[{"type":"preprint","_id":"8404","date_created":"2020-09-17T10:27:59Z","oa":1,"doi":"10.1101/2020.03.13.990150","year":"2020","main_file_link":[{"url":"https://doi.org/10.1101/2020.03.13.990150","open_access":"1"}],"status":"public","day":"14","publication":"bioRxiv","oa_version":"Preprint","citation":{"mla":"Weinhäupl, Katharina, et al. “Architecture and Subunit Dynamics of the Mitochondrial TIM9·10·12 Chaperone.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.03.13.990150\">10.1101/2020.03.13.990150</a>.","short":"K. Weinhäupl, Y. Wang, A. Hessel, M. Brennich, K. Lindorff-Larsen, P. Schanda, BioRxiv (n.d.).","ieee":"K. Weinhäupl, Y. Wang, A. Hessel, M. Brennich, K. Lindorff-Larsen, and P. Schanda, “Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","apa":"Weinhäupl, K., Wang, Y., Hessel, A., Brennich, M., Lindorff-Larsen, K., &#38; Schanda, P. (n.d.). Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.03.13.990150\">https://doi.org/10.1101/2020.03.13.990150</a>","chicago":"Weinhäupl, Katharina, Yong Wang, Audrey Hessel, Martha Brennich, Kresten Lindorff-Larsen, and Paul Schanda. “Architecture and Subunit Dynamics of the Mitochondrial TIM9·10·12 Chaperone.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.03.13.990150\">https://doi.org/10.1101/2020.03.13.990150</a>.","ama":"Weinhäupl K, Wang Y, Hessel A, Brennich M, Lindorff-Larsen K, Schanda P. Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.03.13.990150\">10.1101/2020.03.13.990150</a>","ista":"Weinhäupl K, Wang Y, Hessel A, Brennich M, Lindorff-Larsen K, Schanda P. Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone. bioRxiv, <a href=\"https://doi.org/10.1101/2020.03.13.990150\">10.1101/2020.03.13.990150</a>."},"extern":"1","date_updated":"2021-01-12T08:19:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Katharina","last_name":"Weinhäupl","full_name":"Weinhäupl, Katharina"},{"last_name":"Wang","first_name":"Yong","full_name":"Wang, Yong"},{"full_name":"Hessel, Audrey","last_name":"Hessel","first_name":"Audrey"},{"full_name":"Brennich, Martha","last_name":"Brennich","first_name":"Martha"},{"first_name":"Kresten","last_name":"Lindorff-Larsen","full_name":"Lindorff-Larsen, Kresten"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"month":"03","publication_status":"submitted","abstract":[{"text":"<jats:p>The mitochondrial Tim chaperones are responsible for the transport of membrane proteins across the inter-membrane space to the inner and outer mitochondrial membranes. TIM9·10, a hexameric 70 kDa protein complex formed by 3 copies of Tim9 and Tim10, guides its clients across the aqueous compartment. The TIM9·10·12 complex is the anchor point at the inner-membrane insertase complex TIM22. The mechanism of client transport by TIM9·10 has been resolved recently, but the structure and subunit composition of the TIM9·10·12 complex remains largely unresolved. Furthermore, the assembly process of the hexameric TIM chaperones from its subunits remained elusive. We investigate the structural and dynamical properties of the Tim subunits, and show that they are highly dynamic. In their non-assembled form, the subunits behave as intrinsically disordered proteins; when the conserved cysteines of the CX<jats:sub>3</jats:sub>C-X<jats:sub><jats:italic>n</jats:italic></jats:sub>-CX<jats:sub>3</jats:sub>C motifs are formed, short marginally stable <jats:italic>α</jats:italic>-helices are formed, which are only fully stabilized upon hexamer formation to the mature chaperone. Subunits are in equilibrium between their hexamer-embedded and a free form, with exchange kinetics on a minutes time scale. Joint NMR, small-angle X-ray scattering and MD simulation data allow us to derive a structural model of the TIM9·10·12 assembly, which has a 2:3:1 stoichiometry (Tim9:Tim10:Tim12) with a conserved hydrophobic client-binding groove and flexible N- and C-terminal tentacles.</jats:p>","lang":"eng"}],"title":"Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Cold Spring Harbor Laboratory","date_published":"2020-03-14T00:00:00Z"},{"publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"status":"public","article_type":"original","type":"journal_article","_id":"8434","date_created":"2020-09-17T14:00:33Z","author":[{"last_name":"Dimchev","first_name":"Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A"},{"full_name":"Amiri, Behnam","last_name":"Amiri","first_name":"Behnam"},{"first_name":"Ashley C.","last_name":"Humphries","full_name":"Humphries, Ashley C."},{"first_name":"Matthias","last_name":"Schaks","full_name":"Schaks, Matthias"},{"last_name":"Dimchev","first_name":"Vanessa","full_name":"Dimchev, Vanessa"},{"first_name":"Theresia E. B.","last_name":"Stradal","full_name":"Stradal, Theresia E. B."},{"full_name":"Faix, Jan","last_name":"Faix","first_name":"Jan"},{"last_name":"Krause","first_name":"Matthias","full_name":"Krause, Matthias"},{"full_name":"Way, Michael","first_name":"Michael","last_name":"Way"},{"full_name":"Falcke, Martin","first_name":"Martin","last_name":"Falcke"},{"last_name":"Rottner","first_name":"Klemens","full_name":"Rottner, Klemens"}],"oa_version":"Published Version","quality_controlled":"1","project":[{"call_identifier":"FWF","grant_number":"M02495","_id":"2674F658-B435-11E9-9278-68D0E5697425","name":"Protein structure and function in filopodia across scales"}],"volume":133,"article_processing_charge":"No","language":[{"iso":"eng"}],"article_number":"jcs239020","file":[{"file_name":"2020_JournalCellScience_Dimchev.pdf","content_type":"application/pdf","date_updated":"2020-10-11T22:30:02Z","date_created":"2020-09-17T14:07:51Z","creator":"dernst","file_id":"8435","checksum":"ba917e551acc4ece2884b751434df9ae","file_size":13493302,"access_level":"open_access","relation":"main_file","embargo":"2020-10-10"}],"issue":"7","month":"04","has_accepted_license":"1","doi":"10.1242/jcs.239020","year":"2020","day":"09","acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft (DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.). G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program [M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives its core funding from Cancer Research UK [FC001209], theMedical Research Council [FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1]. Deposited in PMC for release after 6months.","oa":1,"publication":"Journal of Cell Science","intvolume":"       133","keyword":["Cell Biology"],"external_id":{"pmid":[" 32094266"],"isi":["000534387800005"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal, T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.239020\">https://doi.org/10.1242/jcs.239020</a>","chicago":"Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks, Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” <i>Journal of Cell Science</i>. The Company of Biologists, 2020. <a href=\"https://doi.org/10.1242/jcs.239020\">https://doi.org/10.1242/jcs.239020</a>.","ista":"Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 133(7), jcs239020.","ama":"Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. <i>Journal of Cell Science</i>. 2020;133(7). doi:<a href=\"https://doi.org/10.1242/jcs.239020\">10.1242/jcs.239020</a>","ieee":"G. A. Dimchev <i>et al.</i>, “Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation,” <i>Journal of Cell Science</i>, vol. 133, no. 7. The Company of Biologists, 2020.","short":"G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal, J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133 (2020).","mla":"Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” <i>Journal of Cell Science</i>, vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:<a href=\"https://doi.org/10.1242/jcs.239020\">10.1242/jcs.239020</a>."},"department":[{"_id":"FlSc"}],"date_updated":"2023-09-05T15:41:48Z","title":"Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation","pmid":1,"publisher":"The Company of Biologists","file_date_updated":"2020-10-11T22:30:02Z","date_published":"2020-04-09T00:00:00Z","ddc":["570"],"isi":1,"publication_status":"published","abstract":[{"lang":"eng","text":"Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin-binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex, an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.This article has an associated First Person interview with the first author of the paper. "}]},{"related_material":{"record":[{"status":"public","relation":"research_data","id":"13056"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-18912-9"},{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/","relation":"press_release"}]},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"intvolume":"        11","publication":"Nature Communications","oa":1,"acknowledgement":"We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET).","year":"2020","day":"08","doi":"10.1038/s41467-020-18269-z","abstract":[{"text":"Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a <jats:italic>V</jats:italic><jats:sub><jats:italic>π</jats:italic></jats:sub> as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform.","lang":"eng"}],"publication_status":"published","isi":1,"ddc":["530"],"publisher":"Springer Nature","file_date_updated":"2020-09-18T13:02:37Z","date_published":"2020-09-08T00:00:00Z","title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","date_updated":"2024-08-07T07:11:51Z","department":[{"_id":"JoFi"}],"citation":{"mla":"Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>, vol. 11, 4460, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>.","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460.","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>","ieee":"G. M. Arnold <i>et al.