[{"file":[{"checksum":"b6533c37dc8fbd803ffeca216e0a8b8a","creator":"dernst","file_name":"2019_Development_Guerrero.pdf","date_created":"2019-12-13T07:34:06Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":7797881,"file_id":"7177","date_updated":"2020-07-14T12:47:50Z"}],"publication_status":"published","year":"2019","article_processing_charge":"No","article_number":"dev176297","date_published":"2019-12-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"type":"journal_article","ec_funded":1,"isi":1,"issue":"23","corr_author":"1","month":"12","ddc":["570"],"publication":"Development","status":"public","publisher":"Company of Biologists","abstract":[{"lang":"eng","text":"Cell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube, in which neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we used experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates the effect of interkinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube."}],"has_accepted_license":"1","pmid":1,"date_created":"2019-12-10T14:39:50Z","intvolume":"       146","language":[{"iso":"eng"}],"author":[{"first_name":"Pilar","last_name":"Guerrero","full_name":"Guerrero, Pilar"},{"first_name":"Ruben","last_name":"Perez-Carrasco","full_name":"Perez-Carrasco, Ruben"},{"orcid":"0000-0001-7896-7762","last_name":"Zagórski","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P"},{"full_name":"Page, David","last_name":"Page","first_name":"David"},{"full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","orcid":"0000-0003-4509-4998","first_name":"Anna"},{"last_name":"Briscoe","first_name":"James","full_name":"Briscoe, James"},{"full_name":"Page, Karen M.","last_name":"Page","first_name":"Karen M."}],"title":"Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium","date_updated":"2026-08-12T09:58:11Z","day":"04","file_date_updated":"2020-07-14T12:47:50Z","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"article_type":"original","external_id":{"isi":["000507575700004"],"pmid":["31784457"]},"quality_controlled":"1","oa_version":"Published Version","_id":"7165","volume":146,"department":[{"_id":"AnKi"}],"scopus_import":"1","doi":"10.1242/dev.176297","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” <i>Development</i>. Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/dev.176297\">https://doi.org/10.1242/dev.176297</a>.","short":"P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe, K.M. Page, Development 146 (2019).","mla":"Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” <i>Development</i>, vol. 146, no. 23, dev176297, Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/dev.176297\">10.1242/dev.176297</a>.","ieee":"P. Guerrero <i>et al.</i>, “Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium,” <i>Development</i>, vol. 146, no. 23. Company of Biologists, 2019.","apa":"Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe, J., &#38; Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.176297\">https://doi.org/10.1242/dev.176297</a>","ama":"Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. <i>Development</i>. 2019;146(23). doi:<a href=\"https://doi.org/10.1242/dev.176297\">10.1242/dev.176297</a>","ista":"Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 146(23), dev176297."},"project":[{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"}]},{"publisher":"Company of Biologists","pmid":1,"abstract":[{"lang":"eng","text":"The apical hook is a transiently formed structure that plays a protective role when the germinating seedling penetrates through the soil towards the surface. Crucial for proper bending is the local auxin maxima, which defines the concave (inner) side of the hook curvature. As no sign of asymmetric auxin distribution has been reported in embryonic hypocotyls prior to hook formation, the question of how auxin asymmetry is established in the early phases of seedling germination remains largely unanswered. Here, we analyzed the auxin distribution and expression of PIN auxin efflux carriers from early phases of germination, and show that bending of the root in response to gravity is the crucial initial cue that governs the hypocotyl bending required for apical hook formation. Importantly, polar auxin transport machinery is established gradually after germination starts as a result of tight root-hypocotyl interaction and a proper balance between abscisic acid and gibberellins."}],"date_created":"2019-09-22T22:00:36Z","intvolume":"       146","language":[{"iso":"eng"}],"issue":"17","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"month":"09","publication":"Development","status":"public","ddc":["580"],"oa":1,"type":"journal_article","isi":1,"ec_funded":1,"article_processing_charge":"No","year":"2019","publication_status":"published","article_number":"dev175919","date_published":"2019-09-12T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":146,"department":[{"_id":"EvBe"}],"scopus_import":"1","citation":{"short":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, E. Benková, Development 146 (2019).","chicago":"Zhu, Qiang, Marçal Gallemi, Jiří Pospíšil, Petra Žádníková, Miroslav Strnad, and Eva Benková. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” <i>Development</i>. Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/dev.175919\">https://doi.org/10.1242/dev.175919</a>.","apa":"Zhu, Q., Gallemi, M., Pospíšil, J., Žádníková, P., Strnad, M., &#38; Benková, E. (2019). Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.175919\">https://doi.org/10.1242/dev.175919</a>","ista":"Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. 2019. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. 146(17), dev175919.","ama":"Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. <i>Development</i>. 2019;146(17). doi:<a href=\"https://doi.org/10.1242/dev.175919\">10.1242/dev.175919</a>","ieee":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, and E. Benková, “Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis,” <i>Development</i>, vol. 146, no. 17. Company of Biologists, 2019.","mla":"Zhu, Qiang, et al. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” <i>Development</i>, vol. 146, no. 17, dev175919, Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/dev.175919\">10.1242/dev.175919</a>."},"doi":"10.1242/dev.175919","project":[{"grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"main_file_link":[{"url":"https://doi.org/10.1242/dev.175919","open_access":"1"}],"oa_version":"Published Version","quality_controlled":"1","_id":"6897","article_type":"original","acknowledgement":"We thank Jiri Friml and Phillip Brewer for inspiring discussion and for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility\r\n(BIF), the Life Science Facility (LSF).\r\nThis work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to E.B.). J.P. and M.S. received funds from European Regional Development Fund-Project ‘Centre for Experimental Plant Biology’ (No. CZ.02.1.01/0.0/0.0/16_019/0000738).","publication_identifier":{"eissn":["1477-9129"]},"day":"12","external_id":{"isi":["000486297400011"],"pmid":["31391194"]},"author":[{"full_name":"Zhu, Qiang","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","last_name":"Zhu","first_name":"Qiang"},{"last_name":"Gallemi","orcid":"0000-0003-4675-6893","first_name":"Marçal","full_name":"Gallemi, Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jiří","last_name":"Pospíšil","full_name":"Pospíšil, Jiří"},{"full_name":"Žádníková, Petra","last_name":"Žádníková","first_name":"Petra"},{"full_name":"Strnad, Miroslav","first_name":"Miroslav","last_name":"Strnad"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"date_updated":"2026-08-12T09:57:36Z","title":"Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis"},{"publisher":"Company of Biologists","pmid":1,"date_created":"2020-01-29T16:27:10Z","abstract":[{"text":"The formation of neuronal dendrite branches is fundamental for the wiring and function of the nervous system. Indeed, dendrite branching enhances the coverage of the neuron's receptive field and modulates the initial processing of incoming stimuli. Complex dendrite patterns are achieved in vivo through a dynamic process of de novo branch formation, branch extension and retraction. The first step towards branch formation is the generation of a dynamic filopodium-like branchlet. The mechanisms underlying the initiation of dendrite branchlets are therefore crucial to the shaping of dendrites. Through in vivo time-lapse imaging of the subcellular localization of actin during the process of branching of Drosophila larva sensory neurons, combined with genetic analysis and electron tomography, we have identified the Actin-related protein (Arp) 2/3 complex as the major actin nucleator involved in the initiation of dendrite branchlet formation, under the control of the activator WAVE and of the small GTPase Rac1. Transient recruitment of an Arp2/3 component marks the site of branchlet initiation in vivo. These data position the activation of Arp2/3 as an early hub for the initiation of branchlet formation.","lang":"eng"}],"intvolume":"       146","language":[{"iso":"eng"}],"issue":"7","ddc":["570"],"publication":"Development","status":"public","month":"04","oa":1,"type":"journal_article","isi":1,"publication_status":"published","article_processing_charge":"No","year":"2019","article_number":"dev171397","date_published":"2019-04-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":146,"department":[{"_id":"MiSi"}],"scopus_import":"1","citation":{"ieee":"T. Stürner <i>et al.</i>, “Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo,” <i>Development</i>, vol. 146, no. 7. Company of Biologists, 2019.","mla":"Stürner, Tomke, et al. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” <i>Development</i>, vol. 146, no. 7, dev171397, Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/dev.171397\">10.1242/dev.171397</a>.","ista":"Stürner T, Tatarnikova A, Müller J, Schaffran B, Cuntz H, Zhang Y, Nemethova M, Bogdan S, Small V, Tavosanis G. 2019. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. 146(7), dev171397.","apa":"Stürner, T., Tatarnikova, A., Müller, J., Schaffran, B., Cuntz, H., Zhang, Y., … Tavosanis, G. (2019). Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.171397\">https://doi.org/10.1242/dev.171397</a>","ama":"Stürner T, Tatarnikova A, Müller J, et al. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. <i>Development</i>. 2019;146(7). doi:<a href=\"https://doi.org/10.1242/dev.171397\">10.1242/dev.171397</a>","chicago":"Stürner, Tomke, Anastasia Tatarnikova, Jan Müller, Barbara Schaffran, Hermann Cuntz, Yun Zhang, Maria Nemethova, Sven Bogdan, Vic Small, and Gaia Tavosanis. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” <i>Development</i>. Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/dev.171397\">https://doi.org/10.1242/dev.171397</a>.","short":"T. Stürner, A. Tatarnikova, J. Müller, B. Schaffran, H. Cuntz, Y. Zhang, M. Nemethova, S. Bogdan, V. Small, G. Tavosanis, Development 146 (2019)."},"doi":"10.1242/dev.171397","oa_version":"Published Version","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/dev.171397"}],"_id":"7404","day":"04","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"article_type":"original","external_id":{"pmid":["30910826"],"isi":["000464583200006"]},"author":[{"last_name":"Stürner","first_name":"Tomke","full_name":"Stürner, Tomke"},{"full_name":"Tatarnikova, Anastasia","last_name":"Tatarnikova","first_name":"Anastasia"},{"last_name":"Müller","first_name":"Jan","full_name":"Müller, Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D"},{"full_name":"Schaffran, Barbara","first_name":"Barbara","last_name":"Schaffran"},{"full_name":"Cuntz, Hermann","first_name":"Hermann","last_name":"Cuntz"},{"last_name":"Zhang","first_name":"Yun","full_name":"Zhang, Yun"},{"id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Nemethova, Maria","first_name":"Maria","last_name":"Nemethova"},{"full_name":"Bogdan, Sven","last_name":"Bogdan","first_name":"Sven"},{"first_name":"Vic","last_name":"Small","full_name":"Small, Vic"},{"full_name":"Tavosanis, Gaia","last_name":"Tavosanis","first_name":"Gaia"}],"title":"Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo","date_updated":"2026-08-12T09:57:15Z"},{"language":[{"iso":"eng"}],"intvolume":"         7","date_created":"2022-04-20T15:06:05Z","publisher":"Austrian Pharmacological Society","corr_author":"1","status":"public","month":"09","publication":"Intrinsic Activity","ddc":["570"],"issue":"Suppl. 1","type":"conference_abstract","ec_funded":1,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"A3.27","date_published":"2019-09-11T00:00:00Z","year":"2019","article_processing_charge":"No","keyword":["hippocampus","mossy fibers","readily releasable pool","electron microscopy"],"publication_status":"published","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"708497","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse"},{"_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W01205","name":"Zellkommunikation in Gesundheit und Krankheit"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312"}],"doi":"10.25006/ia.7.s1-a3.27","citation":{"chicago":"Kim, Olena, Carolina Borges Merjane, and Peter M Jonas. “Functional Analysis of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.” In <i>Intrinsic Activity</i>, Vol. 7. Austrian Pharmacological Society, 2019. <a href=\"https://doi.org/10.25006/ia.7.s1-a3.27\">https://doi.org/10.25006/ia.7.s1-a3.27</a>.","short":"O. Kim, C. Borges Merjane, P.M. Jonas, in:, Intrinsic Activity, Austrian Pharmacological Society, 2019.","ieee":"O. Kim, C. Borges Merjane, and P. M. Jonas, “Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy,” in <i>Intrinsic Activity</i>, Innsbruck, Austria, 2019, vol. 7, no. Suppl. 1.","mla":"Kim, Olena, et al. “Functional Analysis of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.” <i>Intrinsic Activity</i>, vol. 7, no. Suppl. 1, A3.27, Austrian Pharmacological Society, 2019, doi:<a href=\"https://doi.org/10.25006/ia.7.s1-a3.27\">10.25006/ia.7.s1-a3.27</a>.","ama":"Kim O, Borges Merjane C, Jonas PM. Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. In: <i>Intrinsic Activity</i>. Vol 7. Austrian Pharmacological Society; 2019. doi:<a href=\"https://doi.org/10.25006/ia.7.s1-a3.27\">10.25006/ia.7.s1-a3.27</a>","ista":"Kim O, Borges Merjane C, Jonas PM. 2019. Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. Intrinsic Activity. ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological Society vol. 7, A3.27.","apa":"Kim, O., Borges Merjane, C., &#38; Jonas, P. M. (2019). Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. In <i>Intrinsic Activity</i> (Vol. 7). Innsbruck, Austria: Austrian Pharmacological Society. <a href=\"https://doi.org/10.25006/ia.7.s1-a3.27\">https://doi.org/10.25006/ia.7.s1-a3.27</a>"},"department":[{"_id":"PeJo"}],"volume":7,"_id":"11222","main_file_link":[{"open_access":"1","url":"https://www.intrinsicactivity.org/2019/7/S1/A3.27/"}],"quality_controlled":"1","oa_version":"Published Version","conference":{"start_date":"2019-09-25","location":"Innsbruck, Austria","name":"ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological Society","end_date":"2019-09-27"},"related_material":{"record":[{"id":"11196","relation":"dissertation_contains","status":"public"}]},"acknowledgement":"This work was supported by the ERC and EU Horizon 2020 (ERC 692692; MSC-IF 708497) and FWF Z 312-B27 Wittgenstein award; W 1205-B09).","publication_identifier":{"issn":["2309-8503"]},"day":"11","date_updated":"2026-09-02T22:30:03Z","title":"Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy","author":[{"first_name":"Olena","last_name":"Kim","orcid":"0000-0003-2344-1039","full_name":"Kim, Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carolina","orcid":"0000-0003-0005-401X","last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87","full_name":"Borges Merjane, Carolina"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M"}]},{"file_date_updated":"2020-07-14T12:47:49Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12897"}]},"article_type":"original","publication_identifier":{"issn":["0730-0301"]},"day":"06","external_id":{"isi":["000498397300007"]},"author":[{"full_name":"Hafner, Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hafner"},{"full_name":"Schumacher, Christian","first_name":"Christian","last_name":"Schumacher"},{"last_name":"Knoop","first_name":"Espen","full_name":"Knoop, Espen"},{"first_name":"Thomas","last_name":"Auzinger","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd"},{"first_name":"Moritz","last_name":"Bächer","full_name":"Bächer, Moritz"}],"date_updated":"2026-09-02T22:30:05Z","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","department":[{"_id":"BeBi"}],"scopus_import":"1","volume":38,"project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"chicago":"Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3355089.3356576\">https://doi.org/10.1145/3355089.3356576</a>.","short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019).","mla":"Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” <i>ACM Transactions on Graphics</i>, vol. 38, no. 6, 157, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3355089.3356576\">10.1145/3355089.3356576</a>.","ieee":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 6. ACM, 2019.","ista":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157.","ama":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. <i>ACM Transactions on Graphics</i>. 2019;38(6). doi:<a href=\"https://doi.org/10.1145/3355089.3356576\">10.1145/3355089.3356576</a>","apa":"Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., &#38; Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3355089.3356576\">https://doi.org/10.1145/3355089.3356576</a>"},"doi":"10.1145/3355089.3356576","_id":"7117","quality_controlled":"1","oa_version":"Submitted Version","ec_funded":1,"isi":1,"type":"journal_article","oa":1,"year":"2019","article_processing_charge":"No","publication_status":"published","file":[{"relation":"supplementary_material","date_created":"2019-11-26T14:24:26Z","checksum":"56a2fb019adcb556d2b022f5e5acb68c","creator":"bbickel","file_name":"xcad_sup_mat_siga19.pdf","file_size":1673176,"content_type":"application/pdf","access_level":"open_access","file_id":"7119","date_updated":"2020-07-14T12:47:49Z","title":"X-CAD Supplemental Material"},{"content_type":"application/pdf","access_level":"open_access","file_size":14563618,"creator":"bbickel","checksum":"5f29d76aceb5102e766cbab9b17d776e","file_name":"XCAD_authors_version.pdf","relation":"main_file","date_created":"2019-11-26T14:24:27Z","date_updated":"2020-07-14T12:47:49Z","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","description":"This is the author's version of the work.","file_id":"7120"},{"file_id":"7121","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-26T14:27:37Z","relation":"main_file","file_name":"XCAD_video.mp4","creator":"bbickel","checksum":"0d31e123286cbec9e28b2001c2bb0d55","file_size":259979129,"access_level":"open_access","content_type":"video/mp4"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-11-06T00:00:00Z","article_number":"157","date_created":"2019-11-26T14:22:09Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models."