--- _id: '14979' abstract: - lang: eng text: Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses. acknowledged_ssus: - _id: ScienComp - _id: LifeSc - _id: EM-Fac acknowledgement: "We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Julia full_name: Datler, Julia id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87 last_name: Datler orcid: 0000-0002-3616-8580 - first_name: Jesse full_name: Hansen, Jesse id: 1063c618-6f9b-11ec-9123-f912fccded63 last_name: Hansen - first_name: Andreas full_name: Thader, Andreas id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87 last_name: Thader - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Lukas W full_name: Bauer, Lukas W id: 0c894dcf-897b-11ed-a09c-8186353224b0 last_name: Bauer - first_name: Victor-Valentin full_name: Hodirnau, Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 2024. doi:10.1038/s41594-023-01201-6 apa: Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., & Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6 chicago: Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6. ieee: J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” Nature Structural & Molecular Biology. Springer Nature, 2024. ista: Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. mla: Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology, Springer Nature, 2024, doi:10.1038/s41594-023-01201-6. short: J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural & Molecular Biology (2024). date_created: 2024-02-12T09:59:45Z date_published: 2024-02-05T00:00:00Z date_updated: 2024-03-05T09:27:47Z day: '05' ddc: - '570' department: - _id: FlSc - _id: ScienComp - _id: EM-Fac doi: 10.1038/s41594-023-01201-6 external_id: pmid: - '38316877' has_accepted_license: '1' keyword: - Molecular Biology - Structural Biology language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41594-023-01201-6 month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid publication: Nature Structural & Molecular Biology publication_identifier: eissn: - 1545-9985 issn: - 1545-9993 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/ status: public title: Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- _id: '13162' article_processing_charge: No author: - first_name: Stefano full_name: Elefante, Stefano id: 490F40CE-F248-11E8-B48F-1D18A9856A87 last_name: Elefante - first_name: Stephan full_name: Stadlbauer, Stephan id: 4D0BC184-F248-11E8-B48F-1D18A9856A87 last_name: Stadlbauer - first_name: Michael F full_name: Alexander, Michael F id: 3A02A8FA-F248-11E8-B48F-1D18A9856A87 last_name: Alexander - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 citation: ama: 'Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :42-42.' apa: 'Elefante, S., Stadlbauer, S., Alexander, M. F., & Schlögl, A. (n.d.). Cryo-EM software packages: A sys-admins point of view. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 42–42). Maribor, Slovenia: EuroCC.' chicago: 'Elefante, Stefano, Stephan Stadlbauer, Michael F Alexander, and Alois Schlögl. “Cryo-EM Software Packages: A Sys-Admins Point of View.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 42–42. EuroCC, n.d.' ieee: 'S. Elefante, S. Stadlbauer, M. F. Alexander, and A. Schlögl, “Cryo-EM software packages: A sys-admins point of view,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 42–42.' ista: 'Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 42–42.' mla: 'Elefante, Stefano, et al. “Cryo-EM Software Packages: A Sys-Admins Point of View.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 42–42.' short: S. Elefante, S. Stadlbauer, M.F. Alexander, A. Schlögl, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 42–42. conference: end_date: 2023-06-15 location: Maribor, Slovenia name: 'ASHPC: Austrian-Slovenian HPC Meeting' start_date: 2023-06-12 date_created: 2023-06-23T11:03:18Z date_published: 2023-07-01T00:00:00Z date_updated: 2023-07-18T09:32:16Z day: '01' ddc: - '000' department: - _id: ScienComp file: - access_level: open_access checksum: 0ab6173cd5c5634ed773cd37ff012681 content_type: application/pdf creator: dernst date_created: 2023-07-18T09:28:30Z date_updated: 2023-07-18T09:28:30Z file_id: '13250' file_name: 2023_ASHPC_Elefante.pdf file_size: 380354 relation: main_file success: 1 file_date_updated: 2023-07-18T09:28:30Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 42-42 publication: ASHPC23 - Austrian-Slovenian HPC Meeting 2023 publication_status: accepted publisher: EuroCC quality_controlled: '1' status: public title: 'Cryo-EM software packages: A sys-admins point of view' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13161' acknowledgement: Thanks to Jesse Hansen for his suggestions on improving the abstract. article_processing_charge: No author: - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Stefano full_name: Elefante, Stefano id: 490F40CE-F248-11E8-B48F-1D18A9856A87 last_name: Elefante - first_name: Victor-Valentin full_name: Hodirnau, Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau citation: ama: 'Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :59-59.' apa: 'Schlögl, A., Elefante, S., & Hodirnau, V.-V. (n.d.). Running Windows-applications on a Linux HPC cluster using WINE. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 59–59). Maribor, Slovenia: EuroCC.' chicago: Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 59–59. EuroCC, n.d. ieee: A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications on a Linux HPC cluster using WINE,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 59–59. ista: 'Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 59–59.' mla: Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 59–59. short: A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 59–59. conference: end_date: 2023-06-15 location: Maribor, Slovenia name: 'ASHPC: Austrian-Slovenian HPC Meeting' start_date: 2023-06-13 date_created: 2023-06-23T11:01:23Z date_published: 2023-07-01T00:00:00Z date_updated: 2023-07-18T09:30:54Z day: '01' ddc: - '000' department: - _id: ScienComp - _id: EM-Fac file: - access_level: open_access checksum: ec8e4295d54171032cdd1b01423eb4a6 content_type: application/pdf creator: dernst date_created: 2023-07-18T09:18:55Z date_updated: 2023-07-18T09:18:55Z file_id: '13249' file_name: 2023_ASHPC_Schloegl.pdf file_size: 316959 relation: main_file success: 1 file_date_updated: 2023-07-18T09:18:55Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 59-59 publication: ASHPC23 - Austrian-Slovenian HPC Meeting 2023 publication_status: inpress publisher: EuroCC quality_controlled: '1' status: public title: Running Windows-applications on a Linux HPC cluster using WINE tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12894' acknowledgement: "The abstracts in this booklet are licenced under a CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/legalcode), except Markus Wallerberger’s contribution at page 21, licenced under a CC BY-SA 4.0 licence (https://creativecommons.org/licenses/by-sa/4.0/legalcode).