[{"volume":5,"quality_controlled":"1","publist_id":"6056","pubrep_id":"700","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"has_accepted_license":"1","date_created":"2018-12-11T11:51:02Z","publication":"eLife","publisher":"eLife Sciences Publications","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Neural oscillations as a signature of efficient coding in the presence of synaptic delays","author":[{"orcid":"0000-0001-7782-4436","first_name":"Matthew J","last_name":"Chalk","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","full_name":"Chalk, Matthew J"},{"full_name":"Gutkin, Boris","first_name":"Boris","last_name":"Gutkin"},{"full_name":"Denève, Sophie","first_name":"Sophie","last_name":"Denève"}],"file":[{"file_size":2819055,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"4874","checksum":"dc52d967dc76174477bb258d84be2899","creator":"system","date_created":"2018-12-12T10:11:20Z","date_updated":"2020-07-14T12:44:42Z","file_name":"IST-2016-700-v1+1_e13824-download.pdf"}],"acknowledgement":"Boris Gutkin acknowledges funding by the Russian Academic Excellence Project '5-100’.","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","intvolume":"         5","citation":{"short":"M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016).","ama":"Chalk MJ, Gutkin B, Denève S. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. <i>eLife</i>. 2016;5(2016JULY). doi:<a href=\"https://doi.org/10.7554/eLife.13824\">10.7554/eLife.13824</a>","ieee":"M. J. Chalk, B. Gutkin, and S. Denève, “Neural oscillations as a signature of efficient coding in the presence of synaptic delays,” <i>eLife</i>, vol. 5, no. 2016JULY. eLife Sciences Publications, 2016.","apa":"Chalk, M. J., Gutkin, B., &#38; Denève, S. (2016). Neural oscillations as a signature of efficient coding in the presence of synaptic delays. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.13824\">https://doi.org/10.7554/eLife.13824</a>","mla":"Chalk, Matthew J., et al. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” <i>ELife</i>, vol. 5, no. 2016JULY, e13824, eLife Sciences Publications, 2016, doi:<a href=\"https://doi.org/10.7554/eLife.13824\">10.7554/eLife.13824</a>.","ista":"Chalk MJ, Gutkin B, Denève S. 2016. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 5(2016JULY), e13824.","chicago":"Chalk, Matthew J, Boris Gutkin, and Sophie Denève. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” <i>ELife</i>. eLife Sciences Publications, 2016. <a href=\"https://doi.org/10.7554/eLife.13824\">https://doi.org/10.7554/eLife.13824</a>."},"scopus_import":1,"file_date_updated":"2020-07-14T12:44:42Z","ddc":["571"],"oa_version":"Published Version","date_published":"2016-07-01T00:00:00Z","publication_status":"published","doi":"10.7554/eLife.13824","month":"07","status":"public","oa":1,"article_number":"e13824","_id":"1266","date_updated":"2021-01-12T06:49:30Z","abstract":[{"text":"Cortical networks exhibit ‘global oscillations’, in which neural spike times are entrained to an underlying oscillatory rhythm, but where individual neurons fire irregularly, on only a fraction of cycles. While the network dynamics underlying global oscillations have been well characterised, their function is debated. Here, we show that such global oscillations are a direct consequence of optimal efficient coding in spiking networks with synaptic delays and noise. To avoid firing unnecessary spikes, neurons need to share information about the network state. Ideally, membrane potentials should be strongly correlated and reflect a ‘prediction error’ while the spikes themselves are uncorrelated and occur rarely. We show that the most efficient representation is when: (i) spike times are entrained to a global Gamma rhythm (implying a consistent representation of the error); but (ii) few neurons fire on each cycle (implying high efficiency), while (iii) excitation and inhibition are tightly balanced. This suggests that cortical networks exhibiting such dynamics are tuned to achieve a maximally efficient population code.","lang":"eng"}],"issue":"2016JULY","year":"2016"},{"title":"Nonexistence of large nuclei in the liquid drop model","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":349464,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4863","checksum":"d740a6a226e0f5f864f40e3e269d3cc0","creator":"system","date_created":"2018-12-12T10:11:09Z","file_name":"IST-2016-698-v1+1_s11005-016-0860-8.pdf","date_updated":"2020-07-14T12:44:42Z"}],"project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"author":[{"full_name":"Frank, Rupert","last_name":"Frank","first_name":"Rupert"},{"first_name":"Rowan","last_name":"Killip","full_name":"Killip, Rowan"},{"full_name":"Nam, Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","acknowledgement":"Open access funding provided by Institute of Science and Technology Austria.\r\n","quality_controlled":"1","volume":106,"publist_id":"6054","pubrep_id":"698","language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"type":"journal_article","page":"1033 - 1036","date_created":"2018-12-11T11:51:02Z","publication":"Letters in Mathematical Physics","has_accepted_license":"1","month":"08","oa":1,"status":"public","_id":"1267","year":"2016","date_updated":"2021-01-12T06:49:30Z","issue":"8","abstract":[{"lang":"eng","text":"We give a simplified proof of the nonexistence of large nuclei in the liquid drop model and provide an explicit bound. Our bound is within a factor of 2.3 of the conjectured value and seems to be the first quantitative result."}],"citation":{"ama":"Frank R, Killip R, Nam P. Nonexistence of large nuclei in the liquid drop model. <i>Letters in Mathematical Physics</i>. 2016;106(8):1033-1036. doi:<a href=\"https://doi.org/10.1007/s11005-016-0860-8\">10.1007/s11005-016-0860-8</a>","ieee":"R. Frank, R. Killip, and P. Nam, “Nonexistence of large nuclei in the liquid drop model,” <i>Letters in Mathematical Physics</i>, vol. 106, no. 8. Springer, pp. 1033–1036, 2016.","short":"R. Frank, R. Killip, P. Nam, Letters in Mathematical Physics 106 (2016) 1033–1036.","chicago":"Frank, Rupert, Rowan Killip, and Phan Nam. “Nonexistence of Large Nuclei in the Liquid Drop Model.” <i>Letters in Mathematical Physics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11005-016-0860-8\">https://doi.org/10.1007/s11005-016-0860-8</a>.","apa":"Frank, R., Killip, R., &#38; Nam, P. (2016). Nonexistence of large nuclei in the liquid drop model. <i>Letters in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s11005-016-0860-8\">https://doi.org/10.1007/s11005-016-0860-8</a>","ista":"Frank R, Killip R, Nam P. 2016. Nonexistence of large nuclei in the liquid drop model. Letters in Mathematical Physics. 106(8), 1033–1036.","mla":"Frank, Rupert, et al. “Nonexistence of Large Nuclei in the Liquid Drop Model.” <i>Letters in Mathematical Physics</i>, vol. 106, no. 8, Springer, 2016, pp. 1033–36, doi:<a href=\"https://doi.org/10.1007/s11005-016-0860-8\">10.1007/s11005-016-0860-8</a>."},"intvolume":"       106","ddc":["510","539"],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:42Z","date_published":"2016-08-01T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1007/s11005-016-0860-8"},{"volume":28,"intvolume":"        28","quality_controlled":"1","citation":{"short":"B. Milutinovic, J. Kurtz, Seminars in Immunology 28 (2016) 328–342.","ieee":"B. Milutinovic and J. Kurtz, “Immune memory in invertebrates,” <i>Seminars in Immunology</i>, vol. 28, no. 4. Academic Press, pp. 328–342, 2016.","ama":"Milutinovic B, Kurtz J. Immune memory in invertebrates. <i>Seminars in Immunology</i>. 2016;28(4):328-342. doi:<a href=\"https://doi.org/10.1016/j.smim.2016.05.004\">10.1016/j.smim.2016.05.004</a>","chicago":"Milutinovic, Barbara, and Joachim Kurtz. “Immune Memory in Invertebrates.” <i>Seminars in Immunology</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.smim.2016.05.004\">https://doi.org/10.1016/j.smim.2016.05.004</a>.","ista":"Milutinovic B, Kurtz J. 2016. Immune memory in invertebrates. Seminars in Immunology. 28(4), 328–342.","apa":"Milutinovic, B., &#38; Kurtz, J. (2016). Immune memory in invertebrates. <i>Seminars in Immunology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.smim.2016.05.004\">https://doi.org/10.1016/j.smim.2016.05.004</a>","mla":"Milutinovic, Barbara, and Joachim Kurtz. “Immune Memory in Invertebrates.” <i>Seminars in Immunology</i>, vol. 28, no. 4, Academic Press, 2016, pp. 328–42, doi:<a href=\"https://doi.org/10.1016/j.smim.2016.05.004\">10.1016/j.smim.2016.05.004</a>."},"publist_id":"6053","scopus_import":1,"type":"journal_article","oa_version":"None","date_published":"2016-08-01T00:00:00Z","department":[{"_id":"SyCr"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.smim.2016.05.004","publication_status":"published","publication":"Seminars in Immunology","date_created":"2018-12-11T11:51:03Z","page":"328 - 342","month":"08","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Academic Press","status":"public","title":"Immune memory in invertebrates","author":[{"first_name":"Barbara","orcid":"0000-0002-8214-4758","last_name":"Milutinovic","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","full_name":"Milutinovic, Barbara"},{"last_name":"Kurtz","first_name":"Joachim","full_name":"Kurtz, Joachim"}],"_id":"1268","issue":"4","acknowledgement":"We would like to thank Mihai Netea for inviting us to contribute to this Theme Issue.","date_updated":"2021-01-12T06:49:30Z","year":"2016","day":"01"},{"ddc":["581"],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:42Z","intvolume":"        91","citation":{"ama":"Benková E. Plant hormones in interactions with the environment. <i>Plant Molecular Biology</i>. 2016;91(6):597. doi:<a href=\"https://doi.org/10.1007/s11103-016-0501-8\">10.1007/s11103-016-0501-8</a>","ieee":"E. Benková, “Plant hormones in interactions with the environment,” <i>Plant Molecular Biology</i>, vol. 91, no. 6. Springer, p. 597, 2016.","short":"E. Benková, Plant Molecular Biology 91 (2016) 597.","apa":"Benková, E. (2016). Plant hormones in interactions with the environment. <i>Plant Molecular Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s11103-016-0501-8\">https://doi.org/10.1007/s11103-016-0501-8</a>","ista":"Benková E. 2016. Plant hormones in interactions with the environment. Plant Molecular Biology. 91(6), 597.","mla":"Benková, Eva. “Plant Hormones in Interactions with the Environment.” <i>Plant Molecular Biology</i>, vol. 91, no. 6, Springer, 2016, p. 597, doi:<a href=\"https://doi.org/10.1007/s11103-016-0501-8\">10.1007/s11103-016-0501-8</a>.","chicago":"Benková, Eva. “Plant Hormones in Interactions with the Environment.” <i>Plant Molecular Biology</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11103-016-0501-8\">https://doi.org/10.1007/s11103-016-0501-8</a>."