[{"status":"public","acknowledgement":"This work is supported in part by NSF CNS 13-30077, NSF CNS 13-29886, NSF CNS 15-45002, NSFC 61303014, NSFC 61202010, and NSFC 91218302.","publication_status":"published","title":"From stateflow simulation to verified implementation: A verification approach and a real-time train controller design","author":[{"first_name":"Yu","last_name":"Jiang","full_name":"Jiang, Yu"},{"first_name":"Yixiao","full_name":"Yang, Yixiao","last_name":"Yang"},{"last_name":"Liu","full_name":"Liu, Han","first_name":"Han"},{"orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui","full_name":"Kong, Hui","last_name":"Kong"},{"last_name":"Gu","full_name":"Gu, Ming","first_name":"Ming"},{"first_name":"Jiaguang","last_name":"Sun","full_name":"Sun, Jiaguang"},{"full_name":"Sha, Lui","last_name":"Sha","first_name":"Lui"}],"_id":"1256","abstract":[{"lang":"eng","text":"Simulink is widely used for model driven development (MDD) of industrial software systems. Typically, the Simulink based development is initiated from Stateflow modeling, followed by simulation, validation and code generation mapped to physical execution platforms. However, recent industrial trends have raised the demands of rigorous verification on safety-critical applications, which is unfortunately challenging for Simulink. In this paper, we present an approach to bridge the Stateflow based model driven development and a well- defined rigorous verification. First, we develop a self- contained toolkit to translate Stateflow model into timed automata, where major advanced modeling features in Stateflow are supported. Taking advantage of the strong verification capability of Uppaal, we can not only find bugs in Stateflow models which are missed by Simulink Design Verifier, but also check more important temporal properties. Next, we customize a runtime verifier for the generated nonintrusive VHDL and C code of Stateflow model for monitoring. The major strength of the customization is the flexibility to collect and analyze runtime properties with a pure software monitor, which opens more opportunities for engineers to achieve high reliability of the target system compared with the traditional act that only relies on Simulink Polyspace. We incorporate these two parts into original Stateflow based MDD seamlessly. In this way, safety-critical properties are both verified at the model level, and at the consistent system implementation level with physical execution environment in consideration. We apply our approach on a train controller design, and the verified implementation is tested and deployed on a real hardware platform."}],"doi":"10.1109/RTAS.2016.7461337","file":[{"creator":"system","relation":"main_file","file_size":1293599,"file_name":"IST-2017-780-v1+1_RTAS-42-Camera-Ready.pdf","date_updated":"2020-07-14T12:44:41Z","content_type":"application/pdf","checksum":"42f0462911cc9957f2356b12fb33b4b6","access_level":"open_access","date_created":"2018-12-12T10:12:31Z","file_id":"4949"}],"has_accepted_license":"1","pubrep_id":"780","citation":{"chicago":"Jiang, Yu, Yixiao Yang, Han Liu, Hui Kong, Ming Gu, Jiaguang Sun, and Lui Sha. “From Stateflow Simulation to Verified Implementation: A Verification Approach and a Real-Time Train Controller Design.” IEEE, 2016. <a href=\"https://doi.org/10.1109/RTAS.2016.7461337\">https://doi.org/10.1109/RTAS.2016.7461337</a>.","mla":"Jiang, Yu, et al. <i>From Stateflow Simulation to Verified Implementation: A Verification Approach and a Real-Time Train Controller Design</i>. 7461337, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/RTAS.2016.7461337\">10.1109/RTAS.2016.7461337</a>.","ieee":"Y. Jiang <i>et al.</i>, “From stateflow simulation to verified implementation: A verification approach and a real-time train controller design,” presented at the RTAS: Real-time and Embedded Technology and Applications Symposium, Vienna, Austria, 2016.","apa":"Jiang, Y., Yang, Y., Liu, H., Kong, H., Gu, M., Sun, J., &#38; Sha, L. (2016). From stateflow simulation to verified implementation: A verification approach and a real-time train controller design. Presented at the RTAS: Real-time and Embedded Technology and Applications Symposium, Vienna, Austria: IEEE. <a href=\"https://doi.org/10.1109/RTAS.2016.7461337\">https://doi.org/10.1109/RTAS.2016.7461337</a>","short":"Y. Jiang, Y. Yang, H. Liu, H. Kong, M. Gu, J. Sun, L. Sha, in:, IEEE, 2016.","ama":"Jiang Y, Yang Y, Liu H, et al. From stateflow simulation to verified implementation: A verification approach and a real-time train controller design. In: IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/RTAS.2016.7461337\">10.1109/RTAS.2016.7461337</a>","ista":"Jiang Y, Yang Y, Liu H, Kong H, Gu M, Sun J, Sha L. 2016. From stateflow simulation to verified implementation: A verification approach and a real-time train controller design. RTAS: Real-time and Embedded Technology and Applications Symposium, 7461337."},"day":"27","month":"04","ddc":["005"],"file_date_updated":"2020-07-14T12:44:41Z","oa_version":"Submitted Version","conference":{"name":"RTAS: Real-time and Embedded Technology and Applications Symposium","start_date":"2016-04-11","location":"Vienna, Austria","end_date":"2016-04-14"},"date_updated":"2021-01-12T06:49:26Z","article_number":"7461337","oa":1,"year":"2016","publisher":"IEEE","quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","department":[{"_id":"ToHe"}],"publist_id":"6069","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2016-04-27T00:00:00Z","date_created":"2018-12-11T11:50:58Z","scopus_import":1},{"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","volume":343,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2020-07-14T12:44:42Z","checksum":"4fb2411d9c2f56676123165aad46c828","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":800792,"creator":"system","file_name":"IST-2016-703-v1+1_s00220-016-2600-4.pdf","date_created":"2018-12-12T10:15:02Z","file_id":"5119"}],"oa_version":"Published Version","pubrep_id":"703","citation":{"mla":"Sadel, Christian, and Bálint Virág. “A Central Limit Theorem for Products of Random Matrices and GOE Statistics for the Anderson Model on Long Boxes.” <i>Communications in Mathematical Physics</i>, vol. 343, no. 3, Springer, 2016, pp. 881–919, doi:<a href=\"https://doi.org/10.1007/s00220-016-2600-4\">10.1007/s00220-016-2600-4</a>.","chicago":"Sadel, Christian, and Bálint Virág. “A Central Limit Theorem for Products of Random Matrices and GOE Statistics for the Anderson Model on Long Boxes.” <i>Communications in Mathematical Physics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00220-016-2600-4\">https://doi.org/10.1007/s00220-016-2600-4</a>.","ista":"Sadel C, Virág B. 2016. A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes. Communications in Mathematical Physics. 343(3), 881–919.","short":"C. Sadel, B. Virág, Communications in Mathematical Physics 343 (2016) 881–919.","ama":"Sadel C, Virág B. A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes. <i>Communications in Mathematical Physics</i>. 2016;343(3):881-919. doi:<a href=\"https://doi.org/10.1007/s00220-016-2600-4\">10.1007/s00220-016-2600-4</a>","ieee":"C. Sadel and B. Virág, “A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes,” <i>Communications in Mathematical Physics</i>, vol. 343, no. 3. Springer, pp. 881–919, 2016.","apa":"Sadel, C., &#38; Virág, B. (2016). A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-016-2600-4\">https://doi.org/10.1007/s00220-016-2600-4</a>"},"day":"01","file_date_updated":"2020-07-14T12:44:42Z","ddc":["510","539"],"month":"05","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The work of C. Sadel was supported by NSERC Discovery Grant 92997-2010 RGPIN and by the People Programme (Marie Curie Actions) of the EU 7th Framework Programme FP7/2007-2013, REA Grant 291734.","publication_status":"published","status":"public","ec_funded":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"abstract":[{"lang":"eng","text":"We consider products of random matrices that are small, independent identically distributed perturbations of a fixed matrix (Formula presented.). Focusing on the eigenvalues of (Formula presented.) of a particular size we obtain a limit to a SDE in a critical scaling. Previous results required (Formula presented.) to be a (conjugated) unitary matrix so it could not have eigenvalues of different modulus. From the result we can also obtain a limit SDE for the Markov process given by the action of the random products on the flag manifold. Applying the result to random Schrödinger operators we can improve some results by Valko and Virag showing GOE statistics for the rescaled eigenvalue process of a sequence of Anderson models on long boxes. In particular, we solve a problem posed in their work."