</i>, “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000577280200001"]},"ec_funded":1,"date_created":"2020-09-18T10:56:20Z","_id":"8529","type":"journal_article","article_type":"original","status":"public","publication_identifier":{"issn":["2041-1723"]},"has_accepted_license":"1","month":"09","file":[{"file_name":"2020_NatureComm_Arnold.pdf","content_type":"application/pdf","date_updated":"2020-09-18T13:02:37Z","date_created":"2020-09-18T13:02:37Z","creator":"dernst","file_id":"8530","checksum":"88f92544889eb18bb38e25629a422a86","file_size":1002818,"access_level":"open_access","success":1,"relation":"main_file"}],"article_number":"4460","language":[{"iso":"eng"}],"article_processing_charge":"No","acknowledged_ssus":[{"_id":"NanoFab"}],"volume":11,"quality_controlled":"1","project":[{"name":"Hybrid Optomechanical Technologies","grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Quantum readout techniques and technologies","grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"oa_version":"Published Version","author":[{"full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876","last_name":"Arnold","first_name":"Georg M"},{"first_name":"Matthias","last_name":"Wulf","orcid":"0000-0001-6613-1378","id":"45598606-F248-11E8-B48F-1D18A9856A87","full_name":"Wulf, Matthias"},{"full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","first_name":"Shabir","last_name":"Barzanjeh"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena","first_name":"Elena","last_name":"Redchenko"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","full_name":"Hease, William J","last_name":"Hease","first_name":"William J","orcid":"0000-0001-9868-2166"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid","first_name":"Farid","last_name":"Hassani","orcid":"0000-0001-6937-5773"},{"last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"}]},{"date_created":"2020-09-20T22:01:35Z","article_type":"original","type":"journal_article","_id":"8532","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"status":"public","ec_funded":1,"project":[{"grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020"},{"_id":"25D32BC0-B435-11E9-9278-68D0E5697425","name":"Mechanism of formation and maintenance of input side-dependent asymmetry in the hippocampus"},{"grant_number":"785907","_id":"26436750-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)","call_identifier":"H2020"}],"quality_controlled":"1","oa_version":"Published Version","author":[{"first_name":"David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David"},{"id":"3786AB44-F248-11E8-B48F-1D18A9856A87","full_name":"Montanaro-Punzengruber, Jacqueline-Claire","first_name":"Jacqueline-Claire","last_name":"Montanaro-Punzengruber"},{"first_name":"Pradeep","last_name":"Bhandari","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep"},{"last_name":"Case","first_name":"Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Case, Matthew J"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"}],"month":"09","has_accepted_license":"1","article_number":"6737","file":[{"content_type":"application/pdf","date_updated":"2020-09-21T14:08:58Z","date_created":"2020-09-21T14:08:58Z","file_name":"2020_JournMolecSciences_Kleindienst.pdf","success":1,"relation":"main_file","creator":"dernst","checksum":"2e4f62f3cfe945b7391fc3070e5a289f","file_id":"8551","file_size":5748456,"access_level":"open_access"}],"issue":"18","language":[{"iso":"eng"}],"volume":21,"article_processing_charge":"No","oa":1,"acknowledgement":"This research was funded by Austrian Academy of Sciences, DOC fellowship to D.K., European Research\r\nCouncil Advanced Grant 694539 and European Union Human Brain Project (HBP) SGA2 785907 to R.S.\r\nWe acknowledge Elena Hollergschwandtner for technical support.","day":"14","year":"2020","doi":"10.3390/ijms21186737","scopus_import":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9562"}]},"intvolume":"        21","publication":"International Journal of Molecular Sciences","department":[{"_id":"RySh"}],"date_updated":"2024-03-25T23:30:16Z","citation":{"chicago":"Kleindienst, David, Jacqueline-Claire Montanaro-Punzengruber, Pradeep Bhandari, Matthew J Case, Yugo Fukazawa, and Ryuichi Shigemoto. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” <i>International Journal of Molecular Sciences</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ijms21186737\">https://doi.org/10.3390/ijms21186737</a>.","ama":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. <i>International Journal of Molecular Sciences</i>. 2020;21(18). doi:<a href=\"https://doi.org/10.3390/ijms21186737\">10.3390/ijms21186737</a>","ista":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. 2020. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 21(18), 6737.","apa":"Kleindienst, D., Montanaro-Punzengruber, J.-C., Bhandari, P., Case, M. J., Fukazawa, Y., &#38; Shigemoto, R. (2020). Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms21186737\">https://doi.org/10.3390/ijms21186737</a>","ieee":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M. J. Case, Y. Fukazawa, and R. Shigemoto, “Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses,” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 18. MDPI, 2020.","short":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y. Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020).","mla":"Kleindienst, David, et al. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 18, 6737, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ijms21186737\">10.3390/ijms21186737</a>."},"external_id":{"isi":["000579945300001"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","abstract":[{"text":"The molecular anatomy of synapses defines their characteristics in transmission and plasticity. Precise measurements of the number and distribution of synaptic proteins are important for our understanding of synapse heterogeneity within and between brain regions. Freeze–fracture replica immunogold electron microscopy enables us to analyze them quantitatively on a two-dimensional membrane surface. Here, we introduce Darea software, which utilizes deep learning for analysis of replica images and demonstrate its usefulness for quick measurements of the pre- and postsynaptic areas, density and distribution of gold particles at synapses in a reproducible manner. We used Darea for comparing glutamate receptor and calcium channel distributions between hippocampal CA3-CA1 spine synapses on apical and basal dendrites, which differ in signaling pathways involved in synaptic plasticity. We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA) receptors with size. Interestingly, AMPA and NMDA receptors are segregated within postsynaptic sites and negatively correlated in density among both apical and basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels show similar densities in apical and basal synapses with distributions consistent with an exclusion zone model of calcium channel-release site topography.","lang":"eng"}],"ddc":["570"],"isi":1,"date_published":"2020-09-14T00:00:00Z","publisher":"MDPI","file_date_updated":"2020-09-21T14:08:58Z","title":"Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses"},{"ec_funded":1,"conference":{"start_date":"2020-08-24","end_date":"2020-08-28","location":"Prague, Czech Republic","name":"MFCS: Symposium on Mathematical Foundations of Computer Science"},"type":"conference","_id":"8533","date_created":"2020-09-20T22:01:36Z","license":"https://creativecommons.org/licenses/by/3.0/","publication_identifier":{"issn":["18688969"],"isbn":["9783959771597"]},"status":"public","article_number":"22:1-22:13","file":[{"file_name":"2020_LIPIcs_Chatterjee.pdf","content_type":"application/pdf","date_updated":"2020-09-21T13:57:34Z","date_created":"2020-09-21T13:57:34Z","creator":"dernst","checksum":"bbd7c4f55d45f2ff2a0a4ef0e10a77b1","file_id":"8550","file_size":491374,"access_level":"open_access","success":1,"relation":"main_file"}],"has_accepted_license":"1","month":"08","article_processing_charge":"No","volume":170,"language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","first_name":"Rasmus"},{"last_name":"Jecker","first_name":"Ismael R","full_name":"Jecker, Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425"},{"last_name":"Svoboda","first_name":"Jakub","orcid":"0000-0002-1419-3267","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub"}],"scopus_import":"1","publication":"45th International Symposium on Mathematical Foundations of Computer Science","intvolume":"       170","arxiv":1,"oa":1,"doi":"10.4230/LIPIcs.MFCS.2020.22","year":"2020","day":"18","acknowledgement":"Krishnendu Chatterjee: The research was partially supported by the Vienna Science and\r\nTechnology Fund (WWTF) Project ICT15-003.\r\nIsmaël Jecker: This project has received funding from the European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","ddc":["000"],"abstract":[{"text":"Game of Life is a simple and elegant model to study dynamical system over networks. The model consists of a graph where every vertex has one of two types, namely, dead or alive. A configuration is a mapping of the vertices to the types. An update rule describes how the type of a vertex is updated given the types of its neighbors. In every round, all vertices are updated synchronously, which leads to a configuration update. While in general, Game of Life allows a broad range of update rules, we focus on two simple families of update rules, namely, underpopulation and overpopulation, that model several interesting dynamics studied in the literature. In both settings, a dead vertex requires at least a desired number of live neighbors to become alive. For underpopulation (resp., overpopulation), a live vertex requires at least (resp. at most) a desired number of live neighbors to remain alive. We study the basic computation problems, e.g., configuration reachability, for these two families of rules. For underpopulation rules, we show that these problems can be solved in polynomial time, whereas for overpopulation rules they are PSPACE-complete.","lang":"eng"}],"publication_status":"published","title":"Simplified game of life: Algorithms and complexity","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_published":"2020-08-18T00:00:00Z","file_date_updated":"2020-09-21T13:57:34Z","citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, I.R. Jecker, J. Svoboda, in:, 45th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","mla":"Chatterjee, Krishnendu, et al. “Simplified Game of Life: Algorithms and Complexity.” <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, vol. 170, 22:1-22:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">10.4230/LIPIcs.MFCS.2020.22</a>.","ieee":"K. Chatterjee, R. Ibsen-Jensen, I. R. Jecker, and J. Svoboda, “Simplified game of life: Algorithms and complexity,” in <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Prague, Czech Republic, 2020, vol. 170.","apa":"Chatterjee, K., Ibsen-Jensen, R., Jecker, I. R., &#38; Svoboda, J. (2020). Simplified game of life: Algorithms and complexity. In <i>45th International Symposium on Mathematical Foundations of Computer Science</i> (Vol. 170). Prague, Czech Republic: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">https://doi.org/10.4230/LIPIcs.MFCS.2020.22</a>","ista":"Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. 