},"publication_status":"published","doi":"10.1007/s11103-016-0501-8","date_published":"2016-08-01T00:00:00Z","oa_version":"Published Version","oa":1,"status":"public","month":"08","year":"2016","date_updated":"2021-01-12T06:49:31Z","abstract":[{"lang":"eng","text":"Plants are continuously exposed to a myriad of external signals such as fluctuating nutrients availability, drought, heat, cold, high salinity, or pathogen/pest attacks that can severely affect their development, growth, and fertility. As sessile organisms, plants must therefore be able to sense and rapidly react to these external inputs, activate efficient responses, and adjust development to changing conditions. In recent years, significant progress has been made towards understanding the molecular mechanisms underlying the intricate and complex communication between plants and the environment. It is now becoming increasingly evident that hormones have an important regulatory role in plant adaptation and defense mechanisms."}],"issue":"6","_id":"1269","publist_id":"6052","pubrep_id":"697","quality_controlled":"1","volume":91,"page":"597","date_created":"2018-12-11T11:51:03Z","publication":"Plant Molecular Biology","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"EvBe"}],"type":"journal_article","title":"Plant hormones in interactions with the environment","publisher":"Springer","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"content_type":"application/pdf","relation":"main_file","file_size":297282,"file_name":"IST-2016-697-v1+1_s11103-016-0501-8.pdf","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:18:28Z","checksum":"0ffb7a15c5336b3a55248cc67021a825","creator":"system","file_id":"5349","access_level":"open_access"}],"author":[{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva"}]},{"related_material":{"record":[{"relation":"research_data","status":"public","id":"9869"},{"id":"9870","relation":"research_data","status":"public"},{"id":"9871","relation":"research_data","status":"public"}]},"quality_controlled":"1","volume":11,"pubrep_id":"696","publist_id":"6050","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"PLoS One","date_created":"2018-12-11T11:51:03Z","has_accepted_license":"1","title":"Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","file":[{"relation":"main_file","content_type":"application/pdf","file_size":4950415,"file_id":"4837","checksum":"3d0d55d373096a033bd9cf79288c8586","creator":"system","access_level":"open_access","file_name":"IST-2016-696-v1+1_journal.pone.0163628.PDF","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:10:47Z"}],"author":[{"last_name":"Hillenbrand","first_name":"Patrick","full_name":"Hillenbrand, Patrick"},{"last_name":"Gerland","first_name":"Ulrich","full_name":"Gerland, Ulrich"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","full_name":"Tkacik, Gasper"}],"project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"day":"27","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"The authors would like to thank Thomas Sokolowski and Filipe Tostevin for helpful discussions. PH and UG were funded by the German Excellence Initiative via the program \"Nanosystems Initiative Munich\" (https://www.nano-initiative-munich.de) and the German Research Foundation via the SFB 1032 \"Nanoagents for Spatiotemporal Control of Molecular and Cellular Reactions\" (http://www.sfb1032.physik.uni-muenchen.de). GT was funded by the Austrian Science Fund (FWF P 28844) (http://www.fwf.ac.at).","intvolume":"        11","citation":{"apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628\">https://doi.org/10.1371/journal.pone.0163628</a>","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 11(9), e0163628.","mla":"Hillenbrand, Patrick, et al. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” <i>PLoS One</i>, vol. 11, no. 9, e0163628, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628\">10.1371/journal.pone.0163628</a>.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” <i>PLoS One</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628\">https://doi.org/10.1371/journal.pone.0163628</a>.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016).","ama":"Hillenbrand P, Gerland U, Tkačik G. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. <i>PLoS One</i>. 2016;11(9). doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628\">10.1371/journal.pone.0163628</a>","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information,” <i>PLoS One</i>, vol. 11, no. 9. Public Library of Science, 2016."},"ddc":["571"],"file_date_updated":"2020-07-14T12:44:42Z","scopus_import":1,"date_published":"2016-09-27T00:00:00Z","oa_version":"Published Version","doi":"10.1371/journal.pone.0163628","publication_status":"published","month":"09","oa":1,"status":"public","_id":"1270","article_number":"e0163628","year":"2016","abstract":[{"lang":"eng","text":"A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to infer their global position within a tissue or an organism by reading out local gene expression levels. The patterning system is thus said to encode positional information, a concept that was formalized recently in the framework of information theory. Here we introduce a toy model of patterning in one spatial dimension, which can be seen as an extension of Wolpert's paradigmatic &quot;French Flag&quot; model, to patterning by several interacting, spatially coupled genes subject to intrinsic and extrinsic noise. Our model, a variant of an Ising spin system, allows us to systematically explore expression patterns that optimally encode positional information. We find that optimal patterning systems use positional cues, as in the French Flag model, together with gene-gene interactions to generate combinatorial codes for position which we call &quot;Counter&quot; patterns. Counter patterns can also be stabilized against noise and variations in system size or morphogen dosage by longer-range spatial interactions of the type invoked in the Turing model. The simple setup proposed here qualitatively captures many of the experimentally observed properties of biological patterning systems and allows them to be studied in a single, theoretically consistent framework."}],"issue":"9","date_updated":"2023-02-23T14:11:37Z"},{"scopus_import":1,"file_date_updated":"2020-07-14T12:44:42Z","ddc":["572","576"],"intvolume":"        14","citation":{"short":"A. Diz Muñoz, P. Romanczuk, W. Yu, M. Bergert, K. Ivanovitch, G. Salbreux, C.-P.J. Heisenberg, E. Paluch, BMC Biology 14 (2016).","ieee":"A. Diz Muñoz <i>et al.</i>, “Steering cell migration by alternating blebs and actin-rich protrusions,” <i>BMC Biology</i>, vol. 14, no. 1. BioMed Central, 2016.","ama":"Diz Muñoz A, Romanczuk P, Yu W, et al. Steering cell migration by alternating blebs and actin-rich protrusions. <i>BMC Biology</i>. 2016;14(1). doi:<a href=\"https://doi.org/10.1186/s12915-016-0294-x\">10.1186/s12915-016-0294-x</a>","chicago":"Diz Muñoz, Alba, Pawel Romanczuk, Weimiao Yu, Martin Bergert, Kenzo Ivanovitch, Guillame Salbreux, Carl-Philipp J Heisenberg, and Ewa Paluch. “Steering Cell Migration by Alternating Blebs and Actin-Rich Protrusions.” <i>BMC Biology</i>. BioMed Central, 2016. <a href=\"https://doi.org/10.1186/s12915-016-0294-x\">https://doi.org/10.1186/s12915-016-0294-x</a>.","ista":"Diz Muñoz A, Romanczuk P, Yu W, Bergert M, Ivanovitch K, Salbreux G, Heisenberg C-PJ, Paluch E. 2016. Steering cell migration by alternating blebs and actin-rich protrusions. BMC Biology. 14(1), 74.","apa":"Diz Muñoz, A., Romanczuk, P., Yu, W., Bergert, M., Ivanovitch, K., Salbreux, G., … Paluch, E. (2016). Steering cell migration by alternating blebs and actin-rich protrusions. <i>BMC Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12915-016-0294-x\">https://doi.org/10.1186/s12915-016-0294-x</a>","mla":"Diz Muñoz, Alba, et al. “Steering Cell Migration by Alternating Blebs and Actin-Rich Protrusions.” <i>BMC Biology</i>, vol. 14, no. 1, 74, BioMed Central, 2016, doi:<a href=\"https://doi.org/10.1186/s12915-016-0294-x\">10.1186/s12915-016-0294-x</a>."},"doi":"10.1186/s12915-016-0294-x","publication_status":"published","oa_version":"Published Version","date_published":"2016-09-02T00:00:00Z","status":"public","oa":1,"month":"09","abstract":[{"text":"Background: High directional persistence is often assumed to enhance the efficiency of chemotactic migration. Yet, cells in vivo usually display meandering trajectories with relatively low directional persistence, and the control and function of directional persistence during cell migration in three-dimensional environments are poorly understood. Results: Here, we use mesendoderm progenitors migrating during zebrafish gastrulation as a model system to investigate the control of directional persistence during migration in vivo. We show that progenitor cells alternate persistent run phases with tumble phases that result in cell reorientation. Runs are characterized by the formation of directed actin-rich protrusions and tumbles by enhanced blebbing. Increasing the proportion of actin-rich protrusions or blebs leads to longer or shorter run phases, respectively. Importantly, both reducing and increasing run phases result in larger spatial dispersion of the cells, indicative of reduced migration precision. A physical model quantitatively recapitulating the migratory behavior of mesendoderm progenitors indicates that the ratio of tumbling to run times, and thus the specific degree of directional persistence of migration, are critical for optimizing migration precision. Conclusions: Together, our experiments and model provide mechanistic insight into the control of migration directionality for cells moving in three-dimensional environments that combine different protrusion types, whereby the proportion of blebs to actin-rich protrusions determines the directional persistence and precision of movement by regulating the ratio of tumbling to run times.","lang":"eng"}],"issue":"1","date_updated":"2021-01-12T06:49:32Z","year":"2016","acknowledged_ssus":[{"_id":"LifeSc"}],"article_number":"74","_id":"1271","pubrep_id":"695","publist_id":"6049","volume":14,"quality_controlled":"1","has_accepted_license":"1","publication":"BMC Biology","date_created":"2018-12-11T11:51:04Z","type":"journal_article","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"BioMed Central","title":"Steering cell migration by alternating blebs and actin-rich protrusions","acknowledgement":"We thank K. Lee, C. Norden, A. Webb, and the members of the Paluch lab for\r\ncomments on the manuscript. We are grateful to P. Rørth and Peter Dieterich\r\nfor discussions, S. Ares, Y. Arboleda-Estudillo and S. Schneider for technical help,\r\nM. Biro for help with programming, and the BIOTEC/MPI-CBG and IST zebrafish\r\nand imaging facilities for help and