}],"issue":"3","doi":"10.1007/s00220-016-2600-4","title":"A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes","author":[{"orcid":"0000-0001-8255-3968","full_name":"Sadel, Christian","last_name":"Sadel","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"last_name":"Virág","full_name":"Virág, Bálint","first_name":"Bálint"}],"_id":"1257","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Springer","intvolume":"       343","date_published":"2016-05-01T00:00:00Z","date_created":"2018-12-11T11:50:59Z","scopus_import":1,"department":[{"_id":"LaEr"}],"publist_id":"6067","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"881 - 919","publication":"Communications in Mathematical Physics","date_updated":"2021-01-12T06:49:26Z","year":"2016","oa":1},{"doi":"10.1242/dev.130211","abstract":[{"lang":"eng","text":"When plants grow in close proximity basic resources such as light can become limiting. Under such conditions plants respond to anticipate and/or adapt to the light shortage, a process known as the shade avoidance syndrome (SAS). Following genetic screening using a shade-responsive luciferase reporter line (PHYB:LUC), we identified DRACULA2 (DRA2), which encodes an Arabidopsis homolog of mammalian nucleoporin 98, a component of the nuclear pore complex (NPC). DRA2, together with other nucleoporins, participates positively in the control of the hypocotyl elongation response to plant proximity, a role that can be considered dependent on the nucleocytoplasmic transport of macromolecules (i.e. is transport dependent). In addition, our results reveal a specific role for DRA2 in controlling shade-induced gene expression. We suggest that this novel regulatory role of DRA2 is transport independent and that it might rely on its dynamic localization within and outside of the NPC. These results provide mechanistic insights in to how SAS responses are rapidly established by light conditions. They also indicate that nucleoporins have an active role in plant signaling."}],"year":"2016","issue":"9","_id":"1258","title":"DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis","author":[{"id":"460C6802-F248-11E8-B48F-1D18A9856A87","first_name":"Marcal","full_name":"Gallemi Rovira, Marcal","last_name":"Gallemi Rovira"},{"full_name":"Galstyan, Anahit","last_name":"Galstyan","first_name":"Anahit"},{"first_name":"Sandi","full_name":"Paulišić, Sandi","last_name":"Paulišić"},{"full_name":"Then, Christiane","last_name":"Then","first_name":"Christiane"},{"full_name":"Ferrández Ayela, Almudena","last_name":"Ferrández Ayela","first_name":"Almudena"},{"full_name":"Lorenzo Orts, Laura","last_name":"Lorenzo Orts","first_name":"Laura"},{"first_name":"Irma","last_name":"Roig Villanova","full_name":"Roig Villanova, Irma"},{"first_name":"Xuewen","full_name":"Wang, Xuewen","last_name":"Wang"},{"full_name":"Micol, José","last_name":"Micol","first_name":"José"},{"first_name":"Maria","last_name":"Ponce","full_name":"Ponce, Maria"},{"first_name":"Paul","full_name":"Devlin, Paul","last_name":"Devlin"},{"last_name":"Martínez García","full_name":"Martínez García, Jaime","first_name":"Jaime"}],"page":"1623 - 1631","status":"public","publication_status":"published","acknowledgement":"M.G. received an FPI fellowship from the Spanish Ministerio de Economía y Competitividad (MINECO). A.G. and A.F.-A. received FPU fellowships from the Spanish Ministerio de Educación. S.P. received an FI fellowship from the Agència de Gestió D'ajuts Universitaris i de Recerca (AGAUR - Generalitat de Catalunya). C.T. received a Marie Curie IEF postdoctoral contract funded by the European Commission. I.R.-V. received initially an FPI fellowship from the Spanish MINECO and later a Beatriu de Pinós contract from AGAUR. Our research is supported by grants from the Spanish MINECO-FEDER [BIO2008-00169, BIO2011-23489 and BIO2014-59895-P] and Generalitat de Catalunya [2011-SGR447 and Xarba] to J.F.M.-G., and Generalitat Valenciana [PROMETEO/2009/112, PROMETEOII/2014/006] to M.R.P. and J.L.M. We acknowledge the support of the Spanish MINECO for the ‘Centro de Excelencia Severo Ochoa 2016-2019’ [award SEV-2015-0533]. We thank the CRAG greenhouse service for plant care; Chus Burillo for technical help; Sergi Portolés and Carles Rentero for assistance with mutagenesis; Mark Estelle (UCSD, USA) for providing sar1-4, sar3-1 and sar3-3 seeds; Juanjo López-Moya (CRAG, Barcelona; 35S:HcPro plasmid) and Dolors Ludevid (CRAG; C307 plasmid) for providing DNA plasmids; and Manuel Rodríguez-Concepción (CRAG) and Miguel Blázquez (IBMCP, Valencia, Spain) for comments on the manuscript.","date_updated":"2021-01-12T06:49:27Z","publication":"Development","date_created":"2018-12-11T11:50:59Z","oa_version":"None","scopus_import":1,"date_published":"2016-05-03T00:00:00Z","publist_id":"6068","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"05","citation":{"short":"M. Gallemi, A. Galstyan, S. Paulišić, C. Then, A. Ferrández Ayela, L. Lorenzo Orts, I. Roig Villanova, X. Wang, J. Micol, M. Ponce, P. Devlin, J. Martínez García, Development 143 (2016) 1623–1631.","ama":"Gallemi M, Galstyan A, Paulišić S, et al. DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. <i>Development</i>. 2016;143(9):1623-1631. doi:<a href=\"https://doi.org/10.1242/dev.130211\">10.1242/dev.130211</a>","ista":"Gallemi M, Galstyan A, Paulišić S, Then C, Ferrández Ayela A, Lorenzo Orts L, Roig Villanova I, Wang X, Micol J, Ponce M, Devlin P, Martínez García J. 2016. DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development. 143(9), 1623–1631.","apa":"Gallemi, M., Galstyan, A., Paulišić, S., Then, C., Ferrández Ayela, A., Lorenzo Orts, L., … Martínez García, J. (2016). DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.130211\">https://doi.org/10.1242/dev.130211</a>","ieee":"M. Gallemi <i>et al.</i>, “DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis,” <i>Development</i>, vol. 143, no. 9. Company of Biologists, pp. 1623–1631, 2016.","mla":"Gallemi, Marçal, et al. “DRACULA2 Is a Dynamic Nucleoporin with a Role in Regulating the Shade Avoidance Syndrome in Arabidopsis.” <i>Development</i>, vol. 143, no. 9, Company of Biologists, 2016, pp. 1623–31, doi:<a href=\"https://doi.org/10.1242/dev.130211\">10.1242/dev.130211</a>.","chicago":"Gallemi, Marçal, Anahit Galstyan, Sandi Paulišić, Christiane Then, Almudena Ferrández Ayela, Laura Lorenzo Orts, Irma Roig Villanova, et al. “DRACULA2 Is a Dynamic Nucleoporin with a Role in Regulating the Shade Avoidance Syndrome in Arabidopsis.” <i>Development</i>. Company of Biologists, 2016. <a href=\"https://doi.org/10.1242/dev.130211\">https://doi.org/10.1242/dev.130211</a>."},"day":"03","department":[{"_id":"EvBe"}],"volume":143,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Company of Biologists","intvolume":"       143"},{"article_number":"13","date_updated":"2021-01-12T06:49:27Z","publication":"Mathematical Physics, Analysis and Geometry","year":"2016","oa":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"Springer","intvolume":"        19","date_created":"2018-12-11T11:50:59Z","scopus_import":1,"date_published":"2016-06-01T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6066","department":[{"_id":"RoSe"}],"acknowledgement":"Partial financial support from the DFG grant GRK 1838, as well as the Austrian Science Fund (FWF), project Nr. P 27533-N27 (R.S.), is gratefully acknowledged.","publication_status":"published","status":"public","project":[{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"}],"doi":"10.1007/s11040-016-9209-x","abstract":[{"lang":"eng","text":"We consider the Bogolubov–Hartree–Fock functional for a fermionic many-body system with two-body interactions. For suitable interaction potentials that have a strong enough attractive tail in order to allow for two-body bound states, but are otherwise sufficiently repulsive to guarantee stability of the system, we show that in the low-density limit the ground state of this model consists of a Bose–Einstein condensate of fermion pairs. The latter can be described by means of the Gross–Pitaevskii energy functional."