_version":"Preprint","date_published":"2016-01-29T00:00:00Z","day":"29","_id":"1485","date_updated":"2021-01-12T06:51:04Z","title":"Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis","oa":1,"year":"2016","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"issue":"2","oa":1,"month":"02","intvolume":"        57","year":"2016","article_number":"021101","date_updated":"2021-01-12T06:51:04Z","_id":"1486","type":"journal_article","title":"The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1511.01995"}],"date_published":"2016-02-24T00:00:00Z","publication":"Journal of Mathematical Physics","scopus_import":1,"publisher":"American Institute of Physics","day":"24","language":[{"iso":"eng"}],"publist_id":"5701","department":[{"_id":"RoSe"}],"abstract":[{"text":"We review recent results concerning the mathematical properties of the Bardeen-Cooper-Schrieffer (BCS) functional of superconductivity, which were obtained in a series of papers, partly in collaboration with R. Frank, E. Hamza, S. Naboko, and J. P. Solovej. Our discussion includes, in particular, an investigation of the critical temperature for a general class of interaction potentials, as well as a study of its dependence on external fields. We shall explain how the Ginzburg-Landau model can be derived from the BCS theory in a suitable parameter regime.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2018-12-11T11:52:18Z","volume":57,"doi":"10.1063/1.4941723","quality_controlled":"1","author":[{"first_name":"Christian","full_name":"Hainzl, Christian","last_name":"Hainzl"},{"first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer"}],"status":"public","citation":{"ama":"Hainzl C, Seiringer R. The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. <i>Journal of Mathematical Physics</i>. 2016;57(2). doi:<a href=\"https://doi.org/10.1063/1.4941723\">10.1063/1.4941723</a>","apa":"Hainzl, C., &#38; Seiringer, R. (2016). The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. <i>Journal of Mathematical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4941723\">https://doi.org/10.1063/1.4941723</a>","chicago":"Hainzl, Christian, and Robert Seiringer. “The Bardeen–Cooper–Schrieffer Functional of Superconductivity and Its Mathematical Properties.” <i>Journal of Mathematical Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1063/1.4941723\">https://doi.org/10.1063/1.4941723</a>.","ieee":"C. Hainzl and R. Seiringer, “The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties,” <i>Journal of Mathematical Physics</i>, vol. 57, no. 2. American Institute of Physics, 2016.","ista":"Hainzl C, Seiringer R. 2016. The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. Journal of Mathematical Physics. 57(2), 021101.","short":"C. Hainzl, R. Seiringer, Journal of Mathematical Physics 57 (2016).","mla":"Hainzl, Christian, and Robert Seiringer. “The Bardeen–Cooper–Schrieffer Functional of Superconductivity and Its Mathematical Properties.” <i>Journal of Mathematical Physics</i>, vol. 57, no. 2, 021101, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1063/1.4941723\">10.1063/1.4941723</a>."},"oa_version":"Preprint"},{"issue":"2","month":"02","article_number":"e1002384","intvolume":"        14","pubrep_id":"518","type":"journal_article","ddc":["570"],"file_date_updated":"2020-07-14T12:44:57Z","publication":"PLoS Biology","file":[{"creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"3a5ce0d4e4e36bd6ceb4be761f85644a","file_id":"5129","relation":"main_file","file_name":"IST-2016-518-v1+1_journal.pbio.1002384.PDF","date_updated":"2020-07-14T12:44:57Z","file_size":2879899,"date_created":"2018-12-12T10:15:11Z"}],"scopus_import":1,"publisher":"Public Library of Science","language":[{"iso":"eng"}],"department":[{"_id":"JoCs"}],"publist_id":"5700","abstract":[{"text":"Rhythms with time scales of multiple cycles per second permeate the mammalian brain, yet neuroscientists are not certain of their functional roles. One leading idea is that coherent oscillation between two brain regions facilitates the exchange of information between them. In rats, the hippocampus and the vibrissal sensorimotor system both are characterized by rhythmic oscillation in the theta range, 5–12 Hz. Previous work has been divided as to whether the two rhythms are independent or coherent. To resolve this question, we acquired three measures from rats—whisker motion, hippocampal local field potential (LFP), and barrel cortex unit firing—during a whisker-mediated texture discrimination task and during control conditions (not engaged in a whisker-mediated memory task). Compared to control conditions, the theta band of hippocampal LFP showed a marked increase in power as the rats approached and then palpated the texture. Phase synchronization between whisking and hippocampal LFP increased by almost 50% during approach and texture palpation. In addition, a greater proportion of barrel cortex neurons showed firing that was phase-locked to hippocampal theta while rats were engaged in the discrimination task. Consistent with a behavioral consequence of phase synchronization, the rats identified the texture more rapidly and with lower error likelihood on trials in which there was an increase in theta-whisking coherence at the moment of texture palpation. These results suggest that coherence between the whisking rhythm, barrel cortex firing, and hippocampal LFP is augmented selectively during epochs in which the rat collects sensory information and that such coherence enhances the efficiency of integration of stimulus information into memory and decision-making centers.","lang":"eng"}],"publication_status":"published","citation":{"ista":"Grion N, Akrami A, Zuo Y, Stella F, Diamond M. 2016. Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. PLoS Biology. 