[{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6088","month":"02","oa_version":"Preprint","date_updated":"2021-01-12T06:49:20Z","oa":1,"publication_status":"published","article_number":"022404","_id":"1242","intvolume":"        93","doi":"10.1103/PhysRevE.93.022404","department":[{"_id":"GaTk"}],"acknowledgement":"We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions. This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370 from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W. acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561. G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S.","quality_controlled":"1","citation":{"ieee":"T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic range of transcription factor action by translational regulation,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 93, no. 2. American Institute of Physics, 2016.","ista":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.","ama":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2016;93(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">10.1103/PhysRevE.93.022404</a>","short":"T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016).","chicago":"Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">https://doi.org/10.1103/PhysRevE.93.022404</a>.","mla":"Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 93, no. 2, 022404, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">10.1103/PhysRevE.93.022404</a>.","apa":"Sokolowski, T. R., Walczak, A., Bialek, W., &#38; Tkačik, G. (2016). Extending the dynamic range of transcription factor action by translational regulation. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">https://doi.org/10.1103/PhysRevE.93.022404</a>"},"status":"public","type":"journal_article","title":"Extending the dynamic range of transcription factor action by translational regulation","day":"04","year":"2016","language":[{"iso":"eng"}],"publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","issue":"2","abstract":[{"lang":"eng","text":"A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule acts as an independent sensor of the input concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression."}],"volume":93,"date_published":"2016-02-04T00:00:00Z","author":[{"orcid":"0000-0002-1287-3779","first_name":"Thomas R","last_name":"Sokolowski","id":"3E999752-F248-11E8-B48F-1D18A9856A87","full_name":"Sokolowski, Thomas R"},{"last_name":"Walczak","first_name":"Aleksandra","full_name":"Walczak, Aleksandra"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"}],"date_created":"2018-12-11T11:50:54Z","project":[{"call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"}],"publisher":"American Institute of Physics","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.02562"}],"scopus_import":1},{"related_material":{"record":[{"relation":"dissertation_contains","id":"202","status":"public"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6087","oa_version":"None","month":"02","date_updated":"2023-09-07T11:59:32Z","publication_status":"published","citation":{"chicago":"Pleska, Maros, Long Qian, Reiko Okura, Tobias Bergmiller, Yuichi Wakamoto, Edo Kussell, and Calin C Guet. “Bacterial Autoimmunity Due to a Restriction-Modification System.” <i>Current Biology</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">https://doi.org/10.1016/j.cub.2015.12.041</a>.","ama":"Pleska M, Qian L, Okura R, et al. Bacterial autoimmunity due to a restriction-modification system. <i>Current Biology</i>. 2016;26(3):404-409. doi:<a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">10.1016/j.cub.2015.12.041</a>","short":"M. Pleska, L. Qian, R. Okura, T. Bergmiller, Y. Wakamoto, E. Kussell, C.C. Guet, Current Biology 26 (2016) 404–409.","mla":"Pleska, Maros, et al. “Bacterial Autoimmunity Due to a Restriction-Modification System.” <i>Current Biology</i>, vol. 26, no. 3, Cell Press, 2016, pp. 404–09, doi:<a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">10.1016/j.cub.2015.12.041</a>.","apa":"Pleska, M., Qian, L., Okura, R., Bergmiller, T., Wakamoto, Y., Kussell, E., &#38; Guet, C. C. (2016). Bacterial autoimmunity due to a restriction-modification system. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">https://doi.org/10.1016/j.cub.2015.12.041</a>","ista":"Pleska M, Qian L, Okura R, Bergmiller T, Wakamoto Y, Kussell E, Guet CC. 2016. Bacterial autoimmunity due to a restriction-modification system. Current Biology. 26(3), 404–409.","ieee":"M. Pleska <i>et al.</i>, “Bacterial autoimmunity due to a restriction-modification system,” <i>Current Biology</i>, vol. 26, no. 3. Cell Press, pp. 404–409, 2016."},"status":"public","type":"journal_article","title":"Bacterial autoimmunity due to a restriction-modification system","_id":"1243","page":"404 - 409","intvolume":"        26","doi":"10.1016/j.cub.2015.12.041","department":[{"_id":"CaGu"}],"acknowledgement":"This work was funded by an HFSP Young Investigators’ grant. M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria. R.O. and Y.W. were supported by the Platform for Dynamic Approaches to Living System from MEXT, Japan. We wish to thank I. Kobayashi for providing us with the EcoRI and EcoRV plasmids, and A. Campbell for providing us with the λ vir phage. We thank D. Siekhaus and C. Uhler and members of the C.C.G. and J.P. Bollback laboratories for in-depth discussions. We thank B. Stern for comments on an earlier version of the manuscript. We especially thank B.R. Levin for advice and comments, and the anonymous reviewers for significantly improving the manuscript.","quality_controlled":"1","issue":"3","volume":26,"abstract":[{"lang":"eng","text":"Restriction-modification (RM) systems represent a minimal and ubiquitous biological system of self/non-self discrimination in prokaryotes [1], which protects hosts from exogenous DNA [2]. The mechanism is based on the balance between methyltransferase (M) and cognate restriction endonuclease (R). M tags endogenous DNA as self by methylating short specific DNA sequences called restriction sites, whereas R recognizes unmethylated restriction sites as non-self and introduces a double-stranded DNA break [3]. Restriction sites are significantly underrepresented in prokaryotic genomes [4-7], suggesting that the discrimination mechanism is imperfect and occasionally leads to autoimmunity due to self-DNA cleavage (self-restriction) [8]. Furthermore, RM systems can promote DNA recombination [9] and contribute to genetic variation in microbial populations, thus facilitating adaptive evolution [10]. However, cleavage of self-DNA by RM systems as elements shaping prokaryotic genomes has not been directly detected, and its cause, frequency, and outcome are unknown. We quantify self-restriction caused by two RM systems of Escherichia coli and find that, in agreement with levels of restriction site avoidance, EcoRI, but not EcoRV, cleaves self-DNA at a measurable rate. Self-restriction is a stochastic process, which temporarily induces the SOS response, and is followed by DNA repair, maintaining cell viability. We find that RM systems with higher restriction efficiency against bacteriophage infections exhibit a higher rate of self-restriction, and that this rate can be further increased by stochastic imbalance between R and M. Our results identify molecular noise in RM systems as a factor shaping prokaryotic genomes."}],"date_published":"2016-02-08T00:00:00Z","author":[{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","last_name":"Pleska","first_name":"Maros"},{"last_name":"Qian","first_name":"Long","full_name":"Qian, Long"},{"full_name":"Okura, Reiko","first_name":"Reiko","last_name":"Okura"},{"orcid":"0000-0001-5396-4346","last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yuichi","last_name":"Wakamoto","full_name":"Wakamoto, Yuichi"},{"full_name":"Kussell, Edo","last_name":"Kussell","first_name":"Edo"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C"}],"day":"08","language":[{"iso":"eng"}],"year":"2016","publication":"Current Biology","publisher":"Cell Press","scopus_import":1,"date_created":"2018-12-11T11:50:54Z","project":[{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","grant_number":"24210"}]},{"publication":"PNAS","day":"16","year":"2016","language":[{"iso":"eng"}],"issue":"7","author":[{"full_name":"Recouvreux, Pierre","first_name":"Pierre","last_name":"Recouvreux"},{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779","first_name":"Thomas R","last_name":"Sokolowski"},{"first_name":"Aristea","last_name":"Grammoustianou","full_name":"Grammoustianou, Aristea"},{"full_name":"Tenwolde, Pieter","first_name":"Pieter","last_name":"Tenwolde"},{"last_name":"Dogterom","first_name":"Marileen","full_name":"Dogterom, Marileen"}],"volume":113,"abstract":[{"lang":"eng","text":"Cell polarity refers to a functional spatial organization of proteins that is crucial for the control of essential cellular processes such as growth and division. To establish polarity, cells rely on elaborate regulation networks that control the distribution of proteins at the cell membrane. In fission yeast cells, a microtubule-dependent network has been identified that polarizes the distribution of signaling proteins that restricts growth to cell ends and targets the cytokinetic machinery to the middle of the cell. Although many molecular components have been shown to play a role in this network, it remains unknown which molecular functionalities are minimally required to establish a polarized protein distribution in this system. Here we show that a membrane-binding protein fragment, which distributes homogeneously in wild-type fission yeast cells, can be made to concentrate at cell ends by attaching it to a cytoplasmic microtubule end-binding protein. This concentration results in a polarized pattern of chimera proteins with a spatial extension that is very reminiscent of natural polarity patterns in fission yeast. However, chimera levels fluctuate in response to microtubule dynamics, and disruption of microtubules leads to disappearance of the pattern. Numerical simulations confirm that the combined functionality of membrane anchoring and microtubule tip affinity is in principle sufficient to create polarized patterns. Our chimera protein may thus represent a simple molecular functionality that is able to polarize the membrane, onto which additional layers of molecular complexity may be built to provide the temporal robustness that is typical of natural polarity patterns."