[{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"date_updated":"2020-07-14T12:47:59Z","content_type":"application/pdf","file_name":"2020_eLife_Kierdorf.pdf","date_created":"2020-02-10T08:53:16Z","checksum":"3a072be843f416c7a7d532a51dc0addb","file_size":4959933,"file_id":"7470","creator":"dernst","relation":"main_file","access_level":"open_access"}],"oa":1,"publication_identifier":{"eissn":["2050084X"]},"date_published":"2020-01-20T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"month":"01","article_number":"e51595","oa_version":"Published Version","project":[{"grant_number":"P29638","name":"Drosophila TNFa´s Funktion in Immunzellen","_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"publication":"eLife","has_accepted_license":"1","ddc":["570"],"volume":9,"abstract":[{"lang":"eng","text":"Unpaired ligands are secreted signals that act via a GP130-like receptor, domeless, to activate JAK/STAT signalling in Drosophila. Like many mammalian cytokines, unpaireds can be activated by infection and other stresses and can promote insulin resistance in target tissues. However, the importance of this effect in non-inflammatory physiology is unknown. Here, we identify a requirement for unpaired-JAK signalling as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show basal JAK-STAT signalling activity in the absence of any immune challenge. Plasmatocytes (Drosophila macrophages) are an important source of this tonic signal. Loss of the dome receptor on adult muscles significantly reduces lifespan and causes local and systemic metabolic pathology. These pathologies result from hyperactivation of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine signal that must be received in muscle to control AKT activity and metabolic homeostasis."}],"doi":"10.7554/eLife.51595","day":"20","isi":1,"external_id":{"isi":["000512304800001"]},"date_updated":"2023-08-17T14:36:39Z","year":"2020","citation":{"apa":"Kierdorf, K., Hersperger, F., Sharrock, J., Vincent, C. M., Ustaoglu, P., Dou, J., … Dionne, M. S. (2020). Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.51595\">https://doi.org/10.7554/eLife.51595</a>","ama":"Kierdorf K, Hersperger F, Sharrock J, et al. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.51595\">10.7554/eLife.51595</a>","ieee":"K. Kierdorf <i>et al.</i>, “Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","chicago":"Kierdorf, Katrin, Fabian Hersperger, Jessica Sharrock, Crystal M. Vincent, Pinar Ustaoglu, Jiawen Dou, Attila György, Olaf Groß, Daria E Siekhaus, and Marc S. Dionne. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.51595\">https://doi.org/10.7554/eLife.51595</a>.","short":"K. Kierdorf, F. Hersperger, J. Sharrock, C.M. Vincent, P. Ustaoglu, J. Dou, A. György, O. Groß, D.E. Siekhaus, M.S. Dionne, ELife 9 (2020).","mla":"Kierdorf, Katrin, et al. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” <i>ELife</i>, vol. 9, e51595, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.51595\">10.7554/eLife.51595</a>.","ista":"Kierdorf K, Hersperger F, Sharrock J, Vincent CM, Ustaoglu P, Dou J, György A, Groß O, Siekhaus DE, Dionne MS. 2020. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. eLife. 9, e51595."},"article_type":"original","publisher":"eLife Sciences Publications","file_date_updated":"2020-07-14T12:47:59Z","quality_controlled":"1","title":"Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila","intvolume":"         9","publication_status":"published","article_processing_charge":"No","department":[{"_id":"DaSi"}],"date_created":"2020-02-09T23:00:51Z","author":[{"last_name":"Kierdorf","first_name":"Katrin","full_name":"Kierdorf, Katrin"},{"full_name":"Hersperger, Fabian","first_name":"Fabian","last_name":"Hersperger"},{"full_name":"Sharrock, Jessica","last_name":"Sharrock","first_name":"Jessica"},{"full_name":"Vincent, Crystal M.","last_name":"Vincent","first_name":"Crystal M."},{"full_name":"Ustaoglu, Pinar","last_name":"Ustaoglu","first_name":"Pinar"},{"first_name":"Jiawen","last_name":"Dou","full_name":"Dou, Jiawen"},{"id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1819-198X","full_name":"György, Attila","first_name":"Attila","last_name":"György"},{"full_name":"Groß, Olaf","first_name":"Olaf","last_name":"Groß"},{"first_name":"Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dionne, Marc S.","last_name":"Dionne","first_name":"Marc S."}],"_id":"7466","scopus_import":"1"},{"volume":3,"acknowledgement":"This work was supported by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP (ENE2016-77798-C4-3-R) and the Generalitat de Catalunya through the project 2017SGR1246. D.C. acknowledges support from Universidad Nacional de Colombia. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 754411. M.I. acknowledges financial support from IST Austria.","ddc":["540"],"date_updated":"2023-08-17T14:36:16Z","citation":{"ista":"Cadavid D, Ortega S, Illera S, Liu Y, Ibáñez M, Shavel A, Zhang Y, Li M, López AM, Noriega G, Durá OJ, López De La Torre MA, Prades JD, Cabot A. 2020. Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. ACS Applied Energy Materials. 3(3), 2120–2129.","mla":"Cadavid, Doris, et al. “Influence of the Ligand Stripping on the Transport Properties of Nanoparticle-Based PbSe Nanomaterials.” <i>ACS Applied Energy Materials</i>, vol. 3, no. 3, American Chemical Society, 2020, pp. 2120–29, doi:<a href=\"https://doi.org/10.1021/acsaem.9b02137\">10.1021/acsaem.9b02137</a>.","short":"D. Cadavid, S. Ortega, S. Illera, Y. Liu, M. Ibáñez, A. Shavel, Y. Zhang, M. Li, A.M. López, G. Noriega, O.J. Durá, M.A. López De La Torre, J.D. Prades, A. Cabot, ACS Applied Energy Materials 3 (2020) 2120–2129.","chicago":"Cadavid, Doris, Silvia Ortega, Sergio Illera, Yu Liu, Maria Ibáñez, Alexey Shavel, Yu Zhang, et al. “Influence of the Ligand Stripping on the Transport Properties of Nanoparticle-Based PbSe Nanomaterials.” <i>ACS Applied Energy Materials</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acsaem.9b02137\">https://doi.org/10.1021/acsaem.9b02137</a>.","ieee":"D. Cadavid <i>et al.</i>, “Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials,” <i>ACS Applied Energy Materials</i>, vol. 3, no. 3. American Chemical Society, pp. 2120–2129, 2020.","ama":"Cadavid D, Ortega S, Illera S, et al. Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. <i>ACS Applied Energy Materials</i>. 2020;3(3):2120-2129. doi:<a href=\"https://doi.org/10.1021/acsaem.9b02137\">10.1021/acsaem.9b02137</a>","apa":"Cadavid, D., Ortega, S., Illera, S., Liu, Y., Ibáñez, M., Shavel, A., … Cabot, A. (2020). Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. <i>ACS Applied Energy Materials</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsaem.9b02137\">https://doi.org/10.1021/acsaem.9b02137</a>"},"year":"2020","isi":1,"external_id":{"isi":["000526598300012"]},"doi":"10.1021/acsaem.9b02137","day":"01","abstract":[{"text":"Nanomaterials produced from the bottom-up assembly of nanocrystals may incorporate ∼1020–1021 cm–3 not fully coordinated surface atoms, i.e., ∼1020–1021 cm–3 potential donor or acceptor states that can strongly affect transport properties. Therefore, to exploit the full potential of nanocrystal building blocks to produce functional nanomaterials and thin films, a proper control of their surface chemistry is required. Here, we analyze how the ligand stripping procedure influences the charge and heat transport properties of sintered PbSe nanomaterials produced from the bottom-up assembly of colloidal PbSe nanocrystals. First, we show that the removal of the native organic ligands by thermal decomposition in an inert atmosphere leaves relatively large amounts of carbon at the crystal interfaces. This carbon blocks crystal growth during consolidation and at the same time hampers charge and heat transport through the final nanomaterial. Second, we demonstrate that, by stripping ligands from the nanocrystal surface before consolidation, nanomaterials with larger crystal domains, lower porosity, and higher charge carrier concentrations are obtained, thus resulting in nanomaterials with higher electrical and thermal conductivities. In addition, the ligand displacement leaves the nanocrystal surface unprotected, facilitating oxidation and chalcogen evaporation. The influence of the ligand displacement on the nanomaterial charge transport properties is rationalized here using a two-band model based on the standard Boltzmann transport equation with the relaxation time approximation. Finally, we present an application of the produced functional nanomaterials by modeling, fabricating, and testing a simple PbSe-based thermoelectric device with a ring geometry.","lang":"eng"}],"page":"2120-2129","quality_controlled":"1","ec_funded":1,"file_date_updated":"2022-08-23T08:34:17Z","publisher":"American Chemical Society","article_type":"original","_id":"7467","scopus_import":"1","author":[{"full_name":"Cadavid, Doris","last_name":"Cadavid","first_name":"Doris"},{"full_name":"Ortega, Silvia","first_name":"Silvia","last_name":"Ortega"},{"full_name":"Illera, Sergio","last_name":"Illera","first_name":"Sergio"},{"first_name":"Yu","last_name":"Liu","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shavel, Alexey","last_name":"Shavel","first_name":"Alexey"},{"last_name":"Zhang","first_name":"Yu","full_name":"Zhang, Yu"},{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"full_name":"López, Antonio M.","last_name":"López","first_name":"Antonio M."},{"full_name":"Noriega, Germán","first_name":"Germán","last_name":"Noriega"},{"full_name":"Durá, Oscar Juan","last_name":"Durá","first_name":"Oscar Juan"},{"full_name":"López De La Torre, M. A.","last_name":"López De La Torre","first_name":"M. A."},{"last_name":"Prades","first_name":"Joan Daniel","full_name":"Prades, Joan Daniel"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"issue":"3","publication_status":"published","department":[{"_id":"MaIb"}],"date_created":"2020-02-09T23:00:52Z","article_processing_charge":"No","title":"Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials","intvolume":"         3","file":[{"content_type":"application/pdf","file_name":"2020_ACSAppliedEnergyMat_Cadavid.pdf","date_updated":"2022-08-23T08:34:17Z","checksum":"f23be731a766a480c77c962c1380315c","file_size":6423548,"date_created":"2022-08-23T08:34:17Z","creator":"dernst","file_id":"11942","success":1,"access_level":"open_access","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2020-03-01T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["2574-0962"]},"oa":1,"language":[{"iso":"eng"}],"publication":"ACS Applied Energy Materials","has_accepted_license":"1","oa_version":"Submitted Version","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"month":"03"},{"title":"Replay of behavioral sequences in the medial prefrontal cortex during rule switching","intvolume":"       106","publication_status":"published","article_processing_charge":"No","department":[{"_id":"JoCs"}],"date_created":"2020-02-10T15:45:48Z","author":[{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola","last_name":"Käfer","full_name":"Käfer, Karola"},{"first_name":"Michele","last_name":"Nardin","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"id":"3EA859AE-F248-11E8-B48F-1D18A9856A87","last_name":"Blahna","first_name":"Karel","full_name":"Blahna, Karel"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L"}],"issue":"1","_id":"7472","pmid":1,"scopus_import":"1","article_type":"original","publisher":"Elsevier","page":"P154-165.e6","quality_controlled":"1","ec_funded":1,"abstract":[{"text":"Temporally organized reactivation of experiences during awake immobility periods is thought to underlie cognitive processes like planning and evaluation. While replay of trajectories is well established for the hippocampus, it is unclear whether the medial prefrontal cortex (mPFC) can reactivate sequential behavioral experiences in the awake state to support task execution. We simultaneously recorded from hippocampal and mPFC principal neurons in rats performing a mPFC-dependent rule-switching task on a plus maze. We found that mPFC neuronal activity encoded relative positions between the start and goal. During awake immobility periods, the mPFC replayed temporally organized sequences of these generalized positions, resembling entire spatial trajectories. The occurrence of mPFC trajectory replay positively correlated with rule-switching performance. However, hippocampal and mPFC trajectory replay occurred independently, indicating different functions. These results demonstrate that the mPFC can replay ordered activity patterns representing generalized locations and suggest that mPFC replay might have a role in flexible behavior.","lang":"eng"}],"doi":"10.1016/j.neuron.2020.01.015","day":"08","isi":1,"external_id":{"pmid":["32032512"],"isi":["000525319300016"]},"date_updated":"2023-08-17T14:38:02Z","citation":{"chicago":"Käfer, Karola, Michele Nardin, Karel Blahna, and Jozsef L Csicsvari. “Replay of Behavioral Sequences in the Medial Prefrontal Cortex during Rule Switching.