}],"issue":"2","_id":"1259","title":"Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit","author":[{"full_name":"Bräunlich, Gerhard","last_name":"Bräunlich","first_name":"Gerhard"},{"first_name":"Christian","last_name":"Hainzl","full_name":"Hainzl, Christian"},{"orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"article_processing_charge":"Yes (via OA deal)","volume":19,"has_accepted_license":"1","file":[{"access_level":"open_access","checksum":"9954f685cc25c58d7f1712c67b47ad8d","content_type":"application/pdf","date_updated":"2020-07-14T12:44:42Z","file_name":"IST-2016-702-v1+1_s11040-016-9209-x.pdf","relation":"main_file","file_size":506242,"creator":"system","file_id":"4736","date_created":"2018-12-12T10:09:13Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","ddc":["510","539"],"file_date_updated":"2020-07-14T12:44:42Z","month":"06","citation":{"chicago":"Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Bogolubov–Hartree–Fock Theory for Strongly Interacting Fermions in the Low Density Limit.” <i>Mathematical Physics, Analysis and Geometry</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11040-016-9209-x\">https://doi.org/10.1007/s11040-016-9209-x</a>.","mla":"Bräunlich, Gerhard, et al. “Bogolubov–Hartree–Fock Theory for Strongly Interacting Fermions in the Low Density Limit.” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 19, no. 2, 13, Springer, 2016, doi:<a href=\"https://doi.org/10.1007/s11040-016-9209-x\">10.1007/s11040-016-9209-x</a>.","ama":"Bräunlich G, Hainzl C, Seiringer R. Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit. <i>Mathematical Physics, Analysis and Geometry</i>. 2016;19(2). doi:<a href=\"https://doi.org/10.1007/s11040-016-9209-x\">10.1007/s11040-016-9209-x</a>","ista":"Bräunlich G, Hainzl C, Seiringer R. 2016. Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit. Mathematical Physics, Analysis and Geometry. 19(2), 13.","short":"G. Bräunlich, C. Hainzl, R. Seiringer, Mathematical Physics, Analysis and Geometry 19 (2016).","apa":"Bräunlich, G., Hainzl, C., &#38; Seiringer, R. (2016). Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit. <i>Mathematical Physics, Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-016-9209-x\">https://doi.org/10.1007/s11040-016-9209-x</a>","ieee":"G. Bräunlich, C. Hainzl, and R. Seiringer, “Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit,” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 19, no. 2. Springer, 2016."},"pubrep_id":"702","day":"01"},{"oa":1,"year":"2016","date_updated":"2021-01-12T06:49:28Z","publication":"International Journal of Modern Physics C","article_number":"1650067","article_type":"original","publist_id":"6065","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}],"date_created":"2018-12-11T11:51:00Z","scopus_import":1,"date_published":"2016-06-01T00:00:00Z","external_id":{"arxiv":["1505.02963"]},"publisher":"World Scientific Publishing","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1505.02963"}],"intvolume":"        27","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","_id":"1260","title":"The dual of the space of interactions in neural network models","author":[{"orcid":"0000-0002-5214-4706","last_name":"De Martino","full_name":"De Martino, Daniele","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1142/S0129183116500674","abstract":[{"text":"In this work, the Gardner problem of inferring interactions and fields for an Ising neural network from given patterns under a local stability hypothesis is addressed under a dual perspective. By means of duality arguments, an integer linear system is defined whose solution space is the dual of the Gardner space and whose solutions represent mutually unstable patterns. We propose and discuss Monte Carlo methods in order to find and remove unstable patterns and uniformly sample the space of interactions thereafter. We illustrate the problem on a set of real data and perform ensemble calculation that shows how the emergence of phase dominated by unstable patterns can be triggered in a nonlinear discontinuous way.","lang":"eng"}],"issue":"6","publication_status":"published","status":"public","month":"06","citation":{"ista":"De Martino D. 2016. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 27(6), 1650067.","ama":"De Martino D. The dual of the space of interactions in neural network models. <i>International Journal of Modern Physics C</i>. 2016;27(6). doi:<a href=\"https://doi.org/10.1142/S0129183116500674\">10.1142/S0129183116500674</a>","short":"D. De Martino, International Journal of Modern Physics C 27 (2016).","ieee":"D. De Martino, “The dual of the space of interactions in neural network models,” <i>International Journal of Modern Physics C</i>, vol. 27, no. 6. World Scientific Publishing, 2016.","apa":"De Martino, D. (2016). The dual of the space of interactions in neural network models. <i>International Journal of Modern Physics C</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129183116500674\">https://doi.org/10.1142/S0129183116500674</a>","mla":"De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” <i>International Journal of Modern Physics C</i>, vol. 27, no. 6, 1650067, World Scientific Publishing, 2016, doi:<a href=\"https://doi.org/10.1142/S0129183116500674\">10.1142/S0129183116500674</a>.","chicago":"De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” <i>International Journal of Modern Physics C</i>. World Scientific Publishing, 2016. <a href=\"https://doi.org/10.1142/S0129183116500674\">https://doi.org/10.1142/S0129183116500674</a>."},"day":"01","oa_version":"Preprint","arxiv":1,"volume":27,"article_processing_charge":"No"},{"oa_version":"Preprint","month":"06","day":"10","citation":{"apa":"Maas, J., &#38; Matthes, D. (2016). Long-time behavior of a finite volume discretization for a fourth order diffusion equation. <i>Nonlinearity</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/0951-7715/29/7/1992\">https://doi.org/10.1088/0951-7715/29/7/1992</a>","ieee":"J. Maas and D. Matthes, “Long-time behavior of a finite volume discretization for a fourth order diffusion equation,” <i>Nonlinearity</i>, vol. 29, no. 7. IOP Publishing Ltd., pp. 1992–2023, 2016.","ista":"Maas J, Matthes D. 2016. Long-time behavior of a finite volume discretization for a fourth order diffusion equation. Nonlinearity. 29(7), 1992–2023.","ama":"Maas J, Matthes D. Long-time behavior of a finite volume discretization for a fourth order diffusion equation. <i>Nonlinearity</i>. 2016;29(7):1992-2023. doi:<a href=\"https://doi.org/10.1088/0951-7715/29/7/1992\">10.1088/0951-7715/29/7/1992</a>","short":"J. Maas, D. Matthes, Nonlinearity 29 (2016) 1992–2023.","chicago":"Maas, Jan, and Daniel Matthes. “Long-Time Behavior of a Finite Volume Discretization for a Fourth Order Diffusion Equation.” <i>Nonlinearity</i>. IOP Publishing Ltd., 2016. <a href=\"https://doi.org/10.1088/0951-7715/29/7/1992\">https://doi.org/10.1088/0951-7715/29/7/1992</a>.","mla":"Maas, Jan, and Daniel Matthes. “Long-Time Behavior of a Finite Volume Discretization for a Fourth Order Diffusion Equation.” <i>Nonlinearity</i>, vol. 29, no. 7, IOP Publishing Ltd., 2016, pp. 1992–2023, doi:<a href=\"https://doi.org/10.1088/0951-7715/29/7/1992\">10.1088/0951-7715/29/7/1992</a>."