--- _id: '8793' abstract: - lang: eng text: We study optimal election sequences for repeatedly selecting a (very) small group of leaders among a set of participants (players) with publicly known unique ids. In every time slot, every player has to select exactly one player that it considers to be the current leader, oblivious to the selection of the other players, but with the overarching goal of maximizing a given parameterized global (“social”) payoff function in the limit. We consider a quite generic model, where the local payoff achieved by a given player depends, weighted by some arbitrary but fixed real parameter, on the number of different leaders chosen in a round, the number of players that choose the given player as the leader, and whether the chosen leader has changed w.r.t. the previous round or not. The social payoff can be the maximum, average or minimum local payoff of the players. Possible applications include quite diverse examples such as rotating coordinator-based distributed algorithms and long-haul formation flying of social birds. Depending on the weights and the particular social payoff, optimal sequences can be very different, from simple round-robin where all players chose the same leader alternatingly every time slot to very exotic patterns, where a small group of leaders (at most 2) is elected in every time slot. Moreover, we study the question if and when a single player would not benefit w.r.t. its local payoff when deviating from the given optimal sequence, i.e., when our optimal sequences are Nash equilibria in the restricted strategy space of oblivious strategies. As this is the case for many parameterizations of our model, our results reveal that no punishment is needed to make it rational for the players to optimize the social payoff. acknowledgement: "We are grateful to Matthias Függer and Thomas Nowak for having raised our interest in the problem studied in this paper.\r\nThis work has been supported the Austrian Science Fund (FWF) projects S11405, S11407 (RiSE), and P28182 (ADynNet)." article_processing_charge: No article_type: original author: - first_name: Martin full_name: Zeiner, Martin last_name: Zeiner - first_name: Ulrich full_name: Schmid, Ulrich last_name: Schmid - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: Zeiner M, Schmid U, Chatterjee K. Optimal strategies for selecting coordinators. Discrete Applied Mathematics. 2021;289(1):392-415. doi:10.1016/j.dam.2020.10.022 apa: Zeiner, M., Schmid, U., & Chatterjee, K. (2021). Optimal strategies for selecting coordinators. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2020.10.022 chicago: Zeiner, Martin, Ulrich Schmid, and Krishnendu Chatterjee. “Optimal Strategies for Selecting Coordinators.” Discrete Applied Mathematics. Elsevier, 2021. https://doi.org/10.1016/j.dam.2020.10.022. ieee: M. Zeiner, U. Schmid, and K. Chatterjee, “Optimal strategies for selecting coordinators,” Discrete Applied Mathematics, vol. 289, no. 1. Elsevier, pp. 392–415, 2021. ista: Zeiner M, Schmid U, Chatterjee K. 2021. Optimal strategies for selecting coordinators. Discrete Applied Mathematics. 289(1), 392–415. mla: Zeiner, Martin, et al. “Optimal Strategies for Selecting Coordinators.” Discrete Applied Mathematics, vol. 289, no. 1, Elsevier, 2021, pp. 392–415, doi:10.1016/j.dam.2020.10.022. short: M. Zeiner, U. Schmid, K. Chatterjee, Discrete Applied Mathematics 289 (2021) 392–415. date_created: 2020-11-22T23:01:26Z date_published: 2021-01-31T00:00:00Z date_updated: 2023-08-04T11:12:41Z day: '31' ddc: - '510' department: - _id: KrCh doi: 10.1016/j.dam.2020.10.022 external_id: isi: - '000596823800035' file: - access_level: open_access checksum: f1039ff5a2d6ca116720efdb84ee9d5e content_type: application/pdf creator: dernst date_created: 2021-02-04T11:28:42Z date_updated: 2021-02-04T11:28:42Z file_id: '9089' file_name: 2021_DiscreteApplMath_Zeiner.pdf file_size: 652739 relation: main_file success: 1 file_date_updated: 2021-02-04T11:28:42Z has_accepted_license: '1' intvolume: ' 289' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 392-415 project: - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: Discrete Applied Mathematics publication_identifier: issn: - 0166218X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Optimal strategies for selecting coordinators 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: 289 year: '2021' ... --- _id: '8816' abstract: - lang: eng text: Area-dependent quantum field theory is a modification of two-dimensional topological quantum field theory, where one equips each connected component of a bordism with a positive real number—interpreted as area—which behaves additively under glueing. As opposed to topological theories, in area-dependent theories the state spaces can be infinite-dimensional. We introduce the notion of regularised Frobenius algebras in Hilbert spaces and show that area-dependent theories are in one-to-one correspondence to commutative regularised Frobenius algebras. We also provide a state sum construction for area-dependent theories. Our main example is two-dimensional Yang–Mills theory with compact gauge group, which we treat in detail. acknowledgement: The authors thank Yuki Arano, Nils Carqueville, Alexei Davydov, Reiner Lauterbach, Pau Enrique Moliner, Chris Heunen, André Henriques, Ehud Meir, Catherine Meusburger, Gregor Schaumann, Richard Szabo and Stefan Wagner for helpful discussions and comments. We also thank the referees for their detailed comments which significantly improved the exposition of this paper. LS is supported by the DFG Research Training Group 1670 “Mathematics Inspired by String Theory and Quantum Field Theory”. Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Ingo full_name: Runkel, Ingo last_name: Runkel - first_name: Lorant full_name: Szegedy, Lorant id: 7943226E-220E-11EA-94C7-D59F3DDC885E last_name: Szegedy orcid: 0000-0003-2834-5054 citation: ama: Runkel I, Szegedy L. Area-dependent quantum field theory. Communications in Mathematical Physics. 2021;381(1):83–117. doi:10.1007/s00220-020-03902-1 apa: Runkel, I., & Szegedy, L. (2021). Area-dependent quantum field theory. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-020-03902-1 chicago: Runkel, Ingo, and Lorant Szegedy. “Area-Dependent Quantum Field Theory.” Communications in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s00220-020-03902-1. ieee: I. Runkel and L. Szegedy, “Area-dependent quantum field theory,” Communications in Mathematical Physics, vol. 381, no. 1. Springer Nature, pp. 83–117, 2021. ista: Runkel I, Szegedy L. 2021. Area-dependent quantum field theory. Communications in Mathematical Physics. 381(1), 83–117. mla: Runkel, Ingo, and Lorant Szegedy. “Area-Dependent Quantum Field Theory.” Communications in Mathematical Physics, vol. 381, no. 1, Springer Nature, 2021, pp. 83–117, doi:10.1007/s00220-020-03902-1. short: I. Runkel, L. Szegedy, Communications in Mathematical Physics 381 (2021) 83–117. date_created: 2020-11-29T23:01:17Z date_published: 2021-01-01T00:00:00Z date_updated: 2023-08-04T11:13:35Z day: '01' ddc: - '510' department: - _id: MiLe doi: 10.1007/s00220-020-03902-1 external_id: isi: - '000591139000001' file: - access_level: open_access checksum: 6f451f9c2b74bedbc30cf884a3e02670 content_type: application/pdf creator: dernst date_created: 2021-02-03T15:00:30Z date_updated: 2021-02-03T15:00:30Z file_id: '9081' file_name: 2021_CommMathPhys_Runkel.pdf file_size: 790526 relation: main_file success: 1 file_date_updated: 2021-02-03T15:00:30Z has_accepted_license: '1' intvolume: ' 381' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 83–117 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Communications in Mathematical Physics publication_identifier: eissn: - '14320916' issn: - '00103616' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Area-dependent quantum field theory 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: 381 year: '2021' ... --- _id: '8818' abstract: - lang: eng text: The hippocampus has a major role in encoding and consolidating long-term memories, and undergoes plastic changes during sleep1. These changes require precise homeostatic control by subcortical neuromodulatory structures2. The underlying mechanisms of this phenomenon, however, remain unknown. Here, using multi-structure recordings in macaque monkeys, we show that the brainstem transiently modulates hippocampal network events through phasic pontine waves known as pontogeniculooccipital waves (PGO waves). Two physiologically distinct types of PGO wave appear to occur sequentially, selectively influencing high-frequency ripples and low-frequency theta events, respectively. The two types of PGO wave are associated with opposite hippocampal spike-field coupling, prompting periods of high neural synchrony of neural populations during periods of ripple and theta instances. The coupling between PGO waves and ripples, classically associated with distinct sleep stages, supports the notion that a global coordination mechanism of hippocampal sleep dynamics by cholinergic pontine transients may promote systems and synaptic memory consolidation as well as synaptic homeostasis. acknowledgement: We thank O. Eschenko and M. Constantinou for providing feedback on earlier versions of this work, and J. Werner and M. Schnabel for technical support during the development of this study. This research was supported by the Max Planck Society. article_processing_charge: No article_type: original author: - first_name: Juan F full_name: Ramirez Villegas, Juan F id: 44B06F76-F248-11E8-B48F-1D18A9856A87 last_name: Ramirez Villegas - first_name: Michel full_name: Besserve, Michel last_name: Besserve - first_name: Yusuke full_name: Murayama, Yusuke last_name: Murayama - first_name: Henry C. full_name: Evrard, Henry C. last_name: Evrard - first_name: Axel full_name: Oeltermann, Axel last_name: Oeltermann - first_name: Nikos K. full_name: Logothetis, Nikos K. last_name: Logothetis citation: ama: Ramirez Villegas JF, Besserve M, Murayama Y, Evrard HC, Oeltermann A, Logothetis NK. Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. Nature. 2021;589(7840):96-102. doi:10.1038/s41586-020-2914-4 apa: Ramirez Villegas, J. F., Besserve, M., Murayama, Y., Evrard, H. C., Oeltermann, A., & Logothetis, N. K. (2021). Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. Nature. Springer Nature. https://doi.org/10.1038/s41586-020-2914-4 chicago: Ramirez Villegas, Juan F, Michel Besserve, Yusuke Murayama, Henry C. Evrard, Axel Oeltermann, and Nikos K. Logothetis. “Coupling of Hippocampal Theta and Ripples with Pontogeniculooccipital Waves.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-020-2914-4. ieee: J. F. Ramirez Villegas, M. Besserve, Y. Murayama, H. C. Evrard, A. Oeltermann, and N. K. Logothetis, “Coupling of hippocampal theta and ripples with pontogeniculooccipital waves,” Nature, vol. 589, no. 7840. Springer Nature, pp. 96–102, 2021. ista: Ramirez Villegas JF, Besserve M, Murayama Y, Evrard HC, Oeltermann A, Logothetis NK. 2021. Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. Nature. 589(7840), 96–102. mla: Ramirez Villegas, Juan F., et al. “Coupling of Hippocampal Theta and Ripples with Pontogeniculooccipital Waves.” Nature, vol. 589, no. 7840, Springer Nature, 2021, pp. 96–102, doi:10.1038/s41586-020-2914-4. short: J.F. Ramirez Villegas, M. Besserve, Y. Murayama, H.C. Evrard, A. Oeltermann, N.K. Logothetis, Nature 589 (2021) 96–102. date_created: 2020-11-29T23:01:19Z date_published: 2021-01-07T00:00:00Z date_updated: 2023-08-04T11:13:08Z day: '07' department: - _id: JoCs doi: 10.1038/s41586-020-2914-4 external_id: isi: - '000591047800005' pmid: - '33208951' intvolume: ' 589' isi: 1 issue: '7840' language: - iso: eng month: '01' oa_version: None page: 96-102 pmid: 1 publication: Nature publication_identifier: eissn: - '14764687' issn: - '00280836' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41586-020-03068-9 scopus_import: '1' status: public title: Coupling of hippocampal theta and ripples with pontogeniculooccipital waves type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 589 year: '2021' ... --- _id: '8773' abstract: - lang: eng text: Let g be a complex semisimple Lie algebra. We give a classification of contravariant forms on the nondegenerate Whittaker g-modules Y(χ,η) introduced by Kostant. We prove that the set of all contravariant forms on Y(χ,η) forms a vector space whose dimension is given by the cardinality of the Weyl group of g. We also describe a procedure for parabolically inducing contravariant forms. As a corollary, we deduce the existence of the Shapovalov form on a Verma module, and provide a formula for the dimension of the space of contravariant forms on the degenerate Whittaker modules M(χ,η) introduced by McDowell. acknowledgement: "We would like to thank Peter Trapa for useful discussions, and Dragan Milicic and Arun Ram for valuable feedback on the structure of the paper. The first author acknowledges the support of the European Unions Horizon 2020 research and innovation programme under the Marie Skodowska-Curie Grant Agreement No. 754411. The second author is\r\nsupported by the National Science Foundation Award No. 1803059." article_processing_charge: No article_type: original author: - first_name: Adam full_name: Brown, Adam id: 70B7FDF6-608D-11E9-9333-8535E6697425 last_name: Brown - first_name: Anna full_name: Romanov, Anna last_name: Romanov citation: ama: Brown A, Romanov A. Contravariant forms on Whittaker modules. Proceedings of the American Mathematical Society. 2021;149(1):37-52. doi:10.1090/proc/15205 apa: Brown, A., & Romanov, A. (2021). Contravariant forms on Whittaker modules. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/15205 chicago: Brown, Adam, and Anna Romanov. “Contravariant Forms on Whittaker Modules.” Proceedings of the American Mathematical Society. American Mathematical Society, 2021. https://doi.org/10.1090/proc/15205. ieee: A. Brown and A. Romanov, “Contravariant forms on Whittaker modules,” Proceedings of the American Mathematical Society, vol. 149, no. 1. American Mathematical Society, pp. 37–52, 2021. ista: Brown A, Romanov A. 2021. Contravariant forms on Whittaker modules. Proceedings of the American Mathematical Society. 149(1), 37–52. mla: Brown, Adam, and Anna Romanov. “Contravariant Forms on Whittaker Modules.” Proceedings of the American Mathematical Society, vol. 149, no. 1, American Mathematical Society, 2021, pp. 37–52, doi:10.1090/proc/15205. short: A. Brown, A. Romanov, Proceedings of the American Mathematical Society 149 (2021) 37–52. date_created: 2020-11-19T10:17:40Z date_published: 2021-01-01T00:00:00Z date_updated: 2023-08-04T11:11:47Z day: '01' department: - _id: HeEd doi: 10.1090/proc/15205 ec_funded: 1 external_id: arxiv: - '1910.08286' isi: - '000600416300004' intvolume: ' 149' isi: 1 issue: '1' keyword: - Applied Mathematics - General Mathematics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1910.08286 month: '01' oa: 1 oa_version: Preprint page: 37-52 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Proceedings of the American Mathematical Society publication_identifier: eissn: - 1088-6826 issn: - 0002-9939 publication_status: published publisher: American Mathematical Society quality_controlled: '1' status: public title: Contravariant forms on Whittaker modules type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 149 year: '2021' ... --- _id: '8792' abstract: - lang: eng text: This paper is concerned with a non-isothermal Cahn-Hilliard model based on a microforce balance. The model was derived by A. Miranville and G. Schimperna starting from the two fundamental laws of Thermodynamics, following M. Gurtin's two-scale approach. The main working assumptions are made on the behaviour of the heat flux as the absolute temperature tends to zero and to infinity. A suitable Ginzburg-Landau free energy is considered. Global-in-time existence for the initial-boundary value problem associated to the entropy formulation and, in a subcase, also to the weak formulation of the model is proved by deriving suitable a priori estimates and by showing weak sequential stability of families of approximating solutions. At last, some highlights are given regarding a possible approximation scheme compatible with the a-priori estimates available for the system. acknowledgement: G. Schimperna has been partially supported by GNAMPA (Gruppo Nazionale per l'Analisi Matematica, la Probabilità e le loro Applicazioni) of INdAM (Istituto Nazionale di Alta Matematica). article_processing_charge: No article_type: original author: - first_name: Alice full_name: Marveggio, Alice id: 25647992-AA84-11E9-9D75-8427E6697425 last_name: Marveggio - first_name: Giulio full_name: Schimperna, Giulio last_name: Schimperna citation: ama: Marveggio A, Schimperna G. On a non-isothermal Cahn-Hilliard model based on a microforce balance. Journal of Differential Equations. 2021;274(2):924-970. doi:10.1016/j.jde.2020.10.030 apa: Marveggio, A., & Schimperna, G. (2021). On a non-isothermal Cahn-Hilliard model based on a microforce balance. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2020.10.030 chicago: Marveggio, Alice, and Giulio Schimperna. “On a Non-Isothermal Cahn-Hilliard Model Based on a Microforce Balance.” Journal of Differential Equations. Elsevier, 2021. https://doi.org/10.1016/j.jde.2020.10.030. ieee: A. Marveggio and G. Schimperna, “On a non-isothermal Cahn-Hilliard model based on a microforce balance,” Journal of Differential Equations, vol. 274, no. 2. Elsevier, pp. 924–970, 2021. ista: Marveggio A, Schimperna G. 2021. On a non-isothermal Cahn-Hilliard model based on a microforce balance. Journal of Differential Equations. 274(2), 924–970. mla: Marveggio, Alice, and Giulio Schimperna. “On a Non-Isothermal Cahn-Hilliard Model Based on a Microforce Balance.” Journal of Differential Equations, vol. 274, no. 2, Elsevier, 2021, pp. 924–70, doi:10.1016/j.jde.2020.10.030. short: A. Marveggio, G. Schimperna, Journal of Differential Equations 274 (2021) 924–970. date_created: 2020-11-22T23:01:26Z date_published: 2021-02-15T00:00:00Z date_updated: 2023-08-04T11:12:16Z day: '15' department: - _id: JuFi doi: 10.1016/j.jde.2020.10.030 external_id: arxiv: - '2004.02618' isi: - '000600845300023' intvolume: ' 274' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2004.02618 month: '02' oa: 1 oa_version: Preprint page: 924-970 publication: Journal of Differential Equations publication_identifier: eissn: - '10902732' issn: - '00220396' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: On a non-isothermal Cahn-Hilliard model based on a microforce balance type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 274 year: '2021' ... --- _id: '8912' abstract: - lang: eng text: "For automata, synchronization, the problem of bringing an automaton to a particular state regardless of its initial state, is important. It has several applications in practice and is related to a fifty-year-old conjecture on the length of the shortest synchronizing word. Although using shorter words increases the effectiveness in practice, finding a shortest one (which is not necessarily unique) is NP-hard. For this reason, there exist various heuristics in the literature. However, high-quality heuristics such as SynchroP producing relatively shorter sequences are very expensive and can take hours when the automaton has tens of thousands of states. The SynchroP heuristic has been frequently used as a benchmark to evaluate the performance of the new heuristics. In this work, we first improve the runtime of SynchroP and its variants by using algorithmic techniques. We then focus on adapting SynchroP for many-core architectures,\r\nand overall, we obtain more than 1000× speedup on GPUs compared to naive sequential implementation that has been frequently used as a benchmark to evaluate new heuristics in the literature. We also propose two SynchroP variants and evaluate their performance." acknowledgement: This work was supported by The Scientific and Technological Research Council of Turkey (TUBITAK) [grant number 114E569]. This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). We would like to thank the authors of (Roman & Szykula, 2015) for providing their heuristics implementations, which we used to compare our SynchroP implementation as given in Table 11. article_number: '114203' article_processing_charge: No article_type: original author: - first_name: Naci E full_name: Sarac, Naci E id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425 last_name: Sarac - first_name: Ömer Faruk full_name: Altun, Ömer Faruk last_name: Altun - first_name: Kamil Tolga full_name: Atam, Kamil Tolga last_name: Atam - first_name: Sertac full_name: Karahoda, Sertac last_name: Karahoda - first_name: Kamer full_name: Kaya, Kamer last_name: Kaya - first_name: Hüsnü full_name: Yenigün, Hüsnü last_name: Yenigün citation: ama: Sarac NE, Altun ÖF, Atam KT, Karahoda S, Kaya K, Yenigün H. Boosting expensive synchronizing heuristics. Expert Systems with Applications. 2021;167(4). doi:10.1016/j.eswa.2020.114203 apa: Sarac, N. E., Altun, Ö. F., Atam, K. T., Karahoda, S., Kaya, K., & Yenigün, H. (2021). Boosting expensive synchronizing heuristics. Expert Systems with Applications. Elsevier. https://doi.org/10.1016/j.eswa.2020.114203 chicago: Sarac, Naci E, Ömer Faruk Altun, Kamil Tolga Atam, Sertac Karahoda, Kamer Kaya, and Hüsnü Yenigün. “Boosting Expensive Synchronizing Heuristics.” Expert Systems with Applications. Elsevier, 2021. https://doi.org/10.1016/j.eswa.2020.114203. ieee: N. E. Sarac, Ö. F. Altun, K. T. Atam, S. Karahoda, K. Kaya, and H. Yenigün, “Boosting expensive synchronizing heuristics,” Expert Systems with Applications, vol. 167, no. 4. Elsevier, 2021. ista: Sarac NE, Altun ÖF, Atam KT, Karahoda S, Kaya K, Yenigün H. 2021. Boosting expensive synchronizing heuristics. Expert Systems with Applications. 167(4), 114203. mla: Sarac, Naci E., et al. “Boosting Expensive Synchronizing Heuristics.” Expert Systems with Applications, vol. 167, no. 4, 114203, Elsevier, 2021, doi:10.1016/j.eswa.2020.114203. short: N.E. Sarac, Ö.F. Altun, K.T. Atam, S. Karahoda, K. Kaya, H. Yenigün, Expert Systems with Applications 167 (2021). date_created: 2020-12-02T13:34:25Z date_published: 2021-04-01T00:00:00Z date_updated: 2023-08-04T11:19:00Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1016/j.eswa.2020.114203 external_id: isi: - '000640531100038' file: - access_level: open_access checksum: 600c2f81bc898a725bcfa7cf26ff4fed content_type: application/pdf creator: esarac date_created: 2020-12-02T13:33:51Z date_updated: 2020-12-02T13:33:51Z file_id: '8913' file_name: synchroPaperRevised.pdf file_size: 634967 relation: main_file file_date_updated: 2020-12-02T13:33:51Z has_accepted_license: '1' intvolume: ' 167' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Expert Systems with Applications publication_identifier: issn: - '09574174' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Boosting expensive synchronizing heuristics type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 167 year: '2021' ... --- _id: '8928' abstract: - lang: eng text: Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available. acknowledgement: This work was supported by the EU Marie Curie Career Integration grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant Breeding division of INRA, in partnership with Gautier Semences. CF was supported by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding (University of Torino), the Biotechnology Department (University of Verona), the CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC ) for managing and providing the genetic resources, to Marie‐Christine Daunay and Alain Palloix (INRA UR1052) for assistance in choosing the biological material used, to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France) for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques Lagnel (INRA UR1052) for their Bioinformatics assistance. article_processing_charge: No article_type: original author: - first_name: Stéphanie full_name: Arnoux, Stéphanie last_name: Arnoux - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Christopher full_name: Sauvage, Christopher last_name: Sauvage citation: ama: Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 2021;34(2):270-283. doi:10.1111/jeb.13723 apa: Arnoux, S., Fraisse, C., & Sauvage, C. (2021). Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13723 chicago: Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13723. ieee: S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication histories in three Solanaceae species,” Journal of Evolutionary Biology, vol. 34, no. 2. Wiley, pp. 270–283, 2021. ista: Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2), 270–283. mla: Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal of Evolutionary Biology, vol. 34, no. 2, Wiley, 2021, pp. 270–83, doi:10.1111/jeb.13723. short: S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283. date_created: 2020-12-06T23:01:16Z date_published: 2021-02-01T00:00:00Z date_updated: 2023-08-04T11:19:26Z day: '01' department: - _id: NiBa doi: 10.1111/jeb.13723 external_id: isi: - '000587769700001' pmid: - '33107098' intvolume: ' 34' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/jeb.13723 month: '02' oa: 1 oa_version: Published Version page: 270-283 pmid: 1 project: - _id: 2662AADE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02463 name: Sex chromosomes and species barriers publication: Journal of Evolutionary Biology publication_identifier: eissn: - '14209101' issn: - 1010061X publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '13065' relation: research_data status: public scopus_import: '1' status: public title: Genomic inference of complex domestication histories in three Solanaceae species type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 34 year: '2021' ... --- _id: '8992' abstract: - lang: eng text: The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational modification, regulating physiological and developmental auxin output at all levels. In this review, we comprehensively discuss earlier and recent advances in our understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases participating in auxin action. We provide insights into the mechanisms by which reversible protein phosphorylation defines developmental auxin responses, discuss current challenges, and provide our perspectives on future directions involving the integration of the control of protein phosphorylation into the molecular auxin network. acknowledgement: This work was supported by the European Union’s Horizon 2020 Program (ERC grant agreement no. 742985 to J.F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). C.L. is supported by the Austrian Science Fund (FWF; P 31493). article_processing_charge: No article_type: original author: - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Tan S, Luschnig C, Friml J. Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. Molecular Plant. 2021;14(1):151-165. doi:10.1016/j.molp.2020.11.004' apa: 'Tan, S., Luschnig, C., & Friml, J. (2021). Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.11.004' chicago: 'Tan, Shutang, Christian Luschnig, and Jiří Friml. “Pho-View of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.” Molecular Plant. Elsevier, 2021. https://doi.org/10.1016/j.molp.2020.11.004.' ieee: 'S. Tan, C. Luschnig, and J. Friml, “Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling,” Molecular Plant, vol. 14, no. 1. Elsevier, pp. 151–165, 2021.' ista: 'Tan S, Luschnig C, Friml J. 2021. Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. Molecular Plant. 14(1), 151–165.' mla: 'Tan, Shutang, et al. “Pho-View of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.” Molecular Plant, vol. 14, no. 1, Elsevier, 2021, pp. 151–65, doi:10.1016/j.molp.2020.11.004.' short: S. Tan, C. Luschnig, J. Friml, Molecular Plant 14 (2021) 151–165. date_created: 2021-01-03T23:01:23Z date_published: 2021-01-04T00:00:00Z date_updated: 2023-08-04T11:21:13Z day: '04' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.molp.2020.11.004 ec_funded: 1 external_id: isi: - '000605359400014' pmid: - '33186755' file: - access_level: open_access checksum: 917e60e57092f22e16beac70b1775ea6 content_type: application/pdf creator: dernst date_created: 2021-01-07T14:03:53Z date_updated: 2021-01-07T14:03:53Z file_id: '8995' file_name: 2020_MolecularPlant_Tan.pdf file_size: 871088 relation: main_file success: 1 file_date_updated: 2021-01-07T14:03:53Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 151-165 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 256FEF10-B435-11E9-9278-68D0E5697425 grant_number: 723-2015 name: Long Term Fellowship publication: Molecular Plant publication_identifier: eissn: - '17529867' issn: - '16742052' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2021' ... --- _id: '8988' abstract: - lang: eng text: The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: EM-Fac acknowledgement: "We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky, Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging facility, the life science facility, and Armel Nicolas from the mass spec facility at the Institute of Science and Technology (IST) Austria for technical support. C.D. acknowledges funding from the IST fellowship program; this work was supported by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. " article_number: e2010054118 article_processing_charge: No article_type: original author: - first_name: Christian F full_name: Düllberg, Christian F id: 459064DC-F248-11E8-B48F-1D18A9856A87 last_name: Düllberg orcid: 0000-0001-6335-9748 - first_name: Albert full_name: Auer, Albert id: 3018E8C2-F248-11E8-B48F-1D18A9856A87 last_name: Auer orcid: 0000-0002-3580-2906 - first_name: Nikola full_name: Canigova, Nikola id: 3795523E-F248-11E8-B48F-1D18A9856A87 last_name: Canigova orcid: 0000-0002-8518-5926 - first_name: Katrin full_name: Loibl, Katrin id: 3760F32C-F248-11E8-B48F-1D18A9856A87 last_name: Loibl orcid: 0000-0002-2429-7668 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. PNAS. 2021;118(1). doi:10.1073/pnas.2010054118 apa: Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., & Loose, M. (2021). In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2010054118 chicago: Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” PNAS. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2010054118. ieee: C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1,” PNAS, vol. 118, no. 1. National Academy of Sciences, 2021. ista: Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. PNAS. 118(1), e2010054118. mla: Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” PNAS, vol. 118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:10.1073/pnas.2010054118. short: C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, PNAS 118 (2021). date_created: 2021-01-03T23:01:23Z date_published: 2021-01-05T00:00:00Z date_updated: 2023-08-04T11:20:46Z day: '05' department: - _id: MaLo - _id: MiSi doi: 10.1073/pnas.2010054118 external_id: isi: - '000607270100018' pmid: - '33443153' intvolume: ' 118' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.2010054118 month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2599F062-B435-11E9-9278-68D0E5697425 grant_number: RGY0083/2016 name: Reconstitution of cell polarity and axis determination in a cell-free system publication: PNAS publication_identifier: eissn: - '10916490' issn: - '00278424' publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1 type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 118 year: '2021' ... --- _id: '8927' abstract: - lang: eng text: The recent outbreak of coronavirus disease 2019 (COVID‐19), caused by the Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) has resulted in a world‐wide pandemic. Disseminated lung injury with the development of acute respiratory distress syndrome (ARDS) is the main cause of mortality in COVID‐19. Although liver failure does not seem to occur in the absence of pre‐existing liver disease, hepatic involvement in COVID‐19 may correlate with overall disease severity and serve as a prognostic factor for the development of ARDS. The spectrum of liver injury in COVID‐19 may range from direct infection by SARS‐CoV‐2, indirect involvement by systemic inflammation, hypoxic changes, iatrogenic causes such as drugs and ventilation to exacerbation of underlying liver disease. This concise review discusses the potential pathophysiological mechanisms for SARS‐CoV‐2 hepatic tropism as well as acute and possibly long‐term liver injury in COVID‐19. acknowledgement: This work was supported by grant F7310‐B21 from the Austrian Science Foundation (to MT). We thank Jelena Remetic, Claudia D. Fuchs, Veronika Mlitz and Daniel Steinacher, for their valuable input and discussion. Figure 1 and Figure 2 have been created with BioRender.com. article_processing_charge: No article_type: original author: - first_name: Alexander D. full_name: Nardo, Alexander D. last_name: Nardo - first_name: Mathias full_name: Schneeweiss-Gleixner, Mathias last_name: Schneeweiss-Gleixner - first_name: May M full_name: Bakail, May M id: FB3C3F8E-522F-11EA-B186-22963DDC885E last_name: Bakail orcid: 0000-0002-9592-1587 - first_name: Emmanuel D. full_name: Dixon, Emmanuel D. last_name: Dixon - first_name: Sigurd F. full_name: Lax, Sigurd F. last_name: Lax - first_name: Michael full_name: Trauner, Michael last_name: Trauner citation: ama: Nardo AD, Schneeweiss-Gleixner M, Bakail MM, Dixon ED, Lax SF, Trauner M. Pathophysiological mechanisms of liver injury in COVID-19. Liver International. 2021;41(1):20-32. doi:10.1111/liv.14730 apa: Nardo, A. D., Schneeweiss-Gleixner, M., Bakail, M. M., Dixon, E. D., Lax, S. F., & Trauner, M. (2021). Pathophysiological mechanisms of liver injury in COVID-19. Liver International. Wiley. https://doi.org/10.1111/liv.14730 chicago: Nardo, Alexander D., Mathias Schneeweiss-Gleixner, May M Bakail, Emmanuel D. Dixon, Sigurd F. Lax, and Michael Trauner. “Pathophysiological Mechanisms of Liver Injury in COVID-19.” Liver International. Wiley, 2021. https://doi.org/10.1111/liv.14730. ieee: A. D. Nardo, M. Schneeweiss-Gleixner, M. M. Bakail, E. D. Dixon, S. F. Lax, and M. Trauner, “Pathophysiological mechanisms of liver injury in COVID-19,” Liver International, vol. 41, no. 1. Wiley, pp. 20–32, 2021. ista: Nardo AD, Schneeweiss-Gleixner M, Bakail MM, Dixon ED, Lax SF, Trauner M. 2021. Pathophysiological mechanisms of liver injury in COVID-19. Liver International. 41(1), 20–32. mla: Nardo, Alexander D., et al. “Pathophysiological Mechanisms of Liver Injury in COVID-19.” Liver International, vol. 41, no. 1, Wiley, 2021, pp. 20–32, doi:10.1111/liv.14730. short: A.D. Nardo, M. Schneeweiss-Gleixner, M.M. Bakail, E.D. Dixon, S.F. Lax, M. Trauner, Liver International 41 (2021) 20–32. date_created: 2020-12-06T23:01:16Z date_published: 2021-01-01T00:00:00Z date_updated: 2023-08-04T11:19:51Z day: '01' ddc: - '570' department: - _id: CampIT doi: 10.1111/liv.14730 external_id: isi: - '000594239200001' file: - access_level: open_access checksum: 6e4f21b77ef22c854e016240974fc473 content_type: application/pdf creator: dernst date_created: 2021-02-04T12:01:45Z date_updated: 2021-02-04T12:01:45Z file_id: '9091' file_name: 2021_Liver_Nardo.pdf file_size: 930414 relation: main_file success: 1 file_date_updated: 2021-02-04T12:01:45Z has_accepted_license: '1' intvolume: ' 41' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 20-32 publication: Liver International publication_identifier: eissn: - '14783231' issn: - '14783223' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Pathophysiological mechanisms of liver injury in COVID-19 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 41 year: '2021' ... --- _id: '13356' abstract: - lang: eng text: 'Self-assembly of nanoparticles can be mediated by polymers, but has so far led almost exclusively to nanoparticle aggregates that are amorphous. Here, we employed Coulombic interactions to generate a range of composite materials from mixtures of charged nanoparticles and oppositely charged polymers. The assembly behavior of these nanoparticle/polymer composites depends on their order of addition: polymers added to nanoparticles give rise to stable aggregates, but nanoparticles added to polymers disassemble the initially formed aggregates. The amorphous aggregates were transformed into crystalline ones by transiently increasing the ionic strength of the solution. The morphology of the resulting crystals depended on the length of the polymer: short polymer chains mediated the self-assembly of nanoparticles into strongly faceted crystals, whereas long chains led to pseudospherical nanoparticle/polymer assemblies, within which the crystalline order of nanoparticles was retained.' article_processing_charge: No article_type: original author: - first_name: Tong full_name: Bian, Tong last_name: Bian - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Bian T, Klajn R. Morphology control in crystalline nanoparticle–polymer aggregates. Annals of the New York Academy of Sciences. 2021;1505(1):191-201. doi:10.1111/nyas.14674 apa: Bian, T., & Klajn, R. (2021). Morphology control in crystalline nanoparticle–polymer aggregates. Annals of the New York Academy of Sciences. Wiley. https://doi.org/10.1111/nyas.14674 chicago: Bian, Tong, and Rafal Klajn. “Morphology Control in Crystalline Nanoparticle–Polymer Aggregates.” Annals of the New York Academy of Sciences. Wiley, 2021. https://doi.org/10.1111/nyas.14674. ieee: T. Bian and R. Klajn, “Morphology control in crystalline nanoparticle–polymer aggregates,” Annals of the New York Academy of Sciences, vol. 1505, no. 1. Wiley, pp. 191–201, 2021. ista: Bian T, Klajn R. 2021. Morphology control in crystalline nanoparticle–polymer aggregates. Annals of the New York Academy of Sciences. 1505(1), 191–201. mla: Bian, Tong, and Rafal Klajn. “Morphology Control in Crystalline Nanoparticle–Polymer Aggregates.” Annals of the New York Academy of Sciences, vol. 1505, no. 1, Wiley, 2021, pp. 191–201, doi:10.1111/nyas.14674. short: T. Bian, R. Klajn, Annals of the New York Academy of Sciences 1505 (2021) 191–201. date_created: 2023-08-01T09:33:39Z date_published: 2021-12-01T00:00:00Z date_updated: 2023-08-07T10:01:10Z day: '01' ddc: - '540' doi: 10.1111/nyas.14674 extern: '1' external_id: pmid: - '34427923' intvolume: ' 1505' issue: '1' keyword: - History and Philosophy of Science - General Biochemistry - Genetics and Molecular Biology - General Neuroscience language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/nyas.14674 month: '12' oa: 1 oa_version: Published Version page: 191-201 pmid: 1 publication: Annals of the New York Academy of Sciences publication_identifier: eissn: - 1749-6632 issn: - 0077-8923 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Morphology control in crystalline nanoparticle–polymer aggregates type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1505 year: '2021' ... --- _id: '13359' abstract: - lang: eng text: Dissipative self-assembly is ubiquitous in nature, where it gives rise to complex structures and functions such as self-healing, homeostasis, and camouflage. These phenomena are enabled by the continuous conversion of energy stored in chemical fuels, such as ATP. Over the past decade, an increasing number of synthetic chemically driven systems have been reported that mimic the features of their natural counterparts. At the same time, it has been shown that dissipative self-assembly can also be fueled by light; these optically fueled systems have been developed in parallel to the chemically fueled ones. In this perspective, we critically compare these two classes of systems. Despite the complementarity and fundamental differences between these two modes of dissipative self-assembly, our analysis reveals that multiple analogies exist between chemically and light-fueled systems. We hope that these considerations will facilitate further development of the field of dissipative self-assembly. article_processing_charge: No article_type: original author: - first_name: Maren full_name: Weißenfels, Maren last_name: Weißenfels - first_name: Julius full_name: Gemen, Julius last_name: Gemen - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: 'Weißenfels M, Gemen J, Klajn R. Dissipative self-assembly: Fueling with chemicals versus light. Chem. 2021;7(1):23-37. doi:10.1016/j.chempr.2020.11.025' apa: 'Weißenfels, M., Gemen, J., & Klajn, R. (2021). Dissipative self-assembly: Fueling with chemicals versus light. Chem. Elsevier. https://doi.org/10.1016/j.chempr.2020.11.025' chicago: 'Weißenfels, Maren, Julius Gemen, and Rafal Klajn. “Dissipative Self-Assembly: Fueling with Chemicals versus Light.” Chem. Elsevier, 2021. https://doi.org/10.1016/j.chempr.2020.11.025.' ieee: 'M. Weißenfels, J. Gemen, and R. Klajn, “Dissipative self-assembly: Fueling with chemicals versus light,” Chem, vol. 7, no. 1. Elsevier, pp. 23–37, 2021.' ista: 'Weißenfels M, Gemen J, Klajn R. 2021. Dissipative self-assembly: Fueling with chemicals versus light. Chem. 7(1), 23–37.' mla: 'Weißenfels, Maren, et al. “Dissipative Self-Assembly: Fueling with Chemicals versus Light.” Chem, vol. 7, no. 1, Elsevier, 2021, pp. 23–37, doi:10.1016/j.chempr.2020.11.025.' short: M. Weißenfels, J. Gemen, R. Klajn, Chem 7 (2021) 23–37. date_created: 2023-08-01T09:35:19Z date_published: 2021-01-14T00:00:00Z date_updated: 2023-08-07T10:04:28Z day: '14' doi: 10.1016/j.chempr.2020.11.025 extern: '1' intvolume: ' 7' issue: '1' keyword: - Materials Chemistry - Biochemistry (medical) - General Chemical Engineering - Environmental Chemistry - Biochemistry - General Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.chempr.2020.11.025 month: '01' oa: 1 oa_version: Published Version page: 23-37 publication: Chem publication_identifier: issn: - 2451-9294 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Dissipative self-assembly: Fueling with chemicals versus light' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2021' ... --- _id: '8966' abstract: - lang: eng text: During development, a single cell is transformed into a highly complex organism through progressive cell division, specification and rearrangement. An important prerequisite for the emergence of patterns within the developing organism is to establish asymmetries at various scales, ranging from individual cells to the entire embryo, eventually giving rise to the different body structures. This becomes especially apparent during gastrulation, when the earliest major lineage restriction events lead to the formation of the different germ layers. Traditionally, the unfolding of the developmental program from symmetry breaking to germ layer formation has been studied by dissecting the contributions of different signaling pathways and cellular rearrangements in the in vivo context of intact embryos. Recent efforts, using the intrinsic capacity of embryonic stem cells to self-assemble and generate embryo-like structures de novo, have opened new avenues for understanding the many ways by which an embryo can be built and the influence of extrinsic factors therein. Here, we discuss and compare divergent and conserved strategies leading to germ layer formation in embryos as compared to in vitro systems, their upstream molecular cascades and the role of extrinsic factors in this process. acknowledgement: We thank Nicoletta Petridou, Diana Pinheiro, Cornelia Schwayer and Stefania Tavano for feedback on the manuscript. Research in the Heisenberg lab is supported by an ERC Advanced Grant (MECSPEC 742573) to C.-P.H. A.S. is a recipient of a DOC Fellowship of the Austrian Academy of Science. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Alexandra full_name: Schauer, Alexandra id: 30A536BA-F248-11E8-B48F-1D18A9856A87 last_name: Schauer orcid: 0000-0001-7659-9142 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Schauer A, Heisenberg C-PJ. Reassembling gastrulation. Developmental Biology. 2021;474:71-81. doi:10.1016/j.ydbio.2020.12.014 apa: Schauer, A., & Heisenberg, C.-P. J. (2021). Reassembling gastrulation. Developmental Biology. Elsevier. https://doi.org/10.1016/j.ydbio.2020.12.014 chicago: Schauer, Alexandra, and Carl-Philipp J Heisenberg. “Reassembling Gastrulation.” Developmental Biology. Elsevier, 2021. https://doi.org/10.1016/j.ydbio.2020.12.014. ieee: A. Schauer and C.-P. J. Heisenberg, “Reassembling gastrulation,” Developmental Biology, vol. 474. Elsevier, pp. 71–81, 2021. ista: Schauer A, Heisenberg C-PJ. 2021. Reassembling gastrulation. Developmental Biology. 474, 71–81. mla: Schauer, Alexandra, and Carl-Philipp J. Heisenberg. “Reassembling Gastrulation.” Developmental Biology, vol. 474, Elsevier, 2021, pp. 71–81, doi:10.1016/j.ydbio.2020.12.014. short: A. Schauer, C.-P.J. Heisenberg, Developmental Biology 474 (2021) 71–81. date_created: 2020-12-22T09:53:34Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-08-07T13:30:01Z day: '01' ddc: - '570' department: - _id: CaHe doi: 10.1016/j.ydbio.2020.12.014 ec_funded: 1 external_id: isi: - '000639461800008' file: - access_level: open_access checksum: fa2a5731fd16ab171b029f32f031c440 content_type: application/pdf creator: kschuh date_created: 2021-08-11T10:28:06Z date_updated: 2021-08-11T10:28:06Z file_id: '9880' file_name: 2021_DevBiology_Schauer.pdf file_size: 1440321 relation: main_file success: 1 file_date_updated: 2021-08-11T10:28:06Z has_accepted_license: '1' intvolume: ' 474' isi: 1 keyword: - Developmental Biology - Cell Biology - Molecular Biology language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '06' oa: 1 oa_version: Published Version page: 71-81 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation - _id: 26B1E39C-B435-11E9-9278-68D0E5697425 grant_number: '25239' name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues' publication: Developmental Biology publication_identifier: issn: - 0012-1606 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '12891' relation: dissertation_contains status: public scopus_import: '1' status: public title: Reassembling gastrulation 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: 474 year: '2021' ... --- _id: '8993' abstract: - lang: eng text: N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism. acknowledgement: "This work was supported by Austrian Science Fund Grant FWF P21533-B20 (to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing access to mass spectrometry instruments at the Vienna BioCenter Core Facilities. We thank PNAS reviewers for the many comments and suggestions that helped to improve this manuscript." article_number: e2020857118 article_processing_charge: No article_type: original author: - first_name: Lindy full_name: Abas, Lindy last_name: Abas - first_name: Martina full_name: Kolb, Martina last_name: Kolb - first_name: Johannes full_name: Stadlmann, Johannes last_name: Stadlmann - first_name: Dorina P. full_name: Janacek, Dorina P. last_name: Janacek - first_name: Kristina full_name: Lukic, Kristina id: 2B04DB84-F248-11E8-B48F-1D18A9856A87 last_name: Lukic orcid: 0000-0003-1581-881X - first_name: Claus full_name: Schwechheimer, Claus last_name: Schwechheimer - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Lukas full_name: Mach, Lukas last_name: Mach - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Ulrich Z. full_name: Hammes, Ulrich Z. last_name: Hammes citation: ama: Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. 2021;118(1). doi:10.1073/pnas.2020857118 apa: Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer, C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2020857118 chicago: Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” PNAS. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2020857118. ieee: L. Abas et al., “Naphthylphthalamic acid associates with and inhibits PIN auxin transporters,” PNAS, vol. 118, no. 1. National Academy of Sciences, 2021. ista: Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. 118(1), e2020857118. mla: Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” PNAS, vol. 118, no. 1, e2020857118, National Academy of Sciences, 2021, doi:10.1073/pnas.2020857118. short: L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer, L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, PNAS 118 (2021). date_created: 2021-01-03T23:01:23Z date_published: 2021-01-05T00:00:00Z date_updated: 2023-08-07T13:29:23Z day: '05' department: - _id: JiFr - _id: LeSa doi: 10.1073/pnas.2020857118 ec_funded: 1 external_id: isi: - '000607270100073' pmid: - '33443187' intvolume: ' 118' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.2020857118 month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: PNAS publication_identifier: eissn: - '10916490' issn: - '00278424' publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1073/pnas.2102232118 scopus_import: '1' status: public title: Naphthylphthalamic acid associates with and inhibits PIN auxin transporters type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 118 year: '2021' ... --- _id: '8999' abstract: - lang: eng text: "In many basic shear flows, such as pipe, Couette, and channel flow, turbulence does not\r\narise from an instability of the laminar state, and both dynamical states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number) the fraction of fluid in laminar motion increases while turbulence recedes and eventually the entire flow relaminarizes. The first step towards understanding the nature of this transition is to determine if the phase change is of either first or second order. In the former case, the turbulent fraction would drop discontinuously to zero as the Reynolds number decreases while in the latter the process would be continuous. For Couette flow, the flow between two parallel plates, earlier studies suggest a discontinuous scenario. In the present study we realize a Couette flow between two concentric cylinders which allows studies to be carried out in large aspect ratios and for extensive observation times. The presented measurements show that the transition in this circular Couette geometry is continuous suggesting that former studies were limited by finite size effects. A further characterization of this transition, in particular its relation to the directed percolation universality class, requires even larger system sizes than presently available. " acknowledgement: "This research was funded by the Central Research Development Fund of the University of\r\nBremen grant number ZF04B /2019/FB04 Avila_Kerstin (“Independent Project for Postdocs”). Shreyas Jalikop is acknowledged for recording some of the lifetime measurements\r\n" article_number: '58' article_processing_charge: No article_type: original author: - first_name: Kerstin full_name: Avila, Kerstin id: fcf74381-53e1-11eb-a6dc-b0e2acf78757 last_name: Avila - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Avila K, Hof B. Second-order phase transition in counter-rotating taylor-couette flow experiment. Entropy. 2021;23(1). doi:10.3390/e23010058 apa: Avila, K., & Hof, B. (2021). Second-order phase transition in counter-rotating taylor-couette flow experiment. Entropy. MDPI. https://doi.org/10.3390/e23010058 chicago: Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating Taylor-Couette Flow Experiment.” Entropy. MDPI, 2021. https://doi.org/10.3390/e23010058. ieee: K. Avila and B. Hof, “Second-order phase transition in counter-rotating taylor-couette flow experiment,” Entropy, vol. 23, no. 1. MDPI, 2021. ista: Avila K, Hof B. 2021. Second-order phase transition in counter-rotating taylor-couette flow experiment. Entropy. 23(1), 58. mla: Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating Taylor-Couette Flow Experiment.” Entropy, vol. 23, no. 1, 58, MDPI, 2021, doi:10.3390/e23010058. short: K. Avila, B. Hof, Entropy 23 (2021). date_created: 2021-01-10T23:01:17Z date_published: 2021-01-01T00:00:00Z date_updated: 2023-08-07T13:31:07Z day: '01' ddc: - '530' department: - _id: BjHo doi: 10.3390/e23010058 external_id: isi: - '000610135400001' pmid: - '33396499' file: - access_level: open_access checksum: 3ba3dd8b7eecff713b72c5e9ba30d626 content_type: application/pdf creator: dernst date_created: 2021-01-11T07:50:32Z date_updated: 2021-01-11T07:50:32Z file_id: '9003' file_name: 2021_Entropy_Avila.pdf file_size: 9456389 relation: main_file success: 1 file_date_updated: 2021-01-11T07:50:32Z has_accepted_license: '1' intvolume: ' 23' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Entropy publication_identifier: eissn: - 1099-4300 publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Second-order phase transition in counter-rotating taylor-couette flow experiment 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: 23 year: '2021' ... --- _id: '9005' abstract: - lang: eng text: Studies on the experimental realization of two-dimensional anyons in terms of quasiparticles have been restricted, so far, to only anyons on the plane. It is known, however, that the geometry and topology of space can have significant effects on quantum statistics for particles moving on it. Here, we have undertaken the first step toward realizing the emerging fractional statistics for particles restricted to move on the sphere instead of on the plane. We show that such a model arises naturally in the context of quantum impurity problems. In particular, we demonstrate a setup in which the lowest-energy spectrum of two linear bosonic or fermionic molecules immersed in a quantum many-particle environment can coincide with the anyonic spectrum on the sphere. This paves the way toward the experimental realization of anyons on the sphere using molecular impurities. Furthermore, since a change in the alignment of the molecules corresponds to the exchange of the particles on the sphere, such a realization reveals a novel type of exclusion principle for molecular impurities, which could also be of use as a powerful technique to measure the statistics parameter. Finally, our approach opens up a simple numerical route to investigate the spectra of many anyons on the sphere. Accordingly, we present the spectrum of two anyons on the sphere in the presence of a Dirac monopole field. acknowledgement: "We are grateful to A. Ghazaryan for valuable discussions and also thank the anonymous referees for comments. D.L. acknowledges financial support from the G¨oran Gustafsson Foundation (grant no. 1804) and LMU Munich. M.L. gratefully acknowledges financial support\r\nby the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 801770)." article_number: '015301' article_processing_charge: No article_type: original author: - first_name: Morris full_name: Brooks, Morris id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425 last_name: Brooks orcid: 0000-0002-6249-0928 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: D. full_name: Lundholm, D. last_name: Lundholm - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 citation: ama: Brooks M, Lemeshko M, Lundholm D, Yakaboylu E. Molecular impurities as a realization of anyons on the two-sphere. Physical Review Letters. 