}],"publisher":"ACM","language":[{"iso":"eng"}],"intvolume":"        38","issue":"6","publication":"ACM Transactions on Graphics","ddc":["000"],"month":"11","status":"public"},{"external_id":{"isi":["000504652000020"],"pmid":["31786521"]},"day":"20","publication_identifier":{"issn":["2589-0042"]},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11393"}]},"article_type":"original","file_date_updated":"2020-07-14T12:47:57Z","title":"Electron microscopic detection of single membrane proteins by a specific chemical labeling","date_updated":"2026-09-02T22:30:06Z","author":[{"last_name":"Tabata","first_name":"Shigekazu","id":"4427179E-F248-11E8-B48F-1D18A9856A87","full_name":"Tabata, Shigekazu"},{"id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","full_name":"Jevtic, Marijo","last_name":"Jevtic","first_name":"Marijo"},{"full_name":"Kurashige, Nobutaka","first_name":"Nobutaka","last_name":"Kurashige"},{"first_name":"Hirokazu","last_name":"Fuchida","full_name":"Fuchida, Hirokazu"},{"full_name":"Kido, Munetsugu","first_name":"Munetsugu","last_name":"Kido"},{"last_name":"Tani","first_name":"Kazushi","full_name":"Tani, Kazushi"},{"first_name":"Naoki","last_name":"Zenmyo","full_name":"Zenmyo, Naoki"},{"last_name":"Uchinomiya","first_name":"Shohei","full_name":"Uchinomiya, Shohei"},{"id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Harada, Harumi","first_name":"Harumi","orcid":"0000-0001-7429-7896","last_name":"Harada"},{"last_name":"Itakura","first_name":"Makoto","full_name":"Itakura, Makoto"},{"first_name":"Itaru","last_name":"Hamachi","full_name":"Hamachi, Itaru"},{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"last_name":"Ojida","first_name":"Akio","full_name":"Ojida, Akio"}],"project":[{"call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"},{"call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 1","grant_number":"720270"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"S. Tabata, M. Jevtic, N. Kurashige, H. Fuchida, M. Kido, K. Tani, N. Zenmyo, S. Uchinomiya, H. Harada, M. Itakura, I. Hamachi, R. Shigemoto, A. Ojida, IScience 22 (2019) 256–268.","chicago":"Tabata, Shigekazu, Marijo Jevtic, Nobutaka Kurashige, Hirokazu Fuchida, Munetsugu Kido, Kazushi Tani, Naoki Zenmyo, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” <i>IScience</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">https://doi.org/10.1016/j.isci.2019.11.025</a>.","ama":"Tabata S, Jevtic M, Kurashige N, et al. Electron microscopic detection of single membrane proteins by a specific chemical labeling. <i>iScience</i>. 2019;22(12):256-268. doi:<a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">10.1016/j.isci.2019.11.025</a>","ista":"Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. 2019. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 22(12), 256–268.","apa":"Tabata, S., Jevtic, M., Kurashige, N., Fuchida, H., Kido, M., Tani, K., … Ojida, A. (2019). Electron microscopic detection of single membrane proteins by a specific chemical labeling. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">https://doi.org/10.1016/j.isci.2019.11.025</a>","mla":"Tabata, Shigekazu, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” <i>IScience</i>, vol. 22, no. 12, Elsevier, 2019, pp. 256–68, doi:<a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">10.1016/j.isci.2019.11.025</a>.","ieee":"S. Tabata <i>et al.</i>, “Electron microscopic detection of single membrane proteins by a specific chemical labeling,” <i>iScience</i>, vol. 22, no. 12. Elsevier, pp. 256–268, 2019."},"doi":"10.1016/j.isci.2019.11.025","scopus_import":"1","department":[{"_id":"RySh"}],"volume":22,"_id":"7391","oa_version":"Published Version","quality_controlled":"1","ec_funded":1,"type":"journal_article","isi":1,"oa":1,"page":"256-268","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-12-20T00:00:00Z","publication_status":"published","year":"2019","article_processing_charge":"No","file":[{"file_name":"2019_iScience_Tabata.pdf","checksum":"f3e90056a49f09b205b1c4f8c739ffd1","creator":"dernst","relation":"main_file","date_created":"2020-02-04T10:48:36Z","content_type":"application/pdf","access_level":"open_access","file_size":7197776,"file_id":"7448","date_updated":"2020-07-14T12:47:57Z"}],"language":[{"iso":"eng"}],"intvolume":"        22","abstract":[{"text":"Electron microscopy (EM) is a technology that enables visualization of single proteins at a nanometer resolution. However, current protein analysis by EM mainly relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised by large size of antibody, precluding precise detection of protein location in biological samples. Here, we develop a specific chemical labeling method for EM detection of proteins at single-molecular level. Rational design of α-helical peptide tag and probe structure provided a complementary reaction pair that enabled specific cysteine conjugation of the tag. The developed chemical labeling with gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency and detectability of high-density clusters of tag-fused G protein-coupled receptors in freeze-fracture replicas compared with immunogold labeling. Furthermore, in ultrathin sections, the spatial resolution of the chemical labeling was significantly higher than that of antibody-mediated labeling. These results demonstrate substantial advantages of the chemical labeling approach for single protein visualization by EM.","lang":"eng"}],"has_accepted_license":"1","pmid":1,"date_created":"2020-01-29T15:56:56Z","publisher":"Elsevier","ddc":["570"],"corr_author":"1","publication":"iScience","status":"public","month":"12","issue":"12"},{"_id":"6713","oa_version":"Published Version","quality_controlled":"1","department":[{"_id":"NiBa"}],"scopus_import":"1","volume":8,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.7554/eLife.42014","citation":{"chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.42014\">https://doi.org/10.7554/eLife.42014</a>.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, ELife 8 (2019).","ieee":"J. P. Castro <i>et al.</i>, “An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","mla":"Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” <i>ELife</i>, vol. 8, e42014, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.42014\">10.7554/eLife.42014</a>.","ama":"Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.42014\">10.7554/eLife.42014</a>","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 8, e42014.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.42014\">https://doi.org/10.7554/eLife.42014</a>"},"author":[{"full_name":"Castro, João Pl","last_name":"Castro","first_name":"João Pl"},{"full_name":"Yancoskie, Michelle N.","first_name":"Michelle N.","last_name":"Yancoskie"},{"first_name":"Marta","last_name":"Marchini","full_name":"Marchini, Marta"},{"first_name":"Stefanie","last_name":"Belohlavy","orcid":"0000-0002-9849-498X","full_name":"Belohlavy, Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Layla","last_name":"Hiramatsu","full_name":"Hiramatsu, Layla"},{"first_name":"Marek","last_name":"Kučka","full_name":"Kučka, Marek"},{"full_name":"Beluch, William H.","last_name":"Beluch","first_name":"William H."},{"full_name":"Naumann, Ronald","first_name":"Ronald","last_name":"Naumann"},{"full_name":"Skuplik, Isabella","first_name":"Isabella","last_name":"Skuplik"},{"last_name":"Cobb","first_name":"John","full_name":"Cobb, John"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rolian, Campbell","first_name":"Campbell","last_name":"Rolian"},{"full_name":"Chan, Yingguang Frank","last_name":"Chan","first_name":"Yingguang Frank"}],"date_updated":"2026-09-02T22:30:09Z","title":"An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","file_date_updated":"2020-07-14T12:47:38Z","related_material":{"record":[{"relation":"research_data","id":"9804","status":"public"},{"id":"11388","relation":"dissertation_contains","status":"public"}]},"day":"06","external_id":{"pmid":["31169497"],"isi":["000473588700001"]},"ddc":["576"],"publication":"eLife","month":"06","status":"public","has_accepted_license":"1","pmid":1,"abstract":[{"lang":"eng","text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response."}],"date_created":"2019-07-28T21:59:17Z","publisher":"eLife Sciences Publications","language":[{"iso":"eng"}],"intvolume":"         8","year":"2019","article_processing_charge":"No","publication_status":"published","file":[{"date_created":"2019-07-29T07:41:18Z","relation":"main_file","creator":"apreinsp","file_name":"2019_eLife_Castro.pdf","checksum":"fa0936fe58f0d9e3f8e75038570e5a17","file_size":6748249,"access_level":"open_access","content_type":"application/pdf","file_id":"6721","date_updated":"2020-07-14T12:47:38Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-06-06T00:00:00Z","article_number":"e42014","type":"journal_article","isi":1,"oa":1},{"_id":"6830","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.08.021","open_access":"1"}],"quality_controlled":"1","oa_version":"Published Version","doi":"10.1016/j.neuron.2019.08.021","citation":{"ista":"Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid. Neuron. 103(5), 750–752.","ama":"Contreras X, Hippenmeyer S. Memo1 tiles the radial glial cell grid. <i>Neuron</i>. 2019;103(5):750-752. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.08.021\">10.1016/j.neuron.2019.08.021</a>","apa":"Contreras, X., &#38; Hippenmeyer, S. (2019). Memo1 tiles the radial glial cell grid. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.08.021\">https://doi.org/10.1016/j.neuron.2019.08.021</a>","ieee":"X. Contreras and S. Hippenmeyer, “Memo1 tiles the radial glial cell grid,” <i>Neuron</i>, vol. 103, no. 5. Elsevier, pp. 750–752, 2019.","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” <i>Neuron</i>, vol. 103, no. 5, Elsevier, 2019, pp. 750–52, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.08.021\">10.1016/j.neuron.2019.08.021</a>.","short":"X. Contreras, S. Hippenmeyer, Neuron 103 (2019) 750–752.","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” <i>Neuron</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.neuron.2019.08.021\">https://doi.org/10.1016/j.neuron.2019.08.021</a>."