},"volume":29,"doi":"10.1088/0951-7715/29/7/1992","issue":"7","abstract":[{"lang":"eng","text":"We consider a non-standard finite-volume discretization of a strongly non-linear fourth order diffusion equation on the d-dimensional cube, for arbitrary . The scheme preserves two important structural properties of the equation: the first is the interpretation as a gradient flow in a mass transportation metric, and the second is an intimate relation to a linear Fokker-Planck equation. Thanks to these structural properties, the scheme possesses two discrete Lyapunov functionals. These functionals approximate the entropy and the Fisher information, respectively, and their dissipation rates converge to the optimal ones in the discrete-to-continuous limit. Using the dissipation, we derive estimates on the long-time asymptotics of the discrete solutions. Finally, we present results from numerical experiments which indicate that our discretization is able to capture significant features of the complex original dynamics, even with a rather coarse spatial resolution."}],"_id":"1261","author":[{"orcid":"0000-0002-0845-1338","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Maas, Jan"},{"full_name":"Matthes, Daniel","last_name":"Matthes","first_name":"Daniel"}],"title":"Long-time behavior of a finite volume discretization for a fourth order diffusion equation","acknowledgement":"This  research  was  supported  by  the  DFG  Collaborative  Research  Centers  TRR  109,   ‘ Discretization in Geometry and Dynamics ’  and 1060  ‘ The Mathematics of Emergent Effects ’ .","status":"public","publication_status":"published","scopus_import":1,"date_created":"2018-12-11T11:51:00Z","date_published":"2016-06-10T00:00:00Z","publist_id":"6062","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JaMa"}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1505.03178"}],"intvolume":"        29","publisher":"IOP Publishing Ltd.","year":"2016","oa":1,"page":"1992 - 2023","date_updated":"2021-01-12T06:49:28Z","publication":"Nonlinearity"},{"related_material":{"record":[{"status":"public","relation":"research_data","id":"9704"}]},"article_number":"20160811","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","date_updated":"2023-02-23T14:05:30Z","year":"2016","oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"Royal Society, The","intvolume":"       283","date_published":"2016-06-29T00:00:00Z","date_created":"2018-12-11T11:51:00Z","scopus_import":1,"department":[{"_id":"SyCr"}],"publist_id":"6060","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","acknowledgement":"This work was supported by the Federal Ministry of Food, Agriculture and Consumer Protection (Germany): Fit Bee project (grant 511-06.01-28-1-71.007-10), the EU: BeeDoc (grant 244956), iDiv (2013 NGS-Fast Track grant W47004118) and the Insect Pollinators Initiative (IPI grant BB/I000100/1 and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Natural Environment Research Council, the Scottish Government and the Wellcome Trust, under the Living with Environmental Change Partnership. We thank A. Abrahams, M. Husemann and A. Soro\r\nfor support in obtaining\r\nV.  destructor\r\n-free honeybees; and BBKA\r\nPresident D. Aston for access to records of colony overwinter\r\n2011–2012 mortality in the UK. We also thank the anonymous refe-\r\nrees and Stephen Martin for comments that led to substantial\r\nimprovement of the manuscript.","status":"public","abstract":[{"lang":"eng","text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline."}],"issue":"1833","doi":"10.1098/rspb.2016.0811","title":"Elevated virulence of an emerging viral genotype as a driver of honeybee loss","author":[{"first_name":"Dino","full_name":"Mcmahon, Dino","last_name":"Mcmahon"},{"first_name":"Myrsini","last_name":"Natsopoulou","full_name":"Natsopoulou, Myrsini"},{"first_name":"Vincent","last_name":"Doublet","full_name":"Doublet, Vincent"},{"first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X"},{"last_name":"Weging","full_name":"Weging, Silvio","first_name":"Silvio"},{"first_name":"Mark","full_name":"Brown, Mark","last_name":"Brown"},{"first_name":"Andreas","last_name":"Gogol Döring","full_name":"Gogol Döring, Andreas"},{"full_name":"Paxton, Robert","last_name":"Paxton","first_name":"Robert"}],"_id":"1262","has_accepted_license":"1","volume":283,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"4708","date_created":"2018-12-12T10:08:46Z","file_name":"IST-2016-701-v1+1_20160811.full.pdf","creator":"system","relation":"main_file","file_size":796872,"access_level":"open_access","content_type":"application/pdf","checksum":"0b0d1be38b497d004064650acb3baced","date_updated":"2020-07-14T12:44:42Z"}],"oa_version":"Published Version","pubrep_id":"701","citation":{"chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The, 2016. <a href=\"https://doi.org/10.1098/rspb.2016.0811\">https://doi.org/10.1098/rspb.2016.0811</a>.","mla":"Mcmahon, Dino, et al. “Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 283, no. 1833, 20160811, Royal Society, The, 2016, doi:<a href=\"https://doi.org/10.1098/rspb.2016.0811\">10.1098/rspb.2016.0811</a>.","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, Proceedings of the Royal Society of London Series B Biological Sciences 283 (2016).","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Elevated virulence of an emerging viral genotype as a driver of honeybee loss. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2016;283(1833). doi:<a href=\"https://doi.org/10.1098/rspb.2016.0811\">10.1098/rspb.2016.0811</a>","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proceedings of the Royal Society of London Series B Biological Sciences. 283(1833), 20160811.","apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Elevated virulence of an emerging viral genotype as a driver of honeybee loss. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rspb.2016.0811\">https://doi.org/10.1098/rspb.2016.0811</a>","ieee":"D. Mcmahon <i>et al.</i>, “Elevated virulence of an emerging viral genotype as a driver of honeybee loss,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 283, no. 1833. Royal Society, The, 2016."},"day":"29","ddc":["576","592"],"file_date_updated":"2020-07-14T12:44:42Z","month":"06"},{"acknowledgement":"Alexander von Humboldt Foundation; Studienstiftung des Deutschen Volkes. We would like to acknowledge our stimulating discussions with Konrad Lehnert and Alessandro Pitanti.","publication_status":"published","status":"public","_id":"1263","author":[{"first_name":"Alfredo","last_name":"Rueda","full_name":"Rueda, Alfredo"},{"first_name":"Florian","full_name":"Sedlmeir, Florian","last_name":"Sedlmeir"},{"last_name":"Collodo","full_name":"Collodo, Michele","first_name":"Michele"},{"last_name":"Vogl","full_name":"Vogl, Ulrich","first_name":"Ulrich"},{"last_name":"Stiller","full_name":"Stiller, Birgit","first_name":"Birgit"},{"last_name":"Schunk","full_name":"Schunk, Gerhard","first_name":"Gerhard"},{"first_name":"Dmitry","full_name":"Strekalov, Dmitry","last_name":"Strekalov"},{"first_name":"Christoph","full_name":"Marquardt, Christoph","last_name":"Marquardt"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"},{"last_name":"Painter","full_name":"Painter, Oskar","first_name":"Oskar"},{"first_name":"Gerd","full_name":"Leuchs, Gerd","last_name":"Leuchs"},{"first_name":"Harald","full_name":"Schwefel, Harald","last_name":"Schwefel"}],"title":"Efficient microwave to optical photon conversion: An electro-optical realization","doi":"10.1364/OPTICA.3.000597","issue":"6","abstract":[{"text":"Linking classical microwave electrical circuits to the optical telecommunication band is at the core of modern communication. Future quantum information networks will require coherent microwave-to-optical conversion to link electronic quantum processors and memories via low-loss optical telecommunication networks. Efficient conversion can be achieved with electro-optical modulators operating at the single microwave photon level. In the standard electro-optic modulation scheme, this is impossible because both up- and down-converted sidebands are necessarily present. Here, we demonstrate true single-sideband up- or down-conversion in a triply resonant whispering gallery mode resonator by explicitly addressing modes with asymmetric free spectral range. Compared to previous experiments, we show a 3 orders of magnitude improvement of the electro-optical conversion efficiency, reaching 0.1% photon number conversion for a 10 GHz microwave tone at 0.42 mW of optical pump power. The presented scheme is fully compatible with existing superconducting 3D circuit quantum electrodynamics technology and can be used for nonclassical state conversion and communication. Our conversion bandwidth is larger than 1 MHz and is not fundamentally limited.","lang":"eng"}],"volume":3,"article_processing_charge":"No","month":"06","day":"20","citation":{"apa":"Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., … Schwefel, H. (2016). Efficient microwave to optical photon conversion: An electro-optical realization. <i>Optica</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/OPTICA.3.000597\">https://doi.org/10.1364/OPTICA.3.000597</a>","ieee":"A. Rueda <i>et al.