2020. Simplified game of life: Algorithms and complexity. 45th International Symposium on Mathematical Foundations of Computer Science. MFCS: Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 170, 22:1-22:13.","ama":"Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. Simplified game of life: Algorithms and complexity. In: <i>45th International Symposium on Mathematical Foundations of Computer Science</i>. Vol 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">10.4230/LIPIcs.MFCS.2020.22</a>","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Ismael R Jecker, and Jakub Svoboda. “Simplified Game of Life: Algorithms and Complexity.” In <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Vol. 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">https://doi.org/10.4230/LIPIcs.MFCS.2020.22</a>."},"date_updated":"2025-06-02T08:53:42Z","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"alternative_title":["LIPIcs"],"external_id":{"arxiv":["2007.02894"]}},{"citation":{"apa":"Jecker, I. R., Kupferman, O., &#38; Mazzocchi, N. (2020). Unary prime languages. In <i>45th International Symposium on Mathematical Foundations of Computer Science</i> (Vol. 170). Prague, Czech Republic: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">https://doi.org/10.4230/LIPIcs.MFCS.2020.51</a>","ama":"Jecker IR, Kupferman O, Mazzocchi N. Unary prime languages. In: <i>45th International Symposium on Mathematical Foundations of Computer Science</i>. Vol 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">10.4230/LIPIcs.MFCS.2020.51</a>","ista":"Jecker IR, Kupferman O, Mazzocchi N. 2020. Unary prime languages. 45th International Symposium on Mathematical Foundations of Computer Science. MFCS: Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 170, 51:1-51:12.","chicago":"Jecker, Ismael R, Orna Kupferman, and Nicolas Mazzocchi. “Unary Prime Languages.” In <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Vol. 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">https://doi.org/10.4230/LIPIcs.MFCS.2020.51</a>.","ieee":"I. R. Jecker, O. Kupferman, and N. Mazzocchi, “Unary prime languages,” in <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Prague, Czech Republic, 2020, vol. 170.","short":"I.R. Jecker, O. Kupferman, N. Mazzocchi, in:, 45th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","mla":"Jecker, Ismael R., et al. “Unary Prime Languages.” <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, vol. 170, 51:1-51:12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">10.4230/LIPIcs.MFCS.2020.51</a>."},"department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T08:19:56Z","alternative_title":["LIPIcs"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"ddc":["000"],"publication_status":"published","abstract":[{"lang":"eng","text":"A regular language L of finite words is composite if there are regular languages L₁,L₂,…,L_t such that L = ⋂_{i = 1}^t L_i and the index (number of states in a minimal DFA) of every language L_i is strictly smaller than the index of L. Otherwise, L is prime. Primality of regular languages was introduced and studied in [O. Kupferman and J. Mosheiff, 2015], where the complexity of deciding the primality of the language of a given DFA was left open, with a doubly-exponential gap between the upper and lower bounds. We study primality for unary regular languages, namely regular languages with a singleton alphabet. A unary language corresponds to a subset of ℕ, making the study of unary prime languages closer to that of primality in number theory. We show that the setting of languages is richer. In particular, while every composite number is the product of two smaller numbers, the number t of languages necessary to decompose a composite unary language induces a strict hierarchy. In addition, a primality witness for a unary language L, namely a word that is not in L but is in all products of languages that contain L and have an index smaller than L’s, may be of exponential length. Still, we are able to characterize compositionality by structural properties of a DFA for L, leading to a LogSpace algorithm for primality checking of unary DFAs."}],"title":"Unary prime languages","date_published":"2020-08-18T00:00:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-09-21T14:17:08Z","oa":1,"doi":"10.4230/LIPIcs.MFCS.2020.51","year":"2020","day":"18","acknowledgement":"Ismaël Jecker: This project has received funding from the European Union’s Horizon\r\n2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No.\r\n754411. Nicolas Mazzocchi: PhD fellowship FRIA from the F.R.S.-FNRS.","scopus_import":"1","publication":"45th International Symposium on Mathematical Foundations of Computer Science","intvolume":"       170","oa_version":"Published Version","project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","author":[{"first_name":"Ismael R","last_name":"Jecker","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","full_name":"Jecker, Ismael R"},{"full_name":"Kupferman, Orna","first_name":"Orna","last_name":"Kupferman"},{"first_name":"Nicolas","last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas"}],"article_number":"51:1-51:12","file":[{"file_name":"2020_LIPIcsMFCS_Jecker.pdf","content_type":"application/pdf","date_created":"2020-09-21T14:17:08Z","date_updated":"2020-09-21T14:17:08Z","checksum":"2dc9e2fad6becd4563aef3e27a473f70","file_id":"8552","creator":"dernst","access_level":"open_access","file_size":597977,"success":1,"relation":"main_file"}],"has_accepted_license":"1","month":"08","volume":170,"article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"8534","type":"conference","date_created":"2020-09-20T22:01:36Z","status":"public","publication_identifier":{"isbn":["9783959771597"],"issn":["18688969"]},"conference":{"name":"MFCS: Symposium on Mathematical Foundations of Computer Science","location":"Prague, Czech Republic","end_date":"2020-08-28","start_date":"2020-08-24"},"ec_funded":1},{"project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"}],"quality_controlled":"1","oa_version":"Published Version","author":[{"id":"486A5A46-F248-11E8-B48F-1D18A9856A87","full_name":"Skrivan, Tomas","last_name":"Skrivan","first_name":"Tomas"},{"first_name":"Andreas","last_name":"Soderstrom","full_name":"Soderstrom, Andreas"},{"full_name":"Johansson, John","first_name":"John","last_name":"Johansson"},{"first_name":"Christoph","last_name":"Sprenger","full_name":"Sprenger, Christoph"},{"first_name":"Ken","last_name":"Museth","full_name":"Museth, Ken"},{"orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"month":"07","has_accepted_license":"1","issue":"4","article_number":"65","file":[{"relation":"main_file","success":1,"file_size":20223953,"access_level":"open_access","creator":"dernst","checksum":"c3a680893f01cc4a9e961ff0a4cfa12f","file_id":"8541","date_updated":"2020-09-21T07:51:44Z","date_created":"2020-09-21T07:51:44Z","content_type":"application/pdf","file_name":"2020_ACM_Skrivan.pdf"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"}],"volume":39,"date_created":"2020-09-20T22:01:37Z","type":"journal_article","_id":"8535","article_type":"original","publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"status":"public","ec_funded":1,"date_updated":"2023-08-22T09:28:27Z","department":[{"_id":"ChWo"}],"citation":{"mla":"Skrivan, Tomas, et al. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4, 65, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3386569.3392466\">10.1145/3386569.3392466</a>.","short":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan, ACM Transactions on Graphics 39 (2020).","apa":"Skrivan, T., Soderstrom, A., Johansson, J., Sprenger, C., Museth, K., &#38; Wojtan, C. (2020). Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3386569.3392466\">https://doi.org/10.1145/3386569.3392466</a>","ista":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. 2020. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 39(4), 65.","ama":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. <i>ACM Transactions on Graphics</i>. 2020;39(4). doi:<a href=\"https://doi.org/10.1145/3386569.3392466\">10.1145/3386569.3392466</a>","chicago":"Skrivan, Tomas, Andreas Soderstrom, John Johansson, Christoph Sprenger, Ken Museth, and Chris Wojtan. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3386569.3392466\">https://doi.org/10.1145/3386569.3392466</a>.","ieee":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, and C. Wojtan, “Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4. Association for Computing Machinery, 2020."