},"scopus_import":"1","department":[{"_id":"SiHi"}],"volume":103,"date_updated":"2026-09-02T22:30:18Z","title":"Memo1 tiles the radial glial cell grid","author":[{"first_name":"Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon"}],"external_id":{"pmid":["31487522"],"isi":["000484400200002"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"7902","status":"public"}]},"article_type":"letter_note","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"day":"04","status":"public","month":"09","publication":"Neuron","ddc":["570"],"issue":"5","language":[{"iso":"eng"}],"intvolume":"       103","date_created":"2019-08-25T22:00:50Z","pmid":1,"publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-09-04T00:00:00Z","year":"2019","article_processing_charge":"No","publication_status":"published","isi":1,"type":"journal_article","oa":1,"page":"750-752"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2019-05-07T00:00:00Z","keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"year":"2019","article_processing_charge":"No","publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":3895187,"file_name":"tesisDoctoradoBC.pdf","creator":"casillas","checksum":"6daf2d2086111aa8fd3fbc919a3e2833","relation":"main_file","date_created":"2019-05-13T09:16:20Z","date_updated":"2021-02-11T11:17:15Z","embargo":"2020-05-08","file_id":"6438"},{"access_level":"closed","content_type":"application/zip","file_size":7365118,"creator":"casillas","checksum":"3d221aaff7559a7060230a1ff610594f","file_name":"tesisDoctoradoBC.zip","date_created":"2019-05-13T09:16:20Z","relation":"source_file","date_updated":"2020-07-14T12:47:30Z","embargo_to":"open_access","file_id":"6439"}],"type":"dissertation","ec_funded":1,"oa":1,"page":"183","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"ddc":["570","006","578","592"],"corr_author":"1","status":"public","month":"05","degree_awarded":"PhD","supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia M","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia M"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","date_created":"2019-05-13T08:58:35Z","abstract":[{"text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2026-04-08T14:02:12Z","title":"Collective defenses of garden ants against a fungal pathogen","author":[{"last_name":"Casillas Perez","first_name":"Barbara E","full_name":"Casillas Perez, Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","file_date_updated":"2021-02-11T11:17:15Z","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"1999","relation":"part_of_dissertation","status":"public"}]},"day":"07","_id":"6435","oa_version":"Published Version","project":[{"name":"Epidemics in ant societies on a chip","grant_number":"771402","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>.","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019.","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","mla":"Casillas Perez, Barbara E. <i>Collective Defenses of Garden Ants against a Fungal Pathogen</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>.","ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>","apa":"Casillas Perez, B. E. (2019). <i>Collective defenses of garden ants against a fungal pathogen</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria."},"doi":"10.15479/AT:ISTA:6435","department":[{"_id":"SyCr"}]},{"volume":177,"department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"BjHo"}],"scopus_import":"1","citation":{"chicago":"Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">https://doi.org/10.1016/j.cell.2019.04.030</a>.","short":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg, Cell 177 (2019) 1463–1479.e18.","mla":"Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” <i>Cell</i>, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">10.1016/j.cell.2019.04.030</a>.","ieee":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg, “Bulk actin dynamics drive phase segregation in zebrafish oocytes,” <i>Cell</i>, vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019.","ista":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18.","ama":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin dynamics drive phase segregation in zebrafish oocytes. <i>Cell</i>. 2019;177(6):1463-1479.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">10.1016/j.cell.2019.04.030</a>","apa":"Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">https://doi.org/10.1016/j.cell.2019.04.030</a>"},"doi":"10.1016/j.cell.2019.04.030","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.04.030","open_access":"1"}],"oa_version":"Published Version","quality_controlled":"1","_id":"6508","article_type":"original","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"acknowledgement":"We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful discussions, and the Bioimaging and zebrafish facilities at IST Austria for their continuous support. This project has received funding from the European Union (European Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science Fund (FWF) (P 31639 to E.H.).","file_date_updated":"2020-10-21T07:22:34Z","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-the-cytoplasm-separates-from-the-yolk/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","id":"8350","status":"public"}]},"day":"30","external_id":{"pmid":["31080065"],"isi":["000469415100013"]},"author":[{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","first_name":"Shayan"},{"last_name":"Kardos","first_name":"Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland"},{"id":"31D2C804-F248-11E8-B48F-1D18A9856A87","full_name":"Xue, Shi-lei","last_name":"Xue","first_name":"Shi-lei"},{"first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"date_updated":"2026-09-02T22:30:19Z","title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes","publisher":"Elsevier","date_created":"2019-06-02T21:59:12Z","has_accepted_license":"1","abstract":[{"text":"Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation.","lang":"eng"}],"pmid":1,"intvolume":"       177","language":[{"iso":"eng"}],"issue":"6","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"ddc":["570"],"status":"public","month":"05","publication":"Cell","page":"1463-1479.e18","oa":1,"ec_funded":1,"type":"journal_article","isi":1,"file":[{"success":1,"file_id":"8686","date_updated":"2020-10-21T07:22:34Z","creator":"dernst","file_name":"2019_Cell_Shamipour_accepted.pdf","checksum":"aea43726d80e35ce3885073a5f05c3e3","relation":"main_file","date_created":"2020-10-21T07:22:34Z","content_type":"application/pdf","access_level":"open_access","file_size":3356292}],"article_processing_charge":"No","year":"2019","publication_status":"published","date_published":"2019-05-30T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"page":"937-952.e18","oa":1,"ec_funded":1,"type":"journal_article","isi":1,"file":[{"file_size":8805878,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-10-21T07:09:45Z","checksum":"33dac4bb77ee630e2666e936b4d57980","creator":"dernst","file_name":"2019_Cell_Schwayer_accepted.pdf","date_updated":"2020-10-21T07:09:45Z","file_id":"8684","success":1}],"article_processing_charge":"No","year":"2019","publication_status":"published","date_published":"2019-10-31T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Cell Press","date_created":"2019-11-12T12:51:06Z","has_accepted_license":"1","pmid":1,"intvolume":"       179","language":[{"iso":"eng"}],"issue":"4","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"month":"10","status":"public","ddc":["570"],"publication":"Cell","related_material":{"link":[{"description":"News auf IST Website","url":"https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","id":"7186","status":"public"},{"status":"public","id":"8350","relation":"dissertation_contains"}]},"file_date_updated":"2020-10-21T07:09:45Z","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"article_type":"original","day":"31","external_id":{"isi":["000493898000012"],"pmid":["31675500"]},"author":[{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226","last_name":"Schwayer","first_name":"Cornelia"},{"last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"},{"id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha","first_name":"Kornelija"},{"full_name":"Schauer, Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer","orcid":"0000-0001-7659-9142","first_name":"Alexandra"},{"last_name":"Balda","first_name":"M","full_name":"Balda, M"},{"full_name":"Tada, M","first_name":"M","last_name":"Tada"},{"full_name":"Matter, K","last_name":"Matter","first_name":"K"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"date_updated":"2026-09-02T22:30:19Z","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","volume":179,"scopus_import":"1","department":[{"_id":"CaHe"},{"_id":"BjHo"}],"citation":{"ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. 2019;179(4):937-952.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>","ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18.","apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>","mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>.","ieee":"C. Schwayer <i>et al.</i>, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” <i>Cell</i>, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019.","short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18.","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>."