--- _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: '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: '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' ... --- _id: '7793' abstract: - lang: eng text: Hormonal signalling in animals often involves direct transcription factor-hormone interactions that modulate gene expression. In contrast, plant hormone signalling is most commonly based on de-repression via the degradation of transcriptional repressors. Recently, we uncovered a non-canonical signalling mechanism for the plant hormone auxin whereby auxin directly affects the activity of the atypical auxin response factor (ARF), ETTIN towards target genes without the requirement for protein degradation. Here we show that ETTIN directly binds auxin, leading to dissociation from co-repressor proteins of the TOPLESS/TOPLESS-RELATED family followed by histone acetylation and induction of gene expression. This mechanism is reminiscent of animal hormone signalling as it affects the activity towards regulation of target genes and provides the first example of a DNA-bound hormone receptor in plants. Whilst auxin affects canonical ARFs indirectly by facilitating degradation of Aux/IAA repressors, direct ETTIN-auxin interactions allow switching between repressive and de-repressive chromatin states in an instantly-reversible manner. article_number: e51787 article_processing_charge: No article_type: original author: - first_name: André full_name: Kuhn, André last_name: Kuhn - first_name: Sigurd full_name: Ramans Harborough, Sigurd last_name: Ramans Harborough - first_name: Heather M full_name: McLaughlin, Heather M last_name: McLaughlin - first_name: Bhavani full_name: Natarajan, Bhavani last_name: Natarajan - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Stefan full_name: Kepinski, Stefan last_name: Kepinski - first_name: Lars full_name: Østergaard, Lars last_name: Østergaard citation: ama: Kuhn A, Ramans Harborough S, McLaughlin HM, et al. Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. eLife. 2020;9. doi:10.7554/elife.51787 apa: Kuhn, A., Ramans Harborough, S., McLaughlin, H. M., Natarajan, B., Verstraeten, I., Friml, J., … Østergaard, L. (2020). Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.51787 chicago: Kuhn, André, Sigurd Ramans Harborough, Heather M McLaughlin, Bhavani Natarajan, Inge Verstraeten, Jiří Friml, Stefan Kepinski, and Lars Østergaard. “Direct ETTIN-Auxin Interaction Controls Chromatin States in Gynoecium Development.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.51787. ieee: A. Kuhn et al., “Direct ETTIN-auxin interaction controls chromatin states in gynoecium development,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Kuhn A, Ramans Harborough S, McLaughlin HM, Natarajan B, Verstraeten I, Friml J, Kepinski S, Østergaard L. 2020. Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. eLife. 9, e51787. mla: Kuhn, André, et al. “Direct ETTIN-Auxin Interaction Controls Chromatin States in Gynoecium Development.” ELife, vol. 9, e51787, eLife Sciences Publications, 2020, doi:10.7554/elife.51787. short: A. Kuhn, S. Ramans Harborough, H.M. McLaughlin, B. Natarajan, I. Verstraeten, J. Friml, S. Kepinski, L. Østergaard, ELife 9 (2020). date_created: 2020-05-04T08:50:47Z date_published: 2020-04-08T00:00:00Z date_updated: 2023-08-21T06:17:12Z day: '08' ddc: - '580' department: - _id: JiFr doi: 10.7554/elife.51787 external_id: isi: - '000527752200001' pmid: - '32267233' file: - access_level: open_access checksum: 15d740de1a741fdcc6ec128c48eed017 content_type: application/pdf creator: dernst date_created: 2020-05-04T09:06:43Z date_updated: 2020-07-14T12:48:03Z file_id: '7794' file_name: 2020_eLife_Kuhn.pdf file_size: 2893082 relation: main_file file_date_updated: 2020-07-14T12:48:03Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '04' 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: Direct ETTIN-auxin interaction controls chromatin states in gynoecium development 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: '7790' abstract: - lang: eng text: "We prove a lower bound for the free energy (per unit volume) of the two-dimensional Bose gas in the thermodynamic limit. We show that the free energy at density \U0001D70C and inverse temperature \U0001D6FD differs from the one of the noninteracting system by the correction term \U0001D70B\U0001D70C\U0001D70C\U0001D6FD\U0001D6FD . Here, is the scattering length of the interaction potential, and \U0001D6FD is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. The result is valid in the dilute limit \U0001D70C and if \U0001D6FD\U0001D70C ." article_number: e20 article_processing_charge: No article_type: original author: - first_name: Andreas full_name: Deuchert, Andreas id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87 last_name: Deuchert orcid: 0000-0003-3146-6746 - first_name: Simon full_name: Mayer, Simon id: 30C4630A-F248-11E8-B48F-1D18A9856A87 last_name: Mayer - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. Forum of Mathematics, Sigma. 2020;8. doi:10.1017/fms.2020.17 apa: Deuchert, A., Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional dilute Bose gas. I. Lower bound. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2020.17 chicago: Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” Forum of Mathematics, Sigma. Cambridge University Press, 2020. https://doi.org/10.1017/fms.2020.17. ieee: A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. I. Lower bound,” Forum of Mathematics, Sigma, vol. 8. Cambridge University Press, 2020. ista: Deuchert A, Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. Forum of Mathematics, Sigma. 8, e20. mla: Deuchert, Andreas, et al. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” Forum of Mathematics, Sigma, vol. 8, e20, Cambridge University Press, 2020, doi:10.1017/fms.2020.17. short: A. Deuchert, S. Mayer, R. Seiringer, Forum of Mathematics, Sigma 8 (2020). date_created: 2020-05-03T22:00:48Z date_published: 2020-03-14T00:00:00Z date_updated: 2023-08-21T06:18:49Z day: '14' ddc: - '510' department: - _id: RoSe doi: 10.1017/fms.2020.17 ec_funded: 1 external_id: arxiv: - '1910.03372' isi: - '000527342000001' file: - access_level: open_access checksum: 8a64da99d107686997876d7cad8cfe1e content_type: application/pdf creator: dernst date_created: 2020-05-04T12:02:41Z date_updated: 2020-07-14T12:48:03Z file_id: '7797' file_name: 2020_ForumMath_Deuchert.pdf file_size: 692530 relation: main_file file_date_updated: 2020-07-14T12:48:03Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Forum of Mathematics, Sigma publication_identifier: eissn: - '20505094' publication_status: published publisher: Cambridge University Press quality_controlled: '1' related_material: record: - id: '7524' relation: earlier_version status: public scopus_import: '1' status: public title: The free energy of the two-dimensional dilute Bose gas. I. Lower bound 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: 8 year: '2020' ... --- _id: '7805' abstract: - lang: eng text: Plants as non-mobile organisms constantly integrate varying environmental signals to flexibly adapt their growth and development. Local fluctuations in water and nutrient availability, sudden changes in temperature or other abiotic and biotic stresses can trigger changes in the growth of plant organs. Multiple mutually interconnected hormonal signaling cascades act as essential endogenous translators of these exogenous signals in the adaptive responses of plants. Although the molecular backbones of hormone transduction pathways have been identified, the mechanisms underlying their interactions are largely unknown. Here, using genome wide transcriptome profiling we identify an auxin and cytokinin cross-talk component; SYNERGISTIC ON AUXIN AND CYTOKININ 1 (SYAC1), whose expression in roots is strictly dependent on both of these hormonal pathways. We show that SYAC1 is a regulator of secretory pathway, whose enhanced activity interferes with deposition of cell wall components and can fine-tune organ growth and sensitivity to soil pathogens. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: We thank Daria Siekhaus, Jiri Friml and Alexander Johnson for critical reading of the manuscript, Peter Pimpl, Christian Luschnig and Liwen Jiang for sharing published material, Lesia Rodriguez Solovey for technical assistance. This work was supported by the Austrian Science Fund (FWF01_I1774S) to A.H., K.Ö., and E.B., the German Research Foundation (DFG; He3424/6-1 to I.H.), by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734] (to N.C.), by the EU in the framework of the Marie-Curie FP7 COFUND People Programme through the award of an AgreenSkills+ fellowship No. 609398 (to J.S.) and by the Scientific Service Units of IST-Austria through resources provided by the Bioimaging Facility, the Life Science Facility. The IJPB benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007). article_number: '2170' article_processing_charge: No article_type: original author: - first_name: Andrej full_name: Hurny, Andrej id: 4DC4AF46-F248-11E8-B48F-1D18A9856A87 last_name: Hurny orcid: 0000-0003-3638-1426 - first_name: Candela full_name: Cuesta, Candela id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Nicola full_name: Cavallari, Nicola id: 457160E6-F248-11E8-B48F-1D18A9856A87 last_name: Cavallari - first_name: Krisztina full_name: Ötvös, Krisztina id: 29B901B0-F248-11E8-B48F-1D18A9856A87 last_name: Ötvös orcid: 0000-0002-5503-4983 - first_name: Jerome full_name: Duclercq, Jerome last_name: Duclercq - first_name: Ladislav full_name: Dokládal, Ladislav last_name: Dokládal - first_name: Juan C full_name: Montesinos López, Juan C id: 310A8E3E-F248-11E8-B48F-1D18A9856A87 last_name: Montesinos López orcid: 0000-0001-9179-6099 - first_name: Marçal full_name: Gallemi, Marçal id: 460C6802-F248-11E8-B48F-1D18A9856A87 last_name: Gallemi orcid: 0000-0003-4675-6893 - first_name: Hana full_name: Semeradova, Hana id: 42FE702E-F248-11E8-B48F-1D18A9856A87 last_name: Semeradova - first_name: Thomas full_name: Rauter, Thomas id: A0385D1A-9376-11EA-A47D-9862C5E3AB22 last_name: Rauter - first_name: Irene full_name: Stenzel, Irene last_name: Stenzel - first_name: Geert full_name: Persiau, Geert last_name: Persiau - first_name: Freia full_name: Benade, Freia last_name: Benade - first_name: Rishikesh full_name: Bhalearo, Rishikesh last_name: Bhalearo - first_name: Eva full_name: Sýkorová, Eva last_name: Sýkorová - first_name: András full_name: Gorzsás, András last_name: Gorzsás - first_name: Julien full_name: Sechet, Julien last_name: Sechet - first_name: Gregory full_name: Mouille, Gregory last_name: Mouille - first_name: Ingo full_name: Heilmann, Ingo last_name: Heilmann - first_name: Geert full_name: De Jaeger, Geert last_name: De Jaeger - first_name: Jutta full_name: Ludwig-Müller, Jutta last_name: Ludwig-Müller - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Hurny A, Cuesta C, Cavallari N, et al. Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. 2020;11. doi:10.1038/s41467-020-15895-5 apa: Hurny, A., Cuesta, C., Cavallari, N., Ötvös, K., Duclercq, J., Dokládal, L., … Benková, E. (2020). Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-15895-5 chicago: Hurny, Andrej, Candela Cuesta, Nicola Cavallari, Krisztina Ötvös, Jerome Duclercq, Ladislav Dokládal, Juan C Montesinos López, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-15895-5. ieee: A. Hurny et al., “Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Hurny A, Cuesta C, Cavallari N, Ötvös K, Duclercq J, Dokládal L, Montesinos López JC, Gallemi M, Semerádová H, Rauter T, Stenzel I, Persiau G, Benade F, Bhalearo R, Sýkorová E, Gorzsás A, Sechet J, Mouille G, Heilmann I, De Jaeger G, Ludwig-Müller J, Benková E. 2020. Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. 11, 2170. mla: Hurny, Andrej, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.” Nature Communications, vol. 11, 2170, Springer Nature, 2020, doi:10.1038/s41467-020-15895-5. short: A. Hurny, C. Cuesta, N. Cavallari, K. Ötvös, J. Duclercq, L. Dokládal, J.C. Montesinos López, M. Gallemi, H. Semerádová, T. Rauter, I. Stenzel, G. Persiau, F. Benade, R. Bhalearo, E. Sýkorová, A. Gorzsás, J. Sechet, G. Mouille, I. Heilmann, G. De Jaeger, J. Ludwig-Müller, E. Benková, Nature Communications 11 (2020). date_created: 2020-05-10T22:00:48Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-08-21T06:21:56Z day: '01' ddc: - '570' department: - _id: EvBe doi: 10.1038/s41467-020-15895-5 ec_funded: 1 external_id: isi: - '000531425900012' pmid: - '32358503' file: - access_level: open_access checksum: 2cba327c9e9416d75cb96be54b0fb441 content_type: application/pdf creator: dernst date_created: 2020-10-06T07:47:53Z date_updated: 2020-10-06T07:47:53Z file_id: '8614' file_name: 2020_NatureComm_Hurny.pdf file_size: 4743576 relation: main_file success: 1 file_date_updated: 2020-10-06T07:47:53Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2542D156-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 1774-B16 name: Hormone cross-talk drives nutrient dependent plant development - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance 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: '7882' abstract: - lang: eng text: A few-body cluster is a building block of a many-body system in a gas phase provided the temperature at most is of the order of the binding energy of this cluster. Here we illustrate this statement by considering a system of tubes filled with dipolar distinguishable particles. We calculate the partition function, which determines the probability to find a few-body cluster at a given temperature. The input for our calculations—the energies of few-body clusters—is estimated using the harmonic approximation. We first describe and demonstrate the validity of our numerical procedure. Then we discuss the results featuring melting of the zero-temperature many-body state into a gas of free particles and few-body clusters. For temperature higher than its binding energy threshold, the dimers overwhelmingly dominate the ensemble, where the remaining probability is in free particles. At very high temperatures free (harmonic oscillator trap-bound) particle dominance is eventually reached. This structure evolution appears both for one and two particles in each layer providing crucial information about the behavior of ultracold dipolar gases. The investigation addresses the transition region between few- and many-body physics as a function of temperature using a system of ten dipoles in five tubes. article_number: '484' article_processing_charge: No article_type: original author: - first_name: Jeremy R. full_name: Armstrong, Jeremy R. last_name: Armstrong - first_name: Aksel S. full_name: Jensen, Aksel S. last_name: Jensen - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 - first_name: Nikolaj T. full_name: Zinner, Nikolaj T. last_name: Zinner citation: ama: Armstrong JR, Jensen AS, Volosniev A, Zinner NT. Clusters in separated tubes of tilted dipoles. Mathematics. 