14(2), e1002384.","ieee":"N. Grion, A. Akrami, Y. Zuo, F. Stella, and M. Diamond, “Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination,” <i>PLoS Biology</i>, vol. 14, no. 2. Public Library of Science, 2016.","short":"N. Grion, A. Akrami, Y. Zuo, F. Stella, M. Diamond, PLoS Biology 14 (2016).","mla":"Grion, Natalia, et al. “Coherence between Rat Sensorimotor System and Hippocampus Is Enhanced during Tactile Discrimination.” <i>PLoS Biology</i>, vol. 14, no. 2, e1002384, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002384\">10.1371/journal.pbio.1002384</a>.","ama":"Grion N, Akrami A, Zuo Y, Stella F, Diamond M. Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. <i>PLoS Biology</i>. 2016;14(2). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002384\">10.1371/journal.pbio.1002384</a>","apa":"Grion, N., Akrami, A., Zuo, Y., Stella, F., &#38; Diamond, M. (2016). Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002384\">https://doi.org/10.1371/journal.pbio.1002384</a>","chicago":"Grion, Natalia, Athena Akrami, Yangfang Zuo, Federico Stella, and Mathew Diamond. “Coherence between Rat Sensorimotor System and Hippocampus Is Enhanced during Tactile Discrimination.” <i>PLoS Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.1002384\">https://doi.org/10.1371/journal.pbio.1002384</a>."},"quality_controlled":"1","oa":1,"has_accepted_license":"1","acknowledgement":"We thank Eric Maris, Demian Battaglia, and Rodrigo Quian Quiroga for useful discussions. We are grateful to Fabrizio Manzino and Marco Gigante for construction of the behavioral apparatus, Igor Perkon for developing custom whisker tracking software and to Francesca Pulecchi for animal care and histological processing.","year":"2016","_id":"1487","date_updated":"2021-01-12T06:51:05Z","title":"Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination","date_published":"2016-02-18T00:00:00Z","day":"18","volume":14,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:52:18Z","doi":"10.1371/journal.pbio.1002384","author":[{"last_name":"Grion","first_name":"Natalia","full_name":"Grion, Natalia"},{"last_name":"Akrami","first_name":"Athena","full_name":"Akrami, Athena"},{"first_name":"Yangfang","full_name":"Zuo, Yangfang","last_name":"Zuo"},{"orcid":"0000-0001-9439-3148","first_name":"Federico","full_name":"Stella, Federico","last_name":"Stella","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Diamond, Mathew","first_name":"Mathew","last_name":"Diamond"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa_version":"Published Version"},{"day":"19","date_published":"2016-02-19T00:00:00Z","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"last_name":"Riccio","first_name":"Paul","full_name":"Riccio, Paul"},{"first_name":"Cristina","full_name":"Cebrián, Cristina","last_name":"Cebrián"},{"last_name":"Zong","full_name":"Zong, Hui","first_name":"Hui"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"last_name":"Costantini","first_name":"Frank","full_name":"Costantini, Frank"}],"doi":"10.1371/journal.pbio.1002382","volume":14,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:52:19Z","year":"2016","acknowledgement":"We thank Silvia Arber, Thomas Jessell, Kenneth M. Murphy, Carlton Bates, Hideki Enomoto, Liqun Luo and Andrew McMahon for mouse strains; Thomas Jessell for antibodies; and Laura Martinez Prat for experimental assistance.","has_accepted_license":"1","oa":1,"title":"Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","_id":"1488","date_updated":"2023-02-23T10:01:08Z","related_material":{"record":[{"status":"deleted","id":"9703","relation":"research_data"}]},"abstract":[{"text":"Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis.","lang":"eng"}],"department":[{"_id":"SiHi"}],"publist_id":"5699","language":[{"iso":"eng"}],"publisher":"Public Library of Science","publication":"PLoS Biology","scopus_import":1,"file":[{"content_type":"application/pdf","checksum":"7f8fa1b3a29f94c0a14dd4465278cdbc","access_level":"open_access","creator":"system","file_id":"5027","relation":"main_file","file_size":5904773,"date_created":"2018-12-12T10:13:42Z","date_updated":"2020-07-14T12:44:57Z","file_name":"IST-2016-517-v1+1_journal.pbio.1002382_1_.PDF"}],"file_date_updated":"2020-07-14T12:44:57Z","citation":{"short":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, PLoS Biology 14 (2016).","mla":"Riccio, Paul, et al. “Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” <i>PLoS Biology</i>, vol. 14, no. 2, e1002382, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002382\">10.1371/journal.pbio.1002382</a>.","ista":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2016. Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. PLoS Biology. 14(2), e1002382.","ieee":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis,” <i>PLoS Biology</i>, vol. 14, no. 2. Public Library of Science, 2016.","apa":"Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., &#38; Costantini, F. (2016). Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002382\">https://doi.org/10.1371/journal.pbio.1002382</a>","chicago":"Riccio, Paul, Cristina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank Costantini. “Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” <i>PLoS Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.1002382\">https://doi.org/10.1371/journal.pbio.1002382</a>.","ama":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. <i>PLoS Biology</i>. 2016;14(2). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002382\">10.1371/journal.pbio.1002382</a>"},"quality_controlled":"1","publication_status":"published","article_number":"e1002382","intvolume":"        14","pubrep_id":"517","month":"02","issue":"2","type":"journal_article","ddc":["570"]},{"_id":"1489","date_updated":"2021-01-12T06:51:05Z","title":"Local spectral statistics of Gaussian matrices with correlated entries","article_processing_charge":"Yes (via OA deal)","oa":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). Oskari H. Ajanki was Partially supported by ERC Advanced Grant RANMAT No. 338804, and SFB-TR 12 Grant of the German Research Council. László Erdős was Partially supported by ERC Advanced Grant RANMAT No. 338804. Torben Krüger was Partially supported by ERC Advanced Grant RANMAT No. 338804, and SFB-TR 12 Grant of the German Research Council.","project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"year":"2016","has_accepted_license":"1","doi":"10.1007/s10955-016-1479-y","volume":163,"date_created":"2018-12-11T11:52:19Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"full_name":"Ajanki, Oskari H","first_name":"Oskari H","last_name":"Ajanki","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös"},{"orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87"}],"status":"public","day":"01","date_published":"2016-04-01T00:00:00Z","type":"journal_article","ddc":["510"],"ec_funded":1,"page":"280 - 302","issue":"2","pubrep_id":"516","intvolume":"       163","month":"04","publication_status":"published","citation":{"short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Journal of Statistical Physics 163 (2016) 280–302.","mla":"Ajanki, Oskari H., et al. “Local Spectral Statistics of Gaussian Matrices with Correlated Entries.” <i>Journal of Statistical Physics</i>, vol. 163, no. 2, Springer, 2016, pp. 280–302, doi:<a href=\"https://doi.org/10.1007/s10955-016-1479-y\">10.1007/s10955-016-1479-y</a>.","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Local spectral statistics of Gaussian matrices with correlated entries,” <i>Journal of Statistical Physics</i>, vol. 163, no. 2. Springer, pp. 280–302, 2016.","ista":"Ajanki OH, Erdös L, Krüger TH. 2016. Local spectral statistics of Gaussian matrices with correlated entries. Journal of Statistical Physics. 163(2), 280–302.","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Local Spectral Statistics of Gaussian Matrices with Correlated Entries.” <i>Journal of Statistical Physics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s10955-016-1479-y\">https://doi.org/10.1007/s10955-016-1479-y</a>.","apa":"Ajanki, O. H., Erdös, L., &#38; Krüger, T. H. (2016). Local spectral statistics of Gaussian matrices with correlated entries. <i>Journal of Statistical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s10955-016-1479-y\">https://doi.org/10.1007/s10955-016-1479-y</a>","ama":"Ajanki OH, Erdös L, Krüger TH. Local spectral statistics of Gaussian matrices with correlated entries. <i>Journal of Statistical Physics</i>. 2016;163(2):280-302. doi:<a href=\"https://doi.org/10.1007/s10955-016-1479-y\">10.1007/s10955-016-1479-y</a>"},"quality_controlled":"1","publisher":"Springer","scopus_import":1,"publication":"Journal of Statistical Physics","file":[{"file_id":"4869","access_level":"open_access","creator":"system","checksum":"7139598dcb1cafbe6866bd2bfd732b33","content_type":"application/pdf","date_updated":"2020-07-14T12:44:57Z","file_name":"IST-2016-516-v1+1_s10955-016-1479-y.pdf","file_size":660602,"date_created":"2018-12-12T10:11:16Z","relation":"main_file"}],"file_date_updated":"2020-07-14T12:44:57Z","abstract":[{"text":"We prove optimal local law, bulk universality and non-trivial decay for the off-diagonal elements of the resolvent for a class of translation invariant Gaussian random matrix ensembles with correlated entries. ","lang":"eng"}],"department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"publist_id":"5698"},{"quality_controlled":"1","citation":{"ista":"Russo E, Teijeira A, Vaahtomeri K, Willrodt A, Bloch J, Nitschké M, Santambrogio L, Kerjaschki D, Sixt MK, Halin C. 2016. Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. Cell Reports. 14(7), 1723–1734.","ieee":"E. Russo <i>et al.</i>, “Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels,” <i>Cell Reports</i>, vol. 14, no. 7. Cell Press, pp. 1723–1734, 2016.","short":"E. Russo, A. Teijeira, K. Vaahtomeri, A. Willrodt, J. Bloch, M. Nitschké, L. Santambrogio, D. Kerjaschki, M.K. Sixt, C. Halin, Cell Reports 14 (2016) 1723–1734.","mla":"Russo, Erica, et al. “Intralymphatic CCL21 Promotes Tissue Egress of Dendritic Cells through Afferent Lymphatic Vessels.” <i>Cell Reports</i>, vol. 14, no. 7, Cell Press, 2016, pp. 1723–34, doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.01.048\">10.1016/j.celrep.2016.01.048</a>.","ama":"Russo E, Teijeira A, Vaahtomeri K, et al. Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. <i>Cell Reports</i>. 2016;14(7):1723-1734. doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.01.048\">10.1016/j.celrep.2016.01.048</a>","chicago":"Russo, Erica, Alvaro Teijeira, Kari Vaahtomeri, Ann Willrodt, Joël Bloch, Maximilian Nitschké, Laura Santambrogio, Dontscho Kerjaschki, Michael K Sixt, and Cornelia Halin. “Intralymphatic CCL21 Promotes Tissue Egress of Dendritic Cells through Afferent Lymphatic Vessels.” <i>Cell Reports</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.celrep.2016.01.048\">https://doi.org/10.1016/j.celrep.2016.01.048</a>.","apa":"Russo, E., Teijeira, A., Vaahtomeri, K., Willrodt, A., Bloch, J., Nitschké, M., … Halin, C. (2016). Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2016.01.048\">https://doi.org/10.1016/j.celrep.2016.01.048</a>"},"publication_status":"published","abstract":[{"text":"To induce adaptive immunity, dendritic cells (DCs) migrate through afferent lymphatic vessels (LVs) to draining lymph nodes (dLNs). This process occurs in several consecutive steps. Upon entry into lymphatic capillaries, DCs first actively crawl into downstream collecting vessels. From there, they are next passively and rapidly transported to the dLN by lymph flow. Here, we describe a role for the chemokine CCL21 in intralymphatic DC crawling. Performing time-lapse imaging in murine skin, we found that blockade of CCL21-but not the absence of lymph flow-completely abolished DC migration from capillaries toward collecting vessels and reduced the ability of intralymphatic DCs to emigrate from skin. Moreover, we found that in vitro low laminar flow established a CCL21 gradient along lymphatic endothelial monolayers, thereby inducing downstream-directed DC migration. These findings reveal a role for intralymphatic CCL21 in promoting DC trafficking to dLNs, through the formation of a flow-induced gradient.","lang":"eng"}],"publist_id":"5697","department":[{"_id":"MiSi"}],"language":[{"iso":"eng"}],"publisher":"Cell Press","file_date_updated":"2020-07-14T12:44:58Z","scopus_import":1,"publication":"Cell Reports","file":[{"relation":"main_file","file_name":"IST-2016-515-v1+1_1-s2.0-S2211124716300262-main.pdf","date_updated":"2020-07-14T12:44:58Z","file_size":5489897,"date_created":"2018-12-12T10:12:30Z","creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"c98c1151d5f1e5ce1643a83d8d7f3c29","file_id":"4948"}],"ddc":["570"],"type":"journal_article","intvolume":"        14","pubrep_id":"515","month":"02","page":"1723 - 1734","issue":"7","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"status":"public","author":[{"first_name":"Erica","full_name":"Russo, Erica","last_name":"Russo"},{"first_name":"Alvaro","full_name":"Teijeira, Alvaro","last_name":"Teijeira"},{"last_name":"Vaahtomeri","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari","first_name":"Kari"},{"full_name":"Willrodt, Ann","first_name":"Ann","last_name":"Willrodt"},{"last_name":"Bloch","full_name":"Bloch, Joël","first_name":"Joël"},{"full_name":"Nitschké, Maximilian","first_name":"Maximilian","last_name":"Nitschké"},{"last_name":"Santambrogio","first_name":"Laura","full_name":"Santambrogio, Laura"},{"first_name":"Dontscho","full_name":"Kerjaschki, Dontscho","last_name":"Kerjaschki"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"full_name":"Halin, Cornelia","first_name":"Cornelia","last_name":"Halin"}],"doi":"10.1016/j.celrep.2016.01.048","date_created":"2018-12-11T11:52:19Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":14,"day":"23","date_published":"2016-02-23T00:00:00Z","title":"Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels","date_updated":"2021-01-12T06:51:07Z","_id":"1490","year":"2016","has_accepted_license":"1","oa":1},{"day":"01","date_published":"2016-01-01T00:00:00Z","oa_version":"Submitted Version","author":[{"first_name":"Mathieu","full_name":"Lewin, Mathieu","last_name":"Lewin"},{"last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","full_name":"Nam, Phan"},{"last_name":"Rougerie","first_name":"Nicolas","full_name":"Rougerie, Nicolas"}],"status":"public","doi":"10.1090/tran/6537","date_created":"2018-12-11T11:52:20Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":368,"acknowledgement":"The authors acknowledge financial support from the European Research Council (FP7/2007-2013 Grant Agreement MNIQS 258023) and the ANR (Mathostaq project, ANR-13-JS01-0005-01). The second and third authors have benefited from the hospitality of the Institute for Mathematical Science of the National University of Singapore.","year":"2016","oa":1,"title":"The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases","date_updated":"2021-01-12T06:51:07Z","_id":"1491","abstract":[{"text":"We study the ground state of a trapped Bose gas, starting from the full many-body Schrödinger Hamiltonian, and derive the non-linear Schrödinger energy functional in the limit of a large particle number, when the interaction potential converges slowly to a Dirac delta function. Our method is based on quantitative estimates on the discrepancy between the full many-body energy and its mean-field approximation using Hartree states. These are proved using finite dimensional localization and a quantitative version of the quantum de Finetti theorem. Our approach covers the case of attractive interactions in the regime of stability. In particular, our main new result is a derivation of the 2D attractive non-linear Schrödinger ground state.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"publist_id":"5692","publisher":"American Mathematical Society","scopus_import":1,"publication":"Transactions of the American Mathematical Society","quality_controlled":"1","citation":{"ista":"Lewin M, Nam P, Rougerie N. 2016. The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. Transactions of the American Mathematical Society. 368(9), 6131–6157.","ieee":"M. Lewin, P. Nam, and N. Rougerie, “The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases,” <i>Transactions of the American Mathematical Society</i>, vol. 368, no. 9. American Mathematical Society, pp. 6131–6157, 2016.","mla":"Lewin, Mathieu, et al. “The Mean-Field Approximation and the Non-Linear Schrödinger Functional for Trapped Bose Gases.” <i>Transactions of the American Mathematical Society</i>, vol. 368, no. 9, American Mathematical Society, 2016, pp. 6131–57, doi:<a href=\"https://doi.org/10.1090/tran/6537\">10.1090/tran/6537</a>.","short":"M. Lewin, P. Nam, N. Rougerie, Transactions of the American Mathematical Society 368 (2016) 6131–6157.","ama":"Lewin M, Nam P, Rougerie N. The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. <i>Transactions of the American Mathematical Society</i>. 2016;368(9):6131-6157. doi:<a href=\"https://doi.org/10.1090/tran/6537\">10.1090/tran/6537</a>","apa":"Lewin, M., Nam, P., &#38; Rougerie, N. (2016). The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/6537\">https://doi.org/10.1090/tran/6537</a>","chicago":"Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “The Mean-Field Approximation and the Non-Linear Schrödinger Functional for Trapped Bose Gases.