advice at various stages of this project. This work was supported by the Max Planck Society, the Medical Research Council UK (core funding to the MRC LMCB), and by grants from the Polish Ministry of Science and Higher Education (454/N-MPG/2009/0) to EKP, the Deutsche Forschungsgemeinschaft (HE 3231/6-1 and PA 1590/1-1) to CPH and EKP, a A*Star JCO career development award (12302FG010) to WY and a Damon Runyon fellowship award to ADM (DRG 2157-12). This work was also supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001317), the UK Medical Research Council (FC001317), and the Wellcome Trust (FC001317) to GS.","day":"02","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Diz Muñoz","first_name":"Alba","full_name":"Diz Muñoz, Alba"},{"full_name":"Romanczuk, Pawel","first_name":"Pawel","last_name":"Romanczuk"},{"last_name":"Yu","first_name":"Weimiao","full_name":"Yu, Weimiao"},{"first_name":"Martin","last_name":"Bergert","full_name":"Bergert, Martin"},{"full_name":"Ivanovitch, Kenzo","first_name":"Kenzo","last_name":"Ivanovitch"},{"first_name":"Guillame","last_name":"Salbreux","full_name":"Salbreux, Guillame"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ewa","last_name":"Paluch","full_name":"Paluch, Ewa"}],"project":[{"name":"Analysis of the Formation and Function of Different Cell Protusion Types During Cell Migration in Vivo","_id":"252064B8-B435-11E9-9278-68D0E5697425","grant_number":"HE_3231/6-1"}],"file":[{"file_size":1875695,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"0bfa484ac69a0a560fb9a4589aeda7f6","file_id":"5002","creator":"system","date_created":"2018-12-12T10:13:20Z","file_name":"IST-2016-695-v1+1_s12915-016-0294-x.pdf","date_updated":"2020-07-14T12:44:42Z"}]},{"intvolume":"        13","citation":{"chicago":"Held, Martin, Stefan Huber, and Peter Palfrader. “Generalized Offsetting of Planar Structures Using Skeletons.” <i>Computer-Aided Design and Applications</i>. Taylor and Francis, 2016. <a href=\"https://doi.org/10.1080/16864360.2016.1150718\">https://doi.org/10.1080/16864360.2016.1150718</a>.","mla":"Held, Martin, et al. “Generalized Offsetting of Planar Structures Using Skeletons.” <i>Computer-Aided Design and Applications</i>, vol. 13, no. 5, Taylor and Francis, 2016, pp. 712–21, doi:<a href=\"https://doi.org/10.1080/16864360.2016.1150718\">10.1080/16864360.2016.1150718</a>.","ista":"Held M, Huber S, Palfrader P. 2016. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 13(5), 712–721.","apa":"Held, M., Huber, S., &#38; Palfrader, P. (2016). Generalized offsetting of planar structures using skeletons. <i>Computer-Aided Design and Applications</i>. Taylor and Francis. <a href=\"https://doi.org/10.1080/16864360.2016.1150718\">https://doi.org/10.1080/16864360.2016.1150718</a>","ieee":"M. Held, S. Huber, and P. Palfrader, “Generalized offsetting of planar structures using skeletons,” <i>Computer-Aided Design and Applications</i>, vol. 13, no. 5. Taylor and Francis, pp. 712–721, 2016.","ama":"Held M, Huber S, Palfrader P. Generalized offsetting of planar structures using skeletons. <i>Computer-Aided Design and Applications</i>. 2016;13(5):712-721. doi:<a href=\"https://doi.org/10.1080/16864360.2016.1150718\">10.1080/16864360.2016.1150718</a>","short":"M. Held, S. Huber, P. Palfrader, Computer-Aided Design and Applications 13 (2016) 712–721."},"ddc":["004","516"],"file_date_updated":"2020-07-14T12:44:42Z","scopus_import":1,"date_published":"2016-09-02T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1080/16864360.2016.1150718","month":"09","oa":1,"status":"public","_id":"1272","year":"2016","date_updated":"2021-01-12T06:49:32Z","abstract":[{"lang":"eng","text":"We study different means to extend offsetting based on skeletal structures beyond the well-known constant-radius and mitered offsets supported by Voronoi diagrams and straight skeletons, for which the orthogonal distance of offset elements to their respective input elements is constant and uniform over all input elements. Our main contribution is a new geometric structure, called variable-radius Voronoi diagram, which supports the computation of variable-radius offsets, i.e., offsets whose distance to the input is allowed to vary along the input. We discuss properties of this structure and sketch a prototype implementation that supports the computation of variable-radius offsets based on this new variant of Voronoi diagrams."}],"issue":"5","quality_controlled":"1","volume":13,"publist_id":"6048","pubrep_id":"694","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"type":"journal_article","date_created":"2018-12-11T11:51:04Z","page":"712 - 721","publication":"Computer-Aided Design and Applications","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","title":"Generalized offsetting of planar structures using skeletons","publisher":"Taylor and Francis","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:44:42Z","file_name":"IST-2016-694-v1+1_Generalized_offsetting_of_planar_structures_using_skeletons.pdf","date_created":"2018-12-12T10:16:20Z","file_id":"5206","checksum":"c746f3a48edb62b588d92ea5d0fd2c0e","creator":"system","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":1678369}],"author":[{"full_name":"Held, Martin","last_name":"Held","first_name":"Martin"},{"last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814","first_name":"Stefan","full_name":"Huber, Stefan"},{"full_name":"Palfrader, Peter","first_name":"Peter","last_name":"Palfrader"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"day":"02","acknowledgement":"This work was supported by Austrian Science Fund (FWF): P25816-N15."},{"intvolume":"       143","citation":{"mla":"Porco, Silvana, et al. “Lateral Root Emergence in Arabidopsis Is Dependent on Transcription Factor LBD29 Regulation of Auxin Influx Carrier LAX3.” <i>Development</i>, vol. 143, no. 18, Company of Biologists, 2016, pp. 3340–49, doi:<a href=\"https://doi.org/10.1242/dev.136283\">10.1242/dev.136283</a>.","ista":"Porco S, Larrieu A, Du Y, Gaudinier A, Goh T, Swarup K, Swarup R, Kuempers B, Bishopp A, Lavenus J, Casimiro I, Hill K, Benková E, Fukaki H, Brady S, Scheres B, Peéet B, Bennett M. 2016. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. 143(18), 3340–3349.","apa":"Porco, S., Larrieu, A., Du, Y., Gaudinier, A., Goh, T., Swarup, K., … Bennett, M. (2016). Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.136283\">https://doi.org/10.1242/dev.136283</a>","chicago":"Porco, Silvana, Antoine Larrieu, Yujuan Du, Allison Gaudinier, Tatsuaki Goh, Kamal Swarup, Ranjan Swarup, et al. “Lateral Root Emergence in Arabidopsis Is Dependent on Transcription Factor LBD29 Regulation of Auxin Influx Carrier LAX3.” <i>Development</i>. Company of Biologists, 2016. <a href=\"https://doi.org/10.1242/dev.136283\">https://doi.org/10.1242/dev.136283</a>.","ama":"Porco S, Larrieu A, Du Y, et al. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. <i>Development</i>. 2016;143(18):3340-3349. doi:<a href=\"https://doi.org/10.1242/dev.136283\">10.1242/dev.136283</a>","ieee":"S. Porco <i>et al.</i>, “Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3,” <i>Development</i>, vol. 143, no. 18. Company of Biologists, pp. 3340–3349, 2016.","short":"S. Porco, A. Larrieu, Y. Du, A. Gaudinier, T. Goh, K. Swarup, R. Swarup, B. Kuempers, A. Bishopp, J. Lavenus, I. Casimiro, K. Hill, E. Benková, H. Fukaki, S. Brady, B. Scheres, B. Peéet, M. Bennett, Development 143 (2016) 3340–3349."},"scopus_import":1,"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01595056/","open_access":"1"}],"oa_version":"Preprint","date_published":"2016-09-13T00:00:00Z","publication_status":"published","doi":"10.1242/dev.136283","month":"09","status":"public","oa":1,"_id":"1273","date_updated":"2021-01-12T06:49:32Z","issue":"18","abstract":[{"text":"Lateral root primordia (LRP) originate from pericycle stem cells located deep within parental root tissues. LRP emerge through overlying root tissues by inducing auxin-dependent cell separation and hydraulic changes in adjacent cells. The auxin-inducible auxin influx carrier LAX3 plays a key role concentrating this signal in cells overlying LRP. Delimiting LAX3 expression to two adjacent cell files overlying new LRP is crucial to ensure that auxin-regulated cell separation occurs solely along their shared walls. Multiscale modeling has predicted that this highly focused pattern of expression requires auxin to sequentially induce auxin efflux and influx carriers PIN3 and LAX3, respectively. Consistent with model predictions, we report that auxin-inducible LAX3 expression is regulated indirectly by AUXIN RESPONSE FACTOR 7 (ARF7). Yeast one-hybrid screens revealed that the LAX3 promoter is bound by the transcription factor LBD29, which is a direct target for regulation by ARF7. Disrupting auxin-inducible LBD29 expression or expressing an LBD29-SRDX transcriptional repressor phenocopied the lax3 mutant, resulting in delayed lateral root emergence. We conclude that sequential LBD29 and LAX3 induction by auxin is required to coordinate cell separation and organ emergence.","lang":"eng"}],"year":"2016","volume":143,"quality_controlled":"1","publist_id":"6044","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"EvBe"}],"date_created":"2018-12-11T11:51:04Z","page":"3340 - 3349","publication":"Development","publisher":"Company of Biologists","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3","author":[{"full_name":"Porco, Silvana","last_name":"Porco","first_name":"Silvana"},{"full_name":"Larrieu, Antoine","last_name":"Larrieu","first_name":"Antoine"},{"full_name":"Du, Yujuan","first_name":"Yujuan","last_name":"Du"},{"first_name":"Allison","last_name":"Gaudinier","full_name":"Gaudinier, Allison"},{"first_name":"Tatsuaki","last_name":"Goh","full_name":"Goh, Tatsuaki"},{"last_name":"Swarup","first_name":"Kamal","full_name":"Swarup, Kamal"},{"last_name":"Swarup","first_name":"Ranjan","full_name":"Swarup, Ranjan"},{"full_name":"Kuempers, Britta","last_name":"Kuempers","first_name":"Britta"},{"full_name":"Bishopp, Anthony","first_name":"Anthony","last_name":"Bishopp"},{"first_name":"Julien","last_name":"Lavenus","full_name":"Lavenus, Julien"},{"full_name":"Casimiro, Ilda","first_name":"Ilda","last_name":"Casimiro"},{"full_name":"Hill, Kristine","last_name":"Hill","first_name":"Kristine"},{"full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva"},{"first_name":"Hidehiro","last_name":"Fukaki","full_name":"Fukaki, Hidehiro"},{"first_name":"Siobhan","last_name":"Brady","full_name":"Brady, Siobhan"},{"full_name":"Scheres, Ben","last_name":"Scheres","first_name":"Ben"},{"full_name":"Peéet, Benjamin","last_name":"Peéet","first_name":"Benjamin"},{"last_name":"Bennett","first_name":"Malcolm","full_name":"Bennett, Malcolm"}],"acknowledgement":"We acknowledge the support of glasshouse technicians at the University of\r\nNottingham for help with plant growth and the Nottingham\r\nArabidopsis\r\nStock Centre\r\n(NASC) for providing\r\nArabidopsis\r\nlines. This research was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (to A.B. and M.J.B.); the European Research Council (ERC) Advanced Grant SysArc (to B.S.) and FUTUREROOTS (to M.J.B.); The Royal Society for University and Wolfson Research Fellowship awards (to A.B. and M.J.B.); a Federation of European Biochemical Societies (FEBS) Long-Term Fellowship (to B.P.); an Intra-European Fellowship for Career Development under the 7th framework of the European Commission [IEF-2008-220506 to B.P.]; a European Molecular Biology Organization (EMBO) Long-Term Fellowship (to B.P.); and a European Reintegration Grant under the 7th framework of the European Commission [ERG-2010-276662 to B.P.]; Interuniversity Attraction Poles Programme [initiated by the Belgian Science Policy Office (Federaal Wetenschapsbeleid)] (to M.J.B.); The Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan: Grants-in-Aid for Scientific Research on Innovative Areas [25110330 to H.F.] and a JSPS Research Fellowship for Young Scientists [12J02079 to T.G.]; funds for research performed by S.M.B. and A.G. were provided by University of California, Davis startup funds.","day":"13"},{"citation":{"ieee":"E. Mazur, E. Benková, and J. Friml, “Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","ama":"Mazur E, Benková E, Friml J. Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep33754\">10.1038/srep33754</a>","short":"E. Mazur, E. Benková, J. Friml, Scientific Reports 6 (2016).","chicago":"Mazur, Ewa, Eva Benková, and Jiří Friml. “Vascular Cambium Regeneration and Vessel Formation in Wounded Inflorescence Stems of Arabidopsis.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep33754\">https://doi.org/10.1038/srep33754</a>.","mla":"Mazur, Ewa, et al. “Vascular Cambium Regeneration and Vessel Formation in Wounded Inflorescence Stems of Arabidopsis.” <i>Scientific Reports</i>, vol. 6, 33754, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep33754\">10.1038/srep33754</a>.","apa":"Mazur, E., Benková, E., &#38; Friml, J. (2016). Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep33754\">https://doi.org/10.1038/srep33754</a>","ista":"Mazur E, Benková E, Friml J. 2016. Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. 6, 33754."},"intvolume":"         6","file_date_updated":"2020-07-14T12:44:42Z","scopus_import":"1","ddc":["581"],"oa_version":"Published Version","date_published":"2016-09-21T00:00:00Z","doi":"10.1038/srep33754","publication_status":"published","month":"09","status":"public","oa":1,"article_number":"33754","_id":"1274","abstract":[{"lang":"eng","text":"Synchronized tissue polarization during regeneration or de novo vascular tissue formation is a plant-specific example of intercellular communication and coordinated development. According to the canalization hypothesis, the plant hormone auxin serves as polarizing signal that mediates directional channel formation underlying the spatio-temporal vasculature patterning. A necessary part of canalization is a positive feedback between auxin signaling and polarity of the intercellular auxin flow. The cellular and molecular mechanisms of this process are still poorly understood, not the least, because of a lack of a suitable model system. We show that the main genetic model plant, Arabidopsis (Arabidopsis thaliana) can be used to study the canalization during vascular cambium regeneration and new vasculature formation. We monitored localized auxin responses, directional auxin-transport channels formation, and establishment of new vascular cambium polarity during regenerative processes after stem wounding. The increased auxin response above and around the wound preceded the formation of PIN1 auxin transporter-marked channels from the primarily homogenous tissue and the transient, gradual changes in PIN1 localization preceded the polarity of newly formed vascular tissue. Thus, Arabidopsis is a useful model for studies of coordinated tissue polarization and vasculature formation after wounding allowing for genetic and mechanistic dissection of the canalization hypothesis."}],"date_updated":"2025-05-07T11:12:28Z","year":"2016","volume":6,"quality_controlled":"1","external_id":{"pmid":["27649687"]},"related_material":{"record":[{"id":"545","relation":"later_version","status":"public"}]},"article_processing_charge":"No","pubrep_id":"692","publist_id":"6042","type":"journal_article","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Scientific Reports","date_created":"2018-12-11T11:51:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group","title":"Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis","author":[{"last_name":"Mazur","first_name":"Ewa","full_name":"Mazur, Ewa"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":2895147,"file_name":"IST-2016-692-v1+1_srep33754.pdf","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:13:25Z","creator":"system","checksum":"ee371fbc9124ad93157a95829264e4fe","file_id":"5008","access_level":"open_access"}],"pmid":1,"acknowledgement":"We wish to thank Prof. Ewa U. Kurczyńska for initiation of this work and valuable advices. We thank Martine De Cock for help in preparing the manuscript. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), the European Social Fund (CZ.1.07/2.3.00/20.0043), and the Czech Science Foundation GAČR (GA13-40637 S) to J.F., (GA 13-39982S) to E.B. and E.M. and in part by the European Regional Development Fund (project “CEITEC, Central European Institute of Technology”, CZ.1.05/1.1.00/02.0068).","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"21"},{"oa_version":"None","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2016-09-22T00:00:00Z","department":[{"_id":"CaHe"}],"publication_status":"published","doi":"10.1103/PhysRevLett.117.139802","date_created":"2018-12-11T11:51:05Z","publication":"Physical Review Letters","quality_controlled":"1","citation":{"ista":"Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. 2016. Callan-Jones et al. Reply. Physical Review Letters. 117(13), 139802.","mla":"Callan Jones, Andrew, et al. “Callan-Jones et Al. Reply.” <i>Physical Review Letters</i>, vol. 117, no. 13, 139802, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.117.139802\">10.1103/PhysRevLett.117.139802</a>.","apa":"Callan Jones, A., Ruprecht, V., Wieser, S., Heisenberg, C.-P. J., &#38; Voituriez, R. (2016). Callan-Jones et al. Reply. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.117.139802\">https://doi.org/10.1103/PhysRevLett.117.139802</a>","chicago":"Callan Jones, Andrew, Verena Ruprecht, Stefan Wieser, Carl-Philipp J Heisenberg, and Raphaël Voituriez. “Callan-Jones et Al. Reply.” <i>Physical Review Letters</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevLett.117.139802\">https://doi.org/10.1103/PhysRevLett.117.139802</a>.","ama":"Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. Callan-Jones et al. Reply. <i>Physical Review Letters</i>. 2016;117(13). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.117.139802\">10.1103/PhysRevLett.117.139802</a>","ieee":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P. J. Heisenberg, and R. Voituriez, “Callan-Jones et al. Reply,” <i>Physical Review Letters</i>, vol. 117, no. 13. American Physical Society, 2016.","short":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P.J. Heisenberg, R. Voituriez, Physical Review Letters 117 (2016)."},"intvolume":"       117","volume":117,"scopus_import":1,"publist_id":"6041","article_number":"139802","author":[{"full_name":"Callan Jones, Andrew","first_name":"Andrew","last_name":"Callan Jones"},{"full_name":"Ruprecht, Verena","last_name":"Ruprecht","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","orcid":"0000-0003-4088-8633"},{"full_name":"Wieser, Stefan","last_name":"Wieser","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","orcid":"0000-0002-2670-2217"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"},{"full_name":"Voituriez, Raphaël","last_name":"Voituriez","first_name":"Raphaël"}],"_id":"1275","date_updated":"2021-01-12T06:49:33Z","issue":"13","day":"22","year":"2016","month":"09","status":"public","publisher":"American Physical Society","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Callan-Jones et al. Reply"},{"publisher":"Nature Publishing Group","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex","acknowledgement":"We wish to thank CSC – IT Centre for Science (Espoo, Finland) for computational resources. For financial support, we wish to thank the Academy of Finland (TR, IV and PAP; Center of Excellence in Biomembrane Research (IV, TR)), the Finnish Doctoral Programme in Computational Sciences (KK), the Sigrid Juselius Foundation (IV), the Paulo Foundation (PAP), and the European Research Council (IV, TR; Advanced Grant project CROWDED-PRO-LIPIDS). AO acknowledges The Wellcome Trust International Senior Research Fellowship.","day":"26","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Postila, Pekka","last_name":"Postila","first_name":"Pekka"},{"full_name":"Kaszuba, Karol","first_name":"Karol","last_name":"Kaszuba","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kuleta, Patryk","last_name":"Kuleta","first_name":"Patryk"},{"first_name":"Ilpo","last_name":"Vattulainen","full_name":"Vattulainen, Ilpo"},{"full_name":"Sarewicz, Marcin","last_name":"Sarewicz","first_name":"Marcin"},{"full_name":"Osyczka, Artur","first_name":"Artur","last_name":"Osyczka"},{"last_name":"Róg","first_name":"Tomasz","full_name":"Róg, Tomasz"}],"file":[{"file_name":"IST-2016-691-v1+1_srep33607.pdf","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:17:09Z","checksum":"07c591c1250ebef266333cbc3228b4dd","file_id":"5261","creator":"system","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":1960563}],"publist_id":"6040","pubrep_id":"691","quality_controlled":"1","volume":6,"has_accepted_license":"1","date_created":"2018-12-11T11:51:05Z","publication":"Scientific Reports","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"LeSa"}],"status":"public","oa":1,"month":"09","date_updated":"2021-01-12T06:49:34Z","abstract":[{"lang":"eng","text":"The cytochrome (cyt) bc 1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme's substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Q i-site of the cyt bc 1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Q i-site to facilitate binding of half-protonated semiquinone-a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Q i-site."}],"year":"2016","article_number":"33607","_id":"1276","scopus_import":1,"file_date_updated":"2020-07-14T12:44:42Z","ddc":["576"],"citation":{"short":"P. Postila, K. Kaszuba, P. Kuleta, I. Vattulainen, M. Sarewicz, A. Osyczka, T. Róg, Scientific Reports 6 (2016).","ama":"Postila P, Kaszuba K, Kuleta P, et al. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep33607\">10.1038/srep33607</a>","ieee":"P. Postila <i>et al.</i>, “Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","mla":"Postila, Pekka, et al. “Atomistic Determinants of Co-Enzyme Q Reduction at the Qi-Site of the Cytochrome Bc1 Complex.” <i>Scientific Reports</i>, vol. 6, 33607, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep33607\">10.1038/srep33607</a>.","apa":"Postila, P., Kaszuba, K., Kuleta, P., Vattulainen, I., Sarewicz, M., Osyczka, A., &#38; Róg, T. (2016). Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep33607\">https://doi.org/10.1038/srep33607</a>","ista":"Postila P, Kaszuba K, Kuleta P, Vattulainen I, Sarewicz M, Osyczka A, Róg T. 2016. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports. 6, 33607.","chicago":"Postila, Pekka, Karol Kaszuba, Patryk Kuleta, Ilpo Vattulainen, Marcin Sarewicz, Artur Osyczka, and Tomasz Róg. “Atomistic Determinants of Co-Enzyme Q Reduction at the Qi-Site of the Cytochrome Bc1 Complex.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep33607\">https://doi.org/10.1038/srep33607</a>."},"intvolume":"         6","publication_status":"published","doi":"10.1038/srep33607","oa_version":"Published Version","date_published":"2016-09-26T00:00:00Z"},{"_id":"1277","date_updated":"2021-01-12T06:49:34Z","abstract":[{"lang":"eng","text":"The Arabidopsis thaliana endogenous elicitor peptides (AtPeps) are released into the apoplast after cellular damage caused by pathogens or wounding to induce innate immunity by direct binding to the membrane-localized leucine-rich repeat receptor kinases, PEP RECEPTOR1 (PEPR1) and PEPR2. Although the PEPR-mediated signaling components and responses have been studied extensively, the contributions of the subcellular localization and dynamics of the active PEPRs remain largely unknown. We used live-cell imaging of the fluorescently labeled and bioactive pep1 to visualize the intracellular behavior of the PEPRs in the Arabidopsis root meristem. We found that AtPep1 decorated the plasma membrane (PM) in a receptor-dependent manner and cointernalized with PEPRs. Trafficking of the AtPep1-PEPR1 complexes to the vacuole required neither the trans-Golgi network/early endosome (TGN/EE)-localized vacuolar H+ -ATPase activity nor the function of the brefeldin A-sensitive ADP-ribosylation factor-guanine exchange factors (ARF-GEFs). In addition, AtPep1 and different TGN/EE markers colocalized only rarely, implying that the intracellular route of this receptor-ligand pair is largely independent of the TGN/EE. Inducible overexpression of the Arabidopsis clathrin coat disassembly factor, Auxilin2, which inhibits clathrin-mediated endocytosis (CME), impaired the AtPep1-PEPR1 internalization and compromised AtPep1-mediated responses. Our results show that clathrin function at the PM is required to induce plant defense responses, likely through CME of cell surface-located signaling components.\r\n"}],"issue":"39","year":"2016","month":"09","status":"public","oa":1,"oa_version":"Preprint","date_published":"2016-09-27T00:00:00Z","publication_status":"published","doi":"10.1073/pnas.1605588113","citation":{"chicago":"Ortiz Morea, Fausto, Daniel Savatin, Wim Dejonghe, Rahul Kumar, Yu Luo, Maciek Adamowski, Jos Van Begin, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1605588113\">https://doi.org/10.1073/pnas.1605588113</a>.","ista":"Ortiz Morea F, Savatin D, Dejonghe W, Kumar R, Luo Y, Adamowski M, Van Begin J, Dressano K, De Oliveira G, Zhao X, Lu Q, Madder A, Friml J, De Moura D, Russinova E. 2016. Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. 113(39), 11028–11033.","apa":"Ortiz Morea, F., Savatin, D., Dejonghe, W., Kumar, R., Luo, Y., Adamowski, M., … Russinova, E. (2016). Danger-associated peptide signaling in Arabidopsis requires clathrin. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1605588113\">https://doi.org/10.1073/pnas.1605588113</a>","mla":"Ortiz Morea, Fausto, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” <i>PNAS</i>, vol. 113, no. 39, National Academy of Sciences, 2016, pp. 11028–33, doi:<a href=\"https://doi.org/10.1073/pnas.1605588113\">10.1073/pnas.1605588113</a>.","short":"F. Ortiz Morea, D. Savatin, W. Dejonghe, R. Kumar, Y. Luo, M. Adamowski, J. Van Begin, K. Dressano, G. De Oliveira, X. Zhao, Q. Lu, A. Madder, J. Friml, D. De Moura, E. Russinova, PNAS 113 (2016) 11028–11033.","ieee":"F. Ortiz Morea <i>et al.</i>, “Danger-associated peptide signaling in Arabidopsis requires clathrin,” <i>PNAS</i>, vol. 113, no. 39. National Academy of Sciences, pp. 11028–11033, 2016.","ama":"Ortiz Morea F, Savatin D, Dejonghe W, et al. Danger-associated peptide signaling in Arabidopsis requires clathrin. <i>PNAS</i>. 2016;113(39):11028-11033. doi:<a href=\"https://doi.org/10.1073/pnas.1605588113\">10.1073/pnas.1605588113</a>"},"intvolume":"       113","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047203/","open_access":"1"}],"author":[{"last_name":"Ortiz Morea","first_name":"Fausto","full_name":"Ortiz Morea, Fausto"},{"full_name":"Savatin, Daniel","first_name":"Daniel","last_name":"Savatin"},{"first_name":"Wim","last_name":"Dejonghe","full_name":"Dejonghe, Wim"},{"full_name":"Kumar, Rahul","last_name":"Kumar","first_name":"Rahul"},{"first_name":"Yu","last_name":"Luo","full_name":"Luo, Yu"},{"full_name":"Adamowski, Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","orcid":"0000-0001-6463-5257"},{"full_name":"Van Begin, Jos","first_name":"Jos","last_name":"Van Begin"},{"full_name":"Dressano, Keini","first_name":"Keini","last_name":"Dressano"},{"full_name":"De Oliveira, Guilherme","first_name":"Guilherme","last_name":"De Oliveira"},{"last_name":"Zhao","first_name":"Xiuyang","full_name":"Zhao, Xiuyang"},{"full_name":"Lu, Qing","first_name":"Qing","last_name":"Lu"},{"last_name":"Madder","first_name":"Annemieke","full_name":"Madder, Annemieke"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí"},{"full_name":"De Moura, Daniel","last_name":"De Moura","first_name":"Daniel"},{"first_name":"Eugenia","last_name":"Russinova","full_name":"Russinova, Eugenia"}],"acknowledgement":"F.A.O.-M. was supported by special\r\nresearch funding from the Flemish Government for a joint doctorate fellowship\r\nat Ghent University, and funding from the Student Program\r\n–\r\nGraduate Studies\r\nPlan Program from the Coordination for the Improvement of Higher Educa-\r\ntion Personnel, Brazil, for a doctorate fellowship at the University of São Paulo.\r\nX.Z. and Q.L. are indebted to the China Science Council and G.P.d.O. to the\r\n“\r\nCiência sem Fronteiras\r\n”\r\nfor predoctoral fellowships. R.K. and Y.L. have re-\r\nceived postdoctoral fellowships from the Belgian Science Policy Office. This\r\nresearch was supported by Flanders Research Foundation Grant G008416N\r\n(to E.R.) and by the São Paulo Research Foundation and the National Council\r\nfor Scientific and Technological Development (CNPq) (D.S.d.M.). D.S.d.M. is a\r\nresearch fellow of CNPq.\r\nWe thank D. Van Damme, E. Mylle, M. Castro Silva-Filho,\r\nand J. Goeman for providing usefu\r\nl advice and technical assistance;\r\nI. Hara-Nishimura, J. Lin, G. Jürgens, M. A. Johnson, and P. Bozhkov for sharing\r\npublished materials; and M. Nowack and M. Fendrych for kindly donating the\r\npUBQ10::ATG8-YFP\r\n-expressing marker line.","day":"27","publisher":"National Academy of Sciences","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Danger-associated peptide signaling in Arabidopsis requires clathrin","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"date_created":"2018-12-11T11:51:06Z","page":"11028 - 11033","publication":"PNAS","volume":113,"quality_controlled":"1","publist_id":"6039"},{"date_published":"2016-10-06T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1371/journal.pone.0164037","citation":{"short":"H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, S. Nagao, PLoS One 11 (2016).","ama":"Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. <i>PLoS One</i>. 2016;11(10). doi:<a href=\"https://doi.org/10.1371/journal.pone.0164037\">10.1371/journal.pone.0164037</a>","ieee":"H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, and S. Nagao, “Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies,” <i>PLoS One</i>, vol. 11, no. 10. Public Library of Science, 2016.","chicago":"Matsuno, Hitomi, Moeko Kudoh, Akiya Watakabe, Tetsuo Yamamori, Ryuichi Shigemoto, and Soichi Nagao. “Distribution and Structure of Synapses on Medial Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” <i>PLoS One</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0164037\">https://doi.org/10.1371/journal.pone.0164037</a>.","mla":"Matsuno, Hitomi, et al. “Distribution and Structure of Synapses on Medial Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” <i>PLoS One</i>, vol. 11, no. 10, e0164037, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0164037\">10.1371/journal.pone.0164037</a>.","apa":"Matsuno, H., Kudoh, M., Watakabe, A., Yamamori, T., Shigemoto, R., &#38; Nagao, S. (2016). Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0164037\">https://doi.org/10.1371/journal.pone.0164037</a>","ista":"Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. 2016. Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. PLoS One. 11(10), e0164037."},"intvolume":"        11","ddc":["570","571"],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:42Z","_id":"1278","article_number":"e0164037","year":"2016","date_updated":"2021-01-12T06:49:34Z","issue":"10","abstract":[{"lang":"eng","text":"Adaptations of vestibulo-ocular and optokinetic response eye movements have been studied as an experimental model of cerebellum-dependent motor learning. Several previous physiological and pharmacological studies have consistently suggested that the cerebellar flocculus (FL) Purkinje cells (P-cells) and the medial vestibular nucleus (MVN) neurons targeted by FL (FL-targeted MVN neurons) may respectively maintain the memory traces of short- and long-term adaptation. To study the basic structures of the FL-MVN synapses by light microscopy (LM) and electron microscopy (EM), we injected green florescence protein (GFP)-expressing lentivirus into FL to anterogradely label the FL P-cell axons in C57BL/6J mice. The FL P-cell axonal boutons were distributed in the magnocellular MVN and in the border region of parvocellular MVN and prepositus hypoglossi (PrH). In the magnocellular MVN, the FL-P cell axons mainly terminated on somata and proximal dendrites. On the other hand, in the parvocellular MVN/PrH, the FL P-cell axonal synaptic boutons mainly terminated on the relatively small-diameter (&lt; 1 μm) distal dendrites of MVN neurons, forming symmetrical synapses. The majority of such parvocellular MVN/PrH neurons were determined to be glutamatergic by immunocytochemistry and in-situ hybridization of GFP expressing transgenic mice. To further examine the spatial relationship between the synapses of FL P-cells and those of vestibular nerve on the neurons of the parvocellular MVN/ PrH, we added injections of biotinylated dextran amine into the semicircular canal and anterogradely labeled vestibular nerve axons in some mice. The MVN dendrites receiving the FL P-cell axonal synaptic boutons often closely apposed vestibular nerve synaptic boutons in both LM and EM studies. Such a partial overlap of synaptic boutons of FL P-cell axons with those of vestibular nerve axons in the distal dendrites of MVN neurons suggests that inhibitory synapses of FL P-cells may influence the function of neighboring excitatory synapses of vestibular nerve in the parvocellular MVN/PrH neurons."