2021;126(1). doi:10.1103/PhysRevLett.126.015301 apa: Brooks, M., Lemeshko, M., Lundholm, D., & Yakaboylu, E. (2021). Molecular impurities as a realization of anyons on the two-sphere. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.126.015301 chicago: Brooks, Morris, Mikhail Lemeshko, D. Lundholm, and Enderalp Yakaboylu. “Molecular Impurities as a Realization of Anyons on the Two-Sphere.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.126.015301. ieee: M. Brooks, M. Lemeshko, D. Lundholm, and E. Yakaboylu, “Molecular impurities as a realization of anyons on the two-sphere,” Physical Review Letters, vol. 126, no. 1. American Physical Society, 2021. ista: Brooks M, Lemeshko M, Lundholm D, Yakaboylu E. 2021. Molecular impurities as a realization of anyons on the two-sphere. Physical Review Letters. 126(1), 015301. mla: Brooks, Morris, et al. “Molecular Impurities as a Realization of Anyons on the Two-Sphere.” Physical Review Letters, vol. 126, no. 1, 015301, American Physical Society, 2021, doi:10.1103/PhysRevLett.126.015301. short: M. Brooks, M. Lemeshko, D. Lundholm, E. Yakaboylu, Physical Review Letters 126 (2021). date_created: 2021-01-17T23:01:10Z date_published: 2021-01-08T00:00:00Z date_updated: 2023-08-07T13:32:10Z day: '08' department: - _id: MiLe - _id: RoSe doi: 10.1103/PhysRevLett.126.015301 ec_funded: 1 external_id: arxiv: - '2009.05948' isi: - '000606325000003' intvolume: ' 126' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2009.05948 month: '01' oa: 1 oa_version: Preprint project: - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication: Physical Review Letters publication_identifier: eissn: - '10797114' issn: - '00319007' publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/dancing-molecules-and-two-dimensional-particles/ record: - id: '12390' relation: dissertation_contains status: public scopus_import: '1' status: public title: Molecular impurities as a realization of anyons on the two-sphere type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 126 year: '2021' ... --- _id: '9009' abstract: - lang: eng text: Recent advancements in live cell imaging technologies have identified the phenomenon of intracellular propagation of late apoptotic events, such as cytochrome c release and caspase activation. The mechanism, prevalence, and speed of apoptosis propagation remain unclear. Additionally, no studies have demonstrated propagation of the pro-apoptotic protein, BAX. To evaluate the role of BAX in intracellular apoptotic propagation, we used high speed live-cell imaging to visualize fluorescently tagged-BAX recruitment to mitochondria in four immortalized cell lines. We show that propagation of mitochondrial BAX recruitment occurs in parallel to cytochrome c and SMAC/Diablo release and is affected by cellular morphology, such that cells with processes are more likely to exhibit propagation. The initiation of propagation events is most prevalent in the distal tips of processes, while the rate of propagation is influenced by the 2-dimensional width of the process. Propagation was rarely observed in the cell soma, which exhibited near synchronous recruitment of BAX. Propagation velocity is not affected by mitochondrial volume in segments of processes, but is negatively affected by mitochondrial density. There was no evidence of a propagating wave of increased levels of intracellular calcium ions. Alternatively, we did observe a uniform increase in superoxide build-up in cellular mitochondria, which was released as a propagating wave simultaneously with the propagating recruitment of BAX to the mitochondrial outer membrane. acknowledgement: This work was supported by National Institute of Health grants R01 EY030123, P30 EY016665, and T32 GM081061, an unrestricted research grant from Research to Prevent Blindness, Inc., and the Frederick A. Davis Endowment from the Department of Ophthalmology and Visual Sciences at the University of Wisconsin-Madison. article_processing_charge: No article_type: original author: - first_name: Joshua A. full_name: Grosser, Joshua A. last_name: Grosser - first_name: Margaret E full_name: Maes, Margaret E id: 3838F452-F248-11E8-B48F-1D18A9856A87 last_name: Maes orcid: 0000-0001-9642-1085 - first_name: Robert W. full_name: Nickells, Robert W. last_name: Nickells citation: ama: Grosser JA, Maes ME, Nickells RW. Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. Apoptosis. 2021;26(2):132-145. doi:10.1007/s10495-020-01654-w apa: Grosser, J. A., Maes, M. E., & Nickells, R. W. (2021). Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. Apoptosis. Springer Nature. https://doi.org/10.1007/s10495-020-01654-w chicago: Grosser, Joshua A., Margaret E Maes, and Robert W. Nickells. “Characteristics of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.” Apoptosis. Springer Nature, 2021. https://doi.org/10.1007/s10495-020-01654-w. ieee: J. A. Grosser, M. E. Maes, and R. W. Nickells, “Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis,” Apoptosis, vol. 26, no. 2. Springer Nature, pp. 132–145, 2021. ista: Grosser JA, Maes ME, Nickells RW. 2021. Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. Apoptosis. 26(2), 132–145. mla: Grosser, Joshua A., et al. “Characteristics of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.” Apoptosis, vol. 26, no. 2, Springer Nature, 2021, pp. 132–45, doi:10.1007/s10495-020-01654-w. short: J.A. Grosser, M.E. Maes, R.W. Nickells, Apoptosis 26 (2021) 132–145. date_created: 2021-01-17T23:01:11Z date_published: 2021-02-01T00:00:00Z date_updated: 2023-08-07T13:32:40Z day: '01' department: - _id: SaSi doi: 10.1007/s10495-020-01654-w external_id: isi: - '000606722600001' pmid: - '33426618' intvolume: ' 26' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082518/ month: '02' oa: 1 oa_version: Submitted Version page: 132-145 pmid: 1 publication: Apoptosis publication_identifier: eissn: - 1573-675X issn: - 1360-8185 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 26 year: '2021' ... --- _id: '9038' abstract: - lang: eng text: 'Layered materials in which individual atomic layers are bonded by weak van der Waals forces (vdW materials) constitute one of the most prominent platforms for materials research. Particularly, polar vdW crystals, such as hexagonal boron nitride (h-BN), alpha-molybdenum trioxide (α-MoO3) or alpha-vanadium pentoxide (α-V2O5), have received significant attention in nano-optics, since they support phonon polaritons (PhPs)―light coupled to lattice vibrations― with strong electromagnetic confinement and low optical losses. Recently, correlative far- and near-field studies of α-MoO3 have been demonstrated as an effective strategy to accurately extract the permittivity of this material. Here, we use this accurately characterized and low-loss polaritonic material to sense its local dielectric environment, namely silica (SiO2), one of the most widespread substrates in nanotechnology. By studying the propagation of PhPs on α-MoO3 flakes with different thicknesses laying on SiO2 substrates via near-field microscopy (s-SNOM), we extract locally the infrared permittivity of SiO2. Our work reveals PhPs nanoimaging as a versatile method for the quantitative characterization of the local optical properties of dielectric substrates, crucial for understanding and predicting the response of nanomaterials and for the future scalability of integrated nanophotonic devices. ' acknowledgement: "P.A.-M. acknowledges financial support through JAE Intro program from the Superior\r\nCouncil of Scientific Investigations and the Spanish Ministry of Science and Innovation (grant number JAEINT_20_00589). G.Á.-P. and J.T.-G. acknowledge financial support through the Severo Ochoa Program from the Government of the Principality of Asturias (grant numbers PA-20-PF-BP19-053 and PA-18-PF-BP17-126, respectively). J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain (RYC2018-026196-I) and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00)." article_number: '120' article_processing_charge: No article_type: original author: - first_name: Patricia full_name: Aguilar-Merino, Patricia last_name: Aguilar-Merino - first_name: Gonzalo full_name: Álvarez-Pérez, Gonzalo last_name: Álvarez-Pérez - first_name: Javier full_name: Taboada-Gutiérrez, Javier last_name: Taboada-Gutiérrez - first_name: Jiahua full_name: Duan, Jiahua last_name: Duan - first_name: Ivan full_name: Prieto Gonzalez, Ivan id: 2A307FE2-F248-11E8-B48F-1D18A9856A87 last_name: Prieto Gonzalez orcid: 0000-0002-7370-5357 - first_name: Luis Manuel full_name: Álvarez-Prado, Luis Manuel last_name: Álvarez-Prado - first_name: Alexey Y. full_name: Nikitin, Alexey Y. last_name: Nikitin - first_name: Javier full_name: Martín-Sánchez, Javier last_name: Martín-Sánchez - first_name: Pablo full_name: Alonso-González, Pablo last_name: Alonso-González citation: ama: Aguilar-Merino P, Álvarez-Pérez G, Taboada-Gutiérrez J, et al. Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. Nanomaterials. 2021;11(1). doi:10.3390/nano11010120 apa: Aguilar-Merino, P., Álvarez-Pérez, G., Taboada-Gutiérrez, J., Duan, J., Prieto Gonzalez, I., Álvarez-Prado, L. M., … Alonso-González, P. (2021). Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. Nanomaterials. MDPI. https://doi.org/10.3390/nano11010120 chicago: Aguilar-Merino, Patricia, Gonzalo Álvarez-Pérez, Javier Taboada-Gutiérrez, Jiahua Duan, Ivan Prieto Gonzalez, Luis Manuel Álvarez-Prado, Alexey Y. Nikitin, Javier Martín-Sánchez, and Pablo Alonso-González. “Extracting the Infrared Permittivity of SiO2 Substrates Locally by Near-Field Imaging of Phonon Polaritons in a van Der Waals Crystal.” Nanomaterials. MDPI, 2021. https://doi.org/10.3390/nano11010120. ieee: P. Aguilar-Merino et al., “Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal,” Nanomaterials, vol. 11, no. 1. MDPI, 2021. ista: Aguilar-Merino P, Álvarez-Pérez G, Taboada-Gutiérrez J, Duan J, Prieto Gonzalez I, Álvarez-Prado LM, Nikitin AY, Martín-Sánchez J, Alonso-González P. 2021. Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. Nanomaterials. 11(1), 120. mla: Aguilar-Merino, Patricia, et al. “Extracting the Infrared Permittivity of SiO2 Substrates Locally by Near-Field Imaging of Phonon Polaritons in a van Der Waals Crystal.” Nanomaterials, vol. 11, no. 1, 120, MDPI, 2021, doi:10.3390/nano11010120. short: P. Aguilar-Merino, G. Álvarez-Pérez, J. Taboada-Gutiérrez, J. Duan, I. Prieto Gonzalez, L.M. Álvarez-Prado, A.Y. Nikitin, J. Martín-Sánchez, P. Alonso-González, Nanomaterials 11 (2021). date_created: 2021-01-24T23:01:09Z date_published: 2021-01-07T00:00:00Z date_updated: 2023-08-07T13:35:50Z day: '07' ddc: - '620' department: - _id: NanoFab doi: 10.3390/nano11010120 external_id: isi: - '000610636600001' pmid: - '33430225' file: - access_level: open_access checksum: 1edc13eeda83df5cd9fff9504727b1f5 content_type: application/pdf creator: dernst date_created: 2021-01-25T08:02:32Z date_updated: 2021-01-25T08:02:32Z file_id: '9042' file_name: 2020_Nanomaterials_Aguilar_Merino.pdf file_size: 2730267 relation: main_file success: 1 file_date_updated: 2021-01-25T08:02:32Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Nanomaterials publication_identifier: eissn: - '20794991' publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal 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: '2021' ... --- _id: '9020' abstract: - lang: eng text: 'We study dynamics and thermodynamics of ion transport in narrow, water-filled channels, considered as effective 1D Coulomb systems. The long range nature of the inter-ion interactions comes about due to the dielectric constants mismatch between the water and the surrounding medium, confining the electric filed to stay mostly within the water-filled channel. Statistical mechanics of such Coulomb systems is dominated by entropic effects which may be accurately accounted for by mapping onto an effective quantum mechanics. In presence of multivalent ions the corresponding quantum mechanics appears to be non-Hermitian. In this review we discuss a framework for semiclassical calculations for the effective non-Hermitian Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line to closed cycles on a complex Riemann surfaces where direct calculations are not attainable. We circumvent this issue by applying tools from algebraic topology, such as the Picard-Fuchs equation. We discuss how its solutions relate to the thermodynamics and correlation functions of multivalent solutions within narrow, water-filled channels. ' acknowledgement: "A.K. was supported by NSF grants DMR-2037654. T.G. acknowledges funding from the Institute of Science and Technology (IST) Austria, and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411.\r\nWe are indebted to Boris Shklovskii for introducing us to the problem, and Alexander Gorsky and Peter Koroteev for introducing us to the Picard-Fuchs methods. A very special thanks goes to Michael Janas for several years of excellent collaboration on these topics. TG thanks Michael Kreshchuk for introduction to the exact WKB method and great collaboration on related projects. Figure 3 and Figure 4 are reproduced from Reference [25] with friendly permission by the Russian Academy of Sciences. Figure 2, Figure 4, Figure 5, Figure 6, and Figure 8 are reproduced from Reference [26] with friendly permission by IOP Publishing." article_number: e23010125 article_processing_charge: Yes article_type: original author: - first_name: Tobias full_name: Gulden, Tobias id: 1083E038-9F73-11E9-A4B5-532AE6697425 last_name: Gulden orcid: 0000-0001-6814-7541 - first_name: Alex full_name: Kamenev, Alex last_name: Kamenev citation: ama: Gulden T, Kamenev A. Dynamics of ion channels via non-hermitian quantum mechanics. Entropy. 2021;23(1). doi:10.3390/e23010125 apa: Gulden, T., & Kamenev, A. (2021). Dynamics of ion channels via non-hermitian quantum mechanics. Entropy. MDPI. https://doi.org/10.3390/e23010125 chicago: Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian Quantum Mechanics.” Entropy. MDPI, 2021. https://doi.org/10.3390/e23010125. ieee: T. Gulden and A. Kamenev, “Dynamics of ion channels via non-hermitian quantum mechanics,” Entropy, vol. 23, no. 1. MDPI, 2021. ista: Gulden T, Kamenev A. 2021. Dynamics of ion channels via non-hermitian quantum mechanics. Entropy. 23(1), e23010125. mla: Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian Quantum Mechanics.” Entropy, vol. 23, no. 1, e23010125, MDPI, 2021, doi:10.3390/e23010125. short: T. Gulden, A. Kamenev, Entropy 23 (2021). date_created: 2021-01-19T11:12:06Z date_published: 2021-01-19T00:00:00Z date_updated: 2023-08-07T13:34:18Z day: '19' ddc: - '530' department: - _id: MaSe doi: 10.3390/e23010125 ec_funded: 1 external_id: arxiv: - '2012.01390' isi: - '000610122000001' file: - access_level: open_access checksum: 6cd0e706156827c45c740534bd32c179 content_type: application/pdf creator: tgulden date_created: 2021-01-19T11:11:14Z date_updated: 2021-01-19T11:11:14Z file_id: '9021' file_name: Final published paper.pdf file_size: 981285 relation: main_file file_date_updated: 2021-01-19T11:11:14Z has_accepted_license: '1' intvolume: ' 23' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Entropy publication_identifier: eissn: - 1099-4300 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: Dynamics of ion channels via non-hermitian quantum mechanics 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: 23 year: '2021' ... --- _id: '9037' abstract: - lang: eng text: "We continue our study of ‘no‐dimension’ analogues of basic theorems in combinatorial and convex geometry in Banach spaces. We generalize some results of the paper (Adiprasito, Bárány and Mustafa, ‘Theorems of Carathéodory, Helly, and Tverberg without dimension’, Proceedings of the Thirtieth Annual ACM‐SIAM Symposium on Discrete Algorithms (Society for Industrial and Applied Mathematics, San Diego, California, 2019) 2350–2360) and prove no‐dimension versions of the colored Tverberg theorem, the selection lemma and the weak \U0001D700 ‐net theorem in Banach spaces of type \U0001D45D>1 . To prove these results, we use the original ideas of Adiprasito, Bárány and Mustafa for the Euclidean case, our no‐dimension version of the Radon theorem and slightly modified version of the celebrated Maurey lemma." acknowledgement: "I wish to thank Imre Bárány for bringing the problem to my attention. I am grateful to Marton Naszódi and Igor Tsiutsiurupa for useful remarks and help with the text.\r\nThe author acknowledges the financial support from the Ministry of Educational and Science of the Russian Federation in the framework of MegaGrant no 075‐15‐2019‐1926." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Grigory full_name: Ivanov, Grigory id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E last_name: Ivanov citation: ama: Ivanov G. No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. Bulletin of the London Mathematical Society. 2021;53(2):631-641. doi:10.1112/blms.12449 apa: Ivanov, G. (2021). No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. Bulletin of the London Mathematical Society. London Mathematical Society. https://doi.org/10.1112/blms.12449 chicago: Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach Spaces of Type P.” Bulletin of the London Mathematical Society. London Mathematical Society, 2021. https://doi.org/10.1112/blms.12449. ieee: G. Ivanov, “No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p,” Bulletin of the London Mathematical Society, vol. 53, no. 2. London Mathematical Society, pp. 631–641, 2021. ista: Ivanov G. 2021. No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. Bulletin of the London Mathematical Society. 53(2), 631–641. mla: Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach Spaces of Type P.” Bulletin of the London Mathematical Society, vol. 53, no. 2, London Mathematical Society, 2021, pp. 631–41, doi:10.1112/blms.12449. short: G. Ivanov, Bulletin of the London Mathematical Society 53 (2021) 631–641. date_created: 2021-01-24T23:01:08Z date_published: 2021-04-01T00:00:00Z date_updated: 2023-08-07T13:35:20Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.1112/blms.12449 external_id: arxiv: - '1912.08561' isi: - '000607265100001' file: - access_level: open_access checksum: e6ceaa6470d835eb4c211cbdd38fdfd1 content_type: application/pdf creator: kschuh date_created: 2021-08-06T09:59:45Z date_updated: 2021-08-06T09:59:45Z file_id: '9796' file_name: 2021_BLMS_Ivanov.pdf file_size: 194550 relation: main_file success: 1 file_date_updated: 2021-08-06T09:59:45Z has_accepted_license: '1' intvolume: ' 53' isi: 1 issue: '2' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 631-641 publication: Bulletin of the London Mathematical Society publication_identifier: eissn: - '14692120' issn: - '00246093' publication_status: published publisher: London Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: No-dimension Tverberg's theorem and its corollaries in Banach spaces of type p 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: 53 year: '2021' ... --- _id: '9046' acknowledgement: Our work was supported by the Swedish Research Council (grant 2017-01527) to DIA article_number: e1009172 article_processing_charge: No article_type: original author: - first_name: Roderich full_name: Römhild, Roderich id: 68E56E44-62B0-11EA-B963-444F3DDC885E last_name: Römhild orcid: 0000-0001-9480-5261 - first_name: Dan I. full_name: Andersson, Dan I. last_name: Andersson citation: ama: Römhild R, Andersson DI. Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. PLoS Pathogens. 2021;17(1). doi:10.1371/journal.ppat.1009172 apa: Römhild, R., & Andersson, D. I. (2021). Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1009172 chicago: Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.” PLoS Pathogens. Public Library of Science, 2021. https://doi.org/10.1371/journal.ppat.1009172. ieee: R. Römhild and D. I. Andersson, “Mechanisms and therapeutic potential of collateral sensitivity to antibiotics,” PLoS Pathogens, vol. 17, no. 1. Public Library of Science, 2021. ista: Römhild R, Andersson DI. 2021. Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. PLoS Pathogens. 17(1), e1009172. mla: Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.” PLoS Pathogens, vol. 17, no. 1, e1009172, Public Library of Science, 2021, doi:10.1371/journal.ppat.1009172. short: R. Römhild, D.I. Andersson, PLoS Pathogens 17 (2021). date_created: 2021-01-31T23:01:21Z date_published: 2021-01-14T00:00:00Z date_updated: 2023-08-07T13:36:55Z day: '14' ddc: - '570' department: - _id: CaGu doi: 10.1371/journal.ppat.1009172 external_id: isi: - '000610190400007' pmid: - '33444399' file: - access_level: open_access checksum: d745d7f8fcbb9b95fea16a36f94dee31 content_type: application/pdf creator: dernst date_created: 2021-02-03T12:13:03Z date_updated: 2021-02-03T12:13:03Z file_id: '9070' file_name: 2021_PlosPathogens_Roemhild.pdf file_size: 570066 relation: main_file success: 1 file_date_updated: 2021-02-03T12:13:03Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Pathogens publication_identifier: eissn: - '15537374' issn: - '15537366' publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Mechanisms and therapeutic potential of collateral sensitivity to antibiotics 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: 17 year: '2021' ... --- _id: '9047' abstract: - lang: eng text: This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N1−1/μ) , where N is the block length and μ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 or 1. acknowledgement: M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305, IIS-1741162, and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council of Canada (NSERC) and by Huawei. The authors would like to thank the anonymous reviewers for their comments that helped improving the quality of the manuscript. article_processing_charge: No article_type: original author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: John M. full_name: Cioffi, John M. last_name: Cioffi - first_name: Andrea full_name: Goldsmith, Andrea last_name: Goldsmith citation: ama: Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. Sublinear latency for simplified successive cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. 2021;20(1):18-27. doi:10.1109/TWC.2020.3022922 apa: Mondelli, M., Hashemi, S. A., Cioffi, J. M., & Goldsmith, A. (2021). Sublinear latency for simplified successive cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. IEEE. https://doi.org/10.1109/TWC.2020.3022922 chicago: Mondelli, Marco, Seyyed Ali Hashemi, John M. Cioffi, and Andrea Goldsmith. “Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.” IEEE Transactions on Wireless Communications. IEEE, 2021. https://doi.org/10.1109/TWC.2020.3022922. ieee: M. Mondelli, S. A. Hashemi, J. M. Cioffi, and A. Goldsmith, “Sublinear latency for simplified successive cancellation decoding of polar codes,” IEEE Transactions on Wireless Communications, vol. 20, no. 1. IEEE, pp. 18–27, 2021. ista: Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. 2021. Sublinear latency for simplified successive cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. 20(1), 18–27. mla: Mondelli, Marco, et al. “Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.” IEEE Transactions on Wireless Communications, vol. 20, no. 1, IEEE, 2021, pp. 18–27, doi:10.1109/TWC.2020.3022922. short: M. Mondelli, S.A. Hashemi, J.M. Cioffi, A. Goldsmith, IEEE Transactions on Wireless Communications 20 (2021) 18–27. date_created: 2021-01-31T23:01:21Z date_published: 2021-01-01T00:00:00Z date_updated: 2023-08-07T13:36:25Z day: '01' department: - _id: MaMo doi: 10.1109/TWC.2020.3022922 external_id: arxiv: - '1909.04892' isi: - '000607808800002' intvolume: ' 20' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1909.04892 month: '01' oa: 1 oa_version: Preprint page: 18-27 publication: IEEE Transactions on Wireless Communications publication_identifier: eissn: - '15582248' issn: - '15361276' publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '8536' relation: earlier_version status: public scopus_import: '1' status: public title: Sublinear latency for simplified successive cancellation decoding of polar codes type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 20 year: '2021' ... --- _id: '9036' abstract: - lang: eng text: In this short note, we prove that the square root of the quantum Jensen-Shannon divergence is a true metric on the cone of positive matrices, and hence in particular on the quantum state space. acknowledgement: D. Virosztek was supported by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 846294, and partially supported by the Hungarian National Research, Development and Innovation Office (NKFIH) via grants no. K124152, and no. KH129601. article_number: '107595' article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Virosztek, Daniel id: 48DB45DA-F248-11E8-B48F-1D18A9856A87 last_name: Virosztek orcid: 0000-0003-1109-5511 citation: ama: Virosztek D. The metric property of the quantum Jensen-Shannon divergence. Advances in Mathematics. 2021;380(3). doi:10.1016/j.aim.2021.107595 apa: Virosztek, D. (2021). The metric property of the quantum Jensen-Shannon divergence. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2021.107595 chicago: Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.” Advances in Mathematics. Elsevier, 2021. https://doi.org/10.1016/j.aim.2021.107595. ieee: D. Virosztek, “The metric property of the quantum Jensen-Shannon divergence,” Advances in Mathematics, vol. 380, no. 3. Elsevier, 2021. ista: Virosztek D. 2021. The metric property of the quantum Jensen-Shannon divergence. Advances in Mathematics. 