}],"date_published":"2016-02-16T00:00:00Z","date_created":"2018-12-11T11:50:55Z","publisher":"National Academy of Sciences","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/"}],"scopus_import":1,"oa_version":"Submitted Version","month":"02","publist_id":"6085","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publication_status":"published","date_updated":"2021-01-12T06:49:21Z","doi":"10.1073/pnas.1419248113","_id":"1244","page":"1811 - 1816","intvolume":"       113","acknowledgement":"We thank Sophie Martin, Ken Sawin, Stephen Huisman,\r\nand Damian Brunner for strains; Julianne\r\nTeapal, Marcel Janson, Sergio Rincon,\r\nand Phong Tran for technical assistance; Andrew Mugler and Bela Mulder for\r\ndiscussions; and Sander Tans, Phong Tran,\r\nand Anne Paoletti for critical reading\r\nof the manuscript. This work is part of the research program of the\r\n“\r\nStichting\r\nvoor Fundamenteel Onderzoek de Materie,\r\n”\r\nwhich is financially supported by\r\nthe\r\n“\r\nNederlandse organisatie voor Wete\r\nnschappelijk Onderzoek (NWO).\r\n”","quality_controlled":"1","department":[{"_id":"GaTk"}],"citation":{"mla":"Recouvreux, Pierre, et al. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” <i>PNAS</i>, vol. 113, no. 7, National Academy of Sciences, 2016, pp. 1811–16, doi:<a href=\"https://doi.org/10.1073/pnas.1419248113\">10.1073/pnas.1419248113</a>.","apa":"Recouvreux, P., Sokolowski, T. R., Grammoustianou, A., Tenwolde, P., &#38; Dogterom, M. (2016). Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1419248113\">https://doi.org/10.1073/pnas.1419248113</a>","short":"P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom, PNAS 113 (2016) 1811–1816.","chicago":"Recouvreux, Pierre, Thomas R Sokolowski, Aristea Grammoustianou, Pieter Tenwolde, and Marileen Dogterom. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1419248113\">https://doi.org/10.1073/pnas.1419248113</a>.","ama":"Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. <i>PNAS</i>. 2016;113(7):1811-1816. doi:<a href=\"https://doi.org/10.1073/pnas.1419248113\">10.1073/pnas.1419248113</a>","ieee":"P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom, “Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells,” <i>PNAS</i>, vol. 113, no. 7. National Academy of Sciences, pp. 1811–1816, 2016.","ista":"Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 113(7), 1811–1816."},"title":"Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells","type":"journal_article","status":"public"},{"oa_version":"None","month":"02","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6083","conference":{"name":"CSCW: Computer Supported Cooperative Work and Social Computing","start_date":"2016-02-26","end_date":"2016-03-02","location":"San Francisco, CA, USA"},"publication_status":"published","date_updated":"2021-01-12T06:49:22Z","doi":"10.1145/2818052.2869122","intvolume":"        26","page":"365 - 368","_id":"1245","quality_controlled":"1","acknowledgement":"ERC Start Grant Graph Games 279307 supported this  research. ","department":[{"_id":"KrCh"}],"citation":{"ista":"Pandey V, Chatterjee K. 2016. Game-theoretic models identify useful principles for peer collaboration in online learning platforms. Proceedings of the ACM Conference on Computer Supported Cooperative Work. CSCW: Computer Supported Cooperative Work and Social Computing vol. 26, 365–368.","ieee":"V. Pandey and K. Chatterjee, “Game-theoretic models identify useful principles for peer collaboration in online learning platforms,” in <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i>, San Francisco, CA, USA, 2016, vol. 26, no. Februar-2016, pp. 365–368.","apa":"Pandey, V., &#38; Chatterjee, K. (2016). Game-theoretic models identify useful principles for peer collaboration in online learning platforms. In <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i> (Vol. 26, pp. 365–368). San Francisco, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2818052.2869122\">https://doi.org/10.1145/2818052.2869122</a>","mla":"Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify Useful Principles for Peer Collaboration in Online Learning Platforms.” <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i>, vol. 26, no. Februar-2016, ACM, 2016, pp. 365–68, doi:<a href=\"https://doi.org/10.1145/2818052.2869122\">10.1145/2818052.2869122</a>.","chicago":"Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify Useful Principles for Peer Collaboration in Online Learning Platforms.” In <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i>, 26:365–68. ACM, 2016. <a href=\"https://doi.org/10.1145/2818052.2869122\">https://doi.org/10.1145/2818052.2869122</a>.","ama":"Pandey V, Chatterjee K. Game-theoretic models identify useful principles for peer collaboration in online learning platforms. In: <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i>. Vol 26. ACM; 2016:365-368. doi:<a href=\"https://doi.org/10.1145/2818052.2869122\">10.1145/2818052.2869122</a>","short":"V. Pandey, K. Chatterjee, in:, Proceedings of the ACM Conference on Computer Supported Cooperative Work, ACM, 2016, pp. 365–368."},"title":"Game-theoretic models identify useful principles for peer collaboration in online learning platforms","type":"conference","status":"public","publication":"Proceedings of the ACM Conference on Computer Supported Cooperative Work","year":"2016","language":[{"iso":"eng"}],"day":"27","ec_funded":1,"issue":"Februar-2016","author":[{"last_name":"Pandey","first_name":"Vineet","full_name":"Pandey, Vineet"},{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"date_published":"2016-02-27T00:00:00Z","volume":26,"abstract":[{"lang":"eng","text":"To facilitate collaboration in massive online classrooms, instructors must make many decisions. For instance, the following parameters need to be decided when designing a peer-feedback system where students review each others' essays: the number of students each student must provide feedback to, an algorithm to map feedback providers to receivers, constraints that ensure students do not become free-riders (receiving feedback but not providing it), the best times to receive feedback to improve learning etc. While instructors can answer these questions by running experiments or invoking past experience, game-theoretic models with data from online learning platforms can identify better initial designs for further improvements. As an example, we explore the design space of a peer feedback system by modeling it using game theory. Our simulations show that incentivizing students to provide feedback requires the value obtained from receiving a feedback to exceed the cost of providing it by a large factor (greater than 7). Furthermore, hiding feedback from low-effort students incentivizes them to provide more feedback."}],"date_created":"2018-12-11T11:50:55Z","project":[{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"publisher":"ACM","scopus_import":1},{"date_created":"2018-12-11T11:50:55Z","scopus_import":1,"publisher":"Nature Publishing Group","file":[{"file_id":"5061","date_created":"2018-12-12T10:14:11Z","creator":"system","checksum":"ca76236cb1aae22cb90c65313e2c5e98","relation":"main_file","date_updated":"2020-07-14T12:44:41Z","content_type":"application/pdf","file_name":"IST-2016-707-v1+1_srep22665.pdf","file_size":1425165,"access_level":"open_access"}],"publication":"Scientific Reports","language":[{"iso":"eng"}],"year":"2016","day":"07","author":[{"first_name":"Irina","last_name":"Kabakova","full_name":"Kabakova, Irina"},{"full_name":"De Hoogh, Anouk","last_name":"De Hoogh","first_name":"Anouk"},{"full_name":"Van Der Wel, Ruben","first_name":"Ruben","last_name":"Van Der Wel"},{"id":"45598606-F248-11E8-B48F-1D18A9856A87","full_name":"Wulf, Matthias","last_name":"Wulf","first_name":"Matthias","orcid":"0000-0001-6613-1378"},{"full_name":"Le Feber, Boris","last_name":"Le Feber","first_name":"Boris"},{"full_name":"Kuipers, Laurens","first_name":"Laurens","last_name":"Kuipers"}],"date_published":"2016-03-07T00:00:00Z","volume":6,"abstract":[{"lang":"eng","text":"Near-field imaging is a powerful tool to investigate the complex structure of light at the nanoscale. Recent advances in near-field imaging have indicated the possibility for the complete reconstruction of both electric and magnetic components of the evanescent field. Here we study the electro-magnetic field structure of surface plasmon polariton waves propagating along subwavelength gold nanowires by performing phase- and polarization-resolved near-field microscopy in collection mode. By applying the optical reciprocity theorem, we describe the signal collected by the probe as an overlap integral of the nanowire's evanescent field and the probe's response function. As a result, we find that the probe's sensitivity to the magnetic field is approximately equal to its sensitivity to the electric field. Through rigorous modeling of the nanowire mode as well as the aperture probe response function, we obtain a good agreement between experimentally measured signals and a numerical model. Our findings provide a better understanding of aperture-based near-field imaging of the nanoscopic plasmonic and photonic structures and are helpful for the interpretation of future near-field experiments."