--- _id: '7369' abstract: - lang: eng text: Neuronal responses to complex stimuli and tasks can encompass a wide range of time scales. Understanding these responses requires measures that characterize how the information on these response patterns are represented across multiple temporal resolutions. In this paper we propose a metric – which we call multiscale relevance (MSR) – to capture the dynamical variability of the activity of single neurons across different time scales. The MSR is a non-parametric, fully featureless indicator in that it uses only the time stamps of the firing activity without resorting to any a priori covariate or invoking any specific structure in the tuning curve for neural activity. When applied to neural data from the mEC and from the ADn and PoS regions of freely-behaving rodents, we found that neurons having low MSR tend to have low mutual information and low firing sparsity across the correlates that are believed to be encoded by the region of the brain where the recordings were made. In addition, neurons with high MSR contain significant information on spatial navigation and allow to decode spatial position or head direction as efficiently as those neurons whose firing activity has high mutual information with the covariate to be decoded and significantly better than the set of neurons with high local variations in their interspike intervals. Given these results, we propose that the MSR can be used as a measure to rank and select neurons for their information content without the need to appeal to any a priori covariate. acknowledgement: This research was supported by the Kavli Foundation and the Centre of Excellence scheme of the Research Council of Norway (Centre for Neural Computation). RJC is currently receiving funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Ryan J full_name: Cubero, Ryan J id: 850B2E12-9CD4-11E9-837F-E719E6697425 last_name: Cubero orcid: 0000-0003-0002-1867 - first_name: Matteo full_name: Marsili, Matteo last_name: Marsili - first_name: Yasser full_name: Roudi, Yasser last_name: Roudi citation: ama: Cubero RJ, Marsili M, Roudi Y. Multiscale relevance and informative encoding in neuronal spike trains. Journal of Computational Neuroscience. 2020;48:85-102. doi:10.1007/s10827-020-00740-x apa: Cubero, R. J., Marsili, M., & Roudi, Y. (2020). Multiscale relevance and informative encoding in neuronal spike trains. Journal of Computational Neuroscience. Springer Nature. https://doi.org/10.1007/s10827-020-00740-x chicago: Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” Journal of Computational Neuroscience. Springer Nature, 2020. https://doi.org/10.1007/s10827-020-00740-x. ieee: R. J. Cubero, M. Marsili, and Y. Roudi, “Multiscale relevance and informative encoding in neuronal spike trains,” Journal of Computational Neuroscience, vol. 48. Springer Nature, pp. 85–102, 2020. ista: Cubero RJ, Marsili M, Roudi Y. 2020. Multiscale relevance and informative encoding in neuronal spike trains. Journal of Computational Neuroscience. 48, 85–102. mla: Cubero, Ryan J., et al. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” Journal of Computational Neuroscience, vol. 48, Springer Nature, 2020, pp. 85–102, doi:10.1007/s10827-020-00740-x. short: R.J. Cubero, M. Marsili, Y. Roudi, Journal of Computational Neuroscience 48 (2020) 85–102. date_created: 2020-01-28T10:34:00Z date_published: 2020-02-01T00:00:00Z date_updated: 2023-08-17T14:35:22Z day: '01' ddc: - '004' - '519' - '570' department: - _id: SaSi doi: 10.1007/s10827-020-00740-x ec_funded: 1 external_id: isi: - '000515321800006' file: - access_level: open_access checksum: 036e9451d6cd0c190ad25791bf82393b content_type: application/pdf creator: rcubero date_created: 2020-01-28T09:31:09Z date_updated: 2020-07-14T12:47:56Z file_id: '7380' file_name: 10827_2020_740_MOESM1_ESM.pdf file_size: 1941355 relation: supplementary_material - access_level: open_access checksum: 4dd8b1fd4b54486f79d82ac7b2a412b2 content_type: application/pdf creator: rcubero date_created: 2020-01-28T09:31:09Z date_updated: 2020-07-14T12:47:56Z file_id: '7381' file_name: Cubero2020_Article_MultiscaleRelevanceAndInformat.pdf file_size: 3257880 relation: main_file file_date_updated: 2020-07-14T12:47:56Z has_accepted_license: '1' intvolume: ' 48' isi: 1 keyword: - Time series analysis - Multiple time scale analysis - Spike train data - Information theory - Bayesian decoding language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 85-102 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of Computational Neuroscience publication_identifier: eissn: - 1573-6873 issn: - 0929-5313 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Multiscale relevance and informative encoding in neuronal spike trains 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 48 year: '2020' ... --- _id: '7364' abstract: - lang: eng text: We present nsCouette, a highly scalable software tool to solve the Navier–Stokes equations for incompressible fluid flow between differentially heated and independently rotating, concentric cylinders. It is based on a pseudospectral spatial discretization and dynamic time-stepping. It is implemented in modern Fortran with a hybrid MPI-OpenMP parallelization scheme and thus designed to compute turbulent flows at high Reynolds and Rayleigh numbers. An additional GPU implementation (C-CUDA) for intermediate problem sizes and a version for pipe flow (nsPipe) are also provided. article_number: '100395' article_processing_charge: No article_type: original author: - first_name: Jose M full_name: Lopez Alonso, Jose M id: 40770848-F248-11E8-B48F-1D18A9856A87 last_name: Lopez Alonso orcid: 0000-0002-0384-2022 - first_name: Daniel full_name: Feldmann, Daniel last_name: Feldmann - first_name: Markus full_name: Rampp, Markus last_name: Rampp - first_name: Alberto full_name: Vela-Martín, Alberto last_name: Vela-Martín - first_name: Liang full_name: Shi, Liang id: 374A3F1A-F248-11E8-B48F-1D18A9856A87 last_name: Shi - first_name: Marc full_name: Avila, Marc last_name: Avila citation: ama: Lopez Alonso JM, Feldmann D, Rampp M, Vela-Martín A, Shi L, Avila M. nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. SoftwareX. 2020;11. doi:10.1016/j.softx.2019.100395 apa: Lopez Alonso, J. M., Feldmann, D., Rampp, M., Vela-Martín, A., Shi, L., & Avila, M. (2020). nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. SoftwareX. Elsevier. https://doi.org/10.1016/j.softx.2019.100395 chicago: Lopez Alonso, Jose M, Daniel Feldmann, Markus Rampp, Alberto Vela-Martín, Liang Shi, and Marc Avila. “NsCouette – A High-Performance Code for Direct Numerical Simulations of Turbulent Taylor–Couette Flow.” SoftwareX. Elsevier, 2020. https://doi.org/10.1016/j.softx.2019.100395. ieee: J. M. Lopez Alonso, D. Feldmann, M. Rampp, A. Vela-Martín, L. Shi, and M. Avila, “nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow,” SoftwareX, vol. 11. Elsevier, 2020. ista: Lopez Alonso JM, Feldmann D, Rampp M, Vela-Martín A, Shi L, Avila M. 2020. nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. SoftwareX. 11, 100395. mla: Lopez Alonso, Jose M., et al. “NsCouette – A High-Performance Code for Direct Numerical Simulations of Turbulent Taylor–Couette Flow.” SoftwareX, vol. 11, 100395, Elsevier, 2020, doi:10.1016/j.softx.2019.100395. short: J.M. Lopez Alonso, D. Feldmann, M. Rampp, A. Vela-Martín, L. Shi, M. Avila, SoftwareX 11 (2020). date_created: 2020-01-26T23:00:35Z date_published: 2020-01-17T00:00:00Z date_updated: 2023-08-17T14:29:59Z day: '17' ddc: - '000' department: - _id: BjHo doi: 10.1016/j.softx.2019.100395 external_id: arxiv: - '1908.00587' isi: - '000552271200011' file: - access_level: open_access checksum: 2af1a1a3cc33557b345145276f221668 content_type: application/pdf creator: dernst date_created: 2020-01-27T07:32:46Z date_updated: 2020-07-14T12:47:56Z file_id: '7365' file_name: 2020_SoftwareX_Lopez.pdf file_size: 679707 relation: main_file file_date_updated: 2020-07-14T12:47:56Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: SoftwareX publication_identifier: eissn: - '23527110' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow 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: 11 year: '2020' ... --- _id: '7431' abstract: - lang: eng text: 'In many real-world systems, information can be transmitted in two qualitatively different ways: by copying or by transformation. Copying occurs when messages are transmitted without modification, e.g. when an offspring receives an unaltered copy of a gene from its parent. Transformation occurs when messages are modified systematically during transmission, e.g. when mutational biases occur during genetic replication. Standard information-theoretic measures do not distinguish these two modes of information transfer, although they may reflect different mechanisms and have different functional consequences. Starting from a few simple axioms, we derive a decomposition of mutual information into the information transmitted by copying versus the information transmitted by transformation. We begin with a decomposition that applies when the source and destination of the channel have the same set of messages and a notion of message identity exists. We then generalize our decomposition to other kinds of channels, which can involve different source and destination sets and broader notions of similarity. In addition, we show that copy information can be interpreted as the minimal work needed by a physical copying process, which is relevant for understanding the physics of replication. We use the proposed decomposition to explore a model of amino acid substitution rates. Our results apply to any system in which the fidelity of copying, rather than simple predictability, is of critical relevance.' acknowledgement: "AK was supported by Grant No. FQXi-RFP-1622 from the FQXi foundation, and Grant No. CHE-1648973 from the U.S.\r\nNational Science Foundation. AK would like to thank the Santa Fe Institute for supporting this research. The authors\r\nthank Jordi Fortuny, Rudolf Hanel, Joshua Garland, and Blai Vidiella for helpful discussions, as well as the anonymous\r\nreviewers for their insightful suggestions. " article_number: '0623' article_processing_charge: No article_type: original author: - first_name: Artemy full_name: Kolchinsky, Artemy last_name: Kolchinsky - first_name: Bernat full_name: Corominas-Murtra, Bernat id: 43BE2298-F248-11E8-B48F-1D18A9856A87 last_name: Corominas-Murtra orcid: 0000-0001-9806-5643 citation: ama: Kolchinsky A, Corominas-Murtra B. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 2020;17(162). doi:10.1098/rsif.2019.0623 apa: Kolchinsky, A., & Corominas-Murtra, B. (2020). Decomposing information into copying versus transformation. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2019.0623 chicago: Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” Journal of the Royal Society Interface. The Royal Society, 2020. https://doi.org/10.1098/rsif.2019.0623. ieee: A. Kolchinsky and B. Corominas-Murtra, “Decomposing information into copying versus transformation,” Journal of the Royal Society Interface, vol. 17, no. 162. The Royal Society, 2020. ista: Kolchinsky A, Corominas-Murtra B. 2020. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 17(162), 0623. mla: Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” Journal of the Royal Society Interface, vol. 17, no. 162, 0623, The Royal Society, 2020, doi:10.1098/rsif.2019.0623. short: A. Kolchinsky, B. Corominas-Murtra, Journal of the Royal Society Interface 17 (2020). date_created: 2020-02-02T23:01:03Z date_published: 2020-01-29T00:00:00Z date_updated: 2023-08-17T14:31:28Z day: '29' department: - _id: EdHa doi: 10.1098/rsif.2019.0623 external_id: arxiv: - '1903.10693' isi: - '000538369800002' pmid: - '31964273' intvolume: ' 17' isi: 1 issue: '162' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1903.10693 month: '01' oa: 1 oa_version: Preprint pmid: 1 publication: Journal of the Royal Society Interface publication_identifier: eissn: - '17425662' publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: Decomposing information into copying versus transformation type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2020' ... --- _id: '7389' abstract: - lang: eng text: "Recently Kloeckner described the structure of the isometry group of the quadratic Wasserstein space W_2(R^n). It turned out that the case of the real line is exceptional in the sense that there exists an exotic isometry flow. Following this line of investigation, we compute Isom(W_p(R)), the isometry group of the Wasserstein space\r\nW_p(R) for all p \\in [1,\\infty) \\setminus {2}. We show that W_2(R) is also exceptional regarding the\r\nparameter p: W_p(R) is isometrically rigid if and only if p is not equal to 2. Regarding the underlying\r\nspace, we prove that the exceptionality of p = 2 disappears if we replace R by the compact\r\ninterval [0,1]. Surprisingly, in that case, W_p([0,1]) is isometrically rigid if and only if\r\np is not equal to 1. Moreover, W_1([0,1]) admits isometries that split mass, and Isom(W_1([0,1]))\r\ncannot be embedded into Isom(W_1(R))." article_processing_charge: No article_type: original author: - first_name: Gyorgy Pal full_name: Geher, Gyorgy Pal last_name: Geher - first_name: Tamas full_name: Titkos, Tamas last_name: Titkos - first_name: Daniel full_name: Virosztek, Daniel id: 48DB45DA-F248-11E8-B48F-1D18A9856A87 last_name: Virosztek orcid: 0000-0003-1109-5511 citation: ama: Geher GP, Titkos T, Virosztek D. Isometric study of Wasserstein spaces - the real line. Transactions of the American Mathematical Society. 2020;373(8):5855-5883. doi:10.1090/tran/8113 apa: Geher, G. P., Titkos, T., & Virosztek, D. (2020). Isometric study of Wasserstein spaces - the real line. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/8113 chicago: Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Isometric Study of Wasserstein Spaces - the Real Line.” Transactions of the American Mathematical Society. American Mathematical Society, 2020. https://doi.org/10.1090/tran/8113. ieee: G. P. Geher, T. Titkos, and D. Virosztek, “Isometric study of Wasserstein spaces - the real line,” Transactions of the American Mathematical Society, vol. 373, no. 8. American Mathematical Society, pp. 5855–5883, 2020. ista: Geher GP, Titkos T, Virosztek D. 2020. Isometric study of Wasserstein spaces - the real line. Transactions of the American Mathematical Society. 373(8), 5855–5883. mla: Geher, Gyorgy Pal, et al. “Isometric Study of Wasserstein Spaces - the Real Line.” Transactions of the American Mathematical Society, vol. 373, no. 8, American Mathematical Society, 2020, pp. 5855–83, doi:10.1090/tran/8113. short: G.P. Geher, T. Titkos, D. Virosztek, Transactions of the American Mathematical Society 373 (2020) 5855–5883. date_created: 2020-01-29T10:20:46Z date_published: 2020-08-01T00:00:00Z date_updated: 2023-08-17T14:31:03Z day: '01' ddc: - '515' department: - _id: LaEr doi: 10.1090/tran/8113 ec_funded: 1 external_id: arxiv: - '2002.00859' isi: - '000551418100018' intvolume: ' 373' isi: 1 issue: '8' keyword: - Wasserstein space - isometric embeddings - isometric rigidity - exotic isometry flow language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2002.00859 month: '08' oa: 1 oa_version: Preprint page: 5855-5883 project: - _id: 26A455A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '846294' name: Geometric study of Wasserstein spaces and free probability publication: Transactions of the American Mathematical Society publication_identifier: eissn: - '10886850' issn: - '00029947' publication_status: published publisher: American Mathematical Society quality_controlled: '1' status: public title: Isometric study of Wasserstein spaces - the real line type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 373 year: '2020' ... --- _id: '7467' abstract: - lang: eng text: Nanomaterials produced from the bottom-up assembly of nanocrystals may incorporate ∼1020–1021 cm–3 not fully coordinated surface atoms, i.e., ∼1020–1021 cm–3 potential donor or acceptor states that can strongly affect transport properties. Therefore, to exploit the full potential of nanocrystal building blocks to produce functional nanomaterials and thin films, a proper control of their surface chemistry is required. Here, we analyze how the ligand stripping procedure influences the charge and heat transport properties of sintered PbSe nanomaterials produced from the bottom-up assembly of colloidal PbSe nanocrystals. First, we show that the removal of the native organic ligands by thermal decomposition in an inert atmosphere leaves relatively large amounts of carbon at the crystal interfaces. This carbon blocks crystal growth during consolidation and at the same time hampers charge and heat transport through the final nanomaterial. Second, we demonstrate that, by stripping ligands from the nanocrystal surface before consolidation, nanomaterials with larger crystal domains, lower porosity, and higher charge carrier concentrations are obtained, thus resulting in nanomaterials with higher electrical and thermal conductivities. In addition, the ligand displacement leaves the nanocrystal surface unprotected, facilitating oxidation and chalcogen evaporation. The influence of the ligand displacement on the nanomaterial charge transport properties is rationalized here using a two-band model based on the standard Boltzmann transport equation with the relaxation time approximation. Finally, we present an application of the produced functional nanomaterials by modeling, fabricating, and testing a simple PbSe-based thermoelectric device with a ring geometry. acknowledgement: This work was supported by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP (ENE2016-77798-C4-3-R) and the Generalitat de Catalunya through the project 2017SGR1246. D.C. acknowledges support from Universidad Nacional de Colombia. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 754411. M.I. acknowledges financial support from IST Austria. article_processing_charge: No article_type: original author: - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Silvia full_name: Ortega, Silvia last_name: Ortega - first_name: Sergio full_name: Illera, Sergio last_name: Illera - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Yu full_name: Zhang, Yu last_name: Zhang - first_name: Mengyao full_name: Li, Mengyao last_name: Li - first_name: Antonio M. full_name: López, Antonio M. last_name: López - first_name: Germán full_name: Noriega, Germán last_name: Noriega - first_name: Oscar Juan full_name: Durá, Oscar Juan last_name: Durá - first_name: M. A. full_name: López De La Torre, M. A. last_name: López De La Torre - first_name: Joan Daniel full_name: Prades, Joan Daniel last_name: Prades - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Cadavid D, Ortega S, Illera S, et al. Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. ACS Applied Energy Materials. 2020;3(3):2120-2129. doi:10.1021/acsaem.9b02137 apa: Cadavid, D., Ortega, S., Illera, S., Liu, Y., Ibáñez, M., Shavel, A., … Cabot, A. (2020). Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. ACS Applied Energy Materials. American Chemical Society. https://doi.org/10.1021/acsaem.9b02137 chicago: Cadavid, Doris, Silvia Ortega, Sergio Illera, Yu Liu, Maria Ibáñez, Alexey Shavel, Yu Zhang, et al. “Influence of the Ligand Stripping on the Transport Properties of Nanoparticle-Based PbSe Nanomaterials.” ACS Applied Energy Materials. American Chemical Society, 2020. https://doi.org/10.1021/acsaem.9b02137. ieee: D. Cadavid et al., “Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials,” ACS Applied Energy Materials, vol. 3, no. 3. American Chemical Society, pp. 2120–2129, 2020. ista: Cadavid D, Ortega S, Illera S, Liu Y, Ibáñez M, Shavel A, Zhang Y, Li M, López AM, Noriega G, Durá OJ, López De La Torre MA, Prades JD, Cabot A. 2020. Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. ACS Applied Energy Materials. 3(3), 2120–2129. mla: Cadavid, Doris, et al. “Influence of the Ligand Stripping on the Transport Properties of Nanoparticle-Based PbSe Nanomaterials.” ACS Applied Energy Materials, vol. 3, no. 3, American Chemical Society, 2020, pp. 2120–29, doi:10.1021/acsaem.9b02137. short: D. Cadavid, S. Ortega, S. Illera, Y. Liu, M. Ibáñez, A. Shavel, Y. Zhang, M. Li, A.M. López, G. Noriega, O.J. Durá, M.A. López De La Torre, J.D. Prades, A. Cabot, ACS Applied Energy Materials 3 (2020) 2120–2129. date_created: 2020-02-09T23:00:52Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-08-17T14:36:16Z day: '01' ddc: - '540' department: - _id: MaIb doi: 10.1021/acsaem.9b02137 ec_funded: 1 external_id: isi: - '000526598300012' file: - access_level: open_access checksum: f23be731a766a480c77c962c1380315c content_type: application/pdf creator: dernst date_created: 2022-08-23T08:34:17Z date_updated: 2022-08-23T08:34:17Z file_id: '11942' file_name: 2020_ACSAppliedEnergyMat_Cadavid.pdf file_size: 6423548 relation: main_file success: 1 file_date_updated: 2022-08-23T08:34:17Z has_accepted_license: '1' intvolume: ' 3' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 2120-2129 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: ACS Applied Energy Materials publication_identifier: eissn: - 2574-0962 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 3 year: '2020' ... --- _id: '7465' abstract: - lang: eng text: The flexible development of plants is characterized by a high capacity for post-embryonic organ formation and tissue regeneration, processes, which require tightly regulated intercellular communication and coordinated tissue (re-)polarization. The phytohormone auxin, the main driver for these processes, is able to establish polarized auxin transport channels, which are characterized by the expression and polar, subcellular localization of the PIN1 auxin transport proteins. These channels are demarcating the position of future vascular strands necessary for organ formation and tissue regeneration. Major progress has been made in the last years to understand how PINs can change their polarity in different contexts and thus guide auxin flow through the plant. However, it still remains elusive how auxin mediates the establishment of auxin conducting channels and the formation of vascular tissue and which cellular processes are involved. By the means of sophisticated regeneration experiments combined with local auxin applications in Arabidopsis thaliana inflorescence stems we show that (i) PIN subcellular dynamics, (ii) PIN internalization by clathrin-mediated trafficking and (iii) an intact actin cytoskeleton required for post-endocytic trafficking are indispensable for auxin channel formation, de novo vascular formation and vascular regeneration after wounding. These observations provide novel insights into cellular mechanism of coordinated tissue polarization during auxin canalization. article_number: '110414' article_processing_charge: No article_type: original author: - first_name: Ewa full_name: Mazur, Ewa last_name: Mazur - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Huibin full_name: Han, Huibin id: 31435098-F248-11E8-B48F-1D18A9856A87 last_name: Han - first_name: Hélène S. full_name: Robert, Hélène S. last_name: Robert - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. Plant Science. 2020;293(4). doi:10.1016/j.plantsci.2020.110414 apa: Mazur, E., Gallei, M. C., Adamowski, M., Han, H., Robert, H. S., & Friml, J. (2020). Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2020.110414 chicago: Mazur, Ewa, Michelle C Gallei, Maciek Adamowski, Huibin Han, Hélène S. Robert, and Jiří Friml. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” Plant Science. Elsevier, 2020. https://doi.org/10.1016/j.plantsci.2020.110414. ieee: E. Mazur, M. C. Gallei, M. Adamowski, H. Han, H. S. Robert, and J. Friml, “Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis,” Plant Science, vol. 293, no. 4. Elsevier, 2020. ista: Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. 