380(3), 107595. mla: Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.” Advances in Mathematics, vol. 380, no. 3, 107595, Elsevier, 2021, doi:10.1016/j.aim.2021.107595. short: D. Virosztek, Advances in Mathematics 380 (2021). date_created: 2021-01-22T17:55:17Z date_published: 2021-03-26T00:00:00Z date_updated: 2023-08-07T13:34:48Z day: '26' department: - _id: LaEr doi: 10.1016/j.aim.2021.107595 ec_funded: 1 external_id: arxiv: - '1910.10447' isi: - '000619676100035' intvolume: ' 380' isi: 1 issue: '3' keyword: - General Mathematics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1910.10447 month: '03' oa: 1 oa_version: Preprint project: - _id: 26A455A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '846294' name: Geometric study of Wasserstein spaces and free probability publication: Advances in Mathematics publication_identifier: issn: - 0001-8708 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: The metric property of the quantum Jensen-Shannon divergence type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 380 year: '2021' ... --- _id: '9101' abstract: - lang: eng text: 'Behavioral predispositions are innate tendencies of animals to behave in a given way without the input of learning. They increase survival chances and, due to environmental and ecological challenges, may vary substantially even between closely related taxa. These differences are likely to be especially pronounced in long-lived species like crocodilians. This order is particularly relevant for comparative cognition due to its phylogenetic proximity to birds. Here we compared early life behavioral predispositions in two Alligatoridae species. We exposed American alligator and spectacled caiman hatchlings to three different novel situations: a novel object, a novel environment that was open and a novel environment with a shelter. This was then repeated a week later. During exposure to the novel environments, alligators moved around more and explored a larger range of the arena than the caimans. When exposed to the novel object, the alligators reduced the mean distance to the novel object in the second phase, while the caimans further increased it, indicating diametrically opposite ontogenetic development in behavioral predispositions. Although all crocodilian hatchlings face comparable challenges, e.g., high predation pressure, the effectiveness of parental protection might explain the observed pattern. American alligators are apex predators capable of protecting their offspring against most dangers, whereas adult spectacled caimans are frequently predated themselves. Their distancing behavior might be related to increased predator avoidance and also explain the success of invasive spectacled caimans in the natural habitats of other crocodilians.' acknowledgement: We thank Jamie Gilks and Terry Miles for their support at Crocodiles of the World. We are grateful to the Department of Cognitive Biology, University of Vienna for provision of working space and hardware. Finally, we would like to thank Cliodhna Quigley, Rachael Harrison and Urs A. Reber for discussion. Open Access funding provided by Lund University. This project was funded by the Marietta Blau grant (BMFWF) to S. A. R. article_processing_charge: No article_type: original author: - first_name: Stephan A. full_name: Reber, Stephan A. last_name: Reber - first_name: Jinook full_name: Oh, Jinook id: 403169A4-080F-11EA-9993-BF3F3DDC885E last_name: Oh orcid: 0000-0001-7425-2372 - first_name: Judith full_name: Janisch, Judith last_name: Janisch - first_name: Colin full_name: Stevenson, Colin last_name: Stevenson - first_name: Shaun full_name: Foggett, Shaun last_name: Foggett - first_name: Anna full_name: Wilkinson, Anna last_name: Wilkinson citation: ama: Reber SA, Oh J, Janisch J, Stevenson C, Foggett S, Wilkinson A. Early life differences in behavioral predispositions in two Alligatoridae species. Animal Cognition. 2021;24(4):753-764. doi:10.1007/s10071-020-01461-5 apa: Reber, S. A., Oh, J., Janisch, J., Stevenson, C., Foggett, S., & Wilkinson, A. (2021). Early life differences in behavioral predispositions in two Alligatoridae species. Animal Cognition. Springer Nature. https://doi.org/10.1007/s10071-020-01461-5 chicago: Reber, Stephan A., Jinook Oh, Judith Janisch, Colin Stevenson, Shaun Foggett, and Anna Wilkinson. “Early Life Differences in Behavioral Predispositions in Two Alligatoridae Species.” Animal Cognition. Springer Nature, 2021. https://doi.org/10.1007/s10071-020-01461-5. ieee: S. A. Reber, J. Oh, J. Janisch, C. Stevenson, S. Foggett, and A. Wilkinson, “Early life differences in behavioral predispositions in two Alligatoridae species,” Animal Cognition, vol. 24, no. 4. Springer Nature, pp. 753–764, 2021. ista: Reber SA, Oh J, Janisch J, Stevenson C, Foggett S, Wilkinson A. 2021. Early life differences in behavioral predispositions in two Alligatoridae species. Animal Cognition. 24(4), 753–764. mla: Reber, Stephan A., et al. “Early Life Differences in Behavioral Predispositions in Two Alligatoridae Species.” Animal Cognition, vol. 24, no. 4, Springer Nature, 2021, pp. 753–64, doi:10.1007/s10071-020-01461-5. short: S.A. Reber, J. Oh, J. Janisch, C. Stevenson, S. Foggett, A. Wilkinson, Animal Cognition 24 (2021) 753–764. date_created: 2021-02-07T23:01:13Z date_published: 2021-07-01T00:00:00Z date_updated: 2023-08-07T13:41:08Z day: '01' ddc: - '590' department: - _id: SyCr doi: 10.1007/s10071-020-01461-5 external_id: isi: - '000608382100001' file: - access_level: open_access checksum: d9dfa0d1de6d684692b041d936dd858e content_type: application/pdf creator: dernst date_created: 2021-02-09T07:40:14Z date_updated: 2021-02-09T07:40:14Z file_id: '9107' file_name: 2021_AnimalCognition_Reber.pdf file_size: 1117991 relation: main_file success: 1 file_date_updated: 2021-02-09T07:40:14Z has_accepted_license: '1' intvolume: ' 24' isi: 1 issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 753-764 publication: Animal Cognition publication_identifier: eissn: - '14359456' issn: - '14359448' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Early life differences in behavioral predispositions in two Alligatoridae species 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: 24 year: '2021' ... --- _id: '9100' abstract: - lang: eng text: 'Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we ''dive under the surface'' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.' acknowledgement: "We would like to thank all the participants in the speciation symposium of the Marine Evolution Conference in Sweden for the interesting discussions and to all the contributors to this special\r\nissue. We thank Nicolas Bierne and Wolf Blanckenhorn (reviewer and editor, respectively) for valuable suggestions during the revision of the manuscript, and Roger K. Butlin and Anja M. Westram for very helpful comments on a previous draft. We would also like to thank Wolf Blanckenhorn and Nicola Cook, the Editor in Chief and the Managing Editor of the Journal of Evolutionary Biology, respectively, for the encouragement and support in putting together this special issue, and to all reviewers involved. RF was financed by the European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement Number 706376 and is currently financed by the FEDER Funds through the Operational Competitiveness Factors Program COMPETE and by National Funds through the Foundation for Science and Technology (FCT) within the scope of the project ‘Hybrabbid' (PTDC/BIA-EVL/30628/2017-POCI-01-0145-FEDER-030628). KJ was funded by the Swedish\r\nResearch Council, VR. SS was supported by NERC and ERC funding awarded to Roger K. Butlin." article_processing_charge: No article_type: original author: - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski citation: ama: 'Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 2021;34(1):4-15. doi:10.1111/jeb.13756' apa: 'Faria, R., Johannesson, K., & Stankowski, S. (2021). Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13756' chicago: 'Faria, Rui, Kerstin Johannesson, and Sean Stankowski. “Speciation in Marine Environments: Diving under the Surface.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13756.' ieee: 'R. Faria, K. Johannesson, and S. Stankowski, “Speciation in marine environments: Diving under the surface,” Journal of Evolutionary Biology, vol. 34, no. 1. Wiley, pp. 4–15, 2021.' ista: 'Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 34(1), 4–15.' mla: 'Faria, Rui, et al. “Speciation in Marine Environments: Diving under the Surface.” Journal of Evolutionary Biology, vol. 34, no. 1, Wiley, 2021, pp. 4–15, doi:10.1111/jeb.13756.' short: R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology 34 (2021) 4–15. date_created: 2021-02-07T23:01:13Z date_published: 2021-01-18T00:00:00Z date_updated: 2023-08-07T13:42:08Z day: '18' ddc: - '570' department: - _id: NiBa doi: 10.1111/jeb.13756 external_id: isi: - '000608367500001' file: - access_level: open_access checksum: 5755856a5368d4b4cdd6fad5ab27f4d1 content_type: application/pdf creator: dernst date_created: 2021-02-09T09:04:02Z date_updated: 2021-02-09T09:04:02Z file_id: '9108' file_name: 2021_JourEvolBiology_Faria.pdf file_size: 561340 relation: main_file success: 1 file_date_updated: 2021-02-09T09:04:02Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 4-15 publication: Journal of Evolutionary Biology publication_identifier: eissn: - '14209101' issn: - 1010061X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Speciation in marine environments: Diving under the surface' 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: 34 year: '2021' ... --- _id: '9093' abstract: - lang: eng text: We employ the Gross-Pitaevskii equation to study acoustic emission generated in a uniform Bose gas by a static impurity. The impurity excites a sound-wave packet, which propagates through the gas. We calculate the shape of this wave packet in the limit of long wave lengths, and argue that it is possible to extract properties of the impurity by observing this shape. We illustrate here this possibility for a Bose gas with a trapped impurity atom -- an example of a relevant experimental setup. Presented results are general for all one-dimensional systems described by the nonlinear Schrödinger equation and can also be used in nonatomic systems, e.g., to analyze light propagation in nonlinear optical media. Finally, we calculate the shape of the sound-wave packet for a three-dimensional Bose gas assuming a spherically symmetric perturbation. acknowledgement: "We acknowledge fruitful discussions with Dr. Simos Mistakidis regarding beyond mean-field\r\neffects in our system. We also thank Prof. Maxim Olshanii for valuable suggestions to improve\r\nthe manuscript.O.V.M acknowledges the support from the National Science Foundation\r\nthrough grants No. PHY-1402249, No. PHY-1607221, and No. PHY-1912542 and the\r\nBinational (US-Israel) Science Foundation through grant No. 2015616, as well as by the Israel\r\nScience Foundation (grant No. 1287/17) and from the German Aeronautics and Space Administration\r\n(DLR) through Grant No. 50WM1957. This work has also received funding from\r\nthe DFG Project No.413495248 [VO 2437/1-1] and European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411\r\n(A. G. V.)" article_number: '025' article_processing_charge: No article_type: original author: - first_name: Oleksandr full_name: Marchukov, Oleksandr last_name: Marchukov - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Marchukov O, Volosniev A. Shape of a sound wave in a weakly-perturbed Bose gas. SciPost Physics. 2021;10(2). doi:10.21468/scipostphys.10.2.025 apa: Marchukov, O., & Volosniev, A. (2021). Shape of a sound wave in a weakly-perturbed Bose gas. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.10.2.025 chicago: Marchukov, Oleksandr, and Artem Volosniev. “Shape of a Sound Wave in a Weakly-Perturbed Bose Gas.” SciPost Physics. SciPost Foundation, 2021. https://doi.org/10.21468/scipostphys.10.2.025. ieee: O. Marchukov and A. Volosniev, “Shape of a sound wave in a weakly-perturbed Bose gas,” SciPost Physics, vol. 10, no. 2. SciPost Foundation, 2021. ista: Marchukov O, Volosniev A. 2021. Shape of a sound wave in a weakly-perturbed Bose gas. SciPost Physics. 10(2), 025. mla: Marchukov, Oleksandr, and Artem Volosniev. “Shape of a Sound Wave in a Weakly-Perturbed Bose Gas.” SciPost Physics, vol. 10, no. 2, 025, SciPost Foundation, 2021, doi:10.21468/scipostphys.10.2.025. short: O. Marchukov, A. Volosniev, SciPost Physics 10 (2021). date_created: 2021-02-04T12:39:24Z date_published: 2021-02-03T00:00:00Z date_updated: 2023-08-07T13:39:37Z day: '03' ddc: - '530' department: - _id: MiLe doi: 10.21468/scipostphys.10.2.025 ec_funded: 1 external_id: arxiv: - '2004.08075' isi: - '000646783100027' file: - access_level: open_access checksum: 9fd614b7ab49999e7267874df2582f7e content_type: application/pdf creator: dernst date_created: 2021-02-09T07:06:22Z date_updated: 2021-02-09T07:06:22Z file_id: '9105' file_name: 2021_SciPostPhysics_Marchukov.pdf file_size: 666512 relation: main_file success: 1 file_date_updated: 2021-02-09T07:06:22Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: SciPost Physics publication_identifier: issn: - 2542-4653 publication_status: published publisher: SciPost Foundation quality_controlled: '1' status: public title: Shape of a sound wave in a weakly-perturbed Bose gas tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2021' ... --- _id: '8689' abstract: - lang: eng text: 'This paper continues the discussion started in [CK19] concerning Arnold''s legacy on classical KAM theory and (some of) its modern developments. We prove a detailed and explicit `global'' Arnold''s KAM Theorem, which yields, in particular, the Whitney conjugacy of a non{degenerate, real{analytic, nearly-integrable Hamiltonian system to an integrable system on a closed, nowhere dense, positive measure subset of the phase space. Detailed measure estimates on the Kolmogorov''s set are provided in the case the phase space is: (A) a uniform neighbourhood of an arbitrary (bounded) set times the d-torus and (B) a domain with C2 boundary times the d-torus. All constants are explicitly given.' article_processing_charge: No article_type: original author: - first_name: Luigi full_name: Chierchia, Luigi last_name: Chierchia - first_name: Edmond full_name: Koudjinan, Edmond id: 52DF3E68-AEFA-11EA-95A4-124A3DDC885E last_name: Koudjinan orcid: 0000-0003-2640-4049 citation: ama: Chierchia L, Koudjinan E. V.I. Arnold’s “‘Global’” KAM theorem and geometric measure estimates. Regular and Chaotic Dynamics. 2021;26(1):61-88. doi:10.1134/S1560354721010044 apa: Chierchia, L., & Koudjinan, E. (2021). V.I. Arnold’s “‘Global’” KAM theorem and geometric measure estimates. Regular and Chaotic Dynamics. Springer Nature. https://doi.org/10.1134/S1560354721010044 chicago: Chierchia, Luigi, and Edmond Koudjinan. “V.I. Arnold’s ‘“Global”’ KAM Theorem and Geometric Measure Estimates.” Regular and Chaotic Dynamics. Springer Nature, 2021. https://doi.org/10.1134/S1560354721010044. ieee: L. Chierchia and E. Koudjinan, “V.I. Arnold’s ‘“Global”’ KAM theorem and geometric measure estimates,” Regular and Chaotic Dynamics, vol. 26, no. 1. Springer Nature, pp. 61–88, 2021. ista: Chierchia L, Koudjinan E. 2021. V.I. Arnold’s ‘“Global”’ KAM theorem and geometric measure estimates. Regular and Chaotic Dynamics. 26(1), 61–88. mla: Chierchia, Luigi, and Edmond Koudjinan. “V.I. Arnold’s ‘“Global”’ KAM Theorem and Geometric Measure Estimates.” Regular and Chaotic Dynamics, vol. 26, no. 1, Springer Nature, 2021, pp. 61–88, doi:10.1134/S1560354721010044. short: L. Chierchia, E. Koudjinan, Regular and Chaotic Dynamics 26 (2021) 61–88. date_created: 2020-10-21T14:56:47Z date_published: 2021-02-03T00:00:00Z date_updated: 2023-08-07T13:37:27Z day: '03' ddc: - '515' department: - _id: VaKa doi: 10.1134/S1560354721010044 external_id: arxiv: - '2010.13243' isi: - '000614454700004' intvolume: ' 26' isi: 1 issue: '1' keyword: - Nearly{integrable Hamiltonian systems - perturbation theory - KAM Theory - Arnold's scheme - Kolmogorov's set - primary invariant tori - Lagrangian tori - measure estimates - small divisors - integrability on nowhere dense sets - Diophantine frequencies. language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2010.13243 month: '02' oa: 1 oa_version: Preprint page: 61-88 publication: Regular and Chaotic Dynamics publication_identifier: issn: - 1560-3547 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: V.I. Arnold's ''Global'' KAM theorem and geometric measure estimates type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 26 year: '2021' ... --- _id: '9099' abstract: - lang: eng text: We show that on an Abelian variety over an algebraically closed field of positive characteristic, the obstruction to lifting an automorphism to a field of characteristic zero as a morphism vanishes if and only if it vanishes for lifting it as a derived autoequivalence. We also compare the deformation space of these two types of deformations. acknowledgement: I would like to thank Piotr Achinger, Daniel Huybrechts, Katrina Honigs, Marcin Lara, and Maciek Zdanowicz for the mathematical discussions, Tamas Hausel for hosting me in his research group at IST Austria, and the referees for their valuable suggestions. This research has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie Grant Agreement No. 754411. article_processing_charge: No article_type: original author: - first_name: Tanya K full_name: Srivastava, Tanya K id: 4D046628-F248-11E8-B48F-1D18A9856A87 last_name: Srivastava citation: ama: Srivastava TK. Lifting automorphisms on Abelian varieties as derived autoequivalences. Archiv der Mathematik. 2021;116(5):515-527. doi:10.1007/s00013-020-01564-y apa: Srivastava, T. K. (2021). Lifting automorphisms on Abelian varieties as derived autoequivalences. Archiv Der Mathematik. Springer Nature. https://doi.org/10.1007/s00013-020-01564-y chicago: Srivastava, Tanya K. “Lifting Automorphisms on Abelian Varieties as Derived Autoequivalences.” Archiv Der Mathematik. Springer Nature, 2021. https://doi.org/10.1007/s00013-020-01564-y. ieee: T. K. Srivastava, “Lifting automorphisms on Abelian varieties as derived autoequivalences,” Archiv der Mathematik, vol. 116, no. 5. Springer Nature, pp. 515–527, 2021. ista: Srivastava TK. 2021. Lifting automorphisms on Abelian varieties as derived autoequivalences. Archiv der Mathematik. 116(5), 515–527. mla: Srivastava, Tanya K. “Lifting Automorphisms on Abelian Varieties as Derived Autoequivalences.” Archiv Der Mathematik, vol. 116, no. 5, Springer Nature, 2021, pp. 515–27, doi:10.1007/s00013-020-01564-y. short: T.K. Srivastava, Archiv Der Mathematik 116 (2021) 515–527. date_created: 2021-02-07T23:01:13Z date_published: 2021-05-01T00:00:00Z date_updated: 2023-08-07T13:42:38Z day: '01' department: - _id: TaHa doi: 10.1007/s00013-020-01564-y ec_funded: 1 external_id: arxiv: - '2001.07762' isi: - '000612580200001' intvolume: ' 116' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2001.07762 month: '05' oa: 1 oa_version: Preprint page: 515-527 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Archiv der Mathematik publication_identifier: eissn: - '14208938' issn: - 0003889X publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Lifting automorphisms on Abelian varieties as derived autoequivalences type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 116 year: '2021' ... --- _id: '9098' abstract: - lang: eng text: "We study properties of the volume of projections of the n-dimensional\r\ncross-polytope $\\crosp^n = \\{ x \\in \\R^n \\mid |x_1| + \\dots + |x_n| \\leqslant 1\\}.$ We prove that the projection of $\\crosp^n$ onto a k-dimensional coordinate subspace has the maximum possible volume for k=2 and for k=3.\r\nWe obtain the exact lower bound on the volume of such a projection onto a two-dimensional plane. Also, we show that there exist local maxima which are not global ones for the volume of a projection of $\\crosp^n$ onto a k-dimensional subspace for any n>k⩾2." acknowledgement: Research was supported by the Russian Foundation for Basic Research, project 18-01-00036A (Theorems 1.5 and 5.3) and by the Ministry of Education and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926 (Theorems 1.2 and 7.3). article_number: '112312' article_processing_charge: No article_type: original author: - first_name: Grigory full_name: Ivanov, Grigory id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E last_name: Ivanov citation: ama: Ivanov G. On the volume of projections of the cross-polytope. Discrete Mathematics. 2021;344(5). doi:10.1016/j.disc.2021.112312 apa: Ivanov, G. (2021). On the volume of projections of the cross-polytope. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2021.112312 chicago: Ivanov, Grigory. “On the Volume of Projections of the Cross-Polytope.” Discrete Mathematics. Elsevier, 2021. https://doi.org/10.1016/j.disc.2021.112312. ieee: G. Ivanov, “On the volume of projections of the cross-polytope,” Discrete Mathematics, vol. 344, no. 5. Elsevier, 2021. ista: Ivanov G. 2021. On the volume of projections of the cross-polytope. Discrete Mathematics. 344(5), 112312. mla: Ivanov, Grigory. “On the Volume of Projections of the Cross-Polytope.” Discrete Mathematics, vol. 344, no. 5, 112312, Elsevier, 2021, doi:10.1016/j.disc.2021.112312. short: G. Ivanov, Discrete Mathematics 344 (2021). date_created: 2021-02-07T23:01:12Z date_published: 2021-05-01T00:00:00Z date_updated: 2023-08-07T13:40:37Z day: '01' department: - _id: UlWa doi: 10.1016/j.disc.2021.112312 external_id: arxiv: - '1808.09165' isi: - '000633365200001' intvolume: ' 344' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1808.09165 month: '05' oa: 1 oa_version: Preprint publication: Discrete Mathematics publication_identifier: issn: - 0012365X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: On the volume of projections of the cross-polytope type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 344 year: '2021' ... --- _id: '9188' abstract: - lang: eng text: Genomic imprinting is an epigenetic mechanism that results in parental allele-specific expression of ~1% of all genes in mouse and human. Imprinted genes are key developmental regulators and play pivotal roles in many biological processes such as nutrient transfer from the mother to offspring and neuronal development. Imprinted genes are also involved in human disease, including neurodevelopmental disorders, and often occur in clusters that are regulated by a common imprint control region (ICR). In extra-embryonic tissues ICRs can act over large distances, with the largest surrounding Igf2r spanning over 10 million base-pairs. Besides classical imprinted expression that shows near exclusive maternal or paternal expression, widespread biased imprinted expression has been identified mainly in brain. In this review we discuss recent developments mapping cell type specific imprinted expression in extra-embryonic tissues and neocortex in the mouse. We highlight the advantages of using an inducible uniparental chromosome disomy (UPD) system to generate cells carrying either two maternal or two paternal copies of a specific chromosome to analyze the functional consequences of genomic imprinting. Mosaic Analysis with Double Markers (MADM) allows fluorescent labeling and concomitant induction of UPD sparsely in specific cell types, and thus to over-express or suppress all imprinted genes on that chromosome. To illustrate the utility of this technique, we explain how MADM-induced UPD revealed new insights about the function of the well-studied Cdkn1c imprinted gene, and how MADM-induced UPDs led to identification of highly cell type specific phenotypes related to perturbed imprinted expression in the mouse neocortex. Finally, we give an outlook on how MADM could be used to probe cell type specific imprinted expression in other tissues in mouse, particularly in extra-embryonic tissues. acknowledgement: We thank Melissa Stouffer for critically reading the manuscript. This work was supported by IST Austria institutional funds; NÖ Forschung und Bildung n[f + b] life science call grant (C13-002) to S.H. and the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H. article_number: '104986' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler - first_name: Quanah full_name: Hudson, Quanah last_name: Hudson - first_name: Susanne full_name: Laukoter, Susanne id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87 last_name: Laukoter - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Pauler F, Hudson Q, Laukoter S, Hippenmeyer S. Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond. Neurochemistry International. 2021;145(5). doi:10.1016/j.neuint.2021.104986 apa: Pauler, F., Hudson, Q., Laukoter, S., & Hippenmeyer, S. (2021). Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond. Neurochemistry International. Elsevier. https://doi.org/10.1016/j.neuint.2021.104986 chicago: Pauler, Florian, Quanah Hudson, Susanne Laukoter, and Simon Hippenmeyer. “Inducible Uniparental Chromosome Disomy to Probe Genomic Imprinting at Single-Cell Level in Brain and Beyond.” Neurochemistry International. Elsevier, 2021. https://doi.org/10.1016/j.neuint.2021.104986. ieee: F. Pauler, Q. Hudson, S. Laukoter, and S. Hippenmeyer, “Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond,” Neurochemistry International, vol. 145, no. 5. Elsevier, 2021. ista: Pauler F, Hudson Q, Laukoter S, Hippenmeyer S. 2021. Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond. Neurochemistry International. 