}],"file_date_updated":"2020-07-14T12:44:41Z","quality_controlled":"1","acknowledgement":"This work is supported part of the research program of the Netherlands Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization for Scientific Research (NWO), and part of this work has been funded by the project ‘SPANGL4Q’, which acknowledges the financial support of the Future and Emerging Technologies (FET) program within the Seventh Framework Programme for Research of the European Commission, under FETOpen grant number: FP7-284743. L.K. acknowledges funding from ERC Advanced, Investigator Grant (no. 240438-CONSTANS).","department":[{"_id":"JoFi"}],"doi":"10.1038/srep22665","intvolume":"         6","_id":"1246","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Imaging of electric and magnetic fields near plasmonic nanowires","pubrep_id":"707","type":"journal_article","status":"public","citation":{"mla":"Kabakova, Irina, et al. “Imaging of Electric and Magnetic Fields near Plasmonic Nanowires.” <i>Scientific Reports</i>, vol. 6, 22665, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep22665\">10.1038/srep22665</a>.","apa":"Kabakova, I., De Hoogh, A., Van Der Wel, R., Wulf, M., Le Feber, B., &#38; Kuipers, L. (2016). Imaging of electric and magnetic fields near plasmonic nanowires. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep22665\">https://doi.org/10.1038/srep22665</a>","short":"I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, L. Kuipers, Scientific Reports 6 (2016).","chicago":"Kabakova, Irina, Anouk De Hoogh, Ruben Van Der Wel, Matthias Wulf, Boris Le Feber, and Laurens Kuipers. “Imaging of Electric and Magnetic Fields near Plasmonic Nanowires.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep22665\">https://doi.org/10.1038/srep22665</a>.","ama":"Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. Imaging of electric and magnetic fields near plasmonic nanowires. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep22665\">10.1038/srep22665</a>","ista":"Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. 2016. Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports. 6, 22665.","ieee":"I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, and L. Kuipers, “Imaging of electric and magnetic fields near plasmonic nanowires,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016."},"publication_status":"published","oa":1,"ddc":["539"],"date_updated":"2021-01-12T06:49:22Z","month":"03","oa_version":"Published Version","publist_id":"6082","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"22665","has_accepted_license":"1"},{"doi":"10.1073/pnas.1501343112","page":"2768 - 2773","_id":"1247","intvolume":"       113","acknowledgement":"This work was supported by the Ghent University Special Research Fund (M.K.), the European Research Council (Project ERC-2011-StG-20101109-PSDP) (to J.F.), and the Körber European Science Foun-\r\ndation (J.F.). S.D.G. is indebted to the Agency for Science and Technology for\r\na predoctoral fellowship.","quality_controlled":"1","department":[{"_id":"JiFr"}],"citation":{"mla":"Karampelias, Michael, et al. “ROTUNDA3 Function in Plant Development by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” <i>PNAS</i>, vol. 113, no. 10, National Academy of Sciences, 2016, pp. 2768–73, doi:<a href=\"https://doi.org/10.1073/pnas.1501343112\">10.1073/pnas.1501343112</a>.","apa":"Karampelias, M., Neyt, P., De Groeve, S., Aesaert, S., Coussens, G., Rolčík, J., … Van Lijsebettens, M. (2016). ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1501343112\">https://doi.org/10.1073/pnas.1501343112</a>","chicago":"Karampelias, Michael, Pia Neyt, Steven De Groeve, Stijn Aesaert, Griet Coussens, Jakub Rolčík, Leonardo Bruno, et al. “ROTUNDA3 Function in Plant Development by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1501343112\">https://doi.org/10.1073/pnas.1501343112</a>.","short":"M. Karampelias, P. Neyt, S. De Groeve, S. Aesaert, G. Coussens, J. Rolčík, L. Bruno, N. De Winne, A. Van Minnebruggen, M. Van Montagu, M. Ponce, J. Micol, J. Friml, G. De Jaeger, M. Van Lijsebettens, PNAS 113 (2016) 2768–2773.","ama":"Karampelias M, Neyt P, De Groeve S, et al. ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. <i>PNAS</i>. 2016;113(10):2768-2773. doi:<a href=\"https://doi.org/10.1073/pnas.1501343112\">10.1073/pnas.1501343112</a>","ista":"Karampelias M, Neyt P, De Groeve S, Aesaert S, Coussens G, Rolčík J, Bruno L, De Winne N, Van Minnebruggen A, Van Montagu M, Ponce M, Micol J, Friml J, De Jaeger G, Van Lijsebettens M. 2016. ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 113(10), 2768–2773.","ieee":"M. Karampelias <i>et al.</i>, “ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling,” <i>PNAS</i>, vol. 113, no. 10. National Academy of Sciences, pp. 2768–2773, 2016."},"title":"ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling","type":"journal_article","status":"public","month":"03","oa_version":"Submitted Version","publist_id":"6081","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publication_status":"published","date_updated":"2021-01-12T06:49:22Z","date_created":"2018-12-11T11:50:56Z","project":[{"name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300"}],"publisher":"National Academy of Sciences","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791031/"}],"scopus_import":1,"publication":"PNAS","day":"08","year":"2016","language":[{"iso":"eng"}],"ec_funded":1,"issue":"10","author":[{"full_name":"Karampelias, Michael","last_name":"Karampelias","first_name":"Michael"},{"first_name":"Pia","last_name":"Neyt","full_name":"Neyt, Pia"},{"full_name":"De Groeve, Steven","first_name":"Steven","last_name":"De Groeve"},{"full_name":"Aesaert, Stijn","last_name":"Aesaert","first_name":"Stijn"},{"first_name":"Griet","last_name":"Coussens","full_name":"Coussens, Griet"},{"full_name":"Rolčík, Jakub","last_name":"Rolčík","first_name":"Jakub"},{"full_name":"Bruno, Leonardo","last_name":"Bruno","first_name":"Leonardo"},{"full_name":"De Winne, Nancy","first_name":"Nancy","last_name":"De Winne"},{"first_name":"Annemie","last_name":"Van Minnebruggen","full_name":"Van Minnebruggen, Annemie"},{"full_name":"Van Montagu, Marc","last_name":"Van Montagu","first_name":"Marc"},{"first_name":"Maria","last_name":"Ponce","full_name":"Ponce, Maria"},{"first_name":"José","last_name":"Micol","full_name":"Micol, José"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí"},{"last_name":"De Jaeger","first_name":"Geert","full_name":"De Jaeger, Geert"},{"full_name":"Van Lijsebettens, Mieke","last_name":"Van Lijsebettens","first_name":"Mieke"}],"volume":113,"abstract":[{"text":"The shaping of organs in plants depends on the intercellular flow of the phytohormone auxin, of which the directional signaling is determined by the polar subcellular localization of PIN-FORMED (PIN) auxin transport proteins. Phosphorylation dynamics of PIN proteins are affected by the protein phosphatase 2A (PP2A) and the PINOID kinase, which act antagonistically to mediate their apical-basal polar delivery. Here, we identified the ROTUNDA3 (RON3) protein as a regulator of the PP2A phosphatase activity in Arabidopsis thaliana. The RON3 gene was map-based cloned starting from the ron3-1 leaf mutant and found to be a unique, plant-specific gene coding for a protein with high and dispersed proline content. The ron3-1 and ron3-2 mutant phenotypes [i.e., reduced apical dominance, primary root length, lateral root emergence, and growth; increased ectopic stages II, IV, and V lateral root primordia; decreased auxin maxima in indole-3-acetic acid (IAA)-treated root apical meristems; hypergravitropic root growth and response; increased IAA levels in shoot apices; and reduced auxin accumulation in root meristems] support a role for RON3 in auxin biology. The affinity-purified PP2A complex with RON3 as bait suggested that RON3 might act in PIN transporter trafficking. Indeed, pharmacological interference with vesicle trafficking processes revealed that single ron3-2 and double ron3-2 rcn1 mutants have altered PIN polarity and endocytosis in specific cells. Our data indicate that RON3 contributes to auxin-mediated development by playing a role in PIN recycling and polarity establishment through regulation of the PP2A complex activity.","lang":"eng"}],"date_published":"2016-03-08T00:00:00Z"},{"publication":"Annual Review of Condensed Matter Physics","language":[{"iso":"eng"}],"year":"2016","day":"10","author":[{"orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"last_name":"Bialek","first_name":"William","full_name":"Bialek, William"}],"date_published":"2016-03-10T00:00:00Z","volume":7,"abstract":[{"text":"Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been possible to measure, directly, the flow of information in biological networks, or more generally where information-theoretic ideas have been used to guide the analysis of experiments. Systems of interest range from single molecules (the sequence diversity in families of proteins) to groups of organisms (the distribution of velocities in flocks of birds), and all scales in between. Many of these analyses are motivated by the