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2016. <a href=\"https://doi.org/10.1090/tran/6537\">https://doi.org/10.1090/tran/6537</a>."},"publication_status":"published","intvolume":"       368","month":"01","page":"6131 - 6157","issue":"9","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1405.3220"}],"type":"journal_article"},{"citation":{"mla":"Marhavý, Peter, et al. “Targeted Cell Elimination Reveals an Auxin-Guided Biphasic Mode of Lateral Root Initiation.” <i>Genes and Development</i>, vol. 30, no. 4, Cold Spring Harbor Laboratory Press, 2016, pp. 471–83, doi:<a href=\"https://doi.org/10.1101/gad.276964.115\">10.1101/gad.276964.115</a>.","short":"P. Marhavý, J.C. Montesinos López, A. Abuzeineh, D. Van Damme, J. Vermeer, J. Duclercq, H. Rakusova, P. Marhavá, J. Friml, N. Geldner, E. Benková, Genes and Development 30 (2016) 471–483.","ieee":"P. Marhavý <i>et al.</i>, “Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation,” <i>Genes and Development</i>, vol. 30, no. 4. Cold Spring Harbor Laboratory Press, pp. 471–483, 2016.","ista":"Marhavý P, Montesinos López JC, Abuzeineh A, Van Damme D, Vermeer J, Duclercq J, Rakusova H, Marhavá P, Friml J, Geldner N, Benková E. 2016. Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development. 30(4), 471–483.","apa":"Marhavý, P., Montesinos López, J. C., Abuzeineh, A., Van Damme, D., Vermeer, J., Duclercq, J., … Benková, E. (2016). Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.276964.115\">https://doi.org/10.1101/gad.276964.115</a>","chicago":"Marhavý, Peter, Juan C Montesinos López, Anas Abuzeineh, Daniël Van Damme, Joop Vermeer, Jérôme Duclercq, Hana Rakusova, et al. “Targeted Cell Elimination Reveals an Auxin-Guided Biphasic Mode of Lateral Root Initiation.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2016. <a href=\"https://doi.org/10.1101/gad.276964.115\">https://doi.org/10.1101/gad.276964.115</a>.","ama":"Marhavý P, Montesinos López JC, Abuzeineh A, et al. Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. <i>Genes and Development</i>. 2016;30(4):471-483. doi:<a href=\"https://doi.org/10.1101/gad.276964.115\">10.1101/gad.276964.115</a>"},"quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"To sustain a lifelong ability to initiate organs, plants retain pools of undifferentiated cells with a preserved prolif eration capacity. The root pericycle represents a unique tissue with conditional meristematic activity, and its tight control determines initiation of lateral organs. Here we show that the meristematic activity of the pericycle is constrained by the interaction with the adjacent endodermis. Release of these restraints by elimination of endo dermal cells by single-cell ablation triggers the pericycle to re-enter the cell cycle. We found that endodermis removal substitutes for the phytohormone auxin-dependent initiation of the pericycle meristematic activity. However, auxin is indispensable to steer the cell division plane orientation of new organ-defining divisions. We propose a dual, spatiotemporally distinct role for auxin during lateral root initiation. In the endodermis, auxin releases constraints arising from cell-to-cell interactions that compromise the pericycle meristematic activity, whereas, in the pericycle, auxin defines the orientation of the cell division plane to initiate lateral roots."}],"publist_id":"5691","language":[{"iso":"eng"}],"department":[{"_id":"EvBe"}],"publisher":"Cold Spring Harbor Laboratory Press","scopus_import":1,"publication":"Genes and Development","file":[{"file_id":"5883","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","checksum":"ea394498ee56270e021d1028a29358a0","date_updated":"2020-07-14T12:44:58Z","file_name":"2016_GeneDev_Marhavy.pdf","date_created":"2019-01-25T09:56:11Z","file_size":2757636,"relation":"main_file"}],"file_date_updated":"2020-07-14T12:44:58Z","type":"journal_article","ddc":["570"],"intvolume":"        30","month":"03","page":"471 - 483","acknowledged_ssus":[{"_id":"LifeSc"}],"issue":"4","oa_version":"Published Version","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"status":"public","author":[{"full_name":"Marhavy, Peter","first_name":"Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavy"},{"id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","full_name":"Montesinos López, Juan C","first_name":"Juan C","orcid":"0000-0001-9179-6099"},{"first_name":"Anas","full_name":"Abuzeineh, Anas","last_name":"Abuzeineh"},{"last_name":"Van Damme","full_name":"Van Damme, Daniël","first_name":"Daniël"},{"last_name":"Vermeer","full_name":"Vermeer, Joop","first_name":"Joop"},{"last_name":"Duclercq","full_name":"Duclercq, Jérôme","first_name":"Jérôme"},{"full_name":"Rakusova, Hana","first_name":"Hana","last_name":"Rakusova"},{"last_name":"Marhavá","id":"44E59624-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavá, Petra","first_name":"Petra"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Geldner, Niko","first_name":"Niko","last_name":"Geldner"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"doi":"10.1101/gad.276964.115","volume":30,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:52:20Z","external_id":{"pmid":["    26883363"]},"day":"01","date_published":"2016-03-01T00:00:00Z","title":"Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation","_id":"1492","date_updated":"2021-01-12T06:51:08Z","acknowledgement":"This work was supported by a European Research Council Starting Inde-pendent Research grant (ERC-2007-Stg-207362-HCPO to J.D.), Research Foundation-Flanders (G033711N to A.A.), and the Austrian Science Fund (FWF01_I1774S to E.B.). P.M. is indebted to the Federation of European Biochemical Sciences for a Long-Term Fellowship. ","year":"2016","has_accepted_license":"1","oa":1},{"ddc":["510","530"],"type":"journal_article","ec_funded":1,"issue":"1","intvolume":"        19","pubrep_id":"514","article_number":"3","month":"03","publication_status":"published","quality_controlled":"1","citation":{"short":"S.P. Petrat, P. Pickl, Mathematical Physics, Analysis and Geometry 19 (2016).","mla":"Petrat, Sören P., and Peter Pickl. “A New Method and a New Scaling for Deriving Fermionic Mean-Field Dynamics.” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 19, no. 1, 3, Springer, 2016, doi:<a href=\"https://doi.org/10.1007/s11040-016-9204-2\">10.1007/s11040-016-9204-2</a>.","ieee":"S. P. Petrat and P. Pickl, “A new method and a new scaling for deriving fermionic mean-field dynamics,” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 19, no. 1. Springer, 2016.","ista":"Petrat SP, Pickl P. 2016. A new method and a new scaling for deriving fermionic mean-field dynamics. Mathematical Physics, Analysis and Geometry. 19(1), 3.","chicago":"Petrat, Sören P, and Peter Pickl. “A New Method and a New Scaling for Deriving Fermionic Mean-Field Dynamics.” <i>Mathematical Physics, Analysis and Geometry</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11040-016-9204-2\">https://doi.org/10.1007/s11040-016-9204-2</a>.","apa":"Petrat, S. P., &#38; Pickl, P. (2016). A new method and a new scaling for deriving fermionic mean-field dynamics. <i>Mathematical Physics, Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-016-9204-2\">https://doi.org/10.1007/s11040-016-9204-2</a>","ama":"Petrat SP, Pickl P. A new method and a new scaling for deriving fermionic mean-field dynamics. <i>Mathematical Physics, Analysis and Geometry</i>. 2016;19(1). doi:<a href=\"https://doi.org/10.1007/s11040-016-9204-2\">10.1007/s11040-016-9204-2</a>"},"publisher":"Springer","file":[{"file_id":"5246","creator":"system","access_level":"open_access","checksum":"eb5d2145ef0d377c4f78bf06e18f4529","content_type":"application/pdf","file_name":"IST-2016-514-v1+1_s11040-016-9204-2.pdf","date_updated":"2020-07-14T12:44:58Z","file_size":911310,"date_created":"2018-12-12T10:16:55Z","relation":"main_file"}],"file_date_updated":"2020-07-14T12:44:58Z","publication":"Mathematical Physics, Analysis and Geometry","scopus_import":1,"abstract":[{"lang":"eng","text":"We introduce a new method for deriving the time-dependent Hartree or Hartree-Fock equations as an effective mean-field dynamics from the microscopic Schrödinger equation for fermionic many-particle systems in quantum mechanics. The method is an adaption of the method used in Pickl (Lett. Math. Phys. 97 (2) 151–164 2011) for bosonic systems to fermionic systems. It is based on a Gronwall type estimate for a suitable measure of distance between the microscopic solution and an antisymmetrized product state. We use this method to treat a new mean-field limit for fermions with long-range interactions in a large volume. Some of our results hold for singular attractive or repulsive interactions. We can also treat Coulomb interaction assuming either a mild singularity cutoff or certain regularity conditions on the solutions to the Hartree(-Fock) equations. In the considered limit, the kinetic and interaction energy are of the same order, while the average force is subleading. For some interactions, we prove that the Hartree(-Fock) dynamics is a more accurate approximation than a simpler dynamics that one would expect from the subleading force. With our method we also treat the mean-field limit coupled to a semiclassical limit, which was discussed in the literature before, and we recover some of the previous results. All results hold for initial data close (but not necessarily equal) to antisymmetrized product states and we always provide explicit rates of convergence."}],"department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"publist_id":"5690","date_updated":"2021-01-12T06:51:08Z","_id":"1493","title":"A new method and a new scaling for deriving fermionic mean-field dynamics","article_processing_charge":"Yes (via OA deal)","oa":1,"year":"2016","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","has_accepted_license":"1","doi":"10.1007/s11040-016-9204-2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:52:20Z","volume":19,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"last_name":"Petrat","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9166-5889","full_name":"Petrat, Sören P","first_name":"Sören P"},{"last_name":"Pickl","first_name":"Peter","full_name":"Pickl, Peter"}],"day":"01","date_published":"2016-03-01T00:00:00Z"},{"project":[{"grant_number":"306589","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"_id":"2511D90C-B435-11E9-9278-68D0E5697425","name":"Astrophysical instability of currents and turbulences","grant_number":"SFB 963  TP A8"}],"acknowledgement":"We thank P. Maier for providing valuable ideas and supporting us in the technical aspects. Discussions with D. Barkley, Y. Duguet, B. Eckhart, N. Goldenfeld, P. Manneville and K. Takeuchi are gratefully acknowledged. We acknowledge the Deutsche Forschungsgemeinschaft (Project No. FOR 1182), and the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589 for financial support. L.S. and B.H. acknowledge research funding by Deutsche Forschungsgemeinschaft (DFG) under Grant No. SFB 963/1 (project A8). Numerical simulations were performed thanks to the CPU time allocations of JUROPA in Juelich Supercomputing Center (project HGU17) and of the Max Planck Computing and Data Facility (Garching, Germany). Excellent technical support from M. Rampp on the hybrid code nsCouette is