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000583700300038"]},"abstract":[{"text":"We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation.","lang":"eng"}],"publication_status":"published","isi":1,"ddc":["000"],"file_date_updated":"2020-09-21T07:51:44Z","date_published":"2020-07-08T00:00:00Z","publisher":"Association for Computing Machinery","title":"Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces","oa":1,"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176 and Marie SkłodowskaCurie Grant Agreement No. 665385.","day":"08","doi":"10.1145/3386569.3392466","year":"2020","scopus_import":"1","intvolume":"        39","publication":"ACM Transactions on Graphics"},{"month":"06","article_number":"401-406","language":[{"iso":"eng"}],"volume":"2020-June","article_processing_charge":"No","quality_controlled":"1","oa_version":"Preprint","author":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","first_name":"Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020"},{"full_name":"Hashemi, Seyyed Ali","first_name":"Seyyed Ali","last_name":"Hashemi"},{"last_name":"Cioffi","first_name":"John","full_name":"Cioffi, John"},{"last_name":"Goldsmith","first_name":"Andrea","full_name":"Goldsmith, Andrea"}],"conference":{"end_date":"2020-06-26","start_date":"2020-06-21","location":"Los Angeles, CA, United States","name":"ISIT: Internation Symposium on Information Theory"},"date_created":"2020-09-20T22:01:37Z","_id":"8536","type":"conference","publication_identifier":{"isbn":["9781728164328"],"issn":["21578095"]},"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1909.04892"}],"publication_status":"published","abstract":[{"lang":"eng","text":"This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N 1−1/µ ), where N is the block length and µ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 and 1."}],"date_published":"2020-06-01T00:00:00Z","publisher":"IEEE","title":"Simplified successive cancellation decoding of polar codes has sublinear latency","department":[{"_id":"MaMo"}],"date_updated":"2023-08-07T13:36:24Z","citation":{"short":"M. Mondelli, S.A. Hashemi, J. Cioffi, A. Goldsmith, in:, IEEE International Symposium on Information Theory - Proceedings, IEEE, 2020.","mla":"Mondelli, Marco, et al. “Simplified Successive Cancellation Decoding of Polar Codes Has Sublinear Latency.” <i>IEEE International Symposium on Information Theory - Proceedings</i>, vol. 2020–June, 401–406, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">10.1109/ISIT44484.2020.9174141</a>.","apa":"Mondelli, M., Hashemi, S. A., Cioffi, J., &#38; Goldsmith, A. (2020). Simplified successive cancellation decoding of polar codes has sublinear latency. In <i>IEEE International Symposium on Information Theory - Proceedings</i> (Vol. 2020–June). Los Angeles, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">https://doi.org/10.1109/ISIT44484.2020.9174141</a>","ista":"Mondelli M, Hashemi SA, Cioffi J, Goldsmith A. 2020. Simplified successive cancellation decoding of polar codes has sublinear latency. IEEE International Symposium on Information Theory - Proceedings. ISIT: Internation Symposium on Information Theory vol. 2020–June, 401–406.","chicago":"Mondelli, Marco, Seyyed Ali Hashemi, John Cioffi, and Andrea Goldsmith. “Simplified Successive Cancellation Decoding of Polar Codes Has Sublinear Latency.” In <i>IEEE International Symposium on Information Theory - Proceedings</i>, Vol. 2020–June. IEEE, 2020. <a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">https://doi.org/10.1109/ISIT44484.2020.9174141</a>.","ama":"Mondelli M, Hashemi SA, Cioffi J, Goldsmith A. Simplified successive cancellation decoding of polar codes has sublinear latency. In: <i>IEEE International Symposium on Information Theory - Proceedings</i>. Vol 2020-June. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">10.1109/ISIT44484.2020.9174141</a>","ieee":"M. Mondelli, S. A. Hashemi, J. Cioffi, and A. Goldsmith, “Simplified successive cancellation decoding of polar codes has sublinear latency,” in <i>IEEE International Symposium on Information Theory - Proceedings</i>, Los Angeles, CA, United States, 2020, vol. 2020–June."},"external_id":{"arxiv":["1909.04892"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","related_material":{"record":[{"status":"public","relation":"later_version","id":"9047"}]},"arxiv":1,"publication":"IEEE International Symposium on Information Theory - Proceedings","oa":1,"acknowledgement":"M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305, IIS-1741162 and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council of Canada (NSERC) and by Huawei.","year":"2020","doi":"10.1109/ISIT44484.2020.9174141","day":"01"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"arxiv":["2001.02934"]},"citation":{"ieee":"A. Akopyan, R. Schwartz, and S. Tabachnikov, “Billiards in ellipses revisited,” <i>European Journal of Mathematics</i>. Springer Nature, 2020.","ista":"Akopyan A, Schwartz R, Tabachnikov S. 2020. Billiards in ellipses revisited. European Journal of Mathematics.","ama":"Akopyan A, Schwartz R, Tabachnikov S. Billiards in ellipses revisited. <i>European Journal of Mathematics</i>. 2020. doi:<a href=\"https://doi.org/10.1007/s40879-020-00426-9\">10.1007/s40879-020-00426-9</a>","chicago":"Akopyan, Arseniy, Richard Schwartz, and Serge Tabachnikov. “Billiards in Ellipses Revisited.” <i>European Journal of Mathematics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s40879-020-00426-9\">https://doi.org/10.1007/s40879-020-00426-9</a>.","apa":"Akopyan, A., Schwartz, R., &#38; Tabachnikov, S. (2020). Billiards in ellipses revisited. <i>European Journal of Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40879-020-00426-9\">https://doi.org/10.1007/s40879-020-00426-9</a>","short":"A. Akopyan, R. Schwartz, S. Tabachnikov, European Journal of Mathematics (2020).","mla":"Akopyan, Arseniy, et al. “Billiards in Ellipses Revisited.” <i>European Journal of Mathematics</i>, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1007/s40879-020-00426-9\">10.1007/s40879-020-00426-9</a>."},"date_updated":"2021-12-02T15:10:17Z","department":[{"_id":"HeEd"}],"title":"Billiards in ellipses revisited","date_published":"2020-09-09T00:00:00Z","publisher":"Springer Nature","abstract":[{"text":"We prove some recent experimental observations of Dan Reznik concerning periodic billiard orbits in ellipses. For example, the sum of cosines of the angles of a periodic billiard polygon remains constant in the 1-parameter family of such polygons (that exist due to the Poncelet porism). In our proofs, we use geometric and complex analytic methods.","lang":"eng"}],"publication_status":"published","doi":"10.1007/s40879-020-00426-9","day":"09","year":"2020","acknowledgement":" This paper would not be written if not for Dan Reznik’s curiosity and persistence; we are very grateful to him. We also thank R. Garcia and J. Koiller for interesting discussions. It is a pleasure to thank the Mathematical Institute of the University of Heidelberg for its stimulating atmosphere. ST thanks M. Bialy for interesting discussions and the Tel Aviv\r\nUniversity for its invariable hospitality. AA was supported by European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). RS is supported by NSF Grant DMS-1807320. ST was supported by NSF grant DMS-1510055 and SFB/TRR 191.","oa":1,"publication":"European Journal of Mathematics","arxiv":1,"scopus_import":"1","author":[{"orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schwartz, Richard","last_name":"Schwartz","first_name":"Richard"},{"full_name":"Tabachnikov, Serge","last_name":"Tabachnikov","first_name":"Serge"}],"oa_version":"Preprint","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"eissn":["2199-6768"],"issn":["2199-675X"]},"main_file_link":[{"url":"https://arxiv.org/abs/2001.02934","open_access":"1"}],"status":"public","_id":"8538","type":"journal_article","article_type":"original","date_created":"2020-09-20T22:01:38Z","ec_funded":1},{"page":"663-671","year":"2020","doi":"10.24033/asens.2431","day":"01","oa":1,"publication":"Annales Scientifiques de l'Ecole Normale Superieure","intvolume":"        53","arxiv":1,"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["1708.08013"],"isi":["000592182600004"]},"citation":{"ieee":"C. Su, G. Zhao, and C. Zhong, “On the K-theory stable bases of the springer resolution,” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>, vol. 53, no. 3. Société Mathématique de France, pp. 663–671, 2020.","ista":"Su C, Zhao G, Zhong C. 2020. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 53(3), 663–671.","chicago":"Su, C., Gufang Zhao, and C. Zhong. “On the K-Theory Stable Bases of the Springer Resolution.” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. Société Mathématique de France, 2020. <a href=\"https://doi.org/10.24033/asens.2431\">https://doi.org/10.24033/asens.2431</a>.","ama":"Su C, Zhao G, Zhong C. On the K-theory stable bases of the springer resolution. <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. 2020;53(3):663-671. doi:<a href=\"https://doi.org/10.24033/asens.2431\">10.24033/asens.2431</a>","apa":"Su, C., Zhao, G., &#38; Zhong, C. (2020). On the K-theory stable bases of the springer resolution. <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. Société Mathématique de France. <a href=\"https://doi.org/10.24033/asens.2431\">https://doi.org/10.24033/asens.2431</a>","short":"C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure 53 (2020) 663–671.","mla":"Su, C., et al. “On the K-Theory Stable Bases of the Springer Resolution.” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>, vol. 53, no. 3, Société Mathématique de France, 2020, pp. 663–71, doi:<a href=\"https://doi.org/10.24033/asens.2431\">10.24033/asens.2431</a>."},"date_updated":"2023-08-22T09:27:57Z","department":[{"_id":"TaHa"}],"title":"On the K-theory stable bases of the springer resolution","date_published":"2020-06-01T00:00:00Z","publisher":"Société Mathématique de France","isi":1,"abstract":[{"text":"Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions.","lang":"eng"},{"text":"Les bases stables cohomologiques et K-théoriques proviennent de l’étude de la cohomologie quantique et de la K-théorie quantique. La formule de restriction pour les bases stables cohomologiques a joué un rôle important dans le calcul de la connexion quantique du fibré cotangent de variétés de drapeaux partielles. Dans cet article, nous étudions les bases stables K-théoriques de fibré cotangents des variétés de drapeaux. Nous décrivons ces bases en fonction de l’action de l’algèbre de Hecke affine et de l’algèbre de Kostant-Kumar. En utilisant cette description algébrique et la méthode des polynômes de racine, nous donnons une formule de restriction des bases stables. Nous l’appliquons\r\npour obtenir la formule de restriction pour les variétés de drapeaux partielles. Nous construisons également une relation entre la base stable et la base de Casselman dans les représentations de la série principale du groupe dual de Langlands p-adique. Comme une application, nous donnons une formule close pour la matrice de transition entre la base de Casselman et les fonctions caractéristiques. ","lang":"fre"}],"publication_status":"published","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08013"}],"publication_identifier":{"issn":["0012-9593"]},"_id":"8539","type":"journal_article","article_type":"original","date_created":"2020-09-20T22:01:38Z","author":[{"full_name":"Su, C.","last_name":"Su","first_name":"C."