</i>, “Efficient microwave to optical photon conversion: An electro-optical realization,” <i>Optica</i>, vol. 3, no. 6. Optica Publishing Group, pp. 597–604, 2016.","short":"A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov, C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, Optica 3 (2016) 597–604.","ista":"Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D, Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Efficient microwave to optical photon conversion: An electro-optical realization. Optica. 3(6), 597–604.","ama":"Rueda A, Sedlmeir F, Collodo M, et al. Efficient microwave to optical photon conversion: An electro-optical realization. <i>Optica</i>. 2016;3(6):597-604. doi:<a href=\"https://doi.org/10.1364/OPTICA.3.000597\">10.1364/OPTICA.3.000597</a>","chicago":"Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit Stiller, Gerhard Schunk, Dmitry Strekalov, et al. “Efficient Microwave to Optical Photon Conversion: An Electro-Optical Realization.” <i>Optica</i>. Optica Publishing Group, 2016. <a href=\"https://doi.org/10.1364/OPTICA.3.000597\">https://doi.org/10.1364/OPTICA.3.000597</a>.","mla":"Rueda, Alfredo, et al. “Efficient Microwave to Optical Photon Conversion: An Electro-Optical Realization.” <i>Optica</i>, vol. 3, no. 6, Optica Publishing Group, 2016, pp. 597–604, doi:<a href=\"https://doi.org/10.1364/OPTICA.3.000597\">10.1364/OPTICA.3.000597</a>."},"oa_version":"Published Version","date_updated":"2023-10-17T12:17:15Z","publication":"Optica","page":"597 - 604","oa":1,"year":"2016","intvolume":"         3","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1364/OPTICA.3.000597"}],"publisher":"Optica Publishing Group","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publist_id":"6061","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JoFi"}],"scopus_import":"1","date_created":"2018-12-11T11:51:01Z","date_published":"2016-06-20T00:00:00Z"},{"volume":171,"oa_version":"Submitted Version","month":"07","citation":{"chicago":"Sancho Andrés, Gloria, Esther Soriano Ortega, Caiji Gao, Joan Bernabé Orts, Madhumitha Narasimhan, Anna Müller, Ricardo Tejos, et al. “Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1104/pp.16.00373\">https://doi.org/10.1104/pp.16.00373</a>.","mla":"Sancho Andrés, Gloria, et al. “Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” <i>Plant Physiology</i>, vol. 171, no. 3, American Society of Plant Biologists, 2016, pp. 1965–82, doi:<a href=\"https://doi.org/10.1104/pp.16.00373\">10.1104/pp.16.00373</a>.","ieee":"G. Sancho Andrés <i>et al.</i>, “Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier,” <i>Plant Physiology</i>, vol. 171, no. 3. American Society of Plant Biologists, pp. 1965–1982, 2016.","apa":"Sancho Andrés, G., Soriano Ortega, E., Gao, C., Bernabé Orts, J., Narasimhan, M., Müller, A., … Marcote, M. (2016). Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.16.00373\">https://doi.org/10.1104/pp.16.00373</a>","ista":"Sancho Andrés G, Soriano Ortega E, Gao C, Bernabé Orts J, Narasimhan M, Müller A, Tejos R, Jiang L, Friml J, Aniento F, Marcote M. 2016. Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. 171(3), 1965–1982.","short":"G. Sancho Andrés, E. Soriano Ortega, C. Gao, J. Bernabé Orts, M. Narasimhan, A. Müller, R. Tejos, L. Jiang, J. Friml, F. Aniento, M. Marcote, Plant Physiology 171 (2016) 1965–1982.","ama":"Sancho Andrés G, Soriano Ortega E, Gao C, et al. Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. <i>Plant Physiology</i>. 2016;171(3):1965-1982. doi:<a href=\"https://doi.org/10.1104/pp.16.00373\">10.1104/pp.16.00373</a>"},"day":"01","ec_funded":1,"publication_status":"published","acknowledgement":"We thank Dr. R. Offringa (Leiden University) for providing the GST-\r\nPIN-CL construct; Sandra Richter and Gerd Jurgens (University of Tübin-\r\ngen) for providing the estradiol-inducible PIN1-RFP construct and the\r\ngnl1 mutant expressing BFA-sensitive GNL1; F.J. Santonja (University of Valencia)\r\nfor help with the statistical analysis; Jurgen Kleine-Vehn, Elke Barbez, and\r\nEva Benkova for helpful discussions; the Salk Institute Genomic Analysis\r\nLaboratory for providing the sequence-indexed Arabidopsis T-DNA in-\r\nsertion mutants; and the greenhouse section and the microscopy section\r\nof SCSIE (University of Valencia) and Pilar Selvi for excellent technical\r\nassistance.","status":"public","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"doi":"10.1104/pp.16.00373","abstract":[{"lang":"eng","text":"n contrast with the wealth of recent reports about the function of μ-adaptins and clathrin adaptor protein (AP) complexes, there is very little information about the motifs that determine the sorting of membrane proteins within clathrin-coated vesicles in plants. Here, we investigated putative sorting signals in the large cytosolic loop of the Arabidopsis (Arabidopsis thaliana) PIN-FORMED1 (PIN1) auxin transporter, which are involved in binding μ-adaptins and thus in PIN1 trafficking and localization. We found that Phe-165 and Tyr-280, Tyr-328, and Tyr-394 are involved in the binding of different μ-adaptins in vitro. However, only Phe-165, which binds μA(μ2)- and μD(μ3)-adaptin, was found to be essential for PIN1 trafficking and localization in vivo. The PIN1:GFP-F165A mutant showed reduced endocytosis but also localized to intracellular structures containing several layers of membranes and endoplasmic reticulum (ER) markers, suggesting that they correspond to ER or ER-derived membranes. While PIN1:GFP localized normally in a μA (μ2)-adaptin mutant, it accumulated in big intracellular structures containing LysoTracker in a μD (μ3)-adaptin mutant, consistent with previous results obtained with mutants of other subunits of the AP-3 complex. Our data suggest that Phe-165, through the binding of μA (μ2)- and μD (μ3)-adaptin, is important for PIN1 endocytosis and for PIN1 trafficking along the secretory pathway, respectively."}],"issue":"3","_id":"1264","title":"Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier","author":[{"first_name":"Gloria","last_name":"Sancho Andrés","full_name":"Sancho Andrés, Gloria"},{"first_name":"Esther","last_name":"Soriano Ortega","full_name":"Soriano Ortega, Esther"},{"last_name":"Gao","full_name":"Gao, Caiji","first_name":"Caiji"},{"last_name":"Bernabé Orts","full_name":"Bernabé Orts, Joan","first_name":"Joan"},{"orcid":"0000-0002-8600-0671","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Müller, Anna","last_name":"Müller","id":"420AB15A-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"first_name":"Liwen","last_name":"Jiang","full_name":"Jiang, Liwen"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí"},{"first_name":"Fernando","last_name":"Aniento","full_name":"Aniento, Fernando"},{"first_name":"Maria","last_name":"Marcote","full_name":"Marcote, Maria"}],"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"American Society of Plant Biologists","intvolume":"       171","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936568/"}],"date_created":"2018-12-11T11:51:01Z","scopus_import":1,"date_published":"2016-07-01T00:00:00Z","publist_id":"6059","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"page":"1965 - 1982","date_updated":"2021-01-12T06:49:29Z","publication":"Plant Physiology","year":"2016","oa":1},{"publisher":"American Association for the Advancement of Science","intvolume":"         9","volume":9,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"ista":"Elsayad K, Werner S, Gallemi M, Kong J, Guajardo E, Zhang L, Jaillais Y, Greb T, Belkhadir Y. 2016. Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. 9(435), rs5.","short":"K. Elsayad, S. Werner, M. Gallemi, J. Kong, E. Guajardo, L. Zhang, Y. Jaillais, T. Greb, Y. Belkhadir, Science Signaling 9 (2016).","ama":"Elsayad K, Werner S, Gallemi M, et al. Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. <i>Science Signaling</i>. 2016;9(435). doi:<a href=\"https://doi.org/10.1126/scisignal.aaf6326\">10.1126/scisignal.aaf6326</a>","ieee":"K. Elsayad <i>et al.</i>, “Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging,” <i>Science Signaling</i>, vol. 9, no. 435. American Association for the Advancement of Science, 2016.","apa":"Elsayad, K., Werner, S., Gallemi, M., Kong, J., Guajardo, E., Zhang, L., … Belkhadir, Y. (2016). Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. <i>Science Signaling</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scisignal.aaf6326\">https://doi.org/10.1126/scisignal.aaf6326</a>","chicago":"Elsayad, Kareem, Stephanie Werner, Marçal Gallemi, Jixiang Kong, Edmundo Guajardo, Lijuan Zhang, Yvon Jaillais, Thomas Greb, and Youssef Belkhadir. “Mapping the Subcellular Mechanical Properties of Live Cells in Tissues with Fluorescence Emission-Brillouin Imaging.” <i>Science Signaling</i>. American Association for the Advancement of Science, 2016. <a href=\"https://doi.org/10.1126/scisignal.aaf6326\">https://doi.org/10.1126/scisignal.aaf6326</a>.","mla":"Elsayad, Kareem, et al. “Mapping the Subcellular Mechanical Properties of Live Cells in Tissues with Fluorescence Emission-Brillouin Imaging.” <i>Science Signaling</i>, vol. 9, no. 435, rs5, American Association for the Advancement of Science, 2016, doi:<a href=\"https://doi.org/10.1126/scisignal.aaf6326\">10.1126/scisignal.aaf6326</a>."},"day":"05","department":[{"_id":"EvBe"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6057","month":"07","date_published":"2016-07-05T00:00:00Z","oa_version":"None","date_created":"2018-12-11T11:51:02Z","scopus_import":1,"publication":"Science Signaling","date_updated":"2021-01-12T06:49:29Z","publication_status":"published","status":"public","article_number":"rs5","title":"Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging","author":[{"last_name":"Elsayad","full_name":"Elsayad, Kareem","first_name":"Kareem"},{"first_name":"Stephanie","full_name":"Werner, Stephanie","last_name":"Werner"},{"first_name":"Marcal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","last_name":"Gallemi Rovira","full_name":"Gallemi Rovira, Marcal"},{"full_name":"Kong, Jixiang","last_name":"Kong","first_name":"Jixiang"},{"first_name":"Edmundo","full_name":"Guajardo, Edmundo","last_name":"Guajardo"},{"last_name":"Zhang","full_name":"Zhang, Lijuan","first_name":"Lijuan"},{"full_name":"Jaillais, Yvon","last_name":"Jaillais","first_name":"Yvon"},{"first_name":"Thomas","full_name":"Greb, Thomas","last_name":"Greb"},{"last_name":"Belkhadir","full_name":"Belkhadir, Youssef","first_name":"Youssef"}],"_id":"1265","abstract":[{"text":"Extracellular matrices (ECMs) are central to the advent of multicellular life, and their mechanical propertiesare modulated by and impinge on intracellular signaling pathways that regulate vital cellular functions. High spatial-resolution mapping of mechanical properties in live cells is, however, extremely challenging. Thus, our understanding of how signaling pathways process physiological signals to generate appropriate mechanical responses is limited. We introduce fluorescence emission-Brillouin scattering imaging (FBi), a method for the parallel and all-optical measurements of mechanical properties and fluorescence at the submicrometer scale in living organisms. Using FBi, we showed thatchanges in cellular hydrostatic pressure and cytoplasm viscoelasticity modulate the mechanical signatures of plant ECMs. We further established that the measured &quot;stiffness&quot; of plant ECMs is symmetrically patternedin hypocotyl cells undergoing directional growth. Finally, application of this method to Arabidopsis thaliana with photoreceptor mutants revealed that red and far-red light signals are essential modulators of ECM viscoelasticity. By mapping the viscoelastic signatures of a complex ECM, we provide proof of principlefor the organism-wide applicability of FBi for measuring the mechanical outputs of intracellular signaling pathways. As such, our work has implications for investigations of mechanosignaling pathways and developmental biology.","lang":"eng"}],"issue":"435","year":"2016","doi":"10.1126/scisignal.aaf6326"},{"oa_version":"Published Version","month":"07","ddc":["571"],"file_date_updated":"2020-07-14T12:44:42Z","day":"01","pubrep_id":"700","citation":{"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>","short":"M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016).","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.","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>.","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>."},"volume":5,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2018-12-12T10:11:20Z","file_id":"4874","checksum":"dc52d967dc76174477bb258d84be2899","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:42Z","relation":"main_file","file_size":2819055,"creator":"system","file_name":"IST-2016-700-v1+1_e13824-download.pdf"}],"doi":"10.7554/eLife.13824","issue":"2016JULY","abstract":[{"lang":"eng","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."}],"_id":"1266","author":[{"first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","last_name":"Chalk","full_name":"Chalk, Matthew J","orcid":"0000-0001-7782-4436"},{"first_name":"Boris","last_name":"Gutkin","full_name":"Gutkin, Boris"},{"full_name":"Denève, Sophie","last_name":"Denève","first_name":"Sophie"}],"title":"Neural oscillations as a signature of efficient coding in the presence of synaptic delays","status":"public","acknowledgement":"Boris Gutkin acknowledges funding by the Russian Academic Excellence Project '5-100’.","publication_status":"published","scopus_import":1,"date_created":"2018-12-11T11:51:02Z","date_published":"2016-07-01T00:00:00Z","publist_id":"6056","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","intvolume":"         5","publisher":"eLife Sciences Publications","year":"2016","oa":1,"article_number":"e13824","date_updated":"2021-01-12T06:49:30Z","publication":"eLife"},{"oa_version":"Published Version","citation":{"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.","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>","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>","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.","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>.","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>."},"pubrep_id":"698","day":"01","month":"08","ddc":["510","539"],"file_date_updated":"2020-07-14T12:44:42Z","has_accepted_license":"1","volume":106,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"4863","date_created":"2018-12-12T10:11:09Z","file_name":"IST-2016-698-v1+1_s11005-016-0860-8.pdf","creator":"system","relation":"main_file","file_size":349464,"date_updated":"2020-07-14T12:44:42Z","access_level":"open_access","content_type":"application/pdf","checksum":"d740a6a226e0f5f864f40e3e269d3cc0"}],"abstract":[{"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.","lang":"eng"}],"issue":"8","doi":"10.1007/s11005-016-0860-8","title":"Nonexistence of large nuclei in the liquid drop model","author":[{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert"},{"first_name":"Rowan","full_name":"Killip, Rowan","last_name":"Killip"},{"last_name":"Nam","full_name":"Nam, Phan","first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87"}],"_id":"1267","status":"public","acknowledgement":"Open access funding provided by Institute of Science and Technology Austria.