2020. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. Plant Science. 293(4), 110414. mla: Mazur, Ewa, et al. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” Plant Science, vol. 293, no. 4, 110414, Elsevier, 2020, doi:10.1016/j.plantsci.2020.110414. short: E. Mazur, M.C. Gallei, M. Adamowski, H. Han, H.S. Robert, J. Friml, Plant Science 293 (2020). date_created: 2020-02-09T23:00:50Z date_published: 2020-04-01T00:00:00Z date_updated: 2023-08-17T14:37:32Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.plantsci.2020.110414 ec_funded: 1 external_id: isi: - '000520609800009' file: - access_level: open_access checksum: f7f27c6a8fea985ceb9279be2204461c content_type: application/pdf creator: dernst date_created: 2020-02-10T08:59:36Z date_updated: 2020-07-14T12:47:59Z file_id: '7471' file_name: 2020_PlantScience_Mazur.pdf file_size: 3499069 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' intvolume: ' 293' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Plant Science publication_identifier: eissn: - '18732259' issn: - '01689452' publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '11626' relation: dissertation_contains status: public scopus_import: '1' status: public title: Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 293 year: '2020' ... --- _id: '7466' abstract: - lang: eng text: Unpaired ligands are secreted signals that act via a GP130-like receptor, domeless, to activate JAK/STAT signalling in Drosophila. Like many mammalian cytokines, unpaireds can be activated by infection and other stresses and can promote insulin resistance in target tissues. However, the importance of this effect in non-inflammatory physiology is unknown. Here, we identify a requirement for unpaired-JAK signalling as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show basal JAK-STAT signalling activity in the absence of any immune challenge. Plasmatocytes (Drosophila macrophages) are an important source of this tonic signal. Loss of the dome receptor on adult muscles significantly reduces lifespan and causes local and systemic metabolic pathology. These pathologies result from hyperactivation of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine signal that must be received in muscle to control AKT activity and metabolic homeostasis. article_number: e51595 article_processing_charge: No article_type: original author: - first_name: Katrin full_name: Kierdorf, Katrin last_name: Kierdorf - first_name: Fabian full_name: Hersperger, Fabian last_name: Hersperger - first_name: Jessica full_name: Sharrock, Jessica last_name: Sharrock - first_name: Crystal M. full_name: Vincent, Crystal M. last_name: Vincent - first_name: Pinar full_name: Ustaoglu, Pinar last_name: Ustaoglu - first_name: Jiawen full_name: Dou, Jiawen last_name: Dou - first_name: Attila full_name: György, Attila id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87 last_name: György orcid: 0000-0002-1819-198X - first_name: Olaf full_name: Groß, Olaf last_name: Groß - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Marc S. full_name: Dionne, Marc S. last_name: Dionne citation: ama: Kierdorf K, Hersperger F, Sharrock J, et al. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. eLife. 2020;9. doi:10.7554/eLife.51595 apa: Kierdorf, K., Hersperger, F., Sharrock, J., Vincent, C. M., Ustaoglu, P., Dou, J., … Dionne, M. S. (2020). Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51595 chicago: Kierdorf, Katrin, Fabian Hersperger, Jessica Sharrock, Crystal M. Vincent, Pinar Ustaoglu, Jiawen Dou, Attila György, Olaf Groß, Daria E Siekhaus, and Marc S. Dionne. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.51595. ieee: K. Kierdorf et al., “Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Kierdorf K, Hersperger F, Sharrock J, Vincent CM, Ustaoglu P, Dou J, György A, Groß O, Siekhaus DE, Dionne MS. 2020. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. eLife. 9, e51595. mla: Kierdorf, Katrin, et al. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” ELife, vol. 9, e51595, eLife Sciences Publications, 2020, doi:10.7554/eLife.51595. short: K. Kierdorf, F. Hersperger, J. Sharrock, C.M. Vincent, P. Ustaoglu, J. Dou, A. György, O. Groß, D.E. Siekhaus, M.S. Dionne, ELife 9 (2020). date_created: 2020-02-09T23:00:51Z date_published: 2020-01-20T00:00:00Z date_updated: 2023-08-17T14:36:39Z day: '20' ddc: - '570' department: - _id: DaSi doi: 10.7554/eLife.51595 external_id: isi: - '000512304800001' file: - access_level: open_access checksum: 3a072be843f416c7a7d532a51dc0addb content_type: application/pdf creator: dernst date_created: 2020-02-10T08:53:16Z date_updated: 2020-07-14T12:47:59Z file_id: '7470' file_name: 2020_eLife_Kierdorf.pdf file_size: 4959933 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 253B6E48-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29638 name: Drosophila TNFa´s Funktion in Immunzellen publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2020' ... --- _id: '7472' abstract: - lang: eng text: Temporally organized reactivation of experiences during awake immobility periods is thought to underlie cognitive processes like planning and evaluation. While replay of trajectories is well established for the hippocampus, it is unclear whether the medial prefrontal cortex (mPFC) can reactivate sequential behavioral experiences in the awake state to support task execution. We simultaneously recorded from hippocampal and mPFC principal neurons in rats performing a mPFC-dependent rule-switching task on a plus maze. We found that mPFC neuronal activity encoded relative positions between the start and goal. During awake immobility periods, the mPFC replayed temporally organized sequences of these generalized positions, resembling entire spatial trajectories. The occurrence of mPFC trajectory replay positively correlated with rule-switching performance. However, hippocampal and mPFC trajectory replay occurred independently, indicating different functions. These results demonstrate that the mPFC can replay ordered activity patterns representing generalized locations and suggest that mPFC replay might have a role in flexible behavior. acknowledged_ssus: - _id: M-Shop acknowledgement: We thank Todor Asenov and Thomas Menner from the Machine Shop for the drive design and production, Hugo Malagon-Vina for assistance in maze automatization, Jago Wallenschus for taking the images of the histology, and Federico Stella and Juan Felipe Ramirez-Villegas for comments on an earlier version of the manuscript. This work was supported by the EU-FP7 MC-ITN IN-SENS (grant 607616 ). article_processing_charge: No article_type: original author: - first_name: Karola full_name: Käfer, Karola id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87 last_name: Käfer - first_name: Michele full_name: Nardin, Michele id: 30BD0376-F248-11E8-B48F-1D18A9856A87 last_name: Nardin orcid: 0000-0001-8849-6570 - first_name: Karel full_name: Blahna, Karel id: 3EA859AE-F248-11E8-B48F-1D18A9856A87 last_name: Blahna - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: Käfer K, Nardin M, Blahna K, Csicsvari JL. Replay of behavioral sequences in the medial prefrontal cortex during rule switching. Neuron. 2020;106(1):P154-165.e6. doi:10.1016/j.neuron.2020.01.015 apa: Käfer, K., Nardin, M., Blahna, K., & Csicsvari, J. L. (2020). Replay of behavioral sequences in the medial prefrontal cortex during rule switching. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.01.015 chicago: Käfer, Karola, Michele Nardin, Karel Blahna, and Jozsef L Csicsvari. “Replay of Behavioral Sequences in the Medial Prefrontal Cortex during Rule Switching.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.01.015. ieee: K. Käfer, M. Nardin, K. Blahna, and J. L. Csicsvari, “Replay of behavioral sequences in the medial prefrontal cortex during rule switching,” Neuron, vol. 106, no. 1. Elsevier, p. P154–165.e6, 2020. ista: Käfer K, Nardin M, Blahna K, Csicsvari JL. 2020. Replay of behavioral sequences in the medial prefrontal cortex during rule switching. Neuron. 106(1), P154–165.e6. mla: Käfer, Karola, et al. “Replay of Behavioral Sequences in the Medial Prefrontal Cortex during Rule Switching.” Neuron, vol. 106, no. 1, Elsevier, 2020, p. P154–165.e6, doi:10.1016/j.neuron.2020.01.015. short: K. Käfer, M. Nardin, K. Blahna, J.L. Csicsvari, Neuron 106 (2020) P154–165.e6. date_created: 2020-02-10T15:45:48Z date_published: 2020-04-08T00:00:00Z date_updated: 2023-08-17T14:38:02Z day: '08' department: - _id: JoCs doi: 10.1016/j.neuron.2020.01.015 ec_funded: 1 external_id: isi: - '000525319300016' pmid: - '32032512' intvolume: ' 106' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.neuron.2020.01.015 month: '04' oa: 1 oa_version: Published Version page: P154-165.e6 pmid: 1 project: - _id: 257BBB4C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '607616' name: Inter-and intracellular signalling in schizophrenia publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/this-brain-area-helps-us-decide/ scopus_import: '1' status: public title: Replay of behavioral sequences in the medial prefrontal cortex during rule switching type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 106 year: '2020' ... --- _id: '7388' abstract: - lang: eng text: We give a Wong-Zakai type characterisation of the solutions of quasilinear heat equations driven by space-time white noise in 1 + 1 dimensions. In order to show that the renormalisation counterterms are local in the solution, a careful arrangement of a few hundred terms is required. The main tool in this computation is a general ‘integration by parts’ formula that provides a number of linear identities for the renormalisation constants. article_processing_charge: No article_type: original author: - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser citation: ama: Gerencser M. Nondivergence form quasilinear heat equations driven by space-time white noise. Annales de l’Institut Henri Poincaré C, Analyse non linéaire. 2020;37(3):663-682. doi:10.1016/j.anihpc.2020.01.003 apa: Gerencser, M. (2020). Nondivergence form quasilinear heat equations driven by space-time white noise. Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire. Elsevier. https://doi.org/10.1016/j.anihpc.2020.01.003 chicago: Gerencser, Mate. “Nondivergence Form Quasilinear Heat Equations Driven by Space-Time White Noise.” Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire. Elsevier, 2020. https://doi.org/10.1016/j.anihpc.2020.01.003. ieee: M. Gerencser, “Nondivergence form quasilinear heat equations driven by space-time white noise,” Annales de l’Institut Henri Poincaré C, Analyse non linéaire, vol. 37, no. 3. Elsevier, pp. 663–682, 2020. ista: Gerencser M. 2020. Nondivergence form quasilinear heat equations driven by space-time white noise. Annales de l’Institut Henri Poincaré C, Analyse non linéaire. 37(3), 663–682. mla: Gerencser, Mate. “Nondivergence Form Quasilinear Heat Equations Driven by Space-Time White Noise.” Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire, vol. 37, no. 3, Elsevier, 2020, pp. 663–82, doi:10.1016/j.anihpc.2020.01.003. short: M. Gerencser, Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire 37 (2020) 663–682. date_created: 2020-01-29T09:39:41Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-08-17T14:35:46Z day: '01' department: - _id: JaMa doi: 10.1016/j.anihpc.2020.01.003 external_id: arxiv: - '1902.07635' isi: - '000531049800007' intvolume: ' 37' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.07635 month: '05' oa: 1 oa_version: Preprint page: 663-682 publication: Annales de l'Institut Henri Poincaré C, Analyse non linéaire publication_identifier: issn: - 0294-1449 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Nondivergence form quasilinear heat equations driven by space-time white noise type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 37 year: '2020' ... --- _id: '7487' abstract: - lang: eng text: 'Glutaminase (GA) catalyzes the first step in mitochondrial glutaminolysis playing a key role in cancer metabolic reprogramming. Humans express two types of GA isoforms: GLS and GLS2. GLS isozymes have been consistently related to cell proliferation, but the role of GLS2 in cancer remains poorly understood. GLS2 is repressed in many tumor cells and a better understanding of its function in tumorigenesis may further the development of new therapeutic approaches. We analyzed GLS2 expression in HCC, GBM and neuroblastoma cells, as well as in monkey COS-7 cells. We studied GLS2 expression after induction of differentiation with phorbol ester (PMA) and transduction with the full-length cDNA of GLS2. In parallel, we investigated cell cycle progression and levels of p53, p21 and c-Myc proteins. Using the baculovirus system, human GLS2 protein was overexpressed, purified and analyzed for posttranslational modifications employing a proteomics LC-MS/MS platform. We have demonstrated a dual targeting of GLS2 in human cancer cells. Immunocytochemistry and subcellular fractionation gave consistent results demonstrating nuclear and mitochondrial locations, with the latter being predominant. Nuclear targeting was confirmed in cancer cells overexpressing c-Myc- and GFP-tagged GLS2 proteins. We assessed the subnuclear location finding a widespread distribution of GLS2 in the nucleoplasm without clear overlapping with specific nuclear substructures. GLS2 expression and nuclear accrual notably increased by treatment of SH-SY5Y cells with PMA and it correlated with cell cycle arrest at G2/M, upregulation of tumor suppressor p53 and p21 protein. A similar response was obtained by overexpression of GLS2 in T98G glioma cells, including downregulation of oncogene c-Myc. Furthermore, human GLS2 was identified as being hypusinated by MS analysis, a posttranslational modification which may be relevant for its nuclear targeting and/or function. Our studies provide evidence for a tumor suppressor role of GLS2 in certain types of cancer. The data imply that GLS2 can be regarded as a highly mobile and multilocalizing protein translocated to both mitochondria and nuclei. Upregulation of GLS2 in cancer cells induced an antiproliferative response with cell cycle arrest at the G2/M phase.' article_number: '2259' article_processing_charge: No article_type: original author: - first_name: Amada R. full_name: López De La Oliva, Amada R. last_name: López De La Oliva - first_name: José A. full_name: Campos-Sandoval, José A. last_name: Campos-Sandoval - first_name: María C. full_name: Gómez-García, María C. last_name: Gómez-García - first_name: Carolina full_name: Cardona, Carolina last_name: Cardona - first_name: Mercedes full_name: Martín-Rufián, Mercedes last_name: Martín-Rufián - first_name: Fernando J. full_name: Sialana, Fernando J. last_name: Sialana - first_name: Laura full_name: Castilla, Laura last_name: Castilla - first_name: Narkhyun full_name: Bae, Narkhyun id: 3A5F7CD8-F248-11E8-B48F-1D18A9856A87 last_name: Bae - first_name: Carolina full_name: Lobo, Carolina last_name: Lobo - first_name: Ana full_name: Peñalver, Ana last_name: Peñalver - first_name: Marina full_name: García-Frutos, Marina last_name: García-Frutos - first_name: David full_name: Carro, David last_name: Carro - first_name: Victoria full_name: Enrique, Victoria last_name: Enrique - first_name: José C. full_name: Paz, José C. last_name: Paz - first_name: Raghavendra G. full_name: Mirmira, Raghavendra G. last_name: Mirmira - first_name: Antonia full_name: Gutiérrez, Antonia last_name: Gutiérrez - first_name: Francisco J. full_name: Alonso, Francisco J. last_name: Alonso - first_name: Juan A. full_name: Segura, Juan A. last_name: Segura - first_name: José M. full_name: Matés, José M. last_name: Matés - first_name: Gert full_name: Lubec, Gert last_name: Lubec - first_name: Javier full_name: Márquez, Javier last_name: Márquez citation: ama: López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, et al. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific reports. 2020;10(1). doi:10.1038/s41598-020-58264-4 apa: López De La Oliva, A. R., Campos-Sandoval, J. A., Gómez-García, M. C., Cardona, C., Martín-Rufián, M., Sialana, F. J., … Márquez, J. (2020). Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-58264-4 chicago: López De La Oliva, Amada R., José A. Campos-Sandoval, María C. Gómez-García, Carolina Cardona, Mercedes Martín-Rufián, Fernando J. Sialana, Laura Castilla, et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-58264-4. ieee: A. R. López De La Oliva et al., “Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation,” Scientific reports, vol. 10, no. 1. Springer Nature, 2020. ista: López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, Cardona C, Martín-Rufián M, Sialana FJ, Castilla L, Bae N, Lobo C, Peñalver A, García-Frutos M, Carro D, Enrique V, Paz JC, Mirmira RG, Gutiérrez A, Alonso FJ, Segura JA, Matés JM, Lubec G, Márquez J. 2020. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific reports. 10(1), 2259. mla: López De La Oliva, Amada R., et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” Scientific Reports, vol. 10, no. 1, 2259, Springer Nature, 2020, doi:10.1038/s41598-020-58264-4. short: A.R. López De La Oliva, J.A. Campos-Sandoval, M.C. Gómez-García, C. Cardona, M. Martín-Rufián, F.J. Sialana, L. Castilla, N. Bae, C. Lobo, A. Peñalver, M. García-Frutos, D. Carro, V. Enrique, J.C. Paz, R.G. Mirmira, A. Gutiérrez, F.J. Alonso, J.A. Segura, J.M. Matés, G. Lubec, J. Márquez, Scientific Reports 10 (2020). date_created: 2020-02-16T23:00:49Z date_published: 2020-02-10T00:00:00Z date_updated: 2023-08-18T06:35:13Z day: '10' ddc: - '570' department: - _id: CaBe doi: 10.1038/s41598-020-58264-4 external_id: isi: - '000560694800012' pmid: - '32042057' file: - access_level: open_access checksum: c780bd87476a9c9e12668ff66de3dc96 content_type: application/pdf creator: dernst date_created: 2020-02-18T07:43:21Z date_updated: 2020-07-14T12:47:59Z file_id: '7495' file_name: 2020_ScientificReport_Lopez.pdf file_size: 4703751 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Scientific reports publication_identifier: eissn: - '20452322' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41598-020-80651-0 scopus_import: '1' status: public title: Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2020' ... --- _id: '7490' abstract: - lang: eng text: In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the plasma membrane but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes. acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: EM-Fac article_number: e52067 article_processing_charge: No article_type: original author: - first_name: Madhumitha full_name: Narasimhan, Madhumitha id: 44BF24D0-F248-11E8-B48F-1D18A9856A87 last_name: Narasimhan orcid: 0000-0002-8600-0671 - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - first_name: Roshan full_name: Prizak, Roshan id: 4456104E-F248-11E8-B48F-1D18A9856A87 last_name: Prizak - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Barbara E full_name: Casillas Perez, Barbara E id: 351ED2AA-F248-11E8-B48F-1D18A9856A87 last_name: Casillas Perez - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Narasimhan M, Johnson AJ, Prizak R, et al. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife. 2020;9. doi:10.7554/eLife.52067 apa: Narasimhan, M., Johnson, A. J., Prizak, R., Kaufmann, W., Tan, S., Casillas Perez, B. E., & Friml, J. (2020). Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.52067 chicago: Narasimhan, Madhumitha, Alexander J Johnson, Roshan Prizak, Walter Kaufmann, Shutang Tan, Barbara E Casillas Perez, and Jiří Friml. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.52067. ieee: M. Narasimhan et al., “Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Narasimhan M, Johnson AJ, Prizak R, Kaufmann W, Tan S, Casillas Perez BE, Friml J. 2020. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife. 9, e52067. mla: Narasimhan, Madhumitha, et al. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” ELife, vol. 9, e52067, eLife Sciences Publications, 2020, doi:10.7554/eLife.52067. short: M. Narasimhan, A.J. Johnson, R. Prizak, W. Kaufmann, S. Tan, B.E. Casillas Perez, J. Friml, ELife 9 (2020). date_created: 2020-02-16T23:00:50Z date_published: 2020-01-23T00:00:00Z date_updated: 2023-08-18T06:33:07Z day: '23' ddc: - '570' - '580' department: - _id: JiFr - _id: GaTk - _id: EM-Fac - _id: SyCr doi: 10.7554/eLife.52067 ec_funded: 1 external_id: isi: - '000514104100001' pmid: - '31971511' file: - access_level: open_access checksum: 2052daa4be5019534f3a42f200a09f32 content_type: application/pdf creator: dernst date_created: 2020-02-18T07:21:16Z date_updated: 2020-07-14T12:47:59Z file_id: '7494' file_name: 2020_eLife_Narasimhan.pdf file_size: 7247468 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2020' ... --- _id: '7488' abstract: - lang: eng text: Characteristic or classic phenotype of Cornelia de Lange syndrome (CdLS) is associated with a recognisable facial pattern. However, the heterogeneity in causal genes and the presence of overlapping syndromes have made it increasingly difficult to diagnose only by clinical features. DeepGestalt technology, and its app Face2Gene, is having a growing impact on the diagnosis and management of genetic diseases by analysing the features of affected individuals. Here, we performed a phenotypic study on a cohort of 49 individuals harbouring causative variants in known CdLS genes in order to evaluate Face2Gene utility and sensitivity in the clinical diagnosis of CdLS. Based on the profile images of patients, a diagnosis of CdLS was within the top five predicted syndromes for 97.9% of our cases and even listed as first prediction for 83.7%. The age of patients did not seem to affect the prediction accuracy, whereas our results indicate a correlation between the clinical score and affected genes. Furthermore, each gene presents a different pattern recognition that may be used to develop new neural networks with the goal of separating different genetic subtypes in CdLS. Overall, we conclude that computer-assisted image analysis based on deep learning could support the clinical diagnosis of CdLS. article_number: '1042' article_processing_charge: No article_type: original author: - first_name: Ana full_name: Latorre-Pellicer, Ana last_name: Latorre-Pellicer - first_name: Ángela full_name: Ascaso, Ángela last_name: Ascaso - first_name: Laura full_name: Trujillano, Laura last_name: Trujillano - first_name: Marta full_name: Gil-Salvador, Marta last_name: Gil-Salvador - first_name: Maria full_name: Arnedo, Maria last_name: Arnedo - first_name: Cristina full_name: Lucia-Campos, Cristina last_name: Lucia-Campos - first_name: Rebeca full_name: Antoñanzas-Pérez, Rebeca last_name: Antoñanzas-Pérez - first_name: Iñigo full_name: Marcos-Alcalde, Iñigo last_name: Marcos-Alcalde - first_name: Ilaria full_name: Parenti, Ilaria id: D93538B0-5B71-11E9-AC62-02EBE5697425 last_name: Parenti - first_name: Gloria full_name: Bueno-Lozano, Gloria last_name: Bueno-Lozano - first_name: Antonio full_name: Musio, Antonio last_name: Musio - first_name: Beatriz full_name: Puisac, Beatriz last_name: Puisac - first_name: Frank J. full_name: Kaiser, Frank J. last_name: Kaiser - first_name: Feliciano J. full_name: Ramos, Feliciano J. last_name: Ramos - first_name: Paulino full_name: Gómez-Puertas, Paulino last_name: Gómez-Puertas - first_name: Juan full_name: Pié, Juan last_name: Pié citation: ama: Latorre-Pellicer A, Ascaso Á, Trujillano L, et al. Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. International Journal of Molecular Sciences. 2020;21(3). doi:10.3390/ijms21031042 apa: Latorre-Pellicer, A., Ascaso, Á., Trujillano, L., Gil-Salvador, M., Arnedo, M., Lucia-Campos, C., … Pié, J. (2020). Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21031042 chicago: Latorre-Pellicer, Ana, Ángela Ascaso, Laura Trujillano, Marta Gil-Salvador, Maria Arnedo, Cristina Lucia-Campos, Rebeca Antoñanzas-Pérez, et al. “Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21031042. ieee: A. Latorre-Pellicer et al., “Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes,” International Journal of Molecular Sciences, vol. 21, no. 3. MDPI, 2020. ista: Latorre-Pellicer A, Ascaso Á, Trujillano L, Gil-Salvador M, Arnedo M, Lucia-Campos C, Antoñanzas-Pérez R, Marcos-Alcalde I, Parenti I, Bueno-Lozano G, Musio A, Puisac B, Kaiser FJ, Ramos FJ, Gómez-Puertas P, Pié J. 2020. Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. International Journal of Molecular Sciences. 21(3), 1042. mla: Latorre-Pellicer, Ana, et al. “Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes.” International Journal of Molecular Sciences, vol. 21, no. 3, 1042, MDPI, 2020, doi:10.3390/ijms21031042. short: A. Latorre-Pellicer, Á. Ascaso, L. Trujillano, M. Gil-Salvador, M. Arnedo, C. Lucia-Campos, R. Antoñanzas-Pérez, I. Marcos-Alcalde, I. Parenti, G. Bueno-Lozano, A. Musio, B. Puisac, F.J. Kaiser, F.J. Ramos, P. Gómez-Puertas, J. Pié, International Journal of Molecular Sciences 21 (2020). date_created: 2020-02-16T23:00:49Z date_published: 2020-02-04T00:00:00Z date_updated: 2023-08-18T06:35:41Z day: '04' ddc: - '570' department: - _id: GaNo doi: 10.3390/ijms21031042 external_id: isi: - '000522551606028' file: - access_level: open_access checksum: 0e6658c4fe329d55d4d9bef01c5b15d0 content_type: application/pdf creator: dernst date_created: 2020-02-18T07:49:22Z date_updated: 2020-07-14T12:47:59Z file_id: '7496' file_name: 2020_IntMolecSciences_Latorre.pdf file_size: 4271234 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '3' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: International Journal of Molecular Sciences publication_identifier: eissn: - '14220067' issn: - '16616596' publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2020' ... --- _id: '7505' abstract: - lang: eng text: Neural networks have demonstrated unmatched performance in a range of classification tasks. Despite numerous efforts of the research community, novelty detection remains one of the significant limitations of neural networks. The ability to identify previously unseen inputs as novel is crucial for our understanding of the decisions made by neural networks. At runtime, inputs not falling into any of the categories learned during training cannot be classified correctly by the neural network. Existing approaches treat the neural network as a black box and try to detect novel inputs based on the confidence of the output predictions. However, neural networks are not trained to reduce their confidence for novel inputs, which limits the effectiveness of these approaches. We propose a framework to monitor a neural network by observing the hidden layers. We employ a common abstraction from program analysis - boxes - to identify novel behaviors in the monitored layers, i.e., inputs that cause behaviors outside the box. For each neuron, the boxes range over the values seen in training. The framework is efficient and flexible to achieve a desired trade-off between raising false warnings and detecting novel inputs. We illustrate the performance and the robustness to variability in the unknown classes on popular image-classification benchmarks. acknowledgement: We thank Christoph Lampert and Nikolaus Mayer for fruitful discussions. This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award) and the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie grant agreement No. 754411. alternative_title: - Frontiers in Artificial Intelligence and Applications article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Anna full_name: Lukina, Anna id: CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425 last_name: Lukina - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 citation: ama: 'Henzinger TA, Lukina A, Schilling C. Outside the box: Abstraction-based monitoring of neural networks. In: 24th European Conference on Artificial Intelligence. Vol 325. IOS Press; 2020:2433-2440. doi:10.3233/FAIA200375' apa: 'Henzinger, T. A., Lukina, A., & Schilling, C. (2020). Outside the box: Abstraction-based monitoring of neural networks. In 24th European Conference on Artificial Intelligence (Vol. 325, pp. 2433–2440). Santiago de Compostela, Spain: IOS Press. https://doi.org/10.3233/FAIA200375' chicago: 'Henzinger, Thomas A, Anna Lukina, and Christian Schilling. “Outside the Box: Abstraction-Based Monitoring of Neural Networks.” In 24th European Conference on Artificial Intelligence, 325:2433–40. IOS Press, 2020. https://doi.org/10.3233/FAIA200375.' ieee: 'T. A. Henzinger, A. Lukina, and C. Schilling, “Outside the box: Abstraction-based monitoring of neural networks,” in 24th European Conference on Artificial Intelligence, Santiago de Compostela, Spain, 2020, vol. 325, pp. 2433–2440.' ista: 'Henzinger TA, Lukina A, Schilling C. 2020. Outside the box: Abstraction-based monitoring of neural networks. 24th European Conference on Artificial Intelligence. ECAI: European Conference on Artificial Intelligence, Frontiers in Artificial Intelligence and Applications, vol. 325, 2433–2440.' mla: 'Henzinger, Thomas A., et al. “Outside the Box: Abstraction-Based Monitoring of Neural Networks.” 24th European Conference on Artificial Intelligence, vol. 325, IOS Press, 2020, pp. 2433–40, doi:10.3233/FAIA200375.' short: T.A. Henzinger, A. Lukina, C. Schilling, in:, 24th European Conference on Artificial Intelligence, IOS Press, 2020, pp. 2433–2440. conference: end_date: 2020-09-08 location: Santiago de Compostela, Spain name: 'ECAI: European Conference on Artificial Intelligence' start_date: 2020-08-29 date_created: 2020-02-21T16:44:03Z date_published: 2020-02-24T00:00:00Z date_updated: 2023-08-18T06:38:16Z day: '24' ddc: - '000' department: - _id: ToHe doi: 10.3233/FAIA200375 ec_funded: 1 external_id: arxiv: - '1911.09032' isi: - '000650971303002' file: - access_level: open_access checksum: 80642fa0b6cd7da95dcd87d63789ad5e content_type: application/pdf creator: dernst date_created: 2020-09-21T07:12:32Z date_updated: 2020-09-21T07:12:32Z file_id: '8540' file_name: 2020_ECAI_Henzinger.pdf file_size: 1692214 relation: main_file success: 1 file_date_updated: 2020-09-21T07:12:32Z has_accepted_license: '1' intvolume: ' 325' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '02' oa: 1 oa_version: Published Version page: 2433-2440 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: 24th European Conference on Artificial Intelligence publication_status: published publisher: IOS Press quality_controlled: '1' status: public title: 'Outside the box: Abstraction-based monitoring of neural networks' 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 325 year: '2020' ... --- _id: '7508' abstract: - lang: eng text: In this paper, we introduce a novel method for deriving higher order corrections to the mean-field description of the dynamics of interacting bosons. More precisely, we consider the dynamics of N d-dimensional bosons for large N. The bosons initially form a Bose–Einstein condensate and interact with each other via a pair potential of the form (N−1)−1Ndβv(Nβ·)forβ∈[0,14d). We derive a sequence of N-body functions which approximate the true many-body dynamics in L2(RdN)-norm to arbitrary precision in powers of N−1. The approximating functions are constructed as Duhamel expansions of finite order in terms of the first quantised analogue of a Bogoliubov time evolution. acknowledgement: "Open access funding provided by Institute of Science and Technology (IST Austria).\r\nL.B. gratefully acknowledges the support by the German Research Foundation (DFG) within the Research Training Group 1838 “Spectral Theory and Dynamics of Quantum Systems”, and wishes to thank Stefan Teufel, Sören Petrat and Marcello Porta for helpful discussions. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. N.P. gratefully acknowledges support from NSF grant DMS-1516228 and DMS-1840314. P.P.’s research was funded by DFG Grant no. PI 1114/3-1. Part of this work was done when N.P. and P.P. were visiting CCNU, Wuhan. N.P. and P.P. thank A.S. for his hospitality at CCNU." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lea full_name: Bossmann, Lea id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425 last_name: Bossmann orcid: 0000-0002-6854-1343 - first_name: Nataša full_name: Pavlović, Nataša last_name: Pavlović - first_name: Peter full_name: Pickl, Peter last_name: Pickl - first_name: Avy full_name: Soffer, Avy last_name: Soffer citation: ama: Bossmann L, Pavlović N, Pickl P, Soffer A. Higher order corrections to the mean-field description of the dynamics of interacting bosons. Journal of Statistical Physics. 2020;178:1362-1396. doi:10.1007/s10955-020-02500-8 apa: Bossmann, L., Pavlović, N., Pickl, P., & Soffer, A. (2020). Higher order corrections to the mean-field description of the dynamics of interacting bosons. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-020-02500-8 chicago: Bossmann, Lea, Nataša Pavlović, Peter Pickl, and Avy Soffer. “Higher Order Corrections to the Mean-Field Description of the Dynamics of Interacting Bosons.” Journal of Statistical Physics. Springer Nature, 2020. https://doi.org/10.1007/s10955-020-02500-8. ieee: L. Bossmann, N. Pavlović, P. Pickl, and A. Soffer, “Higher order corrections to the mean-field description of the dynamics of interacting bosons,” Journal of Statistical Physics, vol. 178. Springer Nature, pp. 1362–1396, 2020. ista: Bossmann L, Pavlović N, Pickl P, Soffer A. 2020. Higher order corrections to the mean-field description of the dynamics of interacting bosons. Journal of Statistical Physics. 178, 1362–1396. mla: Bossmann, Lea, et al. “Higher Order Corrections to the Mean-Field Description of the Dynamics of Interacting Bosons.” Journal of Statistical Physics, vol. 178, Springer Nature, 2020, pp. 1362–96, doi:10.1007/s10955-020-02500-8. short: L. Bossmann, N. Pavlović, P. Pickl, A. Soffer, Journal of Statistical Physics 178 (2020) 1362–1396. date_created: 2020-02-23T09:45:51Z date_published: 2020-02-21T00:00:00Z date_updated: 2023-08-18T06:37:46Z day: '21' ddc: - '510' department: - _id: RoSe doi: 10.1007/s10955-020-02500-8 ec_funded: 1 external_id: arxiv: - '1905.06164' isi: - '000516342200001' file: - access_level: open_access checksum: 643e230bf147e64d9cdb3f6cc573679d content_type: application/pdf creator: dernst date_created: 2020-11-20T09:26:46Z date_updated: 2020-11-20T09:26:46Z file_id: '8780' file_name: 2020_JournStatPhysics_Bossmann.pdf file_size: 576726 relation: main_file success: 1 file_date_updated: 2020-11-20T09:26:46Z has_accepted_license: '1' intvolume: ' 178' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 1362-1396 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of Statistical Physics publication_identifier: eissn: - 1572-9613 issn: - 0022-4715 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Higher order corrections to the mean-field description of the dynamics of interacting bosons 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 178 year: '2020' ... --- _id: '7511' abstract: - lang: eng text: Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines. article_number: '876' article_processing_charge: No article_type: original author: - first_name: Beata full_name: Turoňová, Beata last_name: Turoňová - first_name: Wim J.H. full_name: Hagen, Wim J.H. last_name: Hagen - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr orcid: 0000-0003-1756-6564 - first_name: Shyamal full_name: Mosalaganti, Shyamal last_name: Mosalaganti - first_name: J. Wouter full_name: Beugelink, J. Wouter last_name: Beugelink - first_name: Christian E. full_name: Zimmerli, Christian E. last_name: Zimmerli - first_name: Hans Georg full_name: Kräusslich, Hans Georg last_name: Kräusslich - first_name: Martin full_name: Beck, Martin last_name: Beck citation: ama: Turoňová B, Hagen WJH, Obr M, et al. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. 2020;11. doi:10.1038/s41467-020-14535-2 apa: Turoňová, B., Hagen, W. J. H., Obr, M., Mosalaganti, S., Beugelink, J. W., Zimmerli, C. E., … Beck, M. (2020). Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-14535-2 chicago: Turoňová, Beata, Wim J.H. Hagen, Martin Obr, Shyamal Mosalaganti, J. Wouter Beugelink, Christian E. Zimmerli, Hans Georg Kräusslich, and Martin Beck. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-14535-2. ieee: B. Turoňová et al., “Benchmarking tomographic acquisition schemes for high-resolution structural biology,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Turoňová B, Hagen WJH, Obr M, Mosalaganti S, Beugelink JW, Zimmerli CE, Kräusslich HG, Beck M. 2020. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. 11, 876. mla: Turoňová, Beata, et al. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” Nature Communications, vol. 11, 876, Springer Nature, 2020, doi:10.1038/s41467-020-14535-2. short: B. Turoňová, W.J.H. Hagen, M. Obr, S. Mosalaganti, J.W. Beugelink, C.E. Zimmerli, H.G. Kräusslich, M. Beck, Nature Communications 11 (2020). date_created: 2020-02-23T23:00:35Z date_published: 2020-02-13T00:00:00Z date_updated: 2023-08-18T06:36:41Z day: '13' ddc: - '570' department: - _id: FlSc doi: 10.1038/s41467-020-14535-2 external_id: isi: - '000514928000017' file: - access_level: open_access checksum: 2c8d10475e1b0d397500760e28bdf561 content_type: application/pdf creator: dernst date_created: 2020-02-24T14:00:54Z date_updated: 2020-07-14T12:47:59Z file_id: '7517' file_name: 2020_NatureComm_Turonova.pdf file_size: 2027529 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Benchmarking tomographic acquisition schemes for high-resolution structural biology 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '7497' abstract: - lang: eng text: Endophytic fungi can be beneficial to plant growth. However, the molecular mechanisms underlying colonization of Acremonium spp. remain unclear. In this study, a novel endophytic Acremonium strain was isolated from the buds of Panax notoginseng and named Acremonium sp. D212. The Acremonium sp. D212 could colonize the roots of P. notoginseng, enhance the resistance of P. notoginseng to root rot disease, and promote root growth and saponin biosynthesis in P. notoginseng. Acremonium sp. D212 could secrete indole‐3‐acetic acid (IAA) and jasmonic acid (JA), and inoculation with the fungus increased the endogenous levels of IAA and JA in P. notoginseng. Colonization of the Acremonium sp. D212 in the roots of the rice line Nipponbare was dependent on the concentration of methyl jasmonate (MeJA) (2 to 15 μM) and 1‐naphthalenacetic acid (NAA) (10 to 20 μM). Moreover, the roots of the JA signalling‐defective coi1‐18 mutant were colonized by Acremonium sp. D212 to a lesser degree than those of the wild‐type Nipponbare and miR393b‐overexpressing lines, and the colonization was rescued by MeJA but not by NAA. It suggests that the cross‐talk between JA signalling and the auxin biosynthetic pathway plays a crucial role in the colonization of Acremonium sp. D212 in host plants. acknowledgement: We thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for providing generous support with the IAA and JA measurements. We thank Professor Guohua Xu (Nanjing Agricultural University) for generously providing the Nipponbare rice expressing DR5::GUS. We thank Professor Muyuan Zhu (Zhejiang University) for generously providing a rice line expressing 35S::miR393b. We thank Professor Yinong Yang (Pennsylvania State University) for generously providing the rice line coi1-18. This work was supported by grants from the National Natural Science Foundation of China (31660501, 31460453, 31860064 and 31470382), the Major Special Program for Scientific Research, Education Department of Yunnan Province (ZD2015005), the Project sponsored by SRF for ROCS, SEM ([2013] 1792), the Major Science and Technique Programs in Yunnan Province (2016ZF001), the Key Projects of the Applied Basic Research Plan of Yunnan Province (2017FA018), the National Key R&D Program of China (2018YFD0201100) and the China Agriculture Research System (CARS-21). article_processing_charge: No article_type: original author: - first_name: L full_name: Han, L last_name: Han - first_name: X full_name: Zhou, X last_name: Zhou - first_name: Y full_name: Zhao, Y last_name: Zhao - first_name: S full_name: Zhu, S last_name: Zhu - first_name: L full_name: Wu, L last_name: Wu - first_name: Y full_name: He, Y last_name: He - first_name: X full_name: Ping, X last_name: Ping - first_name: X full_name: Lu, X last_name: Lu - first_name: W full_name: Huang, W last_name: Huang - first_name: J full_name: Qian, J last_name: Qian - first_name: L full_name: Zhang, L last_name: Zhang - first_name: X full_name: Jiang, X last_name: Jiang - first_name: D full_name: Zhu, D last_name: Zhu - first_name: C full_name: Luo, C last_name: Luo - first_name: S full_name: Li, S last_name: Li - first_name: Q full_name: Dong, Q last_name: Dong - first_name: Q full_name: Fu, Q last_name: Fu - first_name: K full_name: Deng, K last_name: Deng - first_name: X full_name: Wang, X last_name: Wang - first_name: L full_name: Wang, L last_name: Wang - first_name: S full_name: Peng, S last_name: Peng - first_name: J full_name: Wu, J last_name: Wu - first_name: W full_name: Li, W last_name: Li - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Y full_name: Zhu, Y last_name: Zhu - first_name: X full_name: He, X last_name: He - first_name: Y full_name: Du, Y last_name: Du citation: ama: Han L, Zhou X, Zhao Y, et al. Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. Journal of Integrative Plant Biology. 2020;62(9):1433-1451. doi:10.1111/jipb.12905 apa: Han, L., Zhou, X., Zhao, Y., Zhu, S., Wu, L., He, Y., … Du, Y. (2020). Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.12905 chicago: Han, L, X Zhou, Y Zhao, S Zhu, L Wu, Y He, X Ping, et al. “Colonization of Endophyte Acremonium Sp. D212 in Panax Notoginseng and Rice Mediated by Auxin and Jasmonic Acid.” Journal of Integrative Plant Biology. Wiley, 2020. https://doi.org/10.1111/jipb.12905. ieee: L. Han et al., “Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid,” Journal of Integrative Plant Biology, vol. 62, no. 9. Wiley, pp. 1433–1451, 2020. ista: Han L, Zhou X, Zhao Y, Zhu S, Wu L, He Y, Ping X, Lu X, Huang W, Qian J, Zhang L, Jiang X, Zhu D, Luo C, Li S, Dong Q, Fu Q, Deng K, Wang X, Wang L, Peng S, Wu J, Li W, Friml J, Zhu Y, He X, Du Y. 2020. Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. Journal of Integrative Plant Biology. 62(9), 1433–1451. mla: Han, L., et al. “Colonization of Endophyte Acremonium Sp. D212 in Panax Notoginseng and Rice Mediated by Auxin and Jasmonic Acid.” Journal of Integrative Plant Biology, vol. 62, no. 9, Wiley, 2020, pp. 1433–51, doi:10.1111/jipb.12905. short: L. Han, X. Zhou, Y. Zhao, S. Zhu, L. Wu, Y. He, X. Ping, X. Lu, W. Huang, J. Qian, L. Zhang, X. Jiang, D. Zhu, C. Luo, S. Li, Q. Dong, Q. Fu, K. Deng, X. Wang, L. Wang, S. Peng, J. Wu, W. Li, J. Friml, Y. Zhu, X. He, Y. Du, Journal of Integrative Plant Biology 62 (2020) 1433–1451. date_created: 2020-02-18T10:02:25Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-08-18T06:44:16Z day: '01' department: - _id: JiFr doi: 10.1111/jipb.12905 external_id: isi: - '000515803000001' pmid: - '31912615' intvolume: ' 62' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/jipb.12905 month: '09' oa: 1 oa_version: Published Version page: 1433-1451 pmid: 1 publication: Journal of Integrative Plant Biology publication_identifier: eissn: - 1744-7909 issn: - 1672-9072 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 62 year: '2020' ... --- _id: '7534' abstract: - lang: eng text: 'In the past two decades, our understanding of the transition to turbulence in shear flows with linearly stable laminar solutions has greatly improved. Regarding the susceptibility of the laminar flow, two concepts have been particularly useful: the edge states and the minimal seeds. In this nonlinear picture of the transition, the basin boundary of turbulence is set by the edge state''s stable manifold and this manifold comes closest in energy to the laminar equilibrium at the minimal seed. We begin this paper by presenting numerical experiments in which three-dimensional perturbations are too energetic to trigger turbulence in pipe flow but they do lead to turbulence when their amplitude is reduced. We show that this seemingly counterintuitive observation is in fact consistent with the fully nonlinear description of the transition mediated by the edge state. In order to understand the physical mechanisms behind this process, we measure the turbulent kinetic energy production and dissipation rates as a function of the radial coordinate. Our main observation is that the transition to turbulence relies on the energy amplification away from the wall, as opposed to the turbulence itself, whose energy is predominantly produced near the wall. This observation is further supported by the similar analyses on the minimal seeds and the edge states. Furthermore, we show that the time evolution of production-over-dissipation curves provides a clear distinction between the different initial amplification stages of the transition to turbulence from the minimal seed.' article_number: '023903' article_processing_charge: No article_type: original author: - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Elena full_name: Marensi, Elena last_name: Marensi - first_name: Ashley P. full_name: Willis, Ashley P. last_name: Willis - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Budanur NB, Marensi E, Willis AP, Hof B. Upper edge of chaos and the energetics of transition in pipe flow. Physical Review Fluids. 2020;5(2). doi:10.1103/physrevfluids.5.023903 apa: Budanur, N. B., Marensi, E., Willis, A. P., & Hof, B. (2020). Upper edge of chaos and the energetics of transition in pipe flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/physrevfluids.5.023903 chicago: Budanur, Nazmi B, Elena Marensi, Ashley P. Willis, and Björn Hof. “Upper Edge of Chaos and the Energetics of Transition in Pipe Flow.” Physical Review Fluids. American Physical Society, 2020. https://doi.org/10.1103/physrevfluids.5.023903. ieee: N. B. Budanur, E. Marensi, A. P. Willis, and B. Hof, “Upper edge of chaos and the energetics of transition in pipe flow,” Physical Review Fluids, vol. 5, no. 2. American Physical Society, 2020. ista: Budanur NB, Marensi E, Willis AP, Hof B. 2020. Upper edge of chaos and the energetics of transition in pipe flow. Physical Review Fluids. 5(2), 023903. mla: Budanur, Nazmi B., et al. “Upper Edge of Chaos and the Energetics of Transition in Pipe Flow.” Physical Review Fluids, vol. 5, no. 2, 023903, American Physical Society, 2020, doi:10.1103/physrevfluids.5.023903. short: N.B. Budanur, E. Marensi, A.P. Willis, B. Hof, Physical Review Fluids 5 (2020). date_created: 2020-02-27T10:26:57Z date_published: 2020-02-21T00:00:00Z date_updated: 2023-08-18T06:44:46Z day: '21' department: - _id: BjHo doi: 10.1103/physrevfluids.5.023903 external_id: arxiv: - '1912.09270' isi: - '000515065100001' intvolume: ' 5' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.09270 month: '02' oa: 1 oa_version: Preprint publication: Physical Review Fluids publication_identifier: issn: - 2469-990X publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Upper edge of chaos and the energetics of transition in pipe flow type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 5 year: '2020' ... --- _id: '7512' abstract: - lang: eng text: We consider general self-adjoint polynomials in several independent random matrices whose entries are centered and have the same variance. We show that under certain conditions the local law holds up to the optimal scale, i.e., the eigenvalue density on scales just above the eigenvalue spacing follows the global density of states which is determined by free probability theory. We prove that these conditions hold for general homogeneous polynomials of degree two and for symmetrized products of independent matrices with i.i.d. entries, thus establishing the optimal bulk local law for these classes of ensembles. In particular, we generalize a similar result of Anderson for anticommutator. For more general polynomials our conditions are effectively checkable numerically. acknowledgement: "The authors are grateful to Oskari Ajanki for his invaluable help at the initial stage of this project, to Serban Belinschi for useful discussions, to Alexander Tikhomirov for calling our attention to the model example in Section 6.2 and to the anonymous referee for suggesting to simplify certain proofs. Erdös: Partially funded by ERC Advanced Grant RANMAT No. 338804\r\n" article_number: '108507' article_processing_charge: No article_type: original author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 - first_name: Yuriy full_name: Nemish, Yuriy id: 4D902E6A-F248-11E8-B48F-1D18A9856A87 last_name: Nemish orcid: 0000-0002-7327-856X citation: ama: Erdös L, Krüger TH, Nemish Y. Local laws for polynomials of Wigner matrices. Journal of Functional Analysis. 