},{"last_name":"Zhao","first_name":"Gufang","full_name":"Zhao, Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhong","first_name":"C.","full_name":"Zhong, C."}],"oa_version":"Preprint","quality_controlled":"1","article_processing_charge":"No","volume":53,"language":[{"iso":"eng"}],"issue":"3","month":"06"},{"publication":"bioRxiv","ec_funded":1,"related_material":{"record":[{"status":"public","id":"10614","relation":"later_version"},{"status":"public","id":"8983","relation":"dissertation_contains"}]},"doi":"10.1101/2020.09.18.301481","status":"public","day":"18","year":"2020","main_file_link":[{"url":"https://doi.org/10.1101/2020.09.18.301481","open_access":"1"}],"acknowledgement":"We thank the following for their contributions: The Drosophila Genomics Resource Center supported by NIH grant 2P40OD010949-10A1 for plasmids, K. Brueckner. B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center supported by NIH grant P40OD018537 and the Vienna Drosophila Resource Center for fly stocks, FlyBase (Thurmond et al., 2019) for essential genomic information, and the BDGP in situ database for data (Tomancak et al., 2002, 2007). For antibodies, we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the NIH, and is maintained at the University of Iowa, as well as J. Zeitlinger for her generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for RNA sequencing and analysis and the Life Scientific Service Units at IST Austria for technical support and assistance with microscopy and FACS analysis. We thank C.P. Heisenberg, P. Martin, M. Sixt and Siekhaus group members for discussions and T.Hurd, A. Ratheesh and P. Rangan for comments on the manuscript. A.G. was supported by the Austrian Science Fund (FWF) grant DASI_FWF01_P29638S, D.E.S. by Marie Curie CIG 334077/IRTIM. M.S. is supported by the FWF, PhD program W1212 915 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883). S.W. is supported by an OEAW, DOC fellowship.","type":"preprint","_id":"8557","oa":1,"date_created":"2020-09-23T09:36:47Z","title":"Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance","article_processing_charge":"No","acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"date_published":"2020-09-18T00:00:00Z","month":"09","publication_status":"submitted","abstract":[{"lang":"eng","text":"The infiltration of immune cells into tissues underlies the establishment of tissue resident macrophages, and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio which are themselves required for invasion. Cortical F-actin levels are critical as expressing a dominant active form of Diaphanous, a actin polymerizing Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo imaging shows that Dfos is required to enhance the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the mechanical properties of the macrophage nucleus from affecting tissue entry. We thus identify tuning the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Belyaeva, Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","last_name":"Belyaeva","first_name":"Vera"},{"id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","full_name":"Wachner, Stephanie","first_name":"Stephanie","last_name":"Wachner"},{"first_name":"Igor","last_name":"Gridchyn","orcid":"0000-0002-1807-1929","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","full_name":"Gridchyn, Igor"},{"first_name":"Markus","last_name":"Linder","full_name":"Linder, Markus"},{"last_name":"Emtenani","first_name":"Shamsi","orcid":"0000-0001-6981-6938","id":"49D32318-F248-11E8-B48F-1D18A9856A87","full_name":"Emtenani, Shamsi"},{"first_name":"Attila","last_name":"György","orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","full_name":"György, Attila"},{"first_name":"Maria","last_name":"Sibilia","full_name":"Sibilia, Maria"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","first_name":"Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353"}],"citation":{"ieee":"V. Belyaeva <i>et al.</i>, “Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance,” <i>bioRxiv</i>. .","ista":"Belyaeva V, Wachner S, Gridchyn I, Linder M, Emtenani S, György A, Sibilia M, Siekhaus DE. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv, <a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>.","chicago":"Belyaeva, Vera, Stephanie Wachner, Igor Gridchyn, Markus Linder, Shamsi Emtenani, Attila György, Maria Sibilia, and Daria E Siekhaus. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2020.09.18.301481\">https://doi.org/10.1101/2020.09.18.301481</a>.","ama":"Belyaeva V, Wachner S, Gridchyn I, et al. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>","apa":"Belyaeva, V., Wachner, S., Gridchyn, I., Linder, M., Emtenani, S., György, A., … Siekhaus, D. E. (n.d.). Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2020.09.18.301481\">https://doi.org/10.1101/2020.09.18.301481</a>","short":"V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György, M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.).","mla":"Belyaeva, Vera, et al. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>."},"oa_version":"Preprint","department":[{"_id":"DaSi"},{"_id":"JoCs"}],"project":[{"grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425","name":"Drosophila TNFa´s Funktion in Immunzellen","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions"},{"name":"Tissue barrier penetration is crucial for immunity and metastasis","_id":"26199CA4-B435-11E9-9278-68D0E5697425","grant_number":"24800"}],"date_updated":"2024-03-25T23:30:12Z"},{"author":[{"full_name":"Gavriil, Konstantinos","first_name":"Konstantinos","last_name":"Gavriil"},{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","full_name":"Guseinov, Ruslan","first_name":"Ruslan","last_name":"Guseinov","orcid":"0000-0001-9819-5077"},{"first_name":"Jesus","last_name":"Perez Rodriguez","full_name":"Perez Rodriguez, Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pellis, Davide","first_name":"Davide","last_name":"Pellis"},{"id":"13C09E74-18D9-11E9-8878-32CFE5697425","full_name":"Henderson, Paul M","last_name":"Henderson","first_name":"Paul M","orcid":"0000-0002-5198-7445"},{"full_name":"Rist, Florian","last_name":"Rist","first_name":"Florian"},{"first_name":"Helmut","last_name":"Pottmann","full_name":"Pottmann, Helmut"},{"orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"oa_version":"Submitted Version","language":[{"iso":"eng"}],"volume":39,"article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"}],"month":"11","has_accepted_license":"1","file":[{"relation":"main_file","success":1,"checksum":"c7f67717ad74e670b7daeae732abe151","file_id":"13084","creator":"bbickel","access_level":"open_access","file_size":28964641,"content_type":"application/pdf","date_created":"2023-05-23T20:54:43Z","date_updated":"2023-05-23T20:54:43Z","file_name":"coldglass.pdf"}],"article_number":"208","issue":"6","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"status":"public","date_created":"2020-09-23T11:30:02Z","article_type":"original","type":"journal_article","_id":"8562","ec_funded":1,"external_id":{"arxiv":["2009.03667"],"isi":["000595589100048"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BeBi"}],"date_updated":"2024-02-21T12:43:21Z","citation":{"ama":"Gavriil K, Guseinov R, Perez Rodriguez J, et al. Computational design of cold bent glass façades. <i>ACM Transactions on Graphics</i>. 2020;39(6). doi:<a href=\"https://doi.org/10.1145/3414685.3417843\">10.1145/3414685.3417843</a>","ista":"Gavriil K, Guseinov R, Perez Rodriguez J, Pellis D, Henderson PM, Rist F, Pottmann H, Bickel B. 2020. Computational design of cold bent glass façades. ACM Transactions on Graphics. 39(6), 208.","chicago":"Gavriil, Konstantinos, Ruslan Guseinov, Jesus Perez Rodriguez, Davide Pellis, Paul M Henderson, Florian Rist, Helmut Pottmann, and Bernd Bickel. “Computational Design of Cold Bent Glass Façades.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3414685.3417843\">https://doi.org/10.1145/3414685.3417843</a>.","apa":"Gavriil, K., Guseinov, R., Perez Rodriguez, J., Pellis, D., Henderson, P. M., Rist, F., … Bickel, B. (2020). Computational design of cold bent glass façades. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3414685.3417843\">https://doi.org/10.1145/3414685.3417843</a>","ieee":"K. Gavriil <i>et al.</i>, “Computational design of cold bent glass façades,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 6. Association for Computing Machinery, 2020.","mla":"Gavriil, Konstantinos, et al. “Computational Design of Cold Bent Glass Façades.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 6, 208, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3414685.3417843\">10.1145/3414685.3417843</a>.","short":"K. Gavriil, R. Guseinov, J. Perez Rodriguez, D. Pellis, P.M. Henderson, F. Rist, H. Pottmann, B. Bickel, ACM Transactions on Graphics 39 (2020)."},"file_date_updated":"2023-05-23T20:54:43Z","publisher":"Association for Computing Machinery","date_published":"2020-11-26T00:00:00Z","title":"Computational design of cold bent glass façades","publication_status":"published","abstract":[{"lang":"eng","text":"Cold bent glass is a promising and cost-efficient method for realizing doubly curved glass facades. They are produced by attaching planar glass sheets to curved frames and require keeping the occurring stress within safe limits.