145(5), 104986. mla: Pauler, Florian, et al. “Inducible Uniparental Chromosome Disomy to Probe Genomic Imprinting at Single-Cell Level in Brain and Beyond.” Neurochemistry International, vol. 145, no. 5, 104986, Elsevier, 2021, doi:10.1016/j.neuint.2021.104986. short: F. Pauler, Q. Hudson, S. Laukoter, S. Hippenmeyer, Neurochemistry International 145 (2021). date_created: 2021-02-23T12:31:43Z date_published: 2021-05-01T00:00:00Z date_updated: 2023-08-07T13:48:26Z day: '01' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.neuint.2021.104986 ec_funded: 1 external_id: isi: - '000635575000005' pmid: - '33600873' file: - access_level: open_access checksum: c6d7a40089cd29e289f9b22e75768304 content_type: application/pdf creator: kschuh date_created: 2021-08-11T12:30:38Z date_updated: 2021-08-11T12:30:38Z file_id: '9883' file_name: 2021_NCI_Pauler.pdf file_size: 7083499 relation: main_file success: 1 file_date_updated: 2021-08-11T12:30:38Z has_accepted_license: '1' intvolume: ' 145' isi: 1 issue: '5' keyword: - Cell Biology - Cellular and Molecular Neuroscience language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development - _id: 25D92700-B435-11E9-9278-68D0E5697425 grant_number: LS13-002 name: Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain publication: Neurochemistry International publication_identifier: issn: - 0197-0186 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond 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: 145 year: '2021' ... --- _id: '9158' abstract: - lang: eng text: While several tools have been developed to study the ground state of many-body quantum spin systems, the limitations of existing techniques call for the exploration of new approaches. In this manuscript we develop an alternative analytical and numerical framework for many-body quantum spin ground states, based on the disentanglement formalism. In this approach, observables are exactly expressed as Gaussian-weighted functional integrals over scalar fields. We identify the leading contribution to these integrals, given by the saddle point of a suitable effective action. Analytically, we develop a field-theoretical expansion of the functional integrals, performed by means of appropriate Feynman rules. The expansion can be truncated to a desired order to obtain analytical approximations to observables. Numerically, we show that the disentanglement approach can be used to compute ground state expectation values from classical stochastic processes. While the associated fluctuations grow exponentially with imaginary time and the system size, this growth can be mitigated by means of an importance sampling scheme based on knowledge of the saddle point configuration. We illustrate the advantages and limitations of our methods by considering the quantum Ising model in 1, 2 and 3 spatial dimensions. Our analytical and numerical approaches are applicable to a broad class of systems, bridging concepts from quantum lattice models, continuum field theory, and classical stochastic processes. acknowledgement: "S D N would like to thank M J Bhaseen, J Chalker, B Doyon, V Gritsev, A Lamacraft,\r\nA Michailidis and M Serbyn for helpful feedback and stimulating conversations. S D N\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and\r\nfrom the European Union’s Horizon 2020 research and innovation program under the\r\nMarie Sk\blodowska-Curie Grant Agreement No. 754411. S D N also acknowledges funding\r\nfrom the EPSRC Center for Doctoral Training in Cross-Disciplinary Approaches to Non-\r\nEquilibrium Systems (CANES) under Grant EP/L015854/1. S D N is grateful to IST\r\nAustria for providing open access funding." article_number: '013101' article_processing_charge: No article_type: original author: - first_name: Stefano full_name: De Nicola, Stefano id: 42832B76-F248-11E8-B48F-1D18A9856A87 last_name: De Nicola orcid: 0000-0002-4842-6671 citation: ama: 'De Nicola S. Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation. Journal of Statistical Mechanics: Theory and Experiment. 2021;2021(1). doi:10.1088/1742-5468/abc7c7' apa: 'De Nicola, S. (2021). Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/abc7c7' chicago: 'De Nicola, Stefano. “Disentanglement Approach to Quantum Spin Ground States: Field Theory and Stochastic Simulation.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2021. https://doi.org/10.1088/1742-5468/abc7c7.' ieee: 'S. De Nicola, “Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2021, no. 1. IOP Publishing, 2021.' ista: 'De Nicola S. 2021. Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation. Journal of Statistical Mechanics: Theory and Experiment. 2021(1), 013101.' mla: 'De Nicola, Stefano. “Disentanglement Approach to Quantum Spin Ground States: Field Theory and Stochastic Simulation.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2021, no. 1, 013101, IOP Publishing, 2021, doi:10.1088/1742-5468/abc7c7.' short: 'S. De Nicola, Journal of Statistical Mechanics: Theory and Experiment 2021 (2021).' date_created: 2021-02-17T17:48:46Z date_published: 2021-01-05T00:00:00Z date_updated: 2023-08-07T13:46:28Z day: '05' ddc: - '530' department: - _id: MaSe doi: 10.1088/1742-5468/abc7c7 ec_funded: 1 external_id: isi: - '000605080300001' file: - access_level: open_access checksum: 64e2aae4837790db26e1dd1986c69c07 content_type: application/pdf creator: dernst date_created: 2021-02-19T14:04:40Z date_updated: 2021-02-19T14:04:40Z file_id: '9172' file_name: 2021_JourStatMech_deNicola.pdf file_size: 1693609 relation: main_file success: 1 file_date_updated: 2021-02-19T14:04:40Z has_accepted_license: '1' intvolume: ' 2021' isi: 1 issue: '1' keyword: - Statistics - Probability and Uncertainty - Statistics and Probability - Statistical and Nonlinear Physics language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: 'Journal of Statistical Mechanics: Theory and Experiment' publication_identifier: issn: - 1742-5468 publication_status: published publisher: IOP Publishing quality_controlled: '1' status: public title: 'Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation' 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: 2021 year: '2021' ... --- _id: '9118' abstract: - lang: eng text: Cesium lead halides have intrinsically unstable crystal lattices and easily transform within perovskite and nonperovskite structures. In this work, we explore the conversion of the perovskite CsPbBr3 into Cs4PbBr6 in the presence of PbS at 450 °C to produce doped nanocrystal-based composites with embedded Cs4PbBr6 nanoprecipitates. We show that PbBr2 is extracted from CsPbBr3 and diffuses into the PbS lattice with a consequent increase in the concentration of free charge carriers. This new doping strategy enables the adjustment of the density of charge carriers between 1019 and 1020 cm–3, and it may serve as a general strategy for doping other nanocrystal-based semiconductors. acknowledgement: "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. ICN2\r\nacknowledges funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 823717 − ESTEEM3. M.V.K. acknowledges the support by the European Research Council under the Horizon 2020 Framework Program (ERC Consolidator Grant SCALEHALO\r\nGrant Agreement No. 819740) and by FET-OPEN project no. 862656 (DROP-IT)." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Mariano full_name: Calcabrini, Mariano id: 45D7531A-F248-11E8-B48F-1D18A9856A87 last_name: Calcabrini - first_name: Aziz full_name: Genc, Aziz last_name: Genc - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Tobias full_name: Kleinhanns, Tobias id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425 last_name: Kleinhanns - first_name: Seungho full_name: Lee, Seungho id: BB243B88-D767-11E9-B658-BC13E6697425 last_name: Lee orcid: 0000-0002-6962-8598 - first_name: Dmitry N. full_name: Dirin, Dmitry N. last_name: Dirin - first_name: Quinten A. full_name: Akkerman, Quinten A. last_name: Akkerman - first_name: Maksym V. full_name: Kovalenko, Maksym V. last_name: Kovalenko - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 citation: ama: Calcabrini M, Genc A, Liu Y, et al. Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites. ACS Energy Letters. 2021;6(2):581-587. doi:10.1021/acsenergylett.0c02448 apa: Calcabrini, M., Genc, A., Liu, Y., Kleinhanns, T., Lee, S., Dirin, D. N., … Ibáñez, M. (2021). Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites. ACS Energy Letters. American Chemical Society. https://doi.org/10.1021/acsenergylett.0c02448 chicago: Calcabrini, Mariano, Aziz Genc, Yu Liu, Tobias Kleinhanns, Seungho Lee, Dmitry N. Dirin, Quinten A. Akkerman, Maksym V. Kovalenko, Jordi Arbiol, and Maria Ibáñez. “Exploiting the Lability of Metal Halide Perovskites for Doping Semiconductor Nanocomposites.” ACS Energy Letters. American Chemical Society, 2021. https://doi.org/10.1021/acsenergylett.0c02448. ieee: M. Calcabrini et al., “Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites,” ACS Energy Letters, vol. 6, no. 2. American Chemical Society, pp. 581–587, 2021. ista: Calcabrini M, Genc A, Liu Y, Kleinhanns T, Lee S, Dirin DN, Akkerman QA, Kovalenko MV, Arbiol J, Ibáñez M. 2021. Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites. ACS Energy Letters. 6(2), 581–587. mla: Calcabrini, Mariano, et al. “Exploiting the Lability of Metal Halide Perovskites for Doping Semiconductor Nanocomposites.” ACS Energy Letters, vol. 6, no. 2, American Chemical Society, 2021, pp. 581–87, doi:10.1021/acsenergylett.0c02448. short: M. Calcabrini, A. Genc, Y. Liu, T. Kleinhanns, S. Lee, D.N. Dirin, Q.A. Akkerman, M.V. Kovalenko, J. Arbiol, M. Ibáñez, ACS Energy Letters 6 (2021) 581–587. date_created: 2021-02-14T23:01:14Z date_published: 2021-01-20T00:00:00Z date_updated: 2023-08-07T13:46:00Z day: '20' ddc: - '540' department: - _id: MaIb doi: 10.1021/acsenergylett.0c02448 ec_funded: 1 external_id: isi: - '000619803400036' file: - access_level: open_access checksum: 6fa7374bf8b95fdfe6e6c595322a6689 content_type: application/pdf creator: dernst date_created: 2021-02-17T07:36:52Z date_updated: 2021-02-17T07:36:52Z file_id: '9155' file_name: 2021_ACSEnergyLetters_Calcabrini.pdf file_size: 5071201 relation: main_file success: 1 file_date_updated: 2021-02-17T07:36:52Z has_accepted_license: '1' intvolume: ' 6' isi: 1 issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 581-587 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: ACS Energy Letters publication_identifier: eissn: - 2380-8195 publication_status: published publisher: American Chemical Society quality_controlled: '1' related_material: record: - id: '12885' relation: dissertation_contains status: public scopus_import: '1' status: public title: Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites 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: 6 year: '2021' ... --- _id: '9168' abstract: - lang: eng text: Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems. acknowledged_ssus: - _id: ScienComp acknowledgement: "The computations were performed with the IST Austria High-Performance Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird, and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian Science Foundation FWF grant (Project M 2463-B29)." article_number: iyaa025 article_processing_charge: No article_type: original author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva citation: ama: 'Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 2021;217(2). doi:10.1093/genetics/iyaa025' apa: 'Fraisse, C., & Sachdeva, H. (2021). The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. Genetics Society of America. https://doi.org/10.1093/genetics/iyaa025' chicago: 'Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” Genetics. Genetics Society of America, 2021. https://doi.org/10.1093/genetics/iyaa025.' ieee: 'C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes,” Genetics, vol. 217, no. 2. Genetics Society of America, 2021.' ista: 'Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 217(2), iyaa025.' mla: 'Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” Genetics, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021, doi:10.1093/genetics/iyaa025.' short: C. Fraisse, H. Sachdeva, Genetics 217 (2021). date_created: 2021-02-18T14:41:30Z date_published: 2021-02-01T00:00:00Z date_updated: 2023-08-07T13:47:01Z day: '01' department: - _id: NiBa doi: 10.1093/genetics/iyaa025 external_id: isi: - '000637218100005' intvolume: ' 217' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/genetics/iyaa025 month: '02' oa: 1 oa_version: Published Version project: - _id: 2662AADE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02463 name: Sex chromosomes and species barriers publication: Genetics publication_identifier: issn: - 1943-2631 publication_status: published publisher: Genetics Society of America quality_controlled: '1' status: public title: 'The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 217 year: '2021' ... --- _id: '9113' abstract: - lang: eng text: “Hydrogen economy” could enable a carbon-neutral sustainable energy chain. However, issues with safety, storage, and transport of molecular hydrogen impede its realization. Alcohols as liquid H2 carriers could be enablers, but state-of-the-art reforming is difficult, requiring high temperatures >200 °C and pressures >25 bar, and the resulting H2 is carbonized beyond tolerance levels for direct use in fuel cells. Here, we demonstrate ambient temperature and pressure alcohol reforming in a fuel cell (ARFC) with a simultaneous electrical power output. The alcohol is oxidized at the alkaline anode, where the resulting CO2 is sequestrated as carbonate. Carbon-free H2 is liberated at the acidic cathode. The neutralization energy between the alkaline anode and the acidic cathode drives the process, particularly the unusually high entropy gain (1.27-fold ΔH). The significantly positive temperature coefficient of the resulting electromotive force allows us to harvest a large fraction of the output energy from the surrounding, achieving a thermodynamic efficiency as high as 2.27. MoS2 as the cathode catalyst allows alcohol reforming even under open-air conditions, a challenge that state-of-the-art alcohol reforming failed to overcome. We further show reforming of a wide range of alcohols. The ARFC offers an unprecedented route toward hydrogen economy as CO2 is simultaneously captured and pure H2 produced at mild conditions. acknowledgement: M.O.T. acknowledges DST/TMD/HFC/2 K18/58, DST-SERB, MHRD fast track, and DST Nanomission forfinancialassistance. Z.M.B. acknowledges CSIR-SRF fellowship fromMHRD, India. S.A.F. acknowledges support from IST Austria. article_processing_charge: No article_type: original author: - first_name: Zahid Manzoor full_name: Manzoor Bhat, Zahid Manzoor last_name: Manzoor Bhat - first_name: Ravikumar full_name: Thimmappa, Ravikumar last_name: Thimmappa - first_name: 'Neethu Christudas ' full_name: 'Dargily, Neethu Christudas ' last_name: Dargily - first_name: 'Abdul ' full_name: 'Raafik, Abdul ' last_name: Raafik - first_name: 'Alagar Raja ' full_name: 'Kottaichamy, Alagar Raja ' last_name: Kottaichamy - first_name: 'Mruthyunjayachari Chattanahalli ' full_name: 'Devendrachari, Mruthyunjayachari Chattanahalli ' last_name: Devendrachari - first_name: Mahesh full_name: Itagi, Mahesh last_name: Itagi - first_name: Harish full_name: ' Makri Nimbegondi Kotresh, Harish' last_name: ' Makri Nimbegondi Kotresh' - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: 'Musthafa ' full_name: 'Ottakam Thotiyl, Musthafa ' last_name: Ottakam Thotiyl citation: ama: Manzoor Bhat ZM, Thimmappa R, Dargily NC, et al. Ambient condition alcohol reforming to hydrogen with electricity output. ACS Sustainable Chemistry and Engineering. 2021;9(8):3104-3111. doi:10.1021/acssuschemeng.0c07547 apa: Manzoor Bhat, Z. M., Thimmappa, R., Dargily, N. C., Raafik, A., Kottaichamy, A. R., Devendrachari, M. C., … Ottakam Thotiyl, M. (2021). Ambient condition alcohol reforming to hydrogen with electricity output. ACS Sustainable Chemistry and Engineering. American Chemical Society. https://doi.org/10.1021/acssuschemeng.0c07547 chicago: Manzoor Bhat, Zahid Manzoor, Ravikumar Thimmappa, Neethu Christudas Dargily, Abdul Raafik, Alagar Raja Kottaichamy, Mruthyunjayachari Chattanahalli Devendrachari, Mahesh Itagi, Harish Makri Nimbegondi Kotresh, Stefan Alexander Freunberger, and Musthafa Ottakam Thotiyl. “Ambient Condition Alcohol Reforming to Hydrogen with Electricity Output.” ACS Sustainable Chemistry and Engineering. American Chemical Society, 2021. https://doi.org/10.1021/acssuschemeng.0c07547. ieee: Z. M. Manzoor Bhat et al., “Ambient condition alcohol reforming to hydrogen with electricity output,” ACS Sustainable Chemistry and Engineering, vol. 9, no. 8. American Chemical Society, pp. 3104–3111, 2021. ista: Manzoor Bhat ZM, Thimmappa R, Dargily NC, Raafik A, Kottaichamy AR, Devendrachari MC, Itagi M, Makri Nimbegondi Kotresh H, Freunberger SA, Ottakam Thotiyl M. 2021. Ambient condition alcohol reforming to hydrogen with electricity output. ACS Sustainable Chemistry and Engineering. 9(8), 3104–3111. mla: Manzoor Bhat, Zahid Manzoor, et al. “Ambient Condition Alcohol Reforming to Hydrogen with Electricity Output.” ACS Sustainable Chemistry and Engineering, vol. 9, no. 8, American Chemical Society, 2021, pp. 3104–11, doi:10.1021/acssuschemeng.0c07547. short: Z.M. Manzoor Bhat, R. Thimmappa, N.C. Dargily, A. Raafik, A.R. Kottaichamy, M.C. Devendrachari, M. Itagi, H. Makri Nimbegondi Kotresh, S.A. Freunberger, M. Ottakam Thotiyl, ACS Sustainable Chemistry and Engineering 9 (2021) 3104–3111. date_created: 2021-02-12T09:20:18Z date_published: 2021-02-11T00:00:00Z date_updated: 2023-08-07T13:43:19Z day: '11' department: - _id: StFr doi: 10.1021/acssuschemeng.0c07547 external_id: isi: - '000625460400010' intvolume: ' 9' isi: 1 issue: '8' language: - iso: eng month: '02' oa_version: None page: 3104-3111 publication: ACS Sustainable Chemistry and Engineering publication_identifier: eissn: - 2168-0485 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Ambient condition alcohol reforming to hydrogen with electricity output type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2021' ... --- _id: '9119' abstract: - lang: eng text: 'We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.' article_processing_charge: No article_type: original author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Iva full_name: Popovic, Iva last_name: Popovic - first_name: Clément full_name: Mazoyer, Clément last_name: Mazoyer - first_name: Bruno full_name: Spataro, Bruno last_name: Spataro - first_name: Stéphane full_name: Delmotte, Stéphane last_name: Delmotte - first_name: Jonathan full_name: Romiguier, Jonathan last_name: Romiguier - first_name: Étienne full_name: Loire, Étienne last_name: Loire - first_name: Alexis full_name: Simon, Alexis last_name: Simon - first_name: Nicolas full_name: Galtier, Nicolas last_name: Galtier - first_name: Laurent full_name: Duret, Laurent last_name: Duret - first_name: Nicolas full_name: Bierne, Nicolas last_name: Bierne - first_name: Xavier full_name: Vekemans, Xavier last_name: Vekemans - first_name: Camille full_name: Roux, Camille last_name: Roux citation: ama: 'Fraisse C, Popovic I, Mazoyer C, et al. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. 2021;21:2629-2644. doi:10.1111/1755-0998.13323' apa: 'Fraisse, C., Popovic, I., Mazoyer, C., Spataro, B., Delmotte, S., Romiguier, J., … Roux, C. (2021). DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13323' chicago: 'Fraisse, Christelle, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stéphane Delmotte, Jonathan Romiguier, Étienne Loire, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” Molecular Ecology Resources. Wiley, 2021. https://doi.org/10.1111/1755-0998.13323.' ieee: 'C. Fraisse et al., “DILS: Demographic inferences with linked selection by using ABC,” Molecular Ecology Resources, vol. 21. Wiley, pp. 2629–2644, 2021.' ista: 'Fraisse C, Popovic I, Mazoyer C, Spataro B, Delmotte S, Romiguier J, Loire É, Simon A, Galtier N, Duret L, Bierne N, Vekemans X, Roux C. 2021. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. 21, 2629–2644.' mla: 'Fraisse, Christelle, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” Molecular Ecology Resources, vol. 21, Wiley, 2021, pp. 2629–44, doi:10.1111/1755-0998.13323.' short: C. Fraisse, I. Popovic, C. Mazoyer, B. Spataro, S. Delmotte, J. Romiguier, É. Loire, A. Simon, N. Galtier, L. Duret, N. Bierne, X. Vekemans, C. Roux, Molecular Ecology Resources 21 (2021) 2629–2644. date_created: 2021-02-14T23:01:14Z date_published: 2021-01-15T00:00:00Z date_updated: 2023-08-07T13:45:18Z day: '15' department: - _id: NiBa doi: 10.1111/1755-0998.13323 external_id: isi: - '000614183100001' intvolume: ' 21' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2 month: '01' oa: 1 oa_version: Preprint page: 2629-2644 publication: Molecular Ecology Resources publication_identifier: eissn: - '17550998' issn: - 1755098X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'DILS: Demographic inferences with linked selection by using ABC' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2021' ... --- _id: '9173' abstract: - lang: eng text: We show that Hilbert schemes of points on supersingular Enriques surface in characteristic 2, Hilbn(X), for n ≥ 2 are simply connected, symplectic varieties but are not irreducible symplectic as the hodge number h2,0 > 1, even though a supersingular Enriques surface is an irreducible symplectic variety. These are the classes of varieties which appear only in characteristic 2 and they show that the hodge number formula for G¨ottsche-Soergel does not hold over haracteristic 2. It also gives examples of varieties with trivial canonical class which are neither irreducible symplectic nor Calabi-Yau, thereby showing that there are strictly more classes of simply connected varieties with trivial canonical class in characteristic 2 than over C as given by Beauville-Bogolomov decomposition theorem. acknowledgement: I would like to thank M. Zdanwociz for various mathematical discussions which lead to this article, Tamas Hausel for hosting me in his research group at IST Austria and the anonymous referee for their helpful suggestions and comments. This research has received funding from the European Union's Horizon 2020 Marie Sklodowska-Curie Actions Grant No. 754411 and Institue of Science and Technology Austria IST-PLUS Grant No. 754411. article_number: '102957' article_processing_charge: No article_type: original author: - first_name: Tanya K full_name: Srivastava, Tanya K id: 4D046628-F248-11E8-B48F-1D18A9856A87 last_name: Srivastava citation: ama: Srivastava TK. Pathologies of the Hilbert scheme of points of a supersingular Enriques surface. Bulletin des Sciences Mathematiques. 2021;167(03). doi:10.1016/j.bulsci.2021.102957 apa: Srivastava, T. K. (2021). Pathologies of the Hilbert scheme of points of a supersingular Enriques surface. Bulletin Des Sciences Mathematiques. Elsevier. https://doi.org/10.1016/j.bulsci.2021.102957 chicago: Srivastava, Tanya K. “Pathologies of the Hilbert Scheme of Points of a Supersingular Enriques Surface.” Bulletin Des Sciences Mathematiques. Elsevier, 2021. https://doi.org/10.1016/j.bulsci.2021.102957. ieee: T. K. Srivastava, “Pathologies of the Hilbert scheme of points of a supersingular Enriques surface,” Bulletin des Sciences Mathematiques, vol. 167, no. 03. Elsevier, 2021. ista: Srivastava TK. 2021. Pathologies of the Hilbert scheme of points of a supersingular Enriques surface. Bulletin des Sciences Mathematiques. 167(03), 102957. mla: Srivastava, Tanya K. “Pathologies of the Hilbert Scheme of Points of a Supersingular Enriques Surface.” Bulletin Des Sciences Mathematiques, vol. 167, no. 03, 102957, Elsevier, 2021, doi:10.1016/j.bulsci.2021.102957. short: T.K. Srivastava, Bulletin Des Sciences Mathematiques 167 (2021). date_created: 2021-02-21T23:01:20Z date_published: 2021-03-01T00:00:00Z date_updated: 2023-08-07T13:47:48Z day: '01' department: - _id: TaHa doi: 10.1016/j.bulsci.2021.102957 ec_funded: 1 external_id: arxiv: - '2010.08976' isi: - '000623881600009' intvolume: ' 167' isi: 1 issue: '03' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2010.08976 month: '03' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Bulletin des Sciences Mathematiques publication_identifier: issn: - 0007-4497 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Pathologies of the Hilbert scheme of points of a supersingular Enriques surface type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 167 year: '2021' ... --- _id: '9200' abstract: - lang: eng text: Formal design of embedded and cyber-physical systems relies on mathematical modeling. In this paper, we consider the model class of hybrid automata whose dynamics are defined by affine differential equations. Given a set of time-series data, we present an algorithmic approach to synthesize a hybrid automaton exhibiting behavior that is close to the data, up to a specified precision, and changes in synchrony with the data. A fundamental problem in our synthesis algorithm is to check membership of a time series in a hybrid automaton. Our solution integrates reachability and optimization techniques for affine dynamical systems to obtain both a sufficient and a necessary condition for membership, combined in a refinement framework. The algorithm processes one time series at a time and hence can be interrupted, provide an intermediate result, and be resumed. We report experimental results demonstrating the applicability of our synthesis approach. acknowledgement: This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. article_processing_charge: No author: - first_name: Miriam full_name: Garcia Soto, Miriam id: 4B3207F6-F248-11E8-B48F-1D18A9856A87 last_name: Garcia Soto orcid: 0000-0003-2936-5719 - 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: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 citation: ama: 'Garcia Soto M, Henzinger TA, Schilling C. Synthesis of hybrid automata with affine dynamics from time-series data. In: HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control. Association for Computing Machinery; 2021:2102.12734. doi:10.1145/3447928.3456704' apa: 'Garcia Soto, M., Henzinger, T. A., & Schilling, C. (2021). Synthesis of hybrid automata with affine dynamics from time-series data. In HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control (p. 2102.12734). Nashville, TN, United States: Association for Computing Machinery. https://doi.org/10.1145/3447928.3456704' chicago: 'Garcia Soto, Miriam, Thomas A Henzinger, and Christian Schilling. “Synthesis of Hybrid Automata with Affine Dynamics from Time-Series Data.” In HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control, 2102.12734. Association for Computing Machinery, 2021. https://doi.org/10.1145/3447928.3456704.' ieee: 'M. Garcia Soto, T. A. Henzinger, and C. Schilling, “Synthesis of hybrid automata with affine dynamics from time-series data,” in HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control, Nashville, TN, United States, 2021, p. 2102.12734.' ista: 'Garcia Soto M, Henzinger TA, Schilling C. 2021. Synthesis of hybrid automata with affine dynamics from time-series data. HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control. HSCC: International Conference on Hybrid Systems Computation and Control, 2102.12734.' mla: 'Garcia Soto, Miriam, et al. “Synthesis of Hybrid Automata with Affine Dynamics from Time-Series Data.” HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control, Association for Computing Machinery, 2021, p. 2102.12734, doi:10.1145/3447928.3456704.' short: 'M. Garcia Soto, T.A. Henzinger, C. Schilling, in:, HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control, Association for Computing Machinery, 2021, p. 2102.12734.' conference: end_date: 2021-05-21 location: Nashville, TN, United States name: 'HSCC: International Conference on Hybrid Systems Computation and Control' start_date: 2021-05-19 date_created: 2021-02-26T16:30:39Z date_published: 2021-05-01T00:00:00Z date_updated: 2023-08-07T13:49:33Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1145/3447928.3456704 ec_funded: 1 external_id: arxiv: - '2102.12734' isi: - '000932821700028' file: - access_level: open_access checksum: 4c1202c1abf71384c3ee6fea88c2f80e content_type: application/pdf creator: kschuh date_created: 2021-05-25T13:53:22Z date_updated: 2021-05-25T13:53:22Z file_id: '9424' file_name: 2021_HSCC_Soto.pdf file_size: 1474786 relation: main_file success: 1 file_date_updated: 2021-05-25T13:53:22Z has_accepted_license: '1' isi: 1 keyword: - hybrid automaton - membership - system identification language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '2102.12734' 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: 'HSCC ''21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control' publication_identifier: isbn: - '9781450383394' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Synthesis of hybrid automata with affine dynamics from time-series data tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9205' abstract: - lang: eng text: Cryo-EM grid preparation is an important bottleneck in protein structure determination, especially for membrane proteins, typically requiring screening of a large number of conditions. We systematically investigated the effects of buffer components, blotting conditions and grid types on the outcome of grid preparation of five different membrane protein samples. Aggregation was the most common type of problem which was addressed by changing detergents, salt concentration or reconstitution of proteins into nanodiscs or amphipols. We show that the optimal concentration of detergent is between 0.05 and 0.4% and that the presence of a low concentration of detergent with a high critical micellar concentration protects the proteins from denaturation at the air-water interface. Furthermore, we discuss the strategies for achieving an adequate ice thickness, particle coverage and orientation distribution on free ice and on support films. Our findings provide a clear roadmap for comprehensive screening of conditions for cryo-EM grid preparation of membrane proteins. acknowledged_ssus: - _id: EM-Fac acknowledgement: We thank the Electron Microscopy Facilities at the Institute of Science and Technology Austria and at the Vienna Biocenter for providing access and training for the electron microscopes. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385 . article_number: '102139' 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: Julia full_name: Steiner, Julia id: 3BB67EB0-F248-11E8-B48F-1D18A9856A87 last_name: Steiner - 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, Steiner J, Sazanov LA. Cryo-EM grid optimization for membrane proteins. iScience. 2021;24(3). doi:10.1016/j.isci.2021.102139 apa: Kampjut, D., Steiner, J., & Sazanov, L. A. (2021). Cryo-EM grid optimization for membrane proteins. IScience. Elsevier. https://doi.org/10.1016/j.isci.2021.102139 chicago: Kampjut, Domen, Julia Steiner, and Leonid A Sazanov. “Cryo-EM Grid Optimization for Membrane Proteins.” IScience. Elsevier, 2021. https://doi.org/10.1016/j.isci.2021.102139. ieee: D. Kampjut, J. Steiner, and L. A. Sazanov, “Cryo-EM grid optimization for membrane proteins,” iScience, vol. 24, no. 3. Elsevier, 2021. ista: Kampjut D, Steiner J, Sazanov LA. 2021. Cryo-EM grid optimization for membrane proteins. iScience. 24(3), 102139. mla: Kampjut, Domen, et al. “Cryo-EM Grid Optimization for Membrane Proteins.” IScience, vol. 24, no. 3, 102139, Elsevier, 2021, doi:10.1016/j.isci.2021.102139. short: D. Kampjut, J. Steiner, L.A. Sazanov, IScience 24 (2021). date_created: 2021-02-28T23:01:24Z date_published: 2021-03-19T00:00:00Z date_updated: 2023-08-07T13:54:06Z day: '19' ddc: - '570' department: - _id: LeSa doi: 10.1016/j.isci.2021.102139 ec_funded: 1 external_id: isi: - '000631646000012' pmid: - '33665558' file: - access_level: open_access checksum: 50585447386fe5842f07ab9b3a66e7e9 content_type: application/pdf creator: dernst date_created: 2021-03-03T07:38:14Z date_updated: 2021-03-03T07:38:14Z file_id: '9219' file_name: 2021_iScience_Kampjut.pdf file_size: 7431411 relation: main_file success: 1 file_date_updated: 2021-03-03T07:38:14Z has_accepted_license: '1' intvolume: ' 24' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: iScience publication_identifier: eissn: - '25890042' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Cryo-EM grid optimization for membrane proteins 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: 24 year: '2021' ... --- _id: '9207' abstract: - lang: eng text: "In this paper we experimentally study the transitional range of Reynolds numbers in\r\nplane Couette–Poiseuille flow, focusing our attention on the localized turbulent structures\r\ntriggered by a strong impulsive jet and the large-scale flow generated around these\r\nstructures. We present a detailed investigation of the large-scale flow and show how\r\nits amplitude depends on Reynolds number and amplitude perturbation. In addition,\r\nwe characterize the initial dynamics of the localized turbulent spot, which includes the\r\ncoupling between the small and large scales, as well as the dependence of the advection\r\nspeed on the large-scale flow generated around the spot. Finally, we provide the first\r\nexperimental measurements of the large-scale flow around an oblique turbulent band." acknowledgement: "We thank Y. Duguet, S. Gomé, G. Lemoult, T. Liu, B. Semin and L.S. Tuckerman for\r\nfruitful discussions. \r\nThis work was supported by a grant, TRANSFLOW, provided by the Agence Nationale de\r\nla Recherche (ANR). A.M.P. was partially supported by the French Embassy in Russia (I.I. Mechnikov scholarship) and by the Russian Science Foundation (project no. 18-79-00189). L.K. was partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411." article_number: A24 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lukasz full_name: Klotz, Lukasz id: 2C9AF1C2-F248-11E8-B48F-1D18A9856A87 last_name: Klotz orcid: 0000-0003-1740-7635 - first_name: A. M. full_name: Pavlenko, A. M. last_name: Pavlenko - first_name: J. E. full_name: Wesfreid, J. E. last_name: Wesfreid citation: ama: 'Klotz L, Pavlenko AM, Wesfreid JE. Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow. Journal of Fluid Mechanics. 2021;912. doi:10.1017/jfm.2020.1089' apa: 'Klotz, L., Pavlenko, A. M., & Wesfreid, J. E. (2021). Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2020.1089' chicago: 'Klotz, Lukasz, A. M. Pavlenko, and J. E. Wesfreid. “Experimental Measurements in Plane Couette-Poiseuille Flow: Dynamics of the Large- and Small-Scale Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2020.1089.' ieee: 'L. Klotz, A. M. Pavlenko, and J. E. Wesfreid, “Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow,” Journal of Fluid Mechanics, vol. 912. Cambridge University Press, 2021.' ista: 'Klotz L, Pavlenko AM, Wesfreid JE. 2021. Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow. Journal of Fluid Mechanics. 912, A24.' mla: 'Klotz, Lukasz, et al. “Experimental Measurements in Plane Couette-Poiseuille Flow: Dynamics of the Large- and Small-Scale Flow.” Journal of Fluid Mechanics, vol. 912, A24, Cambridge University Press, 2021, doi:10.1017/jfm.2020.1089.' short: L. Klotz, A.M. Pavlenko, J.E. Wesfreid, Journal of Fluid Mechanics 912 (2021). date_created: 2021-02-28T23:01:25Z date_published: 2021-02-15T00:00:00Z date_updated: 2023-08-07T13:55:40Z day: '15' ddc: - '530' department: - _id: BjHo doi: 10.1017/jfm.2020.1089 ec_funded: 1 external_id: isi: - '000618034400001' file: - access_level: open_access checksum: b8020d6338667673e34fde0608913dd2 content_type: application/pdf creator: dernst date_created: 2021-03-03T09:49:34Z date_updated: 2021-03-03T09:49:34Z file_id: '9220' file_name: 2021_JourFluidMechanics_Klotz.pdf file_size: 4124471 relation: main_file success: 1 file_date_updated: 2021-03-03T09:49:34Z has_accepted_license: '1' intvolume: ' 912' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of Fluid Mechanics publication_identifier: eissn: - 1469-7645 issn: - 0022-1120 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow' 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: 912 year: '2021' ... --- _id: '9206' abstract: - lang: eng text: 'The precise engineering of thermoelectric materials using nanocrystals as their building blocks has proven to be an excellent strategy to increase energy conversion efficiency. Here we present a synthetic route to produce Sb-doped PbS colloidal nanoparticles. These nanoparticles are then consolidated into nanocrystalline PbS:Sb using spark plasma sintering. We demonstrate that the introduction of Sb significantly influences the size, geometry, crystal lattice and especially the carrier concentration of PbS. The increase of charge carrier concentration achieved with the introduction of Sb translates into an increase of the electrical and thermal conductivities and a decrease of the Seebeck coefficient. Overall, PbS:Sb nanomaterial were characterized by two-fold higher thermoelectric figures of merit than undoped PbS. ' acknowledgement: "This work was supported by European Regional Development Funds and the Framework 7\r\nprogram under project UNION (FP7-NMP 310250). GSN acknowledges support from the US National Science Foundation under grant No. DMR-1748188. DC acknowledges support from COLCIENCIAS under project 120480863414. " article_number: '853' article_processing_charge: No article_type: original author: - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Kaya full_name: Wei, Kaya last_name: Wei - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Yu full_name: Zhang, Yu last_name: Zhang - first_name: Mengyao full_name: Li, Mengyao last_name: Li - first_name: Aziz full_name: Genç, Aziz last_name: Genç - first_name: Taisiia full_name: Berestok, Taisiia last_name: Berestok - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: George S. full_name: Nolas, George S. last_name: Nolas - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Cadavid D, Wei K, Liu Y, et al. Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks. Materials. 2021;14(4). doi:10.3390/ma14040853 apa: Cadavid, D., Wei, K., Liu, Y., Zhang, Y., Li, M., Genç, A., … Cabot, A. (2021). Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks. Materials. MDPI. https://doi.org/10.3390/ma14040853 chicago: Cadavid, Doris, Kaya Wei, Yu Liu, Yu Zhang, Mengyao Li, Aziz Genç, Taisiia Berestok, et al. “Synthesis, Bottom up Assembly and Thermoelectric Properties of Sb-Doped PbS Nanocrystal Building Blocks.” Materials. MDPI, 2021. https://doi.org/10.3390/ma14040853. ieee: D. Cadavid et al., “Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks,” Materials, vol. 14, no. 4. MDPI, 2021. ista: Cadavid D, Wei K, Liu Y, Zhang Y, Li M, Genç A, Berestok T, Ibáñez M, Shavel A, Nolas GS, Cabot A. 2021. Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks. Materials. 14(4), 853. mla: Cadavid, Doris, et al. “Synthesis, Bottom up Assembly and Thermoelectric Properties of Sb-Doped PbS Nanocrystal Building Blocks.” Materials, vol. 14, no. 4, 853, MDPI, 2021, doi:10.3390/ma14040853. short: D. Cadavid, K. Wei, Y. Liu, Y. Zhang, M. Li, A. Genç, T. Berestok, M. Ibáñez, A. Shavel, G.S. Nolas, A. Cabot, Materials 14 (2021). date_created: 2021-02-28T23:01:24Z date_published: 2021-02-10T00:00:00Z date_updated: 2023-08-07T13:50:03Z day: '10' ddc: - '540' department: - _id: MaIb doi: 10.3390/ma14040853 external_id: isi: - '000624094100001' file: - access_level: open_access checksum: 76d6c7f97b810ce504ab151c9bf3524e content_type: application/pdf creator: dernst date_created: 2021-03-03T07:32:01Z date_updated: 2021-03-03T07:32:01Z file_id: '9218' file_name: 2021_Materials_Cadavid.pdf file_size: 2722517 relation: main_file success: 1 file_date_updated: 2021-03-03T07:32:01Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '4' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Materials publication_identifier: eissn: - 1996-1944 publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2021' ... --- _id: '9226' abstract: - lang: eng text: 'Half a century after Lewis Wolpert''s seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?' acknowledgement: This work was supported in part by the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030), by the National Institutes of Health (R01GM097275) and by the Fonds zur Förderung der wissenschaftlichen Forschung (FWF P28844). Deposited in PMC for release after 12 months. article_number: dev176065 article_processing_charge: No article_type: original author: - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor citation: ama: Tkačik G, Gregor T. The many bits of positional information. Development. 2021;148(2). doi:10.1242/dev.176065 apa: Tkačik, G., & Gregor, T. (2021). The many bits of positional information. Development. The Company of Biologists. https://doi.org/10.1242/dev.176065 chicago: Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” Development. The Company of Biologists, 2021. https://doi.org/10.1242/dev.176065. ieee: G. Tkačik and T. Gregor, “The many bits of positional information,” Development, vol. 148, no. 2. The Company of Biologists, 2021. ista: Tkačik G, Gregor T. 2021. The many bits of positional information. Development. 148(2), dev176065. mla: Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” Development, vol. 148, no. 2, dev176065, The Company of Biologists, 2021, doi:10.1242/dev.176065. short: G. Tkačik, T. Gregor, Development 148 (2021). date_created: 2021-03-07T23:01:25Z date_published: 2021-02-01T00:00:00Z date_updated: 2023-08-07T13:57:30Z day: '01' department: - _id: GaTk doi: 10.1242/dev.176065 external_id: isi: - '000613906000007' pmid: - '33526425' intvolume: ' 148' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1242/dev.176065 month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Development publication_identifier: eissn: - 1477-9129 publication_status: published publisher: The Company of Biologists quality_controlled: '1' scopus_import: '1' status: public title: The many bits of positional information type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 148 year: '2021' ... --- _id: '9240' abstract: - lang: eng text: A stochastic PDE, describing mesoscopic fluctuations in systems of weakly interacting inertial particles of finite volume, is proposed and analysed in any finite dimension . It is a regularised and inertial version of the Dean–Kawasaki model. A high-probability well-posedness theory for this model is developed. This theory improves significantly on the spatial scaling restrictions imposed in an earlier work of the same authors, which applied only to significantly larger particles in one dimension. The well-posedness theory now applies in d-dimensions when the particle-width ϵ is proportional to for and N is the number of particles. This scaling is optimal in a certain Sobolev norm. Key tools of the analysis are fractional Sobolev spaces, sharp bounds on Bessel functions, separability of the regularisation in the d-spatial dimensions, and use of the Faà di Bruno's formula. acknowledgement: All authors thank the anonymous referee for his/her careful reading of the manuscript and valuable suggestions. This paper was motivated by stimulating discussions at the First Berlin–Leipzig Workshop on Fluctuating Hydrodynamics in August 2019 with Ana Djurdjevac, Rupert Klein and Ralf Kornhuber. JZ gratefully acknowledges funding by a Royal Society Wolfson Research Merit Award. FC gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Federico full_name: Cornalba, Federico id: 2CEB641C-A400-11E9-A717-D712E6697425 last_name: Cornalba - first_name: Tony full_name: Shardlow, Tony last_name: Shardlow - first_name: Johannes full_name: Zimmer, Johannes last_name: Zimmer citation: ama: Cornalba F, Shardlow T, Zimmer J. Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions. Journal of Differential Equations. 2021;284(5):253-283. doi:10.1016/j.jde.2021.02.048 apa: Cornalba, F., Shardlow, T., & Zimmer, J. (2021). Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2021.02.048 chicago: Cornalba, Federico, Tony Shardlow, and Johannes Zimmer. “Well-Posedness for a Regularised Inertial Dean–Kawasaki Model for Slender Particles in Several Space Dimensions.” Journal of Differential Equations. Elsevier, 2021. https://doi.org/10.1016/j.jde.2021.02.048. ieee: F. Cornalba, T. Shardlow, and J. Zimmer, “Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions,” Journal of Differential Equations, vol. 284, no. 5. Elsevier, pp. 253–283, 2021. ista: Cornalba F, Shardlow T, Zimmer J. 2021. Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions. Journal of Differential Equations. 284(5), 253–283. mla: Cornalba, Federico, et al. “Well-Posedness for a Regularised Inertial Dean–Kawasaki Model for Slender Particles in Several Space Dimensions.” Journal of Differential Equations, vol. 284, no. 5, Elsevier, 2021, pp. 253–83, doi:10.1016/j.jde.2021.02.048. short: F. Cornalba, T. Shardlow, J. Zimmer, Journal of Differential Equations 284 (2021) 253–283. date_created: 2021-03-14T23:01:32Z date_published: 2021-05-25T00:00:00Z date_updated: 2023-08-07T14:08:05Z day: '25' ddc: - '510' department: - _id: JuFi doi: 10.1016/j.jde.2021.02.048 ec_funded: 1 external_id: isi: - '000634823300010' file: - access_level: open_access checksum: c630b691fb9e716b02aa6103a9794ec8 content_type: application/pdf creator: dernst date_created: 2021-03-22T07:18:01Z date_updated: 2021-03-22T07:18:01Z file_id: '9267' file_name: 2021_JourDiffEquations_Cornalba.pdf file_size: 473310 relation: main_file success: 1 file_date_updated: 2021-03-22T07:18:01Z has_accepted_license: '1' intvolume: ' 284' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 253-283 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of Differential Equations publication_identifier: eissn: - 1090-2732 issn: - 0022-0396 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions 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: 284 year: '2021' ... --- _id: '9253' abstract: - lang: eng text: In March 2020, the Austrian government introduced a widespread lock-down in response to the COVID-19 pandemic. Based on subjective impressions and anecdotal evidence, Austrian public and private life came to a sudden halt. Here we assess the effect of the lock-down quantitatively for all regions in Austria and present an analysis of daily changes of human mobility throughout Austria using near-real-time anonymized mobile phone data. We describe an efficient data aggregation pipeline and analyze the mobility by quantifying mobile-phone traffic at specific point of interests (POIs), analyzing individual trajectories and investigating the cluster structure of the origin-destination graph. We found a reduction of commuters at Viennese metro stations of over 80% and the number of devices with a radius of gyration of less than 500 m almost doubled. The results of studying crowd-movement behavior highlight considerable changes in the structure of mobility networks, revealed by a higher modularity and an increase from 12 to 20 detected communities. We demonstrate the relevance of mobility data for epidemiological studies by showing a significant correlation of the outflow from the town of Ischgl (an early COVID-19 hotspot) and the reported COVID-19 cases with an 8-day time lag. This research indicates that mobile phone usage data permits the moment-by-moment quantification of mobility behavior for a whole country. We emphasize the need to improve the availability of such data in anonymized form to empower rapid response to combat COVID-19 and future pandemics. article_processing_charge: No author: - first_name: Georg full_name: Heiler, Georg last_name: Heiler - first_name: Tobias full_name: Reisch, Tobias last_name: Reisch - first_name: Jan full_name: Hurt, Jan last_name: Hurt - first_name: Mohammad full_name: Forghani, Mohammad last_name: Forghani - first_name: Aida full_name: Omani, Aida last_name: Omani - first_name: Allan full_name: Hanbury, Allan last_name: Hanbury - first_name: Farid full_name: Karimipour, Farid id: 2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425 last_name: Karimipour orcid: 0000-0001-6746-4174 citation: ama: 'Heiler G, Reisch T, Hurt J, et al. Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic. In: 2020 IEEE International Conference on Big Data. IEEE; 2021:3123-3132. doi:10.1109/bigdata50022.2020.9378374' apa: 'Heiler, G., Reisch, T., Hurt, J., Forghani, M., Omani, A., Hanbury, A., & Karimipour, F. (2021). Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic. In 2020 IEEE International Conference on Big Data (pp. 3123–3132). Atlanta, GA, United States: IEEE. https://doi.org/10.1109/bigdata50022.2020.9378374' chicago: Heiler, Georg, Tobias Reisch, Jan Hurt, Mohammad Forghani, Aida Omani, Allan Hanbury, and Farid Karimipour. “Country-Wide Mobility Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In 2020 IEEE International Conference on Big Data, 3123–32. IEEE, 2021. https://doi.org/10.1109/bigdata50022.2020.9378374. ieee: G. Heiler et al., “Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic,” in 2020 IEEE International Conference on Big Data, Atlanta, GA, United States, 2021, pp. 3123–3132. ista: 'Heiler G, Reisch T, Hurt J, Forghani M, Omani A, Hanbury A, Karimipour F. 2021. Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic. 2020 IEEE International Conference on Big Data. Big Data: International Conference on Big Data, 3123–3132.' mla: Heiler, Georg, et al. “Country-Wide Mobility Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” 2020 IEEE International Conference on Big Data, IEEE, 2021, pp. 3123–32, doi:10.1109/bigdata50022.2020.9378374. short: G. Heiler, T. Reisch, J. Hurt, M. Forghani, A. Omani, A. Hanbury, F. Karimipour, in:, 2020 IEEE International Conference on Big Data, IEEE, 2021, pp. 3123–3132. conference: end_date: 2020-12-13 location: Atlanta, GA, United States name: 'Big Data: International Conference on Big Data' start_date: 2020-12-10 date_created: 2021-03-21T11:34:07Z date_published: 2021-03-19T00:00:00Z date_updated: 2023-08-07T14:00:13Z day: '19' department: - _id: HeEd doi: 10.1109/bigdata50022.2020.9378374 external_id: arxiv: - '2008.10064' isi: - '000662554703032' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2008.10064 month: '03' oa: 1 oa_version: Preprint page: 3123-3132 publication: 2020 IEEE International Conference on Big Data publication_identifier: isbn: - '9781728162515' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9228' abstract: - lang: eng text: Legacy conferences are costly and time consuming, and exclude scientists lacking various resources or abilities. During the 2020 pandemic, we created an online conference platform, Neuromatch Conferences (NMC), aimed at developing technological and cultural changes to make conferences more democratic, scalable, and accessible. We discuss the lessons we learned. acknowledgement: We thank all of our volunteers from the NMC conferences (list of names in the appendix). We also thank the NSF for support from 1734220 to B.W., and DARPA for support to T.A. article_processing_charge: No article_type: original author: - first_name: Titipat full_name: Achakulvisut, Titipat last_name: Achakulvisut - first_name: Tulakan full_name: Ruangrong, Tulakan last_name: Ruangrong - first_name: Patrick full_name: Mineault, Patrick last_name: Mineault - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Megan A.K. full_name: Peters, Megan A.K. last_name: Peters - first_name: Panayiota full_name: Poirazi, Panayiota last_name: Poirazi - first_name: Christopher full_name: Rozell, Christopher last_name: Rozell - first_name: Brad full_name: Wyble, Brad last_name: Wyble - first_name: Dan F.M. full_name: Goodman, Dan F.M. last_name: Goodman - first_name: Konrad Paul full_name: Kording, Konrad Paul last_name: Kording citation: ama: 'Achakulvisut T, Ruangrong T, Mineault P, et al. Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. Trends in Cognitive Sciences. 2021;25(4):265-268. doi:10.1016/j.tics.2021.01.007' apa: 'Achakulvisut, T., Ruangrong, T., Mineault, P., Vogels, T. P., Peters, M. A. K., Poirazi, P., … Kording, K. P. (2021). Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. Trends in Cognitive Sciences. Elsevier. https://doi.org/10.1016/j.tics.2021.01.007' chicago: 'Achakulvisut, Titipat, Tulakan Ruangrong, Patrick Mineault, Tim P Vogels, Megan A.K. Peters, Panayiota Poirazi, Christopher Rozell, Brad Wyble, Dan F.M. Goodman, and Konrad Paul Kording. “Towards Democratizing and Automating Online Conferences: Lessons from the Neuromatch Conferences.” Trends in Cognitive Sciences. Elsevier, 2021. https://doi.org/10.1016/j.tics.2021.01.007.' ieee: 'T. Achakulvisut et al., “Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences,” Trends in Cognitive Sciences, vol. 25, no. 4. Elsevier, pp. 265–268, 2021.' ista: 'Achakulvisut T, Ruangrong T, Mineault P, Vogels TP, Peters MAK, Poirazi P, Rozell C, Wyble B, Goodman DFM, Kording KP. 2021. Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. Trends in Cognitive Sciences. 25(4), 265–268.' mla: 'Achakulvisut, Titipat, et al. “Towards Democratizing and Automating Online Conferences: Lessons from the Neuromatch Conferences.” Trends in Cognitive Sciences, vol. 25, no. 4, Elsevier, 2021, pp. 265–68, doi:10.1016/j.tics.2021.01.007.' short: T. Achakulvisut, T. Ruangrong, P. Mineault, T.P. Vogels, M.A.K. Peters, P. Poirazi, C. Rozell, B. Wyble, D.F.M. Goodman, K.P. Kording, Trends in Cognitive Sciences 25 (2021) 265–268. date_created: 2021-03-07T23:01:25Z date_published: 2021-04-01T00:00:00Z date_updated: 2023-08-07T13:59:07Z day: '01' ddc: - '570' department: - _id: TiVo doi: 10.1016/j.tics.2021.01.007 external_id: isi: - '000627418000001' pmid: - '33608214' file: - access_level: open_access checksum: 87e39ea7bd266b976e8631b66979214d content_type: application/pdf creator: dernst date_created: 2022-05-27T07:31:24Z date_updated: 2022-05-27T07:31:24Z file_id: '11415' file_name: 2021_TrendsCognitiveSciences_Achakulvisut.pdf file_size: 380720 relation: main_file success: 1 file_date_updated: 2022-05-27T07:31:24Z has_accepted_license: '1' intvolume: ' 25' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 265-268 pmid: 1 publication: Trends in Cognitive Sciences publication_identifier: eissn: - 1879-307X issn: - 1364-6613 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 25 year: '2021' ... --- _id: '9224' abstract: - lang: eng text: We re-examine attempts to study the many-body localization transition using measures that are physically natural on the ergodic/quantum chaotic regime of the phase diagram. Using simple scaling arguments and an analysis of various models for which rigorous results are available, we find that these measures can be particularly adversely affected by the strong finite-size effects observed in nearly all numerical studies of many-body localization. This severely impacts their utility in probing the transition and the localized phase. In light of this analysis, we discuss a recent study (Šuntajs et al., 2020) of the behaviour of the Thouless energy and level repulsion in disordered spin chains, and its implications for the question of whether MBL is a true phase of matter. article_number: '168415' article_processing_charge: No article_type: original author: - first_name: D. A. full_name: Abanin, D. A. last_name: Abanin - first_name: J. H. full_name: Bardarson, J. H. last_name: Bardarson - first_name: G. full_name: De Tomasi, G. last_name: De Tomasi - first_name: S. full_name: Gopalakrishnan, S. last_name: Gopalakrishnan - first_name: V. full_name: Khemani, V. last_name: Khemani - first_name: S. A. full_name: Parameswaran, S. A. last_name: Parameswaran - first_name: F. full_name: Pollmann, F. last_name: Pollmann - first_name: A. C. full_name: Potter, A. C. last_name: Potter - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: R. full_name: Vasseur, R. last_name: Vasseur citation: ama: 'Abanin DA, Bardarson JH, De Tomasi G, et al. Distinguishing localization from chaos: Challenges in finite-size systems. Annals of Physics. 