2020;8(4). doi:10.3390/math8040484 apa: Armstrong, J. R., Jensen, A. S., Volosniev, A., & Zinner, N. T. (2020). Clusters in separated tubes of tilted dipoles. Mathematics. MDPI. https://doi.org/10.3390/math8040484 chicago: Armstrong, Jeremy R., Aksel S. Jensen, Artem Volosniev, and Nikolaj T. Zinner. “Clusters in Separated Tubes of Tilted Dipoles.” Mathematics. MDPI, 2020. https://doi.org/10.3390/math8040484. ieee: J. R. Armstrong, A. S. Jensen, A. Volosniev, and N. T. Zinner, “Clusters in separated tubes of tilted dipoles,” Mathematics, vol. 8, no. 4. MDPI, 2020. ista: Armstrong JR, Jensen AS, Volosniev A, Zinner NT. 2020. Clusters in separated tubes of tilted dipoles. Mathematics. 8(4), 484. mla: Armstrong, Jeremy R., et al. “Clusters in Separated Tubes of Tilted Dipoles.” Mathematics, vol. 8, no. 4, 484, MDPI, 2020, doi:10.3390/math8040484. short: J.R. Armstrong, A.S. Jensen, A. Volosniev, N.T. Zinner, Mathematics 8 (2020). date_created: 2020-05-24T22:01:00Z date_published: 2020-04-01T00:00:00Z date_updated: 2023-08-21T06:23:36Z day: '01' ddc: - '510' department: - _id: MiLe doi: 10.3390/math8040484 ec_funded: 1 external_id: isi: - '000531824100024' file: - access_level: open_access checksum: a05a7df724522203d079673a0d4de4bc content_type: application/pdf creator: dernst date_created: 2020-05-25T14:42:22Z date_updated: 2020-07-14T12:48:04Z file_id: '7887' file_name: 2020_Mathematics_Armstrong.pdf file_size: 990540 relation: main_file file_date_updated: 2020-07-14T12:48:04Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Mathematics publication_identifier: eissn: - '22277390' publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Clusters in separated tubes of tilted dipoles 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: 8 year: '2020' ... --- _id: '7804' abstract: - lang: eng text: Besides pro-inflammatory roles, the ancient cytokine interleukin-17 (IL-17) modulates neural circuit function. We investigate IL-17 signaling in neurons, and the extent it can alter organismal phenotypes. We combine immunoprecipitation and mass spectrometry to biochemically characterize endogenous signaling complexes that function downstream of IL-17 receptors in C. elegans neurons. We identify the paracaspase MALT-1 as a critical output of the pathway. MALT1 mediates signaling from many immune receptors in mammals, but was not previously implicated in IL-17 signaling or nervous system function. C. elegans MALT-1 forms a complex with homologs of Act1 and IRAK and appears to function both as a scaffold and a protease. MALT-1 is expressed broadly in the C. elegans nervous system, and neuronal IL-17–MALT-1 signaling regulates multiple phenotypes, including escape behavior, associative learning, immunity and longevity. Our data suggest MALT1 has an ancient role modulating neural circuit function downstream of IL-17 to remodel physiology and behavior. article_number: '2099' article_processing_charge: No article_type: original author: - first_name: Sean M. full_name: Flynn, Sean M. last_name: Flynn - first_name: Changchun full_name: Chen, Changchun last_name: Chen - first_name: Murat full_name: Artan, Murat id: C407B586-6052-11E9-B3AE-7006E6697425 last_name: Artan orcid: 0000-0001-8945-6992 - first_name: Stephen full_name: Barratt, Stephen last_name: Barratt - first_name: Alastair full_name: Crisp, Alastair last_name: Crisp - first_name: Geoffrey M. full_name: Nelson, Geoffrey M. last_name: Nelson - first_name: Sew Yeu full_name: Peak-Chew, Sew Yeu last_name: Peak-Chew - first_name: Farida full_name: Begum, Farida last_name: Begum - first_name: Mark full_name: Skehel, Mark last_name: Skehel - 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: Flynn SM, Chen C, Artan M, et al. MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. 2020;11. doi:10.1038/s41467-020-15872-y apa: Flynn, S. M., Chen, C., Artan, M., Barratt, S., Crisp, A., Nelson, G. M., … de Bono, M. (2020). MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-15872-y chicago: Flynn, Sean M., Changchun Chen, Murat Artan, Stephen Barratt, Alastair Crisp, Geoffrey M. Nelson, Sew Yeu Peak-Chew, Farida Begum, Mark Skehel, and Mario de Bono. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior, Immunity and Longevity.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-15872-y. ieee: S. M. Flynn et al., “MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Flynn SM, Chen C, Artan M, Barratt S, Crisp A, Nelson GM, Peak-Chew SY, Begum F, Skehel M, de Bono M. 2020. MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. 11, 2099. mla: Flynn, Sean M., et al. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior, Immunity and Longevity.” Nature Communications, vol. 11, 2099, Springer Nature, 2020, doi:10.1038/s41467-020-15872-y. short: S.M. Flynn, C. Chen, M. Artan, S. Barratt, A. Crisp, G.M. Nelson, S.Y. Peak-Chew, F. Begum, M. Skehel, M. de Bono, Nature Communications 11 (2020). date_created: 2020-05-10T22:00:47Z date_published: 2020-04-29T00:00:00Z date_updated: 2023-08-21T06:21:14Z day: '29' ddc: - '570' department: - _id: MaDe doi: 10.1038/s41467-020-15872-y external_id: isi: - '000531855500029' file: - access_level: open_access checksum: dce367abf2c1a1d15f58fe6f7de82893 content_type: application/pdf creator: dernst date_created: 2020-05-11T10:36:33Z date_updated: 2020-07-14T12:48:03Z file_id: '7817' file_name: 2020_NatureComm_Flynn.pdf file_size: 4609120 relation: main_file file_date_updated: 2020-07-14T12:48:03Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '04' 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: MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity 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: '7875' abstract: - lang: eng text: 'Cells navigating through complex tissues face a fundamental challenge: while multiple protrusions explore different paths, the cell needs to avoid entanglement. How a cell surveys and then corrects its own shape is poorly understood. Here, we demonstrate that spatially distinct microtubule dynamics regulate amoeboid cell migration by locally promoting the retraction of protrusions. In migrating dendritic cells, local microtubule depolymerization within protrusions remote from the microtubule organizing center triggers actomyosin contractility controlled by RhoA and its exchange factor Lfc. Depletion of Lfc leads to aberrant myosin localization, thereby causing two effects that rate-limit locomotion: (1) impaired cell edge coordination during path finding and (2) defective adhesion resolution. Compromised shape control is particularly hindering in geometrically complex microenvironments, where it leads to entanglement and ultimately fragmentation of the cell body. We thus demonstrate that microtubules can act as a proprioceptive device: they sense cell shape and control actomyosin retraction to sustain cellular coherence.' acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: PreCl acknowledgement: "The authors thank the Scientific Service Units (Life Sciences, Bioimaging, Preclinical) of the Institute of Science and Technology Austria for excellent support. This work was funded by the European Research Council (ERC StG 281556 and CoG 724373), two grants from the Austrian\r\nScience Fund (FWF; P29911 and DK Nanocell W1250-B20 to M. Sixt) and by the German Research Foundation (DFG SFB1032 project B09) to O. Thorn-Seshold and D. Trauner. J. Renkawitz was supported by ISTFELLOW funding from the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under the Research Executive Agency grant agreement (291734) and a European Molecular Biology Organization long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409), E. Kiermaier by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC 2151—390873048, and H. Hacker by the American Lebanese Syrian Associated ¨Charities. K.-D. Fischer was supported by the Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes graduate school funded by the Ministry of Economics, Science, and Digitisation of the State Saxony-Anhalt and by the European Funds for Social and Regional Development." article_number: e201907154 article_processing_charge: No article_type: original author: - first_name: Aglaja full_name: Kopf, Aglaja id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87 last_name: Kopf orcid: 0000-0002-2187-6656 - first_name: Jörg full_name: Renkawitz, Jörg id: 3F0587C8-F248-11E8-B48F-1D18A9856A87 last_name: Renkawitz orcid: 0000-0003-2856-3369 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Irute full_name: Girkontaite, Irute last_name: Girkontaite - first_name: Kerry full_name: Tedford, Kerry last_name: Tedford - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Oliver full_name: Thorn-Seshold, Oliver last_name: Thorn-Seshold - first_name: Dirk full_name: Trauner, Dirk id: E8F27F48-3EBA-11E9-92A1-B709E6697425 last_name: Trauner - first_name: Hans full_name: Häcker, Hans last_name: Häcker - first_name: Klaus Dieter full_name: Fischer, Klaus Dieter last_name: Fischer - first_name: Eva full_name: Kiermaier, Eva id: 3EB04B78-F248-11E8-B48F-1D18A9856A87 last_name: Kiermaier orcid: 0000-0001-6165-5738 - 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: Kopf A, Renkawitz J, Hauschild R, et al. Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. 2020;219(6). doi:10.1083/jcb.201907154 apa: Kopf, A., Renkawitz, J., Hauschild, R., Girkontaite, I., Tedford, K., Merrin, J., … Sixt, M. K. (2020). Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201907154 chicago: Kopf, Aglaja, Jörg Renkawitz, Robert Hauschild, Irute Girkontaite, Kerry Tedford, Jack Merrin, Oliver Thorn-Seshold, et al. “Microtubules Control Cellular Shape and Coherence in Amoeboid Migrating Cells.” The Journal of Cell Biology. Rockefeller University Press, 2020. https://doi.org/10.1083/jcb.201907154. ieee: A. Kopf et al., “Microtubules control cellular shape and coherence in amoeboid migrating cells,” The Journal of Cell Biology, vol. 219, no. 6. Rockefeller University Press, 2020. ista: Kopf A, Renkawitz J, Hauschild R, Girkontaite I, Tedford K, Merrin J, Thorn-Seshold O, Trauner D, Häcker H, Fischer KD, Kiermaier E, Sixt MK. 2020. Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. 219(6), e201907154. mla: Kopf, Aglaja, et al. “Microtubules Control Cellular Shape and Coherence in Amoeboid Migrating Cells.” The Journal of Cell Biology, vol. 219, no. 6, e201907154, Rockefeller University Press, 2020, doi:10.1083/jcb.201907154. short: A. Kopf, J. Renkawitz, R. Hauschild, I. Girkontaite, K. Tedford, J. Merrin, O. Thorn-Seshold, D. Trauner, H. Häcker, K.D. Fischer, E. Kiermaier, M.K. Sixt, The Journal of Cell Biology 219 (2020). date_created: 2020-05-24T22:00:56Z date_published: 2020-06-01T00:00:00Z date_updated: 2023-08-21T06:28:17Z day: '01' ddc: - '570' department: - _id: MiSi - _id: Bio - _id: NanoFab doi: 10.1083/jcb.201907154 ec_funded: 1 external_id: isi: - '000538141100020' pmid: - '32379884' file: - access_level: open_access checksum: cb0b9c77842ae1214caade7b77e4d82d content_type: application/pdf creator: dernst date_created: 2020-11-24T13:25:13Z date_updated: 2020-11-24T13:25:13Z file_id: '8801' file_name: 2020_JCellBiol_Kopf.pdf file_size: 7536712 relation: main_file success: 1 file_date_updated: 2020-11-24T13:25:13Z has_accepted_license: '1' intvolume: ' 219' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular navigation along spatial gradients - _id: 26018E70-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29911 name: Mechanical adaptation of lamellipodial actin - _id: 252C3B08-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W 1250-B20 name: Nano-Analytics of Cellular Systems - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25A48D24-B435-11E9-9278-68D0E5697425 grant_number: ALTF 1396-2014 name: Molecular and system level view of immune cell migration publication: The Journal of Cell Biology publication_identifier: eissn: - 1540-8140 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: Microtubules control cellular shape and coherence in amoeboid migrating cells 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: 219 year: '2020' ... --- _id: '7888' abstract: - lang: eng text: Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order. article_number: e55190 article_processing_charge: No article_type: original author: - first_name: Alexandra full_name: Schauer, Alexandra id: 30A536BA-F248-11E8-B48F-1D18A9856A87 last_name: Schauer orcid: 0000-0001-7659-9142 - first_name: Diana C full_name: Nunes Pinheiro, Diana C id: 2E839F16-F248-11E8-B48F-1D18A9856A87 last_name: Nunes Pinheiro orcid: 0000-0003-4333-7503 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 2020;9. doi:10.7554/elife.55190 apa: Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., & Heisenberg, C.