}],"month":"10","oa":1,"status":"public","language":[{"iso":"eng"}],"department":[{"_id":"RySh"}],"type":"journal_article","date_created":"2018-12-11T11:51:06Z","publication":"PLoS One","has_accepted_license":"1","quality_controlled":"1","volume":11,"publist_id":"6038","article_processing_charge":"No","pubrep_id":"689","article_type":"original","file":[{"file_name":"IST-2016-689-v1+1_journal.pone.0164037.PDF","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:17:16Z","creator":"system","checksum":"7c0ba0ca6d79844059158059d2a38d25","file_id":"5269","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":3657084}],"author":[{"first_name":"Hitomi","last_name":"Matsuno","full_name":"Matsuno, Hitomi"},{"first_name":"Moeko","last_name":"Kudoh","full_name":"Kudoh, Moeko"},{"last_name":"Watakabe","first_name":"Akiya","full_name":"Watakabe, Akiya"},{"first_name":"Tetsuo","last_name":"Yamamori","full_name":"Yamamori, Tetsuo"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"},{"full_name":"Nagao, Soichi","first_name":"Soichi","last_name":"Nagao"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"06","acknowledgement":"This work was supported by RIKEN [to SN]; Grant-in-Aid from the Japan Society for the Promotion of Science, https://www.jsps.go.jp/english/e-grants/ [22300112 to SN].","title":"Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies","publisher":"Public Library of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publist_id":"6037","pubrep_id":"690","volume":11,"quality_controlled":"1","has_accepted_license":"1","date_created":"2018-12-11T11:51:06Z","publication":"PLoS One","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JoCs"}],"publisher":"Public Library of Science","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734] via the IST FELLOWSHIP awarded to Dr. Krisztián A. Kovács and the European Research Council starting grant (acronym: HIPECMEM Project reference: 281511) awarded to Dr. Jozsef Csicsvari. We thank Lauri Viljanto for technical help in building the ripple detector.","day":"19","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Krisztián","last_name":"Kovács","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","full_name":"Kovács, Krisztián"},{"id":"426376DC-F248-11E8-B48F-1D18A9856A87","last_name":"O'Neill","first_name":"Joseph","full_name":"O'Neill, Joseph"},{"last_name":"Schönenberger","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","full_name":"Schönenberger, Philipp"},{"full_name":"Penttonen, Markku","first_name":"Markku","last_name":"Penttonen"},{"first_name":"Dámaris K","orcid":"0000-0002-8602-4374","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","last_name":"Rangel Guerrero","full_name":"Rangel Guerrero, Dámaris K"},{"full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":4353592,"creator":"system","file_id":"5009","checksum":"395895ecb2216e9c39135abaa56b28b3","access_level":"open_access","file_name":"IST-2016-690-v1+1_journal.pone.0164675.PDF","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:13:26Z"}],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:42Z","ddc":["570","571"],"citation":{"ista":"Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari JL. 2016. Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. PLoS One. 11(10), e0164675.","mla":"Kovács, Krisztián, et al. “Optogenetically Blocking Sharp Wave Ripple Events in Sleep Does Not Interfere with the Formation of Stable Spatial Representation in the CA1 Area of the Hippocampus.” <i>PLoS One</i>, vol. 11, no. 10, e0164675, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0164675\">10.1371/journal.pone.0164675</a>.","apa":"Kovács, K., O’Neill, J., Schönenberger, P., Penttonen, M., Rangel Guerrero, D. K., &#38; Csicsvari, J. L. (2016). Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0164675\">https://doi.org/10.1371/journal.pone.0164675</a>","chicago":"Kovács, Krisztián, Joseph O’Neill, Philipp Schönenberger, Markku Penttonen, Dámaris K Rangel Guerrero, and Jozsef L Csicsvari. “Optogenetically Blocking Sharp Wave Ripple Events in Sleep Does Not Interfere with the Formation of Stable Spatial Representation in the CA1 Area of the Hippocampus.” <i>PLoS One</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0164675\">https://doi.org/10.1371/journal.pone.0164675</a>.","short":"K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D.K. Rangel Guerrero, J.L. Csicsvari, PLoS One 11 (2016).","ama":"Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari JL. Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. <i>PLoS One</i>. 2016;11(10). doi:<a href=\"https://doi.org/10.1371/journal.pone.0164675\">10.1371/journal.pone.0164675</a>","ieee":"K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D. K. Rangel Guerrero, and J. L. Csicsvari, “Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus,” <i>PLoS One</i>, vol. 11, no. 10. Public Library of Science, 2016."},"intvolume":"        11","publication_status":"published","doi":"10.1371/journal.pone.0164675","oa_version":"Published Version","date_published":"2016-10-19T00:00:00Z","status":"public","oa":1,"month":"10","ec_funded":1,"date_updated":"2021-01-12T06:49:35Z","abstract":[{"text":"During hippocampal sharp wave/ripple (SWR) events, previously occurring, sensory inputdriven neuronal firing patterns are replayed. Such replay is thought to be important for plasticity- related processes and consolidation of memory traces. It has previously been shown that the electrical stimulation-induced disruption of SWR events interferes with learning in rodents in different experimental paradigms. On the other hand, the cognitive map theory posits that the plastic changes of the firing of hippocampal place cells constitute the electrophysiological counterpart of the spatial learning, observable at the behavioral level. Therefore, we tested whether intact SWR events occurring during the sleep/rest session after the first exploration of a novel environment are needed for the stabilization of the CA1 code, which process requires plasticity. We found that the newly-formed representation in the CA1 has the same level of stability with optogenetic SWR blockade as with a control manipulation that delivered the same amount of light into the brain. Therefore our results suggest that at least in the case of passive exploratory behavior, SWR-related plasticity is dispensable for the stability of CA1 ensembles.","lang":"eng"}],"issue":"10","year":"2016","article_number":"e0164675","_id":"1279"},{"publication":"Communications on Pure and Applied Mathematics","date_created":"2018-12-11T11:51:07Z","page":"1815 - 1881","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"type":"journal_article","publist_id":"6036","volume":69,"day":"01","acknowledgement":"The work of P.B. was partially supported by National Sci-\r\nence Foundation Grant DMS-1208859.  The work of L.E. was partially supported\r\nby ERC Advanced Grant RANMAT 338804.  The work of H.-T. Y. was partially\r\nsupported by National Science Foundation Grant DMS-1307444 and a Simons In-\r\nvestigator award.  The work of J.Y. was partially supported by National Science\r\nFoundation Grant DMS-1207961.  The major part of this research was conducted\r\nwhen all authors were visiting IAS and were also supported by National Science\r\nFoundation Grant DMS-1128255.","author":[{"last_name":"Bourgade","first_name":"Paul","full_name":"Bourgade, Paul"},{"orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László"},{"last_name":"Yau","first_name":"Horngtzer","full_name":"Yau, Horngtzer"},{"full_name":"Yin, Jun","first_name":"Jun","last_name":"Yin"}],"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"title":"Fixed energy universality for generalized wigner matrices","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley-Blackwell","doi":"10.1002/cpa.21624","publication_status":"published","date_published":"2016-10-01T00:00:00Z","oa_version":"Preprint","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1407.5606","open_access":"1"}],"citation":{"chicago":"Bourgade, Paul, László Erdös, Horngtzer Yau, and Jun Yin. “Fixed Energy Universality for Generalized Wigner Matrices.” <i>Communications on Pure and Applied Mathematics</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1002/cpa.21624\">https://doi.org/10.1002/cpa.21624</a>.","ista":"Bourgade P, Erdös L, Yau H, Yin J. 2016. Fixed energy universality for generalized wigner matrices. Communications on Pure and Applied Mathematics. 69(10), 1815–1881.","apa":"Bourgade, P., Erdös, L., Yau, H., &#38; Yin, J. (2016). Fixed energy universality for generalized wigner matrices. <i>Communications on Pure and Applied Mathematics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cpa.21624\">https://doi.org/10.1002/cpa.21624</a>","mla":"Bourgade, Paul, et al. “Fixed Energy Universality for Generalized Wigner Matrices.” <i>Communications on Pure and Applied Mathematics</i>, vol. 69, no. 10, Wiley-Blackwell, 2016, pp. 1815–81, doi:<a href=\"https://doi.org/10.1002/cpa.21624\">10.1002/cpa.21624</a>.","ama":"Bourgade P, Erdös L, Yau H, Yin J. Fixed energy universality for generalized wigner matrices. <i>Communications on Pure and Applied Mathematics</i>. 2016;69(10):1815-1881. doi:<a href=\"https://doi.org/10.1002/cpa.21624\">10.1002/cpa.21624</a>","ieee":"P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Fixed energy universality for generalized wigner matrices,” <i>Communications on Pure and Applied Mathematics</i>, vol. 69, no. 10. Wiley-Blackwell, pp. 1815–1881, 2016.","short":"P. Bourgade, L. Erdös, H. Yau, J. Yin, Communications on Pure and Applied Mathematics 69 (2016) 1815–1881."