appreciated.","year":"2016","title":"Directed percolation phase transition to sustained turbulence in Couette flow","date_updated":"2021-01-12T06:51:08Z","_id":"1494","date_published":"2016-02-15T00:00:00Z","day":"15","author":[{"first_name":"Grégoire M","full_name":"Lemoult, Grégoire M","last_name":"Lemoult","id":"4787FE80-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shi","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","first_name":"Liang","full_name":"Shi, Liang"},{"last_name":"Avila","first_name":"Kerstin","full_name":"Avila, Kerstin"},{"last_name":"Jalikop","id":"44A1D772-F248-11E8-B48F-1D18A9856A87","first_name":"Shreyas V","full_name":"Jalikop, Shreyas V"},{"first_name":"Marc","full_name":"Avila, Marc","last_name":"Avila"},{"orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"status":"public","oa_version":"None","date_created":"2018-12-11T11:52:21Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":12,"doi":"10.1038/nphys3675","month":"02","intvolume":"        12","issue":"3","page":"254 - 258","ec_funded":1,"type":"journal_article","department":[{"_id":"BjHo"}],"publist_id":"5685","language":[{"iso":"eng"}],"abstract":[{"text":"Turbulence is one of the most frequently encountered non-equilibrium phenomena in nature, yet characterizing the transition that gives rise to turbulence in basic shear flows has remained an elusive task. Although, in recent studies, critical points marking the onset of sustained turbulence have been determined for several such flows, the physical nature of the transition could not be fully explained. In extensive experimental and computational studies we show for the example of Couette flow that the onset of turbulence is a second-order phase transition and falls into the directed percolation universality class. Consequently, the complex laminar–turbulent patterns distinctive for the onset of turbulence in shear flows result from short-range interactions of turbulent domains and are characterized by universal critical exponents. More generally, our study demonstrates that even high-dimensional systems far from equilibrium such as turbulence exhibit universality at onset and that here the collective dynamics obeys simple rules.","lang":"eng"}],"publication":"Nature Physics","scopus_import":1,"publisher":"Nature Publishing Group","quality_controlled":"1","citation":{"ieee":"G. M. Lemoult, L. Shi, K. Avila, S. V. Jalikop, M. Avila, and B. Hof, “Directed percolation phase transition to sustained turbulence in Couette flow,” <i>Nature Physics</i>, vol. 12, no. 3. Nature Publishing Group, pp. 254–258, 2016.","ista":"Lemoult GM, Shi L, Avila K, Jalikop SV, Avila M, Hof B. 2016. Directed percolation phase transition to sustained turbulence in Couette flow. Nature Physics. 12(3), 254–258.","mla":"Lemoult, Grégoire M., et al. “Directed Percolation Phase Transition to Sustained Turbulence in Couette Flow.” <i>Nature Physics</i>, vol. 12, no. 3, Nature Publishing Group, 2016, pp. 254–58, doi:<a href=\"https://doi.org/10.1038/nphys3675\">10.1038/nphys3675</a>.","short":"G.M. Lemoult, L. Shi, K. Avila, S.V. Jalikop, M. Avila, B. Hof, Nature Physics 12 (2016) 254–258.","ama":"Lemoult GM, Shi L, Avila K, Jalikop SV, Avila M, Hof B. Directed percolation phase transition to sustained turbulence in Couette flow. <i>Nature Physics</i>. 2016;12(3):254-258. doi:<a href=\"https://doi.org/10.1038/nphys3675\">10.1038/nphys3675</a>","chicago":"Lemoult, Grégoire M, Liang Shi, Kerstin Avila, Shreyas V Jalikop, Marc Avila, and Björn Hof. “Directed Percolation Phase Transition to Sustained Turbulence in Couette Flow.” <i>Nature Physics</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nphys3675\">https://doi.org/10.1038/nphys3675</a>.","apa":"Lemoult, G. M., Shi, L., Avila, K., Jalikop, S. V., Avila, M., &#38; Hof, B. (2016). Directed percolation phase transition to sustained turbulence in Couette flow. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nphys3675\">https://doi.org/10.1038/nphys3675</a>"},"publication_status":"published"},{"date_updated":"2021-01-12T06:51:09Z","_id":"1496","title":"Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model","oa":1,"year":"2016","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"acknowledgement":"This  research  was  supported  in  part  by  FCT, Portugal, through Project No. PTDC/FIS/117606/2010, financed by the European Community  Fund  FEDER  through  the  COMPETE. ","date_created":"2018-12-11T11:52:21Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":93,"doi":"10.1103/PhysRevA.93.032502","author":[{"last_name":"Amaro","full_name":"Amaro, Pedro","first_name":"Pedro"},{"full_name":"Fratini, Filippo","first_name":"Filippo","last_name":"Fratini"},{"first_name":"Laleh","full_name":"Safari, Laleh","last_name":"Safari","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Machado","first_name":"Jorge","full_name":"Machado, Jorge"},{"last_name":"Guerra","full_name":"Guerra, Mauro","first_name":"Mauro"},{"first_name":"Paul","full_name":"Indelicato, Paul","last_name":"Indelicato"},{"full_name":"Santos, José","first_name":"José","last_name":"Santos"}],"status":"public","oa_version":"Preprint","date_published":"2016-03-07T00:00:00Z","day":"07","type":"journal_article","main_file_link":[{"url":"http://arxiv.org/abs/1508.06169","open_access":"1"}],"issue":"3","ec_funded":1,"month":"03","intvolume":"        93","article_number":"032502","publication_status":"published","quality_controlled":"1","citation":{"ama":"Amaro P, Fratini F, Safari L, et al. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2016;93(3). doi:<a href=\"https://doi.org/10.1103/PhysRevA.93.032502\">10.1103/PhysRevA.93.032502</a>","apa":"Amaro, P., Fratini, F., Safari, L., Machado, J., Guerra, M., Indelicato, P., &#38; Santos, J. (2016). Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.93.032502\">https://doi.org/10.1103/PhysRevA.93.032502</a>","chicago":"Amaro, Pedro, Filippo Fratini, Laleh Safari, Jorge Machado, Mauro Guerra, Paul Indelicato, and José Santos. “Relativistic Evaluation of the Two-Photon Decay of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential Model.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevA.93.032502\">https://doi.org/10.1103/PhysRevA.93.032502</a>.","ista":"Amaro P, Fratini F, Safari L, Machado J, Guerra M, Indelicato P, Santos J. 2016. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. Physical Review A - Atomic, Molecular, and Optical Physics. 93(3), 032502.","ieee":"P. Amaro <i>et al.</i>, “Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 93, no. 3. American Physical Society, 2016.","short":"P. Amaro, F. Fratini, L. Safari, J. Machado, M. Guerra, P. Indelicato, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016).","mla":"Amaro, Pedro, et al. “Relativistic Evaluation of the Two-Photon Decay of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential Model.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 93, no. 3, 032502, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevA.93.032502\">10.1103/PhysRevA.93.032502</a>."},"scopus_import":1,"publication":"Physical Review A - Atomic, Molecular, and Optical Physics","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publist_id":"5683","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The two-photon 1s2 2s 2p 3P0 1s22s2 1S0 transition in berylliumlike ions is theoretically investigated within a fully relativistic framework and a second-order perturbation theory. We focus our analysis on how electron correlation, as well as the negative-energy spectrum, can affect the forbidden E1M1 decay rate. For this purpose, we include the electronic correlation via an effective local potential and within a single configuration-state model. Due to its experimental interest, evaluations of decay rates are performed for berylliumlike xenon and uranium. We find that the negative-energy contribution can be neglected at the present level of accuracy in the evaluation of the decay rate. On the other hand, if contributions of electronic correlation are not carefully taken into account, it may change the lifetime of the metastable state by up to 20%. By performing a full-relativistic jj-coupling calculation, we found a decrease of the decay rate by two orders of magnitude compared to non-relativistic LS-coupling calculations, for the selected heavy ions."}]},{"file":[{"relation":"main_file","date_updated":"2020-07-14T12:45:00Z","file_name":"IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf","date_created":"2018-12-12T10:16:51Z","file_size":957466,"access_level":"open_access","creator":"system","checksum":"41c9b5d72e7fe4624dd22dfe622337d5","content_type":"application/pdf","file_id":"5241"}],"publication":"Genetics","scopus_import":"1","file_date_updated":"2020-07-14T12:45:00Z","publisher":"Genetics Society of America","publist_id":"5658","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"},{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno."}],"publication_status":"published","article_type":"original","citation":{"ama":"Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating blockwise likelihoods under the coalescent. <i>Genetics</i>. 2016;202(2):775-786. doi:<a href=\"https://doi.org/10.1534/genetics.115.183814\">10.1534/genetics.115.183814</a>","chicago":"Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.183814\">https://doi.org/10.1534/genetics.115.183814</a>.","apa":"Lohse, K., Chmelik, M., Martin, S., &#38; Barton, N. H. (2016). Efficient strategies for calculating blockwise likelihoods under the coalescent. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.183814\">https://doi.org/10.1534/genetics.115.183814</a>","ista":"Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786.","ieee":"K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for calculating blockwise likelihoods under the coalescent,” <i>Genetics</i>, vol. 202, no. 2. Genetics Society of America, pp. 775–786, 2016.","short":"K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.","mla":"Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” <i>Genetics</i>, vol. 202, no. 2, Genetics Society of America, 2016, pp. 775–86, doi:<a href=\"https://doi.org/10.1534/genetics.115.183814\">10.1534/genetics.115.183814</a>."},"quality_controlled":"1","issue":"2","ec_funded":1,"page":"775 - 786","month":"02","intvolume":"       202","pubrep_id":"561","type":"journal_article","ddc":["570"],"date_published":"2016-02-01T00:00:00Z","day":"01","external_id":{"pmid":["26715666"]},"volume":202,"date_created":"2018-12-11T11:52:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1534/genetics.115.183814","status":"public","author":[{"first_name":"Konrad","full_name":"Lohse, Konrad","last_name":"Lohse"},{"full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Martin","first_name":"Simon","full_name":"Martin, Simon"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"oa_version":"Preprint","oa":1,"has_accepted_license":"1","project":[{"call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"}],"year":"2016","acknowledgement":"We thank Lynsey Bunnefeld for discussions throughout the project and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on an earlier version of this manuscript. This work was supported by funding from the\r\nUnited Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant from the European\r\nResearch Council (250152) (to N.H.B.).","_id":"1518","date_updated":"2025-05-28T11:42:48Z","title":"Efficient strategies for calculating blockwise likelihoods under the coalescent","article_processing_charge":"No"}]