\r\nHowever, it is very challenging to navigate the design space of cold bent glass panels due to the fragility of the material, which impedes the form-finding for practically feasible and aesthetically pleasing cold bent glass facades. We propose an interactive, data-driven approach for designing cold bent glass facades that can be seamlessly integrated into a typical architectural design pipeline. Our method allows non-expert users to interactively edit a parametric surface while providing real-time feedback on the deformed shape and maximum stress of cold bent glass panels. Designs are automatically refined to minimize several fairness criteria while maximal stresses are kept within glass limits. We achieve interactive frame rates by using a differentiable Mixture Density Network trained from more than a million simulations. Given a curved boundary, our regression model is capable of handling multistable\r\nconfigurations and accurately predicting the equilibrium shape of the panel and its corresponding maximal stress. We show predictions are highly accurate and validate our results with a physical realization of a cold bent glass surface."}],"isi":1,"ddc":["000"],"acknowledgement":"We thank IST Austria’s Scientific Computing team for their support, Corinna Datsiou and Sophie Pennetier for their expert input on the practical applications of cold bent glass, and Zaha Hadid Architects and Waagner Biro for providing the architectural datasets. Photo of Fondation Louis Vuitton by Francisco Anzola / CC BY 2.0 / cropped.\r\nPhoto of Opus by Danica O. Kus. This project has received funding from the European Union’s\r\nHorizon 2020 research and innovation program under grant agreement No 675789 - Algebraic Representations in Computer-Aided Design for complEx Shapes (ARCADES), from the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, and SFB-Transregio “Discretization in Geometry and Dynamics” through grant I 2978 of the Austrian Science Fund (FWF). F. Rist and K. Gavriil have been partially supported by KAUST baseline funding.","year":"2020","day":"26","doi":"10.1145/3414685.3417843","oa":1,"arxiv":1,"intvolume":"        39","publication":"ACM Transactions on Graphics","scopus_import":"1","related_material":{"record":[{"id":"8366","relation":"dissertation_contains","status":"public"},{"id":"8761","relation":"research_data","status":"public"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/bend-dont-break/","relation":"press_release"}]}},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8740"}]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","year":"2020","doi":"10.15479/AT:ISTA:8563","day":"19","status":"public","_id":"8563","type":"research_data","oa":1,"date_created":"2020-09-23T14:39:54Z","title":"Optogenetic alteration of hippocampal network activity","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-10-19T10:12:29Z","date_published":"2020-10-19T00:00:00Z","file":[{"relation":"main_file","success":1,"creator":"jozsef","checksum":"a16098a6d172f9c42ab5af5f6991668c","file_id":"8564","file_size":145243906,"access_level":"open_access","content_type":"application/x-compressed","date_updated":"2020-09-23T14:36:17Z","date_created":"2020-09-23T14:36:17Z","file_name":"upload.tgz"},{"success":1,"relation":"main_file","file_size":11648,"access_level":"open_access","creator":"jozsef","checksum":"0bfc54b7e14c0694cd081617318ba606","file_id":"8675","date_updated":"2020-10-19T10:12:29Z","date_created":"2020-10-19T10:12:29Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"redme.docx"}],"ddc":["570"],"month":"10","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Supplementary data  provided for the provided for the publication:\r\nIgor Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. Elife."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1807-1929","first_name":"Igor","last_name":"Gridchyn","full_name":"Gridchyn, Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87"},{"id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","full_name":"Schönenberger, Philipp","first_name":"Philipp","last_name":"Schönenberger"}],"contributor":[{"first_name":"Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_leader"}],"citation":{"ieee":"J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020.","ista":"Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8563\">10.15479/AT:ISTA:8563</a>.","chicago":"Csicsvari, Jozsef L, Igor Gridchyn, and Philipp Schönenberger. “Optogenetic Alteration of Hippocampal Network Activity.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8563\">https://doi.org/10.15479/AT:ISTA:8563</a>.","ama":"Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal network activity. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8563\">10.15479/AT:ISTA:8563</a>","apa":"Csicsvari, J. L., Gridchyn, I., &#38; Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8563\">https://doi.org/10.15479/AT:ISTA:8563</a>","short":"J.L. Csicsvari, I. Gridchyn, P. Schönenberger, (2020).","mla":"Csicsvari, Jozsef L., et al. <i>Optogenetic Alteration of Hippocampal Network Activity</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8563\">10.15479/AT:ISTA:8563</a>."},"oa_version":"Published Version","department":[{"_id":"JoCs"}],"date_updated":"2024-02-21T12:43:41Z"},{"publication":"Nature Communications","intvolume":"        11","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-020-19720-x","relation":"erratum"}]},"day":"24","year":"2020","doi":"10.1038/s41467-020-18610-6","oa":1,"title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","date_published":"2020-09-24T00:00:00Z","file_date_updated":"2020-09-28T13:16:15Z","publisher":"Springer Nature","isi":1,"ddc":["530"],"publication_status":"published","abstract":[{"lang":"eng","text":"Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries."}],"external_id":{"isi":["000573756600004"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"C. Prehal <i>et al.</i>, “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ama":"Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18610-6\">10.1038/s41467-020-18610-6</a>","ista":"Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 11, 4838.","chicago":"Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18610-6\">https://doi.org/10.1038/s41467-020-18610-6</a>.","apa":"Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger, S. A., &#38; Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition in nanoporous carbons. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18610-6\">https://doi.org/10.1038/s41467-020-18610-6</a>","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","mla":"Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” <i>Nature Communications</i>, vol. 11, 4838, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18610-6\">10.1038/s41467-020-18610-6</a>."},"department":[{"_id":"StFr"}],"date_updated":"2023-08-22T09:37:24Z","publication_identifier":{"issn":["2041-1723"]},"status":"public","article_type":"original","type":"journal_article","_id":"8568","date_created":"2020-09-25T07:23:13Z","volume":11,"article_processing_charge":"No","language":[{"iso":"eng"}],"article_number":"4838","file":[{"file_size":1822469,"access_level":"open_access","creator":"dernst","file_id":"8585","checksum":"eada7bc8dd16a49390137cff882ef328","relation":"main_file","success":1,"file_name":"2020_NatureComm_Prehal.pdf","date_updated":"2020-09-28T13:16:15Z","date_created":"2020-09-28T13:16:15Z","content_type":"application/pdf"}],"month":"09","has_accepted_license":"1","author":[{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"full_name":"Fitzek, Harald","last_name":"Fitzek","first_name":"Harald"},{"last_name":"Kothleitner","first_name":"Gerald","full_name":"Kothleitner, Gerald"},{"full_name":"Presser, Volker","first_name":"Volker","last_name":"Presser"},{"last_name":"Gollas","first_name":"Bernhard","full_name":"Gollas, Bernhard"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319"},{"last_name":"Abbas","first_name":"Qamar","full_name":"Abbas, Qamar"}],"oa_version":"Published Version","quality_controlled":"1"},{"has_accepted_license":"1","month":"09","issue":"9","article_number":"574382","file":[{"creator":"dernst","checksum":"01f731824194c94c81a5da360d997073","file_id":"8584","file_size":5527139,"access_level":"open_access","success":1,"relation":"main_file","file_name":"2020_Frontiers_Hansen.pdf","content_type":"application/pdf","date_updated":"2020-09-28T13:11:17Z","date_created":"2020-09-28T13:11:17Z"}],"language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","volume":8,"project":[{"grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444","call_identifier":"FP7"}],"quality_controlled":"1","oa_version":"Published Version","author":[{"last_name":"Hansen","first_name":"Andi H","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"ec_funded":1,"date_created":"2020-09-26T06:11:07Z","_id":"8569","type":"journal_article","article_type":"original","publication_identifier":{"issn":["2296-634X"]},"status":"public","abstract":[{"text":"Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final target lamina, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating the specific sequential steps of radial neuronal migration in vivo are however still unclear, let alone the effects and interactions with the extracellular environment. In any in vivo context, cells will always be exposed to a complex extracellular environment consisting of (1) secreted factors acting as potential signaling cues, (2) the extracellular matrix, and (3) other cells providing cell–cell interaction through receptors and/or direct physical stimuli. Most studies so far have described and focused mainly on intrinsic cell-autonomous gene functions in neuronal migration but there is accumulating evidence that non-cell-autonomous-, local-, systemic-, and/or whole tissue-wide effects substantially contribute to the regulation of radial neuronal migration. These non-cell-autonomous effects may differentially affect cortical neuron migration in distinct cellular environments. However, the cellular and molecular natures of such non-cell-autonomous mechanisms are mostly unknown. Furthermore, physical forces due to collective migration and/or community effects (i.e., interactions with surrounding cells) may play important roles in neocortical projection neuron migration. In this concise review, we first outline distinct models of non-cell-autonomous interactions of cortical projection neurons along their radial migration trajectory during development. We then summarize experimental assays and platforms that can be utilized to visualize and potentially probe non-cell-autonomous mechanisms. Lastly, we define key questions to address in the future.","lang":"eng"}],"publication_status":"published","ddc":["570"],"isi":1,"file_date_updated":"2020-09-28T13:11:17Z","publisher":"Frontiers","date_published":"2020-09-25T00:00:00Z","pmid":1,"title":"Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex","date_updated":"2024-03-25T23:30:23Z","department":[{"_id":"SiHi"}],"citation":{"short":"A.H. Hansen, S. Hippenmeyer, Frontiers in Cell and Developmental Biology 8 (2020).","mla":"Hansen, Andi H., and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” <i>Frontiers in Cell and Developmental Biology</i>, vol. 8, no. 9, 574382, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fcell.2020.574382\">10.3389/fcell.2020.574382</a>.","apa":"Hansen, A. H., &#38; Hippenmeyer, S. (2020). Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. <i>Frontiers in Cell and Developmental Biology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fcell.2020.574382\">https://doi.org/10.3389/fcell.2020.574382</a>","chicago":"Hansen, Andi H, and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” <i>Frontiers in Cell and Developmental Biology</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fcell.2020.574382\">https://doi.org/10.3389/fcell.2020.574382</a>.","ama":"Hansen AH, Hippenmeyer S. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. <i>Frontiers in Cell and Developmental Biology</i>. 2020;8(9). doi:<a href=\"https://doi.org/10.3389/fcell.2020.574382\">10.3389/fcell.2020.574382</a>","ista":"Hansen AH, Hippenmeyer S. 2020. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. 8(9), 574382.","ieee":"A. H. Hansen and S. Hippenmeyer, “Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex,” <i>Frontiers in Cell and Developmental Biology</i>, vol. 8, no. 9. Frontiers, 2020."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000577915900001"],"pmid":["33102480"]},"related_material":{"record":[{"id":"9962","relation":"dissertation_contains","status":"public"}]},"scopus_import":"1","intvolume":"         8","publication":"Frontiers in Cell and Developmental Biology","oa":1,"acknowledgement":"AH was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA Grant Agreement No. 618444 to SH.","year":"2020","day":"25","doi":"10.3389/fcell.2020.574382"},{"date_updated":"2021-01-12T08:20:06Z","department":[{"_id":"ToHe"}],"citation":{"apa":"Geretti, L., Alexandre Dit Sandretto, J., Althoff, M., Benet, L., Chapoutot, A., Chen, X., … Schilling, C. (2020). ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics. In <i>EPiC Series in Computing</i> (Vol. 74, pp. 49–75). EasyChair. <a href=\"https://doi.org/10.29007/zkf6\">https://doi.org/10.29007/zkf6</a>","chicago":"Geretti, Luca, Julien Alexandre Dit Sandretto, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin Chen, Pieter Collins, et al. “ARCH-COMP20 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In <i>EPiC Series in Computing</i>, 74:49–75. EasyChair, 2020. <a href=\"https://doi.org/10.29007/zkf6\">https://doi.org/10.29007/zkf6</a>.","ista":"Geretti L, Alexandre Dit Sandretto J, Althoff M, Benet L, Chapoutot A, Chen X, Collins P, Forets M, Freire D, Immler F, Kochdumper N, Sanders D, Schilling C. 2020. ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 74, 49–75.","ama":"Geretti L, Alexandre Dit Sandretto J, Althoff M, et al. ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics. In: <i>EPiC Series in Computing</i>. Vol 74. EasyChair; 2020:49-75. doi:<a href=\"https://doi.org/10.29007/zkf6\">10.29007/zkf6</a>","ieee":"L. Geretti <i>et al.</i>, “ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics,” in <i>EPiC Series in Computing</i>, 2020, vol. 74, pp. 49–75.","short":"L. Geretti, J. Alexandre Dit Sandretto, M. Althoff, L. Benet, A. Chapoutot, X. Chen, P. Collins, M. Forets, D. Freire, F. Immler, N. Kochdumper, D. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair, 2020, pp. 49–75.","mla":"Geretti, Luca, et al. “ARCH-COMP20 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” <i>EPiC Series in Computing</i>, vol. 74, EasyChair, 2020, pp. 49–75, doi:<a href=\"https://doi.org/10.29007/zkf6\">10.29007/zkf6</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2020. This year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. These tools are applied to solve reachability analysis problems on six benchmark problems, two of them featuring hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools."}],"publication_status":"published","date_published":"2020-09-25T00:00:00Z","publisher":"EasyChair","title":"ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics","oa":1,"acknowledgement":"Christian Schilling acknowledges support in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award) and the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No. 754411.","page":"49-75","doi":"10.29007/zkf6","year":"2020","day":"25","intvolume":"        74","publication":"EPiC Series in Computing","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","oa_version":"Published Version","author":[{"full_name":"Geretti, Luca","last_name":"Geretti","first_name":"Luca"},{"last_name":"Alexandre Dit Sandretto","first_name":"Julien","full_name":"Alexandre Dit Sandretto, Julien"},{"last_name":"Althoff","first_name":"Matthias","full_name":"Althoff, Matthias"},{"first_name":"Luis","last_name":"Benet","full_name":"Benet, Luis"},{"last_name":"Chapoutot","first_name":"Alexandre","full_name":"Chapoutot, Alexandre"},{"last_name":"Chen","first_name":"Xin","full_name":"Chen, Xin"},{"full_name":"Collins, Pieter","first_name":"Pieter","last_name":"Collins"},{"last_name":"Forets","first_name":"Marcelo","full_name":"Forets, Marcelo"},{"full_name":"Freire, Daniel","last_name":"Freire","first_name":"Daniel"},{"last_name":"Immler","first_name":"Fabian","full_name":"Immler, Fabian"},{"last_name":"Kochdumper","first_name":"Niklas","full_name":"Kochdumper, Niklas"},{"full_name":"Sanders, David","first_name":"David","last_name":"Sanders"},{"orcid":"0000-0003-3658-1065","first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"}],"month":"09","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":74,"date_created":"2020-09-26T14:41:29Z","_id":"8571","type":"conference","status":"public","main_file_link":[{"open_access":"1","url":"https://easychair.org/publications/download/nrdD"}],"ec_funded":1,"conference":{"name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems","end_date":"2020-07-12","start_date":"2020-07-12"}},{"month":"09","volume":74,"article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","project":[{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Althoff","first_name":"Matthias","full_name":"Althoff, Matthias"},{"full_name":"Bak, Stanley","first_name":"Stanley","last_name":"Bak"},{"full_name":"Bao, Zongnan","last_name":"Bao","first_name":"Zongnan"},{"full_name":"Forets, Marcelo","last_name":"Forets","first_name":"Marcelo"},{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"full_name":"Freire, Daniel","first_name":"Daniel","last_name":"Freire"},{"first_name":"Niklas","last_name":"Kochdumper","full_name":"Kochdumper, Niklas"},{"first_name":"Yangge","last_name":"Li","full_name":"Li, Yangge"},{"first_name":"Sayan","last_name":"Mitra","full_name":"Mitra, Sayan"},{"full_name":"Ray, Rajarshi","first_name":"Rajarshi","last_name":"Ray"},{"first_name":"Christian","last_name":"Schilling","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","full_name":"Schilling, Christian"},{"first_name":"Stefan","last_name":"Schupp","full_name":"Schupp, Stefan"},{"full_name":"Wetzlinger, Mark","first_name":"Mark","last_name":"Wetzlinger"}],"conference":{"name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems","end_date":"2020-07-12","start_date":"2020-07-12"},"ec_funded":1,"_id":"8572","type":"conference","date_created":"2020-09-26T14:49:43Z","main_file_link":[{"open_access":"1","url":"https://easychair.org/publications/download/DRpS"}],"status":"public","publication_status":"published","abstract":[{"text":"We present the results of the ARCH 2020 friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. In its fourth edition, eight tools have been applied to solve eight different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, C2E2, HyDRA, Hylaa, Hylaa-Continuous, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.","lang":"eng"}],"title":"ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics","publisher":"EasyChair","date_published":"2020-09-25T00:00:00Z","citation":{"ista":"Althoff M, Bak S, Bao Z, Forets M, Frehse G, Freire D, Kochdumper N, Li Y, Mitra S, Ray R, Schilling C, Schupp S, Wetzlinger M. 2020. ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 74, 16–48.","chicago":"Althoff, Matthias, Stanley Bak, Zongnan Bao, Marcelo Forets, Goran Frehse, Daniel Freire, Niklas Kochdumper, et al. “ARCH-COMP20 Category Report: Continuous and Hybrid Systems with Linear Dynamics.” In <i>EPiC Series in Computing</i>, 74:16–48. EasyChair, 2020. <a href=\"https://doi.org/10.29007/7dt2\">https://doi.org/10.29007/7dt2</a>.","ama":"Althoff M, Bak S, Bao Z, et al. ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics. In: <i>EPiC Series in Computing</i>. Vol 74. EasyChair; 2020:16-48. doi:<a href=\"https://doi.org/10.29007/7dt2\">10.29007/7dt2</a>","apa":"Althoff, M., Bak, S., Bao, Z., Forets, M., Frehse, G., Freire, D., … Wetzlinger, M. (2020). ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics. In <i>EPiC Series in Computing</i> (Vol. 74, pp. 16–48). EasyChair. <a href=\"https://doi.org/10.29007/7dt2\">https://doi.org/10.29007/7dt2</a>","ieee":"M. Althoff <i>et al.</i>, “ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics,” in <i>EPiC Series in Computing</i>, 2020, vol. 74, pp. 16–48.","mla":"Althoff, Matthias, et al. “ARCH-COMP20 Category Report: Continuous and Hybrid Systems with Linear Dynamics.” <i>EPiC Series in Computing</i>, vol. 74, EasyChair, 2020, pp. 16–48, doi:<a href=\"https://doi.org/10.29007/7dt2\">10.29007/7dt2</a>.","short":"M. Althoff, S. Bak, Z. Bao, M. Forets, G. Frehse, D. Freire, N. Kochdumper, Y. Li, S. Mitra, R. Ray, C. Schilling, S. Schupp, M. Wetzlinger, in:, EPiC Series in Computing, EasyChair, 2020, pp. 16–48."