},"intvolume":"        69","year":"2016","abstract":[{"text":"We prove the Wigner-Dyson-Mehta conjecture at fixed energy in the bulk of the spectrum for generalized symmetric and Hermitian Wigner matrices. Previous results concerning the universality of random matrices either require an averaging in the energy parameter or they hold only for Hermitian matrices if the energy parameter is fixed. We develop a homogenization theory of the Dyson Brownian motion and show that microscopic universality follows from mesoscopic statistics.","lang":"eng"}],"issue":"10","date_updated":"2021-01-12T06:49:35Z","_id":"1280","oa":1,"status":"public","ec_funded":1,"month":"10"},{"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047109/","open_access":"1"}],"scopus_import":1,"citation":{"chicago":"Bouguyon, Eléonore, Francine Perrine Walker, Marjorie Pervent, Juliette Rochette, Candela Cuesta, Eva Benková, Alexandre Martinière, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1104/pp.16.01047\">https://doi.org/10.1104/pp.16.01047</a>.","mla":"Bouguyon, Eléonore, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” <i>Plant Physiology</i>, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1237–48, doi:<a href=\"https://doi.org/10.1104/pp.16.01047\">10.1104/pp.16.01047</a>.","apa":"Bouguyon, E., Perrine Walker, F., Pervent, M., Rochette, J., Cuesta, C., Benková, E., … Nacry, P. (2016). Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.16.01047\">https://doi.org/10.1104/pp.16.01047</a>","ista":"Bouguyon E, Perrine Walker F, Pervent M, Rochette J, Cuesta C, Benková E, Martinière A, Bach L, Krouk G, Gojon A, Nacry P. 2016. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. 172(2), 1237–1248.","ieee":"E. Bouguyon <i>et al.</i>, “Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor,” <i>Plant Physiology</i>, vol. 172, no. 2. American Society of Plant Biologists, pp. 1237–1248, 2016.","ama":"Bouguyon E, Perrine Walker F, Pervent M, et al. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. <i>Plant Physiology</i>. 2016;172(2):1237-1248. doi:<a href=\"https://doi.org/10.1104/pp.16.01047\">10.1104/pp.16.01047</a>","short":"E. Bouguyon, F. Perrine Walker, M. Pervent, J. Rochette, C. Cuesta, E. Benková, A. Martinière, L. Bach, G. Krouk, A. Gojon, P. Nacry, Plant Physiology 172 (2016) 1237–1248."},"intvolume":"       172","doi":"10.1104/pp.16.01047","publication_status":"published","oa_version":"Preprint","date_published":"2016-10-01T00:00:00Z","status":"public","oa":1,"month":"10","issue":"2","abstract":[{"lang":"eng","text":"Plants are able to modulate root growth and development to optimize their nitrogen nutrition. In Arabidopsis (Arabidopsis thaliana), the adaptive root response to nitrate (NO3 -) depends on the NRT1.1/NPF6.3 transporter/sensor. NRT1.1 represses emergence of lateral root primordia (LRPs) at low concentration or absence of NO3 - through its auxin transport activity that lowers auxin accumulation in LR. However, these functional data strongly contrast with the known transcriptional regulation of NRT1.1, which is markedly repressed in LRPs in the absence of NO3 -. To explain this discrepancy, we investigated in detail the spatiotemporal expression pattern of the NRT1.1 protein during LRP development and combined local transcript analysis with the use of transgenic lines expressing tagged NRT1.1 proteins. Our results show that although NO3 - stimulates NRT1.1 transcription and probably mRNA stability both in primary root tissues and in LRPs, it acts differentially on protein accumulation, depending on the tissues considered with stimulation in cortex and epidermis of the primary root and a strong repression in LRPs and to a lower extent at the primary root tip. This demonstrates that NRT1.1 is strongly regulated at the posttranscriptional level by tissue-specific mechanisms. These mechanisms are crucial for controlling the large palette of adaptive responses to NO3 - mediated by NRT1.1 as they ensure that the protein is present in the proper tissue under the specific conditions where it plays a signaling role in this particular tissue."}],"date_updated":"2021-01-12T06:49:36Z","year":"2016","_id":"1281","publist_id":"6035","quality_controlled":"1","volume":172,"publication":"Plant Physiology","date_created":"2018-12-11T11:51:07Z","page":"1237 - 1248","type":"journal_article","department":[{"_id":"EvBe"}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"American Society of Plant Biologists","title":"Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor","acknowledgement":"This work was supported by the Agropolis Foundation (RHIZOPOLIS project to A.G. and P.N., and RTRA 2009-2011 project to F.P.-W.), the Knowledge Biobase Economy European project (KBBE-005-002 Root enhancement for crop improvement to M.P. and P.N.), and the European EURoot project (FP7-KBBE-2011-5 to J.R., A.G., and P.N.). We thank Carine Alcon for the help with analysis of confocal images, Xavier\r\nDumont for assistance with Arabidopsis transformations, staff members of the\r\nInstitut de Biologie Intégrative des Plantes for technical assistance with biological\r\nmaterial culture, and students and trainees for assistance with laboratory work.\r\nConfocal observations were made at the Montpellier RIO Imaging facility.","day":"01","author":[{"full_name":"Bouguyon, Eléonore","first_name":"Eléonore","last_name":"Bouguyon"},{"last_name":"Perrine Walker","first_name":"Francine","full_name":"Perrine Walker, Francine"},{"last_name":"Pervent","first_name":"Marjorie","full_name":"Pervent, Marjorie"},{"full_name":"Rochette, Juliette","first_name":"Juliette","last_name":"Rochette"},{"full_name":"Cuesta, Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","last_name":"Cuesta","orcid":"0000-0003-1923-2410","first_name":"Candela"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Martinière","first_name":"Alexandre","full_name":"Martinière, Alexandre"},{"last_name":"Bach","first_name":"Lien","full_name":"Bach, Lien"},{"last_name":"Krouk","first_name":"Gabriel","full_name":"Krouk, Gabriel"},{"last_name":"Gojon","first_name":"Alain","full_name":"Gojon, Alain"},{"first_name":"Philippe","last_name":"Nacry","full_name":"Nacry, Philippe"}]},{"author":[{"full_name":"Gundert, Anna","first_name":"Anna","last_name":"Gundert"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner"}],"_id":"1282","issue":"2","abstract":[{"lang":"eng","text":"We consider higher-dimensional generalizations of the normalized Laplacian and the adjacency matrix of graphs and study their eigenvalues for the Linial–Meshulam model Xk(n, p) of random k-dimensional simplicial complexes on n vertices. We show that for p = Ω(logn/n), the eigenvalues of each of the matrices are a.a.s. concentrated around two values. The main tool, which goes back to the work of Garland, are arguments that relate the eigenvalues of these matrices to those of graphs that arise as links of (k - 2)-dimensional faces. Garland’s result concerns the Laplacian; we develop an analogous result for the adjacency matrix. The same arguments apply to other models of random complexes which allow for dependencies between the choices of k-dimensional simplices. In the second part of the paper, we apply this to the question of possible higher-dimensional analogues of the discrete Cheeger inequality, which in the classical case of graphs relates the eigenvalues of a graph and its edge expansion. It is very natural to ask whether this generalizes to higher dimensions and, in particular, whether the eigenvalues of the higher-dimensional Laplacian capture the notion of coboundary expansion—a higher-dimensional generalization of edge expansion that arose in recent work of Linial and Meshulam and of Gromov; this question was raised, for instance, by Dotterrer and Kahle. We show that this most straightforward version of a higher-dimensional discrete Cheeger inequality fails, in quite a strong way: For every k ≥ 2 and n ∈ N, there is a k-dimensional complex Yn k on n vertices that has strong spectral expansion properties (all nontrivial eigenvalues of the normalised k-dimensional Laplacian lie in the interval [1−O(1/√1), 1+0(1/√1]) but whose coboundary expansion is bounded from above by O(log n/n) and so tends to zero as n → ∞; moreover, Yn k can be taken to have vanishing integer homology in dimension less than k."}],"date_updated":"2021-01-12T06:49:36Z","year":"2016","day":"01","month":"10","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Springer","oa":1,"title":"On eigenvalues of random complexes","oa_version":"Preprint","type":"journal_article","date_published":"2016-10-01T00:00:00Z","department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"doi":"10.1007/s11856-016-1419-1","publication_status":"published","publication":"Israel Journal of Mathematics","date_created":"2018-12-11T11:51:07Z","page":"545 - 582","citation":{"short":"A. Gundert, U. Wagner, Israel Journal of Mathematics 216 (2016) 545–582.","ama":"Gundert A, Wagner U. On eigenvalues of random complexes. <i>Israel Journal of Mathematics</i>. 2016;216(2):545-582. doi:<a href=\"https://doi.org/10.1007/s11856-016-1419-1\">10.1007/s11856-016-1419-1</a>","ieee":"A. Gundert and U. Wagner, “On eigenvalues of random complexes,” <i>Israel Journal of Mathematics</i>, vol. 216, no. 2. Springer, pp. 545–582, 2016.","mla":"Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” <i>Israel Journal of Mathematics</i>, vol. 216, no. 2, Springer, 2016, pp. 545–82, doi:<a href=\"https://doi.org/10.1007/s11856-016-1419-1\">10.1007/s11856-016-1419-1</a>.","apa":"Gundert, A., &#38; Wagner, U. (2016). On eigenvalues of random complexes. <i>Israel Journal of Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s11856-016-1419-1\">https://doi.org/10.1007/s11856-016-1419-1</a>","ista":"Gundert A, Wagner U. 2016. On eigenvalues of random complexes. Israel Journal of Mathematics. 216(2), 545–582.","chicago":"Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” <i>Israel Journal of Mathematics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11856-016-1419-1\">https://doi.org/10.1007/s11856-016-1419-1</a>."