-P. J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.55190 chicago: Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55190. ieee: A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish embryonic explants undergo genetically encoded self-assembly,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190. mla: Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife, vol. 9, e55190, eLife Sciences Publications, 2020, doi:10.7554/elife.55190. short: A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife 9 (2020). date_created: 2020-05-25T15:01:40Z date_published: 2020-04-06T00:00:00Z date_updated: 2023-08-21T06:25:49Z day: '06' ddc: - '570' department: - _id: CaHe - _id: Bio doi: 10.7554/elife.55190 ec_funded: 1 external_id: isi: - '000531544400001' pmid: - '32250246' file: - access_level: open_access checksum: f6aad884cf706846ae9357fcd728f8b5 content_type: application/pdf creator: dernst date_created: 2020-05-25T15:15:43Z date_updated: 2020-07-14T12:48:04Z file_id: '7890' file_name: 2020_eLife_Schauer.pdf file_size: 7744848 relation: main_file file_date_updated: 2020-07-14T12:48:04Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation - _id: 26B1E39C-B435-11E9-9278-68D0E5697425 grant_number: '25239' name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues' - _id: 26520D1E-B435-11E9-9278-68D0E5697425 grant_number: ALTF 850-2017 name: Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation - _id: 266BC5CE-B435-11E9-9278-68D0E5697425 grant_number: LT000429 name: Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' related_material: record: - id: '12891' relation: dissertation_contains status: public scopus_import: '1' status: public title: Zebrafish embryonic explants undergo genetically encoded self-assembly 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: '7877' abstract: - lang: eng text: The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations inNIPBLaccount for most cases ofthe rare developmental disorder Cornelia de Lange syndrome (CdLS). Here we report aMAU2 variant causing CdLS, a deletion of seven amino acids that impairs the interaction between MAU2 and the NIPBL N terminus.Investigating this interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable fornormal cohesin and NIPBL function in cells with a NIPBL early truncating mutation. Despite a predicted fataloutcome of an out-of-frame single nucleotide duplication inNIPBL, engineered in two different cell lines,alternative translation initiation yields a form of NIPBL missing N-terminal residues. This form cannot interactwith MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals that cohesin loading can occur independently of functional NIPBL/MAU2 complexes and highlights a novel mechanism protectiveagainst out-of-frame mutations that is potentially relevant for other genetic conditions. article_number: '107647' article_processing_charge: No article_type: original author: - first_name: Ilaria full_name: Parenti, Ilaria id: D93538B0-5B71-11E9-AC62-02EBE5697425 last_name: Parenti - first_name: Farah full_name: Diab, Farah last_name: Diab - first_name: Sara Ruiz full_name: Gil, Sara Ruiz last_name: Gil - first_name: Eskeatnaf full_name: Mulugeta, Eskeatnaf last_name: Mulugeta - first_name: Valentina full_name: Casa, Valentina last_name: Casa - first_name: Riccardo full_name: Berutti, Riccardo last_name: Berutti - first_name: Rutger W.W. full_name: Brouwer, Rutger W.W. last_name: Brouwer - first_name: Valerie full_name: Dupé, Valerie last_name: Dupé - first_name: Juliane full_name: Eckhold, Juliane last_name: Eckhold - first_name: Elisabeth full_name: Graf, Elisabeth last_name: Graf - first_name: Beatriz full_name: Puisac, Beatriz last_name: Puisac - first_name: Feliciano full_name: Ramos, Feliciano last_name: Ramos - first_name: Thomas full_name: Schwarzmayr, Thomas last_name: Schwarzmayr - first_name: Macarena Moronta full_name: Gines, Macarena Moronta last_name: Gines - first_name: Thomas full_name: Van Staveren, Thomas last_name: Van Staveren - first_name: Wilfred F.J. full_name: Van Ijcken, Wilfred F.J. last_name: Van Ijcken - first_name: Tim M. full_name: Strom, Tim M. last_name: Strom - first_name: Juan full_name: Pié, Juan last_name: Pié - first_name: Erwan full_name: Watrin, Erwan last_name: Watrin - first_name: Frank J. full_name: Kaiser, Frank J. last_name: Kaiser - first_name: Kerstin S. full_name: Wendt, Kerstin S. last_name: Wendt citation: ama: Parenti I, Diab F, Gil SR, et al. MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports. 2020;31(7). doi:10.1016/j.celrep.2020.107647 apa: Parenti, I., Diab, F., Gil, S. R., Mulugeta, E., Casa, V., Berutti, R., … Wendt, K. S. (2020). MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2020.107647 chicago: Parenti, Ilaria, Farah Diab, Sara Ruiz Gil, Eskeatnaf Mulugeta, Valentina Casa, Riccardo Berutti, Rutger W.W. Brouwer, et al. “MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome.” Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.107647. ieee: I. Parenti et al., “MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome,” Cell Reports, vol. 31, no. 7. Elsevier, 2020. ista: Parenti I, Diab F, Gil SR, Mulugeta E, Casa V, Berutti R, Brouwer RWW, Dupé V, Eckhold J, Graf E, Puisac B, Ramos F, Schwarzmayr T, Gines MM, Van Staveren T, Van Ijcken WFJ, Strom TM, Pié J, Watrin E, Kaiser FJ, Wendt KS. 2020. MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports. 31(7), 107647. mla: Parenti, Ilaria, et al. “MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome.” Cell Reports, vol. 31, no. 7, 107647, Elsevier, 2020, doi:10.1016/j.celrep.2020.107647. short: I. Parenti, F. Diab, S.R. Gil, E. Mulugeta, V. Casa, R. Berutti, R.W.W. Brouwer, V. Dupé, J. Eckhold, E. Graf, B. Puisac, F. Ramos, T. Schwarzmayr, M.M. Gines, T. Van Staveren, W.F.J. Van Ijcken, T.M. Strom, J. Pié, E. Watrin, F.J. Kaiser, K.S. Wendt, Cell Reports 31 (2020). date_created: 2020-05-24T22:00:57Z date_published: 2020-05-19T00:00:00Z date_updated: 2023-08-21T06:27:47Z day: '19' ddc: - '570' department: - _id: GaNo doi: 10.1016/j.celrep.2020.107647 external_id: isi: - '000535655200005' file: - access_level: open_access checksum: 64d8f7467731ee5c166b10b939b8310b content_type: application/pdf creator: dernst date_created: 2020-05-26T11:05:01Z date_updated: 2020-07-14T12:48:04Z file_id: '7892' file_name: 2020_CellReports_Parenti.pdf file_size: 4695682 relation: main_file file_date_updated: 2020-07-14T12:48:04Z has_accepted_license: '1' intvolume: ' 31' isi: 1 issue: '7' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Cell Reports publication_identifier: eissn: - '22111247' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome 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: 31 year: '2020' ... --- _id: '7878' abstract: - lang: eng text: Type 1 metabotropic glutamate receptors (mGluR1s) are key elements in neuronal signaling. While their function is well documented in slices, requirements for their activation in vivo are poorly understood. We examine this question in adult mice in vivo using 2-photon imaging of cerebellar molecular layer interneurons (MLIs) expressing GCaMP. In anesthetized mice, parallel fiber activation evokes beam-like Cai rises in postsynaptic MLIs which depend on co-activation of mGluR1s and ionotropic glutamate receptors (iGluRs). In awake mice, blocking mGluR1 decreases Cai rises associated with locomotion. In vitro studies and freeze-fracture electron microscopy show that the iGluR-mGluR1 interaction is synergistic and favored by close association of the two classes of receptors. Altogether our results suggest that mGluR1s, acting in synergy with iGluRs, potently contribute to processing cerebellar neuronal signaling under physiological conditions. article_number: e56839 article_processing_charge: No article_type: original author: - first_name: Jin full_name: Bao, Jin last_name: Bao - first_name: Michael full_name: Graupner, Michael last_name: Graupner - first_name: Guadalupe full_name: Astorga, Guadalupe last_name: Astorga - first_name: Thibault full_name: Collin, Thibault last_name: Collin - first_name: Abdelali full_name: Jalil, Abdelali last_name: Jalil - first_name: Dwi Wahyu full_name: Indriati, Dwi Wahyu last_name: Indriati - first_name: Jonathan full_name: Bradley, Jonathan last_name: Bradley - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Isabel full_name: Llano, Isabel last_name: Llano citation: ama: Bao J, Graupner M, Astorga G, et al. Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. eLife. 2020;9. doi:10.7554/eLife.56839 apa: Bao, J., Graupner, M., Astorga, G., Collin, T., Jalil, A., Indriati, D. W., … Llano, I. (2020). Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.56839 chicago: Bao, Jin, Michael Graupner, Guadalupe Astorga, Thibault Collin, Abdelali Jalil, Dwi Wahyu Indriati, Jonathan Bradley, Ryuichi Shigemoto, and Isabel Llano. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56839. ieee: J. Bao et al., “Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Bao J, Graupner M, Astorga G, Collin T, Jalil A, Indriati DW, Bradley J, Shigemoto R, Llano I. 2020. Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. eLife. 9, e56839. mla: Bao, Jin, et al. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” ELife, vol. 9, e56839, eLife Sciences Publications, 2020, doi:10.7554/eLife.56839. short: J. Bao, M. Graupner, G. Astorga, T. Collin, A. Jalil, D.W. Indriati, J. Bradley, R. Shigemoto, I. Llano, ELife 9 (2020). date_created: 2020-05-24T22:00:58Z date_published: 2020-05-13T00:00:00Z date_updated: 2023-08-21T06:26:50Z day: '13' ddc: - '570' department: - _id: RySh doi: 10.7554/eLife.56839 external_id: isi: - '000535191600001' pmid: - '32401196' file: - access_level: open_access checksum: 8ea99bb6660cc407dbdb00c173b01683 content_type: application/pdf creator: dernst date_created: 2020-05-26T09:34:54Z date_updated: 2020-07-14T12:48:04Z file_id: '7891' file_name: 2020_eLife_Bao.pdf file_size: 4832050 relation: main_file file_date_updated: 2020-07-14T12:48:04Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo 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: '7880' abstract: - lang: eng text: 'Following its evoked release, dopamine (DA) signaling is rapidly terminated by presynaptic reuptake, mediated by the cocaine-sensitive DA transporter (DAT). DAT surface availability is dynamically regulated by endocytic trafficking, and direct protein kinase C (PKC) activation acutely diminishes DAT surface expression by accelerating DAT internalization. Previous cell line studies demonstrated that PKC-stimulated DAT endocytosis requires both Ack1 inactivation, which releases a DAT-specific endocytic brake, and the neuronal GTPase, Rit2, which binds DAT. However, it is unknown whether Rit2 is required for PKC-stimulated DAT endocytosis in DAergic terminals or whether there are region- and/or sex-dependent differences in PKC-stimulated DAT trafficking. Moreover, the mechanisms by which Rit2 controls PKC-stimulated DAT endocytosis are unknown. Here, we directly examined these important questions. Ex vivo studies revealed that PKC activation acutely decreased DAT surface expression selectively in ventral, but not dorsal, striatum. AAV-mediated, conditional Rit2 knockdown in DAergic neurons impacted baseline DAT surface:intracellular distribution in DAergic terminals from female ventral, but not dorsal, striatum. Further, Rit2 was required for PKC-stimulated DAT internalization in both male and female ventral striatum. FRET and surface pulldown studies in cell lines revealed that PKC activation drives DAT-Rit2 surface dissociation and that the DAT N terminus is required for both PKC-mediated DAT-Rit2 dissociation and DAT internalization. Finally, we found that Rit2 and Ack1 independently converge on DAT to facilitate PKC-stimulated DAT endocytosis. Together, our data provide greater insight into mechanisms that mediate PKC-regulated DAT internalization and reveal unexpected region-specific differences in PKC-stimulated DAT trafficking in bona fide DAergic terminals. ' article_processing_charge: No article_type: original author: - first_name: Rita R. full_name: Fagan, Rita R. last_name: Fagan - first_name: Patrick J. full_name: Kearney, Patrick J. last_name: Kearney - first_name: Carolyn G. full_name: Sweeney, Carolyn G. last_name: Sweeney - first_name: Dino full_name: Luethi, Dino last_name: Luethi - first_name: Florianne E full_name: Schoot Uiterkamp, Florianne E id: 3526230C-F248-11E8-B48F-1D18A9856A87 last_name: Schoot Uiterkamp - first_name: Klaus full_name: Schicker, Klaus last_name: Schicker - first_name: Brian S. full_name: Alejandro, Brian S. last_name: Alejandro - first_name: Lauren C. full_name: O'Connor, Lauren C. last_name: O'Connor - first_name: Harald H. full_name: Sitte, Harald H. last_name: Sitte - first_name: Haley E. full_name: Melikian, Haley E. last_name: Melikian citation: ama: 'Fagan RR, Kearney PJ, Sweeney CG, et al. Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological Chemistry. 2020;295(16):5229-5244. doi:10.1074/jbc.RA120.012628' apa: 'Fagan, R. R., Kearney, P. J., Sweeney, C. G., Luethi, D., Schoot Uiterkamp, F. E., Schicker, K., … Melikian, H. E. (2020). Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological Chemistry. ASBMB Publications. https://doi.org/10.1074/jbc.RA120.012628' chicago: 'Fagan, Rita R., Patrick J. Kearney, Carolyn G. Sweeney, Dino Luethi, Florianne E Schoot Uiterkamp, Klaus Schicker, Brian S. Alejandro, Lauren C. O’Connor, Harald H. Sitte, and Haley E. Melikian. “Dopamine Transporter Trafficking and Rit2 GTPase: Mechanism of Action and in Vivo Impact.” Journal of Biological Chemistry. ASBMB Publications, 2020. https://doi.org/10.1074/jbc.RA120.012628.' ieee: 'R. R. Fagan et al., “Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact,” Journal of Biological Chemistry, vol. 295, no. 16. ASBMB Publications, pp. 5229–5244, 2020.' ista: 'Fagan RR, Kearney PJ, Sweeney CG, Luethi D, Schoot Uiterkamp FE, Schicker K, Alejandro BS, O’Connor LC, Sitte HH, Melikian HE. 2020. Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological Chemistry. 295(16), 5229–5244.' mla: 'Fagan, Rita R., et al. “Dopamine Transporter Trafficking and Rit2 GTPase: Mechanism of Action and in Vivo Impact.” Journal of Biological Chemistry, vol. 295, no. 16, ASBMB Publications, 2020, pp. 5229–44, doi:10.1074/jbc.RA120.012628.' short: R.R. Fagan, P.J. Kearney, C.G. Sweeney, D. Luethi, F.E. Schoot Uiterkamp, K. Schicker, B.S. Alejandro, L.C. O’Connor, H.H. Sitte, H.E. Melikian, Journal of Biological Chemistry 295 (2020) 5229–5244. date_created: 2020-05-24T22:00:59Z date_published: 2020-04-17T00:00:00Z date_updated: 2023-08-21T06:26:22Z day: '17' department: - _id: SaSi doi: 10.1074/jbc.RA120.012628 external_id: isi: - '000530288000006' pmid: - '32132171' intvolume: ' 295' isi: 1 issue: '16' language: - iso: eng main_file_link: - open_access: '1' url: https://escholarship.umassmed.edu/oapubs/4187 month: '04' oa: 1 oa_version: Submitted Version page: 5229-5244 pmid: 1 publication: Journal of Biological Chemistry publication_identifier: eissn: - 1083351X issn: - '00219258' publication_status: published publisher: ASBMB Publications quality_controlled: '1' scopus_import: '1' status: public title: 'Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 295 year: '2020' ... --- _id: '7876' abstract: - lang: eng text: 'In contrast to lymph nodes, the lymphoid regions of the spleen—the white pulp—are located deep within the organ, yielding the trafficking paths of T cells in the white pulp largely invisible. In an intravital microscopy tour de force reported in this issue of Immunity, Chauveau et al. show that T cells perform unidirectional, perivascular migration through the enigmatic marginal zone bridging channels. ' article_processing_charge: No article_type: original author: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann citation: ama: 'Sixt MK, Lämmermann T. T cells: Bridge-and-channel commute to the white pulp. Immunity. 2020;52(5):721-723. doi:10.1016/j.immuni.2020.04.020' apa: 'Sixt, M. K., & Lämmermann, T. (2020). T cells: Bridge-and-channel commute to the white pulp. Immunity. Elsevier. https://doi.org/10.1016/j.immuni.2020.04.020' chicago: 'Sixt, Michael K, and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute to the White Pulp.” Immunity. Elsevier, 2020. https://doi.org/10.1016/j.immuni.2020.04.020.' ieee: 'M. K. Sixt and T. Lämmermann, “T cells: Bridge-and-channel commute to the white pulp,” Immunity, vol. 52, no. 5. Elsevier, pp. 721–723, 2020.' ista: 'Sixt MK, Lämmermann T. 2020. T cells: Bridge-and-channel commute to the white pulp. Immunity. 