idea that biological systems may have evolved to optimize the gathering and representation of information, and we review the experimental evidence for this optimization, again across a wide range of scales.","lang":"eng"}],"date_created":"2018-12-11T11:50:56Z","project":[{"grant_number":"P 25651-N26","call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://arxiv.org/abs/1412.8752","open_access":"1"}],"publisher":"Annual Reviews","scopus_import":1,"oa_version":"Preprint","month":"03","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6080","oa":1,"publication_status":"published","date_updated":"2021-01-12T06:49:23Z","doi":"10.1146/annurev-conmatphys-031214-014803","intvolume":"         7","page":"89 - 117","_id":"1248","quality_controlled":"1","acknowledgement":"Our work was supported in part by the US\r\nNational Science Foundation (PHY–1305525 and CCF–\r\n0939370), by the Austrian Science Foundation (FWF\r\nP25651), by the Human Frontiers Science Program, and\r\nby the Simons and Swartz Foundations.","department":[{"_id":"GaTk"}],"citation":{"short":"G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.","chicago":"Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” <i>Annual Review of Condensed Matter Physics</i>. Annual Reviews, 2016. <a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">https://doi.org/10.1146/annurev-conmatphys-031214-014803</a>.","ama":"Tkačik G, Bialek W. Information processing in living systems. <i>Annual Review of Condensed Matter Physics</i>. 2016;7:89-117. doi:<a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">10.1146/annurev-conmatphys-031214-014803</a>","apa":"Tkačik, G., &#38; Bialek, W. (2016). Information processing in living systems. <i>Annual Review of Condensed Matter Physics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">https://doi.org/10.1146/annurev-conmatphys-031214-014803</a>","mla":"Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” <i>Annual Review of Condensed Matter Physics</i>, vol. 7, Annual Reviews, 2016, pp. 89–117, doi:<a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">10.1146/annurev-conmatphys-031214-014803</a>.","ieee":"G. Tkačik and W. Bialek, “Information processing in living systems,” <i>Annual Review of Condensed Matter Physics</i>, vol. 7. Annual Reviews, pp. 89–117, 2016.","ista":"Tkačik G, Bialek W. 2016. Information processing in living systems. Annual Review of Condensed Matter Physics. 7, 89–117."},"title":"Information processing in living systems","status":"public","type":"journal_article"},{"day":"29","year":"2016","language":[{"iso":"eng"}],"publication":"Biophysical Journal","abstract":[{"text":"Actin and myosin assemble into a thin layer of a highly dynamic network underneath the membrane of eukaryotic cells. This network generates the forces that drive cell- and tissue-scale morphogenetic processes. The effective material properties of this active network determine large-scale deformations and other morphogenetic events. For example, the characteristic time of stress relaxation (the Maxwell time τM) in the actomyosin sets the timescale of large-scale deformation of the cortex. Similarly, the characteristic length of stress propagation (the hydrodynamic length λ) sets the length scale of slow deformations, and a large hydrodynamic length is a prerequisite for long-ranged cortical flows. Here we introduce a method to determine physical parameters of the actomyosin cortical layer in vivo directly from laser ablation experiments. For this we investigate the cortical response to laser ablation in the one-cell-stage Caenorhabditis elegans embryo and in the gastrulating zebrafish embryo. These responses can be interpreted using a coarse-grained physical description of the cortex in terms of a two-dimensional thin film of an active viscoelastic gel. To determine the Maxwell time τM, the hydrodynamic length λ, the ratio of active stress ζΔμ, and per-area friction γ, we evaluated the response to laser ablation in two different ways: by quantifying flow and density fields as a function of space and time, and by determining the time evolution of the shape of the ablated region. Importantly, both methods provide best-fit physical parameters that are in close agreement with each other and that are similar to previous estimates in the two systems. Our method provides an accurate and robust means for measuring physical parameters of the actomyosin cortical layer. It can be useful for investigations of actomyosin mechanics at the cellular-scale, but also for providing insights into the active mechanics processes that govern tissue-scale morphogenesis.","lang":"eng"}],"volume":110,"date_published":"2016-03-29T00:00:00Z","author":[{"first_name":"Arnab","last_name":"Saha","full_name":"Saha, Arnab"},{"first_name":"Masatoshi","last_name":"Nishikawa","full_name":"Nishikawa, Masatoshi"},{"first_name":"Martin","last_name":"Behrndt","full_name":"Behrndt, Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"first_name":"Frank","last_name":"Julicher","full_name":"Julicher, Frank"},{"last_name":"Grill","first_name":"Stephan","full_name":"Grill, Stephan"}],"issue":"6","file_date_updated":"2020-07-14T12:44:41Z","project":[{"grant_number":"I 930-B20","call_identifier":"FWF","name":"Control of Epithelial Cell Layer Spreading in Zebrafish","_id":"252ABD0A-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:50:56Z","scopus_import":1,"file":[{"relation":"main_file","checksum":"c408cf2e25a25c8d711cffea524bda55","creator":"system","date_created":"2018-12-12T10:10:54Z","file_id":"4845","file_size":1965645,"access_level":"open_access","file_name":"IST-2016-706-v1+1_1-s2.0-S0006349516001582-main.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:41Z"}],"publisher":"Biophysical Society","ddc":["572","576"],"date_updated":"2021-01-12T06:49:23Z","publication_status":"published","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6079","oa_version":"Published Version","month":"03","has_accepted_license":"1","department":[{"_id":"CaHe"}],"acknowledgement":"S.W.G. acknowledges support by grant no. 281903 from the European Research Council and by grant No. GR-7271/2-1 from the Deutsche Forschungsgemeinschaft. S.W.G. and C.-P.H. acknowledge support through a grant from the Fonds zur Förderung der Wissenschaftlichen Forschung and the Deutsche Forschungsgemeinschaft (No. I930-B20). We are grateful to Daniel Dickinson for providing the LP133 C. elegans strain. We thank G. Salbreux, V. K. Krishnamurthy, and J. S. Bois for fruitful discussions.","quality_controlled":"1","_id":"1249","page":"1421 - 1429","intvolume":"       110","doi":"10.1016/j.bpj.2016.02.013","type":"journal_article","status":"public","pubrep_id":"706","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Determining physical properties of the cell cortex","citation":{"chicago":"Saha, Arnab, Masatoshi Nishikawa, Martin Behrndt, Carl-Philipp J Heisenberg, Frank Julicher, and Stephan Grill. “Determining Physical Properties of the Cell Cortex.” <i>Biophysical Journal</i>. Biophysical Society, 2016. <a href=\"https://doi.org/10.1016/j.bpj.2016.02.013\">https://doi.org/10.1016/j.bpj.2016.02.013</a>.","short":"A. Saha, M. Nishikawa, M. Behrndt, C.-P.J. Heisenberg, F. Julicher, S. Grill, Biophysical Journal 110 (2016) 1421–1429.","ama":"Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. Determining physical properties of the cell cortex. <i>Biophysical Journal</i>. 2016;110(6):1421-1429. doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.02.013\">10.1016/j.bpj.2016.02.013</a>","mla":"Saha, Arnab, et al. “Determining Physical Properties of the Cell Cortex.” <i>Biophysical Journal</i>, vol. 110, no. 6, Biophysical Society, 2016, pp. 1421–29, doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.02.013\">10.1016/j.bpj.2016.02.013</a>.","apa":"Saha, A., Nishikawa, M., Behrndt, M., Heisenberg, C.-P. J., Julicher, F., &#38; Grill, S. (2016). Determining physical properties of the cell cortex. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2016.02.013\">https://doi.org/10.1016/j.bpj.2016.02.013</a>","ista":"Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. 2016. Determining physical properties of the cell cortex. Biophysical Journal. 110(6), 1421–1429.","ieee":"A. Saha, M. Nishikawa, M. Behrndt, C.-P. J. Heisenberg, F. Julicher, and S. Grill, “Determining physical properties of the cell cortex,” <i>Biophysical Journal</i>, vol. 110, no. 6. Biophysical Society, pp. 1421–1429, 2016."}},{"acknowledgement":"This manuscript is dedicated to the memory of Alex Böhm, who was a great friend and a passionate biologist. Alex passed away after the initial submission of this manuscript. We thank Vesna Olivera and Ursula Sauder from the Zentrum für Mikroskopie Uni Basel for excellent service, and Olin Silander, Nikki Freed, and Nela Nikolic for helpful discussions. This work was supported by the Swiss National Science Foundation grants to M. Ackermann and Urs Jenal (supporting AB).","quality_controlled":"1","department":[{"_id":"CaGu"}],"doi":"10.1371/journal.pgen.1005974","_id":"1250","intvolume":"        12","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Genetic manipulation of glycogen allocation affects replicative lifespan in E coli","type":"journal_article","status":"public","pubrep_id":"705","citation":{"ieee":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Genetic manipulation of glycogen allocation affects replicative lifespan in E coli,” <i>PLoS Genetics</i>, vol. 12, no. 4. Public Library of Science, 2016.","ista":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. 12(4), e1005974.","mla":"Boehm, Alex, et al. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” <i>PLoS Genetics</i>, vol. 12, no. 4, e1005974, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005974\">10.1371/journal.pgen.1005974</a>.","apa":"Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., &#38; Ackermann, M. (2016). Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005974\">https://doi.org/10.1371/journal.pgen.1005974</a>","chicago":"Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” <i>PLoS Genetics</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pgen.1005974\">https://doi.org/10.1371/journal.pgen.1005974</a>.","short":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, PLoS Genetics 12 (2016).","ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. <i>PLoS Genetics</i>. 2016;12(4). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005974\">10.1371/journal.pgen.1005974</a>"},"publication_status":"published","oa":1,"ddc":["576","579"],"date_updated":"2023-02-23T14:11:39Z","month":"04","oa_version":"Published Version","publist_id":"6077","related_material":{"record":[{"status":"public","id":"9873","relation":"research_data"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"e1005974","has_accepted_license":"1","date_created":"2018-12-11T11:50:56Z","scopus_import":1,"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:44:41Z","access_level":"open_access","file_size":6273249,"file_name":"IST-2016-705-v1+1_journal.pgen.1005974.PDF","file_id":"5067","relation":"main_file","checksum":"53d22b2b39e5adc243d34f18b2615a85","creator":"system","date_created":"2018-12-12T10:14:17Z"}],"publisher":"Public Library of Science","publication":"PLoS Genetics","day":"19","language":[{"iso":"eng"}],"year":"2016","author":[{"first_name":"Alex","last_name":"Boehm","full_name":"Boehm, Alex"},{"first_name":"Markus","last_name":"Arnoldini","full_name":"Arnoldini, Markus"},{"full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","first_name":"Tobias","last_name":"Bergmiller"},{"full_name":"Röösli, Thomas","last_name":"Röösli","first_name":"Thomas"},{"full_name":"Bigosch, Colette","first_name":"Colette","last_name":"Bigosch"},{"full_name":"Ackermann, Martin","first_name":"Martin","last_name":"Ackermann"}],"abstract":[{"lang":"eng","text":"In bacteria, replicative aging manifests as a difference in growth or survival between the two cells emerging from division. One cell can be regarded as an aging mother with a decreased potential for future survival and division, the other as a rejuvenated daughter. Here, we aimed at investigating some of the processes involved in aging in the bacterium Escherichia coli, where the two types of cells can be distinguished by the age of their cell poles. We found that certain changes in the regulation of the carbohydrate metabolism can affect aging. A mutation in the carbon storage regulator gene, csrA, leads to a dramatically shorter replicative lifespan; csrA mutants stop dividing once their pole exceeds an age of about five divisions. These old-pole cells accumulate glycogen at their old cell poles; after their last division, they do not contain a chromosome, presumably because of spatial exclusion by the glycogen aggregates. The new-pole daughters produced by these aging mothers are born young; they only express the deleterious phenotype once their pole is old. These results demonstrate how manipulations of nutrient allocation can lead to the exclusion of the chromosome and limit replicative lifespan in E. coli, and illustrate how mutations can have phenotypic effects that are specific for cells with old poles. This raises the question how bacteria can avoid the accumulation of such mutations in their genomes over evolutionary times, and how they can achieve the long replicative lifespans that have recently been reported."}],"volume":12,"date_published":"2016-04-19T00:00:00Z","file_date_updated":"2020-07-14T12:44:41Z","issue":"4"},{"author":[{"last_name":"Zhu","first_name":"Jinsheng","full_name":"Zhu, Jinsheng"},{"full_name":"Bailly, Aurélien","last_name":"Bailly","first_name":"Aurélien"},{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"full_name":"Sovero, Valpuri","first_name":"Valpuri","last_name":"Sovero"},{"first_name":"Martin","last_name":"Di Donato","full_name":"Di Donato, Martin"},{"first_name":"Pei","last_name":"Ge","full_name":"Ge, Pei"},{"full_name":"Oehri, Jacqueline","first_name":"Jacqueline","last_name":"Oehri"},{"full_name":"Aryal, Bibek","first_name":"Bibek","last_name":"Aryal"},{"full_name":"Hao, Pengchao","first_name":"Pengchao","last_name":"Hao"},{"last_name":"Linnert","first_name":"Miriam","full_name":"Linnert, Miriam"},{"full_name":"Burgardt, Noelia","last_name":"Burgardt","first_name":"Noelia"},{"first_name":"Christian","last_name":"Lücke","full_name":"Lücke, Christian"},{"last_name":"Weiwad","first_name":"Matthias","full_name":"Weiwad, Matthias"},{"full_name":"Michel, Max","last_name":"Michel","first_name":"Max"},{"last_name":"Weiergräber","first_name":"Oliver","full_name":"Weiergräber, Oliver"},{"full_name":"Pollmann, Stephan","first_name":"Stephan","last_name":"Pollmann"},{"first_name":"Elisa","last_name":"Azzarello","full_name":"Azzarello, Elisa"},{"last_name":"Mancuso","first_name":"Stefano","full_name":"Mancuso, Stefano"},{"last_name":"Ferro","first_name":"Noel","full_name":"Ferro, Noel"},{"first_name":"Yoichiro","last_name":"Fukao","full_name":"Fukao, Yoichiro"},{"first_name":"Céline","last_name":"Hoffmann","full_name":"Hoffmann, Céline"},{"full_name":"Wedlich Söldner, Roland","last_name":"Wedlich Söldner","first_name":"Roland"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"last_name":"Thomas","first_name":"Clément","full_name":"Thomas, Clément"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"}],"abstract":[{"lang":"eng","text":"Plant growth and architecture is regulated by the polar distribution of the hormone auxin. Polarity and flexibility of this process is provided by constant cycling of auxin transporter vesicles along actin filaments, coordinated by a positive auxinactin feedback loop. Both polar auxin transport and vesicle cycling are inhibited by synthetic auxin transport inhibitors, such as 1-Nnaphthylphthalamic acid (NPA), counteracting the effect of auxin; however, underlying targets and mechanisms are unclear. Using NMR, we map the NPA binding surface on the Arabidopsis thaliana ABCB chaperone TWISTED DWARF1 (TWD1).We identify ACTIN7 as a relevant, although likely indirect, TWD1 interactor, and show TWD1-dependent regulation of actin filament organization and dynamics and that TWD1 is required for NPA-mediated actin cytoskeleton remodeling. The TWD1-ACTIN7 axis controls plasma membrane presence of efflux transporters, and as a consequence act7 and twd1 share developmental and physiological phenotypes indicative of defects in auxin transport. These can be phenocopied by NPA treatment or by chemical actin (de)stabilization. We provide evidence that TWD1 determines downstreamlocations of auxin efflux transporters by adjusting actin filament debundling and dynamizing processes and mediating NPA action on the latter. This function appears to be evolutionary conserved since TWD1 expression in budding yeast alters actin polarization and cell polarity and provides NPA sensitivity."}],"volume":28,"date_published":"2016-04-01T00:00:00Z","issue":"4","publication":"Plant Cell","day":"01","year":"2016","language":[{"iso":"eng"}],"scopus_import":1,"publisher":"American Society of Plant Biologists","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863381/","open_access":"1"}],"date_created":"2018-12-11T11:50:57Z","oa":1,"publication_status":"published","date_updated":"2021-01-12T06:49:24Z","oa_version":"Submitted Version","month":"04","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6078","title":"TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics","status":"public","type":"journal_article","citation":{"short":"J. Zhu, A. Bailly, M. Zwiewka, V. Sovero, M. Di Donato, P. Ge, J. Oehri, B. Aryal, P. Hao, M. Linnert, N. Burgardt, C. Lücke, M. Weiwad, M. Michel, O. Weiergräber, S. Pollmann, E. Azzarello, S. Mancuso, N. Ferro, Y. Fukao, C. Hoffmann, R. Wedlich Söldner, J. Friml, C. Thomas, M. Geisler, Plant Cell 28 (2016) 930–948.","chicago":"Zhu, Jinsheng, Aurélien Bailly, Marta Zwiewka, Valpuri Sovero, Martin Di Donato, Pei Ge, Jacqueline Oehri, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” <i>Plant Cell</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1105/tpc.15.00726\">https://doi.org/10.1105/tpc.15.00726</a>.","ama":"Zhu J, Bailly A, Zwiewka M, et al. TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. <i>Plant Cell</i>. 2016;28(4):930-948. doi:<a href=\"https://doi.org/10.1105/tpc.15.00726\">10.1105/tpc.15.00726</a>","mla":"Zhu, Jinsheng, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” <i>Plant Cell</i>, vol. 28, no. 4, American Society of Plant Biologists, 2016, pp. 930–48, doi:<a href=\"https://doi.org/10.1105/tpc.15.00726\">10.1105/tpc.15.00726</a>.","apa":"Zhu, J., Bailly, A., Zwiewka, M., Sovero, V., Di Donato, M., Ge, P., … Geisler, M. (2016). TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.15.00726\">https://doi.org/10.1105/tpc.15.00726</a>","ista":"Zhu J, Bailly A, Zwiewka M, Sovero V, Di Donato M, Ge P, Oehri J, Aryal B, Hao P, Linnert M, Burgardt N, Lücke C, Weiwad M, Michel M, Weiergräber O, Pollmann S, Azzarello E, Mancuso S, Ferro N, Fukao Y, Hoffmann C, Wedlich Söldner R, Friml J, Thomas C, Geisler M. 2016. TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. 28(4), 930–948.","ieee":"J. Zhu <i>et al.