--- _id: '8674' abstract: - lang: eng text: 'Extrasynaptic actions of glutamate are limited by high-affinity transporters expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point transmission in excitatory circuits. Memory formation in the brain is associated with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic glutamate actions is poorly understood. Here, we used advanced imaging methods, in situ and in vivo, to find that a classical synaptic memory mechanism, long-term potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical glutamate sensors combined with patch-clamp and 3D molecular localization reveal that LTP induction thus prompts spatial retreat of astroglial glutamate transporters, boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk. The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes. We have therefore uncovered a mechanism by which a memory trace at one synapse could alter signal handling by multiple neighboring connections.' acknowledgement: We thank J. Angibaud for organotypic cultures and R. Chereau and J. Tonnesen for help with the STED microscope; also D. Gonzales and the Neurocentre Magendie INSERM U1215 Genotyping Platform, for breeding management and genotyping. This work was supported by the Wellcome Trust Principal Fellowships 101896 and 212251, ERC Advanced Grant 323113, ERC Proof-of-Concept Grant 767372, EC FP7 ITN 606950, and EU CSA 811011 (D.A.R.); NRW-Rückkehrerpogramm, UCL Excellence Fellowship, German Research Foundation (DFG) SPP1757 and SFB1089 (C.H.); Human Frontiers Science Program (C.H., C.J.J., and H.J.); EMBO Long-Term Fellowship (L.B.); Marie Curie FP7 PIRG08-GA-2010-276995 (A.P.), ASTROMODULATION (S.R.); Equipe FRM DEQ 201 303 26519, Conseil Régional d’Aquitaine R12056GG, INSERM (S.H.R.O.); ANR SUPERTri, ANR Castro (ANR-17-CE16-0002), R-13-BSV4-0007-01, Université de Bordeaux, labex BRAIN (S.H.R.O. and U.V.N.); CNRS (A.P., S.H.R.O., and U.V.N.); HFSP, ANR CEXC, and France-BioImaging ANR-10-INSB-04 (U.V.N.); and FP7 MemStick Project No. 201600 (M.G.S.). article_processing_charge: No article_type: original author: - first_name: Christian full_name: Henneberger, Christian last_name: Henneberger - first_name: Lucie full_name: Bard, Lucie last_name: Bard - first_name: Aude full_name: Panatier, Aude last_name: Panatier - first_name: James P. full_name: Reynolds, James P. last_name: Reynolds - first_name: Olga full_name: Kopach, Olga last_name: Kopach - first_name: Nikolay I. full_name: Medvedev, Nikolay I. last_name: Medvedev - first_name: Daniel full_name: Minge, Daniel last_name: Minge - first_name: Michel K. full_name: Herde, Michel K. last_name: Herde - first_name: Stefanie full_name: Anders, Stefanie last_name: Anders - first_name: Igor full_name: Kraev, Igor last_name: Kraev - first_name: Janosch P. full_name: Heller, Janosch P. last_name: Heller - first_name: Sylvain full_name: Rama, Sylvain last_name: Rama - first_name: Kaiyu full_name: Zheng, Kaiyu last_name: Zheng - first_name: Thomas P. full_name: Jensen, Thomas P. last_name: Jensen - first_name: Inmaculada full_name: Sanchez-Romero, Inmaculada id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87 last_name: Sanchez-Romero - first_name: Colin J. full_name: Jackson, Colin J. last_name: Jackson - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Ole Petter full_name: Ottersen, Ole Petter last_name: Ottersen - first_name: Erlend Arnulf full_name: Nagelhus, Erlend Arnulf last_name: Nagelhus - first_name: Stephane H.R. full_name: Oliet, Stephane H.R. last_name: Oliet - first_name: Michael G. full_name: Stewart, Michael G. last_name: Stewart - first_name: U. VAlentin full_name: Nägerl, U. VAlentin last_name: Nägerl - first_name: 'Dmitri A. ' full_name: 'Rusakov, Dmitri A. ' last_name: Rusakov citation: ama: Henneberger C, Bard L, Panatier A, et al. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 2020;108(5):P919-936.E11. doi:10.1016/j.neuron.2020.08.030 apa: Henneberger, C., Bard, L., Panatier, A., Reynolds, J. P., Kopach, O., Medvedev, N. I., … Rusakov, D. A. (2020). LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.08.030 chicago: Henneberger, Christian, Lucie Bard, Aude Panatier, James P. Reynolds, Olga Kopach, Nikolay I. Medvedev, Daniel Minge, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.08.030. ieee: C. Henneberger et al., “LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia,” Neuron, vol. 108, no. 5. Elsevier, p. P919–936.E11, 2020. ista: Henneberger C, Bard L, Panatier A, Reynolds JP, Kopach O, Medvedev NI, Minge D, Herde MK, Anders S, Kraev I, Heller JP, Rama S, Zheng K, Jensen TP, Sanchez-Romero I, Jackson CJ, Janovjak HL, Ottersen OP, Nagelhus EA, Oliet SHR, Stewart MG, Nägerl UVa, Rusakov DA. 2020. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 108(5), P919–936.E11. mla: Henneberger, Christian, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron, vol. 108, no. 5, Elsevier, 2020, p. P919–936.E11, doi:10.1016/j.neuron.2020.08.030. short: C. Henneberger, L. Bard, A. Panatier, J.P. Reynolds, O. Kopach, N.I. Medvedev, D. Minge, M.K. Herde, S. Anders, I. Kraev, J.P. Heller, S. Rama, K. Zheng, T.P. Jensen, I. Sanchez-Romero, C.J. Jackson, H.L. Janovjak, O.P. Ottersen, E.A. Nagelhus, S.H.R. Oliet, M.G. Stewart, U.Va. Nägerl, D.A. Rusakov, Neuron 108 (2020) P919–936.E11. date_created: 2020-10-18T22:01:38Z date_published: 2020-12-09T00:00:00Z date_updated: 2023-08-22T09:59:29Z day: '09' ddc: - '570' department: - _id: HaJa doi: 10.1016/j.neuron.2020.08.030 external_id: isi: - '000603428000010' pmid: - '32976770' file: - access_level: open_access checksum: 054562bb50165ef9a1f46631c1c5e36b content_type: application/pdf creator: dernst date_created: 2020-12-10T14:42:09Z date_updated: 2020-12-10T14:42:09Z file_id: '8939' file_name: 2020_Neuron_Henneberger.pdf file_size: 7518960 relation: main_file success: 1 file_date_updated: 2020-12-10T14:42:09Z has_accepted_license: '1' intvolume: ' 108' isi: 1 issue: '5' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '12' oa: 1 oa_version: Published Version page: P919-936.E11 pmid: 1 publication: Neuron publication_identifier: eissn: - '10974199' issn: - '08966273' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia 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: 108 year: '2020' ... --- _id: '8652' abstract: - lang: eng text: Nature creates electrons with two values of the spin projection quantum number. In certain applications, it is important to filter electrons with one spin projection from the rest. Such filtering is not trivial, since spin-dependent interactions are often weak, and cannot lead to any substantial effect. Here we propose an efficient spin filter based upon scattering from a two-dimensional crystal, which is made of aligned point magnets. The polarization of the outgoing electron flux is controlled by the crystal, and reaches maximum at specific values of the parameters. In our scheme, polarization increase is accompanied by higher reflectivity of the crystal. High transmission is feasible in scattering from a quantum cavity made of two crystals. Our findings can be used for studies of low-energy spin-dependent scattering from two-dimensional ordered structures made of magnetic atoms or aligned chiral molecules. acknowledgement: "This work has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V. and A.G.). M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting\r\nGrant No. 801770 (ANGULON)." article_number: '178' article_processing_charge: Yes article_type: original author: - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Ghazaryan A, Lemeshko M, Volosniev A. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 2020;3. doi:10.1038/s42005-020-00445-8 apa: Ghazaryan, A., Lemeshko, M., & Volosniev, A. (2020). Filtering spins by scattering from a lattice of point magnets. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-020-00445-8 chicago: Ghazaryan, Areg, Mikhail Lemeshko, and Artem Volosniev. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics. Springer Nature, 2020. https://doi.org/10.1038/s42005-020-00445-8. ieee: A. Ghazaryan, M. Lemeshko, and A. Volosniev, “Filtering spins by scattering from a lattice of point magnets,” Communications Physics, vol. 3. Springer Nature, 2020. ista: Ghazaryan A, Lemeshko M, Volosniev A. 2020. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 3, 178. mla: Ghazaryan, Areg, et al. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics, vol. 3, 178, Springer Nature, 2020, doi:10.1038/s42005-020-00445-8. short: A. Ghazaryan, M. Lemeshko, A. Volosniev, Communications Physics 3 (2020). date_created: 2020-10-13T09:48:59Z date_published: 2020-10-09T00:00:00Z date_updated: 2023-08-22T09:58:46Z day: '09' ddc: - '530' department: - _id: MiLe doi: 10.1038/s42005-020-00445-8 ec_funded: 1 external_id: isi: - '000581681000001' file: - access_level: open_access checksum: 60cd35b99f0780acffc7b6060e49ec8b content_type: application/pdf creator: dernst date_created: 2020-10-14T15:16:28Z date_updated: 2020-10-14T15:16:28Z file_id: '8662' file_name: 2020_CommPhysics_Ghazaryan.pdf file_size: 1462934 relation: main_file success: 1 file_date_updated: 2020-10-14T15:16:28Z has_accepted_license: '1' intvolume: ' 3' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _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: Communications Physics publication_identifier: issn: - 2399-3650 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Filtering spins by scattering from a lattice of point magnets 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: 3 year: '2020' ... --- _id: '8669' abstract: - lang: eng text: Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development. article_number: '5037' article_processing_charge: No article_type: original author: - first_name: Magdalena K. full_name: Sznurkowska, Magdalena K. last_name: Sznurkowska - 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: Roberta full_name: Azzarelli, Roberta last_name: Azzarelli - first_name: Lemonia full_name: Chatzeli, Lemonia last_name: Chatzeli - first_name: Tatsuro full_name: Ikeda, Tatsuro last_name: Ikeda - first_name: Shosei full_name: Yoshida, Shosei last_name: Yoshida - first_name: Anna full_name: Philpott, Anna last_name: Philpott - first_name: Benjamin D full_name: Simons, Benjamin D last_name: Simons citation: ama: Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 2020;11. doi:10.1038/s41467-020-18837-3 apa: Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T., Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18837-3 chicago: Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18837-3. ieee: M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 11, 5037. mla: Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications, vol. 11, 5037, Springer Nature, 2020, doi:10.1038/s41467-020-18837-3. short: M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida, A. Philpott, B.D. Simons, Nature Communications 11 (2020). date_created: 2020-10-18T22:01:35Z date_published: 2020-10-07T00:00:00Z date_updated: 2023-08-22T10:18:17Z day: '07' ddc: - '570' department: - _id: EdHa doi: 10.1038/s41467-020-18837-3 external_id: isi: - '000577244600003' pmid: - '33028844' file: - access_level: open_access checksum: 0ecc0eab72d2d50694852579611a6624 content_type: application/pdf creator: dernst date_created: 2020-10-19T11:27:46Z date_updated: 2020-10-19T11:27:46Z file_id: '8677' file_name: 2020_NatureComm_Sznurkowska.pdf file_size: 5540540 relation: main_file success: 1 file_date_updated: 2020-10-19T11:27:46Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Tracing the cellular basis of islet specification in mouse pancreas 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: '8672' abstract: - lang: eng text: Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions. acknowledgement: This work was supported by the Medical Research Council UK (MRC Program award MC_UU_12018/5 ), the European Research Council (starting grant 311637 -MorphoCorDiv and consolidator grant 820188 -NanoMechShape to E.K.P.), and the Leverhulme Trust (Leverhulme Prize in Biological Sciences to E.K.P.). K.J.C. acknowledges support from the Royal Society (Royal Society Research Fellowship). A.C. acknowledges support from EMBO ( ALTF 2015-563 ), the Wellcome Trust ( 201334/Z/16/Z ), and the Fondation Bettencourt-Schueller (Prix Jeune Chercheur, 2015). article_processing_charge: No article_type: original author: - first_name: Agathe full_name: Chaigne, Agathe last_name: Chaigne - first_name: Céline full_name: Labouesse, Céline last_name: Labouesse - first_name: Ian J. full_name: White, Ian J. last_name: White - first_name: Meghan full_name: Agnew, Meghan last_name: Agnew - 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: Kevin J. full_name: Chalut, Kevin J. last_name: Chalut - first_name: Ewa K. full_name: Paluch, Ewa K. last_name: Paluch citation: ama: Chaigne A, Labouesse C, White IJ, et al. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 2020;55(2):195-208. doi:10.1016/j.devcel.2020.09.001 apa: Chaigne, A., Labouesse, C., White, I. J., Agnew, M., Hannezo, E. B., Chalut, K. J., & Paluch, E. K. (2020). Abscission couples cell division to embryonic stem cell fate. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.09.001 chicago: Chaigne, Agathe, Céline Labouesse, Ian J. White, Meghan Agnew, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.09.001. ieee: A. Chaigne et al., “Abscission couples cell division to embryonic stem cell fate,” Developmental Cell, vol. 55, no. 2. Elsevier, pp. 195–208, 2020. ista: Chaigne A, Labouesse C, White IJ, Agnew M, Hannezo EB, Chalut KJ, Paluch EK. 2020. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 55(2), 195–208. mla: Chaigne, Agathe, et al. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell, vol. 55, no. 2, Elsevier, 2020, pp. 195–208, doi:10.1016/j.devcel.2020.09.001. short: A. Chaigne, C. Labouesse, I.J. White, M. Agnew, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Developmental Cell 55 (2020) 195–208. date_created: 2020-10-18T22:01:37Z date_published: 2020-10-26T00:00:00Z date_updated: 2023-08-22T10:16:58Z day: '26' ddc: - '570' department: - _id: EdHa doi: 10.1016/j.devcel.2020.09.001 external_id: isi: - '000582501100012' pmid: - '32979313' file: - access_level: open_access checksum: 88e1a031a61689165d19a19c2f16d795 content_type: application/pdf creator: dernst date_created: 2021-02-04T10:20:02Z date_updated: 2021-02-04T10:20:02Z file_id: '9086' file_name: 2020_DevelopmCell_Chaigne.pdf file_size: 6929686 relation: main_file success: 1 file_date_updated: 2021-02-04T10:20:02Z has_accepted_license: '1' intvolume: ' 55' isi: 1 issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 195-208 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - '18781551' issn: - '15345807' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Abscission couples cell division to embryonic stem cell fate 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: 55 year: '2020' ... --- _id: '8697' abstract: - lang: eng text: In the computation of the material properties of random alloys, the method of 'special quasirandom structures' attempts to approximate the properties of the alloy on a finite volume with higher accuracy by replicating certain statistics of the random atomic lattice in the finite volume as accurately as possible. In the present work, we provide a rigorous justification for a variant of this method in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach is based on a recent analysis of a related variance reduction method in stochastic homogenization of linear elliptic PDEs and the locality properties of the TFW model. Concerning the latter, we extend an exponential locality result by Nazar and Ortner to include point charges, a result that may be of independent interest. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Michael full_name: Kniely, Michael id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87 last_name: Kniely orcid: 0000-0001-5645-4333 citation: ama: Fischer JL, Kniely M. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 2020;33(11):5733-5772. doi:10.1088/1361-6544/ab9728 apa: Fischer, J. L., & Kniely, M. (2020). Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/ab9728 chicago: Fischer, Julian L, and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity. IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab9728. ieee: J. L. Fischer and M. Kniely, “Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model,” Nonlinearity, vol. 33, no. 11. IOP Publishing, pp. 5733–5772, 2020. ista: Fischer JL, Kniely M. 2020. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 33(11), 5733–5772. mla: Fischer, Julian L., and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity, vol. 33, no. 11, IOP Publishing, 2020, pp. 5733–72, doi:10.1088/1361-6544/ab9728. short: J.L. Fischer, M. Kniely, Nonlinearity 33 (2020) 5733–5772. date_created: 2020-10-25T23:01:16Z date_published: 2020-11-01T00:00:00Z date_updated: 2023-08-22T10:38:38Z day: '01' ddc: - '510' department: - _id: JuFi doi: 10.1088/1361-6544/ab9728 external_id: arxiv: - '1906.12245' isi: - '000576492700001' file: - access_level: open_access checksum: ed90bc6eb5f32ee6157fef7f3aabc057 content_type: application/pdf creator: cziletti date_created: 2020-10-27T12:09:57Z date_updated: 2020-10-27T12:09:57Z file_id: '8710' file_name: 2020_Nonlinearity_Fischer.pdf file_size: 1223899 relation: main_file success: 1 file_date_updated: 2020-10-27T12:09:57Z has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '11' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '11' oa: 1 oa_version: Published Version page: 5733-5772 publication: Nonlinearity publication_identifier: eissn: - '13616544' issn: - '09517715' publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 33 year: '2020' ... --- _id: '8680' abstract: - lang: eng text: Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning. acknowledgement: "We thank the members of the Megason and Heisenberg labs for critical discussions of and technical assistance during the work and B. Appel, S. Holley, J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship of the Company of Biologists, a Collaborative Research grant from the Burroughs Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.)." article_processing_charge: No article_type: original author: - first_name: Tony Y.-C. full_name: Tsai, Tony Y.-C. last_name: Tsai - first_name: Mateusz K full_name: Sikora, Mateusz K id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87 last_name: Sikora - first_name: Peng full_name: Xia, Peng id: 4AB6C7D0-F248-11E8-B48F-1D18A9856A87 last_name: Xia orcid: 0000-0002-5419-7756 - first_name: Tugba full_name: Colak-Champollion, Tugba last_name: Colak-Champollion - first_name: Holger full_name: Knaut, Holger last_name: Knaut - 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 - first_name: Sean G. full_name: Megason, Sean G. last_name: Megason citation: ama: Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 2020;370(6512):113-116. doi:10.1126/science.aba6637 apa: Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg, C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aba6637 chicago: Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion, Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637. ieee: T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association for the Advancement of Science, pp. 113–116, 2020. ista: Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ, Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 370(6512), 113–116. mla: Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637. short: T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J. Heisenberg, S.G. Megason, Science 370 (2020) 113–116. date_created: 2020-10-19T14:09:38Z date_published: 2020-10-02T00:00:00Z date_updated: 2023-08-22T10:36:35Z day: '02' department: - _id: CaHe doi: 10.1126/science.aba6637 ec_funded: 1 external_id: isi: - '000579169000053' intvolume: ' 370' isi: 1 issue: '6512' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/803635v1 month: '10' oa: 1 oa_version: Preprint page: 113-116 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 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/sticking-together/ scopus_import: '1' status: public title: An adhesion code ensures robust pattern formation during tissue morphogenesis type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 370 year: '2020' ... --- _id: '8707' abstract: - lang: eng text: Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data. acknowledgement: 'Work in the Vaquerizas laboratory is funded by the Max Planck Society, the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN to J.M.V.) and the Medical Research Council in the UK. This research was partially funded by the European Union’s H2020 Framework Programme through the European Research Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R. The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia, Innovación y Universidades to the European Molecular Biology Laboratory partnership, the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from the European Regional Development Fund corresponding to the 2014–2020 Smart Growth Operating Program. S.G. thanks the support from the Company of Biologists (grant no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship programme.' article_processing_charge: No article_type: original author: - first_name: Silvia full_name: ' Galan, Silvia' last_name: ' Galan' - first_name: Nick N full_name: Machnik, Nick N id: 3591A0AA-F248-11E8-B48F-1D18A9856A87 last_name: Machnik orcid: 0000-0001-6617-9742 - first_name: Kai full_name: Kruse, Kai last_name: Kruse - first_name: Noelia full_name: Díaz, Noelia last_name: Díaz - first_name: Marc A full_name: Marti-Renom, Marc A last_name: Marti-Renom - first_name: Juan M full_name: Vaquerizas, Juan M last_name: Vaquerizas citation: ama: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y apa: Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas, J. M. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-020-00712-y chicago: Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature, 2020. https://doi.org/10.1038/s41588-020-00712-y. ieee: S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M. Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature, pp. 1247–1255, 2020. ista: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 52, 1247–1255. mla: Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer Nature, 2020, pp. 1247–55, doi:10.1038/s41588-020-00712-y. short: S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas, Nature Genetics 52 (2020) 1247–1255. date_created: 2020-10-25T23:01:20Z date_published: 2020-10-19T00:00:00Z date_updated: 2023-08-22T10:37:10Z day: '19' department: - _id: FyKo doi: 10.1038/s41588-020-00712-y external_id: isi: - '000579693500004' pmid: - '33077914' intvolume: ' 52' isi: 1 language: - iso: eng month: '10' oa_version: None page: 1247-1255 pmid: 1 publication: Nature Genetics publication_identifier: eissn: - '15461718' issn: - '10614036' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 52 year: '2020' ... --- _id: '8679' abstract: - lang: eng text: A central goal of artificial intelligence in high-stakes decision-making applications is to design a single algorithm that simultaneously expresses generalizability by learning coherent representations of their world and interpretable explanations of its dynamics. Here, we combine brain-inspired neural computation principles and scalable deep learning architectures to design compact neural controllers for task-specific compartments of a full-stack autonomous vehicle control system. We discover that a single algorithm with 19 control neurons, connecting 32 encapsulated input features to outputs by 253 synapses, learns to map high-dimensional inputs into steering commands. This system shows superior generalizability, interpretability and robustness compared with orders-of-magnitude larger black-box learning systems. The obtained neural agents enable high-fidelity autonomy for task-specific parts of a complex autonomous system. article_processing_charge: No article_type: original author: - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Ramin full_name: Hasani, Ramin last_name: Hasani - first_name: Alexander full_name: Amini, Alexander last_name: Amini - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Daniela full_name: Rus, Daniela last_name: Rus - first_name: Radu full_name: Grosu, Radu last_name: Grosu citation: ama: Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2020;2:642-652. doi:10.1038/s42256-020-00237-3 apa: Lechner, M., Hasani, R., Amini, A., Henzinger, T. A., Rus, D., & Grosu, R. (2020). Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. Springer Nature. https://doi.org/10.1038/s42256-020-00237-3 chicago: Lechner, Mathias, Ramin Hasani, Alexander Amini, Thomas A Henzinger, Daniela Rus, and Radu Grosu. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature Machine Intelligence. Springer Nature, 2020. https://doi.org/10.1038/s42256-020-00237-3. ieee: M. Lechner, R. Hasani, A. Amini, T. A. Henzinger, D. Rus, and R. Grosu, “Neural circuit policies enabling auditable autonomy,” Nature Machine Intelligence, vol. 2. Springer Nature, pp. 642–652, 2020. ista: Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. 2020. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2, 642–652. mla: Lechner, Mathias, et al. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature Machine Intelligence, vol. 2, Springer Nature, 2020, pp. 642–52, doi:10.1038/s42256-020-00237-3. short: M. Lechner, R. Hasani, A. Amini, T.A. Henzinger, D. Rus, R. Grosu, Nature Machine Intelligence 2 (2020) 642–652. date_created: 2020-10-19T13:46:06Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-08-22T10:36:06Z day: '01' department: - _id: ToHe doi: 10.1038/s42256-020-00237-3 external_id: isi: - '000583337200011' intvolume: ' 2' isi: 1 language: - iso: eng month: '10' oa_version: None page: 642-652 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Nature Machine Intelligence publication_identifier: eissn: - 2522-5839 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/new-deep-learning-models/ scopus_import: '1' status: public title: Neural circuit policies enabling auditable autonomy type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 2 year: '2020' ... --- _id: '8670' abstract: - lang: eng text: The α–z Rényi relative entropies are a two-parameter family of Rényi relative entropies that are quantum generalizations of the classical α-Rényi relative entropies. In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α, z) for which the data processing inequality (DPI) is valid. In this paper, we give algebraic conditions for the equality in DPI. For the full range of parameters (α, z), we give necessary conditions and sufficient conditions. For most parameters, we give equivalent conditions. This generalizes and strengthens the results of Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)]. acknowledgement: This research was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. The author would like to thank Anna Vershynina and Sarah Chehade for their helpful comments. article_number: '102201' article_processing_charge: No article_type: original author: - first_name: Haonan full_name: Zhang, Haonan id: D8F41E38-9E66-11E9-A9E2-65C2E5697425 last_name: Zhang citation: ama: Zhang H. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 2020;61(10). doi:10.1063/5.0022787 apa: Zhang, H. (2020). Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0022787 chicago: Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0022787. ieee: H. Zhang, “Equality conditions of data processing inequality for α-z Rényi relative entropies,” Journal of Mathematical Physics, vol. 61, no. 10. AIP Publishing, 2020. ista: Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 61(10), 102201. mla: Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics, vol. 61, no. 10, 102201, AIP Publishing, 2020, doi:10.1063/5.0022787. short: H. Zhang, Journal of Mathematical Physics 61 (2020). date_created: 2020-10-18T22:01:36Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-08-22T10:32:29Z day: '01' department: - _id: JaMa doi: 10.1063/5.0022787 ec_funded: 1 external_id: arxiv: - '2007.06644' isi: - '000578529200001' intvolume: ' 61' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2007.06644 month: '10' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of Mathematical Physics publication_identifier: issn: - '00222488' publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Equality conditions of data processing inequality for α-z Rényi relative entropies type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 61 year: '2020' ... --- _id: '8698' abstract: - lang: eng text: The brain represents and reasons probabilistically about complex stimuli and motor actions using a noisy, spike-based neural code. A key building block for such neural computations, as well as the basis for supervised and unsupervised learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional neural activity patterns. Despite progress in statistical modeling of neural responses and deep learning, current approaches either do not scale to large neural populations or cannot be implemented using biologically realistic mechanisms. Inspired by the sparse and random connectivity of real neuronal circuits, we present a model for neural codes that accurately estimates the likelihood of individual spiking patterns and has a straightforward, scalable, efficient, learnable, and realistic neural implementation. This model’s performance on simultaneously recorded spiking activity of >100 neurons in the monkey visual and prefrontal cortices is comparable with or better than that of state-of-the-art models. Importantly, the model can be learned using a small number of samples and using a local learning rule that utilizes noise intrinsic to neural circuits. Slower, structural changes in random connectivity, consistent with rewiring and pruning processes, further improve the efficiency and sparseness of the resulting neural representations. Our results merge insights from neuroanatomy, machine learning, and theoretical neuroscience to suggest random sparse connectivity as a key design principle for neuronal computation. acknowledgement: We thank Udi Karpas, Roy Harpaz, Tal Tamir, Adam Haber, and Amir Bar for discussions and suggestions; and especially Oren Forkosh and Walter Senn for invaluable discussions of the learning rule. This work was supported by European Research Council Grant 311238 (to E.S.) and Israel Science Foundation Grant 1629/12 (to E.S.); as well as research support from Martin Kushner Schnur and Mr. and Mrs. Lawrence Feis (E.S.); National Institute of Mental Health Grant R01MH109180 (to R.K.); a Pew Scholarship in Biomedical Sciences (to R.K.); Simons Collaboration on the Global Brain Grant 542997 (to R.K. and E.S.); and a CRCNS (Collaborative Research in Computational Neuroscience) grant (to R.K. and E.S.). article_processing_charge: No article_type: original author: - first_name: Ori full_name: Maoz, Ori last_name: Maoz - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Mohamad Saleh full_name: Esteki, Mohamad Saleh last_name: Esteki - first_name: Roozbeh full_name: Kiani, Roozbeh last_name: Kiani - first_name: Elad full_name: Schneidman, Elad last_name: Schneidman citation: ama: Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):25066-25073. doi:10.1073/pnas.1912804117 apa: Maoz, O., Tkačik, G., Esteki, M. S., Kiani, R., & Schneidman, E. (2020). Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1912804117 chicago: Maoz, Ori, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1912804117. ieee: O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic neural representations with randomly connected circuits,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 25066–25073, 2020. ista: Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. 2020. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 25066–25073. mla: Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 25066–73, doi:10.1073/pnas.1912804117. short: O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 25066–25073. date_created: 2020-10-25T23:01:16Z date_published: 2020-10-06T00:00:00Z date_updated: 2023-08-22T12:11:23Z day: '06' ddc: - '570' department: - _id: GaTk doi: 10.1073/pnas.1912804117 external_id: isi: - '000579045200012' pmid: - '32948691' file: - access_level: open_access checksum: c6a24fdecf3f28faf447078e7a274a88 content_type: application/pdf creator: cziletti date_created: 2020-10-27T14:57:50Z date_updated: 2020-10-27T14:57:50Z file_id: '8713' file_name: 2020_PNAS_Maoz.pdf file_size: 1755359 relation: main_file success: 1 file_date_updated: 2020-10-27T14:57:50Z has_accepted_license: '1' intvolume: ' 117' isi: 1 issue: '40' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '10' oa: 1 oa_version: Published Version page: 25066-25073 pmid: 1 publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - '10916490' issn: - '00278424' publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Learning probabilistic neural representations with randomly connected circuits 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: 117 year: '2020' ... --- _id: '8704' abstract: - lang: eng text: Traditional robotic control suits require profound task-specific knowledge for designing, building and testing control software. The rise of Deep Learning has enabled end-to-end solutions to be learned entirely from data, requiring minimal knowledge about the application area. We design a learning scheme to train end-to-end linear dynamical systems (LDS)s by gradient descent in imitation learning robotic domains. We introduce a new regularization loss component together with a learning algorithm that improves the stability of the learned autonomous system, by forcing the eigenvalues of the internal state updates of an LDS to be negative reals. We evaluate our approach on a series of real-life and simulated robotic experiments, in comparison to linear and nonlinear Recurrent Neural Network (RNN) architectures. Our results show that our stabilizing method significantly improves test performance of LDS, enabling such linear models to match the performance of contemporary nonlinear RNN architectures. A video of the obstacle avoidance performance of our method on a mobile robot, in unseen environments, compared to other methods can be viewed at https://youtu.be/mhEsCoNao5E. acknowledgement: M.L. is supported in parts by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). R.H., and R.G. are partially supported by the Horizon-2020 ECSELProject grant No. 783163 (iDev40), and the Austrian Research Promotion Agency (FFG), Project No. 860424. R.H. and D.R. is partially supported by the Boeing Company. alternative_title: - ICRA article_processing_charge: No author: - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Ramin full_name: Hasani, Ramin last_name: Hasani - first_name: Daniela full_name: Rus, Daniela last_name: Rus - first_name: Radu full_name: Grosu, Radu last_name: Grosu citation: ama: 'Lechner M, Hasani R, Rus D, Grosu R. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In: Proceedings - IEEE International Conference on Robotics and Automation. IEEE; 2020:5446-5452. doi:10.1109/ICRA40945.2020.9196608' apa: 'Lechner, M., Hasani, R., Rus, D., & Grosu, R. (2020). Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In Proceedings - IEEE International Conference on Robotics and Automation (pp. 5446–5452). Paris, France: IEEE. https://doi.org/10.1109/ICRA40945.2020.9196608' chicago: Lechner, Mathias, Ramin Hasani, Daniela Rus, and Radu Grosu. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” In Proceedings - IEEE International Conference on Robotics and Automation, 5446–52. IEEE, 2020. https://doi.org/10.1109/ICRA40945.2020.9196608. ieee: M. Lechner, R. Hasani, D. Rus, and R. Grosu, “Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme,” in Proceedings - IEEE International Conference on Robotics and Automation, Paris, France, 2020, pp. 5446–5452. ista: 'Lechner M, Hasani R, Rus D, Grosu R. 2020. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, , 5446–5452.' mla: Lechner, Mathias, et al. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–52, doi:10.1109/ICRA40945.2020.9196608. short: M. Lechner, R. Hasani, D. Rus, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–5452. conference: end_date: 2020-08-31 location: Paris, France name: 'ICRA: International Conference on Robotics and Automation' start_date: 2020-05-31 date_created: 2020-10-25T23:01:19Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-08-22T10:40:15Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1109/ICRA40945.2020.9196608 external_id: isi: - '000712319503110' file: - access_level: open_access checksum: fccf7b986ac78046918a298cc6849a50 content_type: application/pdf creator: dernst date_created: 2020-11-06T10:58:49Z date_updated: 2020-11-06T10:58:49Z file_id: '8733' file_name: 2020_ICRA_Lechner.pdf file_size: 1070010 relation: main_file success: 1 file_date_updated: 2020-11-06T10:58:49Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 5446-5452 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Proceedings - IEEE International Conference on Robotics and Automation publication_identifier: isbn: - '9781728173955' issn: - '10504729' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2020' ... --- _id: '8700' abstract: - lang: eng text: Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency. acknowledgement: We would like to thank the staff of CCU Genome for sequencing, Tat’yana Pestova, Christopher Helen, and Lyudmila Yur’evna Frolova for the plasmids provided, as well as the laboratory staff for productive discussion of the results. We also thank former laboratory employees Yuliya Vladimirovna Bocharova and Polina Nikolaevna Kryuchkova for the exceptional contribution to the present work. article_processing_charge: No article_type: original author: - first_name: E. E. full_name: Sokolova, E. E. last_name: Sokolova - first_name: Petr full_name: Vlasov, Petr id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87 last_name: Vlasov - first_name: T. V. full_name: Egorova, T. V. last_name: Egorova - first_name: A. V. full_name: Shuvalov, A. V. last_name: Shuvalov - first_name: E. Z. full_name: Alkalaeva, E. Z. last_name: Alkalaeva citation: ama: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 2020;54(5):739-748. doi:10.1134/S0026893320050088 apa: Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320050088 chicago: Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320050088. ieee: E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” Molecular Biology, vol. 54, no. 5. Springer Nature, pp. 739–748, 2020. ista: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 54(5), 739–748. mla: Sokolova, E. E., et al. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology, vol. 54, no. 5, Springer Nature, 2020, pp. 739–48, doi:10.1134/S0026893320050088. short: E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular Biology 54 (2020) 739–748. date_created: 2020-10-25T23:01:17Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-08-22T10:39:38Z day: '01' department: - _id: FyKo doi: 10.1134/S0026893320050088 external_id: isi: - '000579441200009' intvolume: ' 54' isi: 1 issue: '5' language: - iso: eng month: '09' oa_version: None page: 739-748 publication: Molecular Biology publication_identifier: eissn: - '16083245' issn: - '00268933' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8701' relation: original status: public scopus_import: '1' status: public title: The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 54 year: '2020' ... --- _id: '8701' abstract: - lang: eng text: Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency. article_processing_charge: No article_type: original author: - first_name: E. E. full_name: Sokolova, E. E. last_name: Sokolova - first_name: Petr full_name: Vlasov, Petr id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87 last_name: Vlasov - first_name: T. V. full_name: Egorova, T. V. last_name: Egorova - first_name: A. V. full_name: Shuvalov, A. V. last_name: Shuvalov - first_name: E. Z. full_name: Alkalaeva, E. Z. last_name: Alkalaeva citation: ama: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 2020;54(5):837-848. doi:10.31857/S0026898420050080 apa: Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420050080 chicago: Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420050080. ieee: E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” Molekuliarnaia biologiia, vol. 54, no. 5. Russian Academy of Sciences, pp. 837–848, 2020. ista: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 54(5), 837–848. mla: Sokolova, E. E., et al. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia biologiia, vol. 54, no. 5, Russian Academy of Sciences, 2020, pp. 837–48, doi:10.31857/S0026898420050080. short: E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 837–848. date_created: 2020-10-25T23:01:17Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-08-22T10:39:37Z day: '01' department: - _id: FyKo doi: 10.31857/S0026898420050080 external_id: pmid: - '33009793' intvolume: ' 54' issue: '5' language: - iso: rus month: '09' oa_version: None page: 837-848 pmid: 1 publication: Molekuliarnaia biologiia publication_identifier: issn: - '00268984' publication_status: published publisher: Russian Academy of Sciences quality_controlled: '1' related_material: record: - id: '8700' relation: translation status: public scopus_import: '1' status: public title: The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 54 year: '2020' ... --- _id: '8699' abstract: - lang: eng text: In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground state to the details of the local lattice structure shows a large potential for the manipulation of the functional properties by inducing local lattice distortions. We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and at the ligand sites to unveil the response of the low-energy elementary excitations. We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films displays large softening along the [h,0] direction, while along the [h,h] direction it shows hardening. This evolution reveals a renormalization of the magnetic interactions caused by a strain-driven cross-over from anisotropic to isotropic interactions between the magnetic moments. Moreover, we detect dispersive electron–hole pair excitations which shift to lower (higher) energies upon compressive (tensile) strain, manifesting a reduction (increase) in the size of the charge gap. This behavior shows an intimate coupling between charge excitations and lattice distortions in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals. Our work highlights the central role played by the lattice degrees of freedom in determining both the pseudospin and charge excitations of Sr2IrO4 and provides valuable information toward the control of the ground state of complex oxides in the presence of high spin–orbit coupling. acknowledgement: 'We gratefully acknowledge C. Sahle for experimental support at the ID20 beamline of the ESRF. The soft X-ray experiments were carried out at the ADRESS beamline of the Swiss Light Source, Paul Scherrer Institut (PSI). E. Paris and T.S. thank X. Lu and C. Monney for valuable discussions. The work at PSI is supported by the Swiss National Science Foundation (SNSF) through Project 200021_178867, the NCCR (National Centre of Competence in Research) MARVEL (Materials’ Revolution: Computational Design and Discovery of Novel Materials) and the Sinergia network Mott Physics Beyond the Heisenberg Model (MPBH) (SNSF Research Grants CRSII2_160765/1 and CRSII2_141962). K.W. acknowledges support by the Narodowe Centrum Nauki Projects 2016/22/E/ST3/00560 and 2016/23/B/ST3/00839. E.M.P. and M.N. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreements 754411 and 701647, respectively. M.R. was supported by the Swiss National Science Foundation under Project 200021 – 182695. This research used resources of the APS, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357.' article_processing_charge: No article_type: original author: - first_name: Eugenio full_name: Paris, Eugenio last_name: Paris - first_name: Yi full_name: Tseng, Yi last_name: Tseng - first_name: Ekaterina full_name: Paerschke, Ekaterina id: 8275014E-6063-11E9-9B7F-6338E6697425 last_name: Paerschke orcid: 0000-0003-0853-8182 - first_name: Wenliang full_name: Zhang, Wenliang last_name: Zhang - first_name: Mary H full_name: Upton, Mary H last_name: Upton - first_name: Anna full_name: Efimenko, Anna last_name: Efimenko - first_name: Katharina full_name: Rolfs, Katharina last_name: Rolfs - first_name: Daniel E full_name: McNally, Daniel E last_name: McNally - first_name: Laura full_name: Maurel, Laura last_name: Maurel - first_name: Muntaser full_name: Naamneh, Muntaser last_name: Naamneh - first_name: Marco full_name: Caputo, Marco last_name: Caputo - first_name: Vladimir N full_name: Strocov, Vladimir N last_name: Strocov - first_name: Zhiming full_name: Wang, Zhiming last_name: Wang - first_name: Diego full_name: Casa, Diego last_name: Casa - first_name: Christof W full_name: Schneider, Christof W last_name: Schneider - first_name: Ekaterina full_name: Pomjakushina, Ekaterina last_name: Pomjakushina - first_name: Krzysztof full_name: Wohlfeld, Krzysztof last_name: Wohlfeld - first_name: Milan full_name: Radovic, Milan last_name: Radovic - first_name: Thorsten full_name: Schmitt, Thorsten last_name: Schmitt citation: ama: Paris E, Tseng Y, Paerschke E, et al. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):24764-24770. doi:10.1073/pnas.2012043117 apa: Paris, E., Tseng, Y., Paerschke, E., Zhang, W., Upton, M. H., Efimenko, A., … Schmitt, T. (2020). Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2012043117 chicago: Paris, Eugenio, Yi Tseng, Ekaterina Paerschke, Wenliang Zhang, Mary H Upton, Anna Efimenko, Katharina Rolfs, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2012043117. ieee: E. Paris et al., “Strain engineering of the charge and spin-orbital interactions in Sr2IrO4,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 24764–24770, 2020. ista: Paris E, Tseng Y, Paerschke E, Zhang W, Upton MH, Efimenko A, Rolfs K, McNally DE, Maurel L, Naamneh M, Caputo M, Strocov VN, Wang Z, Casa D, Schneider CW, Pomjakushina E, Wohlfeld K, Radovic M, Schmitt T. 2020. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 24764–24770. mla: Paris, Eugenio, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 24764–70, doi:10.1073/pnas.2012043117. short: E. Paris, Y. Tseng, E. Paerschke, W. Zhang, M.H. Upton, A. Efimenko, K. Rolfs, D.E. McNally, L. Maurel, M. Naamneh, M. Caputo, V.N. Strocov, Z. Wang, D. Casa, C.W. Schneider, E. Pomjakushina, K. Wohlfeld, M. Radovic, T. Schmitt, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 24764–24770. date_created: 2020-10-25T23:01:17Z date_published: 2020-10-06T00:00:00Z date_updated: 2023-08-22T12:11:52Z day: '06' ddc: - '530' department: - _id: MiLe doi: 10.1073/pnas.2012043117 ec_funded: 1 external_id: arxiv: - '2009.12262' isi: - '000579059100029' pmid: - '32958669' file: - access_level: open_access checksum: 1638fa36b442e2868576c6dd7d6dc505 content_type: application/pdf creator: cziletti date_created: 2020-10-28T11:53:12Z date_updated: 2020-10-28T11:53:12Z file_id: '8715' file_name: 2020_PNAS_Paris.pdf file_size: 1176522 relation: main_file success: 1 file_date_updated: 2020-10-28T11:53:12Z has_accepted_license: '1' intvolume: ' 117' isi: 1 issue: '40' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 24764-24770 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - '10916490' issn: - '00278424' publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Strain engineering of the charge and spin-orbital interactions in Sr2IrO4 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: 117 year: '2020' ... --- _id: '8737' abstract: - lang: eng text: Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions. acknowledged_ssus: - _id: LifeSc - _id: EM-Fac acknowledgement: We thank J. Novacek (CEITEC Brno) and V.-V. Hodirnau (IST Austria) for their help with collecting cryo-EM datasets. We thank the IST Life Science and Electron Microscopy Facilities for providing equipment. This work has been supported by iNEXT,project number 653706, funded by the Horizon 2020 program of the European Union. This article reflects only the authors’view,and the European Commission is not responsible for any use that may be made of the information it contains. CIISB research infrastructure project LM2015043 funded by MEYS CR is gratefully acknowledged for the financial support of the measurements at the CF Cryo-electron Microscopy and Tomography CEITEC MU.This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement no. 665385 article_number: eabc4209 article_processing_charge: No article_type: original author: - first_name: Domen full_name: Kampjut, Domen id: 37233050-F248-11E8-B48F-1D18A9856A87 last_name: Kampjut - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Kampjut D, Sazanov LA. The coupling mechanism of mammalian respiratory complex I. Science. 2020;370(6516). doi:10.1126/science.abc4209 apa: Kampjut, D., & Sazanov, L. A. (2020). The coupling mechanism of mammalian respiratory complex I. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abc4209 chicago: Kampjut, Domen, and Leonid A Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.abc4209. ieee: D. Kampjut and L. A. Sazanov, “The coupling mechanism of mammalian respiratory complex I,” Science, vol. 370, no. 6516. American Association for the Advancement of Science, 2020. ista: Kampjut D, Sazanov LA. 2020. The coupling mechanism of mammalian respiratory complex I. Science. 370(6516), eabc4209. mla: Kampjut, Domen, and Leonid A. Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” Science, vol. 370, no. 6516, eabc4209, American Association for the Advancement of Science, 2020, doi:10.1126/science.abc4209. short: D. Kampjut, L.A. Sazanov, Science 370 (2020). date_created: 2020-11-08T23:01:23Z date_published: 2020-10-30T00:00:00Z date_updated: 2023-08-22T12:35:38Z day: '30' ddc: - '572' department: - _id: LeSa doi: 10.1126/science.abc4209 ec_funded: 1 external_id: isi: - '000583031800004' pmid: - '32972993' file: - access_level: open_access checksum: 658ba90979ca9528a2efdfac8547047a content_type: application/pdf creator: lsazanov date_created: 2020-11-26T18:47:58Z date_updated: 2020-11-26T18:47:58Z file_id: '8820' file_name: Full_manuscript_with_SI_opt_red.pdf file_size: 7618987 relation: main_file success: 1 file_date_updated: 2020-11-26T18:47:58Z has_accepted_license: '1' intvolume: ' 370' isi: 1 issue: '6516' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version pmid: 1 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Science publication_identifier: eissn: - '10959203' publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: The coupling mechanism of mammalian respiratory complex I type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 370 year: '2020' ... --- _id: '8722' abstract: - lang: eng text: "Load imbalance pervasively exists in distributed deep learning training systems, either caused by the inherent imbalance in learned tasks or by the system itself. Traditional synchronous Stochastic Gradient Descent (SGD)\r\nachieves good accuracy for a wide variety of tasks, but relies on global