},"doi":"10.1016/j.cell.2019.10.006","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"oa_version":"Submitted Version","quality_controlled":"1","_id":"7001"},{"author":[{"last_name":"Kopf","orcid":"0000-0002-2187-6656","first_name":"Aglaja","full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-06-18T17:44:11Z","title":"The implication of cytoskeletal dynamics on leukocyte migration","related_material":{"link":[{"url":"https://ist.ac.at/en/news/feeling-like-a-cell/","relation":"press_release"}],"record":[{"status":"public","relation":"part_of_dissertation","id":"6877"},{"relation":"part_of_dissertation","id":"6328","status":"public"},{"id":"15","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2020-10-17T22:30:03Z","publication_identifier":{"isbn":["978-3-99078-002-2"],"eissn":["2663-337X"]},"day":"24","OA_place":"publisher","oa_version":"Published Version","_id":"6891","department":[{"_id":"MiSi"}],"citation":{"short":"A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration, Institute of Science and Technology Austria, 2019.","chicago":"Kopf, Aglaja. “The Implication of Cytoskeletal Dynamics on Leukocyte Migration.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6891\">https://doi.org/10.15479/AT:ISTA:6891</a>.","ista":"Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria.","ama":"Kopf A. The implication of cytoskeletal dynamics on leukocyte migration. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6891\">10.15479/AT:ISTA:6891</a>","apa":"Kopf, A. (2019). <i>The implication of cytoskeletal dynamics on leukocyte migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6891\">https://doi.org/10.15479/AT:ISTA:6891</a>","ieee":"A. Kopf, “The implication of cytoskeletal dynamics on leukocyte migration,” Institute of Science and Technology Austria, 2019.","mla":"Kopf, Aglaja. <i>The Implication of Cytoskeletal Dynamics on Leukocyte Migration</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6891\">10.15479/AT:ISTA:6891</a>."},"doi":"10.15479/AT:ISTA:6891","project":[{"name":"Nano-Analytics of Cellular Systems","grant_number":"W01250-B20","call_identifier":"FWF","_id":"265E2996-B435-11E9-9278-68D0E5697425"}],"file":[{"relation":"source_file","date_created":"2019-10-15T05:28:42Z","creator":"akopf","checksum":"00d100d6468e31e583051e0a006b640c","file_name":"Kopf_PhD_Thesis.docx","file_size":74735267,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_id":"6950","embargo_to":"open_access","date_updated":"2020-10-17T22:30:03Z"},{"date_updated":"2020-10-17T22:30:03Z","embargo":"2020-10-16","file_id":"6951","file_size":52787224,"access_level":"open_access","content_type":"application/pdf","date_created":"2019-10-15T05:28:47Z","relation":"main_file","creator":"akopf","checksum":"5d1baa899993ae6ca81aebebe1797000","file_name":"Kopf_PhD_Thesis1.pdf"}],"article_processing_charge":"No","keyword":["cell biology","immunology","leukocyte","migration","microfluidics"],"year":"2019","publication_status":"published","date_published":"2019-07-24T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"171","oa":1,"type":"dissertation","degree_awarded":"PhD","corr_author":"1","status":"public","ddc":["570"],"month":"07","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"date_created":"2019-09-19T08:19:44Z","abstract":[{"text":"While cells of mesenchymal or epithelial origin perform their effector functions in a purely anchorage dependent manner, cells derived from the hematopoietic lineage are not committed to operate only within a specific niche. Instead, these cells are able to function autonomously of the molecular composition in a broad range of tissue compartments. By this means, cells of the hematopoietic lineage retain the capacity to disseminate into connective tissue and recirculate between organs, building the foundation for essential processes such as tissue regeneration or immune surveillance. \r\nCells of the immune system, specifically leukocytes, are extraordinarily good at performing this task. These cells are able to flexibly shift their mode of migration between an adhesion-mediated and an adhesion-independent manner, instantaneously accommodating for any changes in molecular composition of the external scaffold. The key component driving directed leukocyte migration is the chemokine receptor 7, which guides the cell along gradients of chemokine ligand. Therefore, the physical destination of migrating leukocytes is purely deterministic, i.e. given by global directional cues such as chemokine gradients. \r\nNevertheless, these cells typically reside in three-dimensional scaffolds of inhomogeneous complexity, raising the question whether cells are able to locally discriminate between multiple optional migration routes. Current literature provides evidence that leukocytes, specifically dendritic cells, do indeed probe their surrounding by virtue of multiple explorative protrusions. However, it remains enigmatic how these cells decide which one is the more favorable route to follow and what are the key players involved in performing this task. Due to the heterogeneous environment of most tissues, and the vast adaptability of migrating leukocytes, at this time it is not clear to what extent leukocytes are able to optimize their migratory strategy by adapting their level of adhesiveness. And, given the fact that leukocyte migration is characterized by branched cell shapes in combination with high migration velocities, it is reasonable to assume that these cells require fine tuned shape maintenance mechanisms that tightly coordinate protrusion and adhesion dynamics in a spatiotemporal manner. \r\nTherefore, this study aimed to elucidate how rapidly migrating leukocytes opt for an ideal migratory path while maintaining a continuous cell shape and balancing adhesive forces to efficiently navigate through complex microenvironments. \r\nThe results of this study unraveled a role for the microtubule cytoskeleton in promoting the decision making process during path finding and for the first time point towards a microtubule-mediated function in cell shape maintenance of highly ramified cells such as dendritic cells. Furthermore, we found that migrating low-adhesive leukocytes are able to instantaneously adapt to increased tensile load by engaging adhesion receptors. This response was only occurring tangential to the substrate while adhesive properties in the vertical direction were not increased. As leukocytes are primed for rapid migration velocities, these results demonstrate that leukocyte integrins are able to confer a high level of traction forces parallel to the cell membrane along the direction of migration without wasting energy in gluing the cell to the substrate. \r\nThus, the data in the here presented thesis provide new insights into the pivotal role of cytoskeletal dynamics and the mechanisms of force transduction during leukocyte migration. \r\nThereby the here presented results help to further define fundamental principles underlying leukocyte migration and open up potential therapeutic avenues of clinical relevance.\r\n","lang":"eng"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-04-25T00:00:00Z","article_processing_charge":"No","year":"2019","publication_status":"published","isi":1,"ec_funded":1,"type":"journal_article","oa":1,"page":"546-550","acknowledged_ssus":[{"_id":"SSU"}],"month":"04","publication":"Nature","status":"public","language":[{"iso":"eng"}],"intvolume":"       568","pmid":1,"date_created":"2019-04-17T06:52:28Z","abstract":[{"text":"During metazoan development, immune surveillance and cancer dissemination, cells migrate in complex three-dimensional microenvironments1,2,3. These spaces are crowded by cells and extracellular matrix, generating mazes with differently sized gaps that are typically smaller than the diameter of the migrating cell4,5. Most mesenchymal and epithelial cells and some—but not all—cancer cells actively generate their migratory path using pericellular tissue proteolysis6. By contrast, amoeboid cells such as leukocytes use non-destructive strategies of locomotion7, raising the question how these extremely fast cells navigate through dense tissues. Here we reveal that leukocytes sample their immediate vicinity for large pore sizes, and are thereby able to choose the path of least resistance. This allows them to circumnavigate local obstacles while effectively following global directional cues such as chemotactic gradients. Pore-size discrimination is facilitated by frontward positioning of the nucleus, which enables the cells to use their bulkiest compartment as a mechanical gauge. Once the nucleus and the closely associated microtubule organizing centre pass the largest pore, cytoplasmic protrusions still lingering in smaller pores are retracted. These retractions are coordinated by dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning in front of the microtubule organizing centre is a typical feature of amoeboid migration, our findings link the fundamental organization of cellular polarity to the strategy of locomotion.","lang":"eng"}],"publisher":"Springer Nature","date_updated":"2026-09-02T22:30:22Z","title":"Nuclear positioning facilitates amoeboid migration along the path of least resistance","author":[{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg","first_name":"Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz"},{"orcid":"0000-0002-2187-6656","last_name":"Kopf","first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","full_name":"Kopf, Aglaja"},{"first_name":"Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A"},{"first_name":"Ingrid","last_name":"de Vries","full_name":"de Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Driscoll, Meghan K.","first_name":"Meghan K.","last_name":"Driscoll"},{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","orcid":"0000-0001-5145-4609","first_name":"Jack"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522"},{"last_name":"Welf","first_name":"Erik S.","full_name":"Welf, Erik S."