</i>, “TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics,” <i>Plant Cell</i>, vol. 28, no. 4. American Society of Plant Biologists, pp. 930–948, 2016."},"acknowledgement":" This work was supported by grants from the European Social Fund (CZ.1.07/2.3.00/20.0043), the Czech Science Foundation GAČR (GA13-40637S) to J.F. and M.Z., the Ministry of Education, Youth, and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) to M.Z., the Ministry for Higher Education and Research of Luxembourg (REC-LOCM-20140703) to C.T., the Partial Funding Program for Short Stays Abroad of CONICET Argentina (to N.I.B.), Swiss National Funds, the Pool de Recherche of the University of Fribourg, and the Novartis Foundation (all to M.G.). ","quality_controlled":"1","department":[{"_id":"JiFr"}],"doi":"10.1105/tpc.15.00726","_id":"1251","page":"930 - 948","intvolume":"        28"},{"arxiv":1,"oa_version":"Preprint","month":"04","publist_id":"6075","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"date_updated":"2022-05-24T09:35:58Z","publication_identifier":{"issn":["1088-6826"]},"article_processing_charge":"No","citation":{"ieee":"S. Harker, H. Kokubu, K. Mischaikow, and P. Pilarczyk, “Inducing a map on homology from a correspondence,” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4. American Mathematical Society, pp. 1787–1801, 2016.","ista":"Harker S, Kokubu H, Mischaikow K, Pilarczyk P. 2016. Inducing a map on homology from a correspondence. Proceedings of the American Mathematical Society. 144(4), 1787–1801.","mla":"Harker, Shaun, et al. “Inducing a Map on Homology from a Correspondence.” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4, American Mathematical Society, 2016, pp. 1787–801, doi:<a href=\"https://doi.org/10.1090/proc/12812\">10.1090/proc/12812</a>.","apa":"Harker, S., Kokubu, H., Mischaikow, K., &#38; Pilarczyk, P. (2016). Inducing a map on homology from a correspondence. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/12812\">https://doi.org/10.1090/proc/12812</a>","short":"S. Harker, H. Kokubu, K. Mischaikow, P. Pilarczyk, Proceedings of the American Mathematical Society 144 (2016) 1787–1801.","ama":"Harker S, Kokubu H, Mischaikow K, Pilarczyk P. Inducing a map on homology from a correspondence. <i>Proceedings of the American Mathematical Society</i>. 2016;144(4):1787-1801. doi:<a href=\"https://doi.org/10.1090/proc/12812\">10.1090/proc/12812</a>","chicago":"Harker, Shaun, Hiroshi Kokubu, Konstantin Mischaikow, and Pawel Pilarczyk. “Inducing a Map on Homology from a Correspondence.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2016. <a href=\"https://doi.org/10.1090/proc/12812\">https://doi.org/10.1090/proc/12812</a>."},"title":"Inducing a map on homology from a correspondence","type":"journal_article","status":"public","doi":"10.1090/proc/12812","external_id":{"arxiv":["1411.7563"]},"page":"1787 - 1801","_id":"1252","intvolume":"       144","acknowledgement":"The authors gratefully acknowledge the support of the Lorenz Center which\r\nprovided an opportunity for us to discuss in depth the work of this paper. Research leading to these results has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Funda¸c˜ao para a Ciˆencia e a Tecnologia (FCT) in the framework of the research\r\nproject FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008),\r\nas well as from the People Programme (Marie Curie Actions) of the European\r\nUnion’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033 (supporting PP). The work of the first and third author has\r\nbeen partially supported by NSF grants NSF-DMS-0835621, 0915019, 1125174,\r\n1248071, and contracts from AFOSR and DARPA. The work of the second author\r\nwas supported by Grant-in-Aid for Scientific Research (No. 25287029), Ministry of\r\nEducation, Science, Technology, Culture and Sports, Japan.","quality_controlled":"1","department":[{"_id":"HeEd"}],"issue":"4","author":[{"full_name":"Harker, Shaun","last_name":"Harker","first_name":"Shaun"},{"first_name":"Hiroshi","last_name":"Kokubu","full_name":"Kokubu, Hiroshi"},{"full_name":"Mischaikow, Konstantin","last_name":"Mischaikow","first_name":"Konstantin"},{"full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","last_name":"Pilarczyk","first_name":"Pawel"}],"abstract":[{"text":"We study the homomorphism induced in homology by a closed correspondence between topological spaces, using projections from the graph of the correspondence to its domain and codomain. We provide assumptions under which the homomorphism induced by an outer approximation of a continuous map coincides with the homomorphism induced in homology by the map. In contrast to more classical results we do not require that the projection to the domain have acyclic preimages. Moreover, we show that it is possible to retrieve correct homological information from a correspondence even if some data is missing or perturbed. Finally, we describe an application to combinatorial maps that are either outer approximations of continuous maps or reconstructions of such maps from a finite set of data points.","lang":"eng"}],"volume":144,"date_published":"2016-04-01T00:00:00Z","publication":"Proceedings of the American Mathematical Society","day":"01","language":[{"iso":"eng"}],"year":"2016","ec_funded":1,"publisher":"American Mathematical Society","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1411.7563"}],"scopus_import":"1","project":[{"_id":"255F06BE-B435-11E9-9278-68D0E5697425","name":"Persistent Homology - Images, Data and Maps","grant_number":"622033","call_identifier":"FP7"}],"article_type":"original","date_created":"2018-12-11T11:50:57Z"},{"author":[{"full_name":"Tsai, Lihuei","first_name":"Lihuei","last_name":"Tsai"},{"last_name":"Siegert","first_name":"Sandra","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"volume":73,"abstract":[{"lang":"eng","text":"This article provides an introduction to the role of microRNAs in the nervous system and outlines their potential involvement in the pathophysiology of schizophrenia, which is hypothesized to arise owing to environmental factors and genetic predisposition."}],"date_published":"2016-04-01T00:00:00Z","file_date_updated":"2020-07-14T12:44:41Z","issue":"4","publication":"JAMA Psychiatry","day":"01","year":"2016","language":[{"iso":"eng"}],"scopus_import":"1","file":[{"file_name":"IST-2018-981-v1+1_YNP150011_annotatedproof_FINAL.pdf","file_size":601679,"access_level":"open_access","date_updated":"2020-07-14T12:44:41Z","content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:17:24Z","checksum":"649aee381f30f7ef7e9efa912d41c2e3","relation":"main_file","file_id":"5278"}],"publisher":"American Medical Association","pmid":1,"date_created":"2018-12-11T11:50:58Z","has_accepted_license":"1","oa":1,"publication_status":"published","ddc":["576","610"],"date_updated":"2024-02-14T12:07:22Z","publication_identifier":{"issn":["2168-622X"]},"oa_version":"Submitted Version","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6074","title":"How MicroRNAs Are involved in splitting the mind","type":"journal_article","status":"public","pubrep_id":"981","article_processing_charge":"No","citation":{"mla":"Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting the Mind.” <i>JAMA Psychiatry</i>, vol. 73, no. 4, American Medical Association, 2016, pp. 409–10, doi:<a href=\"https://doi.org/10.1001/jamapsychiatry.2015.3144\">10.1001/jamapsychiatry.2015.3144</a>.","apa":"Tsai, L., &#38; Siegert, S. (2016). How MicroRNAs Are involved in splitting the mind. <i>JAMA Psychiatry</i>. American Medical Association. <a href=\"https://doi.org/10.1001/jamapsychiatry.2015.3144\">https://doi.org/10.1001/jamapsychiatry.2015.3144</a>","ama":"Tsai L, Siegert S. How MicroRNAs Are involved in splitting the mind. <i>JAMA Psychiatry</i>. 2016;73(4):409-410. doi:<a href=\"https://doi.org/10.1001/jamapsychiatry.2015.3144\">10.1001/jamapsychiatry.2015.3144</a>","chicago":"Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting the Mind.” <i>JAMA Psychiatry</i>. American Medical Association, 2016. <a href=\"https://doi.org/10.1001/jamapsychiatry.2015.3144\">https://doi.org/10.1001/jamapsychiatry.2015.3144</a>.","short":"L. Tsai, S. Siegert, JAMA Psychiatry 73 (2016) 409–410.","ista":"Tsai L, Siegert S. 2016. How MicroRNAs Are involved in splitting the mind. JAMA Psychiatry. 73(4), 409–410.","ieee":"L. Tsai and S. Siegert, “How MicroRNAs Are involved in splitting the mind,” <i>JAMA Psychiatry</i>, vol. 73, no. 4. American Medical Association, pp. 409–410, 2016."},"quality_controlled":"1","department":[{"_id":"SaSi"}],"doi":"10.1001/jamapsychiatry.2015.3144","external_id":{"pmid":["26963490"]},"page":"409 - 410","_id":"1253","intvolume":"        73"},{"project":[{"call_identifier":"FP7","grant_number":"622033","name":"Persistent Homology - Images, Data and Maps","_id":"255F06BE-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:50:58Z","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.00116"}],"publisher":"Taylor and Francis","ec_funded":1,"language":[{"iso":"eng"}],"year":"2016","day":"02","publication":"Experimental Mathematics","date_published":"2016-04-02T00:00:00Z","abstract":[{"lang":"eng","text":"We use rigorous numerical techniques to compute a lower bound for the exponent of expansivity outside a neighborhood of the critical point for thousands of intervals of parameter values in the quadratic family. We first compute a radius of the critical neighborhood outside which the map is uniformly expanding. This radius is taken as small as possible, yet large enough for our numerical procedure to succeed in proving that the expansivity exponent outside this neighborhood is positive. Then, for each of the intervals, we compute a lower bound for this expansivity exponent, valid for all the parameters in that interval. We illustrate and study the distribution of the radii and the expansivity exponents. The results of our computations are mathematically rigorous. The source code of the software and the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/."