synchronization to accumulate the gradients at every training step. In this paper, we propose eager-SGD, which relaxes the global synchronization for\r\ndecentralized accumulation. To implement eager-SGD, we propose to use two partial collectives: solo and majority. With solo allreduce, the faster processes contribute their gradients eagerly without waiting for the slower processes, whereas with majority allreduce, at least half of the participants must contribute gradients before continuing, all without using a central parameter server. We theoretically prove the convergence of the algorithms and describe the partial collectives in detail. Experimental results on load-imbalanced environments (CIFAR-10, ImageNet, and UCF101 datasets) show\r\nthat eager-SGD achieves 1.27x speedup over the state-of-the-art synchronous SGD, without losing accuracy." article_processing_charge: No author: - first_name: Shigang full_name: Li, Shigang last_name: Li - first_name: Tal Ben-Nun full_name: Tal Ben-Nun, Tal Ben-Nun last_name: Tal Ben-Nun - first_name: Salvatore Di full_name: Girolamo, Salvatore Di last_name: Girolamo - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Torsten full_name: Hoefler, Torsten last_name: Hoefler citation: ama: 'Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. Taming unbalanced training workloads in deep learning with partial collective operations. In: Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2020:45-61. doi:10.1145/3332466.3374528' apa: 'Li, S., Tal Ben-Nun, T. B.-N., Girolamo, S. D., Alistarh, D.-A., & Hoefler, T. (2020). Taming unbalanced training workloads in deep learning with partial collective operations. In Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 45–61). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374528' chicago: Li, Shigang, Tal Ben-Nun Tal Ben-Nun, Salvatore Di Girolamo, Dan-Adrian Alistarh, and Torsten Hoefler. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” In Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 45–61. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374528. ieee: S. Li, T. B.-N. Tal Ben-Nun, S. D. Girolamo, D.-A. Alistarh, and T. Hoefler, “Taming unbalanced training workloads in deep learning with partial collective operations,” in Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Diego, CA, United States, 2020, pp. 45–61. ista: 'Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. 2020. Taming unbalanced training workloads in deep learning with partial collective operations. Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 45–61.' mla: Li, Shigang, et al. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61, doi:10.1145/3332466.3374528. short: S. Li, T.B.-N. Tal Ben-Nun, S.D. Girolamo, D.-A. Alistarh, T. Hoefler, in:, Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61. conference: end_date: 2020-02-26 location: San Diego, CA, United States name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming' start_date: 2020-02-22 date_created: 2020-11-05T15:25:30Z date_published: 2020-02-01T00:00:00Z date_updated: 2023-08-22T12:13:48Z day: '01' department: - _id: DaAl doi: 10.1145/3332466.3374528 ec_funded: 1 external_id: arxiv: - '1908.04207' isi: - '000564476500004' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1908.04207 month: '02' oa: 1 oa_version: Preprint page: 45-61 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' status: public title: Taming unbalanced training workloads in deep learning with partial collective operations type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2020' ... --- _id: '8744' abstract: - lang: eng text: Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding. acknowledgement: 'We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe, Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG graduate college: CLiC.' article_number: '5569' article_processing_charge: No article_type: original author: - first_name: Linda full_name: Schulte, Linda last_name: Schulte - first_name: Jiafei full_name: Mao, Jiafei last_name: Mao - first_name: Julian full_name: Reitz, Julian last_name: Reitz - first_name: Sridhar full_name: Sreeramulu, Sridhar last_name: Sreeramulu - first_name: Denis full_name: Kudlinzki, Denis last_name: Kudlinzki - first_name: Victor-Valentin full_name: Hodirnau, Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau - first_name: Jakob full_name: Meier-Credo, Jakob last_name: Meier-Credo - first_name: Krishna full_name: Saxena, Krishna last_name: Saxena - first_name: Florian full_name: Buhr, Florian last_name: Buhr - first_name: Julian D. full_name: Langer, Julian D. last_name: Langer - first_name: Martin full_name: Blackledge, Martin last_name: Blackledge - first_name: Achilleas S. full_name: Frangakis, Achilleas S. last_name: Frangakis - first_name: Clemens full_name: Glaubitz, Clemens last_name: Glaubitz - first_name: Harald full_name: Schwalbe, Harald last_name: Schwalbe citation: ama: Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 2020;11. doi:10.1038/s41467-020-19372-x apa: Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V., … Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19372-x chicago: Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki, Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19372-x. ieee: L. Schulte et al., “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 11, 5569. mla: Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications, vol. 11, 5569, Springer Nature, 2020, doi:10.1038/s41467-020-19372-x. short: L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau, J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis, C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020). date_created: 2020-11-09T07:49:36Z date_published: 2020-11-04T00:00:00Z date_updated: 2023-08-22T12:36:07Z day: '04' ddc: - '570' department: - _id: EM-Fac doi: 10.1038/s41467-020-19372-x external_id: isi: - '000592028600001' file: - access_level: open_access checksum: b2688f0347e69e6629bba582077278c5 content_type: application/pdf creator: dernst date_created: 2020-11-09T07:56:24Z date_updated: 2020-11-09T07:56:24Z file_id: '8745' file_name: 2020_NatureComm_Schulte.pdf file_size: 1670898 relation: main_file success: 1 file_date_updated: 2020-11-09T07:56:24Z has_accepted_license: '1' intvolume: ' 11' isi: 1 keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Cysteine oxidation and disulfide formation in the ribosomal exit tunnel 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: '8747' abstract: - lang: eng text: "Appropriately designed nanocomposites allow improving the thermoelectric performance by several mechanisms, including phonon scattering, modulation doping and energy filtering, while additionally promoting better mechanical properties than those of crystalline materials. Here, a strategy for producing Bi2Te3–Cu2xTe nanocomposites based on the consolidation of heterostructured nanoparticles is described and the thermoelectric properties of the obtained materials are investigated. We first detail a two-step solution-based process to produce Bi2Te3–Cu2xTe heteronanostructures, based on the growth of Cu2xTe nanocrystals on the surface of Bi2Te3 nanowires. We characterize the structural and chemical properties of the synthesized nanostructures and of the nanocomposites\r\nproduced by hot-pressing the particles at moderate temperatures. Besides, the transport properties of the nanocomposites are investigated as a function of the amount of Cu introduced. Overall, the presence of Cu decreases the material thermal conductivity through promotion of phonon scattering, modulates the charge carrier concentration through electron spillover, and increases the Seebeck coefficient through filtering of charge carriers at energy barriers. These effects result in an improvement of over 50% of the thermoelectric figure of merit of Bi2Te3." acknowledgement: "This work was supported by the European Regional Development Funds and by the Spanish Ministerio de Economı´a y\r\nCompetitividad through the project SEHTOP (ENE2016-77798-C4-3-R). Y. Z. and X. H., thank the China Scholarship Council for scholarship support. M. C. has received funding from the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. M. I. acknowledges financial support from IST Austria. Y. L. acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie grant agreement no. 754411. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project ENE2017-85087-C3. ICN2 is supported by the Severo Ochoa program from the Spanish MINECO (grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat \r\nAuto`noma de Barcelona Materials Science PhD program." article_processing_charge: No article_type: original author: - first_name: Yu full_name: Zhang, Yu last_name: Zhang - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Mariano full_name: Calcabrini, Mariano last_name: Calcabrini - first_name: Congcong full_name: Xing, Congcong last_name: Xing - first_name: Xu full_name: Han, Xu last_name: Han - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Zhang Y, Liu Y, Calcabrini M, et al. Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. Journal of Materials Chemistry C. 2020;8(40):14092-14099. doi:10.1039/D0TC02182B apa: Zhang, Y., Liu, Y., Calcabrini, M., Xing, C., Han, X., Arbiol, J., … Cabot, A. (2020). Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. Journal of Materials Chemistry C. Royal Society of Chemistry. https://doi.org/10.1039/D0TC02182B chicago: Zhang, Yu, Yu Liu, Mariano Calcabrini, Congcong Xing, Xu Han, Jordi Arbiol, Doris Cadavid, Maria Ibáñez, and Andreu Cabot. “Bismuth Telluride-Copper Telluride Nanocomposites from Heterostructured Building Blocks.” Journal of Materials Chemistry C. Royal Society of Chemistry, 2020. https://doi.org/10.1039/D0TC02182B. ieee: Y. Zhang et al., “Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks,” Journal of Materials Chemistry C, vol. 8, no. 40. Royal Society of Chemistry, pp. 14092–14099, 2020. ista: Zhang Y, Liu Y, Calcabrini M, Xing C, Han X, Arbiol J, Cadavid D, Ibáñez M, Cabot A. 2020. Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. Journal of Materials Chemistry C. 8(40), 14092–14099. mla: Zhang, Yu, et al. “Bismuth Telluride-Copper Telluride Nanocomposites from Heterostructured Building Blocks.” Journal of Materials Chemistry C, vol. 8, no. 40, Royal Society of Chemistry, 2020, pp. 14092–99, doi:10.1039/D0TC02182B. short: Y. Zhang, Y. Liu, M. Calcabrini, C. Xing, X. Han, J. Arbiol, D. Cadavid, M. Ibáñez, A. Cabot, Journal of Materials Chemistry C 8 (2020) 14092–14099. date_created: 2020-11-09T08:37:51Z date_published: 2020-10-28T00:00:00Z date_updated: 2023-08-22T12:41:05Z day: '28' department: - _id: MaIb doi: 10.1039/D0TC02182B ec_funded: 1 external_id: isi: - '000581559100015' intvolume: ' 8' isi: 1 issue: '40' language: - iso: eng month: '10' oa_version: None page: 14092-14099 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of Materials Chemistry C publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 8 year: '2020' ... --- _id: '8767' abstract: - lang: eng text: Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring. acknowledgement: 'We thank Igor Erovenko for many helpful comments on an earlier version of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation (A.M.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.' article_number: e1008402 article_processing_charge: No article_type: original author: - first_name: Kamran full_name: Kaveh, Kamran last_name: Kaveh - first_name: Alex full_name: McAvoy, Alex last_name: McAvoy - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin A. full_name: Nowak, Martin A. last_name: Nowak citation: ama: Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 2020;16(11). doi:10.1371/journal.pcbi.1008402 apa: Kaveh, K., McAvoy, A., Chatterjee, K., & Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008402 chicago: Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1008402. ieee: K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” PLOS Computational Biology, vol. 16, no. 11. Public Library of Science, 2020. ista: Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402. mla: Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1008402. short: K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020). date_created: 2020-11-18T07:20:23Z date_published: 2020-11-05T00:00:00Z date_updated: 2023-08-22T12:49:18Z day: '05' ddc: - '000' department: - _id: KrCh doi: 10.1371/journal.pcbi.1008402 external_id: isi: - '000591317200004' file: - access_level: open_access checksum: 555456dd0e47bcf9e0994bcb95577e88 content_type: application/pdf creator: dernst date_created: 2020-11-18T07:26:10Z date_updated: 2020-11-18T07:26:10Z file_id: '8768' file_name: 2020_PlosCompBio_Kaveh.pdf file_size: 2498594 relation: main_file success: 1 file_date_updated: 2020-11-18T07:26:10Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '11' keyword: - Ecology - Modelling and Simulation - Computational Theory and Mathematics - Genetics - Ecology - Evolution - Behavior and Systematics - Molecular Biology - Cellular and Molecular Neuroscience language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: PLOS Computational Biology publication_identifier: eissn: - 1553-7358 issn: - 1553-734X publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: The Moran process on 2-chromatic graphs 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: 16 year: '2020' ... --- _id: '8750' abstract: - lang: eng text: "Efficiently handling time-triggered and possibly nondeterministic switches\r\nfor hybrid systems reachability is a challenging task. In this paper we present\r\nan approach based on conservative set-based enclosure of the dynamics that can\r\nhandle systems with uncertain parameters and inputs, where the uncertainties\r\nare bound to given intervals. The method is evaluated on the plant model of an\r\nexperimental electro-mechanical braking system with periodic controller. In\r\nthis model, the fast-switching controller dynamics requires simulation time\r\nscales of the order of nanoseconds. Accurate set-based computations for\r\nrelatively large time horizons are known to be expensive. However, by\r\nappropriately decoupling the time variable with respect to the spatial\r\nvariables, and enclosing the uncertain parameters using interval matrix maps\r\nacting on zonotopes, we show that the computation time can be lowered to 5000\r\ntimes faster with respect to previous works. This is a step forward in formal\r\nverification of hybrid systems because reduced run-times allow engineers to\r\nintroduce more expressiveness in their models with a relatively inexpensive\r\ncomputational cost." article_number: '9314994' article_processing_charge: No author: - first_name: Marcelo full_name: Forets, Marcelo last_name: Forets - first_name: Daniel full_name: Freire, Daniel last_name: Freire - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 citation: ama: 'Forets M, Freire D, Schilling C. Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions. In: 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE; 2020. doi:10.1109/MEMOCODE51338.2020.9314994' apa: 'Forets, M., Freire, D., & Schilling, C. (2020). Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions. In 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. Virtual Conference: IEEE. https://doi.org/10.1109/MEMOCODE51338.2020.9314994' chicago: Forets, Marcelo, Daniel Freire, and Christian Schilling. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with  Time-Triggered Transitions.” In 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE, 2020. https://doi.org/10.1109/MEMOCODE51338.2020.9314994. ieee: M. Forets, D. Freire, and C. Schilling, “Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions,” in 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, Virtual Conference, 2020. ista: 'Forets M, Freire D, Schilling C. 2020. Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions. 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. MEMOCODE: Conference on Formal Methods and Models for System Design, 9314994.' mla: Forets, Marcelo, et al. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with  Time-Triggered Transitions.” 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, 9314994, IEEE, 2020, doi:10.1109/MEMOCODE51338.2020.9314994. short: M. Forets, D. Freire, C. Schilling, in:, 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, IEEE, 2020. conference: end_date: 2020-12-04 location: Virtual Conference name: 'MEMOCODE: Conference on Formal Methods and Models for System Design' start_date: 2020-12-02 date_created: 2020-11-10T07:04:57Z date_published: 2020-12-04T00:00:00Z date_updated: 2023-08-22T12:48:18Z day: '04' department: - _id: ToHe doi: 10.1109/MEMOCODE51338.2020.9314994 ec_funded: 1 external_id: arxiv: - '2006.12325' isi: - '000661920400013' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2006.12325 month: '12' oa: 1 oa_version: Preprint project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: 18th ACM-IEEE International Conference on Formal Methods and Models for System Design publication_identifier: isbn: - '9781728191485' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2020' ...