2020;278(12). doi:10.1016/j.jfa.2020.108507 apa: Erdös, L., Krüger, T. H., & Nemish, Y. (2020). Local laws for polynomials of Wigner matrices. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2020.108507 chicago: Erdös, László, Torben H Krüger, and Yuriy Nemish. “Local Laws for Polynomials of Wigner Matrices.” Journal of Functional Analysis. Elsevier, 2020. https://doi.org/10.1016/j.jfa.2020.108507. ieee: L. Erdös, T. H. Krüger, and Y. Nemish, “Local laws for polynomials of Wigner matrices,” Journal of Functional Analysis, vol. 278, no. 12. Elsevier, 2020. ista: Erdös L, Krüger TH, Nemish Y. 2020. Local laws for polynomials of Wigner matrices. Journal of Functional Analysis. 278(12), 108507. mla: Erdös, László, et al. “Local Laws for Polynomials of Wigner Matrices.” Journal of Functional Analysis, vol. 278, no. 12, 108507, Elsevier, 2020, doi:10.1016/j.jfa.2020.108507. short: L. Erdös, T.H. Krüger, Y. Nemish, Journal of Functional Analysis 278 (2020). date_created: 2020-02-23T23:00:36Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-18T06:36:10Z day: '01' department: - _id: LaEr doi: 10.1016/j.jfa.2020.108507 ec_funded: 1 external_id: arxiv: - '1804.11340' isi: - '000522798900001' intvolume: ' 278' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.11340 month: '07' oa: 1 oa_version: Preprint project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Journal of Functional Analysis publication_identifier: eissn: - '10960783' issn: - '00221236' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Local laws for polynomials of Wigner matrices type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 278 year: '2020' ... --- _id: '7509' abstract: - lang: eng text: "In this paper we study the joint convexity/concavity of the trace functions Ψp,q,s(A,B)=Tr(Bq2K∗ApKBq2)s, p,q,s∈R,\r\nwhere A and B are positive definite matrices and K is any fixed invertible matrix. We will give full range of (p,q,s)∈R3 for Ψp,q,s to be jointly convex/concave for all K. As a consequence, we confirm a conjecture of Carlen, Frank and Lieb. In particular, we confirm a weaker conjecture of Audenaert and Datta and obtain the full range of (α,z) for α-z Rényi relative entropies to be monotone under completely positive trace preserving maps. We also give simpler proofs of many known results, including the concavity of Ψp,0,1/p for 0Advances in Mathematics. 2020;365. doi:10.1016/j.aim.2020.107053 apa: Zhang, H. (2020). From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2020.107053 chicago: Zhang, Haonan. “From Wigner-Yanase-Dyson Conjecture to Carlen-Frank-Lieb Conjecture.” Advances in Mathematics. Elsevier, 2020. https://doi.org/10.1016/j.aim.2020.107053. ieee: H. Zhang, “From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture,” Advances in Mathematics, vol. 365. Elsevier, 2020. ista: Zhang H. 2020. From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. Advances in Mathematics. 365, 107053. mla: Zhang, Haonan. “From Wigner-Yanase-Dyson Conjecture to Carlen-Frank-Lieb Conjecture.” Advances in Mathematics, vol. 365, 107053, Elsevier, 2020, doi:10.1016/j.aim.2020.107053. short: H. Zhang, Advances in Mathematics 365 (2020). date_created: 2020-02-23T21:43:50Z date_published: 2020-05-13T00:00:00Z date_updated: 2023-08-18T06:37:09Z day: '13' ddc: - '515' department: - _id: JaMa doi: 10.1016/j.aim.2020.107053 ec_funded: 1 external_id: arxiv: - '1811.01205' isi: - '000522798000001' intvolume: ' 365' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1811.01205 month: '05' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Advances in Mathematics publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 365 year: '2020' ... --- _id: '7546' abstract: - lang: eng text: The extent to which behavior is shaped by experience varies between individuals. Genetic differences contribute to this variation, but the neural mechanisms are not understood. Here, we dissect natural variation in the behavioral flexibility of two Caenorhabditis elegans wild strains. In one strain, a memory of exposure to 21% O2 suppresses CO2-evoked locomotory arousal; in the other, CO2 evokes arousal regardless of previous O2 experience. We map that variation to a polymorphic dendritic scaffold protein, ARCP-1, expressed in sensory neurons. ARCP-1 binds the Ca2+-dependent phosphodiesterase PDE-1 and co-localizes PDE-1 with molecular sensors for CO2 at dendritic ends. Reducing ARCP-1 or PDE-1 activity promotes CO2 escape by altering neuropeptide expression in the BAG CO2 sensors. Variation in ARCP-1 alters behavioral plasticity in multiple paradigms. Our findings are reminiscent of genetic accommodation, an evolutionary process by which phenotypic flexibility in response to environmental variation is reset by genetic change. article_processing_charge: No article_type: original author: - first_name: Isabel full_name: Beets, Isabel last_name: Beets - first_name: Gaotian full_name: Zhang, Gaotian last_name: Zhang - first_name: Lorenz A. full_name: Fenk, Lorenz A. last_name: Fenk - first_name: Changchun full_name: Chen, Changchun last_name: Chen - first_name: Geoffrey M. full_name: Nelson, Geoffrey M. last_name: Nelson - first_name: Marie-Anne full_name: Félix, Marie-Anne last_name: Félix - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Beets I, Zhang G, Fenk LA, et al. Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression. Neuron. 2020;105(1):106-121.e10. doi:10.1016/j.neuron.2019.10.001 apa: Beets, I., Zhang, G., Fenk, L. A., Chen, C., Nelson, G. M., Félix, M.-A., & de Bono, M. (2020). Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2019.10.001 chicago: Beets, Isabel, Gaotian Zhang, Lorenz A. Fenk, Changchun Chen, Geoffrey M. Nelson, Marie-Anne Félix, and Mario de Bono. “Natural Variation in a Dendritic Scaffold Protein Remodels Experience-Dependent Plasticity by Altering Neuropeptide Expression.” Neuron. Cell Press, 2020. https://doi.org/10.1016/j.neuron.2019.10.001. ieee: I. Beets et al., “Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression,” Neuron, vol. 105, no. 1. Cell Press, p. 106–121.e10, 2020. ista: Beets I, Zhang G, Fenk LA, Chen C, Nelson GM, Félix M-A, de Bono M. 2020. Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression. Neuron. 105(1), 106–121.e10. mla: Beets, Isabel, et al. “Natural Variation in a Dendritic Scaffold Protein Remodels Experience-Dependent Plasticity by Altering Neuropeptide Expression.” Neuron, vol. 105, no. 1, Cell Press, 2020, p. 106–121.e10, doi:10.1016/j.neuron.2019.10.001. short: I. Beets, G. Zhang, L.A. Fenk, C. Chen, G.M. Nelson, M.-A. Félix, M. de Bono, Neuron 105 (2020) 106–121.e10. date_created: 2020-02-28T10:43:39Z date_published: 2020-01-08T00:00:00Z date_updated: 2023-08-18T06:46:23Z day: '08' ddc: - '570' department: - _id: MaDe doi: 10.1016/j.neuron.2019.10.001 external_id: isi: - '000507341300012' pmid: - '31757604' file: - access_level: open_access checksum: 799bfd297a008753a688b30d3958fa48 content_type: application/pdf creator: dernst date_created: 2020-03-02T15:43:57Z date_updated: 2020-07-14T12:48:00Z file_id: '7558' file_name: 2020_Neuron_Beets.pdf file_size: 3294066 relation: main_file file_date_updated: 2020-07-14T12:48:00Z has_accepted_license: '1' intvolume: ' 105' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 106-121.e10 pmid: 1 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Cell Press quality_controlled: '1' status: public title: Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 105 year: '2020' ... --- _id: '7563' abstract: - lang: eng text: "We introduce “state space persistence analysis” for deducing the symbolic dynamics of time series data obtained from high-dimensional chaotic attractors. To this end, we adapt a topological data analysis technique known as persistent homology for the characterization of state space projections of chaotic trajectories and periodic orbits. By comparing the shapes along a chaotic trajectory to those of the periodic orbits, state space persistence analysis quantifies the shape similarity of chaotic trajectory segments and periodic orbits. We demonstrate the method by applying it to the three-dimensional Rössler system and a 30-dimensional discretization of the Kuramoto–Sivashinsky partial differential equation in (1+1) dimensions.\r\nOne way of studying chaotic attractors systematically is through their symbolic dynamics, in which one partitions the state space into qualitatively different regions and assigns a symbol to each such region.1–3 This yields a “coarse-grained” state space of the system, which can then be reduced to a Markov chain encoding all possible transitions between the states of the system. While it is possible to obtain the symbolic dynamics of low-dimensional chaotic systems with standard tools such as Poincaré maps, when applied to high-dimensional systems such as turbulent flows, these tools alone are not sufficient to determine symbolic dynamics.4,5 In this paper, we develop “state space persistence analysis” and demonstrate that it can be utilized to infer the symbolic dynamics in very high-dimensional settings." article_number: '033109' article_processing_charge: No article_type: original author: - first_name: Gökhan full_name: Yalniz, Gökhan id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425 last_name: Yalniz orcid: 0000-0002-8490-9312 - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 citation: ama: Yalniz G, Budanur NB. Inferring symbolic dynamics of chaotic flows from persistence. Chaos. 2020;30(3). doi:10.1063/1.5122969 apa: Yalniz, G., & Budanur, N. B. (2020). Inferring symbolic dynamics of chaotic flows from persistence. Chaos. AIP Publishing. https://doi.org/10.1063/1.5122969 chicago: Yalniz, Gökhan, and Nazmi B Budanur. “Inferring Symbolic Dynamics of Chaotic Flows from Persistence.” Chaos. AIP Publishing, 2020. https://doi.org/10.1063/1.5122969. ieee: G. Yalniz and N. B. Budanur, “Inferring symbolic dynamics of chaotic flows from persistence,” Chaos, vol. 30, no. 3. AIP Publishing, 2020. ista: Yalniz G, Budanur NB. 2020. Inferring symbolic dynamics of chaotic flows from persistence. Chaos. 30(3), 033109. mla: Yalniz, Gökhan, and Nazmi B. Budanur. “Inferring Symbolic Dynamics of Chaotic Flows from Persistence.” Chaos, vol. 30, no. 3, 033109, AIP Publishing, 2020, doi:10.1063/1.5122969. short: G. Yalniz, N.B. Budanur, Chaos 30 (2020). date_created: 2020-03-04T08:06:25Z date_published: 2020-03-03T00:00:00Z date_updated: 2023-08-18T06:47:16Z day: '03' department: - _id: BjHo doi: 10.1063/1.5122969 external_id: arxiv: - '1910.04584' isi: - '000519254800002' intvolume: ' 30' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1063/1.5122969 month: '03' oa: 1 oa_version: Published Version publication: Chaos publication_identifier: eissn: - 1089-7682 issn: - 1054-1500 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Inferring symbolic dynamics of chaotic flows from persistence type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 30 year: '2020' ... --- _id: '7554' abstract: - lang: eng text: Slicing a Voronoi tessellation in ${R}^n$ with a $k$-plane gives a $k$-dimensional weighted Voronoi tessellation, also known as a power diagram or Laguerre tessellation. Mapping every simplex of the dual weighted Delaunay mosaic to the radius of the smallest empty circumscribed sphere whose center lies in the $k$-plane gives a generalized discrete Morse function. Assuming the Voronoi tessellation is generated by a Poisson point process in ${R}^n$, we study the expected number of simplices in the $k$-dimensional weighted Delaunay mosaic as well as the expected number of intervals of the Morse function, both as functions of a radius threshold. As a by-product, we obtain a new proof for the expected number of connected components (clumps) in a line section of a circular Boolean model in ${R}^n$. article_processing_charge: No article_type: original author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Anton full_name: Nikitenko, Anton id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87 last_name: Nikitenko orcid: 0000-0002-0659-3201 citation: ama: Edelsbrunner H, Nikitenko A. Weighted Poisson–Delaunay mosaics. Theory of Probability and its Applications. 2020;64(4):595-614. doi:10.1137/S0040585X97T989726 apa: Edelsbrunner, H., & Nikitenko, A. (2020). Weighted Poisson–Delaunay mosaics. Theory of Probability and Its Applications. SIAM. https://doi.org/10.1137/S0040585X97T989726 chicago: Edelsbrunner, Herbert, and Anton Nikitenko. “Weighted Poisson–Delaunay Mosaics.” Theory of Probability and Its Applications. SIAM, 2020. https://doi.org/10.1137/S0040585X97T989726. ieee: H. Edelsbrunner and A. Nikitenko, “Weighted Poisson–Delaunay mosaics,” Theory of Probability and its Applications, vol. 64, no. 4. SIAM, pp. 595–614, 2020. ista: Edelsbrunner H, Nikitenko A. 2020. Weighted Poisson–Delaunay mosaics. Theory of Probability and its Applications. 64(4), 595–614. mla: Edelsbrunner, Herbert, and Anton Nikitenko. “Weighted Poisson–Delaunay Mosaics.” Theory of Probability and Its Applications, vol. 64, no. 4, SIAM, 2020, pp. 595–614, doi:10.1137/S0040585X97T989726. short: H. Edelsbrunner, A. Nikitenko, Theory of Probability and Its Applications 64 (2020) 595–614. date_created: 2020-03-01T23:00:39Z date_published: 2020-02-13T00:00:00Z date_updated: 2023-08-18T06:45:48Z day: '13' department: - _id: HeEd doi: 10.1137/S0040585X97T989726 ec_funded: 1 external_id: arxiv: - '1705.08735' isi: - '000551393100007' intvolume: ' 64' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.08735 month: '02' oa: 1 oa_version: Preprint page: 595-614 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: Theory of Probability and its Applications publication_identifier: eissn: - '10957219' issn: - 0040585X publication_status: published publisher: SIAM quality_controlled: '1' scopus_import: '1' status: public title: Weighted Poisson–Delaunay mosaics type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 64 year: '2020' ... --- _id: '7540' abstract: - lang: eng text: ' In vitro propagation of the ornamentally interesting species Wikstroemia gemmata is limited by the recalcitrance to form adventitious roots. In this article, two strategies to improve the rooting capacity of in vitro microcuttings are presented. Firstly, the effect of exogenous auxin was evaluated in both light and dark cultivated stem segments and also the sucrose-content of the medium was varied in order to determine better rooting conditions. Secondly, different spectral lights were evaluated and the effect on shoot growth and root induction demonstrated that the exact spectral composition of light is important for successful in vitro growth and development of Wikstroemia gemmata. We show that exogenous auxin cannot compensate for the poor rooting under unfavorable light conditions. Adapting the culture conditions is therefore paramount for successful industrial propagation of Wikstroemia gemmata. ' article_processing_charge: No article_type: original author: - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: H. full_name: Buyle, H. last_name: Buyle - first_name: S. full_name: Werbrouck, S. last_name: Werbrouck - first_name: M.C. full_name: Van Labeke, M.C. last_name: Van Labeke - first_name: D. full_name: Geelen, D. last_name: Geelen citation: ama: Verstraeten I, Buyle H, Werbrouck S, Van Labeke MC, Geelen D. In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality. Israel Journal of Plant Sciences. 2020;67(1-2):16-26. doi:10.1163/22238980-20191110 apa: Verstraeten, I., Buyle, H., Werbrouck, S., Van Labeke, M. C., & Geelen, D. (2020). In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality. Israel Journal of Plant Sciences. Brill. https://doi.org/10.1163/22238980-20191110 chicago: Verstraeten, Inge, H. Buyle, S. Werbrouck, M.C. Van Labeke, and D. Geelen. “In Vitro Shoot Growth and Adventitious Rooting of Wikstroemia Gemmata Depends on Light Quality.” Israel Journal of Plant Sciences. Brill, 2020. https://doi.org/10.1163/22238980-20191110. ieee: I. Verstraeten, H. Buyle, S. Werbrouck, M. C. Van Labeke, and D. Geelen, “In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality,” Israel Journal of Plant Sciences, vol. 67, no. 1–2. Brill, pp. 16–26, 2020. ista: Verstraeten I, Buyle H, Werbrouck S, Van Labeke MC, Geelen D. 2020. In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality. Israel Journal of Plant Sciences. 67(1–2), 16–26. mla: Verstraeten, Inge, et al. “In Vitro Shoot Growth and Adventitious Rooting of Wikstroemia Gemmata Depends on Light Quality.” Israel Journal of Plant Sciences, vol. 67, no. 1–2, Brill, 2020, pp. 16–26, doi:10.1163/22238980-20191110. short: I. Verstraeten, H. Buyle, S. Werbrouck, M.C. Van Labeke, D. Geelen, Israel Journal of Plant Sciences 67 (2020) 16–26. date_created: 2020-02-28T09:18:01Z date_published: 2020-02-01T00:00:00Z date_updated: 2023-08-18T06:45:15Z day: '01' department: - _id: JiFr doi: 10.1163/22238980-20191110 external_id: isi: - '000525343300004' intvolume: ' 67' isi: 1 issue: 1-2 language: - iso: eng month: '02' oa_version: None page: 16-26 publication: Israel Journal of Plant Sciences publication_identifier: eissn: - 2223-8980 issn: - 0792-9978 publication_status: published publisher: Brill quality_controlled: '1' scopus_import: '1' status: public title: In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 67 year: '2020' ... --- _id: '9779' article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Tamar full_name: Friedlander, Tamar last_name: Friedlander citation: ama: Grah R, Friedlander T. Distribution of crosstalk values. 2020. doi:10.1371/journal.pcbi.1007642.s003 apa: Grah, R., & Friedlander, T. (2020). Distribution of crosstalk values. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s003 chicago: Grah, Rok, and Tamar Friedlander. “Distribution of Crosstalk Values.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s003. ieee: R. Grah and T. Friedlander, “Distribution of crosstalk values.” Public Library of Science, 2020. ista: Grah R, Friedlander T. 2020. Distribution of crosstalk values, Public Library of Science, 10.1371/journal.pcbi.1007642.s003. mla: Grah, Rok, and Tamar Friedlander. Distribution of Crosstalk Values. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s003. short: R. Grah, T. Friedlander, (2020). date_created: 2021-08-06T07:24:37Z date_published: 2020-02-25T00:00:00Z date_updated: 2023-08-18T06:47:47Z day: '25' department: - _id: GaTk doi: 10.1371/journal.pcbi.1007642.s003 month: '02' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '7569' relation: research_data status: public status: public title: Distribution of crosstalk values type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9776' article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Tamar full_name: Friedlander, Tamar last_name: Friedlander citation: ama: Grah R, Friedlander T. Supporting information. 2020. doi:10.1371/journal.pcbi.1007642.s001 apa: Grah, R., & Friedlander, T. (2020). Supporting information. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s001 chicago: Grah, Rok, and Tamar Friedlander. “Supporting Information.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s001. ieee: R. Grah and T. Friedlander, “Supporting information.” Public Library of Science, 2020. ista: Grah R, Friedlander T. 2020. Supporting information, Public Library of Science, 10.1371/journal.pcbi.1007642.s001. mla: Grah, Rok, and Tamar Friedlander. Supporting Information. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s001. short: R. Grah, T. Friedlander, (2020). date_created: 2021-08-06T07:15:04Z date_published: 2020-02-25T00:00:00Z date_updated: 2023-08-18T06:47:47Z day: '25' department: - _id: GaTk doi: 10.1371/journal.pcbi.1007642.s001 month: '02' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '7569' relation: used_in_publication status: public status: public title: Supporting information type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '7570' abstract: - lang: eng text: The relaxation of few-body quantum systems can strongly depend on the initial state when the system’s semiclassical phase space is mixed; i.e., regions of chaotic motion coexist with regular islands. In recent years, there has been much effort to understand the process of thermalization in strongly interacting quantum systems that often lack an obvious semiclassical limit. The time-dependent variational principle (TDVP) allows one to systematically derive an effective classical (nonlinear) dynamical system by projecting unitary many-body dynamics onto a manifold of weakly entangled variational states. We demonstrate that such dynamical systems generally possess mixed phase space. When TDVP errors are small, the mixed phase space leaves a footprint on the exact dynamics of the quantum model. For example, when the system is initialized in a state belonging to a stable periodic orbit or the surrounding regular region, it exhibits persistent many-body quantum revivals. As a proof of principle, we identify new types of “quantum many-body scars,” i.e., initial states that lead to long-time oscillations in a model of interacting Rydberg atoms in one and two dimensions. Intriguingly, the initial states that give rise to most robust revivals are typically entangled states. On the other hand, even when TDVP errors are large, as in the thermalizing tilted-field Ising model, initializing the system in a regular region of phase space leads to a surprising slowdown of thermalization. Our work establishes TDVP as a method for identifying interacting quantum systems with anomalous dynamics in arbitrary dimensions. Moreover, the mixed phase space classical variational equations allow one to find slowly thermalizing initial conditions in interacting models. Our results shed light on a link between classical and quantum chaos, pointing toward possible extensions of the classical Kolmogorov-Arnold-Moser theorem to quantum systems. article_number: '011055' article_processing_charge: No article_type: original author: - first_name: Alexios full_name: Michailidis, Alexios id: 36EBAD38-F248-11E8-B48F-1D18A9856A87 last_name: Michailidis orcid: 0000-0002-8443-1064 - first_name: C. J. full_name: Turner, C. J. last_name: Turner - first_name: Z. full_name: Papić, Z. last_name: Papić - first_name: D. A. full_name: Abanin, D. A. last_name: Abanin - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Michailidis A, Turner CJ, Papić Z, Abanin DA, Serbyn M. Slow quantum thermalization and many-body revivals from mixed phase space. Physical Review X. 2020;10(1). doi:10.1103/physrevx.10.011055 apa: Michailidis, A., Turner, C. J., Papić, Z., Abanin, D. A., & Serbyn, M. (2020). Slow quantum thermalization and many-body revivals from mixed phase space. Physical Review X. American Physical Society. https://doi.org/10.1103/physrevx.10.011055 chicago: Michailidis, Alexios, C. J. Turner, Z. Papić, D. A. Abanin, and Maksym Serbyn. “Slow Quantum Thermalization and Many-Body Revivals from Mixed Phase Space.” Physical Review X. American Physical Society, 2020. https://doi.org/10.1103/physrevx.10.011055. ieee: A. Michailidis, C. J. Turner, Z. Papić, D. A. Abanin, and M. Serbyn, “Slow quantum thermalization and many-body revivals from mixed phase space,” Physical Review X, vol. 10, no. 1. American Physical Society, 2020. ista: Michailidis A, Turner CJ, Papić Z, Abanin DA, Serbyn M. 2020. Slow quantum thermalization and many-body revivals from mixed phase space. Physical Review X. 10(1), 011055. mla: Michailidis, Alexios, et al. “Slow Quantum Thermalization and Many-Body Revivals from Mixed Phase Space.” Physical Review X, vol. 10, no. 1, 011055, American Physical Society, 2020, doi:10.1103/physrevx.10.011055. short: A. Michailidis, C.J. Turner, Z. Papić, D.A. Abanin, M. Serbyn, Physical Review X 10 (2020). date_created: 2020-03-08T18:02:01Z date_published: 2020-03-04T00:00:00Z date_updated: 2023-08-18T07:01:07Z day: '04' ddc: - '530' department: - _id: MaSe doi: 10.1103/physrevx.10.011055 external_id: arxiv: - '1905.08564' isi: - '000517969300001' file: - access_level: open_access checksum: 4b3f2c13873d35230173c73d0e11c408 content_type: application/pdf creator: dernst date_created: 2020-03-12T12:13:07Z date_updated: 2020-07-14T12:48:00Z file_id: '7581' file_name: 2020_PhysicalReviewX_Michailidis.pdf file_size: 17828638 relation: main_file file_date_updated: 2020-07-14T12:48:00Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Physical Review X publication_identifier: issn: - 2160-3308 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/classical-physics-helps-predict-fate-of-interacting-quantum-systems/ scopus_import: '1' status: public title: Slow quantum thermalization and many-body revivals from mixed phase space 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2020' ... --- _id: '7582' abstract: - lang: eng text: Small RNAs (smRNA, 19–25 nucleotides long), which are transcribed by RNA polymerase II, regulate the expression of genes involved in a multitude of processes in eukaryotes. miRNA biogenesis and the proteins involved in the biogenesis pathway differ across plant and animal lineages. The major proteins constituting the biogenesis pathway, namely, the Dicers (DCL/DCR) and Argonautes (AGOs), have been extensively studied. However, the accessory proteins (DAWDLE (DDL), SERRATE (SE), and TOUGH (TGH)) of the pathway that differs across the two lineages remain largely uncharacterized. We present the first detailed report on the molecular evolution and divergence of these proteins across eukaryotes. Although DDL is present in eukaryotes and prokaryotes, SE and TGH appear to be specific to eukaryotes. The addition/deletion of specific domains and/or domain-specific sequence divergence in the three proteins points to the observed functional divergence of these proteins across the two lineages, which correlates with the differences in miRNA length across the two lineages. Our data enhance the current understanding of the structure–function relationship of these proteins and reveals previous unexplored crucial residues in the three proteins that can be used as a basis for further functional characterization. The data presented here on the number of miRNAs in crown eukaryotic lineages are consistent with the notion of the expansion of the number of miRNA-coding genes in animal and plant lineages correlating with organismal complexity. Whether this difference in functionally correlates with the diversification (or presence/absence) of the three proteins studied here or the miRNA signaling in the plant and animal lineages is unclear. Based on our results of the three proteins studied here and previously available data concerning the evolution of miRNA genes in the plant and animal lineages, we believe that miRNAs probably evolved once in the ancestor to crown eukaryotes and have diversified independently in the eukaryotes. article_number: '299' article_processing_charge: No article_type: original author: - first_name: Taraka Ramji full_name: Moturu, Taraka Ramji last_name: Moturu - first_name: Sansrity full_name: Sinha, Sansrity last_name: Sinha - first_name: Hymavathi full_name: Salava, Hymavathi last_name: Salava - first_name: Sravankumar full_name: Thula, Sravankumar last_name: Thula - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Radka Svobodová full_name: Vařeková, Radka Svobodová last_name: Vařeková - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 citation: ama: Moturu TR, Sinha S, Salava H, et al. Molecular evolution and diversification of proteins involved in miRNA maturation pathway. Plants. 2020;9(3). doi:10.3390/plants9030299 apa: Moturu, T. R., Sinha, S., Salava, H., Thula, S., Nodzyński, T., Vařeková, R. S., … Simon, S. (2020). Molecular evolution and diversification of proteins involved in miRNA maturation pathway. Plants. MDPI. https://doi.org/10.3390/plants9030299 chicago: Moturu, Taraka Ramji, Sansrity Sinha, Hymavathi Salava, Sravankumar Thula, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of Proteins Involved in MiRNA Maturation Pathway.” Plants. MDPI, 2020. https://doi.org/10.3390/plants9030299. ieee: T. R. Moturu et al., “Molecular evolution and diversification of proteins involved in miRNA maturation pathway,” Plants, vol. 9, no. 3. MDPI, 2020. ista: Moturu TR, Sinha S, Salava H, Thula S, Nodzyński T, Vařeková RS, Friml J, Simon S. 2020. Molecular evolution and diversification of proteins involved in miRNA maturation pathway. Plants. 9(3), 299. mla: Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of Proteins Involved in MiRNA Maturation Pathway.” Plants, vol. 9, no. 3, 299, MDPI, 2020, doi:10.3390/plants9030299. short: T.R. Moturu, S. Sinha, H. Salava, S. Thula, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Plants 9 (2020). date_created: 2020-03-15T23:00:52Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-08-18T07:07:08Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.3390/plants9030299 ec_funded: 1 external_id: isi: - '000525315000035' pmid: - '32121542' file: - access_level: open_access checksum: 6d5af3e17266a48996b4af4e67e88a85 content_type: application/pdf creator: dernst date_created: 2020-03-23T13:37:00Z date_updated: 2020-07-14T12:48:00Z file_id: '7614' file_name: 2020_Plants_Moturu.pdf file_size: 2373484 relation: main_file file_date_updated: 2020-07-14T12:48:00Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Plants publication_identifier: eissn: - '22237747' publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Molecular evolution and diversification of proteins involved in miRNA maturation pathway 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2020' ... --- _id: '7593' abstract: - lang: eng text: Heterozygous loss of human PAFAH1B1 (coding for LIS1) results in the disruption of neurogenesis and neuronal migration via dysregulation of microtubule (MT) stability and dynein motor function/localization that alters mitotic spindle orientation, chromosomal segregation, and nuclear migration. Recently, human induced pluripotent stem cell (iPSC) models revealed an important role for LIS1 in controlling the length of terminal cell divisions of outer radial glial (oRG) progenitors, suggesting cellular functions of LIS1 in regulating neural progenitor cell (NPC) daughter cell separation. Here we examined the late mitotic stages NPCs in vivo and mouse embryonic fibroblasts (MEFs) in vitro from Pafah1b1-deficient mutants. Pafah1b1-deficient neocortical NPCs and MEFs similarly exhibited cleavage plane displacement with mislocalization of furrow-associated markers, associated with actomyosin dysfunction and cell membrane hyper-contractility. Thus, it suggests LIS1 acts as a key molecular link connecting MTs/dynein and actomyosin, ensuring that cell membrane contractility is tightly controlled to execute proper daughter cell separation. article_number: '51512' article_processing_charge: No article_type: original author: - first_name: Hyang Mi full_name: Moon, Hyang Mi last_name: Moon - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Liqun full_name: Luo, Liqun last_name: Luo - first_name: Anthony full_name: Wynshaw-Boris, Anthony last_name: Wynshaw-Boris citation: ama: Moon HM, Hippenmeyer S, Luo L, Wynshaw-Boris A. LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. eLife. 2020;9. doi:10.7554/elife.51512 apa: Moon, H. M., Hippenmeyer, S., Luo, L., & Wynshaw-Boris, A. (2020). LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.51512 chicago: Moon, Hyang Mi, Simon Hippenmeyer, Liqun Luo, and Anthony Wynshaw-Boris. “LIS1 Determines Cleavage Plane Positioning by Regulating Actomyosin-Mediated Cell Membrane Contractility.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.51512. ieee: H. M. Moon, S. Hippenmeyer, L. Luo, and A. Wynshaw-Boris, “LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Moon HM, Hippenmeyer S, Luo L, Wynshaw-Boris A. 2020. LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. eLife. 9, 51512. mla: Moon, Hyang Mi, et al. “LIS1 Determines Cleavage Plane Positioning by Regulating Actomyosin-Mediated Cell Membrane Contractility.” ELife, vol. 9, 51512, eLife Sciences Publications, 2020, doi:10.7554/elife.51512. short: H.M. Moon, S. Hippenmeyer, L. Luo, A. Wynshaw-Boris, ELife 9 (2020). date_created: 2020-03-20T13:16:41Z date_published: 2020-03-11T00:00:00Z date_updated: 2023-08-18T07:06:31Z day: '11' ddc: - '570' department: - _id: SiHi doi: 10.7554/elife.51512 external_id: isi: - '000522835800001' pmid: - '32159512' file: - access_level: open_access checksum: 396ceb2dd10b102ef4e699666b9342c3 content_type: application/pdf creator: dernst date_created: 2020-09-24T07:03:20Z date_updated: 2020-09-24T07:03:20Z file_id: '8567' file_name: 2020_elife_Moon.pdf file_size: 15089438 relation: main_file success: 1 file_date_updated: 2020-09-24T07:03:20Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/751958 month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2020' ... --- _id: '7600' abstract: - lang: eng text: Directional intercellular transport of the phytohormone auxin mediated by PIN FORMED (PIN) efflux carriers plays essential roles in both coordinating patterning processes and integrating multiple external cues by rapidly redirecting auxin fluxes. Multilevel regulations of PIN activity under internal and external cues are complicated; however, the underlying molecular mechanism remains elusive. Here we demonstrate that 3’-Phosphoinositide-Dependent Protein Kinase1 (PDK1), which is conserved in plants and mammals, functions as a molecular hub integrating the upstream lipid signalling and the downstream substrate activity through phosphorylation. Genetic analysis uncovers that loss-of-function Arabidopsis mutant pdk1.1 pdk1.2 exhibits a plethora of abnormalities in organogenesis and growth, due to the defective PIN-dependent auxin transport. Further cellular and biochemical analyses reveal that PDK1 phosphorylates D6 Protein Kinase to facilitate its activity towards PIN proteins. Our studies establish a lipid-dependent phosphorylation cascade connecting membrane composition-based cellular signalling with plant growth and patterning by regulating morphogenetic auxin fluxes. acknowledged_ssus: - _id: Bio - _id: LifeSc article_processing_charge: No article_type: original author: - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Xixi full_name: Zhang, Xixi id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A last_name: Zhang orcid: 0000-0001-7048-4627 - first_name: Wei full_name: Kong, Wei last_name: Kong - first_name: Xiao-Li full_name: Yang, Xiao-Li last_name: Yang - first_name: Gergely full_name: Molnar, Gergely id: 34F1AF46-F248-11E8-B48F-1D18A9856A87 last_name: Molnar - first_name: Zuzana full_name: Vondráková, Zuzana last_name: Vondráková - first_name: Roberta full_name: Filepová, Roberta last_name: Filepová - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Hong-Wei full_name: Xue, Hong-Wei last_name: Xue citation: ama: Tan S, Zhang X, Kong W, et al. The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. Nature Plants. 2020;6:556-569. doi:10.1038/s41477-020-0648-9 apa: Tan, S., Zhang, X., Kong, W., Yang, X.-L., Molnar, G., Vondráková, Z., … Xue, H.-W. (2020). The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-020-0648-9 chicago: Tan, Shutang, Xixi Zhang, Wei Kong, Xiao-Li Yang, Gergely Molnar, Zuzana Vondráková, Roberta Filepová, Jan Petrášek, Jiří Friml, and Hong-Wei Xue. “The Lipid Code-Dependent Phosphoswitch PDK1–D6PK Activates PIN-Mediated Auxin Efflux in Arabidopsis.” Nature Plants. Springer Nature, 2020. https://doi.org/10.1038/s41477-020-0648-9. ieee: S. Tan et al., “The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis,” Nature Plants, vol. 6. Springer Nature, pp. 556–569, 2020. ista: Tan S, Zhang X, Kong W, Yang X-L, Molnar G, Vondráková Z, Filepová R, Petrášek J, Friml J, Xue H-W. 2020. The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. Nature Plants. 6, 556–569. mla: Tan, Shutang, et al. “The Lipid Code-Dependent Phosphoswitch PDK1–D6PK Activates PIN-Mediated Auxin Efflux in Arabidopsis.” Nature Plants, vol. 6, Springer Nature, 2020, pp. 556–69, doi:10.1038/s41477-020-0648-9. short: S. Tan, X. Zhang, W. Kong, X.-L. Yang, G. Molnar, Z. Vondráková, R. Filepová, J. Petrášek, J. Friml, H.-W. Xue, Nature Plants 6 (2020) 556–569. date_created: 2020-03-21T16:34:16Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-08-18T07:05:57Z day: '01' department: - _id: JiFr doi: 10.1038/s41477-020-0648-9 ec_funded: 1 external_id: isi: - '000531787500006' pmid: - '32393881' intvolume: ' 6' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/755504 month: '05' oa: 1 oa_version: Preprint page: 556-569 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 256FEF10-B435-11E9-9278-68D0E5697425 grant_number: 723-2015 name: Long Term Fellowship publication: Nature Plants publication_identifier: eissn: - '20550278' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41477-020-0719-y scopus_import: '1' status: public title: The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 6 year: '2020' ... --- _id: '7603' abstract: - lang: eng text: Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants. article_number: '91' article_processing_charge: No article_type: original author: - first_name: Barbara Anna full_name: Nimeth, Barbara Anna last_name: Nimeth - first_name: Stefan full_name: Riegler, Stefan id: FF6018E0-D806-11E9-8E43-0B14E6697425 last_name: Riegler orcid: 0000-0003-3413-1343 - first_name: Maria full_name: Kalyna, Maria last_name: Kalyna citation: ama: Nimeth BA, Riegler S, Kalyna M. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 2020;11. doi:10.3389/fpls.2020.00091 apa: Nimeth, B. A., Riegler, S., & Kalyna, M. (2020). Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2020.00091 chicago: Nimeth, Barbara Anna, Stefan Riegler, and Maria Kalyna. “Alternative Splicing and DNA Damage Response in Plants.” Frontiers in Plant Science. Frontiers, 2020. https://doi.org/10.3389/fpls.2020.00091. ieee: B. A. Nimeth, S. Riegler, and M. Kalyna, “Alternative splicing and DNA damage response in plants,” Frontiers in Plant Science, vol. 11. Frontiers, 2020. ista: Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 11, 91. mla: Nimeth, Barbara Anna, et al. “Alternative Splicing and DNA Damage Response in Plants.” Frontiers in Plant Science, vol. 11, 91, Frontiers, 2020, doi:10.3389/fpls.2020.00091. short: B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020). date_created: 2020-03-22T23:00:46Z date_published: 2020-02-19T00:00:00Z date_updated: 2023-08-18T07:05:18Z day: '19' ddc: - '580' department: - _id: FyKo doi: 10.3389/fpls.2020.00091 external_id: isi: - '000518903600001' file: - access_level: open_access checksum: 57c37209f7b6712ced86c0f11b2be74e content_type: application/pdf creator: dernst date_created: 2020-03-23T09:03:40Z date_updated: 2020-07-14T12:48:01Z file_id: '7607' file_name: 2020_FrontiersPlants_Nimeth.pdf file_size: 507414 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Frontiers in Plant Science publication_identifier: eissn: - 1664462X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: Alternative splicing and DNA damage response in plants 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '7586' abstract: - lang: eng text: CLC chloride/proton exchangers may support acidification of endolysosomes and raise their luminal Cl− concentration. Disruption of endosomal ClC‐3 causes severe neurodegeneration. To assess the importance of ClC‐3 Cl−/H+ exchange, we now generate Clcn3unc/unc mice in which ClC‐3 is converted into a Cl− channel. Unlike Clcn3−/− mice, Clcn3unc/unc mice appear normal owing to compensation by ClC‐4 with which ClC‐3 forms heteromers. ClC‐4 protein levels are strongly reduced in Clcn3−/−, but not in Clcn3unc/unc mice because ClC‐3unc binds and stabilizes ClC‐4 like wild‐type ClC‐3. Although mice lacking ClC‐4 appear healthy, its absence in Clcn3unc/unc/Clcn4−/− mice entails even stronger neurodegeneration than observed in Clcn3−/− mice. A fraction of ClC‐3 is found on synaptic vesicles, but miniature postsynaptic currents and synaptic vesicle acidification are not affected in Clcn3unc/unc or Clcn3−/− mice before neurodegeneration sets in. Both, Cl−/H+‐exchange activity and the stabilizing effect on ClC‐4, are central to the biological function of ClC‐3. acknowledgement: "We thank T. Stauber and T. Breiderhoff for cloning expression constructs; K. Räbel, S. Hohensee, and C. Backhaus for technical assistance; R. Jahn (MPIbpc, Göttingen) for providing the equipment required for SV purification; and A\r\nWoehler (MDC, Berlin) for assistance with SV imaging. Supported, in part, by grants from the Deutsche Forschungsgemeinschaft (JE164/9-2, SFB740 TP C5, FOR 2625 (JE164/14-1), NeuroCure Cluster of Excellence), the European Research Council Advanced Grant CYTOVOLION (ERC 294435) and the Prix Louis-Jeantet de Médecine to TJJ, and Peter and Traudl Engelhorn fellowship to ZF." article_number: e103358 article_processing_charge: No article_type: original author: - first_name: Stefanie full_name: Weinert, Stefanie last_name: Weinert - first_name: Niclas full_name: Gimber, Niclas last_name: Gimber - first_name: Dorothea full_name: Deuschel, Dorothea last_name: Deuschel - first_name: Till full_name: Stuhlmann, Till last_name: Stuhlmann - first_name: Dmytro full_name: Puchkov, Dmytro last_name: Puchkov - first_name: Zohreh full_name: Farsi, Zohreh last_name: Farsi - first_name: Carmen F. full_name: Ludwig, Carmen F. last_name: Ludwig - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Karen I. full_name: López-Cayuqueo, Karen I. last_name: López-Cayuqueo - first_name: Rosa full_name: Planells-Cases, Rosa last_name: Planells-Cases - first_name: Thomas J. full_name: Jentsch, Thomas J. last_name: Jentsch citation: ama: Weinert S, Gimber N, Deuschel D, et al. Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration. EMBO Journal. 2020;39. doi:10.15252/embj.2019103358 apa: Weinert, S., Gimber, N., Deuschel, D., Stuhlmann, T., Puchkov, D., Farsi, Z., … Jentsch, T. J. (2020). Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration. EMBO Journal. EMBO Press. https://doi.org/10.15252/embj.2019103358 chicago: Weinert, Stefanie, Niclas Gimber, Dorothea Deuschel, Till Stuhlmann, Dmytro Puchkov, Zohreh Farsi, Carmen F. Ludwig, et al. “Uncoupling Endosomal CLC Chloride/Proton Exchange Causes Severe Neurodegeneration.” EMBO Journal. EMBO Press, 2020. https://doi.org/10.15252/embj.2019103358. ieee: S. Weinert et al., “Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration,” EMBO Journal, vol. 39. EMBO Press, 2020. ista: Weinert S, Gimber N, Deuschel D, Stuhlmann T, Puchkov D, Farsi Z, Ludwig CF, Novarino G, López-Cayuqueo KI, Planells-Cases R, Jentsch TJ. 2020. Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration. EMBO Journal. 39, e103358. mla: Weinert, Stefanie, et al. “Uncoupling Endosomal CLC Chloride/Proton Exchange Causes Severe Neurodegeneration.” EMBO Journal, vol. 39, e103358, EMBO Press, 2020, doi:10.15252/embj.2019103358. short: S. Weinert, N. Gimber, D. Deuschel, T. Stuhlmann, D. Puchkov, Z. Farsi, C.F. Ludwig, G. Novarino, K.I. López-Cayuqueo, R. Planells-Cases, T.J. Jentsch, EMBO Journal 39 (2020). date_created: 2020-03-15T23:00:55Z date_published: 2020-03-02T00:00:00Z date_updated: 2023-08-18T07:07:36Z day: '02' ddc: - '570' department: - _id: GaNo doi: 10.15252/embj.2019103358 external_id: isi: - '000517335000001' pmid: - '32118314' file: - access_level: open_access checksum: 82750a7a93e3740decbce8474004111a content_type: application/pdf creator: dernst date_created: 2020-03-23T13:51:11Z date_updated: 2020-07-14T12:48:00Z file_id: '7615' file_name: 2020_EMBO_Weinert.pdf file_size: 12243278 relation: main_file file_date_updated: 2020-07-14T12:48:00Z has_accepted_license: '1' intvolume: ' 39' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: EMBO Journal publication_identifier: eissn: - '14602075' issn: - '02614189' publication_status: published publisher: EMBO Press quality_controlled: '1' scopus_import: '1' status: public title: Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration 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: 39 year: '2020' ... --- _id: '7618' abstract: - lang: eng text: 'This short note aims to study quantum Hellinger distances investigated recently by Bhatia et al. (Lett Math Phys 109:1777–1804, 2019) with a particular emphasis on barycenters. We introduce the family of generalized quantum Hellinger divergences that are of the form ϕ(A,B)=Tr((1−c)A+cB−AσB), where σ is an arbitrary Kubo–Ando mean, and c∈(0,1) is the weight of σ. We note that these divergences belong to the family of maximal quantum f-divergences, and hence are jointly convex, and satisfy the data processing inequality. We derive a characterization of the barycenter of finitely many positive definite operators for these generalized quantum Hellinger divergences. We note that the characterization of the barycenter as the weighted multivariate 1/2-power mean, that was claimed in Bhatia et al. (2019), is true in the case of commuting operators, but it is not correct in the general case. ' acknowledgement: "J. Pitrik was supported by the Hungarian Academy of Sciences Lendület-Momentum Grant for Quantum\r\nInformation Theory, No. 96 141, and by the Hungarian National Research, Development and Innovation\r\nOffice (NKFIH) via Grants Nos. K119442, K124152 and KH129601. D. Virosztek was supported by the\r\nISTFELLOW program of the Institute of Science and Technology Austria (Project Code IC1027FELL01),\r\nby the European Union’s Horizon 2020 research and innovation program under the Marie\r\nSklodowska-Curie Grant Agreement No. 846294, and partially supported by the Hungarian National\r\nResearch, Development and Innovation Office (NKFIH) via Grants Nos. K124152 and KH129601.\r\nWe are grateful to Milán Mosonyi for drawing our attention to Ref.’s [6,14,15,17,\r\n20,21], for comments on earlier versions of this paper, and for several discussions on the topic. We are\r\nalso grateful to Miklós Pálfia for several discussions; to László Erdös for his essential suggestions on the\r\nstructure and highlights of this paper, and for his comments on earlier versions; and to the anonymous\r\nreferee for his/her valuable comments and suggestions." article_processing_charge: No article_type: original author: - first_name: Jozsef full_name: Pitrik, Jozsef last_name: Pitrik - first_name: Daniel full_name: Virosztek, Daniel id: 48DB45DA-F248-11E8-B48F-1D18A9856A87 last_name: Virosztek orcid: 0000-0003-1109-5511 citation: ama: Pitrik J, Virosztek D. Quantum Hellinger distances revisited. Letters in Mathematical Physics. 2020;110(8):2039-2052. doi:10.1007/s11005-020-01282-0 apa: Pitrik, J., & Virosztek, D. (2020). Quantum Hellinger distances revisited. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-020-01282-0 chicago: Pitrik, Jozsef, and Daniel Virosztek. “Quantum Hellinger Distances Revisited.” Letters in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s11005-020-01282-0. ieee: J. Pitrik and D. Virosztek, “Quantum Hellinger distances revisited,” Letters in Mathematical Physics, vol. 110, no. 8. Springer Nature, pp. 2039–2052, 2020. ista: Pitrik J, Virosztek D. 2020. Quantum Hellinger distances revisited. Letters in Mathematical Physics. 110(8), 2039–2052. mla: Pitrik, Jozsef, and Daniel Virosztek. “Quantum Hellinger Distances Revisited.” Letters in Mathematical Physics, vol. 110, no. 8, Springer Nature, 2020, pp. 2039–52, doi:10.1007/s11005-020-01282-0. short: J. Pitrik, D. Virosztek, Letters in Mathematical Physics 110 (2020) 2039–2052. date_created: 2020-03-25T15:57:48Z date_published: 2020-08-01T00:00:00Z date_updated: 2023-08-18T10:17:26Z day: '01' department: - _id: LaEr doi: 10.1007/s11005-020-01282-0 ec_funded: 1 external_id: arxiv: - '1903.10455' isi: - '000551556000002' intvolume: ' 110' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1903.10455 month: '08' oa: 1 oa_version: Preprint page: 2039-2052 project: - _id: 26A455A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '846294' name: Geometric study of Wasserstein spaces and free probability - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Letters in Mathematical Physics publication_identifier: eissn: - 1573-0530 issn: - 0377-9017 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Quantum Hellinger distances revisited type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 110 year: '2020' ... --- _id: '7632' abstract: - lang: eng text: The posterior parietal cortex (PPC) and frontal motor areas comprise a cortical network supporting goal-directed behaviour, with functions including sensorimotor transformations and decision making. In primates, this network links performed and observed actions via mirror neurons, which fire both when individuals perform an action and when they observe the same action performed by a conspecific. Mirror neurons are believed to be important for social learning, but it is not known whether mirror-like neurons occur in similar networks in other social species, such as rodents, or if they can be measured in such models using paradigms where observers passively view a demonstrator. Therefore, we imaged Ca2+ responses in PPC and secondary motor cortex (M2) while mice performed and observed pellet-reaching and wheel-running tasks, and found that cell populations in both areas robustly encoded several naturalistic behaviours. However, neural responses to the same set of observed actions were absent, although we verified that observer mice were attentive to performers and that PPC neurons responded reliably to visual cues. Statistical modelling also indicated that executed actions outperformed observed actions in predicting neural responses. These results raise the possibility that sensorimotor action recognition in rodents could take place outside of the parieto-frontal circuit, and underscore that detecting socially-driven neural coding depends critically on the species and behavioural paradigm used. article_number: '5559' article_processing_charge: No article_type: original author: - first_name: Tuce full_name: Tombaz, Tuce last_name: Tombaz - first_name: Benjamin A. full_name: Dunn, Benjamin A. last_name: Dunn - first_name: Karoline full_name: Hovde, Karoline last_name: Hovde - first_name: Ryan J full_name: Cubero, Ryan J id: 850B2E12-9CD4-11E9-837F-E719E6697425 last_name: Cubero orcid: 0000-0003-0002-1867 - first_name: Bartul full_name: Mimica, Bartul last_name: Mimica - first_name: Pranav full_name: Mamidanna, Pranav last_name: Mamidanna - first_name: Yasser full_name: Roudi, Yasser last_name: Roudi - first_name: Jonathan R. full_name: Whitlock, Jonathan R. last_name: Whitlock citation: ama: Tombaz T, Dunn BA, Hovde K, et al. Action representation in the mouse parieto-frontal network. Scientific reports. 2020;10(1). doi:10.1038/s41598-020-62089-6 apa: Tombaz, T., Dunn, B. A., Hovde, K., Cubero, R. J., Mimica, B., Mamidanna, P., … Whitlock, J. R. (2020). Action representation in the mouse parieto-frontal network. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-62089-6 chicago: Tombaz, Tuce, Benjamin A. Dunn, Karoline Hovde, Ryan J Cubero, Bartul Mimica, Pranav Mamidanna, Yasser Roudi, and Jonathan R. Whitlock. “Action Representation in the Mouse Parieto-Frontal Network.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-62089-6. ieee: T. Tombaz et al., “Action representation in the mouse parieto-frontal network,” Scientific reports, vol. 10, no. 1. Springer Nature, 2020. ista: Tombaz T, Dunn BA, Hovde K, Cubero RJ, Mimica B, Mamidanna P, Roudi Y, Whitlock JR. 2020. Action representation in the mouse parieto-frontal network. Scientific reports. 10(1), 5559. mla: Tombaz, Tuce, et al. “Action Representation in the Mouse Parieto-Frontal Network.” Scientific Reports, vol. 10, no. 1, 5559, Springer Nature, 2020, doi:10.1038/s41598-020-62089-6. short: T. Tombaz, B.A. Dunn, K. Hovde, R.J. Cubero, B. Mimica, P. Mamidanna, Y. Roudi, J.R. Whitlock, Scientific Reports 10 (2020). date_created: 2020-04-05T22:00:47Z date_published: 2020-03-27T00:00:00Z date_updated: 2023-08-18T10:25:13Z day: '27' ddc: - '570' department: - _id: SaSi doi: 10.1038/s41598-020-62089-6 external_id: isi: - '000560406800007' file: - access_level: open_access checksum: e6cfaaaf7986532132934400038b824a content_type: application/pdf creator: dernst date_created: 2020-04-06T10:44:23Z date_updated: 2020-07-14T12:48:01Z file_id: '7644' file_name: 2020_ScientificReports_Tombaz.pdf file_size: 2621249 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Scientific reports publication_identifier: eissn: - '20452322' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Action representation in the mouse parieto-frontal network 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2020' ... --- _id: '7622' abstract: - lang: eng text: The International Young Physicists' Tournament (IYPT) continued in 2018 in Beijing, China and 2019 in Warsaw, Poland with its 31st and 32nd editions. The IYPT is a modern scientific competition for teams of high school students, also known as the Physics World Cup. It involves long-term theoretical and experimental work focused on solving 17 publicly announced open-ended problems in teams of five. On top of that, teams have to present their solutions in front of other teams and a scientific jury, and get opposed and reviewed by their peers. Here we present a brief information about the competition with a specific focus on one of the IYPT 2018 tasks, the 'Ring Oiler'. This seemingly simple mechanical problem appeared to be of such a complexity that even the dozens of participating teams and jurying scientists were not able to solve all of its subtleties. article_number: '034001' article_processing_charge: No article_type: original author: - first_name: Martin full_name: Plesch, Martin last_name: Plesch - first_name: Samuel full_name: Plesník, Samuel last_name: Plesník - first_name: Natalia full_name: Ruzickova, Natalia id: D2761128-D73D-11E9-A1BF-BA0DE6697425 last_name: Ruzickova citation: ama: Plesch M, Plesník S, Ruzickova N. The IYPT and the “Ring Oiler” problem. European Journal of Physics. 2020;41(3). doi:10.1088/1361-6404/ab6414 apa: Plesch, M., Plesník, S., & Ruzickova, N. (2020). The IYPT and the “Ring Oiler” problem. European Journal of Physics. IOP Publishing. https://doi.org/10.1088/1361-6404/ab6414 chicago: Plesch, Martin, Samuel Plesník, and Natalia Ruzickova. “The IYPT and the ‘Ring Oiler’ Problem.” European Journal of Physics. IOP Publishing, 2020. https://doi.org/10.1088/1361-6404/ab6414. ieee: M. Plesch, S. Plesník, and N. Ruzickova, “The IYPT and the ‘Ring Oiler’ problem,” European Journal of Physics, vol. 41, no. 3. IOP Publishing, 2020. ista: Plesch M, Plesník S, Ruzickova N. 2020. The IYPT and the ‘Ring Oiler’ problem. European Journal of Physics. 41(3), 034001. mla: Plesch, Martin, et al. “The IYPT and the ‘Ring Oiler’ Problem.” European Journal of Physics, vol. 41, no. 3, 034001, IOP Publishing, 2020, doi:10.1088/1361-6404/ab6414. short: M. Plesch, S. Plesník, N. Ruzickova, European Journal of Physics 41 (2020). date_created: 2020-03-31T11:25:04Z date_published: 2020-02-24T00:00:00Z date_updated: 2023-08-18T10:18:29Z day: '24' ddc: - '530' department: - _id: FyKo doi: 10.1088/1361-6404/ab6414 external_id: arxiv: - '1910.03290' isi: - '000537425400001' file: - access_level: open_access checksum: 47dda164e33b6c0c6c3ed14aad298376 content_type: application/pdf creator: dernst date_created: 2020-04-06T08:53:53Z date_updated: 2020-07-14T12:48:01Z file_id: '7641' file_name: 2020_EuropJourPhysics_Plesch.pdf file_size: 1533672 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' intvolume: ' 41' isi: 1 issue: '3' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: European Journal of Physics publication_identifier: eissn: - '13616404' issn: - '01430807' publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: The IYPT and the 'Ring Oiler' problem 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 41 year: '2020' ... --- _id: '7634' abstract: - lang: eng text: Assemblies of colloidal semiconductor nanocrystals (NCs) in the form of thin solid films leverage the size-dependent quantum confinement properties and the wet chemical methods vital for the development of the emerging solution-processable electronics, photonics, and optoelectronics technologies. The ability to control the charge carrier transport in the colloidal NC assemblies is fundamental for altering their electronic and optical properties for the desired applications. Here we demonstrate a strategy to render the solids of narrow-bandgap NC assemblies exclusively electron-transporting by creating a type-II heterojunction via shelling. Electronic transport of molecularly cross-linked PbTe@PbS core@shell NC assemblies is measured using both a conventional solid gate transistor and an electric-double-layer transistor, as well as compared with those of core-only PbTe NCs. In contrast to the ambipolar characteristics demonstrated by many narrow-bandgap NCs, the core@shell NCs exhibit exclusive n-type transport, i.e., drastically suppressed contribution of holes to the overall transport. The PbS shell that forms a type-II heterojunction assists the selective carrier transport by heavy doping of electrons into the PbTe-core conduction level and simultaneously strongly localizes the holes within the NC core valence level. This strongly enhanced n-type transport makes these core@shell NCs suitable for applications where ambipolar characteristics should be actively suppressed, in particular, for thermoelectric and electron-transporting layers in photovoltaic devices. acknowledgement: This work is partly supported by Grants-in-Aid for Scientific Research by Young Scientist A (KAKENHI Wakate-A) No. JP17H04802, Grants-in-Aid for Scientific Research No. JP19H05602 from the Japan Society for the Promotion of Science, and RIKEN Incentive Research Grant (Shoreikadai) 2016. M.V.K. and M.I. acknowledge financial support from the European Union (EU) via FP7 ERC Starting Grant 2012 (Project NANOSOLID, GA No. 306733) and ETH Zurich via ETH career seed grant (SEED-18 16-2). Support from Cambridge Display Technology, Ltd., and Sumitomo Chemical Company is also acknowledged. We thank Mrs. T. Kikitsu and Dr. D. Hashizume (RIKEN-CEMS) for access to the transmission electron microscope facility. article_processing_charge: No article_type: original author: - first_name: Retno full_name: Miranti, Retno last_name: Miranti - first_name: Daiki full_name: Shin, Daiki last_name: Shin - first_name: Ricky Dwi full_name: Septianto, Ricky Dwi last_name: Septianto - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Maksym V. full_name: Kovalenko, Maksym V. last_name: Kovalenko - first_name: Nobuhiro full_name: Matsushita, Nobuhiro last_name: Matsushita - first_name: Yoshihiro full_name: Iwasa, Yoshihiro last_name: Iwasa - first_name: Satria Zulkarnaen full_name: Bisri, Satria Zulkarnaen last_name: Bisri citation: ama: Miranti R, Shin D, Septianto RD, et al. Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies. ACS Nano. 2020;14(3):3242-3250. doi:10.1021/acsnano.9b08687 apa: Miranti, R., Shin, D., Septianto, R. D., Ibáñez, M., Kovalenko, M. V., Matsushita, N., … Bisri, S. Z. (2020). Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.9b08687 chicago: Miranti, Retno, Daiki Shin, Ricky Dwi Septianto, Maria Ibáñez, Maksym V. Kovalenko, Nobuhiro Matsushita, Yoshihiro Iwasa, and Satria Zulkarnaen Bisri. “Exclusive Electron Transport in Core@Shell PbTe@PbS Colloidal Semiconductor Nanocrystal Assemblies.” ACS Nano. American Chemical Society, 2020. https://doi.org/10.1021/acsnano.9b08687. ieee: R. Miranti et al., “Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies,” ACS Nano, vol. 14, no. 3. American Chemical Society, pp. 3242–3250, 2020. ista: Miranti R, Shin D, Septianto RD, Ibáñez M, Kovalenko MV, Matsushita N, Iwasa Y, Bisri SZ. 2020. Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies. ACS Nano. 14(3), 3242–3250. mla: Miranti, Retno, et al. “Exclusive Electron Transport in Core@Shell PbTe@PbS Colloidal Semiconductor Nanocrystal Assemblies.” ACS Nano, vol. 14, no. 3, American Chemical Society, 2020, pp. 3242–50, doi:10.1021/acsnano.9b08687. short: R. Miranti, D. Shin, R.D. Septianto, M. Ibáñez, M.V. Kovalenko, N. Matsushita, Y. Iwasa, S.Z. Bisri, ACS Nano 14 (2020) 3242–3250. date_created: 2020-04-05T22:00:48Z date_published: 2020-03-24T00:00:00Z date_updated: 2023-08-18T10:25:40Z day: '24' department: - _id: MaIb doi: 10.1021/acsnano.9b08687 external_id: isi: - '000526301400057' pmid: - '32073817' intvolume: ' 14' isi: 1 issue: '3' language: - iso: eng month: '03' oa_version: None page: 3242-3250 pmid: 1 publication: ACS Nano publication_identifier: eissn: - 1936-086X publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2020' ... --- _id: '7623' abstract: - lang: eng text: A two-dimensional mathematical model for cells migrating without adhesion capabilities is presented and analyzed. Cells are represented by their cortex, which is modeled as an elastic curve, subject to an internal pressure force. Net polymerization or depolymerization in the cortex is modeled via local addition or removal of material, driving a cortical flow. The model takes the form of a fully nonlinear degenerate parabolic system. An existence analysis is carried out by adapting ideas from the theory of gradient flows. Numerical simulations show that these simple rules can account for the behavior observed in experiments, suggesting a possible mechanical mechanism for adhesion-independent motility. acknowledgement: This work has been supported by the Vienna Science and Technology Fund, Grant no. LS13-029. G.J. and C.S. also acknowledge support by the Austrian Science Fund, Grants no. W1245, F 65, and W1261, as well as by the Fondation Sciences Mathématiques de Paris, and by Paris-Sciences-et-Lettres. article_processing_charge: No article_type: original author: - first_name: Gaspard full_name: Jankowiak, Gaspard last_name: Jankowiak - first_name: Diane full_name: Peurichard, Diane last_name: Peurichard - first_name: Anne full_name: Reversat, Anne id: 35B76592-F248-11E8-B48F-1D18A9856A87 last_name: Reversat orcid: 0000-0003-0666-8928 - first_name: Christian full_name: Schmeiser, Christian last_name: Schmeiser - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Jankowiak G, Peurichard D, Reversat A, Schmeiser C, Sixt MK. Modeling adhesion-independent cell migration. Mathematical Models and Methods in Applied Sciences. 2020;30(3):513-537. doi:10.1142/S021820252050013X apa: Jankowiak, G., Peurichard, D., Reversat, A., Schmeiser, C., & Sixt, M. K. (2020). Modeling adhesion-independent cell migration. Mathematical Models and Methods in Applied Sciences. World Scientific. https://doi.org/10.1142/S021820252050013X chicago: Jankowiak, Gaspard, Diane Peurichard, Anne Reversat, Christian Schmeiser, and Michael K Sixt. “Modeling Adhesion-Independent Cell Migration.” Mathematical Models and Methods in Applied Sciences. World Scientific, 2020. https://doi.org/10.1142/S021820252050013X. ieee: G. Jankowiak, D. Peurichard, A. Reversat, C. Schmeiser, and M. K. Sixt, “Modeling adhesion-independent cell migration,” Mathematical Models and Methods in Applied Sciences, vol. 30, no. 3. World Scientific, pp. 513–537, 2020. ista: Jankowiak G, Peurichard D, Reversat A, Schmeiser C, Sixt MK. 2020. Modeling adhesion-independent cell migration. Mathematical Models and Methods in Applied Sciences. 30(3), 513–537. mla: Jankowiak, Gaspard, et al. “Modeling Adhesion-Independent Cell Migration.” Mathematical Models and Methods in Applied Sciences, vol. 30, no. 3, World Scientific, 2020, pp. 513–37, doi:10.1142/S021820252050013X. short: G. Jankowiak, D. Peurichard, A. Reversat, C. Schmeiser, M.K. Sixt, Mathematical Models and Methods in Applied Sciences 30 (2020) 513–537. date_created: 2020-03-31T11:25:05Z date_published: 2020-03-18T00:00:00Z date_updated: 2023-08-18T10:18:56Z day: '18' department: - _id: MiSi doi: 10.1142/S021820252050013X external_id: arxiv: - '1903.09426' isi: - '000525349900003' intvolume: ' 30' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1903.09426 month: '03' oa: 1 oa_version: Preprint page: 513-537 project: - _id: 25AD6156-B435-11E9-9278-68D0E5697425 grant_number: LS13-029 name: Modeling of Polarization and Motility of Leukocytes in Three-Dimensional Environments publication: Mathematical Models and Methods in Applied Sciences publication_identifier: issn: - '02182025' publication_status: published publisher: World Scientific quality_controlled: '1' scopus_import: '1' status: public title: Modeling adhesion-independent cell migration type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 30 year: '2020' ... --- _id: '7646' abstract: - lang: eng text: In plant cells, environmental stressors promote changes in connectivity between the cortical ER and the PM. Although this process is tightly regulated in space and time, the molecular signals and structural components mediating these changes in inter-organelle communication are only starting to be characterized. In this report, we confirm the presence of a putative tethering complex containing the synaptotagmins 1 and 5 (SYT1 and SYT5) and the Ca2+ and lipid binding protein 1 (CLB1/SYT7). This complex is enriched at ER-PM contact sites (EPCS), have slow responses to changes in extracellular Ca2+, and display severe cytoskeleton-dependent rearrangements in response to the trivalent lanthanum (La3+) and gadolinium (Gd3+) rare earth elements (REEs). Although REEs are generally used as non-selective cation channel blockers at the PM, here we show that the slow internalization of REEs into the cytosol underlies the activation of the Ca2+/Calmodulin intracellular signaling, the accumulation of phosphatidylinositol-4-phosphate (PI4P) at the PM, and the cytoskeleton-dependent rearrangement of the SYT1/SYT5 EPCS complexes. We propose that the observed EPCS rearrangements act as a slow adaptive response to sustained stress conditions, and that this process involves the accumulation of stress-specific phosphoinositides species at the PM. article_processing_charge: No article_type: original author: - first_name: E full_name: Lee, E last_name: Lee - first_name: B full_name: Vila Nova Santana, B last_name: Vila Nova Santana - first_name: E full_name: Samuels, E last_name: Samuels - first_name: F full_name: Benitez-Fuente, F last_name: Benitez-Fuente - first_name: E full_name: Corsi, E last_name: Corsi - first_name: MA full_name: Botella, MA last_name: Botella - first_name: J full_name: Perez-Sancho, J last_name: Perez-Sancho - first_name: S full_name: Vanneste, S last_name: Vanneste - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: A full_name: Macho, A last_name: Macho - first_name: A full_name: Alves Azevedo, A last_name: Alves Azevedo - first_name: A full_name: Rosado, A last_name: Rosado citation: ama: Lee E, Vila Nova Santana B, Samuels E, et al. Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. Journal of Experimental Botany. 2020;71(14):3986–3998. doi:10.1093/jxb/eraa138 apa: Lee, E., Vila Nova Santana, B., Samuels, E., Benitez-Fuente, F., Corsi, E., Botella, M., … Rosado, A. (2020). Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/eraa138 chicago: Lee, E, B Vila Nova Santana, E Samuels, F Benitez-Fuente, E Corsi, MA Botella, J Perez-Sancho, et al. “Rare Earth Elements Induce Cytoskeleton-Dependent and PI4P-Associated Rearrangement of SYT1/SYT5 ER-PM Contact Site Complexes in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2020. https://doi.org/10.1093/jxb/eraa138. ieee: E. Lee et al., “Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis,” Journal of Experimental Botany, vol. 71, no. 14. Oxford University Press, pp. 3986–3998, 2020. ista: Lee E, Vila Nova Santana B, Samuels E, Benitez-Fuente F, Corsi E, Botella M, Perez-Sancho J, Vanneste S, Friml J, Macho A, Alves Azevedo A, Rosado A. 2020. Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. Journal of Experimental Botany. 71(14), 3986–3998. mla: Lee, E., et al. “Rare Earth Elements Induce Cytoskeleton-Dependent and PI4P-Associated Rearrangement of SYT1/SYT5 ER-PM Contact Site Complexes in Arabidopsis.” Journal of Experimental Botany, vol. 71, no. 14, Oxford University Press, 2020, pp. 3986–3998, doi:10.1093/jxb/eraa138. short: E. Lee, B. Vila Nova Santana, E. Samuels, F. Benitez-Fuente, E. Corsi, M. Botella, J. Perez-Sancho, S. Vanneste, J. Friml, A. Macho, A. Alves Azevedo, A. Rosado, Journal of Experimental Botany 71 (2020) 3986–3998. date_created: 2020-04-06T10:57:08Z date_published: 2020-07-06T00:00:00Z date_updated: 2023-08-18T10:27:52Z day: '06' ddc: - '580' department: - _id: JiFr doi: 10.1093/jxb/eraa138 external_id: isi: - '000553125400007' pmid: - '32179893' file: - access_level: open_access checksum: b06aaaa93dc41896da805fe4b75cf3a1 content_type: application/pdf creator: dernst date_created: 2020-10-06T07:41:35Z date_updated: 2020-10-06T07:41:35Z file_id: '8613' file_name: 2020_JourExperimBotany_Lee.pdf file_size: 1916031 relation: main_file success: 1 file_date_updated: 2020-10-06T07:41:35Z has_accepted_license: '1' intvolume: ' 71' isi: 1 issue: '14' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 3986–3998 pmid: 1 publication: Journal of Experimental Botany publication_identifier: eissn: - 1460-2431 issn: - 0022-0957 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 71 year: '2020' ... --- _id: '7656' abstract: - lang: eng text: 'We propose that correlations among neurons are generically strong enough to organize neural activity patterns into a discrete set of clusters, which can each be viewed as a population codeword. Our reasoning starts with the analysis of retinal ganglion cell data using maximum entropy models, showing that the population is robustly in a frustrated, marginally sub-critical, or glassy, state. This leads to an argument that neural populations in many other brain areas might share this structure. Next, we use latent variable models to show that this glassy state possesses well-defined clusters of neural activity. Clusters have three appealing properties: (i) clusters exhibit error correction, i.e., they are reproducibly elicited by the same stimulus despite variability at the level of constituent neurons; (ii) clusters encode qualitatively different visual features than their constituent neurons; and (iii) clusters can be learned by downstream neural circuits in an unsupervised fashion. We hypothesize that these properties give rise to a “learnable” neural code which the cortical hierarchy uses to extract increasingly complex features without supervision or reinforcement.' article_number: '20' article_processing_charge: No article_type: original author: - first_name: Michael J. full_name: Berry, Michael J. last_name: Berry - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: 'Berry MJ, Tkačik G. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 2020;14. doi:10.3389/fncom.2020.00020' apa: 'Berry, M. J., & Tkačik, G. (2020). Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. Frontiers. https://doi.org/10.3389/fncom.2020.00020' chicago: 'Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design Principle for Population Codes.” Frontiers in Computational Neuroscience. Frontiers, 2020. https://doi.org/10.3389/fncom.2020.00020.' ieee: 'M. J. Berry and G. Tkačik, “Clustering of neural activity: A design principle for population codes,” Frontiers in Computational Neuroscience, vol. 14. Frontiers, 2020.' ista: 'Berry MJ, Tkačik G. 2020. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 14, 20.' mla: 'Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design Principle for Population Codes.” Frontiers in Computational Neuroscience, vol. 14, 20, Frontiers, 2020, doi:10.3389/fncom.2020.00020.' short: M.J. Berry, G. Tkačik, Frontiers in Computational Neuroscience 14 (2020). date_created: 2020-04-12T22:00:40Z date_published: 2020-03-13T00:00:00Z date_updated: 2023-08-18T10:30:11Z day: '13' ddc: - '570' department: - _id: GaTk doi: 10.3389/fncom.2020.00020 external_id: isi: - '000525543200001' pmid: - '32231528' file: - access_level: open_access checksum: 2b1da23823eae9cedbb42d701945b61e content_type: application/pdf creator: dernst date_created: 2020-04-14T12:20:39Z date_updated: 2020-07-14T12:48:01Z file_id: '7659' file_name: 2020_Frontiers_Berry.pdf file_size: 4082937 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Computational Neuroscience publication_identifier: eissn: - '16625188' publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: 'Clustering of neural activity: A design principle for population codes' 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2020' ... --- _id: '7638' abstract: - lang: eng text: Following on from our recent work, we investigate a stochastic approach to non-equilibrium quantum spin systems. We show how the method can be applied to a variety of physical observables and for different initial conditions. We provide exact formulae of broad applicability for the time-dependence of expectation values and correlation functions following a quantum quench in terms of averages over classical stochastic processes. We further explore the behavior of the classical stochastic variables in the presence of dynamical quantum phase transitions, including results for their distributions and correlation functions. We provide details on the numerical solution of the associated stochastic differential equations, and examine the growth of fluctuations in the classical description. We discuss the strengths and limitations of the current implementation of the stochastic approach and the potential for further development. article_number: '013106' article_processing_charge: No article_type: original author: - first_name: Stefano full_name: De Nicola, Stefano id: 42832B76-F248-11E8-B48F-1D18A9856A87 last_name: De Nicola orcid: 0000-0002-4842-6671 - first_name: B. full_name: Doyon, B. last_name: Doyon - first_name: M. J. full_name: Bhaseen, M. J. last_name: Bhaseen citation: ama: 'De Nicola S, Doyon B, Bhaseen MJ. Non-equilibrium quantum spin dynamics from classical stochastic processes. Journal of Statistical Mechanics: Theory and Experiment. 2020;2020(1). doi:10.1088/1742-5468/ab6093' apa: 'De Nicola, S., Doyon, B., & Bhaseen, M. J. (2020). Non-equilibrium quantum spin dynamics from classical stochastic processes. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/ab6093' chicago: 'De Nicola, Stefano, B. Doyon, and M. J. Bhaseen. “Non-Equilibrium Quantum Spin Dynamics from Classical Stochastic Processes.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2020. https://doi.org/10.1088/1742-5468/ab6093.' ieee: 'S. De Nicola, B. Doyon, and M. J. Bhaseen, “Non-equilibrium quantum spin dynamics from classical stochastic processes,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2020, no. 1. IOP Publishing, 2020.' ista: 'De Nicola S, Doyon B, Bhaseen MJ. 2020. Non-equilibrium quantum spin dynamics from classical stochastic processes. Journal of Statistical Mechanics: Theory and Experiment. 2020(1), 013106.' mla: 'De Nicola, Stefano, et al. “Non-Equilibrium Quantum Spin Dynamics from Classical Stochastic Processes.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2020, no. 1, 013106, IOP Publishing, 2020, doi:10.1088/1742-5468/ab6093.' short: 'S. De Nicola, B. Doyon, M.J. Bhaseen, Journal of Statistical Mechanics: Theory and Experiment 2020 (2020).' date_created: 2020-04-05T22:00:50Z date_published: 2020-01-22T00:00:00Z date_updated: 2023-08-18T10:27:15Z day: '22' ddc: - '530' department: - _id: MaSe doi: 10.1088/1742-5468/ab6093 ec_funded: 1 external_id: arxiv: - '1909.13142' isi: - '000520187500001' file: - access_level: open_access checksum: 4030e683c15d30b7b4794ec7dc1b6537 content_type: application/pdf creator: dernst date_created: 2020-04-06T13:15:49Z date_updated: 2020-07-14T12:48:01Z file_id: '7648' file_name: 2020_JournStatisticalMech_DeNicola.pdf file_size: 3159026 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' intvolume: ' 2020' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: 'Journal of Statistical Mechanics: Theory and Experiment' publication_identifier: eissn: - '17425468' publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Non-equilibrium quantum spin dynamics from classical stochastic processes type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 2020 year: '2020' ... --- _id: '7637' abstract: - lang: eng text: The evolution of finitely many particles obeying Langevin dynamics is described by Dean–Kawasaki equations, a class of stochastic equations featuring a non-Lipschitz multiplicative noise in divergence form. We derive a regularised Dean–Kawasaki model based on second order Langevin dynamics by analysing a system of particles interacting via a pairwise potential. Key tools of our analysis are the propagation of chaos and Simon's compactness criterion. The model we obtain is a small-noise stochastic perturbation of the undamped McKean–Vlasov equation. We also provide a high-probability result for existence and uniqueness for our model. article_processing_charge: No article_type: original author: - first_name: Federico full_name: Cornalba, Federico id: 2CEB641C-A400-11E9-A717-D712E6697425 last_name: Cornalba orcid: 0000-0002-6269-5149 - first_name: Tony full_name: Shardlow, Tony last_name: Shardlow - first_name: Johannes full_name: Zimmer, Johannes last_name: Zimmer citation: ama: Cornalba F, Shardlow T, Zimmer J. From weakly interacting particles to a regularised Dean-Kawasaki model. Nonlinearity. 2020;33(2):864-891. doi:10.1088/1361-6544/ab5174 apa: Cornalba, F., Shardlow, T., & Zimmer, J. (2020). From weakly interacting particles to a regularised Dean-Kawasaki model. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/ab5174 chicago: Cornalba, Federico, Tony Shardlow, and Johannes Zimmer. “From Weakly Interacting Particles to a Regularised Dean-Kawasaki Model.” Nonlinearity. IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab5174. ieee: F. Cornalba, T. Shardlow, and J. Zimmer, “From weakly interacting particles to a regularised Dean-Kawasaki model,” Nonlinearity, vol. 33, no. 2. IOP Publishing, pp. 864–891, 2020. ista: Cornalba F, Shardlow T, Zimmer J. 2020. From weakly interacting particles to a regularised Dean-Kawasaki model. Nonlinearity. 33(2), 864–891. mla: Cornalba, Federico, et al. “From Weakly Interacting Particles to a Regularised Dean-Kawasaki Model.” Nonlinearity, vol. 33, no. 2, IOP Publishing, 2020, pp. 864–91, doi:10.1088/1361-6544/ab5174. short: F. Cornalba, T. Shardlow, J. Zimmer, Nonlinearity 33 (2020) 864–891. date_created: 2020-04-05T22:00:49Z date_published: 2020-01-10T00:00:00Z date_updated: 2023-08-18T10:26:07Z day: '10' department: - _id: JuFi doi: 10.1088/1361-6544/ab5174 external_id: arxiv: - '1811.06448' isi: - '000508175400001' intvolume: ' 33' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1811.06448 month: '01' oa: 1 oa_version: Preprint page: 864-891 publication: Nonlinearity publication_identifier: eissn: - '13616544' issn: - '09517715' publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: From weakly interacting particles to a regularised Dean-Kawasaki model type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 33 year: '2020' ... --- _id: '7664' abstract: - lang: eng text: Metabotropic γ-aminobutyric acid (GABAB) receptors contribute to the control of network activity and information processing in hippocampal circuits by regulating neuronal excitability and synaptic transmission. The dysfunction in the dentate gyrus (DG) has been implicated in Alzheimer´s disease (AD). Given the involvement of GABAB receptors in AD, to determine their subcellular localisation and possible alteration in granule cells of the DG in a mouse model of AD at 12 months of age, we used high-resolution immunoelectron microscopic analysis. Immunohistochemistry at the light microscopic level showed that the regional and cellular expression pattern of GABAB1 was similar in an AD model mouse expressing mutated human amyloid precursor protein and presenilin1 (APP/PS1) and in age-matched wild type mice. High-resolution immunoelectron microscopy revealed a distance-dependent gradient of immunolabelling for GABAB receptors, increasing from proximal to distal dendrites in both wild type and APP/PS1 mice. However, the overall density of GABAB receptors at the neuronal surface of these postsynaptic compartments of granule cells was significantly reduced in APP/PS1 mice. Parallel to this reduction in surface receptors, we found a significant increase in GABAB1 at cytoplasmic sites. GABAB receptors were also detected at presynaptic sites in the molecular layer of the DG. We also found a decrease in plasma membrane GABAB receptors in axon terminals contacting dendritic spines of granule cells, which was more pronounced in the outer than in the inner molecular layer. Altogether, our data showing post- and presynaptic reduction in surface GABAB receptors in the DG suggest the alteration of the GABAB-mediated modulation of excitability and synaptic transmission in granule cells, which may contribute to the cognitive dysfunctions in the APP/PS1 model of AD article_number: '2459' article_processing_charge: No article_type: original author: - first_name: Alejandro full_name: Martín-Belmonte, Alejandro last_name: Martín-Belmonte - first_name: Carolina full_name: Aguado, Carolina last_name: Aguado - first_name: Rocío full_name: Alfaro-Ruíz, Rocío last_name: Alfaro-Ruíz - first_name: Ana Esther full_name: Moreno-Martínez, Ana Esther last_name: Moreno-Martínez - first_name: Luis full_name: De La Ossa, Luis last_name: De La Ossa - first_name: José full_name: Martínez-Hernández, José last_name: Martínez-Hernández - first_name: Alain full_name: Buisson, Alain last_name: Buisson - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Rafael full_name: Luján, Rafael last_name: Luján citation: ama: Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, et al. Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. International journal of molecular sciences. 2020;21(7). doi:10.3390/ijms21072459 apa: Martín-Belmonte, A., Aguado, C., Alfaro-Ruíz, R., Moreno-Martínez, A. E., De La Ossa, L., Martínez-Hernández, J., … Luján, R. (2020). Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21072459 chicago: Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, Ryuichi Shigemoto, Yugo Fukazawa, and Rafael Luján. “Density of GABAB Receptors Is Reduced in Granule Cells of the Hippocampus in a Mouse Model of Alzheimer’s Disease.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21072459. ieee: A. Martín-Belmonte et al., “Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease,” International journal of molecular sciences, vol. 21, no. 7. MDPI, 2020. ista: Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, Moreno-Martínez AE, De La Ossa L, Martínez-Hernández J, Buisson A, Shigemoto R, Fukazawa Y, Luján R. 2020. Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. International journal of molecular sciences. 21(7), 2459. mla: Martín-Belmonte, Alejandro, et al. “Density of GABAB Receptors Is Reduced in Granule Cells of the Hippocampus in a Mouse Model of Alzheimer’s Disease.” International Journal of Molecular Sciences, vol. 21, no. 7, 2459, MDPI, 2020, doi:10.3390/ijms21072459. short: A. Martín-Belmonte, C. Aguado, R. Alfaro-Ruíz, A.E. Moreno-Martínez, L. De La Ossa, J. Martínez-Hernández, A. Buisson, R. Shigemoto, Y. Fukazawa, R. Luján, International Journal of Molecular Sciences 21 (2020). date_created: 2020-04-19T22:00:55Z date_published: 2020-04-02T00:00:00Z date_updated: 2023-08-21T06:13:19Z day: '02' ddc: - '570' department: - _id: RySh doi: 10.3390/ijms21072459 external_id: isi: - '000535574200201' pmid: - '32252271' file: - access_level: open_access checksum: b9d2f1657d8c4a74b01a62b474d009b0 content_type: application/pdf creator: dernst date_created: 2020-04-20T11:43:18Z date_updated: 2020-07-14T12:48:01Z file_id: '7669' file_name: 2020_JournMolecSciences_Martin_Belmonte.pdf file_size: 2941197 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '7' language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: International journal of molecular sciences publication_identifier: eissn: - '14220067' publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer's disease 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2020' ... --- _id: '7665' abstract: - lang: eng text: Acute brain slice preparation is a powerful experimental model for investigating the characteristics of synaptic function in the brain. Although brain tissue is usually cut at ice-cold temperature (CT) to facilitate slicing and avoid neuronal damage, exposure to CT causes molecular and architectural changes of synapses. To address these issues, we investigated ultrastructural and electrophysiological features of synapses in mouse acute cerebellar slices prepared at ice-cold and physiological temperature (PT). In the slices prepared at CT, we found significant spine loss and reconstruction, synaptic vesicle rearrangement and decrease in synaptic proteins, all of which were not detected in slices prepared at PT. Consistent with these structural findings, slices prepared at PT showed higher release probability. Furthermore, preparation at PT allows electrophysiological recording immediately after slicing resulting in higher detectability of long-term depression (LTD) after motor learning compared with that at CT. These results indicate substantial advantages of the slice preparation at PT for investigating synaptic functions in different physiological conditions. article_number: '63' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Kohgaku full_name: Eguchi, Kohgaku id: 2B7846DC-F248-11E8-B48F-1D18A9856A87 last_name: Eguchi orcid: 0000-0002-6170-2546 - first_name: Philipp full_name: Velicky, Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 - first_name: Elena full_name: Hollergschwandtner, Elena id: 3C054040-F248-11E8-B48F-1D18A9856A87 last_name: Hollergschwandtner - first_name: Makoto full_name: Itakura, Makoto last_name: Itakura - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Eguchi K, Velicky P, Saeckl E, et al. Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. Frontiers in Cellular Neuroscience. 2020;14. doi:10.3389/fncel.2020.00063 apa: Eguchi, K., Velicky, P., Saeckl, E., Itakura, M., Fukazawa, Y., Danzl, J. G., & Shigemoto, R. (2020). Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. Frontiers in Cellular Neuroscience. Frontiers Media. https://doi.org/10.3389/fncel.2020.00063 chicago: Eguchi, Kohgaku, Philipp Velicky, Elena Saeckl, Makoto Itakura, Yugo Fukazawa, Johann G Danzl, and Ryuichi Shigemoto. “Advantages of Acute Brain Slices Prepared at Physiological Temperature in the Characterization of Synaptic Functions.” Frontiers in Cellular Neuroscience. Frontiers Media, 2020. https://doi.org/10.3389/fncel.2020.00063. ieee: K. Eguchi et al., “Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions,” Frontiers in Cellular Neuroscience, vol. 14. Frontiers Media, 2020. ista: Eguchi K, Velicky P, Saeckl E, Itakura M, Fukazawa Y, Danzl JG, Shigemoto R. 2020. Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. Frontiers in Cellular Neuroscience. 14, 63. mla: Eguchi, Kohgaku, et al. “Advantages of Acute Brain Slices Prepared at Physiological Temperature in the Characterization of Synaptic Functions.” Frontiers in Cellular Neuroscience, vol. 14, 63, Frontiers Media, 2020, doi:10.3389/fncel.2020.00063. short: K. Eguchi, P. Velicky, E. Saeckl, M. Itakura, Y. Fukazawa, J.G. Danzl, R. Shigemoto, Frontiers in Cellular Neuroscience 14 (2020). date_created: 2020-04-19T22:00:55Z date_published: 2020-03-19T00:00:00Z date_updated: 2023-08-21T06:12:48Z day: '19' ddc: - '570' department: - _id: JoDa - _id: RySh doi: 10.3389/fncel.2020.00063 ec_funded: 1 external_id: isi: - '000525582200001' file: - access_level: open_access checksum: 1c145123c6f8dc3e2e4bd5a66a1ad60e content_type: application/pdf creator: dernst date_created: 2020-04-20T10:59:49Z date_updated: 2020-07-14T12:48:01Z file_id: '7668' file_name: 2020_FrontiersCellularNeurosc_Eguchi.pdf file_size: 9227283 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 2659CC84-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '793482' name: 'Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission' - _id: 25CA28EA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694539' name: 'In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour' - _id: 265CB4D0-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03600 name: Optical control of synaptic function via adhesion molecules - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Frontiers in Cellular Neuroscience publication_identifier: issn: - '16625102' publication_status: published publisher: Frontiers Media quality_controlled: '1' scopus_import: '1' status: public title: Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2020' ... --- _id: '7663' abstract: - lang: eng text: Wood, as the most abundant carbon dioxide storing bioresource, is currently driven beyond its traditional use through creative innovations and nanotechnology. For many properties the micro- and nanostructure plays a crucial role and one key challenge is control and detection of chemical and physical processes in the confined microstructure and nanopores of the wooden cell wall. In this study, correlative Raman and atomic force microscopy show high potential for tracking in situ molecular rearrangement of wood polymers during compression. More water molecules (interpreted as wider cellulose microfibril distances) and disentangling of hemicellulose chains are detected in the opened cell wall regions, whereas an increase of lignin is revealed in the compressed areas. These results support a new more “loose” cell wall model based on flexible lignin nanodomains and advance our knowledge of the molecular reorganization during deformation of wood for optimized processing and utilization. article_processing_charge: No article_type: original author: - first_name: Martin full_name: Felhofer, Martin last_name: Felhofer - first_name: Peter full_name: Bock, Peter last_name: Bock - first_name: Adya full_name: Singh, Adya last_name: Singh - first_name: Batirtze full_name: Prats Mateu, Batirtze id: 299FE892-F248-11E8-B48F-1D18A9856A87 last_name: Prats Mateu - first_name: Ronald full_name: Zirbs, Ronald last_name: Zirbs - first_name: Notburga full_name: Gierlinger, Notburga last_name: Gierlinger citation: ama: Felhofer M, Bock P, Singh A, Prats Mateu B, Zirbs R, Gierlinger N. Wood deformation leads to rearrangement of molecules at the nanoscale. Nano Letters. 2020;20(4):2647-2653. doi:10.1021/acs.nanolett.0c00205 apa: Felhofer, M., Bock, P., Singh, A., Prats Mateu, B., Zirbs, R., & Gierlinger, N. (2020). Wood deformation leads to rearrangement of molecules at the nanoscale. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c00205 chicago: Felhofer, Martin, Peter Bock, Adya Singh, Batirtze Prats Mateu, Ronald Zirbs, and Notburga Gierlinger. “Wood Deformation Leads to Rearrangement of Molecules at the Nanoscale.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.0c00205. ieee: M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, and N. Gierlinger, “Wood deformation leads to rearrangement of molecules at the nanoscale,” Nano Letters, vol. 20, no. 4. American Chemical Society, pp. 2647–2653, 2020. ista: Felhofer M, Bock P, Singh A, Prats Mateu B, Zirbs R, Gierlinger N. 2020. Wood deformation leads to rearrangement of molecules at the nanoscale. Nano Letters. 20(4), 2647–2653. mla: Felhofer, Martin, et al. “Wood Deformation Leads to Rearrangement of Molecules at the Nanoscale.” Nano Letters, vol. 20, no. 4, American Chemical Society, 2020, pp. 2647–53, doi:10.1021/acs.nanolett.0c00205. short: M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, N. Gierlinger, Nano Letters 20 (2020) 2647–2653. date_created: 2020-04-19T22:00:54Z date_published: 2020-04-08T00:00:00Z date_updated: 2023-08-21T06:12:09Z day: '08' ddc: - '530' department: - _id: MaLo doi: 10.1021/acs.nanolett.0c00205 external_id: isi: - '000526413400055' pmid: - '32196350' file: - access_level: open_access checksum: fe46146a9c4c620592a1932a8599069e content_type: application/pdf creator: dernst date_created: 2020-04-20T10:43:36Z date_updated: 2020-07-14T12:48:01Z file_id: '7667' file_name: 2020_NanoLetters_Felhofer.pdf file_size: 7108014 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' intvolume: ' 20' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 2647-2653 pmid: 1 publication: Nano Letters publication_identifier: eissn: - '15306992' publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Wood deformation leads to rearrangement of molecules at the nanoscale 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 20 year: '2020' ... --- _id: '7666' abstract: - lang: eng text: Generalizing the decomposition of a connected planar graph into a tree and a dual tree, we prove a combinatorial analog of the classic Helmholtz–Hodge decomposition of a smooth vector field. Specifically, we show that for every polyhedral complex, K, and every dimension, p, there is a partition of the set of p-cells into a maximal p-tree, a maximal p-cotree, and a collection of p-cells whose cardinality is the p-th reduced Betti number of K. Given an ordering of the p-cells, this tri-partition is unique, and it can be computed by a matrix reduction algorithm that also constructs canonical bases of cycle and boundary groups. acknowledgement: This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through Grant No. I02979-N35 of the Austrian Science Fund (FWF). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Katharina full_name: Ölsböck, Katharina id: 4D4AA390-F248-11E8-B48F-1D18A9856A87 last_name: Ölsböck orcid: 0000-0002-4672-8297 citation: ama: Edelsbrunner H, Ölsböck K. Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. 2020;64:759-775. doi:10.1007/s00454-020-00188-x apa: Edelsbrunner, H., & Ölsböck, K. (2020). Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00188-x chicago: Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of an Ordered Complex.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00188-x. ieee: H. Edelsbrunner and K. Ölsböck, “Tri-partitions and bases of an ordered complex,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 759–775, 2020. ista: Edelsbrunner H, Ölsböck K. 2020. Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. 64, 759–775. mla: Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of an Ordered Complex.