52(5), 721–723.' mla: 'Sixt, Michael K., and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute to the White Pulp.” Immunity, vol. 52, no. 5, Elsevier, 2020, pp. 721–23, doi:10.1016/j.immuni.2020.04.020.' short: M.K. Sixt, T. Lämmermann, Immunity 52 (2020) 721–723. date_created: 2020-05-24T22:00:57Z date_published: 2020-05-19T00:00:00Z date_updated: 2023-08-21T06:27:18Z day: '19' department: - _id: MiSi doi: 10.1016/j.immuni.2020.04.020 external_id: isi: - '000535371100002' intvolume: ' 52' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://pure.mpg.de/pubman/item/item_3265599_2/component/file_3265620/Sixt%20et%20al..pdf month: '05' oa: 1 oa_version: Published Version page: 721-723 publication: Immunity publication_identifier: eissn: - '10974180' issn: - '10747613' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'T cells: Bridge-and-channel commute to the white pulp' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 52 year: '2020' ... --- _id: '7909' abstract: - lang: eng text: Cell migration entails networks and bundles of actin filaments termed lamellipodia and microspikes or filopodia, respectively, as well as focal adhesions, all of which recruit Ena/VASP family members hitherto thought to antagonize efficient cell motility. However, we find these proteins to act as positive regulators of migration in different murine cell lines. CRISPR/Cas9-mediated loss of Ena/VASP proteins reduced lamellipodial actin assembly and perturbed lamellipodial architecture, as evidenced by changed network geometry as well as reduction of filament length and number that was accompanied by abnormal Arp2/3 complex and heterodimeric capping protein accumulation. Loss of Ena/VASP function also abolished the formation of microspikes normally embedded in lamellipodia, but not of filopodia capable of emanating without lamellipodia. Ena/VASP-deficiency also impaired integrin-mediated adhesion accompanied by reduced traction forces exerted through these structures. Our data thus uncover novel Ena/VASP functions of these actin polymerases that are fully consistent with their promotion of cell migration. article_number: e55351 article_processing_charge: No article_type: original author: - first_name: Julia full_name: Damiano-Guercio, Julia last_name: Damiano-Guercio - first_name: Laëtitia full_name: Kurzawa, Laëtitia last_name: Kurzawa - first_name: Jan full_name: Müller, Jan id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D last_name: Müller - first_name: Georgi A full_name: Dimchev, Georgi A id: 38C393BE-F248-11E8-B48F-1D18A9856A87 last_name: Dimchev orcid: 0000-0001-8370-6161 - first_name: Matthias full_name: Schaks, Matthias last_name: Schaks - first_name: Maria full_name: Nemethova, Maria id: 34E27F1C-F248-11E8-B48F-1D18A9856A87 last_name: Nemethova - first_name: Thomas full_name: Pokrant, Thomas last_name: Pokrant - first_name: Stefan full_name: Brühmann, Stefan last_name: Brühmann - first_name: Joern full_name: Linkner, Joern last_name: Linkner - first_name: Laurent full_name: Blanchoin, Laurent last_name: Blanchoin - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner - first_name: Jan full_name: Faix, Jan last_name: Faix citation: ama: Damiano-Guercio J, Kurzawa L, Müller J, et al. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. eLife. 2020;9. doi:10.7554/eLife.55351 apa: Damiano-Guercio, J., Kurzawa, L., Müller, J., Dimchev, G. A., Schaks, M., Nemethova, M., … Faix, J. (2020). Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.55351 chicago: Damiano-Guercio, Julia, Laëtitia Kurzawa, Jan Müller, Georgi A Dimchev, Matthias Schaks, Maria Nemethova, Thomas Pokrant, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.55351. ieee: J. Damiano-Guercio et al., “Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Damiano-Guercio J, Kurzawa L, Müller J, Dimchev GA, Schaks M, Nemethova M, Pokrant T, Brühmann S, Linkner J, Blanchoin L, Sixt MK, Rottner K, Faix J. 2020. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. eLife. 9, e55351. mla: Damiano-Guercio, Julia, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” ELife, vol. 9, e55351, eLife Sciences Publications, 2020, doi:10.7554/eLife.55351. short: J. Damiano-Guercio, L. Kurzawa, J. Müller, G.A. Dimchev, M. Schaks, M. Nemethova, T. Pokrant, S. Brühmann, J. Linkner, L. Blanchoin, M.K. Sixt, K. Rottner, J. Faix, ELife 9 (2020). date_created: 2020-05-31T22:00:49Z date_published: 2020-05-11T00:00:00Z date_updated: 2023-08-21T06:32:25Z day: '11' ddc: - '570' department: - _id: MiSi doi: 10.7554/eLife.55351 ec_funded: 1 external_id: isi: - '000537208000001' file: - access_level: open_access checksum: d33bd4441b9a0195718ce1ba5d2c48a6 content_type: application/pdf creator: dernst date_created: 2020-06-02T10:35:37Z date_updated: 2020-07-14T12:48:05Z file_id: '7914' file_name: 2020_eLife_Damiano_Guercio.pdf file_size: 10535713 relation: main_file file_date_updated: 2020-07-14T12:48:05Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular navigation along spatial gradients publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion 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: '7908' abstract: - lang: eng text: Volatile anesthetics are widely used for surgery, but neuronal mechanisms of anesthesia remain unidentified. At the calyx of Held in brainstem slices from rats of either sex, isoflurane at clinical doses attenuated EPSCs by decreasing the release probability and the number of readily releasable vesicles. In presynaptic recordings of Ca2+ currents and exocytic capacitance changes, isoflurane attenuated exocytosis by inhibiting Ca2+ currents evoked by a short presynaptic depolarization, whereas it inhibited exocytosis evoked by a prolonged depolarization via directly blocking exocytic machinery downstream of Ca2+ influx. Since the length of presynaptic depolarization can simulate the frequency of synaptic inputs, isoflurane anesthesia is likely mediated by distinct dual mechanisms, depending on input frequencies. In simultaneous presynaptic and postsynaptic action potential recordings, isoflurane impaired the fidelity of repetitive spike transmission, more strongly at higher frequencies. Furthermore, in the cerebrum of adult mice, isoflurane inhibited monosynaptic corticocortical spike transmission, preferentially at a higher frequency. We conclude that dual presynaptic mechanisms operate for the anesthetic action of isoflurane, of which direct inhibition of exocytic machinery plays a low-pass filtering role in spike transmission at central excitatory synapses. article_processing_charge: No article_type: original author: - first_name: Han Ying full_name: Wang, Han Ying last_name: Wang - first_name: Kohgaku full_name: Eguchi, Kohgaku id: 2B7846DC-F248-11E8-B48F-1D18A9856A87 last_name: Eguchi orcid: 0000-0002-6170-2546 - first_name: Takayuki full_name: Yamashita, Takayuki last_name: Yamashita - first_name: Tomoyuki full_name: Takahashi, Tomoyuki last_name: Takahashi citation: ama: Wang HY, Eguchi K, Yamashita T, Takahashi T. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. 2020;40(21):4103-4115. doi:10.1523/JNEUROSCI.2946-19.2020 apa: Wang, H. Y., Eguchi, K., Yamashita, T., & Takahashi, T. (2020). Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2946-19.2020 chicago: Wang, Han Ying, Kohgaku Eguchi, Takayuki Yamashita, and Tomoyuki Takahashi. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.2946-19.2020. ieee: H. Y. Wang, K. Eguchi, T. Yamashita, and T. Takahashi, “Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms,” Journal of Neuroscience, vol. 40, no. 21. Society for Neuroscience, pp. 4103–4115, 2020. ista: Wang HY, Eguchi K, Yamashita T, Takahashi T. 2020. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. 40(21), 4103–4115. mla: Wang, Han Ying, et al. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” Journal of Neuroscience, vol. 40, no. 21, Society for Neuroscience, 2020, pp. 4103–15, doi:10.1523/JNEUROSCI.2946-19.2020. short: H.Y. Wang, K. Eguchi, T. Yamashita, T. Takahashi, Journal of Neuroscience 40 (2020) 4103–4115. date_created: 2020-05-31T22:00:48Z date_published: 2020-05-20T00:00:00Z date_updated: 2023-08-21T06:31:25Z day: '20' ddc: - '570' department: - _id: RySh doi: 10.1523/JNEUROSCI.2946-19.2020 external_id: isi: - '000535694700004' file: - access_level: open_access checksum: 6571607ea9036154b67cc78e848a7f7d content_type: application/pdf creator: dernst date_created: 2020-06-02T09:12:16Z date_updated: 2020-07-14T12:48:05Z file_id: '7912' file_name: 2020_JourNeuroscience_Wang.pdf file_size: 3817360 relation: main_file file_date_updated: 2020-07-14T12:48:05Z has_accepted_license: '1' intvolume: ' 40' isi: 1 issue: '21' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 4103-4115 publication: Journal of Neuroscience publication_identifier: eissn: - '15292401' publication_status: published publisher: Society for Neuroscience quality_controlled: '1' scopus_import: '1' status: public title: Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms 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: 40 year: '2020' ... --- _id: '7931' abstract: - lang: eng text: In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data. article_number: '8635' article_processing_charge: No article_type: original author: - first_name: Leonid A. full_name: Uroshlev, Leonid A. last_name: Uroshlev - first_name: Eldar T. full_name: Abdullaev, Eldar T. last_name: Abdullaev - first_name: Iren R. full_name: Umarova, Iren R. last_name: Umarova - first_name: Irina A. full_name: Il’Icheva, Irina A. last_name: Il’Icheva - first_name: Larisa A. full_name: Panchenko, Larisa A. last_name: Panchenko - first_name: Robert V. full_name: Polozov, Robert V. last_name: Polozov - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Yury D. full_name: Nechipurenko, Yury D. last_name: Nechipurenko - first_name: Sergei L. full_name: Grokhovsky, Sergei L. last_name: Grokhovsky citation: ama: Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 2020;10. doi:10.1038/s41598-020-65406-1 apa: Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-65406-1 chicago: Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva, Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko, and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-65406-1. ieee: L. A. Uroshlev et al., “A method for identification of the methylation level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer Nature, 2020. ista: Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 10, 8635. mla: Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635, Springer Nature, 2020, doi:10.1038/s41598-020-65406-1. short: L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko, R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports 10 (2020). date_created: 2020-06-07T22:00:51Z date_published: 2020-05-25T00:00:00Z date_updated: 2023-08-21T07:00:17Z day: '25' ddc: - '570' department: - _id: FyKo doi: 10.1038/s41598-020-65406-1 external_id: isi: - '000560774200007' file: - access_level: open_access checksum: 099e51611a5b7ca04244d03b2faddf33 content_type: application/pdf creator: dernst date_created: 2020-06-08T06:27:32Z date_updated: 2020-07-14T12:48:05Z file_id: '7947' file_name: 2020_ScientificReports_Uroshlev.pdf file_size: 1001724 relation: main_file file_date_updated: 2020-07-14T12:48:05Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '05' 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: A method for identification of the methylation level of CpG islands from NGS data 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: '7933' abstract: - lang: eng text: We study a mobile quantum impurity, possessing internal rotational degrees of freedom, confined to a ring in the presence of a many-particle bosonic bath. By considering the recently introduced rotating polaron problem, we define the Hamiltonian and examine the energy spectrum. The weak-coupling regime is studied by means of a variational ansatz in the truncated Fock space. The corresponding spectrum indicates that there emerges a coupling between the internal and orbital angular momenta of the impurity as a consequence of the phonon exchange. We interpret the coupling as a phonon-mediated spin-orbit coupling and quantify it by using a correlation function between the internal and the orbital angular momentum operators. The strong-coupling regime is investigated within the Pekar approach, and it is shown that the correlation function of the ground state shows a kink at a critical coupling, that is explained by a sharp transition from the noninteracting state to the states that exhibit strong interaction with the surroundings. The results might find applications in such fields as spintronics or topological insulators where spin-orbit coupling is of crucial importance. article_number: '184104 ' article_processing_charge: No article_type: original author: - first_name: Mikhail full_name: Maslov, Mikhail id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87 last_name: Maslov orcid: 0000-0003-4074-2570 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 citation: ama: Maslov M, Lemeshko M, Yakaboylu E. Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. 2020;101(18). doi:10.1103/PhysRevB.101.184104 apa: Maslov, M., Lemeshko, M., & Yakaboylu, E. (2020). Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.101.184104 chicago: Maslov, Mikhail, Mikhail Lemeshko, and Enderalp Yakaboylu. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.101.184104. ieee: M. Maslov, M. Lemeshko, and E. Yakaboylu, “Synthetic spin-orbit coupling mediated by a bosonic environment,” Physical Review B, vol. 101, no. 18. American Physical Society, 2020. ista: Maslov M, Lemeshko M, Yakaboylu E. 2020. Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. 101(18), 184104. mla: Maslov, Mikhail, et al. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” Physical Review B, vol. 101, no. 18, 184104, American Physical Society, 2020, doi:10.1103/PhysRevB.101.184104. short: M. Maslov, M. Lemeshko, E. Yakaboylu, Physical Review B 101 (2020). date_created: 2020-06-07T22:00:52Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-08-21T07:05:15Z day: '01' department: - _id: MiLe doi: 10.1103/PhysRevB.101.184104 ec_funded: 1 external_id: arxiv: - '1912.03092' isi: - '000530754700003' intvolume: ' 101' isi: 1 issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.03092 month: '05' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication: Physical Review B publication_identifier: eissn: - '24699969' issn: - '24699950' publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Synthetic spin-orbit coupling mediated by a bosonic environment type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 101 year: '2020' ... --- _id: '7942' abstract: - lang: eng text: An understanding of the missing antinodal electronic excitations in the pseudogap state is essential for uncovering the physics of the underdoped cuprate high-temperature superconductors1,2,3,4,5,6. The majority of high-temperature experiments performed thus far, however, have been unable to discern whether the antinodal states are rendered unobservable due to their damping or whether they vanish due to their gapping7,8,9,10,11,12,13,14,15,16,17,18. Here, we distinguish between these two scenarios by using quantum oscillations to examine whether the small Fermi surface pocket, found to occupy only 2% of the Brillouin zone in the underdoped cuprates19,20,21,22,23,24, exists in isolation against a majority of completely gapped density of states spanning the antinodes, or whether it is thermodynamically coupled to a background of ungapped antinodal states. We find that quantum oscillations associated with the small Fermi surface pocket exhibit a signature sawtooth waveform characteristic of an isolated two-dimensional Fermi surface pocket25,26,27,28,29,30,31,32. This finding reveals that the antinodal states are destroyed by a hard gap that extends over the majority of the Brillouin zone, placing strong constraints on a drastic underlying origin of quasiparticle disappearance over almost the entire Brillouin zone in the pseudogap regime7,8,9,10,11,12,13,14,15,16,17,18. acknowledgement: M.H., Y.-T.H. and S.E.S. acknowledge support from the Royal Society, the Winton Programme for the Physics of Sustainability, EPSRC (studentship, grant no. EP/P024947/1 and EPSRC Strategic Equipment grant no. EP/M000524/1) and the European Research Council (grant no. 772891). S.E.S. acknowledges support from the Leverhulme Trust by way of the award of a Philip Leverhulme Prize. H.Z., J.W. and Z.Z. acknowledge support from the National Key Research and Development Program of China (grant no. 2016YFA0401704). A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by the National Science Foundation Cooperative Agreement no. DMR-1644779, the state of Florida and the US Department of Energy. Work performed by M.K.C., R.D.M. and N.H. was supported by the US DOE BES ‘Science of 100 T’ programme. article_processing_charge: No article_type: letter_note author: - first_name: Máté full_name: Hartstein, Máté last_name: Hartstein - first_name: Yu Te full_name: Hsu, Yu Te last_name: Hsu - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Juan full_name: Porras, Juan last_name: Porras - first_name: Toshinao full_name: Loew, Toshinao last_name: Loew - first_name: Matthieu Le full_name: Tacon, Matthieu Le last_name: Tacon - first_name: Huakun full_name: Zuo, Huakun last_name: Zuo - first_name: Jinhua full_name: Wang, Jinhua last_name: Wang - first_name: Zengwei full_name: Zhu, Zengwei last_name: Zhu - first_name: Mun K. full_name: Chan, Mun K. last_name: Chan - first_name: Ross D. full_name: Mcdonald, Ross D. last_name: Mcdonald - first_name: Gilbert G. full_name: Lonzarich, Gilbert G. last_name: Lonzarich - first_name: Bernhard full_name: Keimer, Bernhard last_name: Keimer - first_name: Suchitra E. full_name: Sebastian, Suchitra E. last_name: Sebastian - first_name: Neil full_name: Harrison, Neil last_name: Harrison citation: ama: Hartstein M, Hsu YT, Modic KA, et al. Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. Nature Physics. 2020;16:841-847. doi:10.1038/s41567-020-0910-0 apa: Hartstein, M., Hsu, Y. T., Modic, K. A., Porras, J., Loew, T., Tacon, M. L., … Harrison, N. (2020). Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-020-0910-0 chicago: Hartstein, Máté, Yu Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Nature Physics. Springer Nature, 2020. https://doi.org/10.1038/s41567-020-0910-0. ieee: M. Hartstein et al., “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors,” Nature Physics, vol. 16. Springer Nature, pp. 841–847, 2020. ista: Hartstein M, Hsu YT, Modic KA, Porras J, Loew T, Tacon ML, Zuo H, Wang J, Zhu Z, Chan MK, Mcdonald RD, Lonzarich GG, Keimer B, Sebastian SE, Harrison N. 2020. Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. Nature Physics. 16, 841–847. mla: Hartstein, Máté, et al. “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Nature Physics, vol. 16, Springer Nature, 2020, pp. 841–47, doi:10.1038/s41567-020-0910-0. short: M. Hartstein, Y.T. Hsu, K.A. Modic, J. Porras, T. Loew, M.L. Tacon, H. Zuo, J. Wang, Z. Zhu, M.K. Chan, R.D. Mcdonald, G.G. Lonzarich, B. Keimer, S.E. Sebastian, N. Harrison, Nature Physics 16 (2020) 841–847. date_created: 2020-06-07T22:00:56Z date_published: 2020-08-01T00:00:00Z date_updated: 2023-08-21T07:06:49Z day: '01' department: - _id: KiMo doi: 10.1038/s41567-020-0910-0 external_id: arxiv: - '2005.14123' isi: - '000535464400005' intvolume: ' 16' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2005.14123 month: '08' oa: 1 oa_version: Preprint page: 841-847 publication: Nature Physics publication_identifier: eissn: - '17452481' issn: - '17452473' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '9708' relation: research_data status: public scopus_import: '1' status: public title: Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2020' ... --- _id: '7948' abstract: - lang: eng text: In agricultural systems, nitrate is the main source of nitrogen available for plants. Besides its role as a nutrient, nitrate has been shown to act as a signal molecule for plant growth, development and stress responses. In Arabidopsis, the NRT1.1 nitrate transceptor represses lateral root (LR) development at low nitrate availability by promoting auxin basipetal transport out of the LR primordia (LRPs). In addition, our present study shows that NRT1.1 acts as a negative regulator of the TAR2 auxin biosynthetic gene expression in the root stele. This is expected to repress local auxin biosynthesis and thus to reduce acropetal auxin supply to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin influx carrier, thus preventing cell wall remodeling required for overlying tissues separation during LRP emergence. Both NRT1.1-mediated repression of TAR2 and LAX3 are suppressed at high nitrate availability, resulting in the nitrate induction of TAR2 and LAX3 expression that is required for optimal stimulation of LR development by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately controls several crucial auxin-associated processes required for LRP development, and as a consequence that NRT1.1 plays a much more integrated role than previously anticipated in regulating the nitrate response of root system architecture. article_processing_charge: No article_type: original author: - first_name: A full_name: Maghiaoui, A last_name: Maghiaoui - first_name: E full_name: Bouguyon, E last_name: Bouguyon - first_name: Candela full_name: Cuesta, Candela id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: F full_name: Perrine-Walker, F last_name: Perrine-Walker - first_name: C full_name: Alcon, C last_name: Alcon - first_name: G full_name: Krouk, G last_name: Krouk - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: P full_name: Nacry, P last_name: Nacry - first_name: A full_name: Gojon, A last_name: Gojon - first_name: L full_name: Bach, L last_name: Bach citation: ama: Maghiaoui A, Bouguyon E, Cuesta C, et al. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany. 2020;71(15):4480-4494. doi:10.1093/jxb/eraa242 apa: Maghiaoui, A., Bouguyon, E., Cuesta, C., Perrine-Walker, F., Alcon, C., Krouk, G., … Bach, L. (2020). The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/eraa242 chicago: Maghiaoui, A, E Bouguyon, Candela Cuesta, F Perrine-Walker, C Alcon, G Krouk, Eva Benková, P Nacry, A Gojon, and L Bach. “The Arabidopsis NRT1.1 Transceptor Coordinately Controls Auxin Biosynthesis and Transport to Regulate Root Branching in Response to Nitrate.” Journal of Experimental Botany. Oxford University Press, 2020. https://doi.org/10.1093/jxb/eraa242. ieee: A. Maghiaoui et al., “The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate,” Journal of Experimental Botany, vol. 71, no. 15. Oxford University Press, pp. 4480–4494, 2020. ista: Maghiaoui A, Bouguyon E, Cuesta C, Perrine-Walker F, Alcon C, Krouk G, Benková E, Nacry P, Gojon A, Bach L. 2020. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany. 71(15), 4480–4494. mla: Maghiaoui, A., et al. “The Arabidopsis NRT1.1 Transceptor Coordinately Controls Auxin Biosynthesis and Transport to Regulate Root Branching in Response to Nitrate.” Journal of Experimental Botany, vol. 71, no. 15, Oxford University Press, 2020, pp. 4480–94, doi:10.1093/jxb/eraa242. short: A. Maghiaoui, E. Bouguyon, C. Cuesta, F. Perrine-Walker, C. Alcon, G. Krouk, E. Benková, P. Nacry, A. Gojon, L. Bach, Journal of Experimental Botany 71 (2020) 4480–4494. date_created: 2020-06-08T10:10:28Z date_published: 2020-07-25T00:00:00Z date_updated: 2023-08-21T07:07:30Z day: '25' department: - _id: EvBe doi: 10.1093/jxb/eraa242 external_id: isi: - '000553127600013' pmid: - '32428238' intvolume: ' 71' isi: 1 issue: '15' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.inrae.fr/hal-02619371 month: '07' oa: 1 oa_version: Submitted Version page: 4480-4494 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: The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 71 year: '2020' ... --- _id: '7940' abstract: - lang: eng text: We prove that the Yangian associated to an untwisted symmetric affine Kac–Moody Lie algebra is isomorphic to the Drinfeld double of a shuffle algebra. The latter is constructed in [YZ14] as an algebraic formalism of cohomological Hall algebras. As a consequence, we obtain the Poincare–Birkhoff–Witt (PBW) theorem for this class of affine Yangians. Another independent proof of the PBW theorem is given recently by Guay, Regelskis, and Wendlandt [GRW18]. acknowledgement: Gufang Zhao is affiliated to IST Austria, Hausel group until July of 2018. Supported by the Advanced Grant Arithmetic and Physics of Higgs moduli spaces No. 320593 of the European Research Council. article_processing_charge: No article_type: original author: - first_name: Yaping full_name: Yang, Yaping id: 360D8648-F248-11E8-B48F-1D18A9856A87 last_name: Yang - first_name: Gufang full_name: Zhao, Gufang id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87 last_name: Zhao citation: ama: Yang Y, Zhao G. The PBW theorem for affine Yangians. Transformation Groups. 2020;25:1371-1385. doi:10.1007/s00031-020-09572-6 apa: Yang, Y., & Zhao, G. (2020). The PBW theorem for affine Yangians. Transformation Groups. Springer Nature. https://doi.org/10.1007/s00031-020-09572-6 chicago: Yang, Yaping, and Gufang Zhao. “The PBW Theorem for Affine Yangians.” Transformation Groups. Springer Nature, 2020. https://doi.org/10.1007/s00031-020-09572-6. ieee: Y. Yang and G. Zhao, “The PBW theorem for affine Yangians,” Transformation Groups, vol. 25. Springer Nature, pp. 1371–1385, 2020. ista: Yang Y, Zhao G. 2020. The PBW theorem for affine Yangians. Transformation Groups. 25, 1371–1385. mla: Yang, Yaping, and Gufang Zhao. “The PBW Theorem for Affine Yangians.” Transformation Groups, vol. 25, Springer Nature, 2020, pp. 1371–85, doi:10.1007/s00031-020-09572-6. short: Y. Yang, G. Zhao, Transformation Groups 25 (2020) 1371–1385. date_created: 2020-06-07T22:00:55Z date_published: 2020-12-01T00:00:00Z date_updated: 2023-08-21T07:06:21Z day: '01' department: - _id: TaHa doi: 10.1007/s00031-020-09572-6 ec_funded: 1 external_id: arxiv: - '1804.04375' isi: - '000534874300003' intvolume: ' 25' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.04375 month: '12' oa: 1 oa_version: Preprint page: 1371-1385 project: - _id: 25E549F4-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '320593' name: Arithmetic and physics of Higgs moduli spaces publication: Transformation Groups publication_identifier: eissn: - 1531586X issn: - '10834362' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The PBW theorem for affine Yangians type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 25 year: '2020' ... --- _id: '9708' abstract: - lang: eng text: This research data supports 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file for plotting each figure is provided. article_processing_charge: No author: - first_name: Mate full_name: Hartstein, Mate last_name: Hartstein - first_name: Yu-Te full_name: Hsu, Yu-Te last_name: Hsu - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Juan full_name: Porras, Juan last_name: Porras - first_name: Toshinao full_name: Loew, Toshinao last_name: Loew - first_name: Matthieu full_name: Le Tacon, Matthieu last_name: Le Tacon - first_name: Huakun full_name: Zuo, Huakun last_name: Zuo - first_name: Jinhua full_name: Wang, Jinhua last_name: Wang - first_name: Zengwei full_name: Zhu, Zengwei last_name: Zhu - first_name: Mun full_name: Chan, Mun last_name: Chan - first_name: Ross full_name: McDonald, Ross last_name: McDonald - first_name: Gilbert full_name: Lonzarich, Gilbert last_name: Lonzarich - first_name: Bernhard full_name: Keimer, Bernhard last_name: Keimer - first_name: Suchitra full_name: Sebastian, Suchitra last_name: Sebastian - first_name: Neil full_name: Harrison, Neil last_name: Harrison citation: ama: Hartstein M, Hsu Y-T, Modic KA, et al. Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” 2020. doi:10.17863/cam.50169 apa: Hartstein, M., Hsu, Y.-T., Modic, K. A., Porras, J., Loew, T., Le Tacon, M., … Harrison, N. (2020). Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” Apollo - University of Cambridge. https://doi.org/10.17863/cam.50169 chicago: Hartstein, Mate, Yu-Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Accompanying Dataset for ‘Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.’” Apollo - University of Cambridge, 2020. https://doi.org/10.17863/cam.50169. ieee: M. Hartstein et al., “Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.’” Apollo - University of Cambridge, 2020. ista: Hartstein M, Hsu Y-T, Modic KA, Porras J, Loew T, Le Tacon M, Zuo H, Wang J, Zhu Z, Chan M, McDonald R, Lonzarich G, Keimer B, Sebastian S, Harrison N. 2020. Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors’, Apollo - University of Cambridge, 10.17863/cam.50169. mla: Hartstein, Mate, et al. Accompanying Dataset for “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Apollo - University of Cambridge, 2020, doi:10.17863/cam.50169. short: M. Hartstein, Y.