\r\n" article_processing_charge: No author: - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Andrei full_name: Hornoiu, Andrei id: 77129392-B450-11EA-8745-D4653DDC885E last_name: Hornoiu - first_name: Stefano full_name: Elefante, Stefano id: 490F40CE-F248-11E8-B48F-1D18A9856A87 last_name: Elefante - first_name: Stephan full_name: Stadlbauer, Stephan id: 4D0BC184-F248-11E8-B48F-1D18A9856A87 last_name: Stadlbauer citation: ama: 'Schlögl A, Hornoiu A, Elefante S, Stadlbauer S. Where is the sweet spot? A procurement story of general purpose compute nodes. In: ASHPC22 - Austrian-Slovenian HPC Meeting 2022. EuroCC Austria c/o Universität Wien; 2022:7. doi:10.25365/phaidra.337' apa: 'Schlögl, A., Hornoiu, A., Elefante, S., & Stadlbauer, S. (2022). Where is the sweet spot? A procurement story of general purpose compute nodes. In ASHPC22 - Austrian-Slovenian HPC Meeting 2022 (p. 7). Grundlsee, Austria: EuroCC Austria c/o Universität Wien. https://doi.org/10.25365/phaidra.337' chicago: Schlögl, Alois, Andrei Hornoiu, Stefano Elefante, and Stephan Stadlbauer. “Where Is the Sweet Spot? A Procurement Story of General Purpose Compute Nodes.” In ASHPC22 - Austrian-Slovenian HPC Meeting 2022, 7. EuroCC Austria c/o Universität Wien, 2022. https://doi.org/10.25365/phaidra.337. ieee: A. Schlögl, A. Hornoiu, S. Elefante, and S. Stadlbauer, “Where is the sweet spot? A procurement story of general purpose compute nodes,” in ASHPC22 - Austrian-Slovenian HPC Meeting 2022, Grundlsee, Austria, 2022, p. 7. ista: 'Schlögl A, Hornoiu A, Elefante S, Stadlbauer S. 2022. Where is the sweet spot? A procurement story of general purpose compute nodes. ASHPC22 - Austrian-Slovenian HPC Meeting 2022. ASHPC: Austrian-Slovenian HPC Meeting, 7.' mla: Schlögl, Alois, et al. “Where Is the Sweet Spot? A Procurement Story of General Purpose Compute Nodes.” ASHPC22 - Austrian-Slovenian HPC Meeting 2022, EuroCC Austria c/o Universität Wien, 2022, p. 7, doi:10.25365/phaidra.337. short: A. Schlögl, A. Hornoiu, S. Elefante, S. Stadlbauer, in:, ASHPC22 - Austrian-Slovenian HPC Meeting 2022, EuroCC Austria c/o Universität Wien, 2022, p. 7. conference: end_date: 2022-06-02 location: Grundlsee, Austria name: 'ASHPC: Austrian-Slovenian HPC Meeting' start_date: 2022-05-31 date_created: 2023-05-05T09:13:42Z date_published: 2022-06-02T00:00:00Z date_updated: 2023-05-16T07:42:56Z day: '02' ddc: - '000' department: - _id: ScienComp doi: 10.25365/phaidra.337 file: - access_level: open_access checksum: e3f8c240b85422ce2190e7b203cc2563 content_type: application/pdf creator: schloegl date_created: 2023-05-05T09:06:00Z date_updated: 2023-05-05T09:06:00Z file_id: '12895' file_name: BOOKLET_ASHPC22.pdf file_size: 7180531 relation: main_file success: 1 file_date_updated: 2023-05-05T09:06:00Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '7' publication: ASHPC22 - Austrian-Slovenian HPC Meeting 2022 publication_identifier: isbn: - 978-3-200-08499-5 publication_status: published publisher: EuroCC Austria c/o Universität Wien status: public title: Where is the sweet spot? A procurement story of general purpose compute nodes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '12909' article_processing_charge: No author: - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Stefano full_name: Elefante, Stefano id: 490F40CE-F248-11E8-B48F-1D18A9856A87 last_name: Elefante - first_name: Andrei full_name: Hornoiu, Andrei id: 77129392-B450-11EA-8745-D4653DDC885E last_name: Hornoiu - first_name: Stephan full_name: Stadlbauer, Stephan id: 4D0BC184-F248-11E8-B48F-1D18A9856A87 last_name: Stadlbauer citation: ama: 'Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. Managing software on a heterogenous HPC cluster. In: ASHPC21 – Austrian-Slovenian HPC Meeting 2021. University of Ljubljana; 2021:5. doi:10.3359/2021hpc' apa: 'Schlögl, A., Elefante, S., Hornoiu, A., & Stadlbauer, S. (2021). Managing software on a heterogenous HPC cluster. In ASHPC21 – Austrian-Slovenian HPC Meeting 2021 (p. 5). Virtual: University of Ljubljana. https://doi.org/10.3359/2021hpc' chicago: Schlögl, Alois, Stefano Elefante, Andrei Hornoiu, and Stephan Stadlbauer. “Managing Software on a Heterogenous HPC Cluster.” In ASHPC21 – Austrian-Slovenian HPC Meeting 2021, 5. University of Ljubljana, 2021. https://doi.org/10.3359/2021hpc. ieee: A. Schlögl, S. Elefante, A. Hornoiu, and S. Stadlbauer, “Managing software on a heterogenous HPC cluster,” in ASHPC21 – Austrian-Slovenian HPC Meeting 2021, Virtual, 2021, p. 5. ista: Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. 2021. Managing software on a heterogenous HPC cluster. ASHPC21 – Austrian-Slovenian HPC Meeting 2021. ASHPC - Austrian-Slovenian HPC Meeting, 5. mla: Schlögl, Alois, et al. “Managing Software on a Heterogenous HPC Cluster.” ASHPC21 – Austrian-Slovenian HPC Meeting 2021, University of Ljubljana, 2021, p. 5, doi:10.3359/2021hpc. short: A. Schlögl, S. Elefante, A. Hornoiu, S. Stadlbauer, in:, ASHPC21 – Austrian-Slovenian HPC Meeting 2021, University of Ljubljana, 2021, p. 5. conference: end_date: 2021-06-02 location: Virtual name: ASHPC - Austrian-Slovenian HPC Meeting start_date: 2021-05-31 date_created: 2023-05-05T13:17:36Z date_published: 2021-06-02T00:00:00Z date_updated: 2023-05-16T07:43:54Z day: '02' ddc: - '000' department: - _id: ScienComp doi: 10.3359/2021hpc file: - access_level: open_access checksum: ba73f85858fb9d5737ebc7724646dd45 content_type: application/pdf creator: dernst date_created: 2023-05-16T07:36:34Z date_updated: 2023-05-16T07:36:34Z file_id: '12971' file_name: 2021_ASHPC_Schloegl.pdf file_size: 422761 relation: main_file success: 1 file_date_updated: 2023-05-16T07:36:34Z has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ashpc21/BOOKLET_ASHPC21.pdf month: '06' oa: 1 oa_version: Published Version page: '5' publication: ASHPC21 – Austrian-Slovenian HPC Meeting 2021 publication_identifier: isbn: - 978-961-6980-77-7 - 978-961-6133-48-7 publication_status: published publisher: University of Ljubljana status: public title: Managing software on a heterogenous HPC cluster type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '9329' abstract: - lang: eng text: "Background: To understand information coding in single neurons, it is necessary to analyze subthreshold synaptic events, action potentials (APs), and their interrelation in different behavioral states. However, detecting excitatory postsynaptic potentials (EPSPs) or currents (EPSCs) in behaving animals remains challenging, because of unfavorable signal-to-noise ratio, high frequency, fluctuating amplitude, and variable time course of synaptic events.\r\nNew method: We developed a method for synaptic event detection, termed MOD (Machine-learning Optimal-filtering Detection-procedure), which combines concepts of supervised machine learning and optimal Wiener filtering. Experts were asked to manually score short epochs of data. The algorithm was trained to obtain the optimal filter coefficients of a Wiener filter and the optimal detection threshold. Scored and unscored data were then processed with the optimal filter, and events were detected as peaks above threshold.\r\nResults: We challenged MOD with EPSP traces in vivo in mice during spatial navigation and EPSC traces in vitro in slices under conditions of enhanced transmitter release. The area under the curve (AUC) of the receiver operating characteristics (ROC) curve was, on average, 0.894 for in vivo and 0.969 for in vitro data sets, indicating high detection accuracy and efficiency.\r\nComparison with existing methods: When benchmarked using a (1 − AUC)−1 metric, MOD outperformed previous methods (template-fit, deconvolution, and Bayesian methods) by an average factor of 3.13 for in vivo data sets, but showed comparable (template-fit, deconvolution) or higher (Bayesian) computational efficacy.\r\nConclusions: MOD may become an important new tool for large-scale, real-time analysis of synaptic activity." acknowledged_ssus: - _id: SSU acknowledgement: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J.). We thank Drs. Jozsef Csicsvari, Christoph Lampert, and Federico Stella for critically reading previous manuscript versions. We are also grateful to Drs. Josh Merel and Ben Shababo for their help with applying the Bayesian detection method to our data. We also thank Florian Marr for technical assistance, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support. article_number: '109125' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Xiaomin full_name: Zhang, Xiaomin id: 423EC9C2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: 'Zhang X, Schlögl A, Vandael DH, Jonas PM. MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. 