2021;427(4). doi:10.1016/j.aop.2021.168415' apa: 'Abanin, D. A., Bardarson, J. H., De Tomasi, G., Gopalakrishnan, S., Khemani, V., Parameswaran, S. A., … Vasseur, R. (2021). Distinguishing localization from chaos: Challenges in finite-size systems. Annals of Physics. Elsevier. https://doi.org/10.1016/j.aop.2021.168415' chicago: 'Abanin, D. A., J. H. Bardarson, G. De Tomasi, S. Gopalakrishnan, V. Khemani, S. A. Parameswaran, F. Pollmann, A. C. Potter, Maksym Serbyn, and R. Vasseur. “Distinguishing Localization from Chaos: Challenges in Finite-Size Systems.” Annals of Physics. Elsevier, 2021. https://doi.org/10.1016/j.aop.2021.168415.' ieee: 'D. A. Abanin et al., “Distinguishing localization from chaos: Challenges in finite-size systems,” Annals of Physics, vol. 427, no. 4. Elsevier, 2021.' ista: 'Abanin DA, Bardarson JH, De Tomasi G, Gopalakrishnan S, Khemani V, Parameswaran SA, Pollmann F, Potter AC, Serbyn M, Vasseur R. 2021. Distinguishing localization from chaos: Challenges in finite-size systems. Annals of Physics. 427(4), 168415.' mla: 'Abanin, D. A., et al. “Distinguishing Localization from Chaos: Challenges in Finite-Size Systems.” Annals of Physics, vol. 427, no. 4, 168415, Elsevier, 2021, doi:10.1016/j.aop.2021.168415.' short: D.A. Abanin, J.H. Bardarson, G. De Tomasi, S. Gopalakrishnan, V. Khemani, S.A. Parameswaran, F. Pollmann, A.C. Potter, M. Serbyn, R. Vasseur, Annals of Physics 427 (2021). date_created: 2021-03-07T23:01:25Z date_published: 2021-04-01T00:00:00Z date_updated: 2023-08-07T13:58:30Z day: '01' department: - _id: MaSe doi: 10.1016/j.aop.2021.168415 external_id: arxiv: - '1911.04501' isi: - '000634879800007' intvolume: ' 427' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1911.04501 month: '04' oa: 1 oa_version: Preprint publication: Annals of Physics publication_identifier: eissn: - 1096035X issn: - '00034916' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Distinguishing localization from chaos: Challenges in finite-size systems' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 427 year: '2021' ... --- _id: '9239' abstract: - lang: eng text: 'A graph game proceeds as follows: two players move a token through a graph to produce a finite or infinite path, which determines the payoff of the game. We study bidding games in which in each turn, an auction determines which player moves the token. Bidding games were largely studied in combination with two variants of first-price auctions called “Richman” and “poorman” bidding. We study taxman bidding, which span the spectrum between the two. The game is parameterized by a constant : portion τ of the winning bid is paid to the other player, and portion to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games: we unify, generalize, and simplify previous equivalences between bidding games and a class of stochastic games called random-turn games.' article_processing_charge: No article_type: original author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - 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: Đorđe full_name: Žikelić, Đorđe last_name: Žikelić citation: ama: Avni G, Henzinger TA, Žikelić Đ. Bidding mechanisms in graph games. Journal of Computer and System Sciences. 2021;119(8):133-144. doi:10.1016/j.jcss.2021.02.008 apa: Avni, G., Henzinger, T. A., & Žikelić, Đ. (2021). Bidding mechanisms in graph games. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2021.02.008 chicago: Avni, Guy, Thomas A Henzinger, and Đorđe Žikelić. “Bidding Mechanisms in Graph Games.” Journal of Computer and System Sciences. Elsevier, 2021. https://doi.org/10.1016/j.jcss.2021.02.008. ieee: G. Avni, T. A. Henzinger, and Đ. Žikelić, “Bidding mechanisms in graph games,” Journal of Computer and System Sciences, vol. 119, no. 8. Elsevier, pp. 133–144, 2021. ista: Avni G, Henzinger TA, Žikelić Đ. 2021. Bidding mechanisms in graph games. Journal of Computer and System Sciences. 119(8), 133–144. mla: Avni, Guy, et al. “Bidding Mechanisms in Graph Games.” Journal of Computer and System Sciences, vol. 119, no. 8, Elsevier, 2021, pp. 133–44, doi:10.1016/j.jcss.2021.02.008. short: G. Avni, T.A. Henzinger, Đ. Žikelić, Journal of Computer and System Sciences 119 (2021) 133–144. date_created: 2021-03-14T23:01:32Z date_published: 2021-03-03T00:00:00Z date_updated: 2023-08-07T14:08:34Z day: '03' department: - _id: ToHe doi: 10.1016/j.jcss.2021.02.008 external_id: arxiv: - '1905.03835' isi: - '000634149800009' intvolume: ' 119' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1905.03835 month: '03' oa: 1 oa_version: Preprint page: 133-144 publication: Journal of Computer and System Sciences publication_identifier: eissn: - 1090-2724 issn: - 0022-0000 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '6884' relation: earlier_version status: public scopus_import: '1' status: public title: Bidding mechanisms in graph games type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 119 year: '2021' ... --- _id: '9244' abstract: - lang: eng text: 'Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed tomography (DUCT). As proof of principle, we applied DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized by intrahepatic bile duct paucity, that can spontaneously generate a biliary system in adulthood. DUCT identified increased central biliary branching and peripheral bile duct tortuosity as two compensatory processes occurring in distinct regions of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis, which can reveal novel phenotypes and provide a standardized method of defining liver architecture in mouse models.' acknowledgement: "Work in ERA lab is supported by the Swedish Research Council, the Center of Innovative Medicine (CIMED) Grant, Karolinska Institutet, and the Heart and Lung Foundation, and\r\nthe Daniel Alagille Award from the European Association for the Study of the Liver. One project in ERA lab is funded by ModeRNA, unrelated to this project. The funders have no role in the design or interpretation of the work. SH has been supported by a KI-MU PhD student program, and by a Wera Ekstro¨m Foundation Scholarship. We are grateful for support from Tornspiran foundation to NVH. JK: This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II and CzechNanoLab Research Infrastructure supported by MEYS CR (LM2018110) . UL: The financial support from the Swedish Research Council and ICMC (Integrated CardioMetabolic Center) is acknowledged. JJ: The work was supported by the Grant Agency of Masaryk University (project no. MUNI/A/1565/2018). We thank Kari Huppert and Stacey Huppert for their expertise and help regarding bile duct cannulation and their laboratory hospitality. We also thank Nadja Schultz and Charlotte L Mattsson for their help with common bile duct cannulation. We thank Daniel Holl for his help with trachea cannulation. We thank Nikos Papadogiannakis for his assistance with mild Alagille biopsy samples and discussion. We thank Karolinska Biomedicum Imaging Core, especially Shigeaki Kanatani for his help with image analysis. We thank Jan Masek and Carolina Gutierrez for their scientific input in manuscript writing. We thank Peter Ranefall and the BioImage Informatics (SciLife national facility) for their help writing parts of the MATLAB pipeline.\r\nThe TROMA-III antibody developed by Rolf Kemler was obtained from the Developmental Studies Hybridoma (DSHB) Bank developed under the auspices of NICHD and maintained by The University of Iowa, Department of Biological Sciences, Iowa City, IA52242. We thank Goncalo M Brito for all illustrations. This work was supported by the European Union (European Research Council Starting grant 851288 to E.H.)." article_number: e60916 article_processing_charge: No article_type: original author: - first_name: Simona full_name: Hankeova, Simona last_name: Hankeova - first_name: Jakub full_name: Salplachta, Jakub last_name: Salplachta - first_name: Tomas full_name: Zikmund, Tomas last_name: Zikmund - first_name: Michaela full_name: Kavkova, Michaela last_name: Kavkova - first_name: Noémi full_name: Van Hul, Noémi last_name: Van Hul - first_name: Adam full_name: Brinek, Adam last_name: Brinek - first_name: Veronika full_name: Smekalova, Veronika last_name: Smekalova - first_name: Jakub full_name: Laznovsky, Jakub last_name: Laznovsky - first_name: Feven full_name: Dawit, Feven last_name: Dawit - first_name: Josef full_name: Jaros, Josef last_name: Jaros - first_name: Vítězslav full_name: Bryja, Vítězslav last_name: Bryja - first_name: Urban full_name: Lendahl, Urban last_name: Lendahl - first_name: Ewa full_name: Ellis, Ewa last_name: Ellis - first_name: Antal full_name: Nemeth, Antal last_name: Nemeth - first_name: Björn full_name: Fischler, Björn last_name: Fischler - 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: Jozef full_name: Kaiser, Jozef last_name: Kaiser - first_name: Emma Rachel full_name: Andersson, Emma Rachel last_name: Andersson citation: ama: Hankeova S, Salplachta J, Zikmund T, et al. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. eLife. 2021;10. doi:10.7554/eLife.60916 apa: Hankeova, S., Salplachta, J., Zikmund, T., Kavkova, M., Van Hul, N., Brinek, A., … Andersson, E. R. (2021). DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.60916 chicago: Hankeova, Simona, Jakub Salplachta, Tomas Zikmund, Michaela Kavkova, Noémi Van Hul, Adam Brinek, Veronika Smekalova, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.60916. ieee: S. Hankeova et al., “DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Hankeova S, Salplachta J, Zikmund T, Kavkova M, Van Hul N, Brinek A, Smekalova V, Laznovsky J, Dawit F, Jaros J, Bryja V, Lendahl U, Ellis E, Nemeth A, Fischler B, Hannezo EB, Kaiser J, Andersson ER. 2021. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. eLife. 10, e60916. mla: Hankeova, Simona, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” ELife, vol. 10, e60916, eLife Sciences Publications, 2021, doi:10.7554/eLife.60916. short: S. Hankeova, J. Salplachta, T. Zikmund, M. Kavkova, N. Van Hul, A. Brinek, V. Smekalova, J. Laznovsky, F. Dawit, J. Jaros, V. Bryja, U. Lendahl, E. Ellis, A. Nemeth, B. Fischler, E.B. Hannezo, J. Kaiser, E.R. Andersson, ELife 10 (2021). date_created: 2021-03-14T23:01:34Z date_published: 2021-02-26T00:00:00Z date_updated: 2023-08-07T14:12:54Z day: '26' ddc: - '570' department: - _id: EdHa doi: 10.7554/eLife.60916 ec_funded: 1 external_id: isi: - '000625357100001' pmid: - '33635272' file: - access_level: open_access checksum: 20ccf4dfe46c48cf986794c8bf4fd1cb content_type: application/pdf creator: dernst date_created: 2021-03-22T08:50:33Z date_updated: 2021-03-22T08:50:33Z file_id: '9271' file_name: 2021_eLife_Hankeova.pdf file_size: 9259690 relation: main_file success: 1 file_date_updated: 2021-03-22T08:50:33Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2021' ... --- _id: '9241' abstract: - lang: eng text: 'Volumetric light transport is a pervasive physical phenomenon, and therefore its accurate simulation is important for a broad array of disciplines. While suitable mathematical models for computing the transport are now available, obtaining the necessary material parameters needed to drive such simulations is a challenging task: direct measurements of these parameters from material samples are seldom possible. Building on the inverse scattering paradigm, we present a novel measurement approach which indirectly infers the transport parameters from extrinsic observations of multiple-scattered radiance. The novelty of the proposed approach lies in replacing structured illumination with a structured reflector bonded to the sample, and a robust fitting procedure that largely compensates for potential systematic errors in the calibration of the setup. We show the feasibility of our approach by validating simulations of complex 3D compositions of the measured materials against physical prints, using photo-polymer resins. As presented in this paper, our technique yields colorspace data suitable for accurate appearance reproduction in the area of 3D printing. Beyond that, and without fundamental changes to the basic measurement methodology, it could equally well be used to obtain spectral measurements that are useful for other application areas.' acknowledgement: "H2020 Marie Skłodowska-Curie Actions (642841); European Research Council (715767); Grantová Agentura České Republiky (16-08111S, 16-18964S); Univerzita Karlova v Praze (SVV-2017-260452); Engineering and Physical Sciences Research Council (EP/K023578/1).\r\nWe are grateful to Stratasys Ltd. for access to the voxel-level print interface of the J750\r\nmachine." article_processing_charge: No article_type: original author: - first_name: Oskar full_name: Elek, Oskar last_name: Elek - first_name: Ran full_name: Zhang, Ran id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0002-3808-281X - first_name: Denis full_name: Sumin, Denis last_name: Sumin - first_name: Karol full_name: Myszkowski, Karol last_name: Myszkowski - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Alexander full_name: Wilkie, Alexander last_name: Wilkie - first_name: Jaroslav full_name: Křivánek, Jaroslav last_name: Křivánek - first_name: Tim full_name: Weyrich, Tim last_name: Weyrich citation: ama: Elek O, Zhang R, Sumin D, et al. Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing. Optics Express. 2021;29(5):7568-7588. doi:10.1364/OE.406095 apa: Elek, O., Zhang, R., Sumin, D., Myszkowski, K., Bickel, B., Wilkie, A., … Weyrich, T. (2021). Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing. Optics Express. The Optical Society. https://doi.org/10.1364/OE.406095 chicago: Elek, Oskar, Ran Zhang, Denis Sumin, Karol Myszkowski, Bernd Bickel, Alexander Wilkie, Jaroslav Křivánek, and Tim Weyrich. “Robust and Practical Measurement of Volume Transport Parameters in Solid Photo-Polymer Materials for 3D Printing.” Optics Express. The Optical Society, 2021. https://doi.org/10.1364/OE.406095. ieee: O. Elek et al., “Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing,” Optics Express, vol. 29, no. 5. The Optical Society, pp. 7568–7588, 2021. ista: Elek O, Zhang R, Sumin D, Myszkowski K, Bickel B, Wilkie A, Křivánek J, Weyrich T. 2021. Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing. Optics Express. 29(5), 7568–7588. mla: Elek, Oskar, et al. “Robust and Practical Measurement of Volume Transport Parameters in Solid Photo-Polymer Materials for 3D Printing.” Optics Express, vol. 29, no. 5, The Optical Society, 2021, pp. 7568–88, doi:10.1364/OE.406095. short: O. Elek, R. Zhang, D. Sumin, K. Myszkowski, B. Bickel, A. Wilkie, J. Křivánek, T. Weyrich, Optics Express 29 (2021) 7568–7588. date_created: 2021-03-14T23:01:33Z date_published: 2021-03-01T00:00:00Z date_updated: 2023-08-07T14:11:57Z day: '01' ddc: - '000' department: - _id: BeBi doi: 10.1364/OE.406095 ec_funded: 1 external_id: isi: - '000624968100103' file: - access_level: open_access checksum: a9697ad83136c19ad87e46aa2db63cfd content_type: application/pdf creator: dernst date_created: 2021-03-22T08:15:28Z date_updated: 2021-03-22T08:15:28Z file_id: '9269' file_name: 2021_OpticsExpress_Elek.pdf file_size: 10873700 relation: main_file success: 1 file_date_updated: 2021-03-22T08:15:28Z has_accepted_license: '1' intvolume: ' 29' isi: 1 issue: '5' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 7568-7588 project: - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: Optics Express publication_identifier: eissn: - 1094-4087 publication_status: published publisher: The Optical Society quality_controlled: '1' scopus_import: '1' status: public title: Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing 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: 29 year: '2021' ... --- _id: '9243' abstract: - lang: eng text: Peptidoglycan is an essential component of the bacterial cell envelope that surrounds the cytoplasmic membrane to protect the cell from osmotic lysis. Important antibiotics such as β-lactams and glycopeptides target peptidoglycan biosynthesis. Class A penicillin-binding proteins (PBPs) are bifunctional membrane-bound peptidoglycan synthases that polymerize glycan chains and connect adjacent stem peptides by transpeptidation. How these enzymes work in their physiological membrane environment is poorly understood. Here, we developed a novel Förster resonance energy transfer-based assay to follow in real time both reactions of class A PBPs reconstituted in liposomes or supported lipid bilayers and applied this assay with PBP1B homologues from Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii in the presence or absence of their cognate lipoprotein activator. Our assay will allow unravelling the mechanisms of peptidoglycan synthesis in a lipid-bilayer environment and can be further developed to be used for high-throughput screening for new antimicrobials. acknowledgement: 'We thank Alexander Egan (Newcastle University) for purified proteins LpoB(sol) and LpoPPa(sol), Federico Corona (Newcastle University) for purified MepM, and Oliver Birkholz and Jacob Piehler (Department of Biology and Center of Cellular Nanoanalytics, University of Osnabru¨ ck) for their help with PBP1B reconstitution into polymer-SLBs and initial guidance on single particle tracking. We also acknowledge Christian P Richter and Changjiang You (Department of Biology and Center of Cellular Nanoanalytics, University of Osnabru¨ ck) for providing SLIMfast software and tris-DODA-NTA reagent, respectively. This work was funded by the BBSRC grant BB/R017409/1 (to WV), the European Research Council through grant ERC-2015-StG-679239 (to ML), and long-term fellowships HFSP LT 000824/2016-L4 and EMBO ALTF 1163–2015 (to NB). ' article_number: 1-32 article_processing_charge: No article_type: original author: - first_name: Víctor M. full_name: Hernández-Rocamora, Víctor M. last_name: Hernández-Rocamora - first_name: Natalia S. full_name: Baranova, Natalia S. id: 38661662-F248-11E8-B48F-1D18A9856A87 last_name: Baranova orcid: 0000-0002-3086-9124 - first_name: Katharina full_name: Peters, Katharina last_name: Peters - first_name: Eefjan full_name: Breukink, Eefjan last_name: Breukink - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Waldemar full_name: Vollmer, Waldemar last_name: Vollmer citation: ama: Hernández-Rocamora VM, Baranova NS, Peters K, Breukink E, Loose M, Vollmer W. Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. eLife. 2021;10. doi:10.7554/eLife.61525 apa: Hernández-Rocamora, V. M., Baranova, N. S., Peters, K., Breukink, E., Loose, M., & Vollmer, W. (2021). Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.61525 chicago: Hernández-Rocamora, Víctor M., Natalia S. Baranova, Katharina Peters, Eefjan Breukink, Martin Loose, and Waldemar Vollmer. “Real Time Monitoring of Peptidoglycan Synthesis by Membrane-Reconstituted Penicillin Binding Proteins.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.61525. ieee: V. M. Hernández-Rocamora, N. S. Baranova, K. Peters, E. Breukink, M. Loose, and W. Vollmer, “Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Hernández-Rocamora VM, Baranova NS, Peters K, Breukink E, Loose M, Vollmer W. 2021. Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. eLife. 10, 1–32. mla: Hernández-Rocamora, Víctor M., et al. “Real Time Monitoring of Peptidoglycan Synthesis by Membrane-Reconstituted Penicillin Binding Proteins.” ELife, vol. 10, 1–32, eLife Sciences Publications, 2021, doi:10.7554/eLife.61525. short: V.M. Hernández-Rocamora, N.S. Baranova, K. Peters, E. Breukink, M. Loose, W. Vollmer, ELife 10 (2021). date_created: 2021-03-14T23:01:33Z date_published: 2021-02-24T00:00:00Z date_updated: 2023-08-07T14:10:50Z day: '24' ddc: - '570' department: - _id: MaLo doi: 10.7554/eLife.61525 ec_funded: 1 external_id: isi: - '000627596400001' file: - access_level: open_access checksum: 79897a09bfecd9914d39c4aea2841855 content_type: application/pdf creator: dernst date_created: 2021-03-22T07:36:08Z date_updated: 2021-03-22T07:36:08Z file_id: '9268' file_name: 2021_eLife_HernandezRocamora.pdf file_size: 2314698 relation: main_file success: 1 file_date_updated: 2021-03-22T07:36:08Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 2595697A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '679239' name: Self-Organization of the Bacterial Cell - _id: 2596EAB6-B435-11E9-9278-68D0E5697425 grant_number: ALTF 2015-1163 name: Synthesis of bacterial cell wall - _id: 259B655A-B435-11E9-9278-68D0E5697425 grant_number: LT000824/2016 name: Reconstitution of bacterial cell wall sythesis publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2021' ... --- _id: '9246' abstract: - lang: eng text: We consider the Fröhlich Hamiltonian in a mean-field limit where many bosonic particles weakly couple to the quantized phonon field. For large particle numbers and a suitably small coupling, we show that the dynamics of the system is approximately described by the Landau–Pekar equations. These describe a Bose–Einstein condensate interacting with a classical polarization field, whose dynamics is effected by the condensate, i.e., the back-reaction of the phonons that are created by the particles during the time evolution is of leading order. acknowledgement: "Financial support by the European Research Council (ERC) under the\r\nEuropean Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo 694227; N.L and R.S.), the SNSF Eccellenza Project PCEFP2 181153 (N.L) and the\r\nDeutsche Forschungsgemeinschaft (DFG) through the Research TrainingGroup 1838: Spectral\r\nTheory and Dynamics of Quantum Systems (D.M.) is gratefully acknowledged. N.L.\r\ngratefully acknowledges support from the NCCRSwissMAP and would like to thank Simone\r\nRademacher and Benjamin Schlein for interesting discussions about the time-evolution of\r\nthe polaron at strong coupling. D.M. thanks Marcel Griesemer and Andreas Wünsch for\r\nextensive discussions about the Fröhlich polaron." article_processing_charge: No article_type: original author: - first_name: Nikolai K full_name: Leopold, Nikolai K id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87 last_name: Leopold orcid: 0000-0002-0495-6822 - first_name: David Johannes full_name: Mitrouskas, David Johannes id: cbddacee-2b11-11eb-a02e-a2e14d04e52d last_name: Mitrouskas - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Leopold NK, Mitrouskas DJ, Seiringer R. Derivation of the Landau–Pekar equations in a many-body mean-field limit. Archive for Rational Mechanics and Analysis. 2021;240:383-417. doi:10.1007/s00205-021-01616-9 apa: Leopold, N. K., Mitrouskas, D. J., & Seiringer, R. (2021). Derivation of the Landau–Pekar equations in a many-body mean-field limit. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01616-9 chicago: Leopold, Nikolai K, David Johannes Mitrouskas, and Robert Seiringer. “Derivation of the Landau–Pekar Equations in a Many-Body Mean-Field Limit.” Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01616-9. ieee: N. K. Leopold, D. J. Mitrouskas, and R. Seiringer, “Derivation of the Landau–Pekar equations in a many-body mean-field limit,” Archive for Rational Mechanics and Analysis, vol. 240. Springer Nature, pp. 383–417, 2021. ista: Leopold NK, Mitrouskas DJ, Seiringer R. 2021. Derivation of the Landau–Pekar equations in a many-body mean-field limit. Archive for Rational Mechanics and Analysis. 240, 383–417. mla: Leopold, Nikolai K., et al. “Derivation of the Landau–Pekar Equations in a Many-Body Mean-Field Limit.” Archive for Rational Mechanics and Analysis, vol. 240, Springer Nature, 2021, pp. 383–417, doi:10.1007/s00205-021-01616-9. short: N.K. Leopold, D.J. Mitrouskas, R. Seiringer, Archive for Rational Mechanics and Analysis 240 (2021) 383–417. date_created: 2021-03-14T23:01:34Z date_published: 2021-02-26T00:00:00Z date_updated: 2023-08-07T14:12:27Z day: '26' ddc: - '510' department: - _id: RoSe doi: 10.1007/s00205-021-01616-9 ec_funded: 1 external_id: arxiv: - '2001.03993' isi: - '000622226200001' file: - access_level: open_access checksum: 23449e44dc5132501a5c86e70638800f content_type: application/pdf creator: dernst date_created: 2021-03-22T08:31:29Z date_updated: 2021-03-22T08:31:29Z file_id: '9270' file_name: 2021_ArchRationalMechAnal_Leopold.pdf file_size: 558006 relation: main_file success: 1 file_date_updated: 2021-03-22T08:31:29Z has_accepted_license: '1' intvolume: ' 240' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 383-417 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Archive for Rational Mechanics and Analysis publication_identifier: eissn: - '14320673' issn: - '00039527' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Derivation of the Landau–Pekar equations in a many-body mean-field limit 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: 240 year: '2021' ... --- _id: '9256' abstract: - lang: eng text: We consider the ferromagnetic quantum Heisenberg model in one dimension, for any spin S≥1/2. We give upper and lower bounds on the free energy, proving that at low temperature it is asymptotically equal to the one of an ideal Bose gas of magnons, as predicted by the spin-wave approximation. The trial state used in the upper bound yields an analogous estimate also in the case of two spatial dimensions, which is believed to be sharp at low temperature. acknowledgement: "The work of MN was supported by the National Science Centre (NCN) Project Nr. 2016/21/D/ST1/02430. The work of RS was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227).\r\nOpen access funding provided by Institute of Science and Technology (IST Austria)." article_number: '31' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Marcin M full_name: Napiórkowski, Marcin M id: 4197AD04-F248-11E8-B48F-1D18A9856A87 last_name: Napiórkowski - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Napiórkowski MM, Seiringer R. Free energy asymptotics of the quantum Heisenberg spin chain. Letters in Mathematical Physics. 