}],"volume":25,"author":[{"full_name":"Golmakani, Ali","last_name":"Golmakani","first_name":"Ali"},{"first_name":"Stefano","last_name":"Luzzatto","full_name":"Luzzatto, Stefano"},{"first_name":"Pawel","last_name":"Pilarczyk","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","full_name":"Pilarczyk, Pawel"}],"issue":"2","department":[{"_id":"HeEd"}],"quality_controlled":"1","acknowledgement":"AG and PP were partially supported by Abdus Salam International Centre for Theoretical Physics (ICTP). Additionally, AG was supported by BREUDS, and research conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008); and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033. The  authors  gratefully  acknowledge  the  Department  of\r\nMathematics  of  Kyoto  University  for  providing  access\r\nto  their  server  for  conducting  computations  for  this\r\nproject.","intvolume":"        25","_id":"1254","page":"116 - 124","doi":"10.1080/10586458.2015.1048011","type":"journal_article","status":"public","title":"Uniform expansivity outside a critical neighborhood in the quadratic family","citation":{"ista":"Golmakani A, Luzzatto S, Pilarczyk P. 2016. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 25(2), 116–124.","ieee":"A. Golmakani, S. Luzzatto, and P. Pilarczyk, “Uniform expansivity outside a critical neighborhood in the quadratic family,” <i>Experimental Mathematics</i>, vol. 25, no. 2. Taylor and Francis, pp. 116–124, 2016.","apa":"Golmakani, A., Luzzatto, S., &#38; Pilarczyk, P. (2016). Uniform expansivity outside a critical neighborhood in the quadratic family. <i>Experimental Mathematics</i>. Taylor and Francis. <a href=\"https://doi.org/10.1080/10586458.2015.1048011\">https://doi.org/10.1080/10586458.2015.1048011</a>","mla":"Golmakani, Ali, et al. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” <i>Experimental Mathematics</i>, vol. 25, no. 2, Taylor and Francis, 2016, pp. 116–24, doi:<a href=\"https://doi.org/10.1080/10586458.2015.1048011\">10.1080/10586458.2015.1048011</a>.","ama":"Golmakani A, Luzzatto S, Pilarczyk P. Uniform expansivity outside a critical neighborhood in the quadratic family. <i>Experimental Mathematics</i>. 2016;25(2):116-124. doi:<a href=\"https://doi.org/10.1080/10586458.2015.1048011\">10.1080/10586458.2015.1048011</a>","chicago":"Golmakani, Ali, Stefano Luzzatto, and Pawel Pilarczyk. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” <i>Experimental Mathematics</i>. Taylor and Francis, 2016. <a href=\"https://doi.org/10.1080/10586458.2015.1048011\">https://doi.org/10.1080/10586458.2015.1048011</a>.","short":"A. Golmakani, S. Luzzatto, P. Pilarczyk, Experimental Mathematics 25 (2016) 116–124."},"date_updated":"2021-01-12T06:49:25Z","publication_status":"published","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6071","month":"04","oa_version":"Preprint"},{"publication":"Royal Society Open Science","year":"2016","language":[{"iso":"eng"}],"day":"01","author":[{"last_name":"Peuß","first_name":"Robert","full_name":"Peuß, Robert"},{"full_name":"Wensing, Kristina","last_name":"Wensing","first_name":"Kristina"},{"full_name":"Woestmann, Luisa","first_name":"Luisa","last_name":"Woestmann"},{"last_name":"Eggert","first_name":"Hendrik","full_name":"Eggert, Hendrik"},{"orcid":"0000-0002-8214-4758","first_name":"Barbara","last_name":"Milutinovic","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","full_name":"Milutinovic, Barbara"},{"last_name":"Sroka","first_name":"Marlene","full_name":"Sroka, Marlene"},{"last_name":"Scharsack","first_name":"Jörn","full_name":"Scharsack, Jörn"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"last_name":"Armitage","first_name":"Sophie","full_name":"Armitage, Sophie"}],"date_published":"2016-04-01T00:00:00Z","abstract":[{"text":"Down syndrome cell adhesion molecule 1 (Dscam1) has widereaching and vital neuronal functions although the role it plays in insect and crustacean immunity is less well understood. In this study, we combine different approaches to understand the roles that Dscam1 plays in fitness-related contexts in two model insect species. Contrary to our expectations, we found no short-term modulation of Dscam1 gene expression after haemocoelic or oral bacterial exposure in Tribolium castaneum, or after haemocoelic bacterial exposure in Drosophila melanogaster. Furthermore, RNAi-mediated Dscam1 knockdown and subsequent bacterial exposure did not reduce T. castaneum survival. However, Dscam1 knockdown in larvae resulted in adult locomotion defects, as well as dramatically reduced fecundity in males and females. We suggest that Dscam1 does not always play a straightforward role in immunity, but strongly influences behaviour and fecundity. This study takes a step towards understanding more about the role of this intriguing gene from different phenotypic perspectives.","lang":"eng"}],"volume":3,"file_date_updated":"2020-07-14T12:44:41Z","issue":"4","date_created":"2018-12-11T11:50:58Z","scopus_import":1,"publisher":"Royal Society, The","file":[{"date_updated":"2020-07-14T12:44:41Z","content_type":"application/pdf","file_name":"IST-2016-704-v1+1_160138.full.pdf","access_level":"open_access","file_size":627377,"file_id":"5049","date_created":"2018-12-12T10:14:01Z","creator":"system","checksum":"c3cd84666c8dc0ce6a784f1c82c1cf68","relation":"main_file"}],"oa":1,"publication_status":"published","date_updated":"2021-01-12T06:49:25Z","ddc":["576","592"],"oa_version":"Published Version","month":"04","publist_id":"6070","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"160138","has_accepted_license":"1","quality_controlled":"1","acknowledgement":"We thank Dietmar Schmucker for reading a draft of this manuscript and thank him and his group for\r\nhelpful discussions. We thank Barbara Hasert, Kevin Ferro and Manuel F. Talarico for technical support and helpful\r\ndiscussions. We also thank two anonymous reviewers for their comments. This study was supported by grants from the Volkswagen Stiftung (1/83 516 and AZ 86020: both to S.A.O.A.) and from the DFG priority programme 1399 ‘Host parasite coevolution’ (KU 1929/4-2 to R.P. and J.K.).","department":[{"_id":"SyCr"}],"doi":"10.1098/rsos.160138","intvolume":"         3","_id":"1255","title":"Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pubrep_id":"704","status":"public","type":"journal_article","citation":{"ieee":"R. Peuß <i>et al.</i>, “Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction,” <i>Royal Society Open Science</i>, vol. 3, no. 4. Royal Society, The, 2016.","ista":"Peuß R, Wensing K, Woestmann L, Eggert H, Milutinovic B, Sroka M, Scharsack J, Kurtz J, Armitage S. 2016. Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. Royal Society Open Science. 3(4), 160138.","mla":"Peuß, Robert, et al. “Down Syndrome Cell Adhesion Molecule 1: Testing for a Role in Insect Immunity, Behaviour and Reproduction.” <i>Royal Society Open Science</i>, vol. 3, no. 4, 160138, Royal Society, The, 2016, doi:<a href=\"https://doi.org/10.1098/rsos.160138\">10.1098/rsos.160138</a>.","apa":"Peuß, R., Wensing, K., Woestmann, L., Eggert, H., Milutinovic, B., Sroka, M., … Armitage, S. (2016). Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. <i>Royal Society Open Science</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rsos.160138\">https://doi.org/10.1098/rsos.160138</a>","short":"R. Peuß, K. Wensing, L. Woestmann, H. Eggert, B. Milutinovic, M. Sroka, J. Scharsack, J. Kurtz, S. Armitage, Royal Society Open Science 3 (2016).","ama":"Peuß R, Wensing K, Woestmann L, et al. Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. <i>Royal Society Open Science</i>. 2016;3(4). doi:<a href=\"https://doi.org/10.1098/rsos.160138\">10.1098/rsos.160138</a>","chicago":"Peuß, Robert, Kristina Wensing, Luisa Woestmann, Hendrik Eggert, Barbara Milutinovic, Marlene Sroka, Jörn Scharsack, Joachim Kurtz, and Sophie Armitage. “Down Syndrome Cell Adhesion Molecule 1: Testing for a Role in Insect Immunity, Behaviour and Reproduction.” <i>Royal Society Open Science</i>. Royal Society, The, 2016. <a href=\"https://doi.org/10.1098/rsos.160138\">https://doi.org/10.1098/rsos.160138</a>."}},{"language":[{"iso":"eng"}],"year":"2016","day":"27","date_published":"2016-04-27T00:00:00Z","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."}],"author":[{"full_name":"Jiang, Yu","last_name":"Jiang","first_name":"Yu"},{"full_name":"Yang, Yixiao","first_name":"Yixiao","last_name":"Yang"},{"full_name":"Liu, Han","last_name":"Liu","first_name":"Han"},{"orcid":"0000-0002-3066-6941","first_name":"Hui","last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","full_name":"Kong, Hui"},{"first_name":"Ming","last_name":"Gu","full_name":"Gu, Ming"},{"full_name":"Sun, Jiaguang","last_name":"Sun","first_name":"Jiaguang"},{"first_name":"Lui","last_name":"Sha","full_name":"Sha, Lui"}],"file_date_updated":"2020-07-14T12:44:41Z","date_created":"2018-12-11T11:50:58Z","scopus_import":1,"file":[{"file_size":1293599,"access_level":"open_access","file_name":"IST-2017-780-v1+1_RTAS-42-Camera-Ready.