2021;357(6). doi:10.1016/j.jneumeth.2021.109125' apa: 'Zhang, X., Schlögl, A., Vandael, D. H., & Jonas, P. M. (2021). MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. Elsevier. https://doi.org/10.1016/j.jneumeth.2021.109125' chicago: 'Zhang, Xiaomin, Alois Schlögl, David H Vandael, and Peter M Jonas. “MOD: A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.” Journal of Neuroscience Methods. Elsevier, 2021. https://doi.org/10.1016/j.jneumeth.2021.109125.' ieee: 'X. Zhang, A. Schlögl, D. H. Vandael, and P. M. Jonas, “MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo,” Journal of Neuroscience Methods, vol. 357, no. 6. Elsevier, 2021.' ista: 'Zhang X, Schlögl A, Vandael DH, Jonas PM. 2021. MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. 357(6), 109125.' mla: 'Zhang, Xiaomin, et al. “MOD: A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.” Journal of Neuroscience Methods, vol. 357, no. 6, 109125, Elsevier, 2021, doi:10.1016/j.jneumeth.2021.109125.' short: X. Zhang, A. Schlögl, D.H. Vandael, P.M. Jonas, Journal of Neuroscience Methods 357 (2021). date_created: 2021-04-18T22:01:39Z date_published: 2021-03-09T00:00:00Z date_updated: 2023-08-07T14:36:14Z day: '09' ddc: - '570' department: - _id: PeJo - _id: ScienComp doi: 10.1016/j.jneumeth.2021.109125 ec_funded: 1 external_id: isi: - '000661088500005' file: - access_level: open_access checksum: 2a5800d91b96d08b525e17319dcd5e44 content_type: application/pdf creator: dernst date_created: 2021-04-19T08:30:22Z date_updated: 2021-04-19T08:30:22Z file_id: '9339' file_name: 2021_JourNeuroscienceMeth_Zhang.pdf file_size: 6924738 relation: main_file success: 1 file_date_updated: 2021-04-19T08:30:22Z has_accepted_license: '1' intvolume: ' 357' isi: 1 issue: '6' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '03' oa: 1 oa_version: Published Version project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize publication: Journal of Neuroscience Methods publication_identifier: eissn: - 1872-678X issn: - 0165-0270 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 357 year: '2021' ... --- _id: '10816' abstract: - lang: eng text: Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks. acknowledged_ssus: - _id: SSU acknowledgement: We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and T. Vogels for critically reading earlier versions of the manuscript. We are grateful to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished data. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.). article_processing_charge: No article_type: original author: - first_name: José full_name: Guzmán, José id: 30CC5506-F248-11E8-B48F-1D18A9856A87 last_name: Guzmán orcid: 0000-0003-2209-5242 - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: 'Claudia ' full_name: 'Espinoza Martinez, Claudia ' id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87 last_name: Espinoza Martinez orcid: 0000-0003-4710-2082 - first_name: Xiaomin full_name: Zhang, Xiaomin id: 423EC9C2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang - first_name: Benjamin full_name: Suter, Benjamin id: 4952F31E-F248-11E8-B48F-1D18A9856A87 last_name: Suter orcid: 0000-0002-9885-6936 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 2021;1(12):830-842. doi:10.1038/s43588-021-00157-1 apa: Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., & Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-021-00157-1 chicago: Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science. Springer Nature, 2021. https://doi.org/10.1038/s43588-021-00157-1. ieee: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network,” Nature Computational Science, vol. 1, no. 12. Springer Nature, pp. 830–842, 2021. ista: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 1(12), 830–842. mla: Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science, vol. 1, no. 12, Springer Nature, 2021, pp. 830–42, doi:10.1038/s43588-021-00157-1. short: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, Nature Computational Science 1 (2021) 830–842. date_created: 2022-03-04T08:32:36Z date_published: 2021-12-16T00:00:00Z date_updated: 2023-08-10T22:30:10Z day: '16' ddc: - '610' department: - _id: PeJo doi: 10.1038/s43588-021-00157-1 ec_funded: 1 file: - access_level: open_access checksum: 9fec5b667909ef52be96d502e4f8c2ae content_type: application/pdf creator: patrickd date_created: 2022-06-02T12:51:07Z date_updated: 2022-06-18T22:30:03Z embargo: 2022-06-17 file_id: '11430' file_name: Guzmanetal2021.pdf file_size: 1699466 relation: main_file - access_level: open_access checksum: 52a005b13a114e3c3a28fa6bbe8b1a8d content_type: application/pdf creator: patrickd date_created: 2022-06-02T12:53:47Z date_updated: 2022-06-18T22:30:03Z embargo: 2022-06-17 file_id: '11431' file_name: Guzmanetal2021Suppl.pdf file_size: 3005651 relation: supplementary_material title: Supplementary Material file_date_updated: 2022-06-18T22:30:03Z has_accepted_license: '1' intvolume: ' 1' issue: '12' keyword: - general medicine language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/647800 month: '12' oa: 1 oa_version: Submitted Version page: 830-842 project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize publication: Nature Computational Science publication_identifier: issn: - 2662-8457 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: press_release url: https://ista.ac.at/en/news/spot-the-difference/ record: - id: '10110' relation: software status: public scopus_import: '1' status: public title: How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2021' ... --- _id: '10110' abstract: - lang: eng text: Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks. author: - first_name: José full_name: Guzmán, José id: 30CC5506-F248-11E8-B48F-1D18A9856A87 last_name: Guzmán orcid: 0000-0003-2209-5242 - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: 'Claudia ' full_name: 'Espinoza Martinez, Claudia ' id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87 last_name: Espinoza Martinez orcid: 0000-0003-4710-2082 - first_name: Xiaomin full_name: Zhang, Xiaomin id: 423EC9C2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang - first_name: Benjamin full_name: Suter, Benjamin id: 4952F31E-F248-11E8-B48F-1D18A9856A87 last_name: Suter orcid: 0000-0002-9885-6936 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:10.15479/AT:ISTA:10110 apa: Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., & Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. https://doi.org/10.15479/AT:ISTA:10110 chicago: Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:10110. ieee: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021. ista: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, 10.15479/AT:ISTA:10110. mla: Guzmán, José, et al. How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network. IST Austria, 2021, doi:10.15479/AT:ISTA:10110. short: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021). date_created: 2021-10-08T06:44:22Z date_published: 2021-12-16T00:00:00Z date_updated: 2024-03-27T23:30:11Z day: '16' ddc: - '005' department: - _id: PeJo - _id: ScienComp doi: 10.15479/AT:ISTA:10110 file: - access_level: open_access checksum: f92f8931cad0aa7e411c1715337bf408 content_type: application/x-zip-compressed creator: cchlebak date_created: 2021-10-08T08:46:04Z date_updated: 2021-10-08T08:46:04Z file_id: '10114' file_name: patternseparation-main (1).zip file_size: 332990101 relation: main_file success: 1 file_date_updated: 2021-10-08T08:46:04Z has_accepted_license: '1' license: https://opensource.org/licenses/GPL-3.0 month: '12' oa: 1 publisher: IST Austria related_material: link: - description: News on IST