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">https://doi.org/10.1016/j.neuron.2020.01.015</a>.","ieee":"K. Käfer, M. Nardin, K. Blahna, and J. L. Csicsvari, “Replay of behavioral sequences in the medial prefrontal cortex during rule switching,” <i>Neuron</i>, vol. 106, no. 1. Elsevier, p. P154–165.e6, 2020.","apa":"Käfer, K., Nardin, M., Blahna, K., &#38; Csicsvari, J. L. (2020). Replay of behavioral sequences in the medial prefrontal cortex during rule switching. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">https://doi.org/10.1016/j.neuron.2020.01.015</a>","ama":"Käfer K, Nardin M, Blahna K, Csicsvari JL. Replay of behavioral sequences in the medial prefrontal cortex during rule switching. <i>Neuron</i>. 2020;106(1):P154-165.e6. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">10.1016/j.neuron.2020.01.015</a>","ista":"Käfer K, Nardin M, Blahna K, Csicsvari JL. 2020. Replay of behavioral sequences in the medial prefrontal cortex during rule switching. Neuron. 106(1), P154–165.e6.","mla":"Käfer, Karola, et al. “Replay of Behavioral Sequences in the Medial Prefrontal Cortex during Rule Switching.” <i>Neuron</i>, vol. 106, no. 1, Elsevier, 2020, p. P154–165.e6, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">10.1016/j.neuron.2020.01.015</a>.","short":"K. Käfer, M. Nardin, K. Blahna, J.L. Csicsvari, Neuron 106 (2020) P154–165.e6."},"year":"2020","acknowledgement":"We thank Todor Asenov and Thomas Menner from the Machine Shop for the drive design and production, Hugo Malagon-Vina for assistance in maze automatization, Jago Wallenschus for taking the images of the histology, and Federico Stella and Juan Felipe Ramirez-Villegas for comments on an earlier version of the manuscript. This work was supported by the EU-FP7 MC-ITN IN-SENS (grant 607616 ).","volume":106,"month":"04","acknowledged_ssus":[{"_id":"M-Shop"}],"oa_version":"Published Version","project":[{"name":"Inter-and intracellular signalling in schizophrenia","grant_number":"607616","call_identifier":"FP7","_id":"257BBB4C-B435-11E9-9278-68D0E5697425"}],"publication":"Neuron","language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"issn":["0896-6273"]},"date_published":"2020-04-08T00:00:00Z","type":"journal_article","related_material":{"link":[{"url":"https://ist.ac.at/en/news/this-brain-area-helps-us-decide/","description":"News on IST Homepage","relation":"press_release"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2020.01.015","open_access":"1"}]},{"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/"}],"record":[{"id":"11196","relation":"dissertation_contains","status":"public"}]},"file":[{"access_level":"open_access","relation":"main_file","success":1,"file_id":"8778","creator":"dernst","date_created":"2020-11-20T08:58:53Z","checksum":"3582664addf26859e86ac5bec3e01416","file_size":9712957,"date_updated":"2020-11-20T08:58:53Z","file_name":"2020_Neuron_BorgesMerjane.pdf","content_type":"application/pdf"}],"oa":1,"publication_identifier":{"issn":["0896-6273"]},"date_published":"2020-03-18T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"language":[{"iso":"eng"}],"month":"03","oa_version":"Published Version","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","grant_number":"708497"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Zellkommunikation in Gesundheit und Krankheit","grant_number":"W01205","call_identifier":"FWF","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425"}],"publication":"Neuron","has_accepted_license":"1","ddc":["570"],"volume":105,"acknowledgement":"This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement No. 692692 and Marie Sklodowska-Curie 708497) and from Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27 Wittgenstein award and DK W1205-B09). We thank Johann Danzl and Ryuichi Shigemoto for critically reading the manuscript; Walter Kaufmann, Daniel Gutl, and Vanessa Zheden for extensive EM training, advice, and experimental assistance; Benjamin Suter for substantial help with light stimulation, ImageJ plugins for analysis, and manuscript editing; Florian Marr and Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; Julia König and Paul Wurzinger (Leica Microsystems) for helpful technical discussions; and Taija Makinen for providing the Prox1-CreERT2 mouse line.","abstract":[{"text":"How structural and functional properties of synapses relate to each other is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms of synaptic transmission, and electron microscopy (EM) has provided insight into morphological properties of synapses. Here we describe an enhanced method for functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure freezing. We demonstrate that the improved method can be applied to intact networks in acute brain slices and organotypic slice cultures from mice. As a proof of concept, we probed vesicle pool changes during synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked vesicle pool and the functionally defined readily releasable pool and provide evidence of fast endocytosis at this synapse. Functional EM with acute slices and slice cultures has the potential to reveal the structural and functional mechanisms of transmission in intact, genetically perturbed, and disease-affected synapses.","lang":"eng"}],"doi":"10.1016/j.neuron.2019.12.022","day":"18","isi":1,"external_id":{"pmid":["31928842"],"isi":["000520854700008"]},"date_updated":"2024-03-25T23:30:04Z","citation":{"apa":"Borges Merjane, C., Kim, O., &#38; Jonas, P. M. (2020). Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">https://doi.org/10.1016/j.neuron.2019.12.022</a>","ama":"Borges Merjane C, Kim O, Jonas PM. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. <i>Neuron</i>. 2020;105:992-1006. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">10.1016/j.neuron.2019.12.022</a>","ieee":"C. Borges Merjane, O. Kim, and P. M. Jonas, “Functional electron microscopy (‘Flash and Freeze’) of identified cortical synapses in acute brain slices,” <i>Neuron</i>, vol. 105. Elsevier, pp. 992–1006, 2020.","chicago":"Borges Merjane, Carolina, Olena Kim, and Peter M Jonas. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">https://doi.org/10.1016/j.neuron.2019.12.022</a>.","short":"C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006.","mla":"Borges Merjane, Carolina, et al. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” <i>Neuron</i>, vol. 105, Elsevier, 2020, pp. 992–1006, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">10.1016/j.neuron.2019.12.022</a>.","ista":"Borges Merjane C, Kim O, Jonas PM. 2020. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 105, 992–1006."},"year":"2020","article_type":"original","publisher":"Elsevier","file_date_updated":"2020-11-20T08:58:53Z","page":"992-1006","quality_controlled":"1","ec_funded":1,"title":"Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices","intvolume":"       105","publication_status":"published","department":[{"_id":"PeJo"}],"date_created":"2020-02-10T15:59:45Z","article_processing_charge":"No","author":[{"id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","first_name":"Carolina","full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X"},{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","last_name":"Kim","full_name":"Kim, Olena"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"_id":"7473","pmid":1,"scopus_import":"1"},{"conference":{"start_date":"2020-02-19","name":"AHPC: Austrian High-Performance-Computing Meeting","end_date":"2020-02-21","location":"Klosterneuburg, Austria"},"language":[{"iso":"eng"}],"oa_version":"Published Version","month":"02","has_accepted_license":"1","file":[{"relation":"main_file","access_level":"open_access","file_id":"7504","creator":"schloegl","date_created":"2020-02-19T06:53:38Z","checksum":"49798edb9e57bbd6be18362d1d7b18a9","file_size":90899507,"date_updated":"2020-07-14T12:47:59Z","content_type":"application/pdf","file_name":"BOOKLET_AHPC2020.final.pdf"}],"place":"Klosterneuburg, Austria","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["978-3-99078-004-6"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"book_editor","date_published":"2020-02-19T00:00:00Z","editor":[{"last_name":"Schlögl","first_name":"Alois","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","last_name":"Kiss","first_name":"Janos","full_name":"Kiss, Janos"},{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","full_name":"Elefante, Stefano","last_name":"Elefante","first_name":"Stefano"}],"publisher":"IST Austria","quality_controlled":"1","page":"72","file_date_updated":"2020-07-14T12:47:59Z","article_processing_charge":"No","department":[{"_id":"ScienComp"}],"date_created":"2020-02-11T07:59:04Z","publication_status":"published","title":"Austrian High-Performance-Computing meeting (AHPC2020)","_id":"7474","ddc":["000"],"day":"19","doi":"10.15479/AT:ISTA:7474","abstract":[{"lang":"eng","text":"This booklet is a collection of abstracts presented at the AHPC conference."}],"citation":{"mla":"Schlögl, Alois, et al., editors. <i>Austrian High-Performance-Computing Meeting (AHPC2020)</i>. IST Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7474\">10.15479/AT:ISTA:7474</a>.","short":"A. Schlögl, J. Kiss, S. Elefante, eds., Austrian High-Performance-Computing Meeting (AHPC2020), IST Austria, Klosterneuburg, Austria, 2020.","ista":"Schlögl A, Kiss J, Elefante S eds. 2020. Austrian High-Performance-Computing meeting (AHPC2020), Klosterneuburg, Austria: IST Austria, 72p.","ama":"Schlögl A, Kiss J, Elefante S, eds. <i>Austrian High-Performance-Computing Meeting (AHPC2020)</i>. Klosterneuburg, Austria: IST Austria; 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7474\">10.15479/AT:ISTA:7474</a>","apa":"Schlögl, A., Kiss, J., &#38; Elefante, S. (Eds.). (2020). <i>Austrian High-Performance-Computing meeting (AHPC2020)</i>. Presented at the AHPC: Austrian High-Performance-Computing Meeting, Klosterneuburg, Austria: IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7474\">https://doi.org/10.15479/AT:ISTA:7474</a>","chicago":"Schlögl, Alois, Janos Kiss, and Stefano Elefante, eds. <i>Austrian High-Performance-Computing Meeting (AHPC2020)</i>. Klosterneuburg, Austria: IST Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7474\">https://doi.org/10.15479/AT:ISTA:7474</a>.","ieee":"A. Schlögl, J. Kiss, and S. Elefante, Eds., <i>Austrian High-Performance-Computing meeting (AHPC2020)</i>. Klosterneuburg, Austria: IST Austria, 2020."