\r\n","publication_status":"published","project":[{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"date_published":"2016-08-01T00:00:00Z","date_created":"2018-12-11T11:51:02Z","scopus_import":1,"department":[{"_id":"RoSe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6054","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Springer","intvolume":"       106","year":"2016","oa":1,"page":"1033 - 1036","publication":"Letters in Mathematical Physics","date_updated":"2021-01-12T06:49:30Z"},{"publist_id":"6053","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"08","citation":{"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>.","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>.","ista":"Milutinovic B, Kurtz J. 2016. Immune memory in invertebrates. Seminars in Immunology. 28(4), 328–342.","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>","short":"B. Milutinovic, J. Kurtz, Seminars in Immunology 28 (2016) 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>","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."},"department":[{"_id":"SyCr"}],"day":"01","oa_version":"None","date_created":"2018-12-11T11:51:03Z","scopus_import":1,"date_published":"2016-08-01T00:00:00Z","publisher":"Academic Press","intvolume":"        28","volume":28,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","_id":"1268","title":"Immune memory in invertebrates","author":[{"orcid":"0000-0002-8214-4758","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","full_name":"Milutinovic, Barbara","last_name":"Milutinovic"},{"first_name":"Joachim","full_name":"Kurtz, Joachim","last_name":"Kurtz"}],"doi":"10.1016/j.smim.2016.05.004","year":"2016","issue":"4","date_updated":"2021-01-12T06:49:30Z","publication":"Seminars in Immunology","page":"328 - 342","publication_status":"published","status":"public","acknowledgement":"We would like to thank Mihai Netea for inviting us to contribute to this Theme Issue."},{"volume":91,"has_accepted_license":"1","file":[{"file_id":"5349","date_created":"2018-12-12T10:18:28Z","date_updated":"2020-07-14T12:44:42Z","access_level":"open_access","checksum":"0ffb7a15c5336b3a55248cc67021a825","content_type":"application/pdf","file_name":"IST-2016-697-v1+1_s11103-016-0501-8.pdf","creator":"system","file_size":297282,"relation":"main_file"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","ddc":["581"],"file_date_updated":"2020-07-14T12:44:42Z","month":"08","day":"01","citation":{"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>.","short":"E. Benková, Plant Molecular Biology 91 (2016) 597.","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>","ista":"Benková E. 2016. Plant hormones in interactions with the environment. Plant Molecular Biology. 91(6), 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>","ieee":"E. Benková, “Plant hormones in interactions with the environment,” <i>Plant Molecular Biology</i>, vol. 91, no. 6. Springer, p. 597, 2016."},"pubrep_id":"697","status":"public","publication_status":"published","doi":"10.1007/s11103-016-0501-8","issue":"6","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."}],"_id":"1269","author":[{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"title":"Plant hormones in interactions with the environment","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"        91","publisher":"Springer","scopus_import":1,"date_created":"2018-12-11T11:51:03Z","date_published":"2016-08-01T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6052","department":[{"_id":"EvBe"}],"page":"597","date_updated":"2021-01-12T06:49:31Z","publication":"Plant Molecular Biology","year":"2016","oa":1},{"intvolume":"        11","publisher":"Public Library of Science","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","department":[{"_id":"GaTk"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6050","date_published":"2016-09-27T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:51:03Z","publication":"PLoS One","date_updated":"2023-02-23T14:11:37Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"9869"},{"id":"9870","status":"public","relation":"research_data"},{"status":"public","relation":"research_data","id":"9871"}]},"article_number":"e0163628","oa":1,"year":"2016","file":[{"file_id":"4837","date_created":"2018-12-12T10:10:47Z","file_name":"IST-2016-696-v1+1_journal.pone.0163628.PDF","relation":"main_file","file_size":4950415,"creator":"system","date_updated":"2020-07-14T12:44:42Z","access_level":"open_access","checksum":"3d0d55d373096a033bd9cf79288c8586","content_type":"application/pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","volume":11,"day":"27","pubrep_id":"696","citation":{"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>.","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>","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.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016).","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.","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>"},"file_date_updated":"2020-07-14T12:44:42Z","ddc":["571"],"month":"09","oa_version":"Published Version","project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"status":"public","publication_status":"published","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).","author":[{"first_name":"Patrick","last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick"},{"first_name":"Ulrich","full_name":"Gerland, Ulrich","last_name":"Gerland"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Tkacik, Gasper","last_name":"Tkacik"}],"title":"Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information","_id":"1270","issue":"9","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."}],"doi":"10.1371/journal.pone.0163628"},{"file_date_updated":"2020-07-14T12:44:42Z","ddc":["572","576"],"month":"09","citation":{"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>","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.","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.","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>","short":"A. Diz Muñoz, P. Romanczuk, W. Yu, M. Bergert, K. Ivanovitch, G. Salbreux, C.-P.J. Heisenberg, E. Paluch, BMC Biology 14 (2016).","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>.","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>."},"pubrep_id":"695","day":"02","oa_version":"Published Version","file":[{"file_id":"5002","date_created":"2018-12-12T10:13:20Z","file_name":"IST-2016-695-v1+1_s12915-016-0294-x.pdf","creator":"system","relation":"main_file","file_size":1875695,"access_level":"open_access","content_type":"application/pdf","checksum":"0bfa484ac69a0a560fb9a4589aeda7f6","date_updated":"2020-07-14T12:44:42Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":14,"has_accepted_license":"1","_id":"1271","title":"Steering cell migration by alternating blebs and actin-rich protrusions","author":[{"first_name":"Alba","last_name":"Diz Muñoz","full_name":"Diz Muñoz, Alba"},{"last_name":"Romanczuk","full_name":"Romanczuk, Pawel","first_name":"Pawel"},{"full_name":"Yu, Weimiao","last_name":"Yu","first_name":"Weimiao"},{"last_name":"Bergert","full_name":"Bergert, Martin","first_name":"Martin"},{"last_name":"Ivanovitch","full_name":"Ivanovitch, Kenzo","first_name":"Kenzo"},{"first_name":"Guillame","last_name":"Salbreux","full_name":"Salbreux, Guillame"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"full_name":"Paluch, Ewa","last_name":"Paluch","first_name":"Ewa"}],"doi":"10.1186/s12915-016-0294-x","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","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"}],"status":"public","publication_status":"published","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.