Webpage relation: press_release url: https://ist.ac.at/en/news/spot-the-difference/ record: - id: '10816' relation: used_for_analysis_in status: public status: public title: How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network tmp: legal_code_url: https://www.gnu.org/licenses/gpl-3.0.en.html name: GNU General Public License 3.0 short: GPL 3.0 type: software user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2021' ... --- _id: '7474' abstract: - lang: eng text: This booklet is a collection of abstracts presented at the AHPC conference. article_processing_charge: No citation: ama: 'Schlögl A, Kiss J, Elefante S, eds. Austrian High-Performance-Computing Meeting (AHPC2020). Klosterneuburg, Austria: IST Austria; 2020. doi:10.15479/AT:ISTA:7474' apa: 'Schlögl, A., Kiss, J., & Elefante, S. (Eds.). (2020). Austrian High-Performance-Computing meeting (AHPC2020). Presented at the AHPC: Austrian High-Performance-Computing Meeting, Klosterneuburg, Austria: IST Austria. https://doi.org/10.15479/AT:ISTA:7474' chicago: 'Schlögl, Alois, Janos Kiss, and Stefano Elefante, eds. Austrian High-Performance-Computing Meeting (AHPC2020). Klosterneuburg, Austria: IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:7474.' ieee: 'A. Schlögl, J. Kiss, and S. Elefante, Eds., Austrian High-Performance-Computing meeting (AHPC2020). Klosterneuburg, Austria: IST Austria, 2020.' ista: 'Schlögl A, Kiss J, Elefante S eds. 2020. Austrian High-Performance-Computing meeting (AHPC2020), Klosterneuburg, Austria: IST Austria, 72p.' mla: Schlögl, Alois, et al., editors. Austrian High-Performance-Computing Meeting (AHPC2020). IST Austria, 2020, doi:10.15479/AT:ISTA:7474. short: A. Schlögl, J. Kiss, S. Elefante, eds., Austrian High-Performance-Computing Meeting (AHPC2020), IST Austria, Klosterneuburg, Austria, 2020. conference: end_date: 2020-02-21 location: Klosterneuburg, Austria name: 'AHPC: Austrian High-Performance-Computing Meeting' start_date: 2020-02-19 date_created: 2020-02-11T07:59:04Z date_published: 2020-02-19T00:00:00Z date_updated: 2023-05-16T07:48:28Z day: '19' ddc: - '000' department: - _id: ScienComp doi: 10.15479/AT:ISTA:7474 editor: - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Janos full_name: Kiss, Janos id: 3D3A06F8-F248-11E8-B48F-1D18A9856A87 last_name: Kiss - first_name: Stefano full_name: Elefante, Stefano id: 490F40CE-F248-11E8-B48F-1D18A9856A87 last_name: Elefante file: - access_level: open_access checksum: 49798edb9e57bbd6be18362d1d7b18a9 content_type: application/pdf creator: schloegl date_created: 2020-02-19T06:53:38Z date_updated: 2020-07-14T12:47:59Z file_id: '7504' file_name: BOOKLET_AHPC2020.final.pdf file_size: 90899507 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '72' place: Klosterneuburg, Austria publication_identifier: isbn: - 978-3-99078-004-6 publication_status: published publisher: IST Austria quality_controlled: '1' status: public title: Austrian High-Performance-Computing meeting (AHPC2020) tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: book_editor user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8261' abstract: - lang: eng text: Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion. acknowledged_ssus: - _id: M-Shop - _id: ScienComp - _id: PreCl acknowledgement: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari, Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp recording. We are grateful to Florian Marr for cell labeling, cell reconstruction, and technical assistance; Ben Suter for helpful discussions; Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor Asenov (Machine Shop) for device construction. We also thank the Scientific Service Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical Facility) for efficient support. article_processing_charge: No article_type: original author: - first_name: Xiaomin full_name: Zhang, Xiaomin id: 423EC9C2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 2020;107(6):1212-1225. doi:10.1016/j.neuron.2020.07.006 apa: Zhang, X., Schlögl, A., & Jonas, P. M. (2020). Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.07.006 chicago: Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.07.006. ieee: X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information flow from input to output in hippocampal granule cells,” Neuron, vol. 107, no. 6. Elsevier, pp. 1212–1225, 2020. ista: Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225. mla: Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron, vol. 107, no. 6, Elsevier, 2020, pp. 1212–25, doi:10.1016/j.neuron.2020.07.006. short: X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225. date_created: 2020-08-14T09:36:05Z date_published: 2020-09-23T00:00:00Z date_updated: 2023-08-22T08:30:55Z day: '23' ddc: - '570' department: - _id: PeJo - _id: ScienComp doi: 10.1016/j.neuron.2020.07.006 ec_funded: 1 external_id: isi: - '000579698700009' pmid: - '32763145' file: - access_level: open_access checksum: 44a5960fc083a4cb3488d22224859fdc content_type: application/pdf creator: dernst date_created: 2020-12-04T09:29:21Z date_updated: 2020-12-04T09:29:21Z file_id: '8920' file_name: 2020_Neuron_Zhang.pdf file_size: 3011120 relation: main_file success: 1 file_date_updated: 2020-12-04T09:29:21Z has_accepted_license: '1' intvolume: ' 107' isi: 1 issue: '6' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1212-1225 pmid: 1 project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Website relation: press_release url: https://ist.ac.at/en/news/the-bouncer-in-the-brain/ status: public title: Selective routing of spatial information flow from input to output in hippocampal granule cells tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2020' ... --- _id: '12901' article_processing_charge: No author: - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Janos full_name: Kiss, Janos id: 3D3A06F8-F248-11E8-B48F-1D18A9856A87 last_name: Kiss - first_name: Stefano full_name: Elefante, Stefano id: 490F40CE-F248-11E8-B48F-1D18A9856A87 last_name: Elefante citation: ama: 'Schlögl A, Kiss J, Elefante S. Is Debian suitable for running an HPC Cluster? In: AHPC19 - Austrian HPC Meeting 2019 . Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz; 2019:25.' apa: 'Schlögl, A., Kiss, J., & Elefante, S. (2019). Is Debian suitable for running an HPC Cluster? In AHPC19 - Austrian HPC Meeting 2019 (p. 25). Grundlsee, Austria: Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz.' chicago: Schlögl, Alois, Janos Kiss, and Stefano Elefante. “Is Debian Suitable for Running an HPC Cluster?” In AHPC19 - Austrian HPC Meeting 2019 , 25. Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019. ieee: A. Schlögl, J. Kiss, and S. Elefante, “Is Debian suitable for running an HPC Cluster?,” in AHPC19 - Austrian HPC Meeting 2019 , Grundlsee, Austria, 2019, p. 25. ista: 'Schlögl A, Kiss J, Elefante S. 2019. Is Debian suitable for running an HPC Cluster? AHPC19 - Austrian HPC Meeting 2019 . AHPC: Austrian HPC Meeting, 25.' mla: Schlögl, Alois, et al. “Is Debian Suitable for Running an HPC Cluster?” AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25. short: A. Schlögl, J. Kiss, S. Elefante, in:, AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25. conference: end_date: 2019-02-27 location: Grundlsee, Austria name: 'AHPC: Austrian HPC Meeting' start_date: 2019-02-25 date_created: 2023-05-05T12:48:48Z date_published: 2019-02-27T00:00:00Z date_updated: 2023-05-16T07:29:32Z day: '27' ddc: - '000' department: - _id: ScienComp file: - access_level: open_access checksum: acc8272027faaf30709c51ac5c58ffa4 content_type: application/pdf creator: dernst date_created: 2023-05-16T07:27:09Z date_updated: 2023-05-16T07:27:09Z file_id: '12970' file_name: 2019_AHPC_Schloegl.pdf file_size: 1097603 relation: main_file success: 1 