},"year":"2020","date_updated":"2023-05-16T07:48:28Z"},{"date_created":"2020-02-11T09:07:37Z","article_processing_charge":"No","department":[{"_id":"ChLa"}],"publication_status":"published","oa_version":"Published Version","title":"Functional vs. parametric equivalence of ReLU networks","month":"04","has_accepted_license":"1","publication":"8th International Conference on Learning Representations","_id":"7481","author":[{"full_name":"Bui Thi Mai, Phuong","first_name":"Phuong","last_name":"Bui Thi Mai","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"conference":{"location":"Online","end_date":"2020-04-30","name":"ICLR: International Conference on Learning Representations","start_date":"2020-04-27"},"quality_controlled":"1","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:59Z","day":"26","oa":1,"abstract":[{"lang":"eng","text":"We address the following question:  How redundant is the parameterisation of ReLU networks? Specifically, we consider transformations of the weight space which leave the function implemented by the network intact.  Two such transformations are known for feed-forward architectures:  permutation of neurons within a layer, and positive scaling of all incoming weights of a neuron coupled with inverse scaling of its outgoing weights. In this work, we show for architectures with non-increasing widths that permutation and scaling are in fact the only function-preserving weight transformations.  For any eligible architecture we give an explicit construction of a neural network such that any other network that implements the same function can be obtained from the original one by the application of permutations and rescaling.  The proof relies on a geometric understanding of boundaries between linear regions of ReLU networks, and we hope the developed mathematical tools are of independent interest."}],"year":"2020","citation":{"ista":"Phuong M, Lampert C. 2020. Functional vs. parametric equivalence of ReLU networks. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","short":"M. Phuong, C. Lampert, in:, 8th International Conference on Learning Representations, 2020.","mla":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” <i>8th International Conference on Learning Representations</i>, 2020.","ieee":"M. Phuong and C. Lampert, “Functional vs. parametric equivalence of ReLU networks,” in <i>8th International Conference on Learning Representations</i>, Online, 2020.","chicago":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” In <i>8th International Conference on Learning Representations</i>, 2020.","ama":"Phuong M, Lampert C. Functional vs. parametric equivalence of ReLU networks. In: <i>8th International Conference on Learning Representations</i>. ; 2020.","apa":"Phuong, M., &#38; Lampert, C. (2020). Functional vs. parametric equivalence of ReLU networks. In <i>8th International Conference on Learning Representations</i>. Online."},"date_updated":"2023-09-07T13:29:50Z","type":"conference","date_published":"2020-04-26T00:00:00Z","file":[{"relation":"main_file","access_level":"open_access","file_id":"7482","creator":"bphuong","date_created":"2020-02-11T09:07:27Z","checksum":"8d372ea5defd8cb8fdc430111ed754a9","file_size":405469,"date_updated":"2020-07-14T12:47:59Z","content_type":"application/pdf","file_name":"main.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"9418","relation":"dissertation_contains","status":"public"}],"link":[{"relation":"supplementary_material","url":"https://iclr.cc/virtual_2020/poster_Bylx-TNKvH.html"}]},"ddc":["000"],"status":"public"},{"abstract":[{"lang":"eng","text":"Glutaminase (GA) catalyzes the first step in mitochondrial glutaminolysis playing a key role in cancer metabolic reprogramming. Humans express two types of GA isoforms: GLS and GLS2. GLS isozymes have been consistently related to cell proliferation, but the role of GLS2 in cancer remains poorly understood. GLS2 is repressed in many tumor cells and a better understanding of its function in tumorigenesis may further the development of new therapeutic approaches. We analyzed GLS2 expression in HCC, GBM and neuroblastoma cells, as well as in monkey COS-7 cells. We studied GLS2 expression after induction of differentiation with phorbol ester (PMA) and transduction with the full-length cDNA of GLS2. In parallel, we investigated cell cycle progression and levels of p53, p21 and c-Myc proteins. Using the baculovirus system, human GLS2 protein was overexpressed, purified and analyzed for posttranslational modifications employing a proteomics LC-MS/MS platform. We have demonstrated a dual targeting of GLS2 in human cancer cells. Immunocytochemistry and subcellular fractionation gave consistent results demonstrating nuclear and mitochondrial locations, with the latter being predominant. Nuclear targeting was confirmed in cancer cells overexpressing c-Myc- and GFP-tagged GLS2 proteins. We assessed the subnuclear location finding a widespread distribution of GLS2 in the nucleoplasm without clear overlapping with specific nuclear substructures. GLS2 expression and nuclear accrual notably increased by treatment of SH-SY5Y cells with PMA and it correlated with cell cycle arrest at G2/M, upregulation of tumor suppressor p53 and p21 protein. A similar response was obtained by overexpression of GLS2 in T98G glioma cells, including downregulation of oncogene c-Myc. Furthermore, human GLS2 was identified as being hypusinated by MS analysis, a posttranslational modification which may be relevant for its nuclear targeting and/or function. Our studies provide evidence for a tumor suppressor role of GLS2 in certain types of cancer. The data imply that GLS2 can be regarded as a highly mobile and multilocalizing protein translocated to both mitochondria and nuclei. Upregulation of GLS2 in cancer cells induced an antiproliferative response with cell cycle arrest at the G2/M phase."}],"doi":"10.1038/s41598-020-58264-4","day":"10","isi":1,"external_id":{"isi":["000560694800012"],"pmid":["32042057"]},"date_updated":"2023-08-18T06:35:13Z","year":"2020","citation":{"apa":"López De La Oliva, A. R., Campos-Sandoval, J. A., Gómez-García, M. C., Cardona, C., Martín-Rufián, M., Sialana, F. J., … Márquez, J. (2020). Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-020-58264-4\">https://doi.org/10.1038/s41598-020-58264-4</a>","ama":"López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, et al. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. <i>Scientific reports</i>. 2020;10(1). doi:<a href=\"https://doi.org/10.1038/s41598-020-58264-4\">10.1038/s41598-020-58264-4</a>","chicago":"López De La Oliva, Amada R., José A. Campos-Sandoval, María C. Gómez-García, Carolina Cardona, Mercedes Martín-Rufián, Fernando J. Sialana, Laura Castilla, et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” <i>Scientific Reports</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41598-020-58264-4\">https://doi.org/10.1038/s41598-020-58264-4</a>.","ieee":"A. R. López De La Oliva <i>et al.</i>, “Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation,” <i>Scientific reports</i>, vol. 10, no. 1. Springer Nature, 2020.","short":"A.R. López De La Oliva, J.A. Campos-Sandoval, M.C. Gómez-García, C. Cardona, M. Martín-Rufián, F.J. Sialana, L. Castilla, N. Bae, C. Lobo, A. Peñalver, M. García-Frutos, D. Carro, V. Enrique, J.C. Paz, R.G. Mirmira, A. Gutiérrez, F.J. Alonso, J.A. Segura, J.M. Matés, G. Lubec, J. Márquez, Scientific Reports 10 (2020).","mla":"López De La Oliva, Amada R., et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” <i>Scientific Reports</i>, vol. 10, no. 1, 2259, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41598-020-58264-4\">10.1038/s41598-020-58264-4</a>.","ista":"López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, Cardona C, Martín-Rufián M, Sialana FJ, Castilla L, Bae N, Lobo C, Peñalver A, García-Frutos M, Carro D, Enrique V, Paz JC, Mirmira RG, Gutiérrez A, Alonso FJ, Segura JA, Matés JM, Lubec G, Márquez J. 2020. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific reports. 10(1), 2259."},"ddc":["570"],"volume":10,"title":"Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation","intvolume":"        10","publication_status":"published","date_created":"2020-02-16T23:00:49Z","article_processing_charge":"No","department":[{"_id":"CaBe"}],"author":[{"full_name":"López De La Oliva, Amada R.","first_name":"Amada R.","last_name":"López De La Oliva"},{"full_name":"Campos-Sandoval, José A.","first_name":"José A.","last_name":"Campos-Sandoval"},{"last_name":"Gómez-García","first_name":"María C.","full_name":"Gómez-García, María C."},{"last_name":"Cardona","first_name":"Carolina","full_name":"Cardona, Carolina"},{"full_name":"Martín-Rufián, Mercedes","first_name":"Mercedes","last_name":"Martín-Rufián"},{"first_name":"Fernando J.","last_name":"Sialana","full_name":"Sialana, Fernando J."},{"full_name":"Castilla, Laura","last_name":"Castilla","first_name":"Laura"},{"id":"3A5F7CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Narkhyun","last_name":"Bae","full_name":"Bae, Narkhyun"},{"full_name":"Lobo, Carolina","last_name":"Lobo","first_name":"Carolina"},{"full_name":"Peñalver, Ana","first_name":"Ana","last_name":"Peñalver"},{"full_name":"García-Frutos, Marina","last_name":"García-Frutos","first_name":"Marina"},{"last_name":"Carro","first_name":"David","full_name":"Carro, David"},{"full_name":"Enrique, Victoria","first_name":"Victoria","last_name":"Enrique"},{"full_name":"Paz, José C.","last_name":"Paz","first_name":"José C."},{"full_name":"Mirmira, Raghavendra G.","last_name":"Mirmira","first_name":"Raghavendra G."},{"full_name":"Gutiérrez, Antonia","first_name":"Antonia","last_name":"Gutiérrez"},{"full_name":"Alonso, Francisco J.","first_name":"Francisco J.","last_name":"Alonso"},{"full_name":"Segura, Juan A.","first_name":"Juan A.","last_name":"Segura"},{"last_name":"Matés","first_name":"José M.","full_name":"Matés, José M."},{"last_name":"Lubec","first_name":"Gert","full_name":"Lubec, Gert"},{"full_name":"Márquez, Javier","last_name":"Márquez","first_name":"Javier"}],"issue":"1","_id":"7487","pmid":1,"scopus_import":"1","article_type":"original","publisher":"Springer Nature","file_date_updated":"2020-07-14T12:47:59Z","quality_controlled":"1","oa":1,"publication_identifier":{"eissn":["20452322"]},"date_published":"2020-02-10T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","related_material":{"link":[{"url":"https://doi.org/10.1038/s41598-020-80651-0","relation":"erratum"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":4703751,"checksum":"c780bd87476a9c9e12668ff66de3dc96","date_created":"2020-02-18T07:43:21Z","content_type":"application/pdf","file_name":"2020_ScientificReport_Lopez.pdf","date_updated":"2020-07-14T12:47:59Z","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"7495"}],"month":"02","article_number":"2259","oa_version":"Published Version","publication":"Scientific reports","has_accepted_license":"1","language":[{"iso":"eng"}]},{"article_processing_charge":"No","department":[{"_id":"GaNo"}],"date_created":"2020-02-16T23:00:49Z","publication_status":"published","intvolume":"        21","title":"Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes","scopus_import":"1","_id":"7488","issue":"3","author":[{"first_name":"Ana","last_name":"Latorre-Pellicer","full_name":"Latorre-Pellicer, Ana"},{"full_name":"Ascaso, Ángela","first_name":"Ángela","last_name":"Ascaso"},{"full_name":"Trujillano, Laura","first_name":"Laura","last_name":"Trujillano"},{"full_name":"Gil-Salvador, Marta","first_name":"Marta","last_name":"Gil-Salvador"},{"full_name":"Arnedo, Maria","last_name":"Arnedo","first_name":"Maria"},{"first_name":"Cristina","last_name":"Lucia-Campos","full_name":"Lucia-Campos, Cristina"},{"last_name":"Antoñanzas-Pérez","first_name":"Rebeca","full_name":"Antoñanzas-Pérez, Rebeca"},{"first_name":"Iñigo","last_name":"Marcos-Alcalde","full_name":"Marcos-Alcalde, Iñigo"},{"last_name":"Parenti","first_name":"Ilaria","full_name":"Parenti, Ilaria","id":"D93538B0-5B71-11E9-AC62-02EBE5697425"},{"first_name":"Gloria","last_name":"Bueno-Lozano","full_name":"Bueno-Lozano, Gloria"},{"last_name":"Musio","first_name":"Antonio","full_name":"Musio, Antonio"},{"last_name":"Puisac","first_name":"Beatriz","full_name":"Puisac, Beatriz"},{"full_name":"Kaiser, Frank J.","last_name":"Kaiser","first_name":"Frank J."