},"volume":216,"intvolume":"       216","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1411.4906"}],"publist_id":"6034","scopus_import":1},{"quality_controlled":"1","volume":21,"publist_id":"6033","article_type":"original","pubrep_id":"1018","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"EvBe"}],"has_accepted_license":"1","page":"809 - 811","date_created":"2018-12-11T11:51:08Z","publication":"Trends in Plant Science","publisher":"Cell Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Seedlings’ strategy to overcome a soil barrier","project":[{"grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF"}],"author":[{"id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","last_name":"Zhu","first_name":"Qiang","full_name":"Zhu, Qiang"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":229094,"file_name":"IST-2018-1018-v1+1_Zhu_and_Benkova_TIPS_2016.pdf","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:08:19Z","file_id":"4679","checksum":"4d569977fad7a7f22b7e3424003d2ab1","creator":"system","access_level":"local"}],"acknowledgement":"This work was supported by the Austrian Science Fund (FWF01_I1774S) to E.B., the Natural Science Foundation of Fujian Province (2016J01099), and the Fujian–Taiwan Joint Innovative Center for Germplasm Resources and Cultivation of Crops (FJ 2011 Program, No 2015-75) to Q.Z. The\r\nauthors\r\nthank\r\nIsrael\r\nAusin\r\nand\r\nXu\r\nChen\r\nfor\r\ncritical\r\nreading\r\nof\r\nthe\r\nmanuscript.","day":"01","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"citation":{"apa":"Zhu, Q., &#38; Benková, E. (2016). Seedlings’ strategy to overcome a soil barrier. <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">https://doi.org/10.1016/j.tplants.2016.08.003</a>","ista":"Zhu Q, Benková E. 2016. Seedlings’ strategy to overcome a soil barrier. Trends in Plant Science. 21(10), 809–811.","mla":"Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.” <i>Trends in Plant Science</i>, vol. 21, no. 10, Cell Press, 2016, pp. 809–11, doi:<a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">10.1016/j.tplants.2016.08.003</a>.","chicago":"Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.” <i>Trends in Plant Science</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">https://doi.org/10.1016/j.tplants.2016.08.003</a>.","ieee":"Q. Zhu and E. Benková, “Seedlings’ strategy to overcome a soil barrier,” <i>Trends in Plant Science</i>, vol. 21, no. 10. Cell Press, pp. 809–811, 2016.","ama":"Zhu Q, Benková E. Seedlings’ strategy to overcome a soil barrier. <i>Trends in Plant Science</i>. 2016;21(10):809-811. doi:<a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">10.1016/j.tplants.2016.08.003</a>","short":"Q. Zhu, E. Benková, Trends in Plant Science 21 (2016) 809–811."},"intvolume":"        21","file_date_updated":"2020-07-14T12:44:42Z","scopus_import":1,"ddc":["575"],"oa_version":"Submitted Version","date_published":"2016-10-01T00:00:00Z","publication_status":"published","doi":"10.1016/j.tplants.2016.08.003","month":"10","status":"public","_id":"1283","date_updated":"2021-01-12T06:49:36Z","issue":"10","abstract":[{"lang":"eng","text":"The impact of the plant hormone ethylene on seedling development has long been recognized; however, its ecophysiological relevance is unexplored. Three recent studies demonstrate that ethylene is a critical endogenous integrator of various environmental signals including mechanical stress, light, and oxygen availability during seedling germination and growth through the soil."}],"year":"2016"},{"quality_controlled":"1","citation":{"short":"E. Paluch, I. Aspalter, M.K. Sixt, Annual Review of Cell and Developmental Biology 32 (2016) 469–490.","ama":"Paluch E, Aspalter I, Sixt MK. Focal adhesion-independent cell migration. <i>Annual Review of Cell and Developmental Biology</i>. 2016;32:469-490. doi:<a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">10.1146/annurev-cellbio-111315-125341</a>","ieee":"E. Paluch, I. Aspalter, and M. K. Sixt, “Focal adhesion-independent cell migration,” <i>Annual Review of Cell and Developmental Biology</i>, vol. 32. Annual Reviews, pp. 469–490, 2016.","chicago":"Paluch, Ewa, Irene Aspalter, and Michael K Sixt. “Focal Adhesion-Independent Cell Migration.” <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews, 2016. <a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">https://doi.org/10.1146/annurev-cellbio-111315-125341</a>.","ista":"Paluch E, Aspalter I, Sixt MK. 2016. Focal adhesion-independent cell migration. Annual Review of Cell and Developmental Biology. 32, 469–490.","apa":"Paluch, E., Aspalter, I., &#38; Sixt, M. K. (2016). Focal adhesion-independent cell migration. <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">https://doi.org/10.1146/annurev-cellbio-111315-125341</a>","mla":"Paluch, Ewa, et al. “Focal Adhesion-Independent Cell Migration.” <i>Annual Review of Cell and Developmental Biology</i>, vol. 32, Annual Reviews, 2016, pp. 469–90, doi:<a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">10.1146/annurev-cellbio-111315-125341</a>."},"volume":32,"intvolume":"        32","publist_id":"6031","scopus_import":1,"type":"journal_article","oa_version":"None","language":[{"iso":"eng"}],"date_published":"2016-10-06T00:00:00Z","department":[{"_id":"MiSi"}],"publication_status":"published","doi":"10.1146/annurev-cellbio-111315-125341","date_created":"2018-12-11T11:51:08Z","page":"469 - 490","publication":"Annual Review of Cell and Developmental Biology","month":"10","ec_funded":1,"status":"public","publisher":"Annual Reviews","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Focal adhesion-independent cell migration","project":[{"grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"},{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12","call_identifier":"FWF","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)"}],"author":[{"full_name":"Paluch, Ewa","first_name":"Ewa","last_name":"Paluch"},{"first_name":"Irene","last_name":"Aspalter","full_name":"Aspalter, Irene"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"_id":"1285","date_updated":"2021-01-12T06:49:37Z","acknowledgement":"We would like to thank Dani Bodor for critical comments on the manuscript and Guillaume Salbreux for discussions. The authors are supported by the United Kingdom's Medical Research Council (MRC) (E.K.P. and I.M.A.; core funding to the MRC Laboratory for Molecular Cell Biology), by the European Research Council [ERC GA 311637 (E.K.P.) and ERC GA 281556 (M.S.)], and by a START award from the Austrian Science Foundation (M.S.).","abstract":[{"text":"Cell migration is central to a multitude of physiological processes, including embryonic development, immune surveillance, and wound healing, and deregulated migration is key to cancer dissemination. Decades of investigations have uncovered many of the molecular and physical mechanisms underlying cell migration. Together with protrusion extension and cell body retraction, adhesion to the substrate via specific focal adhesion points has long been considered an essential step in cell migration. Although this is true for cells moving on two-dimensional substrates, recent studies have demonstrated that focal adhesions are not required for cells moving in three dimensions, in which confinement is sufficient to maintain a cell in contact with its substrate. Here, we review the investigations that have led to challenging the requirement of specific adhesions for migration, discuss the physical mechanisms proposed for cell body translocation during focal adhesion-independent migration, and highlight the remaining open questions for the future.","lang":"eng"}],"day":"06","year":"2016"},{"oa_version":"Preprint","date_published":"2016-10-13T00:00:00Z","doi":"10.1103/PhysRevA.94.041601","publication_status":"published","citation":{"chicago":"Midya, Bikashkali, Michał Tomza, Richard Schmidt, and Mikhail Lemeshko. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">https://doi.org/10.1103/PhysRevA.94.041601</a>.","apa":"Midya, B., Tomza, M., Schmidt, R., &#38; Lemeshko, M. (2016). Rotation of cold molecular ions inside a Bose-Einstein condensate. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">https://doi.org/10.1103/PhysRevA.94.041601</a>","mla":"Midya, Bikashkali, et al. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 94, no. 4, 041601, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">10.1103/PhysRevA.94.041601</a>.","ista":"Midya B, Tomza M, Schmidt R, Lemeshko M. 2016. Rotation of cold molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical Physics. 94(4), 041601.","ieee":"B. Midya, M. Tomza, R. Schmidt, and M. Lemeshko, “Rotation of cold molecular ions inside a Bose-Einstein condensate,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 94, no. 4. American Physical Society, 2016.","ama":"Midya B, Tomza M, Schmidt R, Lemeshko M. Rotation of cold molecular ions inside a Bose-Einstein condensate. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2016;94(4). doi:<a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">10.1103/PhysRevA.94.041601</a>","short":"B. Midya, M. Tomza, R. Schmidt, M. Lemeshko, Physical Review A - Atomic, Molecular, and Optical Physics 94 (2016)."},"intvolume":"        94","main_file_link":[{"url":"https://arxiv.org/abs/1607.06092","open_access":"1"}],"scopus_import":1,"article_number":"041601","_id":"1286","issue":"4","abstract":[{"text":"We use recently developed angulon theory [R. Schmidt and M. Lemeshko, Phys. Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001] to study the rotational spectrum of a cyanide molecular anion immersed into Bose-Einstein condensates of rubidium and strontium. Based on ab initio potential energy surfaces, we provide a detailed study of the rotational Lamb shift and many-body-induced fine structure which arise due to dressing of molecular rotation by a field of phonon excitations. We demonstrate that the magnitude of these effects is large enough in order to be observed in modern experiments on cold molecular ions. Furthermore, we introduce a novel method to construct pseudopotentials starting from the ab initio potential energy surfaces, which provides a means to obtain effective coupling constants for low-energy polaron models.","lang":"eng"}],"date_updated":"2021-01-12T06:49:37Z","year":"2016","month":"10","ec_funded":1,"status":"public","oa":1,"type":"journal_article","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"publication":"Physical Review A - Atomic, Molecular, and Optical Physics","date_created":"2018-12-11T11:51:09Z","volume":94,"quality_controlled":"1","publist_id":"6030","author":[{"full_name":"Midya, Bikashkali","first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","last_name":"Midya"},{"full_name":"Tomza, Michał","first_name":"Michał","last_name":"Tomza"},{"first_name":"Richard","last_name":"Schmidt","full_name":"Schmidt, Richard"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"acknowledgement":"The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and the Smithsonian Astrophysical Observatory. B.M. acknowledges financial support received from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 291734. M.T. acknowledges support from the EU Marie Curie COFUND action (ICFOnest), the EU Grants ERC AdG OSYRIS, FP7 SIQS and EQuaM, FETPROACT QUIC, the Spanish Ministry Grants FOQUS (FIS2013-46768-P) and Severo Ochoa (SEV-2015-0522), Generalitat de Catalunya (SGR 874), Fundacio Cellex, the National Science Centre (2015/19/D/ST4/02173), and the PL-Grid Infrastructure.","day":"13","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","title":"Rotation of cold molecular ions inside a Bose-Einstein condensate"}]