file_date_updated: 2023-05-16T07:27:09Z has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc19/BOOKLET_AHPC19.pdf month: '02' oa: 1 oa_version: Published Version page: '25' publication: 'AHPC19 - Austrian HPC Meeting 2019 ' publication_status: published publisher: Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz status: public title: Is Debian suitable for running an HPC Cluster? type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '630' abstract: - lang: eng text: 'Background: Standards have become available to share semantically encoded vital parameters from medical devices, as required for example by personal healthcare records. Standardised sharing of biosignal data largely remains open. Objectives: The goal of this work is to explore available biosignal file format and data exchange standards and profiles, and to conceptualise end-To-end solutions. Methods: The authors reviewed and discussed available biosignal file format standards with other members of international standards development organisations (SDOs). Results: A raw concept for standards based acquisition, storage, archiving and sharing of biosignals was developed. The GDF format may serve for storing biosignals. Signals can then be shared using FHIR resources and may be stored on FHIR servers or in DICOM archives, with DICOM waveforms as one possible format. Conclusion: Currently a group of international SDOs (e.g. HL7, IHE, DICOM, IEEE) is engaged in intensive discussions. This discussion extends existing work that already was adopted by large implementer communities. The concept presented here only reports the current status of the discussion in Austria. The discussion will continue internationally, with results to be expected over the coming years.' alternative_title: - Studies in Health Technology and Informatics author: - first_name: Stefan full_name: Sauermann, Stefan last_name: Sauermann - first_name: Veronika full_name: David, Veronika last_name: David - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Reinhard full_name: Egelkraut, Reinhard last_name: Egelkraut - first_name: Matthias full_name: Frohner, Matthias last_name: Frohner - first_name: Birgit full_name: Pohn, Birgit last_name: Pohn - first_name: Philipp full_name: Urbauer, Philipp last_name: Urbauer - first_name: Alexander full_name: Mense, Alexander last_name: Mense citation: ama: 'Sauermann S, David V, Schlögl A, et al. Biosignals standards and FHIR: The way to go. In: Vol 236. IOS Press; 2017:356-362. doi:10.3233/978-1-61499-759-7-356' apa: 'Sauermann, S., David, V., Schlögl, A., Egelkraut, R., Frohner, M., Pohn, B., … Mense, A. (2017). Biosignals standards and FHIR: The way to go (Vol. 236, pp. 356–362). Presented at the eHealth: Health Informatics Meets eHealth, Vienna, Austria: IOS Press. https://doi.org/10.3233/978-1-61499-759-7-356' chicago: 'Sauermann, Stefan, Veronika David, Alois Schlögl, Reinhard Egelkraut, Matthias Frohner, Birgit Pohn, Philipp Urbauer, and Alexander Mense. “Biosignals Standards and FHIR: The Way to Go,” 236:356–62. IOS Press, 2017. https://doi.org/10.3233/978-1-61499-759-7-356.' ieee: 'S. Sauermann et al., “Biosignals standards and FHIR: The way to go,” presented at the eHealth: Health Informatics Meets eHealth, Vienna, Austria, 2017, vol. 236, pp. 356–362.' ista: 'Sauermann S, David V, Schlögl A, Egelkraut R, Frohner M, Pohn B, Urbauer P, Mense A. 2017. Biosignals standards and FHIR: The way to go. eHealth: Health Informatics Meets eHealth, Studies in Health Technology and Informatics, vol. 236, 356–362.' mla: 'Sauermann, Stefan, et al. Biosignals Standards and FHIR: The Way to Go. Vol. 236, IOS Press, 2017, pp. 356–62, doi:10.3233/978-1-61499-759-7-356.' short: S. Sauermann, V. David, A. Schlögl, R. Egelkraut, M. Frohner, B. Pohn, P. Urbauer, A. Mense, in:, IOS Press, 2017, pp. 356–362. conference: end_date: 2017-05-24 location: Vienna, Austria name: 'eHealth: Health Informatics Meets eHealth' start_date: 2017-05-23 date_created: 2018-12-11T11:47:36Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:06:59Z day: '01' ddc: - '005' department: - _id: ScienComp - _id: PeJo doi: 10.3233/978-1-61499-759-7-356 file: - access_level: open_access checksum: 1254dcc5b04a996d97fad9a726b42727 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:56Z date_updated: 2020-07-14T12:47:27Z file_id: '4913' file_name: IST-2017-906-v1+1_SHTI236-0356.pdf file_size: 443635 relation: main_file file_date_updated: 2020-07-14T12:47:27Z has_accepted_license: '1' intvolume: ' 236' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '01' oa: 1 oa_version: Published Version page: 356 - 362 publication_identifier: isbn: - 978-161499758-0 publication_status: published publisher: IOS Press publist_id: '7164' pubrep_id: '906' quality_controlled: '1' scopus_import: 1 status: public title: 'Biosignals standards and FHIR: The way to go' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 236 year: '2017' ... --- _id: '12905' article_processing_charge: No author: - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Janos full_name: Kiss, Janos id: 3D3A06F8-F248-11E8-B48F-1D18A9856A87 last_name: Kiss citation: ama: 'Schlögl A, Kiss J. Scientific Computing at IST Austria. In: AHPC17 – Austrian HPC Meeting 2017. FSP Scientific Computing; 2017:28.' apa: 'Schlögl, A., & Kiss, J. (2017). Scientific Computing at IST Austria. In AHPC17 – Austrian HPC Meeting 2017 (p. 28). Grundlsee, Austria: FSP Scientific Computing.' chicago: Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” In AHPC17 – Austrian HPC Meeting 2017, 28. FSP Scientific Computing, 2017. ieee: A. Schlögl and J. Kiss, “Scientific Computing at IST Austria,” in AHPC17 – Austrian HPC Meeting 2017, Grundlsee, Austria, 2017, p. 28. ista: 'Schlögl A, Kiss J. 2017. Scientific Computing at IST Austria. AHPC17 – Austrian HPC Meeting 2017. AHPC: Austrian HPC Meeting, 28.' mla: Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28. short: A. Schlögl, J. Kiss, in:, AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28. conference: end_date: 2017-03-03 location: Grundlsee, Austria name: 'AHPC: Austrian HPC Meeting' start_date: 2017-03-01 date_created: 2023-05-05T12:58:53Z date_published: 2017-03-03T00:00:00Z date_updated: 2023-05-16T07:22:23Z day: '03' ddc: - '000' department: - _id: ScienComp file: - access_level: open_access checksum: 7bcc499479d4f4c5ce6c0071c24ca6c6 content_type: application/pdf creator: dernst date_created: 2023-05-16T07:20:50Z date_updated: 2023-05-16T07:20:50Z file_id: '12969' file_name: 2017_AHPC_Schloegl.pdf file_size: 1005486 relation: main_file success: 1 file_date_updated: 2023-05-16T07:20:50Z has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc17/BOOKLET_AHPC17.pdf month: '03' oa: 1 oa_version: Published Version page: '28' publication: AHPC17 – Austrian HPC Meeting 2017 publication_status: published publisher: FSP Scientific Computing status: public title: Scientific Computing at IST Austria type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '10810' abstract: - lang: eng text: "The main goal of the SCP-ECG standard is to address ECG data and related metadata structuring, semantics and syntax, with the objective of facilitating interoperability and thus supporting and promoting the exchange of the relevant information for unary and serial ECG diagnosis. Starting with version V3.0, the standard now also provides support for the storage of continuous, long-term ECG recordings and affords a repository for selected ECG sequences and the related metadata to accommodate stress tests, drug trials and protocol-based ECG recordings. The global and per-lead measurements sections have been extended and three new sections have been introduced for storing beat-by-beat and/or spike-by-spike measurements\r\nand annotations. The used terminology and the provided measurements and annotations have been harmonized with the ISO/IEEE 11073-10102 Annotated ECG standard. Emphasis has also been put on harmonizing the Universal Statement Codes with the CDISC and the categorized AHA statement codes and similarly the drug and implanted devices codes with the ATC and NASPE/BPEG codes. " acknowledgement: The authors are thankful to Drs. Roger Abaecherli, Nikus Kjell, Paul Kligfield, Jay Mason, Patrice Nony, Vito Starc, Anders Thurin and the late Galen Wagner for their in depth review and constructive comments. article_processing_charge: No author: - first_name: Paul full_name: Rubel, Paul last_name: Rubel - first_name: Danilo full_name: Pani, Danilo last_name: Pani - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Jocelyne full_name: Fayn, Jocelyne last_name: Fayn - first_name: Fabio full_name: Badilini, Fabio last_name: Badilini - first_name: Peter full_name: Macfarlane, Peter last_name: Macfarlane - first_name: Alpo full_name: Varri, Alpo last_name: Varri citation: ama: 'Rubel P, Pani D, Schlögl A, et al. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In: 2016 Computing in Cardiology Conference. Vol 43. Computing in Cardiology; 2016:309-312. doi:10.22489/cinc.2016.090-500' apa: 'Rubel, P., Pani, D., Schlögl, A., Fayn, J., Badilini, F., Macfarlane, P., & Varri, A. (2016). SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In 2016 Computing in Cardiology Conference (Vol. 43, pp. 309–312). Vancouver, Canada: Computing in Cardiology. https://doi.org/10.22489/cinc.2016.090-500' chicago: 'Rubel, Paul, Danilo Pani, Alois Schlögl, Jocelyne Fayn, Fabio Badilini, Peter Macfarlane, and Alpo Varri. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” In 2016 Computing in Cardiology Conference, 43:309–12. Computing in Cardiology, 2016. https://doi.org/10.22489/cinc.2016.090-500.' ieee: 'P. Rubel et al., “SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography,” in 2016 Computing in Cardiology Conference, Vancouver, Canada, 2016, vol. 43, pp. 309–312.' ista: 'Rubel P, Pani D, Schlögl A, Fayn J, Badilini F, Macfarlane P, Varri A. 2016. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. 2016 Computing in Cardiology Conference. CinC: Computing in Cardiology vol. 43, 309–312.' mla: 'Rubel, Paul, et al. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” 2016 Computing in Cardiology Conference, vol. 43, Computing in Cardiology, 2016, pp. 309–12, doi:10.22489/cinc.2016.090-500.' short: P. Rubel, D. Pani, A. Schlögl, J. Fayn, F. Badilini, P. Macfarlane, A. Varri, in:, 2016 Computing in Cardiology Conference, Computing in Cardiology, 2016, pp. 309–312. conference: end_date: 2016-09-14 location: Vancouver, Canada name: 'CinC: Computing in Cardiology' start_date: 2016-09-11 date_created: 2022-03-03T10:43:10Z date_published: 2016-03-01T00:00:00Z date_updated: 2022-03-04T07:34:45Z day: '01' department: - _id: CampIT doi: 10.22489/cinc.2016.090-500 intvolume: ' 43' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.22489/cinc.2016.090-500 month: '03' oa: 1 oa_version: Published Version page: 309-312 publication: 2016 Computing in Cardiology Conference publication_identifier: issn: - 2325-887X publication_status: published publisher: Computing in Cardiology quality_controlled: '1' scopus_import: '1' status: public title: 'SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2016' ... --- _id: '1350' abstract: - lang: eng text: "The hippocampal CA3 region plays a key role in learning and memory. Recurrent CA3–CA3\r\nsynapses are thought to be the subcellular substrate of pattern completion. However, the\r\nsynaptic mechanisms of this network computation remain enigmatic. To investigate these mechanisms, we combined functional connectivity analysis with network modeling.\r\nSimultaneous recording fromup to eight CA3 pyramidal neurons revealed that connectivity was sparse, spatially uniform, and highly enriched in disynaptic motifs (reciprocal, convergence,divergence, and chain motifs). Unitary connections were composed of one or two synaptic contacts, suggesting efficient use of postsynaptic space. Real-size modeling indicated that CA3 networks with sparse connectivity, disynaptic motifs, and single-contact connections robustly generated pattern completion.Thus, macro- and microconnectivity contribute to efficient\r\nmemory storage and retrieval in hippocampal networks." acknowledged_ssus: - _id: ScienComp author: - first_name: José full_name: Guzmán, José id: 30CC5506-F248-11E8-B48F-1D18A9856A87 last_name: Guzmán - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Guzmán J, Schlögl A, Frotscher M, Jonas PM. Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. 2016;353(6304):1117-1123. doi:10.1126/science.aaf1836 apa: Guzmán, J., Schlögl, A., Frotscher, M., & Jonas, P. M. (2016). Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aaf1836 chicago: Guzmán, José, Alois Schlögl, Michael Frotscher, and Peter M Jonas. “Synaptic Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aaf1836. ieee: J. Guzmán, A. Schlögl, M. Frotscher, and P. M. Jonas, “Synaptic mechanisms of pattern completion in the hippocampal CA3 network,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1117–1123, 2016. ista: Guzmán J, Schlögl A, Frotscher M, Jonas PM. 2016. Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. 353(6304), 1117–1123. mla: Guzmán, José, et al. “Synaptic Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” Science, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1117–23, doi:10.1126/science.aaf1836. short: J. Guzmán, A. Schlögl, M. Frotscher, P.M. Jonas, Science 353 (2016) 1117–1123. date_created: 2018-12-11T11:51:31Z date_published: 2016-09-09T00:00:00Z date_updated: 2021-01-12T06:50:04Z day: '09' ddc: - '570' department: - _id: ScienComp - _id: PeJo doi: 10.1126/science.aaf1836 ec_funded: 1 file: - access_level: open_access checksum: 89caefa4e181424cbf0aecc835fcc5ec content_type: application/pdf creator: system date_created: 2018-12-12T10:12:27Z date_updated: 2020-07-14T12:44:46Z file_id: '4945' file_name: IST-2017-823-v1+1_aaf1836_CombinedPDF_v2-1.pdf file_size: 19408143 relation: main_file file_date_updated: 2020-07-14T12:44:46Z has_accepted_license: '1' intvolume: ' 353' issue: '6304' language: - iso: eng month: '09' oa: 1 oa_version: Preprint page: 1117 - 1123 project: - _id: 25C0F108-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '268548' name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons - _id: 25C26B1E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P24909-B24 name: Mechanisms of transmitter release at GABAergic synapses publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5899' pubrep_id: '823' quality_controlled: '1' scopus_import: 1 status: public title: Synaptic mechanisms of pattern completion in the hippocampal CA3 network type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 353 year: '2016' ... --- _id: '12903' article_processing_charge: No author: - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Stephan full_name: Stadlbauer, Stephan id: 4D0BC184-F248-11E8-B48F-1D18A9856A87 last_name: Stadlbauer citation: ama: 'Schlögl A, Stadlbauer S. High performance computing at IST Austria: Modelling the human hippocampus. In: AHPC16 - Austrian HPC Meeting 2016. VSC - Vienna Scientific Cluster; 2016:37.' apa: 'Schlögl, A., & Stadlbauer, S. (2016). High performance computing at IST Austria: Modelling the human hippocampus. In AHPC16 - Austrian HPC Meeting 2016 (p. 37). Grundlsee, Austria: VSC - Vienna Scientific Cluster.' chicago: 'Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at IST Austria: Modelling the Human Hippocampus.” In AHPC16 - Austrian HPC Meeting 2016, 37. VSC - Vienna Scientific Cluster, 2016.' ieee: 