-T. Hsu, K.A. Modic, J. Porras, T. Loew, M. Le Tacon, H. Zuo, J. Wang, Z. Zhu, M. Chan, R. McDonald, G. Lonzarich, B. Keimer, S. Sebastian, N. Harrison, (2020). date_created: 2021-07-23T10:00:35Z date_published: 2020-05-29T00:00:00Z date_updated: 2023-08-21T07:06:48Z day: '29' department: - _id: KiMo doi: 10.17863/cam.50169 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.17863/CAM.50169 month: '05' oa: 1 oa_version: Published Version publisher: Apollo - University of Cambridge related_material: record: - id: '7942' relation: used_in_publication status: public status: public title: Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors' 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: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '7955' abstract: - lang: eng text: Simple stochastic games are turn-based 2½-player games with a reachability objective. The basic question asks whether one player can ensure reaching a given target with at least a given probability. A natural extension is games with a conjunction of such conditions as objective. Despite a plethora of recent results on the analysis of systems with multiple objectives, the decidability of this basic problem remains open. In this paper, we present an algorithm approximating the Pareto frontier of the achievable values to a given precision. Moreover, it is an anytime algorithm, meaning it can be stopped at any time returning the current approximation and its error bound. acknowledgement: "Pranav Ashok, Jan Křetínský and Maximilian Weininger were funded in part by TUM IGSSE Grant 10.06 (PARSEC) and the German Research Foundation (DFG) project KR 4890/2-1\r\n“Statistical Unbounded Verification”. Krishnendu Chatterjee was supported by the ERC CoG 863818 (ForM-SMArt) and Vienna Science and Technology Fund (WWTF) Project ICT15-\r\n003. Tobias Winkler was supported by the RTG 2236 UnRAVe." article_processing_charge: No author: - first_name: Pranav full_name: Ashok, Pranav last_name: Ashok - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Jan full_name: Kretinsky, Jan last_name: Kretinsky - first_name: Maximilian full_name: Weininger, Maximilian last_name: Weininger - first_name: Tobias full_name: Winkler, Tobias last_name: Winkler citation: ama: 'Ashok P, Chatterjee K, Kretinsky J, Weininger M, Winkler T. Approximating values of generalized-reachability stochastic games. In: Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science . Association for Computing Machinery; 2020:102-115. doi:10.1145/3373718.3394761' apa: 'Ashok, P., Chatterjee, K., Kretinsky, J., Weininger, M., & Winkler, T. (2020). Approximating values of generalized-reachability stochastic games. In Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 102–115). Saarbrücken, Germany: Association for Computing Machinery. https://doi.org/10.1145/3373718.3394761' chicago: Ashok, Pranav, Krishnendu Chatterjee, Jan Kretinsky, Maximilian Weininger, and Tobias Winkler. “Approximating Values of Generalized-Reachability Stochastic Games.” In Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , 102–15. Association for Computing Machinery, 2020. https://doi.org/10.1145/3373718.3394761. ieee: P. Ashok, K. Chatterjee, J. Kretinsky, M. Weininger, and T. Winkler, “Approximating values of generalized-reachability stochastic games,” in Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , Saarbrücken, Germany, 2020, pp. 102–115. ista: 'Ashok P, Chatterjee K, Kretinsky J, Weininger M, Winkler T. 2020. Approximating values of generalized-reachability stochastic games. Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science . LICS: Symposium on Logic in Computer Science, 102–115.' mla: Ashok, Pranav, et al. “Approximating Values of Generalized-Reachability Stochastic Games.” Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , Association for Computing Machinery, 2020, pp. 102–15, doi:10.1145/3373718.3394761. short: P. Ashok, K. Chatterjee, J. Kretinsky, M. Weininger, T. Winkler, in:, Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , Association for Computing Machinery, 2020, pp. 102–115. conference: end_date: 2020-07-11 location: Saarbrücken, Germany name: 'LICS: Symposium on Logic in Computer Science' start_date: 2020-07-08 date_created: 2020-06-14T22:00:48Z date_published: 2020-07-08T00:00:00Z date_updated: 2023-08-21T08:24:36Z day: '08' ddc: - '000' department: - _id: KrCh doi: 10.1145/3373718.3394761 ec_funded: 1 external_id: arxiv: - '1908.05106' isi: - '000665014900010' file: - access_level: open_access checksum: d0d0288fe991dd16cf5f02598b794240 content_type: application/pdf creator: dernst date_created: 2020-11-25T09:38:14Z date_updated: 2020-11-25T09:38:14Z file_id: '8804' file_name: 2020_LICS_Ashok.pdf file_size: 1001395 relation: main_file success: 1 file_date_updated: 2020-11-25T09:38:14Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 102-115 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication: 'Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science ' publication_identifier: isbn: - '9781450371049' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Approximating values of generalized-reachability stochastic games type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2020' ... --- _id: '7957' abstract: - lang: eng text: "Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain development and function and are characterized by wide genetic and clinical variability. In this review, we discuss the multiple factors that influence the clinical presentation of NDDs, with particular attention to gene vulnerability, mutational load, and the two-hit model. Despite the complex architecture of\r\nmutational events associated with NDDs, the various proteins involved appear to converge on common pathways, such as synaptic plasticity/function, chromatin remodelers and the mammalian target of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind these pathways will hopefully lead to the identification of candidates that could be targeted for treatment approaches." acknowledgement: We wish to thank Jasmin Morandell for generously sharing Figure 2. This work was supported by the European Research Council Starting Grant (grant 715508 ) to G.N. article_processing_charge: No article_type: original author: - first_name: Ilaria full_name: Parenti, Ilaria id: D93538B0-5B71-11E9-AC62-02EBE5697425 last_name: Parenti - first_name: Luis E full_name: Garcia Rabaneda, Luis E id: 33D1B084-F248-11E8-B48F-1D18A9856A87 last_name: Garcia Rabaneda - first_name: Hanna full_name: Schön, Hanna id: C8E17EDC-D7AA-11E9-B7B7-45ECE5697425 last_name: Schön - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: 'Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. 2020;43(8):608-621. doi:10.1016/j.tins.2020.05.004' apa: 'Parenti, I., Garcia Rabaneda, L. E., Schön, H., & Novarino, G. (2020). Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. Elsevier. https://doi.org/10.1016/j.tins.2020.05.004' chicago: 'Parenti, Ilaria, Luis E Garcia Rabaneda, Hanna Schön, and Gaia Novarino. “Neurodevelopmental Disorders: From Genetics to Functional Pathways.” Trends in Neurosciences. Elsevier, 2020. https://doi.org/10.1016/j.tins.2020.05.004.' ieee: 'I. Parenti, L. E. Garcia Rabaneda, H. Schön, and G. Novarino, “Neurodevelopmental disorders: From genetics to functional pathways,” Trends in Neurosciences, vol. 43, no. 8. Elsevier, pp. 608–621, 2020.' ista: 'Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. 2020. Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. 43(8), 608–621.' mla: 'Parenti, Ilaria, et al. “Neurodevelopmental Disorders: From Genetics to Functional Pathways.” Trends in Neurosciences, vol. 43, no. 8, Elsevier, 2020, pp. 608–21, doi:10.1016/j.tins.2020.05.004.' short: I. Parenti, L.E. Garcia Rabaneda, H. Schön, G. Novarino, Trends in Neurosciences 43 (2020) 608–621. date_created: 2020-06-14T22:00:49Z date_published: 2020-08-01T00:00:00Z date_updated: 2023-08-21T08:25:31Z day: '01' ddc: - '570' department: - _id: GaNo doi: 10.1016/j.tins.2020.05.004 ec_funded: 1 external_id: isi: - '000553090600008' pmid: - '32507511' file: - access_level: open_access checksum: 67db0251b1d415ae59005f876fcf9e34 content_type: application/pdf creator: dernst date_created: 2020-11-25T09:43:40Z date_updated: 2020-11-25T09:43:40Z file_id: '8805' file_name: 2020_TrendsNeuroscience_Parenti.pdf file_size: 1439550 relation: main_file success: 1 file_date_updated: 2020-11-25T09:43:40Z has_accepted_license: '1' intvolume: ' 43' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 608-621 pmid: 1 project: - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models publication: Trends in Neurosciences publication_identifier: eissn: - 1878108X issn: - '01662236' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Neurodevelopmental disorders: From genetics to functional pathways' 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: 43 year: '2020' ... --- _id: '7960' abstract: - lang: eng text: Let A={A1,…,An} be a family of sets in the plane. For 0≤i2b be integers. We prove that if each k-wise or (k+1)-wise intersection of sets from A has at most b path-connected components, which all are open, then fk+1=0 implies fk≤cfk−1 for some positive constant c depending only on b and k. These results also extend to two-dimensional compact surfaces. acknowledgement: "We are very grateful to Pavel Paták for many helpful discussions and remarks. We also thank the referees for helpful comments, which greatly improved the presentation.\r\nThe project was supported by ERC Advanced Grant 320924. GK was also partially supported by NSF grant DMS1300120. The research stay of ZP at IST Austria is funded by the project CZ.02.2.69/0.0/0.0/17_050/0008466 Improvement of internationalization in the field of research and development at Charles University, through the support of quality projects MSCA-IF." article_processing_charge: No article_type: original author: - first_name: Gil full_name: Kalai, Gil last_name: Kalai - first_name: Zuzana full_name: Patakova, Zuzana id: 48B57058-F248-11E8-B48F-1D18A9856A87 last_name: Patakova orcid: 0000-0002-3975-1683 citation: ama: Kalai G, Patakova Z. Intersection patterns of planar sets. Discrete and Computational Geometry. 2020;64:304-323. doi:10.1007/s00454-020-00205-z apa: Kalai, G., & Patakova, Z. (2020). Intersection patterns of planar sets. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00205-z chicago: Kalai, Gil, and Zuzana Patakova. “Intersection Patterns of Planar Sets.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00205-z. ieee: G. Kalai and Z. Patakova, “Intersection patterns of planar sets,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 304–323, 2020. ista: Kalai G, Patakova Z. 2020. Intersection patterns of planar sets. Discrete and Computational Geometry. 64, 304–323. mla: Kalai, Gil, and Zuzana Patakova. “Intersection Patterns of Planar Sets.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 304–23, doi:10.1007/s00454-020-00205-z. short: G. Kalai, Z. Patakova, Discrete and Computational Geometry 64 (2020) 304–323. date_created: 2020-06-14T22:00:50Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-08-21T08:26:34Z day: '01' department: - _id: UlWa doi: 10.1007/s00454-020-00205-z external_id: arxiv: - '1907.00885' isi: - '000537329400001' intvolume: ' 64' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1907.00885 month: '09' oa: 1 oa_version: Preprint page: 304-323 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: Intersection patterns of planar sets type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 64 year: '2020' ... --- _id: '7962' abstract: - lang: eng text: 'A string graph is the intersection graph of a family of continuous arcs in the plane. The intersection graph of a family of plane convex sets is a string graph, but not all string graphs can be obtained in this way. We prove the following structure theorem conjectured by Janson and Uzzell: The vertex set of almost all string graphs on n vertices can be partitioned into five cliques such that some pair of them is not connected by any edge (n→∞). We also show that every graph with the above property is an intersection graph of plane convex sets. As a corollary, we obtain that almost all string graphs on n vertices are intersection graphs of plane convex sets.' article_processing_charge: No article_type: original author: - first_name: János full_name: Pach, János id: E62E3130-B088-11EA-B919-BF823C25FEA4 last_name: Pach - first_name: Bruce full_name: Reed, Bruce last_name: Reed - first_name: Yelena full_name: Yuditsky, Yelena last_name: Yuditsky citation: ama: Pach J, Reed B, Yuditsky Y. Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. 2020;63(4):888-917. doi:10.1007/s00454-020-00213-z apa: Pach, J., Reed, B., & Yuditsky, Y. (2020). Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00213-z chicago: Pach, János, Bruce Reed, and Yelena Yuditsky. “Almost All String Graphs Are Intersection Graphs of Plane Convex Sets.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00213-z. ieee: J. Pach, B. Reed, and Y. Yuditsky, “Almost all string graphs are intersection graphs of plane convex sets,” Discrete and Computational Geometry, vol. 63, no. 4. Springer Nature, pp. 888–917, 2020. ista: Pach J, Reed B, Yuditsky Y. 2020. Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. 63(4), 888–917. mla: Pach, János, et al. “Almost All String Graphs Are Intersection Graphs of Plane Convex Sets.” Discrete and Computational Geometry, vol. 63, no. 4, Springer Nature, 2020, pp. 888–917, doi:10.1007/s00454-020-00213-z. short: J. Pach, B. Reed, Y. Yuditsky, Discrete and Computational Geometry 63 (2020) 888–917. date_created: 2020-06-14T22:00:51Z date_published: 2020-06-05T00:00:00Z date_updated: 2023-08-21T08:49:18Z day: '05' department: - _id: HeEd doi: 10.1007/s00454-020-00213-z external_id: arxiv: - '1803.06710' isi: - '000538229000001' intvolume: ' 63' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1803.06710 month: '06' oa: 1 oa_version: Preprint page: 888-917 project: - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: The Wittgenstein Prize 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: Almost all string graphs are intersection graphs of plane convex sets type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 63 year: '2020' ... --- _id: '13460' abstract: - lang: eng text: Binary interaction can cause stellar envelopes to be stripped, which significantly reduces the radius of the star. The orbit of a binary composed of a stripped star and a compact object can therefore be so tight that the gravitational radiation the system produces reaches frequencies accessible to the Laser Interferometer Space Antenna (LISA). Two such stripped stars in tight orbits with white dwarfs are known so far (ZTF J2130+4420 and CD−30°11223), but many more are expected to exist. These binaries provide important constraints for binary evolution models and may be used as LISA verification sources. We develop a Monte Carlo code that uses detailed evolutionary models to simulate the Galactic population of stripped stars in tight orbits with either neutron star or white dwarf companions. We predict 0–100 stripped star + white dwarf binaries and 0–4 stripped star + neutron star binaries with a signal-to-noise ratio >5 after 10 yr of observations with LISA. More than 90% of these binaries are expected to show large radial velocity shifts of ≳200 $\,\mathrm{km}\,{{\rm{s}}}^{-1}$, which are spectroscopically detectable. Photometric variability due to tidal deformation of the stripped star is also expected and has been observed in ZTF J2130+4420 and CD−30°11223. In addition, the stripped star + neutron star binaries are expected to be X-ray bright with LX ≳ 1033–1036 $\,\mathrm{erg}\,{{\rm{s}}}^{-1}$. Our results show that stripped star binaries are promising multimessenger sources for the upcoming electromagnetic and gravitational wave facilities. article_number: '56' article_processing_charge: No article_type: original author: - first_name: Ylva Louise Linsdotter full_name: Götberg, Ylva Louise Linsdotter id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d last_name: Götberg orcid: 0000-0002-6960-6911 - first_name: V. full_name: Korol, V. last_name: Korol - first_name: A. full_name: Lamberts, A. last_name: Lamberts - first_name: T. full_name: Kupfer, T. last_name: Kupfer - first_name: K. full_name: Breivik, K. last_name: Breivik - first_name: B. full_name: Ludwig, B. last_name: Ludwig - first_name: M. R. full_name: Drout, M. R. last_name: Drout citation: ama: 'Götberg YLL, Korol V, Lamberts A, et al. Stars stripped in binaries: The living gravitational-wave sources. The Astrophysical Journal. 