},{"full_name":"Danuser, Gaudenz","first_name":"Gaudenz","last_name":"Danuser"},{"full_name":"Fiolka, Reto","first_name":"Reto","last_name":"Fiolka"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K"}],"external_id":{"isi":["000465594200050"],"pmid":["30944468"]},"article_type":"letter_note","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14697"},{"id":"6891","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/","relation":"press_release","description":"News on IST Homepage"}]},"day":"25","_id":"6328","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/"}],"oa_version":"Submitted Version","quality_controlled":"1","project":[{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"724373","name":"Cellular Navigation Along Spatial Gradients"},{"name":"Nano-Analytics of Cellular Systems","grant_number":"W01250-B20","call_identifier":"FWF","_id":"265FAEBA-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014","_id":"25A48D24-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41586-019-1087-5","citation":{"mla":"Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” <i>Nature</i>, vol. 568, Springer Nature, 2019, pp. 546–50, doi:<a href=\"https://doi.org/10.1038/s41586-019-1087-5\">10.1038/s41586-019-1087-5</a>.","ieee":"J. Renkawitz <i>et al.</i>, “Nuclear positioning facilitates amoeboid migration along the path of least resistance,” <i>Nature</i>, vol. 568. Springer Nature, pp. 546–550, 2019.","ama":"Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid migration along the path of least resistance. <i>Nature</i>. 2019;568:546-550. doi:<a href=\"https://doi.org/10.1038/s41586-019-1087-5\">10.1038/s41586-019-1087-5</a>","ista":"Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 568, 546–550.","apa":"Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin, J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along the path of least resistance. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1087-5\">https://doi.org/10.1038/s41586-019-1087-5</a>","chicago":"Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K. Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1087-5\">https://doi.org/10.1038/s41586-019-1087-5</a>.","short":"J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin, R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550."},"scopus_import":"1","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"volume":568},{"citation":{"ieee":"N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” <i>Physical Review Letters</i>, vol. 122, no. 11. American Physical Society, 2019.","mla":"Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” <i>Physical Review Letters</i>, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">10.1103/PhysRevLett.122.114502</a>.","apa":"Agrawal, N., Choueiri, G. H., &#38; Hof, B. (2019). Transition to turbulence in particle laden flows. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">https://doi.org/10.1103/PhysRevLett.122.114502</a>","ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502.","ama":"Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. <i>Physical Review Letters</i>. 2019;122(11). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">10.1103/PhysRevLett.122.114502</a>","chicago":"Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” <i>Physical Review Letters</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">https://doi.org/10.1103/PhysRevLett.122.114502</a>.","short":"N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019)."},"doi":"10.1103/PhysRevLett.122.114502","volume":122,"department":[{"_id":"BjHo"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.06358"}],"oa_version":"Preprint","quality_controlled":"1","_id":"6189","external_id":{"pmid":["30951357"],"arxiv":["1809.06358"],"isi":["000461922000006"]},"arxiv":1,"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"related_material":{"record":[{"id":"9728","relation":"dissertation_contains","status":"public"}]},"day":"22","date_updated":"2026-09-02T22:30:23Z","title":"Transition to turbulence in particle laden flows","author":[{"last_name":"Agrawal","first_name":"Nishchal","full_name":"Agrawal, Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87"},{"id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H","last_name":"Choueiri","first_name":"George H"},{"first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"       122","language":[{"iso":"eng"}],"publisher":"American Physical Society","date_created":"2019-03-31T21:59:12Z","abstract":[{"text":"Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations.","lang":"eng"}],"pmid":1,"month":"03","status":"public","publication":"Physical Review Letters","issue":"11","oa":1,"type":"journal_article","isi":1,"article_number":"114502","date_published":"2019-03-22T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","year":"2019","publication_status":"published"},{"volume":177,"scopus_import":"1","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.cell.2019.04.015","citation":{"chicago":"Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková, and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">https://doi.org/10.1016/j.cell.2019.04.015</a>.","short":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell 177 (2019) 957–969.e13.","ieee":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml, “Re-activation of stem cell pathways for pattern restoration in plant wound healing,” <i>Cell</i>, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019.","mla":"Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” <i>Cell</i>, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">10.1016/j.cell.2019.04.015</a>.","ista":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4), 957–969.e13.","ama":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation of stem cell pathways for pattern restoration in plant wound healing. <i>Cell</i>. 2019;177(4):957-969.e13. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">10.1016/j.cell.2019.04.015</a>","apa":"Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., &#38; Friml, J. (2019). Re-activation of stem cell pathways for pattern restoration in plant wound healing. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">https://doi.org/10.1016/j.cell.2019.04.015</a>"},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"quality_controlled":"1","oa_version":"Published Version","_id":"6351","file_date_updated":"2020-07-14T12:47:28Z","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"related_material":{"record":[{"status":"public","id":"9992","relation":"dissertation_contains"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/","description":"News on IST Homepage"}]},"day":"02","external_id":{"isi":["000466843000015"],"pmid":["31051107"]},"author":[{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavá, Petra","last_name":"Marhavá","first_name":"Petra"},{"orcid":"0000-0001-8295-2926","last_name":"Hörmayer","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas"},{"full_name":"Yoshida, Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","last_name":"Yoshida","orcid":"0000-0001-6111-9353"},{"orcid":"0000-0001-5227-5741","last_name":"Marhavy","first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavy, Peter"},{"first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"date_updated":"2026-09-02T22:30:24Z","title":"Re-activation of stem cell pathways for pattern restoration in plant wound healing","publisher":"Elsevier","pmid":1,"date_created":"2019-04-28T21:59:14Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing."}],"intvolume":"       177","language":[{"iso":"eng"}],"issue":"4","acknowledged_ssus":[{"_id":"Bio"}],"month":"05","corr_author":"1","status":"public","publication":"Cell","ddc":["570"],"page":"957-969.e13","oa":1,"ec_funded":1,"isi":1,"type":"journal_article","file":[{"file_id":"6411","date_updated":"2020-07-14T12:47:28Z","creator":"dernst","file_name":"2019_Cell_Marhava.pdf","checksum":"4ceba04a96a74f5092ec3ce2c579a0c7","relation":"main_file","date_created":"2019-05-13T06:12:45Z","content_type":"application/pdf","access_level":"open_access","file_size":10272032}],"article_processing_charge":"No","year":"2019","publication_status":"published","date_published":"2019-05-02T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"01","article_type":"original","file_date_updated":"2020-07-14T12:47:45Z","related_material":{"record":[{"status":"public","id":"9992","relation":"dissertation_contains"}]},"publication_identifier":{"issn":["1369-5266"]},"external_id":{"pmid":["31585333"],"isi":["000502890600017"]},"author":[{"full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","first_name":"Lukas"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"title":"Targeted cell ablation-based insights into wound healing and restorative patterning","date_updated":"2026-09-02T22:30:24Z","volume":52,"department":[{"_id":"JiFr"}],"scopus_import":"1","doi":"10.1016/j.pbi.2019.08.006","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">https://doi.org/10.1016/j.pbi.2019.08.006</a>.","short":"L. Hörmayer, J. Friml, Current Opinion in Plant Biology 52 (2019) 124–130.","mla":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” <i>Current Opinion in Plant Biology</i>, vol. 52, Elsevier, 2019, pp. 124–30, doi:<a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">10.1016/j.pbi.2019.08.006</a>.","ieee":"L. Hörmayer and J. Friml, “Targeted cell ablation-based insights into wound healing and restorative patterning,” <i>Current Opinion in Plant Biology</i>, vol. 52. Elsevier, pp. 124–130, 2019.","ista":"Hörmayer L, Friml J. 2019. Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. 52, 124–130.","ama":"Hörmayer L, Friml J. Targeted cell ablation-based insights into wound healing and restorative patterning. <i>Current Opinion in Plant Biology</i>. 2019;52:124-130. doi:<a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">10.1016/j.pbi.2019.08.006</a>","apa":"Hörmayer, L., &#38; Friml, J. (2019). Targeted cell ablation-based insights into wound healing and restorative patterning. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">https://doi.org/10.1016/j.pbi.2019.08.006</a>"},"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Published Version","quality_controlled":"1","_id":"6943","page":"124-130","oa":1,"isi":1,"type":"journal_article","ec_funded":1,"file":[{"date_updated":"2020-07-14T12:47:45Z","file_id":"6946","file_size":1659288,"access_level":"open_access","content_type":"application/pdf","date_created":"2019-10-14T14:48:21Z","relation":"main_file","creator":"dernst","checksum":"d6fd68a6e965f1efe3f0bf2d2070a616","file_name":"2019_CurrentOpinionPlant_Hoermayer.pdf"}],"publication_status":"published","article_processing_charge":"No","year":"2019","date_published":"2019-12-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","date_created":"2019-10-14T07:00:24Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Plants as sessile organisms are constantly under attack by herbivores, rough environmental situations, or mechanical pressure. These challenges often lead to the induction of wounds or destruction of already specified and developed tissues. Additionally, wounding makes plants vulnerable to invasion by pathogens, which is why wound signalling often triggers specific defence responses. To stay competitive or, eventually, survive under these circumstances, plants need to regenerate efficiently, which in rigid, tissue migration-incompatible plant tissues requires post-embryonic patterning and organogenesis. Now, several studies used laser-assisted single cell ablation in the Arabidopsis root tip as a minimal wounding proxy. Here, we discuss their findings and put them into context of a broader spectrum of wound signalling, pathogen responses and tissue as well as organ regeneration."}],"pmid":1,"intvolume":"        52","language":[{"iso":"eng"}],"status":"public","month":"12","corr_author":"1","ddc":["580"],"publication":"Current Opinion in Plant Biology"},{"arxiv":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7258"}]},"publication_identifier":{"issn":["0098-2202"],"eissn":["1528-901X"]},"article_type":"original","day":"01","external_id":{"isi":["000487748600005"],"arxiv":["1809.07625"]},"author":[{"id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","full_name":"Kühnen, Jakob","first_name":"Jakob","orcid":"0000-0003-4312-0179","last_name":"Kühnen"},{"orcid":"0000-0001-5227-4271","last_name":"Scarselli","first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","full_name":"Scarselli, Davide"},{"orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"date_updated":"2026-09-02T22:30:25Z","title":"Relaminarization of pipe flow by means of 3D-printed shaped honeycombs","volume":141,"scopus_import":"1","department":[{"_id":"BjHo"}],"doi":"10.1115/1.4043494","citation":{"mla":"Kühnen, Jakob, et al. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” <i>Journal of Fluids Engineering</i>, vol. 141, no. 11, 111105, ASME, 2019, doi:<a href=\"https://doi.org/10.1115/1.4043494\">10.1115/1.4043494</a>.","ieee":"J. Kühnen, D. Scarselli, and B. Hof, “Relaminarization of pipe flow by means of 3D-printed shaped honeycombs,” <i>Journal of Fluids Engineering</i>, vol. 141, no. 11. ASME, 2019.","ama":"Kühnen J, Scarselli D, Hof B. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. <i>Journal of Fluids Engineering</i>. 2019;141(11). doi:<a href=\"https://doi.org/10.1115/1.4043494\">10.1115/1.4043494</a>","apa":"Kühnen, J., Scarselli, D., &#38; Hof, B. (2019). Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. <i>Journal of Fluids Engineering</i>. ASME. <a href=\"https://doi.org/10.1115/1.4043494\">https://doi.org/10.1115/1.4043494</a>","ista":"Kühnen J, Scarselli D, Hof B. 2019. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 141(11), 111105.","chicago":"Kühnen, Jakob, Davide Scarselli, and Björn Hof. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” <i>Journal of Fluids Engineering</i>. ASME, 2019. <a href=\"https://doi.org/10.1115/1.4043494\">https://doi.org/10.1115/1.4043494</a>.","short":"J. Kühnen, D. Scarselli, B. Hof, Journal of Fluids Engineering 141 (2019)."},"project":[{"call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","grant_number":"306589"}],"main_file_link":[{"url":"https://arxiv.org/abs/1809.07625","open_access":"1"}],"quality_controlled":"1","oa_version":"Preprint","_id":"6486","oa":1,"ec_funded":1,"isi":1,"type":"journal_article","article_processing_charge":"No","year":"2019","publication_status":"published","article_number":"111105","date_published":"2019-11-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ASME","abstract":[{"lang":"eng","text":"Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow."}],"date_created":"2019-05-26T21:59:13Z","intvolume":"       141","language":[{"iso":"eng"}],"issue":"11","acknowledged_ssus":[{"_id":"M-Shop"}],"publication":"Journal of Fluids Engineering","month":"11","status":"public"},{"_id":"6228","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1807.05357","open_access":"1"}],"project":[{"call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","grant_number":"306589"},{"_id":"25104D44-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"737549","name":"Eliminating turbulence in oil pipelines"}],"citation":{"chicago":"Scarselli, Davide, Jakob Kühnen, and Björn Hof. “Relaminarising Pipe Flow by Wall Movement.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2019. <a href=\"https://doi.org/10.1017/jfm.2019.191\">https://doi.org/10.1017/jfm.2019.191</a>.","short":"D. Scarselli, J. Kühnen, B. Hof, Journal of Fluid Mechanics 867 (2019) 934–948.","mla":"Scarselli, Davide, et al. “Relaminarising Pipe Flow by Wall Movement.” <i>Journal of Fluid Mechanics</i>, vol. 867, Cambridge University Press, 2019, pp. 934–48, doi:<a href=\"https://doi.org/10.1017/jfm.2019.191\">10.1017/jfm.2019.191</a>.","ieee":"D. Scarselli, J. Kühnen, and B. Hof, “Relaminarising pipe flow by wall movement,” <i>Journal of Fluid Mechanics</i>, vol. 867. Cambridge University Press, pp. 934–948, 2019.","apa":"Scarselli, D., Kühnen, J., &#38; Hof, B. (2019). Relaminarising pipe flow by wall movement. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2019.191\">https://doi.org/10.1017/jfm.2019.191</a>","ama":"Scarselli D, Kühnen J, Hof B. Relaminarising pipe flow by wall movement. <i>Journal of Fluid Mechanics</i>. 2019;867:934-948. doi:<a href=\"https://doi.org/10.1017/jfm.2019.191\">10.1017/jfm.2019.191</a>","ista":"Scarselli D, Kühnen J, Hof B. 2019. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 867, 934–948."},"doi":"10.1017/jfm.2019.191","scopus_import":"1","department":[{"_id":"BjHo"}],"volume":867,"title":"Relaminarising pipe flow by wall movement","date_updated":"2026-09-02T22:30:25Z","author":[{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271","last_name":"Scarselli","first_name":"Davide"},{"full_name":"Kühnen, Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","last_name":"Kühnen","orcid":"0000-0003-4312-0179","first_name":"Jakob"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754"}],"external_id":{"isi":["000462606100001"],"arxiv":["1807.05357"]},"day":"25","related_material":{"record":[{"status":"public","id":"7258","relation":"dissertation_contains"}],"link":[{"url":"https://doi.org/10.1017/jfm.2019.191","relation":"supplementary_material"}]},"publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"arxiv":1,"month":"05","status":"public","publication":"Journal of Fluid Mechanics","language":[{"iso":"eng"}],"intvolume":"       867","abstract":[{"lang":"eng","text":"Following  the  recent  observation  that  turbulent  pipe  flow  can  be  relaminarised  bya  relatively  simple  modification  of  the  mean  velocity  profile,  we  here  carry  out  aquantitative  experimental  investigation  of  this  phenomenon.  Our  study  confirms  thata  flat  velocity  profile  leads  to  a  collapse  of  turbulence  and  in  order  to  achieve  theblunted  profile  shape,  we  employ  a  moving  pipe  segment  that  is  briefly  and  rapidlyshifted  in  the  streamwise  direction.  The  relaminarisation  threshold  and  the  minimumshift  length  and  speeds  are  determined  as  a  function  of  Reynolds  number.  Althoughturbulence  is  still  active  after  the  acceleration  phase,  the  modulated  profile  possessesa  severely  decreased  lift-up  potential  as  measured  by  transient  growth.  As  shown,this  results  in  an  exponential  decay  of  fluctuations  and  the  flow  relaminarises.  Whilethis  method  can  be  easily  applied  at  low  to  moderate  flow  speeds,  the  minimumstreamwise  length  over  which  the  acceleration  needs  to  act  increases  linearly  with  theReynolds  number."}],"date_created":"2019-04-07T21:59:14Z","publisher":"Cambridge University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-05-25T00:00:00Z","publication_status":"published","year":"2019","article_processing_charge":"No","type":"journal_article","isi":1,"ec_funded":1,"oa":1,"page":"934-948"},{"date_updated":"2026-09-02T22:30:25Z","title":"The entorhinal cognitive map is attracted to goals","author":[{"first_name":"Charlotte N.","orcid":"0000-0001-7237-5109","last_name":"Boccara","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","full_name":"Boccara, Charlotte N."