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6049","department":[{"_id":"CaHe"}],"date_created":"2018-12-11T11:51:04Z","scopus_import":1,"acknowledged_ssus":[{"_id":"LifeSc"}],"date_published":"2016-09-02T00:00:00Z","publisher":"BioMed Central","intvolume":"        14","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"oa":1,"year":"2016","date_updated":"2021-01-12T06:49:32Z","publication":"BMC Biology","article_number":"74"},{"status":"public","publication_status":"published","acknowledgement":"This work was supported by Austrian Science Fund (FWF): P25816-N15.","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","doi":"10.1080/16864360.2016.1150718","title":"Generalized offsetting of planar structures using skeletons","author":[{"full_name":"Held, Martin","last_name":"Held","first_name":"Martin"},{"orcid":"0000-0002-8871-5814","first_name":"Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87","last_name":"Huber","full_name":"Huber, Stefan"},{"last_name":"Palfrader","full_name":"Palfrader, Peter","first_name":"Peter"}],"_id":"1272","has_accepted_license":"1","volume":13,"file":[{"file_id":"5206","date_created":"2018-12-12T10:16:20Z","file_name":"IST-2016-694-v1+1_Generalized_offsetting_of_planar_structures_using_skeletons.pdf","file_size":1678369,"creator":"system","relation":"main_file","date_updated":"2020-07-14T12:44:42Z","access_level":"open_access","checksum":"c746f3a48edb62b588d92ea5d0fd2c0e","content_type":"application/pdf"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","pubrep_id":"694","citation":{"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>.","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>.","short":"M. Held, S. Huber, P. Palfrader, Computer-Aided Design and Applications 13 (2016) 712–721.","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>","ista":"Held M, Huber S, Palfrader P. 2016. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 13(5), 712–721.","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.","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>"},"day":"02","ddc":["004","516"],"file_date_updated":"2020-07-14T12:44:42Z","month":"09","page":"712 - 721","publication":"Computer-Aided Design and Applications","date_updated":"2021-01-12T06:49:32Z","year":"2016","oa":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Taylor and Francis","intvolume":"        13","date_published":"2016-09-02T00:00:00Z","date_created":"2018-12-11T11:51:04Z","scopus_import":1,"department":[{"_id":"HeEd"}],"publist_id":"6048","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"year":"2016","oa":1,"page":"3340 - 3349","publication":"Development","date_updated":"2021-01-12T06:49:32Z","date_published":"2016-09-13T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:51:04Z","department":[{"_id":"EvBe"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6044","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01595056/","open_access":"1"}],"intvolume":"       143","publisher":"Company of Biologists","issue":"18","abstract":[{"lang":"eng","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."}],"doi":"10.1242/dev.136283","author":[{"full_name":"Porco, Silvana","last_name":"Porco","first_name":"Silvana"},{"full_name":"Larrieu, Antoine","last_name":"Larrieu","first_name":"Antoine"},{"last_name":"Du","full_name":"Du, Yujuan","first_name":"Yujuan"},{"full_name":"Gaudinier, Allison","last_name":"Gaudinier","first_name":"Allison"},{"full_name":"Goh, Tatsuaki","last_name":"Goh","first_name":"Tatsuaki"},{"last_name":"Swarup","full_name":"Swarup, Kamal","first_name":"Kamal"},{"first_name":"Ranjan","full_name":"Swarup, Ranjan","last_name":"Swarup"},{"full_name":"Kuempers, Britta","last_name":"Kuempers","first_name":"Britta"},{"last_name":"Bishopp","full_name":"Bishopp, Anthony","first_name":"Anthony"},{"first_name":"Julien","last_name":"Lavenus","full_name":"Lavenus, Julien"},{"last_name":"Casimiro","full_name":"Casimiro, Ilda","first_name":"Ilda"},{"last_name":"Hill","full_name":"Hill, Kristine","first_name":"Kristine"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková"},{"full_name":"Fukaki, Hidehiro","last_name":"Fukaki","first_name":"Hidehiro"},{"full_name":"Brady, Siobhan","last_name":"Brady","first_name":"Siobhan"},{"first_name":"Ben","last_name":"Scheres","full_name":"Scheres, Ben"},{"full_name":"Peéet, Benjamin","last_name":"Peéet","first_name":"Benjamin"},{"full_name":"Bennett, Malcolm","last_name":"Bennett","first_name":"Malcolm"}],"title":"Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3","_id":"1273","status":"public","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.","publication_status":"published","oa_version":"Preprint","day":"13","citation":{"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>","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.","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.","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.","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>.","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>."},"month":"09","volume":143},{"publisher":"Nature Publishing Group","intvolume":"         6","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6042","date_published":"2016-09-21T00:00:00Z","external_id":{"pmid":["27649687"]},"date_created":"2018-12-11T11:51:05Z","scopus_import":"1","publication":"Scientific Reports","date_updated":"2025-05-07T11:12:28Z","related_material":{"record":[{"id":"545","relation":"later_version","status":"public"}]},"article_number":"33754","oa":1,"year":"2016","file":[{"date_created":"2018-12-12T10:13:25Z","file_id":"5008","content_type":"application/pdf","checksum":"ee371fbc9124ad93157a95829264e4fe","access_level":"open_access","date_updated":"2020-07-14T12:44:42Z","relation":"main_file","file_size":2895147,"creator":"system","file_name":"IST-2016-692-v1+1_srep33754.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"No","volume":6,"pubrep_id":"692","citation":{"short":"E. Mazur, E. Benková, J. Friml, Scientific Reports 6 (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>","ista":"Mazur E, Benková E, Friml J. 2016. Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. 6, 33754.","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.","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>","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>."},"day":"21","file_date_updated":"2020-07-14T12:44:42Z","pmid":1,"month":"09","ddc":["581"],"oa_version":"Published Version","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).","status":"public","publication_status":"published","title":"Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis","author":[{"last_name":"Mazur","full_name":"Mazur, Ewa","first_name":"Ewa"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"_id":"1274","abstract":[{"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.","lang":"eng"}],"doi":"10.1038/srep33754"},{"_id":"1275","author":[{"full_name":"Callan Jones, Andrew","last_name":"Callan Jones","first_name":"Andrew"},{"orcid":"0000-0003-4088-8633","last_name":"Ruprecht","full_name":"Ruprecht, Verena","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","last_name":"Wieser","full_name":"Wieser, Stefan","orcid":"0000-0002-2670-2217"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"first_name":"Raphaël","full_name":"Voituriez, Raphaël","last_name":"Voituriez"}],"title":"Callan-Jones et al. Reply","doi":"10.1103/PhysRevLett.117.139802","year":"2016","issue":"13","date_updated":"2021-01-12T06:49:33Z","publication":"Physical Review Letters","article_number":"139802","publication_status":"published","status":"public","publist_id":"6041","month":"09","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"22","department":[{"_id":"CaHe"}],"citation":{"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>.","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>","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.","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>","short":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P.J. Heisenberg, R. Voituriez, Physical Review Letters 117 (2016).","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."},"scopus_import":1,"oa_version":"None","date_created":"2018-12-11T11:51:05Z","date_published":"2016-09-22T00:00:00Z","intvolume":"       117","publisher":"American Physical Society","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","volume":117}]