},"department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T08:20:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"EPiC Series in Computing","intvolume":"        74","oa":1,"doi":"10.29007/7dt2","year":"2020","page":"16-48","day":"25","acknowledgement":"The authors gratefully acknowledge financial support by the European Commission project\r\njustITSELF under grant number 817629, by the Austrian Science Fund (FWF) under grant\r\nZ211-N23 (Wittgenstein Award), by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No. 754411, and by the\r\nScience and Engineering Research Board (SERB) project with file number IMP/2018/000523.\r\nThis material is based upon work supported by the Air Force Office of Scientific Research under\r\naward number FA9550-19-1-0288. Any opinions, finding, and conclusions or recommendations\r\nexpressed in this material are those of the author(s) and do not necessarily reflect the views of\r\nthe United States Air Force."},{"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"year":"2020","doi":"10.15479/AT:ISTA:8574","page":"158","day":"20","oa":1,"file_date_updated":"2020-09-28T07:25:37Z","date_published":"2020-09-20T00:00:00Z","publisher":"Institute of Science and Technology Austria","title":"Local adaptation in metapopulations","publication_status":"published","abstract":[{"text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes,  such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. ","lang":"eng"}],"ddc":["570"],"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"NiBa"}],"date_updated":"2023-09-07T13:11:39Z","citation":{"mla":"Szep, Eniko. <i>Local Adaptation in Metapopulations</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8574\">10.15479/AT:ISTA:8574</a>.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020.","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8574\">10.15479/AT:ISTA:8574</a>","chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8574\">https://doi.org/10.15479/AT:ISTA:8574</a>.","ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","apa":"Szep, E. (2020). <i>Local adaptation in metapopulations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8574\">https://doi.org/10.15479/AT:ISTA:8574</a>"},"publication_identifier":{"eissn":["2663-337X"]},"status":"public","date_created":"2020-09-28T07:33:38Z","type":"dissertation","_id":"8574","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"09","has_accepted_license":"1","file":[{"date_created":"2020-09-28T07:25:35Z","date_updated":"2020-09-28T07:25:35Z","content_type":"application/pdf","file_name":"thesis_EnikoSzep_final.pdf","success":1,"relation":"main_file","access_level":"open_access","file_size":6354833,"checksum":"20e71f015fbbd78fea708893ad634ed0","file_id":"8575","creator":"dernst"},{"content_type":"application/x-zip-compressed","date_updated":"2020-09-28T07:25:37Z","date_created":"2020-09-28T07:25:37Z","file_name":"thesisFiles_EnikoSzep.zip","relation":"source_file","creator":"dernst","file_id":"8576","checksum":"a8de2c14a1bb4e53c857787efbb289e1","file_size":23020401,"access_level":"closed"}],"author":[{"first_name":"Eniko","last_name":"Szep","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko"}],"oa_version":"Published Version"},{"status":"public","publication_identifier":{"eissn":["20770375"]},"date_created":"2020-09-28T08:59:26Z","article_type":"original","_id":"8579","type":"journal_article","author":[{"first_name":"Andreea","last_name":"Andrei","full_name":"Andrei, Andreea"},{"full_name":"Öztürk, Yavuz","last_name":"Öztürk","first_name":"Yavuz"},{"full_name":"Khalfaoui-Hassani, Bahia","first_name":"Bahia","last_name":"Khalfaoui-Hassani"},{"last_name":"Rauch","first_name":"Juna","full_name":"Rauch, Juna"},{"full_name":"Marckmann, Dorian","first_name":"Dorian","last_name":"Marckmann"},{"last_name":"Trasnea","first_name":"Petru Iulian","id":"D560034C-10C4-11EA-ABF4-A4B43DDC885E","full_name":"Trasnea, Petru Iulian"},{"first_name":"Fevzi","last_name":"Daldal","full_name":"Daldal, Fevzi"},{"last_name":"Koch","first_name":"Hans-Georg","full_name":"Koch, Hans-Georg"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"volume":10,"article_processing_charge":"No","month":"09","has_accepted_license":"1","file":[{"content_type":"application/pdf","date_updated":"2020-09-28T11:36:50Z","date_created":"2020-09-28T11:36:50Z","file_name":"2020_Membranes_Andrei.pdf","relation":"main_file","success":1,"creator":"dernst","file_id":"8583","checksum":"ceb43d7554e712dea6f36f9287271737","file_size":4612258,"access_level":"open_access"}],"article_number":"242","issue":"9","day":"01","year":"2020","doi":"10.3390/membranes10090242","oa":1,"intvolume":"        10","publication":"Membranes","scopus_import":"1","external_id":{"isi":["000581446000001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"LeSa"}],"date_updated":"2023-08-22T09:34:06Z","citation":{"short":"A. Andrei, Y. Öztürk, B. Khalfaoui-Hassani, J. Rauch, D. Marckmann, P.I. Trasnea, F. Daldal, H.-G. Koch, Membranes 10 (2020).","mla":"Andrei, Andreea, et al. “Cu Homeostasis in Bacteria: The Ins and Outs.” <i>Membranes</i>, vol. 10, no. 9, 242, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/membranes10090242\">10.3390/membranes10090242</a>.","apa":"Andrei, A., Öztürk, Y., Khalfaoui-Hassani, B., Rauch, J., Marckmann, D., Trasnea, P. I., … Koch, H.-G. (2020). Cu homeostasis in bacteria: The ins and outs. <i>Membranes</i>. MDPI. <a href=\"https://doi.org/10.3390/membranes10090242\">https://doi.org/10.3390/membranes10090242</a>","ista":"Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch H-G. 2020. Cu homeostasis in bacteria: The ins and outs. Membranes. 10(9), 242.","chicago":"Andrei, Andreea, Yavuz Öztürk, Bahia Khalfaoui-Hassani, Juna Rauch, Dorian Marckmann, Petru Iulian Trasnea, Fevzi Daldal, and Hans-Georg Koch. “Cu Homeostasis in Bacteria: The Ins and Outs.” <i>Membranes</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/membranes10090242\">https://doi.org/10.3390/membranes10090242</a>.","ama":"Andrei A, Öztürk Y, Khalfaoui-Hassani B, et al. Cu homeostasis in bacteria: The ins and outs. <i>Membranes</i>. 2020;10(9). doi:<a href=\"https://doi.org/10.3390/membranes10090242\">10.3390/membranes10090242</a>","ieee":"A. Andrei <i>et al.</i>, “Cu homeostasis in bacteria: The ins and outs,” <i>Membranes</i>, vol. 10, no. 9. MDPI, 2020."},"date_published":"2020-09-01T00:00:00Z","publisher":"MDPI","file_date_updated":"2020-09-28T11:36:50Z","title":"Cu homeostasis in bacteria: The ins and outs","publication_status":"published","abstract":[{"text":"Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.","lang":"eng"}],"isi":1,"ddc":["570"]},{"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"article_processing_charge":"Yes (via OA deal)","volume":212,"language":[{"iso":"eng"}],"issue":"3","article_number":"107633","file":[{"relation":"main_file","success":1,"creator":"dernst","file_id":"8937","checksum":"c48cbf594e84fc2f91966ffaafc0918c","file_size":7076870,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-12-10T14:01:10Z","date_created":"2020-12-10T14:01:10Z","file_name":"2020_JourStrucBiology_Faessler.pdf"}],"month":"12","has_accepted_license":"1","author":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","last_name":"Fäßler","first_name":"Florian","orcid":"0000-0001-7149-769X"},{"first_name":"Bettina","last_name":"Zens","full_name":"Zens, Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522"},{"orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"quality_controlled":"1","status":"public","publication_identifier":{"issn":["1047-8477"]},"_id":"8586","type":"journal_article","article_type":"original","date_created":"2020-09-29T13:24:06Z","title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","date_published":"2020-12-01T00:00:00Z","publisher":"Elsevier","file_date_updated":"2020-12-10T14:01:10Z","ddc":["570"],"isi":1,"abstract":[{"lang":"eng","text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications."}],"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000600997800008"]},"citation":{"ieee":"F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy,” <i>Journal of Structural Biology</i>, vol. 212, no. 3. Elsevier, 2020.","chicago":"Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” <i>Journal of Structural Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">https://doi.org/10.1016/j.jsb.2020.107633</a>.","ista":"Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 212(3), 107633.","ama":"Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. <i>Journal of Structural Biology</i>. 2020;212(3). doi:<a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">10.1016/j.jsb.2020.107633</a>","apa":"Fäßler, F., Zens, B., Hauschild, R., &#38; Schur, F. K. (2020). 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">https://doi.org/10.1016/j.jsb.2020.107633</a>","mla":"Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” <i>Journal of Structural Biology</i>, vol. 212, no. 3, 107633, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">10.1016/j.jsb.2020.107633</a>.","short":"F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020)."},"date_updated":"2024-03-25T23:30:04Z","department":[{"_id":"FlSc"}],"publication":"Journal of Structural Biology","intvolume":"       212","related_material":{"record":[{"status":"public","id":"14592","relation":"used_in_publication"},{"status":"public","relation":"dissertation_contains","id":"12491"}]},"keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"scopus_import":"1","day":"01","doi":"10.1016/j.jsb.2020.107633","year":"2020","acknowledgement":"This work was supported by the Austrian Science Fund (FWF, P33367) to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing our grid holders in different experimental setups and Daniel Gütl and the Kondrashov group (IST Austria) for granting us repeated access to their 3D printers. We also thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science) for illustrating the graphical abstract.","oa":1}]