},{"full_name":"Ramos, Feliciano J.","last_name":"Ramos","first_name":"Feliciano J."},{"first_name":"Paulino","last_name":"Gómez-Puertas","full_name":"Gómez-Puertas, Paulino"},{"full_name":"Pié, Juan","first_name":"Juan","last_name":"Pié"}],"publisher":"MDPI","article_type":"original","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:59Z","day":"04","doi":"10.3390/ijms21031042","abstract":[{"lang":"eng","text":"Characteristic or classic phenotype of Cornelia de Lange syndrome (CdLS) is associated with a recognisable facial pattern. However, the heterogeneity in causal genes and the presence of overlapping syndromes have made it increasingly difficult to diagnose only by clinical features. DeepGestalt technology, and its app Face2Gene, is having a growing impact on the diagnosis and management of genetic diseases by analysing the features of affected individuals. Here, we performed a phenotypic study on a cohort of 49 individuals harbouring causative variants in known CdLS genes in order to evaluate Face2Gene utility and sensitivity in the clinical diagnosis of CdLS. Based on the profile images of patients, a diagnosis of CdLS was within the top five predicted syndromes for 97.9% of our cases and even listed as first prediction for 83.7%. The age of patients did not seem to affect the prediction accuracy, whereas our results indicate a correlation between the clinical score and affected genes. Furthermore, each gene presents a different pattern recognition that may be used to develop new neural networks with the goal of separating different genetic subtypes in CdLS. Overall, we conclude that computer-assisted image analysis based on deep learning could support the clinical diagnosis of CdLS."}],"citation":{"apa":"Latorre-Pellicer, A., Ascaso, Á., Trujillano, L., Gil-Salvador, M., Arnedo, M., Lucia-Campos, C., … Pié, J. (2020). Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms21031042\">https://doi.org/10.3390/ijms21031042</a>","ama":"Latorre-Pellicer A, Ascaso Á, Trujillano L, et al. Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. <i>International Journal of Molecular Sciences</i>. 2020;21(3). doi:<a href=\"https://doi.org/10.3390/ijms21031042\">10.3390/ijms21031042</a>","ieee":"A. Latorre-Pellicer <i>et al.</i>, “Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes,” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 3. MDPI, 2020.","chicago":"Latorre-Pellicer, Ana, Ángela Ascaso, Laura Trujillano, Marta Gil-Salvador, Maria Arnedo, Cristina Lucia-Campos, Rebeca Antoñanzas-Pérez, et al. “Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes.” <i>International Journal of Molecular Sciences</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ijms21031042\">https://doi.org/10.3390/ijms21031042</a>.","mla":"Latorre-Pellicer, Ana, et al. “Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes.” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 3, 1042, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ijms21031042\">10.3390/ijms21031042</a>.","short":"A. Latorre-Pellicer, Á. Ascaso, L. Trujillano, M. Gil-Salvador, M. Arnedo, C. Lucia-Campos, R. Antoñanzas-Pérez, I. Marcos-Alcalde, I. Parenti, G. Bueno-Lozano, A. Musio, B. Puisac, F.J. Kaiser, F.J. Ramos, P. Gómez-Puertas, J. Pié, International Journal of Molecular Sciences 21 (2020).","ista":"Latorre-Pellicer A, Ascaso Á, Trujillano L, Gil-Salvador M, Arnedo M, Lucia-Campos C, Antoñanzas-Pérez R, Marcos-Alcalde I, Parenti I, Bueno-Lozano G, Musio A, Puisac B, Kaiser FJ, Ramos FJ, Gómez-Puertas P, Pié J. 2020. Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. International Journal of Molecular Sciences. 21(3), 1042."},"year":"2020","date_updated":"2023-08-18T06:35:41Z","external_id":{"isi":["000522551606028"]},"isi":1,"volume":21,"ddc":["570"],"oa_version":"Published Version","article_number":"1042","month":"02","has_accepted_license":"1","publication":"International Journal of Molecular Sciences","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2020-02-04T00:00:00Z","file":[{"date_created":"2020-02-18T07:49:22Z","file_size":4271234,"checksum":"0e6658c4fe329d55d4d9bef01c5b15d0","date_updated":"2020-07-14T12:47:59Z","content_type":"application/pdf","file_name":"2020_IntMolecSciences_Latorre.pdf","access_level":"open_access","relation":"main_file","file_id":"7496","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public"},{"year":"2020","citation":{"ieee":"J. L. Fischer and S. Hensel, “Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 236. Springer Nature, pp. 967–1087, 2020.","chicago":"Fischer, Julian L, and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00205-019-01486-2\">https://doi.org/10.1007/s00205-019-01486-2</a>.","ama":"Fischer JL, Hensel S. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. <i>Archive for Rational Mechanics and Analysis</i>. 2020;236:967-1087. doi:<a href=\"https://doi.org/10.1007/s00205-019-01486-2\">10.1007/s00205-019-01486-2</a>","apa":"Fischer, J. L., &#38; Hensel, S. (2020). Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-019-01486-2\">https://doi.org/10.1007/s00205-019-01486-2</a>","ista":"Fischer JL, Hensel S. 2020. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. 236, 967–1087.","short":"J.L. Fischer, S. Hensel, Archive for Rational Mechanics and Analysis 236 (2020) 967–1087.","mla":"Fischer, Julian L., and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 236, Springer Nature, 2020, pp. 967–1087, doi:<a href=\"https://doi.org/10.1007/s00205-019-01486-2\">10.1007/s00205-019-01486-2</a>."},"date_updated":"2023-09-07T13:30:45Z","external_id":{"isi":["000511060200001"]},"isi":1,"day":"01","doi":"10.1007/s00205-019-01486-2","abstract":[{"text":"In the present work, we consider the evolution of two fluids separated by a sharp interface in the presence of surface tension—like, for example, the evolution of oil bubbles in water. Our main result is a weak–strong uniqueness principle for the corresponding free boundary problem for the incompressible Navier–Stokes equation: as long as a strong solution exists, any varifold solution must coincide with it. In particular, in the absence of physical singularities, the concept of varifold solutions—whose global in time existence has been shown by Abels (Interfaces Free Bound 9(1):31–65, 2007) for general initial data—does not introduce a mechanism for non-uniqueness. The key ingredient of our approach is the construction of a relative entropy functional capable of controlling the interface error. If the viscosities of the two fluids do not coincide, even for classical (strong) solutions the gradient of the velocity field becomes discontinuous at the interface, introducing the need for a careful additional adaption of the relative entropy.","lang":"eng"}],"volume":236,"ddc":["530","532"],"scopus_import":"1","_id":"7489","author":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Hensel","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian"}],"department":[{"_id":"JuFi"}],"date_created":"2020-02-16T23:00:50Z","article_processing_charge":"Yes (via OA deal)","publication_status":"published","intvolume":"       236","title":"Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension","ec_funded":1,"quality_controlled":"1","page":"967-1087","file_date_updated":"2020-11-20T09:14:22Z","publisher":"Springer Nature","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2020-05-01T00:00:00Z","publication_identifier":{"issn":["00039527"],"eissn":["14320673"]},"oa":1,"file":[{"file_name":"2020_ArchRatMechAn_Fischer.pdf","content_type":"application/pdf","date_updated":"2020-11-20T09:14:22Z","file_size":1897571,"checksum":"f107e21b58f5930876f47144be37cf6c","date_created":"2020-11-20T09:14:22Z","creator":"dernst","file_id":"8779","success":1,"relation":"main_file","access_level":"open_access"}],"status":"public","related_material":{"record":[{"id":"10007","relation":"dissertation_contains","status":"public"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","publication":"Archive for Rational Mechanics and Analysis","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"oa_version":"Published Version","month":"05","language":[{"iso":"eng"}]},{"date_published":"2020-01-23T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["2050-084X"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"relation":"main_file","access_level":"open_access","file_id":"7494","creator":"dernst","date_created":"2020-02-18T07:21:16Z","checksum":"2052daa4be5019534f3a42f200a09f32","file_size":7247468,"date_updated":"2020-07-14T12:47:59Z","content_type":"application/pdf","file_name":"2020_eLife_Narasimhan.pdf"}],"publication":"eLife","has_accepted_license":"1","month":"01","article_number":"e52067","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"oa_version":"Published Version","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"isi":1,"external_id":{"pmid":["31971511"],"isi":["000514104100001"]},"date_updated":"2023-08-18T06:33:07Z","year":"2020","citation":{"apa":"Narasimhan, M., Johnson, A. J., Prizak, R., Kaufmann, W., Tan, S., Casillas Perez, B. E., &#38; Friml, J. (2020). Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.52067\">https://doi.org/10.7554/eLife.52067</a>","ama":"Narasimhan M, Johnson AJ, Prizak R, et al. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.52067\">10.7554/eLife.52067</a>","chicago":"Narasimhan, Madhumitha, Alexander J Johnson, Roshan Prizak, Walter Kaufmann, Shutang Tan, Barbara E Casillas Perez, and Jiří Friml. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.52067\">https://doi.org/10.7554/eLife.52067</a>.","ieee":"M. Narasimhan <i>et al.</i>, “Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","mla":"Narasimhan, Madhumitha, et al. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” <i>ELife</i>, vol. 9, e52067, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.52067\">10.7554/eLife.52067</a>.","short":"M. Narasimhan, A.J. Johnson, R. Prizak, W. Kaufmann, S. Tan, B.E. Casillas Perez, J. Friml, ELife 9 (2020).","ista":"Narasimhan M, Johnson AJ, Prizak R, Kaufmann W, Tan S, Casillas Perez BE, Friml J. 2020. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife. 9, e52067."},"abstract":[{"lang":"eng","text":"In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the plasma membrane but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes."}],"doi":"10.7554/eLife.52067","day":"23","ddc":["570","580"],"volume":9,"author":[{"full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","first_name":"Roshan","full_name":"Prizak, Roshan"},{"first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Casillas Perez, Barbara E","first_name":"Barbara E","last_name":"Casillas Perez","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"}],"_id":"7490","pmid":1,"scopus_import":"1","title":"Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants","intvolume":"         9","publication_status":"published","department":[{"_id":"JiFr"},{"_id":"GaTk"},{"_id":"EM-Fac"},{"_id":"SyCr"}],"article_processing_charge":"No","date_created":"2020-02-16T23:00:50Z","file_date_updated":"2020-07-14T12:47:59Z","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"eLife Sciences Publications"},{"language":[{"iso":"eng"}],"oa_version":"Published Version","month":"09","publication":"Journal of Integrative Plant Biology","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jipb.12905"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"oa":1,"type":"journal_article","date_published":"2020-09-01T00:00:00Z","publisher":"Wiley","article_type":"original","quality_controlled":"1","page":"1433-1451","date_created":"2020-02-18T10:02:25Z","article_processing_charge":"No","department":[{"_id":"JiFr"}],"publication_status":"published","intvolume":"        62","title":"Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid","scopus_import":"1","_id":"7497","pmid":1,"issue":"9","author":[{"full_name":"Han, L","first_name":"L","last_name":"Han"},{"full_name":"Zhou, X","last_name":"Zhou","first_name":"X"},{"first_name":"Y","last_name":"Zhao","full_name":"Zhao, Y"},{"first_name":"S","last_name":"Zhu","full_name":"Zhu, S"},{"first_name":"L","last_name":"Wu","full_name":"Wu, L"},{"full_name":"He, Y","first_name":"Y","last_name":"He"},{"full_name":"Ping, X","first_name":"X","last_name":"Ping"},{"first_name":"X","last_name":"Lu","full_name":"Lu, X"},{"first_name":"W","last_name":"Huang","full_name":"Huang, W"},{"first_name":"J","last_name":"Qian","full_name":"Qian, J"},{"last_name":"Zhang","first_name":"L","full_name":"Zhang, L"},{"first_name":"X","last_name":"Jiang","full_name":"Jiang, X"},{"full_name":"Zhu, D","last_name":"Zhu","first_name":"D"},{"first_name":"C","last_name":"Luo","full_name":"Luo, C"},{"first_name":"S","last_name":"Li","full_name":"Li, S"},{"full_name":"Dong, Q","last_name":"Dong","first_name":"Q"},{"first_name":"Q","last_name":"Fu","full_name":"Fu, Q"},{"first_name":"K","last_name":"Deng","full_name":"Deng, K"},{"full_name":"Wang, X","last_name":"Wang","first_name":"X"},{"full_name":"Wang, L","last_name":"Wang","first_name":"L"},{"last_name":"Peng","first_name":"S","full_name":"Peng, S"},{"full_name":"Wu, J","last_name":"Wu","first_name":"J"},{"first_name":"W","last_name":"Li","full_name":"Li, W"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"Y","last_name":"Zhu","full_name":"Zhu, Y"},{"last_name":"He","first_name":"X","full_name":"He, X"},{"last_name":"Du","first_name":"Y","full_name":"Du, Y"}],"volume":62,"acknowledgement":"We thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for providing generous support with the IAA and JA measurements. We thank Professor Guohua Xu (Nanjing Agricultural University) for generously providing the Nipponbare rice expressing DR5::GUS. We thank Professor Muyuan Zhu (Zhejiang University) for generously providing a rice line expressing 35S::miR393b. We thank Professor Yinong Yang (Pennsylvania State University) for generously providing the rice line coi1-18. This work was supported by grants from the National Natural Science Foundation of China (31660501, 31460453, 31860064 and 31470382), the Major Special Program for Scientific Research, Education Department of Yunnan Province (ZD2015005), the Project sponsored by SRF for ROCS, SEM ([2013] 1792), the Major Science and Technique Programs in Yunnan Province (2016ZF001), the Key Projects of the Applied Basic Research Plan of Yunnan Province (2017FA018), the National Key R&D Program of China (2018YFD0201100) and the China Agriculture Research System (CARS-21).","day":"01","doi":"10.1111/jipb.12905","abstract":[{"text":"Endophytic fungi can be beneficial to plant growth. However, the molecular mechanisms underlying colonization of Acremonium spp. remain unclear. In this study, a novel endophytic Acremonium strain was isolated from the buds of Panax notoginseng and named Acremonium sp. D212. The Acremonium sp. D212 could colonize the roots of P. notoginseng, enhance the resistance of P. notoginseng to root rot disease, and promote root growth and saponin biosynthesis in P. notoginseng. Acremonium sp. D212 could secrete indole‐3‐acetic acid (IAA) and jasmonic acid (JA), and inoculation with the fungus increased the endogenous levels of IAA and JA in P. notoginseng. Colonization of the Acremonium sp. D212 in the roots of the rice line Nipponbare was dependent on the concentration of methyl jasmonate (MeJA) (2 to 15 μM) and 1‐naphthalenacetic acid (NAA) (10 to 20 μM). Moreover, the roots of the JA signalling‐defective coi1‐18 mutant were colonized by Acremonium sp. D212 to a lesser degree than those of the wild‐type Nipponbare and miR393b‐overexpressing lines, and the colonization was rescued by MeJA but not by NAA. It suggests that the cross‐talk between JA signalling and the auxin biosynthetic pathway plays a crucial role in the colonization of Acremonium sp. D212 in host plants.","lang":"eng"}],"citation":{"ama":"Han L, Zhou X, Zhao Y, et al. Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. <i>Journal of Integrative Plant Biology</i>. 2020;62(9):1433-1451. doi:<a href=\"https://doi.org/10.1111/jipb.12905\">10.1111/jipb.12905</a>","apa":"Han, L., Zhou, X., Zhao, Y., Zhu, S., Wu, L., He, Y., … Du, Y. (2020). Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.12905\">https://doi.org/10.1111/jipb.12905</a>","chicago":"Han, L, X Zhou, Y Zhao, S Zhu, L Wu, Y He, X Ping, et al. “Colonization of Endophyte Acremonium Sp. D212 in Panax Notoginseng and Rice Mediated by Auxin and Jasmonic Acid.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/jipb.12905\">https://doi.org/10.1111/jipb.12905</a>.","ieee":"L. Han <i>et al.</i>, “Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid,” <i>Journal of Integrative Plant Biology</i>, vol. 62, no. 9. Wiley, pp. 1433–1451, 2020.","mla":"Han, L., et al. “Colonization of Endophyte Acremonium Sp. D212 in Panax Notoginseng and Rice Mediated by Auxin and Jasmonic Acid.” <i>Journal of Integrative Plant Biology</i>, vol. 62, no. 9, Wiley, 2020, pp. 1433–51, doi:<a href=\"https://doi.org/10.1111/jipb.12905\">10.1111/jipb.12905</a>.","short":"L. Han, X. Zhou, Y. Zhao, S. Zhu, L. Wu, Y. He, X. Ping, X. Lu, W. Huang, J. Qian, L. Zhang, X. Jiang, D. Zhu, C. Luo, S. Li, Q. Dong, Q. Fu, K. Deng, X. Wang, L. Wang, S. Peng, J. Wu, W. Li, J. Friml, Y. Zhu, X. He, Y. Du, Journal of Integrative Plant Biology 62 (2020) 1433–1451.","ista":"Han L, Zhou X, Zhao Y, Zhu S, Wu L, He Y, Ping X, Lu X, Huang W, Qian J, Zhang L, Jiang X, Zhu D, Luo C, Li S, Dong Q, Fu Q, Deng K, Wang X, Wang L, Peng S, Wu J, Li W, Friml J, Zhu Y, He X, Du Y. 2020. Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. Journal of Integrative Plant Biology. 62(9), 1433–1451."},"year":"2020","date_updated":"2023-08-18T06:44:16Z","external_id":{"isi":["000515803000001"],"pmid":["31912615"]},"isi":1},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8822"}]},"status":"public","file":[{"date_created":"2020-11-20T09:32:10Z","file_size":2106888,"checksum":"17de728b0205979feb95ce663ba918c2","date_updated":"2020-11-20T09:32:10Z","file_name":"2020_NewPhytologist_Mazur.pdf","content_type":"application/pdf","access_level":"open_access","success":1,"relation":"main_file","file_id":"8781","creator":"dernst"}],"oa":1,"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"type":"journal_article","date_published":"2020-06-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"month":"06","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"2699E3D2-B435-11E9-9278-68D0E5697425","name":"Cell surface receptor complexes for PIN polarity and auxin-mediated development","grant_number":"25239"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"New Phytologist","ddc":["580"],"acknowledgement":"We thank Mark Estelle, José M. Alonso and the Arabidopsis Stock Centre for providing seeds. We acknowledge the core facility CELLIM of CEITEC supported by the MEYS CR (LM2015062 Czech‐BioImaging) and Plant Sciences Core Facility of CEITEC Masaryk University for help in generating essential data. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement no. 742985) and the Czech Science Foundation GAČR (GA13‐40637S and GA18‐26981S) to JF. JH is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology. The authors declare no competing interests.","volume":226,"abstract":[{"lang":"eng","text":"Plant survival depends on vascular tissues, which originate in a self‐organizing manner as strands of cells co‐directionally transporting the plant hormone auxin. The latter phenomenon (also known as auxin canalization) is classically hypothesized to be regulated by auxin itself via the effect of this hormone on the polarity of its own intercellular transport. Correlative observations supported this concept, but molecular insights remain limited.\r\nIn the current study, we established an experimental system based on the model Arabidopsis thaliana, which exhibits auxin transport channels and formation of vasculature strands in response to local auxin application.\r\nOur methodology permits the genetic analysis of auxin canalization under controllable experimental conditions. By utilizing this opportunity, we confirmed the dependence of auxin canalization on a PIN‐dependent auxin transport and nuclear, TIR1/AFB‐mediated auxin signaling. We also show that leaf venation and auxin‐mediated PIN repolarization in the root require TIR1/AFB signaling.\r\nFurther studies based on this experimental system are likely to yield better understanding of the mechanisms underlying auxin transport polarization in other developmental contexts."}],"day":"01","doi":"10.1111/nph.16446","external_id":{"pmid":["31971254"],"isi":["000514939700001"]},"isi":1,"citation":{"ieee":"E. Mazur, I. Kulik, J. Hajny, and J. Friml, “Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis,” <i>New Phytologist</i>, vol. 226, no. 5. Wiley, pp. 1375–1383, 2020.","chicago":"Mazur, E, Ivan Kulik, Jakub Hajny, and Jiří Friml. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” <i>New Phytologist</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/nph.16446\">https://doi.org/10.1111/nph.16446</a>.","apa":"Mazur, E., Kulik, I., Hajny, J., &#38; Friml, J. (2020). Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16446\">https://doi.org/10.1111/nph.16446</a>","ama":"Mazur E, Kulik I, Hajny J, Friml J. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. <i>New Phytologist</i>. 2020;226(5):1375-1383. doi:<a href=\"https://doi.org/10.1111/nph.16446\">10.1111/nph.16446</a>","ista":"Mazur E, Kulik I, Hajny J, Friml J. 2020. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 226(5), 1375–1383.","mla":"Mazur, E., et al. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” <i>New Phytologist</i>, vol. 226, no. 5, Wiley, 2020, pp. 1375–83, doi:<a href=\"https://doi.org/10.1111/nph.16446\">10.1111/nph.16446</a>.","short":"E. Mazur, I. Kulik, J. Hajny, J. Friml, New Phytologist 226 (2020) 1375–1383."