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 759–75, doi:10.1007/s00454-020-00188-x. short: H. Edelsbrunner, K. Ölsböck, Discrete and Computational Geometry 64 (2020) 759–775. date_created: 2020-04-19T22:00:56Z date_published: 2020-03-20T00:00:00Z date_updated: 2023-08-21T06:13:48Z day: '20' ddc: - '510' department: - _id: HeEd doi: 10.1007/s00454-020-00188-x ec_funded: 1 external_id: isi: - '000520918800001' file: - access_level: open_access checksum: f8cc96e497f00c38340b5dafe0cb91d7 content_type: application/pdf creator: dernst date_created: 2020-11-20T13:22:21Z date_updated: 2020-11-20T13:22:21Z file_id: '8786' file_name: 2020_DiscreteCompGeo_Edelsbrunner.pdf file_size: 701673 relation: main_file success: 1 file_date_updated: 2020-11-20T13:22:21Z has_accepted_license: '1' intvolume: ' 64' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 759-775 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: Discrete and Computational Geometry publication_identifier: eissn: - '14320444' issn: - '01795376' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Tri-partitions and bases of an ordered complex 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 64 year: '2020' ... --- _id: '7683' abstract: - lang: eng text: For any free oriented Borel–Moore homology theory A, we construct an associative product on the A-theory of the stack of Higgs torsion sheaves over a projective curve C. We show that the resulting algebra AHa0C admits a natural shuffle presentation, and prove it is faithful when A is replaced with usual Borel–Moore homology groups. We also introduce moduli spaces of stable triples, heavily inspired by Nakajima quiver varieties, whose A-theory admits an AHa0C-action. These triples can be interpreted as certain sheaves on PC(ωC⊕OC). In particular, we obtain an action of AHa0C on the cohomology of Hilbert schemes of points on T∗C. article_number: '30' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Sasha full_name: Minets, Sasha id: 3E7C5304-F248-11E8-B48F-1D18A9856A87 last_name: Minets orcid: 0000-0003-3883-1806 citation: ama: Minets S. Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. Selecta Mathematica, New Series. 2020;26(2). doi:10.1007/s00029-020-00553-x apa: Minets, S. (2020). Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. Selecta Mathematica, New Series. Springer Nature. https://doi.org/10.1007/s00029-020-00553-x chicago: Minets, Sasha. “Cohomological Hall Algebras for Higgs Torsion Sheaves, Moduli of Triples and Sheaves on Surfaces.” Selecta Mathematica, New Series. Springer Nature, 2020. https://doi.org/10.1007/s00029-020-00553-x. ieee: S. Minets, “Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces,” Selecta Mathematica, New Series, vol. 26, no. 2. Springer Nature, 2020. ista: Minets S. 2020. Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. Selecta Mathematica, New Series. 26(2), 30. mla: Minets, Sasha. “Cohomological Hall Algebras for Higgs Torsion Sheaves, Moduli of Triples and Sheaves on Surfaces.” Selecta Mathematica, New Series, vol. 26, no. 2, 30, Springer Nature, 2020, doi:10.1007/s00029-020-00553-x. short: S. Minets, Selecta Mathematica, New Series 26 (2020). date_created: 2020-04-26T22:00:44Z date_published: 2020-04-15T00:00:00Z date_updated: 2023-08-21T06:14:58Z day: '15' ddc: - '510' department: - _id: TaHa doi: 10.1007/s00029-020-00553-x external_id: arxiv: - '1801.01429' isi: - '000526036400001' file: - access_level: open_access checksum: 2368c4662629b4759295eb365323b2ad content_type: application/pdf creator: dernst date_created: 2020-04-28T10:57:58Z date_updated: 2020-07-14T12:48:02Z file_id: '7690' file_name: 2020_SelectaMathematica_Minets.pdf file_size: 792469 relation: main_file file_date_updated: 2020-07-14T12:48:02Z has_accepted_license: '1' intvolume: ' 26' isi: 1 issue: '2' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Selecta Mathematica, New Series publication_identifier: eissn: - '14209020' issn: - '10221824' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 26 year: '2020' ... --- _id: '7672' abstract: - lang: eng text: Large overpotentials upon discharge and charge of Li-O2 cells have motivated extensive research into heterogeneous solid electrocatalysts or non-carbon electrodes with the aim to improve rate capability, round-trip efficiency and cycle life. These features are equally governed by parasitic reactions, which are now recognized to be caused by the highly reactive singlet oxygen (1O2). However, the link between the presence of electrocatalysts and 1O2 formation in metal-O2 cells is unknown. Here, we show that, compared to pristine carbon black electrodes, a representative selection of electrocatalysts or non-carbon electrodes (noble metal, transition metal compounds) may both slightly reduce or severely increase the 1O2 formation. The individual reaction steps, where the surfaces impact the 1O2 yield are deciphered, showing that 1O2 yield from superoxide disproportionation as well as the decomposition of trace H2O2 are sensitive to catalysts. Transition metal compounds in general are prone to increase 1O2. acknowledgement: S.A.F. thanks the International Society of Electrochemistry for awarding the Tajima Prize 2019 “in recognition of outstanding re- searches on Li-Air batteries by the use of a range of in-situ elec- trochemical methods to achieve comprehensive understanding of the reactions taking place at the oxygen electrode”. This article is dedicated to the special issue of Electrochmica Acta associated with the awarding conference. S.A.F. is indebted to and the Austrian Federal Ministry of Science, Research and Economy and the Austrian Research Promotion Agency (grant No. 845364 ) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 636069). The authors thank J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH and G. Strohmeier for help with HPLC measurements, S. Eder for cyclic voltammetry measurements, and C. Slugovc for discussions and continuous support. We thank S. Borisov for access and advice with fluorescence measurements. We thank EL-Cell GmbH, Hamburg, Germany for providing the PAT-Cell-Press electrochemical cell. article_number: '137175' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Aleksej full_name: Samojlov, Aleksej last_name: Samojlov - first_name: David full_name: Schuster, David last_name: Schuster - first_name: Jürgen full_name: Kahr, Jürgen last_name: Kahr - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Samojlov A, Schuster D, Kahr J, Freunberger SA. Surface and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. 2020;362(12). doi:10.1016/j.electacta.2020.137175 apa: Samojlov, A., Schuster, D., Kahr, J., & Freunberger, S. A. (2020). Surface and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. Elsevier. https://doi.org/10.1016/j.electacta.2020.137175 chicago: Samojlov, Aleksej, David Schuster, Jürgen Kahr, and Stefan Alexander Freunberger. “Surface and Catalyst Driven Singlet Oxygen Formation in Li-O2 Cells.” Electrochimica Acta. Elsevier, 2020. https://doi.org/10.1016/j.electacta.2020.137175. ieee: A. Samojlov, D. Schuster, J. Kahr, and S. A. Freunberger, “Surface and catalyst driven singlet oxygen formation in Li-O2 cells,” Electrochimica Acta, vol. 362, no. 12. Elsevier, 2020. ista: Samojlov A, Schuster D, Kahr J, Freunberger SA. 2020. Surface and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. 362(12), 137175. mla: Samojlov, Aleksej, et al. “Surface and Catalyst Driven Singlet Oxygen Formation in Li-O2 Cells.” Electrochimica Acta, vol. 362, no. 12, 137175, Elsevier, 2020, doi:10.1016/j.electacta.2020.137175. short: A. Samojlov, D. Schuster, J. Kahr, S.A. Freunberger, Electrochimica Acta 362 (2020). date_created: 2020-04-20T19:29:31Z date_published: 2020-12-01T00:00:00Z date_updated: 2023-08-21T06:14:21Z day: '01' ddc: - '540' department: - _id: StFr doi: 10.1016/j.electacta.2020.137175 external_id: isi: - '000582869700060' file: - access_level: open_access checksum: 1ab1aa2024d431e2a089ea336bc08298 content_type: application/pdf creator: dernst date_created: 2020-10-01T13:20:45Z date_updated: 2020-10-01T13:20:45Z file_id: '8593' file_name: 2020_ElectrochimicaActa_Samojlov.pdf file_size: 1404030 relation: main_file success: 1 file_date_updated: 2020-10-01T13:20:45Z has_accepted_license: '1' intvolume: ' 362' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Electrochimica Acta publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Surface and catalyst driven singlet oxygen formation in Li-O2 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: 362 year: '2020' ... --- _id: '7684' article_processing_charge: No article_type: original author: - first_name: Igor full_name: Gridchyn, Igor id: 4B60654C-F248-11E8-B48F-1D18A9856A87 last_name: Gridchyn orcid: 0000-0002-1807-1929 - first_name: Philipp full_name: Schönenberger, Philipp id: 3B9D816C-F248-11E8-B48F-1D18A9856A87 last_name: Schönenberger - first_name: Joseph full_name: O'Neill, Joseph id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. Assembly-specific disruption of hippocampal replay leads to selective memory deficit. Neuron. 2020;106(2):291-300.e6. doi:10.1016/j.neuron.2020.01.021 apa: Gridchyn, I., Schönenberger, P., O’Neill, J., & Csicsvari, J. L. (2020). Assembly-specific disruption of hippocampal replay leads to selective memory deficit. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.01.021 chicago: Gridchyn, Igor, Philipp Schönenberger, Joseph O’Neill, and Jozsef L Csicsvari. “Assembly-Specific Disruption of Hippocampal Replay Leads to Selective Memory Deficit.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.01.021. ieee: I. Gridchyn, P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Assembly-specific disruption of hippocampal replay leads to selective memory deficit,” Neuron, vol. 106, no. 2. Elsevier, p. 291–300.e6, 2020. ista: Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. 2020. Assembly-specific disruption of hippocampal replay leads to selective memory deficit. Neuron. 106(2), 291–300.e6. mla: Gridchyn, Igor, et al. “Assembly-Specific Disruption of Hippocampal Replay Leads to Selective Memory Deficit.” Neuron, vol. 106, no. 2, Elsevier, 2020, p. 291–300.e6, doi:10.1016/j.neuron.2020.01.021. short: I. Gridchyn, P. Schönenberger, J. O’Neill, J.L. Csicsvari, Neuron 106 (2020) 291–300.e6. date_created: 2020-04-26T22:00:45Z date_published: 2020-04-22T00:00:00Z date_updated: 2023-08-21T06:15:31Z day: '22' department: - _id: JoCs doi: 10.1016/j.neuron.2020.01.021 ec_funded: 1 external_id: isi: - '000528268200013' pmid: - '32070475' intvolume: ' 106' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.neuron.2020.01.021 month: '04' oa: 1 oa_version: Published Version page: 291-300.e6 pmid: 1 project: - _id: 257A4776-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281511' name: Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex publication: Neuron publication_identifier: eissn: - '10974199' issn: - '08966273' publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/librarian-of-memory/ scopus_import: '1' status: public title: Assembly-specific disruption of hippocampal replay leads to selective memory deficit type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 106 year: '2020' ... --- _id: '7686' abstract: - lang: eng text: 'The agricultural green revolution spectacularly enhanced crop yield and lodging resistance with modified DELLA-mediated gibberellin signaling. However, this was achieved at the expense of reduced nitrogen-use efficiency (NUE). Recently, Wu et al. revealed novel gibberellin signaling that provides a blueprint for improving tillering and NUE in Green Revolution varieties (GRVs). ' article_processing_charge: No article_type: original author: - first_name: Huidan full_name: Xue, Huidan last_name: Xue - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: Guanghui full_name: Xiao, Guanghui last_name: Xiao citation: ama: 'Xue H, Zhang Y, Xiao G. Neo-gibberellin signaling: Guiding the next generation of the green revolution. Trends in Plant Science. 2020;25(6):520-522. doi:10.1016/j.tplants.2020.04.001' apa: 'Xue, H., Zhang, Y., & Xiao, G. (2020). Neo-gibberellin signaling: Guiding the next generation of the green revolution. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2020.04.001' chicago: 'Xue, Huidan, Yuzhou Zhang, and Guanghui Xiao. “Neo-Gibberellin Signaling: Guiding the next Generation of the Green Revolution.” Trends in Plant Science. Elsevier, 2020. https://doi.org/10.1016/j.tplants.2020.04.001.' ieee: 'H. Xue, Y. Zhang, and G. Xiao, “Neo-gibberellin signaling: Guiding the next generation of the green revolution,” Trends in Plant Science, vol. 25, no. 6. Elsevier, pp. 520–522, 2020.' ista: 'Xue H, Zhang Y, Xiao G. 2020. Neo-gibberellin signaling: Guiding the next generation of the green revolution. Trends in Plant Science. 25(6), 520–522.' mla: 'Xue, Huidan, et al. “Neo-Gibberellin Signaling: Guiding the next Generation of the Green Revolution.” Trends in Plant Science, vol. 25, no. 6, Elsevier, 2020, pp. 520–22, doi:10.1016/j.tplants.2020.04.001.' short: H. Xue, Y. Zhang, G. Xiao, Trends in Plant Science 25 (2020) 520–522. date_created: 2020-04-26T22:00:46Z date_published: 2020-06-01T00:00:00Z date_updated: 2023-08-21T06:16:01Z day: '01' department: - _id: JiFr doi: 10.1016/j.tplants.2020.04.001 external_id: isi: - '000533518400003' pmid: - '32407691' intvolume: ' 25' isi: 1 issue: '6' language: - iso: eng month: '06' oa_version: None page: 520-522 pmid: 1 publication: Trends in Plant Science publication_identifier: issn: - 1360-1385 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Neo-gibberellin signaling: Guiding the next generation of the green revolution' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 25 year: '2020' ... --- _id: '7788' abstract: - lang: eng text: Mutations in NDUFS4, which encodes an accessory subunit of mitochondrial oxidative phosphorylation (OXPHOS) complex I (CI), induce Leigh syndrome (LS). LS is a poorly understood pediatric disorder featuring brain-specific anomalies and early death. To study the LS pathomechanism, we here compared OXPHOS proteomes between various Ndufs4−/− mouse tissues. Ndufs4−/− animals displayed significantly lower CI subunit levels in brain/diaphragm relative to other tissues (liver/heart/kidney/skeletal muscle), whereas other OXPHOS subunit levels were not reduced. Absence of NDUFS4 induced near complete absence of the NDUFA12 accessory subunit, a 50% reduction in other CI subunit levels, and an increase in specific CI assembly factors. Among the latter, NDUFAF2 was most highly increased. Regarding NDUFS4, NDUFA12 and NDUFAF2, identical results were obtained in Ndufs4−/− mouse embryonic fibroblasts (MEFs) and NDUFS4-mutated LS patient cells. Ndufs4−/− MEFs contained active CI in situ but blue-native-PAGE highlighted that NDUFAF2 attached to an inactive CI subcomplex (CI-830) and inactive assemblies of higher MW. In NDUFA12-mutated LS patient cells, NDUFA12 absence did not reduce NDUFS4 levels but triggered NDUFAF2 association to active CI. BN-PAGE revealed no such association in LS patient fibroblasts with mutations in other CI subunit-encoding genes where NDUFAF2 was attached to CI-830 (NDUFS1, NDUFV1 mutation) or not detected (NDUFS7 mutation). Supported by enzymological and CI in silico structural analysis, we conclude that absence of NDUFS4 induces near complete absence of NDUFA12 but not vice versa, and that NDUFAF2 stabilizes active CI in Ndufs4−/− mice and LS patient cells, perhaps in concert with mitochondrial inner membrane lipids. article_number: '148213' article_processing_charge: No article_type: original author: - first_name: Merel J.W. full_name: Adjobo-Hermans, Merel J.W. last_name: Adjobo-Hermans - first_name: Ria full_name: De Haas, Ria last_name: De Haas - first_name: Peter H.G.M. full_name: Willems, Peter H.G.M. last_name: Willems - first_name: Aleksandra full_name: Wojtala, Aleksandra last_name: Wojtala - first_name: Sjenet E. full_name: Van Emst-De Vries, Sjenet E. last_name: Van Emst-De Vries - first_name: Jori A. full_name: Wagenaars, Jori A. last_name: Wagenaars - first_name: Mariel full_name: Van Den Brand, Mariel last_name: Van Den Brand - first_name: Richard J. full_name: Rodenburg, Richard J. last_name: Rodenburg - first_name: Jan A.M. full_name: Smeitink, Jan A.M. last_name: Smeitink - first_name: Leo G. full_name: Nijtmans, Leo G. last_name: Nijtmans - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Mariusz R. full_name: Wieckowski, Mariusz R. last_name: Wieckowski - first_name: Werner J.H. full_name: Koopman, Werner J.H. last_name: Koopman citation: ama: 'Adjobo-Hermans MJW, De Haas R, Willems PHGM, et al. NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. 2020;1861(8). doi:10.1016/j.bbabio.2020.148213' apa: 'Adjobo-Hermans, M. J. W., De Haas, R., Willems, P. H. G. M., Wojtala, A., Van Emst-De Vries, S. E., Wagenaars, J. A., … Koopman, W. J. H. (2020). NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2020.148213' chicago: 'Adjobo-Hermans, Merel J.W., Ria De Haas, Peter H.G.M. Willems, Aleksandra Wojtala, Sjenet E. Van Emst-De Vries, Jori A. Wagenaars, Mariel Van Den Brand, et al. “NDUFS4 Deletion Triggers Loss of NDUFA12 in Ndufs4−/− Mice and Leigh Syndrome Patients: A Stabilizing Role for NDUFAF2.” Biochimica et Biophysica Acta - Bioenergetics. Elsevier, 2020. https://doi.org/10.1016/j.bbabio.2020.148213.' ieee: 'M. J. W. Adjobo-Hermans et al., “NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2,” Biochimica et Biophysica Acta - Bioenergetics, vol. 1861, no. 8. Elsevier, 2020.' ista: 'Adjobo-Hermans MJW, De Haas R, Willems PHGM, Wojtala A, Van Emst-De Vries SE, Wagenaars JA, Van Den Brand M, Rodenburg RJ, Smeitink JAM, Nijtmans LG, Sazanov LA, Wieckowski MR, Koopman WJH. 2020. NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. 1861(8), 148213.' mla: 'Adjobo-Hermans, Merel J. W., et al. “NDUFS4 Deletion Triggers Loss of NDUFA12 in Ndufs4−/− Mice and Leigh Syndrome Patients: A Stabilizing Role for NDUFAF2.” Biochimica et Biophysica Acta - Bioenergetics, vol. 1861, no. 8, 148213, Elsevier, 2020, doi:10.1016/j.bbabio.2020.148213.' short: M.J.W. Adjobo-Hermans, R. De Haas, P.H.G.M. Willems, A. Wojtala, S.E. Van Emst-De Vries, J.A. Wagenaars, M. Van Den Brand, R.J. Rodenburg, J.A.M. Smeitink, L.G. Nijtmans, L.A. Sazanov, M.R. Wieckowski, W.J.H. Koopman, Biochimica et Biophysica Acta - Bioenergetics 1861 (2020). date_created: 2020-05-03T22:00:47Z date_published: 2020-08-01T00:00:00Z date_updated: 2023-08-21T06:19:18Z day: '01' ddc: - '570' department: - _id: LeSa doi: 10.1016/j.bbabio.2020.148213 external_id: isi: - '000540842000012' pmid: - '32335026' file: - access_level: open_access checksum: a9b152381307cf45fe266a8dc5640388 content_type: application/pdf creator: dernst date_created: 2020-05-04T12:25:19Z date_updated: 2020-07-14T12:48:03Z file_id: '7798' file_name: 2020_BBA_Adjobo_Hermans.pdf file_size: 3826792 relation: main_file file_date_updated: 2020-07-14T12:48:03Z has_accepted_license: '1' intvolume: ' 1861' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Biochimica et Biophysica Acta - Bioenergetics publication_identifier: eissn: - '18792650' issn: - '00052728' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2' 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 1861 year: '2020' ... --- _id: '7789' abstract: - lang: eng text: During embryonic and postnatal development, organs and tissues grow steadily to achieve their final size at the end of puberty. However, little is known about the cellular dynamics that mediate postnatal growth. By combining in vivo clonal lineage tracing, proliferation kinetics, single-cell transcriptomics, andin vitro micro-pattern experiments, we resolved the cellular dynamics taking place during postnatal skin epidermis expansion. Our data revealed that harmonious growth is engineered by a single population of developmental progenitors presenting a fixed fate imbalance of self-renewing divisions with an ever-decreasing proliferation rate. Single-cell RNA sequencing revealed that epidermal developmental progenitors form a more uniform population compared with adult stem and progenitor cells. Finally, we found that the spatial pattern of cell division orientation is dictated locally by the underlying collagen fiber orientation. Our results uncover a simple design principle of organ growth where progenitors and differentiated cells expand in harmony with their surrounding tissues. article_processing_charge: No article_type: original author: - first_name: Sophie full_name: Dekoninck, Sophie last_name: Dekoninck - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Alejandro full_name: Sifrim, Alejandro last_name: Sifrim - first_name: Yekaterina A. full_name: Miroshnikova, Yekaterina A. last_name: Miroshnikova - first_name: Mariaceleste full_name: Aragona, Mariaceleste last_name: Aragona - first_name: Milan full_name: Malfait, Milan last_name: Malfait - first_name: Souhir full_name: Gargouri, Souhir last_name: Gargouri - first_name: Charlotte full_name: De Neunheuser, Charlotte last_name: De Neunheuser - first_name: Christine full_name: Dubois, Christine last_name: Dubois - first_name: Thierry full_name: Voet, Thierry last_name: Voet - first_name: Sara A. full_name: Wickström, Sara A. last_name: Wickström - first_name: Benjamin D. full_name: Simons, Benjamin D. last_name: Simons - first_name: Cédric full_name: Blanpain, Cédric last_name: Blanpain citation: ama: Dekoninck S, Hannezo EB, Sifrim A, et al. Defining the design principles of skin epidermis postnatal growth. Cell. 2020;181(3):604-620.e22. doi:10.1016/j.cell.2020.03.015 apa: Dekoninck, S., Hannezo, E. B., Sifrim, A., Miroshnikova, Y. A., Aragona, M., Malfait, M., … Blanpain, C. (2020). Defining the design principles of skin epidermis postnatal growth. Cell. Elsevier. https://doi.org/10.1016/j.cell.2020.03.015 chicago: Dekoninck, Sophie, Edouard B Hannezo, Alejandro Sifrim, Yekaterina A. Miroshnikova, Mariaceleste Aragona, Milan Malfait, Souhir Gargouri, et al. “Defining the Design Principles of Skin Epidermis Postnatal Growth.” Cell. Elsevier, 2020. https://doi.org/10.1016/j.cell.2020.03.015. ieee: S. Dekoninck et al., “Defining the design principles of skin epidermis postnatal growth,” Cell, vol. 181, no. 3. Elsevier, p. 604–620.e22, 2020. ista: Dekoninck S, Hannezo EB, Sifrim A, Miroshnikova YA, Aragona M, Malfait M, Gargouri S, De Neunheuser C, Dubois C, Voet T, Wickström SA, Simons BD, Blanpain C. 2020. Defining the design principles of skin epidermis postnatal growth. Cell. 181(3), 604–620.e22. mla: Dekoninck, Sophie, et al. “Defining the Design Principles of Skin Epidermis Postnatal Growth.” Cell, vol. 181, no. 3, Elsevier, 2020, p. 604–620.e22, doi:10.1016/j.cell.2020.03.015. short: S. Dekoninck, E.B. Hannezo, A. Sifrim, Y.A. Miroshnikova, M. Aragona, M. Malfait, S. Gargouri, C. De Neunheuser, C. Dubois, T. Voet, S.A. Wickström, B.D. Simons, C. Blanpain, Cell 181 (2020) 604–620.e22. date_created: 2020-05-03T22:00:48Z date_published: 2020-04-30T00:00:00Z date_updated: 2023-08-21T06:17:43Z day: '30' ddc: - '570' department: - _id: EdHa doi: 10.1016/j.cell.2020.03.015 external_id: isi: - '000530708400016' pmid: - '32259486' file: - access_level: open_access checksum: e2114902f4e9d75a752e9efb5ae06011 content_type: application/pdf creator: dernst date_created: 2020-05-04T10:20:55Z date_updated: 2020-07-14T12:48:03Z file_id: '7795' file_name: 2020_Cell_Dekoninck.pdf file_size: 17992888 relation: main_file file_date_updated: 2020-07-14T12:48:03Z has_accepted_license: '1' intvolume: ' 181' isi: 1 issue: '3' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 604-620.e22 pmid: 1 publication: Cell publication_identifier: eissn: - '10974172' issn: - '00928674' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Defining the design principles of skin epidermis postnatal growth 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: 181 year: '2020' ...