2020;904(1). doi:10.3847/1538-4357/abbda5' apa: 'Götberg, Y. L. L., Korol, V., Lamberts, A., Kupfer, T., Breivik, K., Ludwig, B., & Drout, M. R. (2020). Stars stripped in binaries: The living gravitational-wave sources. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/abbda5' chicago: 'Götberg, Ylva Louise Linsdotter, V. Korol, A. Lamberts, T. Kupfer, K. Breivik, B. Ludwig, and M. R. Drout. “Stars Stripped in Binaries: The Living Gravitational-Wave Sources.” The Astrophysical Journal. American Astronomical Society, 2020. https://doi.org/10.3847/1538-4357/abbda5.' ieee: 'Y. L. L. Götberg et al., “Stars stripped in binaries: The living gravitational-wave sources,” The Astrophysical Journal, vol. 904, no. 1. American Astronomical Society, 2020.' ista: 'Götberg YLL, Korol V, Lamberts A, Kupfer T, Breivik K, Ludwig B, Drout MR. 2020. Stars stripped in binaries: The living gravitational-wave sources. The Astrophysical Journal. 904(1), 56.' mla: 'Götberg, Ylva Louise Linsdotter, et al. “Stars Stripped in Binaries: The Living Gravitational-Wave Sources.” The Astrophysical Journal, vol. 904, no. 1, 56, American Astronomical Society, 2020, doi:10.3847/1538-4357/abbda5.' short: Y.L.L. Götberg, V. Korol, A. Lamberts, T. Kupfer, K. Breivik, B. Ludwig, M.R. Drout, The Astrophysical Journal 904 (2020). date_created: 2023-08-03T10:12:07Z date_published: 2020-11-20T00:00:00Z date_updated: 2023-08-21T11:32:40Z day: '20' doi: 10.3847/1538-4357/abbda5 extern: '1' external_id: arxiv: - '2006.07382' intvolume: ' 904' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2006.07382 month: '11' oa: 1 oa_version: Preprint publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: American Astronomical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Stars stripped in binaries: The living gravitational-wave sources' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 904 year: '2020' ... --- _id: '7999' abstract: - lang: eng text: 'Linking epigenetic marks to clinical outcomes improves insight into molecular processes, disease prediction, and therapeutic target identification. Here, a statistical approach is presented to infer the epigenetic architecture of complex disease, determine the variation captured by epigenetic effects, and estimate phenotype-epigenetic probe associations jointly. Implicitly adjusting for probe correlations, data structure (cell-count or relatedness), and single-nucleotide polymorphism (SNP) marker effects, improves association estimates and in 9,448 individuals, 75.7% (95% CI 71.70–79.3) of body mass index (BMI) variation and 45.6% (95% CI 37.3–51.9) of cigarette consumption variation was captured by whole blood methylation array data. Pathway-linked probes of blood cholesterol, lipid transport and sterol metabolism for BMI, and xenobiotic stimuli response for smoking, showed >1.5 times larger associations with >95% posterior inclusion probability. Prediction accuracy improved by 28.7% for BMI and 10.2% for smoking over a LASSO model, with age-, and tissue-specificity, implying associations are a phenotypic consequence rather than causal. ' article_number: '2865' article_processing_charge: No article_type: original author: - first_name: D full_name: Trejo Banos, D last_name: Trejo Banos - first_name: DL full_name: McCartney, DL last_name: McCartney - first_name: M full_name: Patxot, M last_name: Patxot - first_name: L full_name: Anchieri, L last_name: Anchieri - first_name: T full_name: Battram, T last_name: Battram - first_name: C full_name: Christiansen, C last_name: Christiansen - first_name: R full_name: Costeira, R last_name: Costeira - first_name: RM full_name: Walker, RM last_name: Walker - first_name: SW full_name: Morris, SW last_name: Morris - first_name: A full_name: Campbell, A last_name: Campbell - first_name: Q full_name: Zhang, Q last_name: Zhang - first_name: DJ full_name: Porteous, DJ last_name: Porteous - first_name: AF full_name: McRae, AF last_name: McRae - first_name: NR full_name: Wray, NR last_name: Wray - first_name: PM full_name: Visscher, PM last_name: Visscher - first_name: CS full_name: Haley, CS last_name: Haley - first_name: KL full_name: Evans, KL last_name: Evans - first_name: IJ full_name: Deary, IJ last_name: Deary - first_name: AM full_name: McIntosh, AM last_name: McIntosh - first_name: G full_name: Hemani, G last_name: Hemani - first_name: JT full_name: Bell, JT last_name: Bell - first_name: RE full_name: Marioni, RE last_name: Marioni - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Trejo Banos D, McCartney D, Patxot M, et al. Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. 2020;11. doi:10.1038/s41467-020-16520-1 apa: Trejo Banos, D., McCartney, D., Patxot, M., Anchieri, L., Battram, T., Christiansen, C., … Robinson, M. R. (2020). Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-16520-1 chicago: Trejo Banos, D, DL McCartney, M Patxot, L Anchieri, T Battram, C Christiansen, R Costeira, et al. “Bayesian Reassessment of the Epigenetic Architecture of Complex Traits.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-16520-1. ieee: D. Trejo Banos et al., “Bayesian reassessment of the epigenetic architecture of complex traits,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Trejo Banos D, McCartney D, Patxot M, Anchieri L, Battram T, Christiansen C, Costeira R, Walker R, Morris S, Campbell A, Zhang Q, Porteous D, McRae A, Wray N, Visscher P, Haley C, Evans K, Deary I, McIntosh A, Hemani G, Bell J, Marioni R, Robinson MR. 2020. Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. 11, 2865. mla: Trejo Banos, D., et al. “Bayesian Reassessment of the Epigenetic Architecture of Complex Traits.” Nature Communications, vol. 11, 2865, Springer Nature, 2020, doi:10.1038/s41467-020-16520-1. short: D. Trejo Banos, D. McCartney, M. Patxot, L. Anchieri, T. Battram, C. Christiansen, R. Costeira, R. Walker, S. Morris, A. Campbell, Q. Zhang, D. Porteous, A. McRae, N. Wray, P. Visscher, C. Haley, K. Evans, I. Deary, A. McIntosh, G. Hemani, J. Bell, R. Marioni, M.R. Robinson, Nature Communications 11 (2020). date_created: 2020-06-22T11:18:25Z date_published: 2020-06-08T00:00:00Z date_updated: 2023-08-22T07:13:09Z day: '08' ddc: - '570' department: - _id: MaRo doi: 10.1038/s41467-020-16520-1 external_id: isi: - '000541702400004' pmid: - '32513961' file: - access_level: open_access checksum: 4c96babd4cfb0d153334f6c598c0bacb content_type: application/pdf creator: dernst date_created: 2020-06-22T11:24:32Z date_updated: 2020-07-14T12:48:07Z file_id: '8000' file_name: 2020_NatureComm_Bayesian.pdf file_size: 1475657 relation: main_file file_date_updated: 2020-07-14T12:48:07Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-020-19099-9 scopus_import: '1' status: public title: Bayesian reassessment of the epigenetic architecture of complex traits 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: '7995' abstract: - lang: eng text: When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple‐effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis , occur in North Atlantic rocky‐shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size‐assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment. acknowledgement: We are very grateful to I. Sencic, L. Brettell, A.‐L. Liabot, J. Galindo, M. Ravinet, and A. Butlin for their help with field sampling and mating experiments. This work was funded by the Natural Environment Research Council, European Research Council and Swedish Research Council VR and we are also very grateful for the support of the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg. The simulations were performed on resources at Chalmers Centre for Computational Science and Engineering (C3SE) provided by the Swedish National Infrastructure for Computing (SNIC). AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie grant agreement no. 797747. article_processing_charge: No article_type: original author: - first_name: Samuel full_name: Perini, Samuel last_name: Perini - first_name: Marina full_name: Rafajlović, Marina last_name: Rafajlović - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 2020;74(7):1482-1497. doi:10.1111/evo.14027 apa: Perini, S., Rafajlović, M., Westram, A. M., Johannesson, K., & Butlin, R. K. (2020). Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. Wiley. https://doi.org/10.1111/evo.14027 chicago: Perini, Samuel, Marina Rafajlović, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution. Wiley, 2020. https://doi.org/10.1111/evo.14027. ieee: S. Perini, M. Rafajlović, A. M. Westram, K. Johannesson, and R. K. Butlin, “Assortative mating, sexual selection, and their consequences for gene flow in Littorina,” Evolution, vol. 74, no. 7. Wiley, pp. 1482–1497, 2020. ista: Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. 2020. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 74(7), 1482–1497. mla: Perini, Samuel, et al. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution, vol. 74, no. 7, Wiley, 2020, pp. 1482–97, doi:10.1111/evo.14027. short: S. Perini, M. Rafajlović, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 74 (2020) 1482–1497. date_created: 2020-06-22T09:14:21Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-22T07:13:38Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/evo.14027 ec_funded: 1 external_id: isi: - '000539780800001' file: - access_level: open_access checksum: 56235bf1e2a9e25f96196bb13b6b754d content_type: application/pdf creator: dernst date_created: 2020-11-25T10:49:48Z date_updated: 2020-11-25T10:49:48Z file_id: '8808' file_name: 2020_Evolution_Perini.pdf file_size: 1080810 relation: main_file success: 1 file_date_updated: 2020-11-25T10:49:48Z has_accepted_license: '1' intvolume: ' 74' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1482-1497 project: - _id: 265B41B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '797747' name: Theoretical and empirical approaches to understanding Parallel Adaptation publication: Evolution publication_identifier: eissn: - '15585646' issn: - '00143820' publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '8809' relation: research_data status: public scopus_import: '1' status: public title: Assortative mating, sexual selection, and their consequences for gene flow in Littorina 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: 74 year: '2020' ... --- _id: '8809' abstract: - lang: eng text: When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment. article_processing_charge: No author: - first_name: Samuel full_name: Perini, Samuel last_name: Perini - first_name: Marina full_name: Rafajlovic, Marina last_name: Rafajlovic - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger full_name: Butlin, Roger last_name: Butlin citation: ama: 'Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:10.5061/dryad.qrfj6q5cn' apa: 'Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., & Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. https://doi.org/10.5061/dryad.qrfj6q5cn' chicago: 'Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. https://doi.org/10.5061/dryad.qrfj6q5cn.' ieee: 'S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020.' ista: 'Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, 10.5061/dryad.qrfj6q5cn.' mla: 'Perini, Samuel, et al. Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina. Dryad, 2020, doi:10.5061/dryad.qrfj6q5cn.' short: S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020). date_created: 2020-11-25T11:07:25Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-22T07:13:37Z day: '01' department: - _id: NiBa doi: 10.5061/dryad.qrfj6q5cn has_accepted_license: '1' license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.qrfj6q5cn month: '07' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '7995' relation: used_in_publication status: public status: public title: 'Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '8001' abstract: - lang: eng text: Post-tetanic potentiation (PTP) is an attractive candidate mechanism for hippocampus-dependent short-term memory. Although PTP has a uniquely large magnitude at hippocampal mossy fiber-CA3 pyramidal neuron synapses, it is unclear whether it can be induced by natural activity and whether its lifetime is sufficient to support short-term memory. We combined in vivo recordings from granule cells (GCs), in vitro paired recordings from mossy fiber terminals and postsynaptic CA3 neurons, and “flash and freeze” electron microscopy. PTP was induced at single synapses and showed a low induction threshold adapted to sparse GC activity in vivo. PTP was mainly generated by enlargement of the readily releasable pool of synaptic vesicles, allowing multiplicative interaction with other plasticity forms. PTP was associated with an increase in the docked vesicle pool, suggesting formation of structural “pool engrams.” Absence of presynaptic activity extended the lifetime of the potentiation, enabling prolonged information storage in the hippocampal network. acknowledged_ssus: - _id: SSU acknowledgement: This project received funding from the European Research Council (ERC) under the European Union Horizon 2020 Research and Innovation Program (grant agreement 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung ( Z 312-B27 , Wittgenstein award to P.J. and V 739-B27 to C.B.