},"year":"2020","date_updated":"2024-03-25T23:30:21Z","article_type":"original","publisher":"Wiley","file_date_updated":"2020-11-20T09:32:10Z","ec_funded":1,"quality_controlled":"1","page":"1375-1383","intvolume":"       226","title":"Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis","date_created":"2020-02-18T10:03:47Z","article_processing_charge":"No","department":[{"_id":"JiFr"}],"publication_status":"published","issue":"5","author":[{"first_name":"E","last_name":"Mazur","full_name":"Mazur, E"},{"full_name":"Kulik, Ivan","last_name":"Kulik","first_name":"Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB"},{"orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","first_name":"Jakub","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"_id":"7500"},{"language":[{"iso":"eng"}],"conference":{"location":"Santiago de Compostela, Spain","end_date":"2020-09-08","start_date":"2020-08-29","name":"ECAI: European Conference on Artificial Intelligence"},"has_accepted_license":"1","publication":"24th European Conference on Artificial Intelligence","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","month":"02","file":[{"file_size":1692214,"checksum":"80642fa0b6cd7da95dcd87d63789ad5e","date_created":"2020-09-21T07:12:32Z","file_name":"2020_ECAI_Henzinger.pdf","content_type":"application/pdf","date_updated":"2020-09-21T07:12:32Z","relation":"main_file","access_level":"open_access","success":1,"creator":"dernst","file_id":"8540"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"type":"conference","date_published":"2020-02-24T00:00:00Z","oa":1,"quality_controlled":"1","ec_funded":1,"page":"2433-2440","file_date_updated":"2020-09-21T07:12:32Z","publisher":"IOS Press","_id":"7505","author":[{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","full_name":"Lukina, Anna","first_name":"Anna","last_name":"Lukina"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling","first_name":"Christian","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065"}],"date_created":"2020-02-21T16:44:03Z","article_processing_charge":"No","department":[{"_id":"ToHe"}],"publication_status":"published","intvolume":"       325","alternative_title":["Frontiers in Artificial Intelligence and Applications"],"title":"Outside the box: Abstraction-based monitoring of neural networks","acknowledgement":"We thank Christoph Lampert and Nikolaus Mayer for fruitful discussions. This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award) and the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie grant agreement No. 754411.","volume":325,"ddc":["000"],"citation":{"apa":"Henzinger, T. A., Lukina, A., &#38; Schilling, C. (2020). Outside the box: Abstraction-based monitoring of neural networks. In <i>24th European Conference on Artificial Intelligence</i> (Vol. 325, pp. 2433–2440). Santiago de Compostela, Spain: IOS Press. <a href=\"https://doi.org/10.3233/FAIA200375\">https://doi.org/10.3233/FAIA200375</a>","ama":"Henzinger TA, Lukina A, Schilling C. Outside the box: Abstraction-based monitoring of neural networks. In: <i>24th European Conference on Artificial Intelligence</i>. Vol 325. IOS Press; 2020:2433-2440. doi:<a href=\"https://doi.org/10.3233/FAIA200375\">10.3233/FAIA200375</a>","ieee":"T. A. Henzinger, A. Lukina, and C. Schilling, “Outside the box: Abstraction-based monitoring of neural networks,” in <i>24th European Conference on Artificial Intelligence</i>, Santiago de Compostela, Spain, 2020, vol. 325, pp. 2433–2440.","chicago":"Henzinger, Thomas A, Anna Lukina, and Christian Schilling. “Outside the Box: Abstraction-Based Monitoring of Neural Networks.” In <i>24th European Conference on Artificial Intelligence</i>, 325:2433–40. IOS Press, 2020. <a href=\"https://doi.org/10.3233/FAIA200375\">https://doi.org/10.3233/FAIA200375</a>.","mla":"Henzinger, Thomas A., et al. “Outside the Box: Abstraction-Based Monitoring of Neural Networks.” <i>24th European Conference on Artificial Intelligence</i>, vol. 325, IOS Press, 2020, pp. 2433–40, doi:<a href=\"https://doi.org/10.3233/FAIA200375\">10.3233/FAIA200375</a>.","short":"T.A. Henzinger, A. Lukina, C. Schilling, in:, 24th European Conference on Artificial Intelligence, IOS Press, 2020, pp. 2433–2440.","ista":"Henzinger TA, Lukina A, Schilling C. 2020. Outside the box: Abstraction-based monitoring of neural networks. 24th European Conference on Artificial Intelligence. ECAI: European Conference on Artificial Intelligence, Frontiers in Artificial Intelligence and Applications, vol. 325, 2433–2440."},"year":"2020","date_updated":"2023-08-18T06:38:16Z","external_id":{"isi":["000650971303002"],"arxiv":["1911.09032"]},"isi":1,"day":"24","doi":"10.3233/FAIA200375","arxiv":1,"abstract":[{"lang":"eng","text":"Neural networks have demonstrated unmatched performance in a range of classification tasks. Despite numerous efforts of the research community, novelty detection remains one of the significant limitations of neural networks. The ability to identify previously unseen inputs as novel is crucial for our understanding of the decisions made by neural networks. At runtime, inputs not falling into any of the categories learned during training cannot be classified correctly by the neural network. Existing approaches treat the neural network as a black box and try to detect novel inputs based on the confidence of the output predictions. However, neural networks are not trained to reduce their confidence for novel inputs, which limits the effectiveness of these approaches. We propose a framework to monitor a neural network by observing the hidden layers. We employ a common abstraction from program analysis - boxes - to identify novel behaviors in the monitored layers, i.e., inputs that cause behaviors outside the box. For each neuron, the boxes range over the values seen in training. The framework is efficient and flexible to achieve a desired trade-off between raising false warnings and detecting novel inputs. We illustrate the performance and the robustness to variability in the unknown classes on popular image-classification benchmarks."}]},{"author":[{"id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","last_name":"Bossmann","first_name":"Lea","full_name":"Bossmann, Lea","orcid":"0000-0002-6854-1343"},{"last_name":"Pavlović","first_name":"Nataša","full_name":"Pavlović, Nataša"},{"first_name":"Peter","last_name":"Pickl","full_name":"Pickl, Peter"},{"full_name":"Soffer, Avy","first_name":"Avy","last_name":"Soffer"}],"scopus_import":"1","_id":"7508","intvolume":"       178","title":"Higher order corrections to the mean-field description of the dynamics of interacting bosons","department":[{"_id":"RoSe"}],"article_processing_charge":"Yes (via OA deal)","date_created":"2020-02-23T09:45:51Z","publication_status":"published","file_date_updated":"2020-11-20T09:26:46Z","ec_funded":1,"quality_controlled":"1","page":"1362-1396","article_type":"original","publisher":"Springer Nature","external_id":{"arxiv":["1905.06164"],"isi":["000516342200001"]},"isi":1,"citation":{"ieee":"L. Bossmann, N. Pavlović, P. Pickl, and A. Soffer, “Higher order corrections to the mean-field description of the dynamics of interacting bosons,” <i>Journal of Statistical Physics</i>, vol. 178. Springer Nature, pp. 1362–1396, 2020.","chicago":"Bossmann, Lea, Nataša Pavlović, Peter Pickl, and Avy Soffer. “Higher Order Corrections to the Mean-Field Description of the Dynamics of Interacting Bosons.” <i>Journal of Statistical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s10955-020-02500-8\">https://doi.org/10.1007/s10955-020-02500-8</a>.","ama":"Bossmann L, Pavlović N, Pickl P, Soffer A. Higher order corrections to the mean-field description of the dynamics of interacting bosons. <i>Journal of Statistical Physics</i>. 2020;178:1362-1396. doi:<a href=\"https://doi.org/10.1007/s10955-020-02500-8\">10.1007/s10955-020-02500-8</a>","apa":"Bossmann, L., Pavlović, N., Pickl, P., &#38; Soffer, A. (2020). Higher order corrections to the mean-field description of the dynamics of interacting bosons. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-020-02500-8\">https://doi.org/10.1007/s10955-020-02500-8</a>","ista":"Bossmann L, Pavlović N, Pickl P, Soffer A. 2020. Higher order corrections to the mean-field description of the dynamics of interacting bosons. Journal of Statistical Physics. 178, 1362–1396.","short":"L. Bossmann, N. Pavlović, P. Pickl, A. Soffer, Journal of Statistical Physics 178 (2020) 1362–1396.","mla":"Bossmann, Lea, et al. “Higher Order Corrections to the Mean-Field Description of the Dynamics of Interacting Bosons.” <i>Journal of Statistical Physics</i>, vol. 178, Springer Nature, 2020, pp. 1362–96, doi:<a href=\"https://doi.org/10.1007/s10955-020-02500-8\">10.1007/s10955-020-02500-8</a>."},"year":"2020","date_updated":"2023-08-18T06:37:46Z","abstract":[{"lang":"eng","text":"In this paper, we introduce a novel method for deriving higher order corrections to the mean-field description of the dynamics of interacting bosons. More precisely, we consider the dynamics of N d-dimensional bosons for large N. The bosons initially form a Bose–Einstein condensate and interact with each other via a pair potential of the form (N−1)−1Ndβv(Nβ·)forβ∈[0,14d). We derive a sequence of N-body functions which approximate the true many-body dynamics in L2(RdN)-norm to arbitrary precision in powers of N−1. The approximating functions are constructed as Duhamel expansions of finite order in terms of the first quantised analogue of a Bogoliubov time evolution."}],"day":"21","arxiv":1,"doi":"10.1007/s10955-020-02500-8","ddc":["510"],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\nL.B. gratefully acknowledges the support by the German Research Foundation (DFG) within the Research Training Group 1838 “Spectral Theory and Dynamics of Quantum Systems”, and wishes to thank Stefan Teufel, Sören Petrat and Marcello Porta for helpful discussions. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. N.P. gratefully acknowledges support from NSF grant DMS-1516228 and DMS-1840314. P.P.’s research was funded by DFG Grant no. PI 1114/3-1. Part of this work was done when N.P. and P.P. were visiting CCNU, Wuhan. N.P. and P.P. thank A.S. for his hospitality at CCNU.","volume":178,"has_accepted_license":"1","publication":"Journal of Statistical Physics","month":"02","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2020-02-21T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["1572-9613"],"issn":["0022-4715"]},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"8780","creator":"dernst","success":1,"relation":"main_file","access_level":"open_access","date_updated":"2020-11-20T09:26:46Z","content_type":"application/pdf","file_name":"2020_JournStatPhysics_Bossmann.pdf","date_created":"2020-11-20T09:26:46Z","file_size":576726,"checksum":"643e230bf147e64d9cdb3f6cc573679d"}]},{"_id":"7509","author":[{"id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","full_name":"Zhang, Haonan","first_name":"Haonan","last_name":"Zhang"}],"article_processing_charge":"No","date_created":"2020-02-23T21:43:50Z","department":[{"_id":"JaMa"}],"publication_status":"published","intvolume":"       365","title":"From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture","ec_funded":1,"quality_controlled":"1","publisher":"Elsevier","article_type":"original","year":"2020","citation":{"ieee":"H. Zhang, “From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture,” <i>Advances in Mathematics</i>, vol. 365. Elsevier, 2020.","chicago":"Zhang, Haonan. “From Wigner-Yanase-Dyson Conjecture to Carlen-Frank-Lieb Conjecture.” <i>Advances in Mathematics</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.aim.2020.107053\">https://doi.org/10.1016/j.aim.2020.107053</a>.","apa":"Zhang, H. (2020). From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2020.107053\">https://doi.org/10.1016/j.aim.2020.107053</a>","ama":"Zhang H. From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. <i>Advances in Mathematics</i>. 