'A. Schlögl and S. Stadlbauer, “High performance computing at IST Austria: Modelling the human hippocampus,” in AHPC16 - Austrian HPC Meeting 2016, Grundlsee, Austria, 2016, p. 37.' ista: 'Schlögl A, Stadlbauer S. 2016. High performance computing at IST Austria: Modelling the human hippocampus. AHPC16 - Austrian HPC Meeting 2016. AHPC: Austrian HPC Meeting, 37.' mla: 'Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at IST Austria: Modelling the Human Hippocampus.” AHPC16 - Austrian HPC Meeting 2016, VSC - Vienna Scientific Cluster, 2016, p. 37.' short: A. Schlögl, S. Stadlbauer, in:, AHPC16 - Austrian HPC Meeting 2016, VSC - Vienna Scientific Cluster, 2016, p. 37. conference: end_date: 2016-02-24 location: Grundlsee, Austria name: 'AHPC: Austrian HPC Meeting' start_date: 2016-02-22 date_created: 2023-05-05T12:54:47Z date_published: 2016-02-24T00:00:00Z date_updated: 2023-05-16T07:15:14Z day: '24' ddc: - '000' department: - _id: ScienComp - _id: PeJo file: - access_level: open_access checksum: 4a7b00362e81358d568f5e216fa03c3e content_type: application/pdf creator: dernst date_created: 2023-05-16T07:03:56Z date_updated: 2023-05-16T07:03:56Z file_id: '12968' file_name: 2016_AHPC_Schloegl.pdf file_size: 1073523 relation: main_file success: 1 file_date_updated: 2023-05-16T07:03:56Z has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc16/BOOKLET_AHPC16.pdf month: '02' oa: 1 oa_version: Published Version page: '37' publication: AHPC16 - Austrian HPC Meeting 2016 publication_status: published publisher: VSC - Vienna Scientific Cluster quality_controlled: '1' status: public title: 'High performance computing at IST Austria: Modelling the human hippocampus' type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '1890' abstract: - lang: eng text: To search for a target in a complex environment is an everyday behavior that ends with finding the target. When we search for two identical targets, however, we must continue the search after finding the first target and memorize its location. We used fixation-related potentials to investigate the neural correlates of different stages of the search, that is, before and after finding the first target. Having found the first target influenced subsequent distractor processing. Compared to distractor fixations before the first target fixation, a negative shift was observed for three subsequent distractor fixations. These results suggest that processing a target in continued search modulates the brain's response, either transiently by reflecting temporary working memory processes or permanently by reflecting working memory retention. acknowledgement: 'Funded by Austrian Science Fund (FWF) Grant Number: P 22189-B18; European Union within the 6th Framework Programme Grant Number: 517590; State government of Styria Grant Number: PN 4055' author: - first_name: Christof full_name: Körner, Christof last_name: Körner - first_name: Verena full_name: Braunstein, Verena last_name: Braunstein - first_name: Matthias full_name: Stangl, Matthias last_name: Stangl - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Christa full_name: Neuper, Christa last_name: Neuper - first_name: Anja full_name: Ischebeck, Anja last_name: Ischebeck citation: ama: 'Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. Psychophysiology. 2014;51(4):385-395. doi:10.1111/psyp.12062' apa: 'Körner, C., Braunstein, V., Stangl, M., Schlögl, A., Neuper, C., & Ischebeck, A. (2014). Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. Psychophysiology. Wiley-Blackwell. https://doi.org/10.1111/psyp.12062' chicago: 'Körner, Christof, Verena Braunstein, Matthias Stangl, Alois Schlögl, Christa Neuper, and Anja Ischebeck. “Sequential Effects in Continued Visual Search: Using Fixation-Related Potentials to Compare Distractor Processing before and after Target Detection.” Psychophysiology. Wiley-Blackwell, 2014. https://doi.org/10.1111/psyp.12062.' ieee: 'C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, and A. Ischebeck, “Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection,” Psychophysiology, vol. 51, no. 4. Wiley-Blackwell, pp. 385–395, 2014.' ista: 'Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. 2014. Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. Psychophysiology. 51(4), 385–395.' mla: 'Körner, Christof, et al. “Sequential Effects in Continued Visual Search: Using Fixation-Related Potentials to Compare Distractor Processing before and after Target Detection.” Psychophysiology, vol. 51, no. 4, Wiley-Blackwell, 2014, pp. 385–95, doi:10.1111/psyp.12062.' short: C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, A. Ischebeck, Psychophysiology 51 (2014) 385–395. date_created: 2018-12-11T11:54:34Z date_published: 2014-02-11T00:00:00Z date_updated: 2021-01-12T06:53:52Z day: '11' ddc: - '000' department: - _id: ScienComp - _id: PeJo doi: 10.1111/psyp.12062 file: - access_level: open_access checksum: 4255b6185e774acce1d99f8e195c564d content_type: application/pdf creator: system date_created: 2018-12-12T10:16:44Z date_updated: 2020-07-14T12:45:20Z file_id: '5233' file_name: IST-2016-442-v1+1_K-rner_et_al-2014-Psychophysiology.pdf file_size: 543243 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 51' issue: '4' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 385 - 395 publication: Psychophysiology publication_status: published publisher: Wiley-Blackwell publist_id: '5205' pubrep_id: '442' scopus_import: 1 status: public title: 'Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2014' ... --- _id: '2230' abstract: - lang: eng text: Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals. article_number: '16' author: - first_name: José full_name: Guzmán, José id: 30CC5506-F248-11E8-B48F-1D18A9856A87 last_name: Guzmán - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Christoph full_name: Schmidt Hieber, Christoph last_name: Schmidt Hieber citation: ama: 'Guzmán J, Schlögl A, Schmidt Hieber C. Stimfit: Quantifying electrophysiological data with Python. Frontiers in Neuroinformatics. 2014;8(FEB). doi:10.3389/fninf.2014.00016' apa: 'Guzmán, J., Schlögl, A., & Schmidt Hieber, C. (2014). Stimfit: Quantifying electrophysiological data with Python. Frontiers in Neuroinformatics. Frontiers Research Foundation. https://doi.org/10.3389/fninf.2014.00016' chicago: 'Guzmán, José, Alois Schlögl, and Christoph Schmidt Hieber. “Stimfit: Quantifying Electrophysiological Data with Python.” Frontiers in Neuroinformatics. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fninf.2014.00016.' ieee: 'J. Guzmán, A. Schlögl, and C. Schmidt Hieber, “Stimfit: Quantifying electrophysiological data with Python,” Frontiers in Neuroinformatics, vol. 8, no. FEB. Frontiers Research Foundation, 2014.' ista: 'Guzmán J, Schlögl A, Schmidt Hieber C. 2014. Stimfit: Quantifying electrophysiological data with Python. Frontiers in Neuroinformatics. 8(FEB), 16.' mla: 'Guzmán, José, et al. “Stimfit: Quantifying Electrophysiological Data with Python.” Frontiers in Neuroinformatics, vol. 8, no. FEB, 16, Frontiers Research Foundation, 2014, doi:10.3389/fninf.2014.00016.' short: J. Guzmán, A. Schlögl, C. Schmidt Hieber, Frontiers in Neuroinformatics 8 (2014). date_created: 2018-12-11T11:56:27Z date_published: 2014-02-21T00:00:00Z date_updated: 2021-01-12T06:56:09Z day: '21' ddc: - '570' department: - _id: ScienComp - _id: PeJo doi: 10.3389/fninf.2014.00016 file: - access_level: open_access checksum: eeca00bba7232ff7d27db83321f6ea30 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:17Z date_updated: 2020-07-14T12:45:34Z file_id: '4935' file_name: IST-2016-425-v1+1_fninf-08-00016.pdf file_size: 2883372 relation: main_file file_date_updated: 2020-07-14T12:45:34Z has_accepted_license: '1' intvolume: ' 8' issue: FEB language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Frontiers in Neuroinformatics publication_identifier: issn: - '16625196' publication_status: published publisher: Frontiers Research Foundation publist_id: '4731' pubrep_id: '425' quality_controlled: '1' scopus_import: 1 status: public title: 'Stimfit: Quantifying electrophysiological data with Python' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2014' ... --- _id: '10396' abstract: - lang: eng text: Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable. article_number: '000010151520134181' article_processing_charge: No article_type: original author: - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: C. full_name: Schmidt-Hieber, C. last_name: Schmidt-Hieber - first_name: S. J. full_name: Guzman, S. J. last_name: Guzman citation: ama: 'Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. 