},{"last_name":"Nardin","orcid":"0000-0001-8849-6570","first_name":"Michele","full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stella","orcid":"0000-0001-9439-3148","first_name":"Federico","full_name":"Stella, Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87"},{"last_name":"O'Neill","first_name":"Joseph","full_name":"O'Neill, Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L"}],"external_id":{"isi":["000462738000034"]},"related_material":{"record":[{"id":"6062","relation":"popular_science","status":"public"},{"id":"11932","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/grid-cells-create-treasure-map-in-rat-brain/","relation":"press_release"}]},"article_type":"original","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"file_date_updated":"2020-07-14T12:47:23Z","day":"29","_id":"6194","quality_controlled":"1","oa_version":"Submitted Version","project":[{"call_identifier":"FP7","_id":"257A4776-B435-11E9-9278-68D0E5697425","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"doi":"10.1126/science.aav4837","citation":{"short":"C.N. Boccara, M. Nardin, F. Stella, J. O’Neill, J.L. Csicsvari, Science 363 (2019) 1443–1447.","chicago":"Boccara, Charlotte N., Michele Nardin, Federico Stella, Joseph O’Neill, and Jozsef L Csicsvari. “The Entorhinal Cognitive Map Is Attracted to Goals.” <i>Science</i>. American Association for the Advancement of Science, 2019. <a href=\"https://doi.org/10.1126/science.aav4837\">https://doi.org/10.1126/science.aav4837</a>.","ama":"Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. The entorhinal cognitive map is attracted to goals. <i>Science</i>. 2019;363(6434):1443-1447. doi:<a href=\"https://doi.org/10.1126/science.aav4837\">10.1126/science.aav4837</a>","ista":"Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. 2019. The entorhinal cognitive map is attracted to goals. Science. 363(6434), 1443–1447.","apa":"Boccara, C. N., Nardin, M., Stella, F., O’Neill, J., &#38; Csicsvari, J. L. (2019). The entorhinal cognitive map is attracted to goals. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aav4837\">https://doi.org/10.1126/science.aav4837</a>","ieee":"C. N. Boccara, M. Nardin, F. Stella, J. O’Neill, and J. L. Csicsvari, “The entorhinal cognitive map is attracted to goals,” <i>Science</i>, vol. 363, no. 6434. American Association for the Advancement of Science, pp. 1443–1447, 2019.","mla":"Boccara, Charlotte N., et al. “The Entorhinal Cognitive Map Is Attracted to Goals.” <i>Science</i>, vol. 363, no. 6434, American Association for the Advancement of Science, 2019, pp. 1443–47, doi:<a href=\"https://doi.org/10.1126/science.aav4837\">10.1126/science.aav4837</a>."},"department":[{"_id":"JoCs"}],"scopus_import":"1","volume":363,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-03-29T00:00:00Z","article_processing_charge":"No","year":"2019","publication_status":"published","file":[{"file_size":9045923,"access_level":"open_access","content_type":"application/pdf","date_created":"2020-05-14T09:11:10Z","relation":"main_file","file_name":"2019_Science_Boccara.pdf","checksum":"5e6b16742cde10a560cfaf2130764da1","creator":"dernst","date_updated":"2020-07-14T12:47:23Z","file_id":"7826"}],"type":"journal_article","ec_funded":1,"isi":1,"oa":1,"page":"1443-1447","month":"03","publication":"Science","ddc":["570"],"status":"public","issue":"6434","language":[{"iso":"eng"}],"intvolume":"       363","has_accepted_license":"1","abstract":[{"text":"Grid cells with their rigid hexagonal firing fields are thought to provide an invariant metric to the hippocampal cognitive map, yet environmental geometrical features have recently been shown to distort the grid structure. Given that the hippocampal role goes beyond space, we tested the influence of nonspatial information on the grid organization. We trained rats to daily learn three new reward locations on a cheeseboard maze while recording from the medial entorhinal cortex and the hippocampal CA1 region. Many grid fields moved toward goal location, leading to long-lasting deformations of the entorhinal map. Therefore, distortions in the grid structure contribute to goal representation during both learning and recall, which demonstrates that grid cells participate in mnemonic coding and do not merely provide a simple metric of space.","lang":"eng"}],"date_created":"2019-04-04T08:39:30Z","publisher":"American Association for the Advancement of Science"},{"month":"06","publication":"Nature","status":"public","acknowledged_ssus":[{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"intvolume":"       570","date_created":"2019-07-07T21:59:20Z","abstract":[{"text":"Mechanical systems facilitate the development of a hybrid quantum technology comprising electrical, optical, atomic and acoustic degrees of freedom1, and entanglement is essential to realize quantum-enabled devices. Continuous-variable entangled fields—known as Einstein–Podolsky–Rosen (EPR) states—are spatially separated two-mode squeezed states that can be used for quantum teleportation and quantum communication2. In the optical domain, EPR states are typically generated using nondegenerate optical amplifiers3, and at microwave frequencies Josephson circuits can serve as a nonlinear medium4,5,6. An outstanding goal is to deterministically generate and distribute entangled states with a mechanical oscillator, which requires a carefully arranged balance between excitation, cooling and dissipation in an ultralow noise environment. Here we observe stationary emission of path-entangled microwave radiation from a parametrically driven 30-micrometre-long silicon nanostring oscillator, squeezing the joint field operators of two thermal modes by 3.40 decibels below the vacuum level. The motion of this micromechanical system correlates up to 50 photons per second per hertz, giving rise to a quantum discord that is robust with respect to microwave noise7. Such generalized quantum correlations of separable states are important for quantum-enhanced detection8 and provide direct evidence of the non-classical nature of the mechanical oscillator without directly measuring its state9. This noninvasive measurement scheme allows to infer information about otherwise inaccessible objects, with potential implications for sensing, open-system dynamics and fundamental tests of quantum gravity. In the future, similar on-chip devices could be used to entangle subsystems on very different energy scales, such as microwave and optical photons.","lang":"eng"}],"publisher":"Nature Publishing Group","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-06-27T00:00:00Z","publication_status":"published","article_processing_charge":"No","year":"2019","ec_funded":1,"isi":1,"type":"journal_article","oa":1,"page":"480-483","_id":"6609","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.05865"}],"project":[{"grant_number":"732894","name":"Hybrid Optomechanical Technologies","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"citation":{"chicago":"Barzanjeh, Shabir, Elena Redchenko, Matilda Peruzzo, Matthias Wulf, Dylan Lewis, Georg M Arnold, and Johannes M Fink. “Stationary Entangled Radiation from Micromechanical Motion.” <i>Nature</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1320-2\">https://doi.org/10.1038/s41586-019-1320-2</a>.","short":"S. Barzanjeh, E. Redchenko, M. Peruzzo, M. Wulf, D. Lewis, G.M. Arnold, J.M. Fink, Nature 570 (2019) 480–483.","ieee":"S. Barzanjeh <i>et al.</i>, “Stationary entangled radiation from micromechanical motion,” <i>Nature</i>, vol. 570. Nature Publishing Group, pp. 480–483, 2019.","mla":"Barzanjeh, Shabir, et al. “Stationary Entangled Radiation from Micromechanical Motion.” <i>Nature</i>, vol. 570, Nature Publishing Group, 2019, pp. 480–83, doi:<a href=\"https://doi.org/10.1038/s41586-019-1320-2\">10.1038/s41586-019-1320-2</a>.","ama":"Barzanjeh S, Redchenko E, Peruzzo M, et al. Stationary entangled radiation from micromechanical motion. <i>Nature</i>. 2019;570:480-483. doi:<a href=\"https://doi.org/10.1038/s41586-019-1320-2\">10.1038/s41586-019-1320-2</a>","ista":"Barzanjeh S, Redchenko E, Peruzzo M, Wulf M, Lewis D, Arnold GM, Fink JM. 2019. Stationary entangled radiation from micromechanical motion. Nature. 570, 480–483.","apa":"Barzanjeh, S., Redchenko, E., Peruzzo, M., Wulf, M., Lewis, D., Arnold, G. M., &#38; Fink, J. M. (2019). Stationary entangled radiation from micromechanical motion. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-019-1320-2\">https://doi.org/10.1038/s41586-019-1320-2</a>"},"doi":"10.1038/s41586-019-1320-2","department":[{"_id":"JoFi"}],"scopus_import":"1","volume":570,"title":"Stationary entangled radiation from micromechanical motion","date_updated":"2026-09-02T22:30:33Z","author":[{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh","first_name":"Shabir"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena","first_name":"Elena","last_name":"Redchenko"},{"full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","orcid":"0000-0002-3415-4628","first_name":"Matilda"},{"first_name":"Matthias","orcid":"0000-0001-6613-1378","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","full_name":"Wulf, Matthias"},{"last_name":"Lewis","first_name":"Dylan","full_name":"Lewis, Dylan"},{"orcid":"0000-0003-1397-7876","last_name":"Arnold","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M"},{"last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000472860000042"],"arxiv":["1809.05865"]},"day":"27","related_material":{"record":[{"id":"18871","relation":"dissertation_contains","status":"public"}]},"arxiv":1}]