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:41Z","checksum":"42f0462911cc9957f2356b12fb33b4b6","relation":"main_file","date_created":"2018-12-12T10:12:31Z","creator":"system","file_id":"4949"}],"publisher":"IEEE","date_updated":"2021-01-12T06:49:26Z","ddc":["005"],"conference":{"location":"Vienna, Austria","name":"RTAS: Real-time and Embedded Technology and Applications Symposium","start_date":"2016-04-11","end_date":"2016-04-14"},"oa":1,"publication_status":"published","publist_id":"6069","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","month":"04","article_number":"7461337","has_accepted_license":"1","department":[{"_id":"ToHe"}],"quality_controlled":"1","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.","_id":"1256","doi":"10.1109/RTAS.2016.7461337","pubrep_id":"780","type":"conference","status":"public","title":"From stateflow simulation to verified implementation: A verification approach and a real-time train controller design","citation":{"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>","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>.","short":"Y. Jiang, Y. Yang, H. Liu, H. Kong, M. Gu, J. Sun, L. Sha, in:, IEEE, 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>","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.","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."}},{"doi":"10.1007/s00220-016-2600-4","intvolume":"       343","page":"881 - 919","_id":"1257","quality_controlled":"1","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.","department":[{"_id":"LaEr"}],"citation":{"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>.","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>","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>","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>.","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.","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."},"article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes","pubrep_id":"703","type":"journal_article","status":"public","month":"05","oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6067","oa":1,"publication_status":"published","date_updated":"2021-01-12T06:49:26Z","ddc":["510","539"],"has_accepted_license":"1","date_created":"2018-12-11T11:50:59Z","project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"file":[{"file_id":"5119","checksum":"4fb2411d9c2f56676123165aad46c828","relation":"main_file","creator":"system","date_created":"2018-12-12T10:15:02Z","content_type":"application/pdf","date_updated":"2020-07-14T12:44:42Z","file_size":800792,"access_level":"open_access","file_name":"IST-2016-703-v1+1_s00220-016-2600-4.pdf"}],"publisher":"Springer","scopus_import":1,"publication":"Communications in Mathematical Physics","language":[{"iso":"eng"}],"year":"2016","day":"01","ec_funded":1,"file_date_updated":"2020-07-14T12:44:42Z","issue":"3","author":[{"id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","full_name":"Sadel, Christian","orcid":"0000-0001-8255-3968","last_name":"Sadel","first_name":"Christian"},{"first_name":"Bálint","last_name":"Virág","full_name":"Virág, Bálint"}],"date_published":"2016-05-01T00:00:00Z","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."}],"volume":343},{"scopus_import":1,"title":"DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis","status":"public","type":"journal_article","citation":{"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.","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>","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>.","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.","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>.","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>"},"publisher":"Company of Biologists","quality_controlled":"1","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.","department":[{"_id":"EvBe"}],"doi":"10.1242/dev.130211","date_created":"2018-12-11T11:50:59Z","intvolume":"       143","_id":"1258","page":"1623 - 1631","author":[{"id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi Rovira, Marcal","first_name":"Marcal","last_name":"Gallemi Rovira"},{"last_name":"Galstyan","first_name":"Anahit","full_name":"Galstyan, Anahit"},{"first_name":"Sandi","last_name":"Paulišić","full_name":"Paulišić, Sandi"},{"full_name":"Then, Christiane","last_name":"Then","first_name":"Christiane"},{"full_name":"Ferrández Ayela, Almudena","first_name":"Almudena","last_name":"Ferrández Ayela"},{"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","last_name":"Wang","full_name":"Wang, Xuewen"},{"first_name":"José","last_name":"Micol","full_name":"Micol, José"},{"full_name":"Ponce, Maria","last_name":"Ponce","first_name":"Maria"},{"full_name":"Devlin, Paul","first_name":"Paul","last_name":"Devlin"},{"full_name":"Martínez García, Jaime","first_name":"Jaime","last_name":"Martínez García"}],"date_published":"2016-05-03T00:00:00Z","volume":143,"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."}],"issue":"9","publication_status":"published","date_updated":"2021-01-12T06:49:27Z","oa_version":"None","month":"05","publication":"Development","year":"2016","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6068","day":"03"},{"day":"01","year":"2016","language":[{"iso":"eng"}],"publication":"Mathematical Physics, Analysis and Geometry","abstract":[{"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.","lang":"eng"}],"volume":19,"date_published":"2016-06-01T00:00:00Z","author":[{"full_name":"Bräunlich, Gerhard","last_name":"Bräunlich","first_name":"Gerhard"},{"full_name":"Hainzl, Christian","last_name":"Hainzl","first_name":"Christian"},{"first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"issue":"2","file_date_updated":"2020-07-14T12:44:42Z","project":[{"grant_number":"P27533_N27","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:50:59Z","scopus_import":1,"publisher":"Springer","file":[{"date_created":"2018-12-12T10:09:13Z","creator":"system","relation":"main_file","checksum":"9954f685cc25c58d7f1712c67b47ad8d","file_id":"4736","file_name":"IST-2016-702-v1+1_s11040-016-9209-x.pdf","access_level":"open_access","file_size":506242,"date_updated":"2020-07-14T12:44:42Z","content_type":"application/pdf"}],"ddc":["510","539"],"date_updated":"2021-01-12T06:49:27Z","oa":1,"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6066","oa_version":"Published Version","month":"06","article_number":"13","has_accepted_license":"1","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.","quality_controlled":"1","_id":"1259","intvolume":"        19","doi":"10.1007/s11040-016-9209-x","status":"public","type":"journal_article","pubrep_id":"702","title":"Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (via OA deal)","citation":{"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.","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.","short":"G. Bräunlich, C. Hainzl, R. Seiringer, Mathematical Physics, Analysis and Geometry 19 (2016).","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>","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>.","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>"}},{"title":"The dual of the space of interactions in neural network models","status":"public","type":"journal_article","citation":{"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>","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>.","short":"D. De Martino, International Journal of Modern Physics C 27 (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>.","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.","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."},"article_processing_charge":"No","quality_controlled":"1","department":[{"_id":"GaTk"}],"external_id":{"arxiv":["1505.02963"]},"doi":"10.1142/S0129183116500674","intvolume":"        27","_id":"1260","article_number":"1650067","arxiv":1,"oa":1,"publication_status":"published","date_updated":"2021-01-12T06:49:28Z","oa_version":"Preprint","month":"06","publist_id":"6065","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1505.02963","open_access":"1"}],"publisher":"World Scientific Publishing","article_type":"original","date_created":"2018-12-11T11:51:00Z","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","last_name":"De Martino","first_name":"Daniele","orcid":"0000-0002-5214-4706"}],"date_published":"2016-06-01T00:00:00Z","abstract":[{"lang":"eng","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."}],"volume":27,"issue":"6","publication":"International Journal of Modern Physics C","language":[{"iso":"eng"}],"year":"2016","day":"01"},{"day":"10","language":[{"iso":"eng"}],"year":"2016","publication":"Nonlinearity","issue":"7","abstract":[{"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.","lang":"eng"}],"volume":29,"date_published":"2016-06-10T00:00:00Z","author":[{"full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan"},{"full_name":"Matthes, Daniel","first_name":"Daniel","last_name":"Matthes"}],"date_created":"2018-12-11T11:51:00Z","publisher":"IOP Publishing Ltd.","main_file_link":[{"url":"https://arxiv.org/abs/1505.03178","open_access":"1"}],"scopus_import":1,"publist_id":"6062","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"06","oa_version":"Preprint","date_updated":"2021-01-12T06:49:28Z","oa":1,"publication_status":"published","_id":"1261","page":"1992 - 2023","intvolume":"        29","doi":"10.1088/0951-7715/29/7/1992","department":[{"_id":"JaMa"}],"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 ’ .","quality_controlled":"1","citation":{"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>.","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>","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.","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."},"type":"journal_article","status":"public","title":"Long-time behavior of a finite volume discretization for a fourth order diffusion equation"}]