2020;365. doi:<a href=\"https://doi.org/10.1016/j.aim.2020.107053\">10.1016/j.aim.2020.107053</a>","ista":"Zhang H. 2020. From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. Advances in Mathematics. 365, 107053.","short":"H. Zhang, Advances in Mathematics 365 (2020).","mla":"Zhang, Haonan. “From Wigner-Yanase-Dyson Conjecture to Carlen-Frank-Lieb Conjecture.” <i>Advances in Mathematics</i>, vol. 365, 107053, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.aim.2020.107053\">10.1016/j.aim.2020.107053</a>."},"date_updated":"2023-08-18T06:37:09Z","external_id":{"arxiv":["1811.01205"],"isi":["000522798000001"]},"isi":1,"day":"13","doi":"10.1016/j.aim.2020.107053","arxiv":1,"abstract":[{"text":"In this paper we study the joint convexity/concavity of the trace functions Ψp,q,s(A,B)=Tr(Bq2K∗ApKBq2)s,  p,q,s∈R,\r\nwhere A and B are positive definite matrices and K is any fixed invertible matrix. We will give full range of (p,q,s)∈R3 for Ψp,q,s to be jointly convex/concave for all K. As a consequence, we confirm a conjecture of Carlen, Frank and Lieb. In particular, we confirm a weaker conjecture of Audenaert and Datta and obtain the full range of (α,z) for α-z Rényi relative entropies to be monotone under completely positive trace preserving maps. We also give simpler proofs of many known results, including the concavity of Ψp,0,1/p for 0<p<1 which was first proved by Epstein using complex analysis. The key is to reduce the problem to the joint convexity/concavity of the trace functions Ψp,1−p,1(A,B)=TrK∗ApKB1−p,  −1≤p≤1, using a variational method. ","lang":"eng"}],"volume":365,"acknowledgement":"The author would like to thank Quanhua Xu, Adam Skalski, Ke Li and Zhi Yin for their valuable comments. He also would like to thank the anonymous referees for pointing out some errors in an earlier version of this paper and for helpful comments and suggestions that make this paper better. The research was partially supported by the NCN (National Centre of Science) grant 2014/14/E/ST1/00525, the French project ISITE-BFC (contract ANR-15-IDEX-03), NSFC No. 11826012, and the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","ddc":["515"],"publication":"Advances in Mathematics","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"oa_version":"Preprint","article_number":"107053","month":"05","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2020-05-13T00:00:00Z","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.01205"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"oa":1,"publication_identifier":{"eissn":["20411723"]},"type":"journal_article","date_published":"2020-02-13T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","file_id":"7517","relation":"main_file","access_level":"open_access","file_name":"2020_NatureComm_Turonova.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:59Z","checksum":"2c8d10475e1b0d397500760e28bdf561","file_size":2027529,"date_created":"2020-02-24T14:00:54Z"}],"article_number":"876","month":"02","oa_version":"Published Version","has_accepted_license":"1","publication":"Nature Communications","language":[{"iso":"eng"}],"abstract":[{"text":"Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines.","lang":"eng"}],"day":"13","doi":"10.1038/s41467-020-14535-2","external_id":{"isi":["000514928000017"]},"isi":1,"citation":{"mla":"Turoňová, Beata, et al. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” <i>Nature Communications</i>, vol. 11, 876, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-14535-2\">10.1038/s41467-020-14535-2</a>.","short":"B. Turoňová, W.J.H. Hagen, M. Obr, S. Mosalaganti, J.W. Beugelink, C.E. Zimmerli, H.G. Kräusslich, M. Beck, Nature Communications 11 (2020).","ista":"Turoňová B, Hagen WJH, Obr M, Mosalaganti S, Beugelink JW, Zimmerli CE, Kräusslich HG, Beck M. 2020. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. 11, 876.","ama":"Turoňová B, Hagen WJH, Obr M, et al. Benchmarking tomographic acquisition schemes for high-resolution structural biology. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-14535-2\">10.1038/s41467-020-14535-2</a>","apa":"Turoňová, B., Hagen, W. J. H., Obr, M., Mosalaganti, S., Beugelink, J. W., Zimmerli, C. E., … Beck, M. (2020). Benchmarking tomographic acquisition schemes for high-resolution structural biology. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-14535-2\">https://doi.org/10.1038/s41467-020-14535-2</a>","ieee":"B. Turoňová <i>et al.</i>, “Benchmarking tomographic acquisition schemes for high-resolution structural biology,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","chicago":"Turoňová, Beata, Wim J.H. Hagen, Martin Obr, Shyamal Mosalaganti, J. Wouter Beugelink, Christian E. Zimmerli, Hans Georg Kräusslich, and Martin Beck. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-14535-2\">https://doi.org/10.1038/s41467-020-14535-2</a>."},"year":"2020","date_updated":"2023-08-18T06:36:41Z","ddc":["570"],"volume":11,"intvolume":"        11","title":"Benchmarking tomographic acquisition schemes for high-resolution structural biology","article_processing_charge":"No","department":[{"_id":"FlSc"}],"date_created":"2020-02-23T23:00:35Z","publication_status":"published","author":[{"full_name":"Turoňová, Beata","first_name":"Beata","last_name":"Turoňová"},{"first_name":"Wim J.H.","last_name":"Hagen","full_name":"Hagen, Wim J.H."},{"id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","full_name":"Obr, Martin","first_name":"Martin","last_name":"Obr"},{"full_name":"Mosalaganti, Shyamal","first_name":"Shyamal","last_name":"Mosalaganti"},{"first_name":"J. Wouter","last_name":"Beugelink","full_name":"Beugelink, J. Wouter"},{"first_name":"Christian E.","last_name":"Zimmerli","full_name":"Zimmerli, Christian E."},{"last_name":"Kräusslich","first_name":"Hans Georg","full_name":"Kräusslich, Hans Georg"},{"last_name":"Beck","first_name":"Martin","full_name":"Beck, Martin"}],"scopus_import":"1","_id":"7511","article_type":"original","publisher":"Springer Nature","file_date_updated":"2020-07-14T12:47:59Z","quality_controlled":"1"},{"main_file_link":[{"url":"https://arxiv.org/abs/1804.11340","open_access":"1"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["10960783"],"issn":["00221236"]},"oa":1,"type":"journal_article","date_published":"2020-07-01T00:00:00Z","language":[{"iso":"eng"}],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"oa_version":"Preprint","article_number":"108507","month":"07","publication":"Journal of Functional Analysis","volume":278,"acknowledgement":"The authors are grateful to Oskari Ajanki for his invaluable help at the initial stage of this project, to Serban Belinschi for useful discussions, to Alexander Tikhomirov for calling our attention to the model example in Section 6.2 and to the anonymous referee for suggesting to simplify certain proofs. Erdös: Partially funded by ERC Advanced Grant RANMAT No. 338804\r\n","day":"01","arxiv":1,"doi":"10.1016/j.jfa.2020.108507","abstract":[{"text":"We consider general self-adjoint polynomials in several independent random matrices whose entries are centered and have the same variance. We show that under certain conditions the local law holds up to the optimal scale, i.e., the eigenvalue density on scales just above the eigenvalue spacing follows the global density of states which is determined by free probability theory. We prove that these conditions hold for general homogeneous polynomials of degree two and for symmetrized products of independent matrices with i.i.d. entries, thus establishing the optimal bulk local law for these classes of ensembles. In particular, we generalize a similar result of Anderson for anticommutator. For more general polynomials our conditions are effectively checkable numerically.","lang":"eng"}],"citation":{"ista":"Erdös L, Krüger TH, Nemish Y. 2020. Local laws for polynomials of Wigner matrices. Journal of Functional Analysis. 278(12), 108507.","mla":"Erdös, László, et al. “Local Laws for Polynomials of Wigner Matrices.” <i>Journal of Functional Analysis</i>, vol. 278, no. 12, 108507, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.jfa.2020.108507\">10.1016/j.jfa.2020.108507</a>.","short":"L. Erdös, T.H. Krüger, Y. Nemish, Journal of Functional Analysis 278 (2020).","ieee":"L. Erdös, T. H. Krüger, and Y. Nemish, “Local laws for polynomials of Wigner matrices,” <i>Journal of Functional Analysis</i>, vol. 278, no. 12. Elsevier, 2020.","chicago":"Erdös, László, Torben H Krüger, and Yuriy Nemish. “Local Laws for Polynomials of Wigner Matrices.” <i>Journal of Functional Analysis</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jfa.2020.108507\">https://doi.org/10.1016/j.jfa.2020.108507</a>.","ama":"Erdös L, Krüger TH, Nemish Y. Local laws for polynomials of Wigner matrices. <i>Journal of Functional Analysis</i>. 2020;278(12). doi:<a href=\"https://doi.org/10.1016/j.jfa.2020.108507\">10.1016/j.jfa.2020.108507</a>","apa":"Erdös, L., Krüger, T. H., &#38; Nemish, Y. (2020). Local laws for polynomials of Wigner matrices. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2020.108507\">https://doi.org/10.1016/j.jfa.2020.108507</a>"},"year":"2020","date_updated":"2023-08-18T06:36:10Z","external_id":{"arxiv":["1804.11340"],"isi":["000522798900001"]},"isi":1,"publisher":"Elsevier","article_type":"original","quality_controlled":"1","ec_funded":1,"date_created":"2020-02-23T23:00:36Z","article_processing_charge":"No","department":[{"_id":"LaEr"}],"publication_status":"published","intvolume":"       278","title":"Local laws for polynomials of Wigner matrices","scopus_import":"1","_id":"7512","issue":"12","author":[{"first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","first_name":"Torben H","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297"},{"id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","full_name":"Nemish, Yuriy","orcid":"0000-0002-7327-856X","last_name":"Nemish","first_name":"Yuriy"}]},{"related_material":{"record":[{"status":"public","id":"7524","relation":"part_of_dissertation"}]},"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"relation":"main_file","access_level":"open_access","file_id":"7515","creator":"dernst","date_created":"2020-02-24T09:15:06Z","file_size":1563429,"checksum":"b4de7579ddc1dbdd44ff3f17c48395f6","date_updated":"2020-07-14T12:47:59Z","content_type":"application/pdf","file_name":"thesis.pdf"},{"date_updated":"2020-07-14T12:47:59Z","content_type":"application/x-zip-compressed","file_name":"thesis_source.zip","date_created":"2020-02-24T09:15:16Z","checksum":"ad7425867b52d7d9e72296e87bc9cb67","file_size":2028038,"file_id":"7516","creator":"dernst","access_level":"closed","relation":"source_file"}],"oa":1,"supervisor":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","date_published":"2020-02-24T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"month":"02","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","has_accepted_license":"1","ddc":["510"],"abstract":[{"lang":"eng","text":"We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.\r\nWe motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks."}],"day":"24","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7514","citation":{"ista":"Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria.","short":"S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020.","mla":"Mayer, Simon. <i>The Free Energy of a Dilute Two-Dimensional Bose Gas</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7514\">10.15479/AT:ISTA:7514</a>.","chicago":"Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7514\">https://doi.org/10.15479/AT:ISTA:7514</a>.","ieee":"S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020.","apa":"Mayer, S. (2020). <i>The free energy of a dilute two-dimensional Bose gas</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7514\">https://doi.org/10.15479/AT:ISTA:7514</a>","ama":"Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7514\">10.15479/AT:ISTA:7514</a>"},"year":"2020","date_updated":"2023-09-07T13:12:42Z","publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:47:59Z","ec_funded":1,"page":"148","alternative_title":["ISTA Thesis"],"title":"The free energy of a dilute two-dimensional Bose gas","department":[{"_id":"RoSe"},{"_id":"GradSch"}],"article_processing_charge":"No","date_created":"2020-02-24T09:17:27Z","publication_status":"published","author":[{"id":"30C4630A-F248-11E8-B48F-1D18A9856A87","full_name":"Mayer, Simon","last_name":"Mayer","first_name":"Simon"}],"_id":"7514"},{"keyword":["Cav2.3","medial habenula (MHb)","interpeduncular nucleus (IPN)"],"language":[{"iso":"eng"}],"month":"02","oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"}],"has_accepted_license":"1","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"access_level":"open_access","relation":"main_file","file_id":"7538","creator":"pbhandari","embargo":"2021-02-28","date_created":"2020-02-28T08:37:53Z","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","checksum":"4589234fdb12b4ad72273b311723a7b4","file_size":9646346,"date_updated":"2021-03-01T23:30:04Z","file_name":"Pradeep Bhandari Thesis.pdf","content_type":"application/pdf"},{"relation":"source_file","access_level":"closed","file_id":"7539","creator":"pbhandari","date_created":"2020-02-28T08:47:14Z","checksum":"aa79490553ca0a5c9b6fbcd152e93928","file_size":35252164,"title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","embargo_to":"open_access","date_updated":"2021-03-01T23:30:04Z","file_name":"Pradeep Bhandari Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"oa":1,"supervisor":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"}],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","date_published":"2020-02-28T00:00:00Z","publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-03-01T23:30:04Z","page":"79","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","alternative_title":["ISTA Thesis"],"department":[{"_id":"RySh"}],"date_created":"2020-02-26T10:56:37Z","article_processing_charge":"No","publication_status":"published","author":[{"id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","first_name":"Pradeep","last_name":"Bhandari","orcid":"0000-0003-0863-4481","full_name":"Bhandari, Pradeep"}],"_id":"7525","ddc":["570"],"abstract":[{"lang":"eng","text":"The medial habenula (MHb) is an evolutionary conserved epithalamic structure important for the modulation of emotional memory. It is involved in regulation of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and feeding behavior. MHb receives inputs from septal regions and projects exclusively to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project to different subnuclei of MHb: the bed nucleus of anterior commissure projects to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore, the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively. Importantly, these projections have unique features of prominent co-release of different neurotransmitters and requirement of a peculiar type of calcium channel for release. In general, synaptic neurotransmission requires an activity-dependent influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels. The calcium channel family most commonly involved in neurotransmitter release comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits, respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements. This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique mechanisms of glutamate release in this pathway. One potential example of such uniqueness is the facilitation of release by GABAB receptor (GBR) activation. Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting presynaptic calcium channels. MHb shows the highest expression levels of GBR in the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are associated with auxiliary subunits, called potassium channel tetramerization domain containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b may be involved in the unique mechanisms of neurotransmitter release mediated by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482. We next found that baclofen, a GBR agonist, has facilitatory effects on release from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed exclusively in ventral MHb may have a role in the facilitatory effects of GBR activation. In a heterologous expression system using HEK cells, we found that KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely in presynaptic active zone in IPN with KCTD12b being present only in rostral/central but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3, KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating that they may form complexes regulating vesicle release in rostral IPN. \r\nOn electrophysiological studies of wild type (WT) mice, we found that paired-pulse ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8 KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO mice, the mean variance analysis revealed significantly lower release probability in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8 and KCTD12b KO mice, and found the facilitation of release remained in both KO mice, indicating that the peculiar effects of the GBR activation in this pathway do not depend on the selective expression of these KCTD subunits in ventral MHb. However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in its termination in the absence of KCTD12b. Consistent with these functional findings, replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn summary, our study provided new insights into the physiological roles of presynaptic Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal circuit. Future studies will be required to identify the exact molecular mechanism underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals. It remains to be determined whether the prominent presence of presynaptic KCTDs at active zone could exert similar neuromodulatory functions in different pathways of the brain.\r\n"}],"day":"28","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7525","citation":{"ieee":"P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway,” Institute of Science and Technology Austria, 2020.","chicago":"Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7525\">https://doi.org/10.15479/AT:ISTA:7525</a>.","ama":"Bhandari P. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7525\">10.15479/AT:ISTA:7525</a>","apa":"Bhandari, P. (2020). <i>Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7525\">https://doi.org/10.15479/AT:ISTA:7525</a>","ista":"Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria.","short":"P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria, 2020.","mla":"Bhandari, Pradeep. <i>Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7525\">10.15479/AT:ISTA:7525</a>."},"year":"2020","date_updated":"2023-09-07T13:20:03Z"},{"issue":"2","author":[{"full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marensi, Elena","first_name":"Elena","last_name":"Marensi"},{"full_name":"Willis, Ashley P.","last_name":"Willis","first_name":"Ashley P."},{"last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"7534","intvolume":"         5","title":"Upper edge of chaos and the energetics of transition in pipe flow","date_created":"2020-02-27T10:26:57Z","article_processing_charge":"No","department":[{"_id":"BjHo"}],"publication_status":"published","quality_controlled":"1","article_type":"original","publisher":"American Physical Society","external_id":{"arxiv":["1912.09270"],"isi":["000515065100001"]},"isi":1,"year":"2020","citation":{"ista":"Budanur NB, Marensi E, Willis AP, Hof B. 2020. Upper edge of chaos and the energetics of transition in pipe flow. Physical Review Fluids. 5(2), 023903.","mla":"Budanur, Nazmi B., et al. “Upper Edge of Chaos and the Energetics of Transition in Pipe Flow.” <i>Physical Review Fluids</i>, vol. 5, no. 2, 023903, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevfluids.5.023903\">10.1103/physrevfluids.5.023903</a>.","short":"N.B. Budanur, E. Marensi, A.P. Willis, B. Hof, Physical Review Fluids 5 (2020).","chicago":"Budanur, Nazmi B, Elena Marensi, Ashley P. Willis, and Björn Hof. “Upper Edge of Chaos and the Energetics of Transition in Pipe Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevfluids.5.023903\">https://doi.org/10.1103/physrevfluids.5.023903</a>.","ieee":"N. B. Budanur, E. Marensi, A. P. Willis, and B. Hof, “Upper edge of chaos and the energetics of transition in pipe flow,” <i>Physical Review Fluids</i>, vol. 5, no. 2. American Physical Society, 2020.","apa":"Budanur, N. B., Marensi, E., Willis, A. P., &#38; Hof, B. (2020). Upper edge of chaos and the energetics of transition in pipe flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevfluids.5.023903\">https://doi.org/10.1103/physrevfluids.5.023903</a>","ama":"Budanur NB, Marensi E, Willis AP, Hof B. Upper edge of chaos and the energetics of transition in pipe flow. <i>Physical Review Fluids</i>. 2020;5(2). doi:<a href=\"https://doi.org/10.1103/physrevfluids.5.023903\">10.1103/physrevfluids.5.023903</a>"},"date_updated":"2023-08-18T06:44:46Z","abstract":[{"text":"In the past two decades, our understanding of the transition to turbulence in shear flows with linearly stable laminar solutions has greatly improved. Regarding the susceptibility of the laminar flow, two concepts have been particularly useful: the edge states and the minimal seeds. In this nonlinear picture of the transition, the basin boundary of turbulence is set by the edge state's stable manifold and this manifold comes closest in energy to the laminar equilibrium at the minimal seed. We begin this paper by presenting numerical experiments in which three-dimensional perturbations are too energetic to trigger turbulence in pipe flow but they do lead to turbulence when their amplitude is reduced. We show that this seemingly counterintuitive observation is in fact consistent with the fully nonlinear description of the transition mediated by the edge state. In order to understand the physical mechanisms behind this process, we measure the turbulent kinetic energy production and dissipation rates as a function of the radial coordinate. Our main observation is that the transition to turbulence relies on the energy amplification away from the wall, as opposed to the turbulence itself, whose energy is predominantly produced near the wall. This observation is further supported by the similar analyses on the minimal seeds and the edge states. Furthermore, we show that the time evolution of production-over-dissipation curves provides a clear distinction between the different initial amplification stages of the transition to turbulence from the minimal seed.","lang":"eng"}],"day":"21","doi":"10.1103/physrevfluids.5.023903","arxiv":1,"volume":5,"publication":"Physical Review Fluids","article_number":"023903","month":"02","oa_version":"Preprint","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2020-02-21T00:00:00Z","oa":1,"publication_identifier":{"issn":["2469-990X"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1912.09270","open_access":"1"}]}]