2013;58(SI-1-Track-G). doi:10.1515/bmt-2013-4181' apa: 'Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., & Guzman, S. J. (2013). Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. Graz, Austria: De Gruyter. https://doi.org/10.1515/bmt-2013-4181' chicago: 'Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” Biomedical Engineering / Biomedizinische Technik. De Gruyter, 2013. https://doi.org/10.1515/bmt-2013-4181.' ieee: 'A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A fast visualization and analysis environment for cellular neurophysiology,” Biomedical Engineering / Biomedizinische Technik, vol. 58, no. SI-1-Track-G. De Gruyter, 2013.' ista: 'Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181.' mla: 'Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” Biomedical Engineering / Biomedizinische Technik, vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:10.1515/bmt-2013-4181.' short: A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering / Biomedizinische Technik 58 (2013). conference: end_date: 2013-09-21 location: Graz, Austria name: 'BMT: Biomedizinische Technik ' start_date: 2013-09-19 date_created: 2021-12-01T14:35:35Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-12-02T12:51:12Z day: '01' ddc: - '005' - '610' department: - _id: PeJo doi: 10.1515/bmt-2013-4181 external_id: pmid: - '24042795' file: - access_level: open_access checksum: cdfc5339b530a25d6079f7223f0b1f16 content_type: application/pdf creator: schloegl date_created: 2021-12-01T14:38:08Z date_updated: 2021-12-01T14:38:08Z file_id: '10397' file_name: Schloegl_Abstract-BMT2013.pdf file_size: 149825 relation: main_file success: 1 file_date_updated: 2021-12-01T14:38:08Z has_accepted_license: '1' intvolume: ' 58' issue: SI-1-Track-G keyword: - biomedical engineering - data analysis - free software language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version pmid: 1 publication: Biomedical Engineering / Biomedizinische Technik publication_identifier: eissn: - 1862-278X issn: - 0013-5585 publication_status: published publisher: De Gruyter quality_controlled: '1' status: public title: 'Stimfit: A fast visualization and analysis environment for cellular neurophysiology' type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 58 year: '2013' ... --- _id: '2954' abstract: - lang: eng text: Spontaneous postsynaptic currents (PSCs) provide key information about the mechanisms of synaptic transmission and the activity modes of neuronal networks. However, detecting spontaneous PSCs in vitro and in vivo has been challenging, because of the small amplitude, the variable kinetics, and the undefined time of generation of these events. Here, we describe a, to our knowledge, new method for detecting spontaneous synaptic events by deconvolution, using a template that approximates the average time course of spontaneous PSCs. A recorded PSC trace is deconvolved from the template, resulting in a series of delta-like functions. The maxima of these delta-like events are reliably detected, revealing the precise onset times of the spontaneous PSCs. Among all detection methods, the deconvolution-based method has a unique temporal resolution, allowing the detection of individual events in high-frequency bursts. Furthermore, the deconvolution-based method has a high amplitude resolution, because deconvolution can substantially increase the signal/noise ratio. When tested against previously published methods using experimental data, the deconvolution-based method was superior for spontaneous PSCs recorded in vivo. Using the high-resolution deconvolution-based detection algorithm, we show that the frequency of spontaneous excitatory postsynaptic currents in dentate gyrus granule cells is 4.5 times higher in vivo than in vitro. acknowledgement: "This work was supported by the Deutsche Forschungsgemeinschaft (TR3/B10) and a European Research Council Advanced grant to P.J.\r\nWe thank H. Hu, S. J. Guzman, and C. Schmidt-Hieber for critically reading the manuscript, I. Koeva and F. Marr for technical support, and E. Kramberger for editorial assistance.\r\n" author: - first_name: Alejandro full_name: Pernia-Andrade, Alejandro id: 36963E98-F248-11E8-B48F-1D18A9856A87 last_name: Pernia-Andrade - first_name: Sarit full_name: Goswami, Sarit id: 3A578F32-F248-11E8-B48F-1D18A9856A87 last_name: Goswami - first_name: Yvonne full_name: Stickler, Yvonne id: 63B76600-E9CC-11E9-9B5F-82450873F7A1 last_name: Stickler - first_name: Ulrich full_name: Fröbe, Ulrich last_name: Fröbe - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Pernia-Andrade A, Goswami S, Stickler Y, Fröbe U, Schlögl A, Jonas PM. A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo. Biophysical Journal. 2012;103(7):1429-1439. doi:10.1016/j.bpj.2012.08.039 apa: Pernia-Andrade, A., Goswami, S., Stickler, Y., Fröbe, U., Schlögl, A., & Jonas, P. M. (2012). A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo. Biophysical Journal. Biophysical. https://doi.org/10.1016/j.bpj.2012.08.039 chicago: Pernia-Andrade, Alejandro, Sarit Goswami, Yvonne Stickler, Ulrich Fröbe, Alois Schlögl, and Peter M Jonas. “A Deconvolution Based Method with High Sensitivity and Temporal Resolution for Detection of Spontaneous Synaptic Currents in Vitro and in Vivo.” Biophysical Journal. Biophysical, 2012. https://doi.org/10.1016/j.bpj.2012.08.039. ieee: A. Pernia-Andrade, S. Goswami, Y. Stickler, U. Fröbe, A. Schlögl, and P. M. Jonas, “A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo,” Biophysical Journal, vol. 103, no. 7. Biophysical, pp. 1429–1439, 2012. ista: Pernia-Andrade A, Goswami S, Stickler Y, Fröbe U, Schlögl A, Jonas PM. 2012. A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo. Biophysical Journal. 103(7), 1429–1439. mla: Pernia-Andrade, Alejandro, et al. “A Deconvolution Based Method with High Sensitivity and Temporal Resolution for Detection of Spontaneous Synaptic Currents in Vitro and in Vivo.” Biophysical Journal, vol. 103, no. 7, Biophysical, 2012, pp. 1429–39, doi:10.1016/j.bpj.2012.08.039. short: A. Pernia-Andrade, S. Goswami, Y. Stickler, U. Fröbe, A. Schlögl, P.M. Jonas, Biophysical Journal 103 (2012) 1429–1439. date_created: 2018-12-11T12:00:32Z date_published: 2012-10-03T00:00:00Z date_updated: 2021-01-12T07:40:01Z day: '03' department: - _id: PeJo - _id: ScienComp doi: 10.1016/j.bpj.2012.08.039 external_id: pmid: - '23062335' intvolume: ' 103' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3471482/ month: '10' oa: 1 oa_version: Submitted Version page: 1429 - 1439 pmid: 1 project: - _id: 25BDE9A4-B435-11E9-9278-68D0E5697425 grant_number: SFB-TR3-TP10B name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen publication: Biophysical Journal publication_status: published publisher: Biophysical publist_id: '3774' quality_controlled: '1' scopus_import: 1 status: public title: A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 103 year: '2012' ...