-M.). We thank Drs. Jozsef Csicsvari, Jose Guzman, Erwin Neher, and Ryuichi Shigemoto for commenting on earlier versions of the manuscript. We are grateful to Walter Kaufmann, Daniel Gütl, and Vanessa Zheden for EM training; Alois Schlögl for programming; Florian Marr for excellent technical assistance and cell reconstruction; Christina Altmutter for technical help; Eleftheria Kralli-Beller for manuscript editing; Taija Makinen for providing the Prox1-CreERT2 mouse line; and the Scientific Service Units of IST Austria for support. article_processing_charge: No article_type: original author: - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: Carolina full_name: Borges Merjane, Carolina id: 4305C450-F248-11E8-B48F-1D18A9856A87 last_name: Borges Merjane orcid: 0000-0003-0005-401X - first_name: Xiaomin full_name: Zhang, Xiaomin id: 423EC9C2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Vandael DH, Borges Merjane C, Zhang X, Jonas PM. Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. 2020;107(3):509-521. doi:10.1016/j.neuron.2020.05.013 apa: Vandael, D. H., Borges Merjane, C., Zhang, X., & Jonas, P. M. (2020). Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.05.013 chicago: Vandael, David H, Carolina Borges Merjane, Xiaomin Zhang, and Peter M Jonas. “Short-Term Plasticity at Hippocampal Mossy Fiber Synapses Is Induced by Natural Activity Patterns and Associated with Vesicle Pool Engram Formation.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.05.013. ieee: D. H. Vandael, C. Borges Merjane, X. Zhang, and P. M. Jonas, “Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation,” Neuron, vol. 107, no. 3. Elsevier, pp. 509–521, 2020. ista: Vandael DH, Borges Merjane C, Zhang X, Jonas PM. 2020. Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. 107(3), 509–521. mla: Vandael, David H., et al. “Short-Term Plasticity at Hippocampal Mossy Fiber Synapses Is Induced by Natural Activity Patterns and Associated with Vesicle Pool Engram Formation.” Neuron, vol. 107, no. 3, Elsevier, 2020, pp. 509–21, doi:10.1016/j.neuron.2020.05.013. short: D.H. Vandael, C. Borges Merjane, X. Zhang, P.M. Jonas, Neuron 107 (2020) 509–521. date_created: 2020-06-22T13:29:05Z date_published: 2020-08-05T00:00:00Z date_updated: 2023-08-22T07:45:25Z day: '05' ddc: - '570' department: - _id: PeJo doi: 10.1016/j.neuron.2020.05.013 ec_funded: 1 external_id: isi: - '000556135600004' pmid: - '32492366' file: - access_level: open_access checksum: 4030b2be0c9625d54694a1e9fb00305e content_type: application/pdf creator: dernst date_created: 2020-11-25T11:23:02Z date_updated: 2020-11-25T11:23:02Z file_id: '8811' file_name: 2020_Neuron_Vandael.pdf file_size: 4390833 relation: main_file success: 1 file_date_updated: 2020-11-25T11:23:02Z has_accepted_license: '1' intvolume: ' 107' isi: 1 issue: '3' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 509-521 pmid: 1 project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize - _id: 2696E7FE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: V00739 name: Structural plasticity at mossy fiber-CA3 synapses publication: Neuron publication_identifier: eissn: - '10974199' 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/possible-physical-trace-of-short-term-memory-found/ scopus_import: '1' status: public title: Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2020' ... --- _id: '13998' abstract: - lang: eng text: The interaction of strong near-infrared (NIR) laser pulses with wide-bandgap dielectrics produces high harmonics in the extreme ultraviolet (XUV) wavelength range. These observations have opened up the possibility of attosecond metrology in solids, which would benefit from a precise measurement of the emission times of individual harmonics with respect to the NIR laser field. Here we show that, when high-harmonics are detected from the input surface of a magnesium oxide crystal, a bichromatic probing of the XUV emission shows a clear synchronization largely consistent with a semiclassical model of electron–hole recollisions in bulk solids. On the other hand, the bichromatic spectrogram of harmonics originating from the exit surface of the 200 μm-thick crystal is strongly modified, indicating the influence of laser field distortions during propagation. Our tracking of sub-cycle electron and hole re-collisions at XUV energies is relevant to the development of solid-state sources of attosecond pulses. article_number: '144003' article_processing_charge: No article_type: original author: - first_name: Giulio full_name: Vampa, Giulio last_name: Vampa - first_name: Jian full_name: Lu, Jian last_name: Lu - first_name: Yong Sing full_name: You, Yong Sing last_name: You - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Mengxi full_name: Wu, Mengxi last_name: Wu - first_name: Hanzhe full_name: Liu, Hanzhe last_name: Liu - first_name: Kenneth J full_name: Schafer, Kenneth J last_name: Schafer - first_name: Mette B full_name: Gaarde, Mette B last_name: Gaarde - first_name: David A full_name: Reis, David A last_name: Reis - first_name: Shambhu full_name: Ghimire, Shambhu last_name: Ghimire citation: ama: 'Vampa G, Lu J, You YS, et al. Attosecond synchronization of extreme ultraviolet high harmonics from crystals. Journal of Physics B: Atomic, Molecular and Optical Physics. 2020;53(14). doi:10.1088/1361-6455/ab8e56' apa: 'Vampa, G., Lu, J., You, Y. S., Baykusheva, D. R., Wu, M., Liu, H., … Ghimire, S. (2020). Attosecond synchronization of extreme ultraviolet high harmonics from crystals. Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing. https://doi.org/10.1088/1361-6455/ab8e56' chicago: 'Vampa, Giulio, Jian Lu, Yong Sing You, Denitsa Rangelova Baykusheva, Mengxi Wu, Hanzhe Liu, Kenneth J Schafer, Mette B Gaarde, David A Reis, and Shambhu Ghimire. “Attosecond Synchronization of Extreme Ultraviolet High Harmonics from Crystals.” Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing, 2020. https://doi.org/10.1088/1361-6455/ab8e56.' ieee: 'G. Vampa et al., “Attosecond synchronization of extreme ultraviolet high harmonics from crystals,” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 53, no. 14. IOP Publishing, 2020.' ista: 'Vampa G, Lu J, You YS, Baykusheva DR, Wu M, Liu H, Schafer KJ, Gaarde MB, Reis DA, Ghimire S. 2020. Attosecond synchronization of extreme ultraviolet high harmonics from crystals. Journal of Physics B: Atomic, Molecular and Optical Physics. 53(14), 144003.' mla: 'Vampa, Giulio, et al. “Attosecond Synchronization of Extreme Ultraviolet High Harmonics from Crystals.” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 53, no. 14, 144003, IOP Publishing, 2020, doi:10.1088/1361-6455/ab8e56.' short: 'G. Vampa, J. Lu, Y.S. You, D.R. Baykusheva, M. Wu, H. Liu, K.J. Schafer, M.B. Gaarde, D.A. Reis, S. Ghimire, Journal of Physics B: Atomic, Molecular and Optical Physics 53 (2020).' date_created: 2023-08-09T13:09:51Z date_published: 2020-06-17T00:00:00Z date_updated: 2023-08-22T07:36:36Z day: '17' doi: 10.1088/1361-6455/ab8e56 extern: '1' external_id: arxiv: - '2001.09951' intvolume: ' 53' issue: '14' keyword: - Condensed Matter Physics - Atomic and Molecular Physics - and Optics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2001.09951 month: '06' oa: 1 oa_version: Preprint publication: 'Journal of Physics B: Atomic, Molecular and Optical Physics' publication_identifier: eissn: - 1361-6455 issn: - 0953-4075 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Attosecond synchronization of extreme ultraviolet high harmonics from crystals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2020' ... --- _id: '8038' abstract: - lang: eng text: Microelectromechanical systems and integrated photonics provide the basis for many reliable and compact circuit elements in modern communication systems. Electro-opto-mechanical devices are currently one of the leading approaches to realize ultra-sensitive, low-loss transducers for an emerging quantum information technology. Here we present an on-chip microwave frequency converter based on a planar aluminum on silicon nitride platform that is compatible with slot-mode coupled photonic crystal cavities. We show efficient frequency conversion between two propagating microwave modes mediated by the radiation pressure interaction with a metalized dielectric nanobeam oscillator. We achieve bidirectional coherent conversion with a total device efficiency of up to ~60%, a dynamic range of 2 × 10^9 photons/s and an instantaneous bandwidth of up to 1.7 kHz. A high fidelity quantum state transfer would be possible if the drive dependent output noise of currently ~14 photons s^−1 Hz^−1 is further reduced. Such a silicon nitride based transducer is in situ reconfigurable and could be used for on-chip classical and quantum signal routing and filtering, both for microwave and hybrid microwave-optical applications. article_number: '034011' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: M. full_name: Kalaee, M. last_name: Kalaee - first_name: R. full_name: Norte, R. last_name: Norte - first_name: A. full_name: Pitanti, A. last_name: Pitanti - first_name: O. full_name: Painter, O. last_name: Painter citation: ama: Fink JM, Kalaee M, Norte R, Pitanti A, Painter O. Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. 2020;5(3). doi:10.1088/2058-9565/ab8dce apa: Fink, J. M., Kalaee, M., Norte, R., Pitanti, A., & Painter, O. (2020). Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. IOP Publishing. https://doi.org/10.1088/2058-9565/ab8dce chicago: Fink, Johannes M, M. Kalaee, R. Norte, A. Pitanti, and O. Painter. “Efficient Microwave Frequency Conversion Mediated by a Photonics Compatible Silicon Nitride Nanobeam Oscillator.” Quantum Science and Technology. IOP Publishing, 2020. https://doi.org/10.1088/2058-9565/ab8dce. ieee: J. M. Fink, M. Kalaee, R. Norte, A. Pitanti, and O. Painter, “Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator,” Quantum Science and Technology, vol. 5, no. 3. IOP Publishing, 2020. ista: Fink JM, Kalaee M, Norte R, Pitanti A, Painter O. 2020. Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. 5(3), 034011. mla: Fink, Johannes M., et al. “Efficient Microwave Frequency Conversion Mediated by a Photonics Compatible Silicon Nitride Nanobeam Oscillator.” Quantum Science and Technology, vol. 5, no. 3, 034011, IOP Publishing, 2020, doi:10.1088/2058-9565/ab8dce. short: J.M. Fink, M. Kalaee, R. Norte, A. Pitanti, O. Painter, Quantum Science and Technology 5 (2020). date_created: 2020-06-29T07:59:35Z date_published: 2020-05-25T00:00:00Z date_updated: 2023-08-22T07:49:01Z day: '25' ddc: - '530' department: - _id: JoFi doi: 10.1088/2058-9565/ab8dce ec_funded: 1 external_id: isi: - '000539300800001' file: - access_level: open_access checksum: 8f25f05053f511f892ae8fa93f341e61 content_type: application/pdf creator: cziletti date_created: 2020-06-30T10:29:10Z date_updated: 2020-07-14T12:48:08Z file_id: '8072' file_name: 2020_QuantumSciTechnol_Fink.pdf file_size: 2600967 relation: main_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '3' language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 26927A52-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F07105 name: Integrating superconducting quantum circuits - _id: 257EB838-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '732894' name: Hybrid Optomechanical Technologies - _id: 2622978C-B435-11E9-9278-68D0E5697425 name: Hybrid Semiconductor - Superconductor Quantum Devices publication: Quantum Science and Technology publication_identifier: eissn: - '20589565' publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator 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: 5 year: '2020' ... --- _id: '8037' abstract: - lang: eng text: 'Genetic perturbations that affect bacterial resistance to antibiotics have been characterized genome-wide, but how do such perturbations interact with subsequent evolutionary adaptation to the drug? Here, we show that strong epistasis between resistance mutations and systematically identified genes can be exploited to control spontaneous resistance evolution. We evolved hundreds of Escherichia coli K-12 mutant populations in parallel, using a robotic platform that tightly controls population size and selection pressure. We find a global diminishing-returns epistasis pattern: strains that are initially more sensitive generally undergo larger resistance gains. However, some gene deletion strains deviate from this general trend and curtail the evolvability of resistance, including deletions of genes for membrane transport, LPS biosynthesis, and chaperones. Deletions of efflux pump genes force evolution on inferior mutational paths, not explored in the wild type, and some of these essentially block resistance evolution. This effect is due to strong negative epistasis with resistance mutations. The identified genes and cellular functions provide potential targets for development of adjuvants that may block spontaneous resistance evolution when combined with antibiotics.' article_number: '3105' article_processing_charge: No article_type: original author: - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 - first_name: Booshini full_name: Fernando, Booshini last_name: Fernando - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Lukacisinova M, Fernando B, Bollenbach MT. Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nature Communications. 2020;11. doi:10.1038/s41467-020-16932-z apa: Lukacisinova, M., Fernando, B., & Bollenbach, M. T. (2020). Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-16932-z chicago: Lukacisinova, Marta, Booshini Fernando, and Mark Tobias Bollenbach. “Highly Parallel Lab Evolution Reveals That Epistasis Can Curb the Evolution of Antibiotic Resistance.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-16932-z. ieee: M. Lukacisinova, B. Fernando, and M. T. Bollenbach, “Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Lukacisinova M, Fernando B, Bollenbach MT. 2020. Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nature Communications. 11, 3105. mla: Lukacisinova, Marta, et al. “Highly Parallel Lab Evolution Reveals That Epistasis Can Curb the Evolution of Antibiotic Resistance.” Nature Communications, vol. 11, 3105, Springer Nature, 2020, doi:10.1038/s41467-020-16932-z. short: M. Lukacisinova, B. Fernando, M.T. Bollenbach, Nature Communications 11 (2020). date_created: 2020-06-29T07:59:35Z date_published: 2020-06-19T00:00:00Z date_updated: 2023-08-22T07:48:30Z day: '19' ddc: - '570' doi: 10.1038/s41467-020-16932-z extern: '1' external_id: isi: - '000545685100002' pmid: - '32561723' file: - access_level: open_access checksum: 4f5f49d63add331d5eb8a2bae477b396 content_type: application/pdf creator: cziletti date_created: 2020-06-30T09:58:50Z date_updated: 2020-07-14T12:48:08Z file_id: '8071' file_name: 2020_NatureComm_Lukacisinova.pdf file_size: 1546491 relation: main_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 25EB3A80-B435-11E9-9278-68D0E5697425 grant_number: RGP0042/2013 name: Revealing the fundamental limits of cell growth publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance 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' ...