2021;111(2). doi:10.1007/s11005-021-01375-4 apa: Napiórkowski, M. M., & Seiringer, R. (2021). Free energy asymptotics of the quantum Heisenberg spin chain. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-021-01375-4 chicago: Napiórkowski, Marcin M, and Robert Seiringer. “Free Energy Asymptotics of the Quantum Heisenberg Spin Chain.” Letters in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s11005-021-01375-4. ieee: M. M. Napiórkowski and R. Seiringer, “Free energy asymptotics of the quantum Heisenberg spin chain,” Letters in Mathematical Physics, vol. 111, no. 2. Springer Nature, 2021. ista: Napiórkowski MM, Seiringer R. 2021. Free energy asymptotics of the quantum Heisenberg spin chain. Letters in Mathematical Physics. 111(2), 31. mla: Napiórkowski, Marcin M., and Robert Seiringer. “Free Energy Asymptotics of the Quantum Heisenberg Spin Chain.” Letters in Mathematical Physics, vol. 111, no. 2, 31, Springer Nature, 2021, doi:10.1007/s11005-021-01375-4. short: M.M. Napiórkowski, R. Seiringer, Letters in Mathematical Physics 111 (2021). date_created: 2021-03-21T23:01:19Z date_published: 2021-03-09T00:00:00Z date_updated: 2023-08-07T14:17:00Z day: '09' ddc: - '510' department: - _id: RoSe doi: 10.1007/s11005-021-01375-4 external_id: isi: - '000626837400001' file: - access_level: open_access checksum: 687fef1525789c0950de90468dd81604 content_type: application/pdf creator: dernst date_created: 2021-03-22T11:01:09Z date_updated: 2021-03-22T11:01:09Z file_id: '9273' file_name: 2021_LettersMathPhysics_Napiorkowski.pdf file_size: 397962 relation: main_file success: 1 file_date_updated: 2021-03-22T11:01:09Z has_accepted_license: '1' intvolume: ' 111' isi: 1 issue: '2' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Letters in Mathematical Physics publication_identifier: eissn: - '15730530' issn: - '03779017' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Free energy asymptotics of the quantum Heisenberg spin chain 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: 111 year: '2021' ... --- _id: '9242' abstract: - lang: eng text: In the recent years important experimental advances in resonant electro-optic modulators as high-efficiency sources for coherent frequency combs and as devices for quantum information transfer have been realized, where strong optical and microwave mode coupling were achieved. These features suggest electro-optic-based devices as candidates for entangled optical frequency comb sources. In the present work, I study the generation of entangled optical frequency combs in millimeter-sized resonant electro-optic modulators. These devices profit from the experimentally proven advantages such as nearly constant optical free spectral ranges over several gigahertz, and high optical and microwave quality factors. The generation of frequency multiplexed quantum channels with spectral bandwidth in the MHz range for conservative parameter values paves the way towards novel uses in long-distance hybrid quantum networks, quantum key distribution, enhanced optical metrology, and quantum computing. acknowledgement: "I thank Prof. Shabir Barzanjeh and Dr. Ulrich Vogl for the fruitful discussions.\r\n" article_number: '023708' article_processing_charge: No article_type: original author: - first_name: Alfredo R full_name: Rueda Sanchez, Alfredo R id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87 last_name: Rueda Sanchez orcid: 0000-0001-6249-5860 citation: ama: Rueda Sanchez AR. Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. Physical Review A. 2021;103(2). doi:10.1103/PhysRevA.103.023708 apa: Rueda Sanchez, A. R. (2021). Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.103.023708 chicago: Rueda Sanchez, Alfredo R. “Frequency-Multiplexed Hybrid Optical Entangled Source Based on the Pockels Effect.” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/PhysRevA.103.023708. ieee: A. R. Rueda Sanchez, “Frequency-multiplexed hybrid optical entangled source based on the Pockels effect,” Physical Review A, vol. 103, no. 2. American Physical Society, 2021. ista: Rueda Sanchez AR. 2021. Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. Physical Review A. 103(2), 023708. mla: Rueda Sanchez, Alfredo R. “Frequency-Multiplexed Hybrid Optical Entangled Source Based on the Pockels Effect.” Physical Review A, vol. 103, no. 2, 023708, American Physical Society, 2021, doi:10.1103/PhysRevA.103.023708. short: A.R. Rueda Sanchez, Physical Review A 103 (2021). date_created: 2021-03-14T23:01:33Z date_published: 2021-02-11T00:00:00Z date_updated: 2023-08-07T14:11:18Z day: '11' department: - _id: JoFi doi: 10.1103/PhysRevA.103.023708 external_id: arxiv: - '2010.05356' isi: - '000617037900013' intvolume: ' 103' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2010.05356 month: '02' oa: 1 oa_version: Preprint publication: Physical Review A publication_identifier: eissn: - 2469-9934 issn: - 2469-9926 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Frequency-multiplexed hybrid optical entangled source based on the Pockels effect type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 103 year: '2021' ... --- _id: '9257' abstract: - lang: eng text: 'The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing emergent kinetics, but this has received considerably less attention. Using recent advances in automatic differentiation, we show how kinetic pathways can be precisely designed by directly differentiating through statistical physics models, namely free energy calculations and molecular dynamics simulations. We consider two systems that are crucial to our understanding of structural self-assembly: bulk crystallization and small nanoclusters. In each case, we are able to assemble precise dynamical features. Using gradient information, we manipulate interactions among constituent particles to tune the rate at which these systems yield specific structures of interest. Moreover, we use this approach to learn nontrivial features about the high-dimensional design space, allowing us to accurately predict when multiple kinetic features can be simultaneously and independently controlled. These results provide a concrete and generalizable foundation for studying nonstructural self-assembly, including kinetic properties as well as other complex emergent properties, in a vast array of systems.' acknowledgement: We thank Agnese Curatolo, Megan Engel, Ofer Kimchi, Seong Ho Pahng, and Roy Frostig for helpful discussions. This material is based on work supported by NSF Graduate Research Fellowship Grant DGE1745303. This research was funded by NSF Grant DMS-1715477, Materials Research Science and Engineering Centers Grant DMR-1420570, and Office of Naval Research Grant N00014-17-1-3029. M.P.B. is an investigator of the Simons Foundation. article_number: e2024083118 article_processing_charge: No article_type: original author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Ella M. full_name: King, Ella M. last_name: King - first_name: Samuel S. full_name: Schoenholz, Samuel S. last_name: Schoenholz - first_name: Ekin D. full_name: Cubuk, Ekin D. last_name: Cubuk - first_name: Michael P. full_name: Brenner, Michael P. last_name: Brenner citation: ama: Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences. 2021;118(10). doi:10.1073/pnas.2024083118 apa: Goodrich, C. P., King, E. M., Schoenholz, S. S., Cubuk, E. D., & Brenner, M. P. (2021). Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2024083118 chicago: Goodrich, Carl Peter, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk, and Michael P. Brenner. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2024083118. ieee: C. P. Goodrich, E. M. King, S. S. Schoenholz, E. D. Cubuk, and M. P. Brenner, “Designing self-assembling kinetics with differentiable statistical physics models,” Proceedings of the National Academy of Sciences, vol. 118, no. 10. National Academy of Sciences, 2021. ista: Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. 2021. Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences. 118(10), e2024083118. mla: Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” Proceedings of the National Academy of Sciences, vol. 118, no. 10, e2024083118, National Academy of Sciences, 2021, doi:10.1073/pnas.2024083118. short: C.P. Goodrich, E.M. King, S.S. Schoenholz, E.D. Cubuk, M.P. Brenner, Proceedings of the National Academy of Sciences 118 (2021). date_created: 2021-03-21T23:01:20Z date_published: 2021-03-09T00:00:00Z date_updated: 2023-08-07T14:19:34Z day: '09' ddc: - '530' department: - _id: CaGo doi: 10.1073/pnas.2024083118 external_id: isi: - '000627429100097' pmid: - '33653960' file: - access_level: open_access checksum: 5be8da2b1c0757feb1057f1a515cf9e0 content_type: application/pdf creator: dernst date_created: 2021-03-22T12:23:54Z date_updated: 2021-03-22T12:23:54Z file_id: '9278' file_name: 2021_PNAS_Goodrich.pdf file_size: 1047954 relation: main_file success: 1 file_date_updated: 2021-03-22T12:23:54Z has_accepted_license: '1' intvolume: ' 118' isi: 1 issue: '10' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Designing self-assembling kinetics with differentiable statistical physics models 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: 118 year: '2021' ... --- _id: '9262' abstract: - lang: eng text: Sequence-specific oligomers with predictable folding patterns, i.e., foldamers, provide new opportunities to mimic α-helical peptides and design inhibitors of protein-protein interactions. One major hurdle of this strategy is to retain the correct orientation of key side chains involved in protein surface recognition. Here, we show that the structural plasticity of a foldamer backbone may notably contribute to the required spatial adjustment for optimal interaction with the protein surface. By using oligoureas as α helix mimics, we designed a foldamer/peptide hybrid inhibitor of histone chaperone ASF1, a key regulator of chromatin dynamics. The crystal structure of its complex with ASF1 reveals a notable plasticity of the urea backbone, which adapts to the ASF1 surface to maintain the same binding interface. One additional benefit of generating ASF1 ligands with nonpeptide oligourea segments is the resistance to proteolysis in human plasma, which was highly improved compared to the cognate α-helical peptide. acknowledgement: 'We thank the Synchrotron SOLEIL, the European Synchrotron Radiation Facility (ESRF), and the French Infrastructure for Integrated Structural Biology (FRISBI) ANR-10-INBS-05. We are particularly grateful to A. Clavier and A. Campalans for help in setting up and performing the cell penetration assays. Funding: Research was funded by the French Centre National de Recherche Scientifique (CNRS), the Commissariat à l’Energie Atomique (CEA), University of Bordeaux, University Paris-Saclay, and the Synchrotron Soleil. The project was supported by the ANR 2007 BREAKABOUND (JC-07-216078), 2011 BIPBIP (ANR-10-BINF-0003), 2012 CHAPINHIB (ANR-12-BSV5-0022-01), 2015 CHIPSET (ANR-15-CE11-008-01), 2015 HIMPP2I (ANR-15-CE07-0010), and the program labeled by the ARC foundation 2016 PGA1*20160203953). M.B. was supported by Canceropole (Paris, France) and a grant for young researchers from La Ligue contre le Cancer. J.M. was supported by La Ligue contre le Cancer.' article_number: eabd9153 article_processing_charge: No article_type: original author: - first_name: Johanne full_name: Mbianda, Johanne last_name: Mbianda - first_name: May M full_name: Bakail, May M id: FB3C3F8E-522F-11EA-B186-22963DDC885E last_name: Bakail orcid: 0000-0002-9592-1587 - first_name: Christophe full_name: André, Christophe last_name: André - first_name: Gwenaëlle full_name: Moal, Gwenaëlle last_name: Moal - first_name: Marie E. full_name: Perrin, Marie E. last_name: Perrin - first_name: Guillaume full_name: Pinna, Guillaume last_name: Pinna - first_name: Raphaël full_name: Guerois, Raphaël last_name: Guerois - first_name: Francois full_name: Becher, Francois last_name: Becher - first_name: Pierre full_name: Legrand, Pierre last_name: Legrand - first_name: Seydou full_name: Traoré, Seydou last_name: Traoré - first_name: Céline full_name: Douat, Céline last_name: Douat - first_name: Gilles full_name: Guichard, Gilles last_name: Guichard - first_name: Françoise full_name: Ochsenbein, Françoise last_name: Ochsenbein citation: ama: Mbianda J, Bakail MM, André C, et al. Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. Science Advances. 2021;7(12). doi:10.1126/sciadv.abd9153 apa: Mbianda, J., Bakail, M. M., André, C., Moal, G., Perrin, M. E., Pinna, G., … Ochsenbein, F. (2021). Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abd9153 chicago: Mbianda, Johanne, May M Bakail, Christophe André, Gwenaëlle Moal, Marie E. Perrin, Guillaume Pinna, Raphaël Guerois, et al. “Optimal Anchoring of a Foldamer Inhibitor of ASF1 Histone Chaperone through Backbone Plasticity.” Science Advances. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/sciadv.abd9153. ieee: J. Mbianda et al., “Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity,” Science Advances, vol. 7, no. 12. American Association for the Advancement of Science, 2021. ista: Mbianda J, Bakail MM, André C, Moal G, Perrin ME, Pinna G, Guerois R, Becher F, Legrand P, Traoré S, Douat C, Guichard G, Ochsenbein F. 2021. Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. Science Advances. 7(12), eabd9153. mla: Mbianda, Johanne, et al. “Optimal Anchoring of a Foldamer Inhibitor of ASF1 Histone Chaperone through Backbone Plasticity.” Science Advances, vol. 7, no. 12, eabd9153, American Association for the Advancement of Science, 2021, doi:10.1126/sciadv.abd9153. short: J. Mbianda, M.M. Bakail, C. André, G. Moal, M.E. Perrin, G. Pinna, R. Guerois, F. Becher, P. Legrand, S. Traoré, C. Douat, G. Guichard, F. Ochsenbein, Science Advances 7 (2021). date_created: 2021-03-22T07:14:03Z date_published: 2021-03-19T00:00:00Z date_updated: 2023-08-07T14:20:26Z day: '19' ddc: - '570' department: - _id: CampIT doi: 10.1126/sciadv.abd9153 external_id: isi: - '000633443000011' pmid: - '33741589' file: - access_level: open_access checksum: 737624cd0e630ffa7c52797a690500e3 content_type: application/pdf creator: dernst date_created: 2021-03-22T12:49:00Z date_updated: 2021-03-22T12:49:00Z file_id: '9280' file_name: 2021_ScienceAdv_Mbianda.pdf file_size: 837156 relation: main_file success: 1 file_date_updated: 2021-03-22T12:49:00Z has_accepted_license: '1' intvolume: ' 7' isi: 1 issue: '12' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: Science Advances publication_identifier: issn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' status: public title: Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 7 year: '2021' ... --- _id: '9259' abstract: - lang: eng text: Gradients of chemokines and growth factors guide migrating cells and morphogenetic processes. Migration of antigen-presenting dendritic cells from the interstitium into the lymphatic system is dependent on chemokine CCL21, which is secreted by endothelial cells of the lymphatic capillary, binds heparan sulfates and forms gradients decaying into the interstitium. Despite the importance of CCL21 gradients, and chemokine gradients in general, the mechanisms of gradient formation are unclear. Studies on fibroblast growth factors have shown that limited diffusion is crucial for gradient formation. Here, we used the mouse dermis as a model tissue to address the necessity of CCL21 anchoring to lymphatic capillary heparan sulfates in the formation of interstitial CCL21 gradients. Surprisingly, the absence of lymphatic endothelial heparan sulfates resulted only in a modest decrease of CCL21 levels at the lymphatic capillaries and did neither affect interstitial CCL21 gradient shape nor dendritic cell migration toward lymphatic capillaries. Thus, heparan sulfates at the level of the lymphatic endothelium are dispensable for the formation of a functional CCL21 gradient. acknowledgement: "This work was supported by Sigrid Juselius fellowship (KV), University of Helsinki 3-year research grant (KV), Academy of Finland Research fellow funding (315710, to KV), the European Research Council (ERC CoG 724373 to MS), and by the Austrian Science foundation (FWF) (Y564-B12 START award to MS).\r\nTaija Mäkinen is acknowledged for providing Prox1CreERT2 transgenic mice and Yu Yamaguchi for providing the conditional Ext1 mouse strain." article_number: '630002' article_processing_charge: No article_type: original author: - first_name: Kari full_name: Vaahtomeri, Kari id: 368EE576-F248-11E8-B48F-1D18A9856A87 last_name: Vaahtomeri orcid: 0000-0001-7829-3518 - first_name: Christine full_name: Moussion, Christine id: 3356F664-F248-11E8-B48F-1D18A9856A87 last_name: Moussion - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Vaahtomeri K, Moussion C, Hauschild R, Sixt MK. Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. Frontiers in Immunology. 2021;12. doi:10.3389/fimmu.2021.630002 apa: Vaahtomeri, K., Moussion, C., Hauschild, R., & Sixt, M. K. (2021). Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2021.630002 chicago: Vaahtomeri, Kari, Christine Moussion, Robert Hauschild, and Michael K Sixt. “Shape and Function of Interstitial Chemokine CCL21 Gradients Are Independent of Heparan Sulfates Produced by Lymphatic Endothelium.” Frontiers in Immunology. Frontiers, 2021. https://doi.org/10.3389/fimmu.2021.630002. ieee: K. Vaahtomeri, C. Moussion, R. Hauschild, and M. K. Sixt, “Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium,” Frontiers in Immunology, vol. 12. Frontiers, 2021. ista: Vaahtomeri K, Moussion C, Hauschild R, Sixt MK. 2021. Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. Frontiers in Immunology. 12, 630002. mla: Vaahtomeri, Kari, et al. “Shape and Function of Interstitial Chemokine CCL21 Gradients Are Independent of Heparan Sulfates Produced by Lymphatic Endothelium.” Frontiers in Immunology, vol. 12, 630002, Frontiers, 2021, doi:10.3389/fimmu.2021.630002. short: K. Vaahtomeri, C. Moussion, R. Hauschild, M.K. Sixt, Frontiers in Immunology 12 (2021). date_created: 2021-03-21T23:01:20Z date_published: 2021-02-25T00:00:00Z date_updated: 2023-08-07T14:18:26Z day: '25' ddc: - '570' department: - _id: MiSi - _id: Bio doi: 10.3389/fimmu.2021.630002 ec_funded: 1 external_id: isi: - '000627134400001' pmid: - '33717158' file: - access_level: open_access checksum: 663f5a48375e42afa4bfef58d42ec186 content_type: application/pdf creator: dernst date_created: 2021-03-22T12:08:26Z date_updated: 2021-03-22T12:08:26Z file_id: '9277' file_name: 2021_FrontiersImmumo_Vaahtomeri.pdf file_size: 3740146 relation: main_file success: 1 file_date_updated: 2021-03-22T12:08:26Z has_accepted_license: '1' intvolume: ' 12' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular navigation along spatial gradients - _id: 25A8E5EA-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 564-B12 name: Cytoskeletal force generation and force transduction of migrating leukocytes publication: Frontiers in Immunology publication_identifier: eissn: - 1664-3224 publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium 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: 12 year: '2021' ... --- _id: '9254' abstract: - lang: eng text: 'Auxin is a key regulator of plant growth and development. Local auxin biosynthesis and intercellular transport generates regional gradients in the root that are instructive for processes such as specification of developmental zones that maintain root growth and tropic responses. Here we present a toolbox to study auxin-mediated root development that features: (i) the ability to control auxin synthesis with high spatio-temporal resolution and (ii) single-cell nucleus tracking and morphokinetic analysis infrastructure. Integration of these two features enables cutting-edge analysis of root development at single-cell resolution based on morphokinetic parameters under normal growth conditions and during cell-type-specific induction of auxin biosynthesis. We show directional auxin flow in the root and refine the contributions of key players in this process. In addition, we determine the quantitative kinetics of Arabidopsis root meristem skewing, which depends on local auxin gradients but does not require PIN2 and AUX1 auxin transporter activities. Beyond the mechanistic insights into root development, the tools developed here will enable biologists to study kinetics and morphology of various critical processes at the single cell-level in whole organisms.' acknowledgement: This work was supported by grants from the Israel Science Foundation (2378/19 to E.S.), the Joint NSFC-ISF Research Grant (3419/20 to E.S. and Z.D.), the Human Frontier Science Program (HFSP—LIY000540/2020 to E.S.), the European Research Council Starting Grant (757683- RobustHormoneTrans to E.S.), PBC postdoctoral fellowships (to Y.H. and M.O.), NIH (GM114660 to Y.Z.), Breast Cancer Research Foundation (BCRF to I.T.). article_number: '1657' article_processing_charge: No article_type: original author: - first_name: Yangjie full_name: Hu, Yangjie last_name: Hu - first_name: Moutasem full_name: Omary, Moutasem last_name: Omary - first_name: Yun full_name: Hu, Yun last_name: Hu - first_name: Ohad full_name: Doron, Ohad last_name: Doron - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer - first_name: Qingguo full_name: Chen, Qingguo last_name: Chen - first_name: Or full_name: Megides, Or last_name: Megides - first_name: Ori full_name: Chekli, Ori last_name: Chekli - first_name: Zhaojun full_name: Ding, Zhaojun last_name: Ding - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Yunde full_name: Zhao, Yunde last_name: Zhao - first_name: Ilan full_name: Tsarfaty, Ilan last_name: Tsarfaty - first_name: Eilon full_name: Shani, Eilon last_name: Shani citation: ama: Hu Y, Omary M, Hu Y, et al. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. 2021;12. doi:10.1038/s41467-021-21802-3 apa: Hu, Y., Omary, M., Hu, Y., Doron, O., Hörmayer, L., Chen, Q., … Shani, E. (2021). Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-21802-3 chicago: Hu, Yangjie, Moutasem Omary, Yun Hu, Ohad Doron, Lukas Hörmayer, Qingguo Chen, Or Megides, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-21802-3. ieee: Y. Hu et al., “Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing,” Nature Communications, vol. 12. Springer Nature, 2021. ista: Hu Y, Omary M, Hu Y, Doron O, Hörmayer L, Chen Q, Megides O, Chekli O, Ding Z, Friml J, Zhao Y, Tsarfaty I, Shani E. 2021. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. 12, 1657. mla: Hu, Yangjie, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” Nature Communications, vol. 12, 1657, Springer Nature, 2021, doi:10.1038/s41467-021-21802-3. short: Y. Hu, M. Omary, Y. Hu, O. Doron, L. Hörmayer, Q. Chen, O. Megides, O. Chekli, Z. Ding, J. Friml, Y. Zhao, I. Tsarfaty, E. Shani, Nature Communications 12 (2021). date_created: 2021-03-21T23:01:19Z date_published: 2021-03-12T00:00:00Z date_updated: 2023-08-07T14:17:55Z day: '12' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-021-21802-3 external_id: isi: - '000630419400048' pmid: - '33712581' file: - access_level: open_access checksum: e1022f3aee349853ded2b2b3e092362d content_type: application/pdf creator: dernst date_created: 2021-03-22T11:18:58Z date_updated: 2021-03-22T11:18:58Z file_id: '9275' file_name: 2021_NatureComm_Hu.pdf file_size: 8602096 relation: main_file success: 1 file_date_updated: 2021-03-22T11:18:58Z has_accepted_license: '1' intvolume: ' 12' isi: 1 language: - iso: eng month: '03' 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: Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing 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: 12 year: '2021' ... --- _id: '9255' abstract: - lang: eng text: Our ability to trust that a random number is truly random is essential for fields as diverse as cryptography and fundamental tests of quantum mechanics. Existing solutions both come with drawbacks—device-independent quantum random number generators (QRNGs) are highly impractical and standard semi-device-independent QRNGs are limited to a specific physical implementation and level of trust. Here we propose a framework for semi-device-independent randomness certification, using a source of trusted vacuum in the form of a signal shutter. It employs a flexible set of assumptions and levels of trust, allowing it to be applied in a wide range of physical scenarios involving both quantum and classical entropy sources. We experimentally demonstrate our protocol with a photonic setup and generate secure random bits under three different assumptions with varying degrees of security and resulting data rates. acknowledgement: We would like to thank Robert Fickler for discussions about the experimental realization and Marek Sýs for running the NIST randomness test on the data we acquired in the experiment. We would like to thank Ugo Zanforlin, Gerald Buller, Daniel White, and Cristian Bonato for their help with the experiment. M. Pivoluska, M. Plesch, and M.M. acknowledge Czech-Austrian project MultiQUEST (I3053-N27 and GF17-33780L). M. Pivoluska and M. Plesch additionally acknowledge the support of VEGA project 2/0136/19. M.F. acknowledges support from the Polish NCN grant Sonata UMO-2014/14/E/ST2/00020, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program ERC AdG CERQUTE (grant agreement No 834266), the State Research Agency (AEI) TRANQI (PID2019-106888GB-I00/10.13039/501100011033), the Government of Spain (FIS2020-TRANQI; Severo Ochoa CEX2019-000910-S), Fundació Cellex, Fundació Mir-Puig, and Generalitat de Catalunya (CERCA, AGAUR). M.M., W.M., N.H.V., and C.F. acknowledge support from the QuantERA ERA-NET Co-fund (FWF Project I3773-N36) and the UK Engineering and Physical Sciences Research Council (EPSRC) (EP/P024114/1). article_number: '50' article_processing_charge: No article_type: original author: - first_name: Matej full_name: Pivoluska, Matej last_name: Pivoluska - first_name: Martin full_name: Plesch, Martin last_name: Plesch - first_name: Máté full_name: Farkas, Máté last_name: Farkas - first_name: Natalia full_name: Ruzickova, Natalia id: D2761128-D73D-11E9-A1BF-BA0DE6697425 last_name: Ruzickova - first_name: Clara full_name: Flegel, Clara last_name: Flegel - first_name: Natalia Herrera full_name: Valencia, Natalia Herrera last_name: Valencia - first_name: Will full_name: Mccutcheon, Will last_name: Mccutcheon - first_name: Mehul full_name: Malik, Mehul last_name: Malik - first_name: Edgar A. full_name: Aguilar, Edgar A. last_name: Aguilar citation: ama: Pivoluska M, Plesch M, Farkas M, et al. Semi-device-independent random number generation with flexible assumptions. npj Quantum Information. 2021;7. doi:10.1038/s41534-021-00387-1 apa: Pivoluska, M., Plesch, M., Farkas, M., Ruzickova, N., Flegel, C., Valencia, N. H., … Aguilar, E. A. (2021). Semi-device-independent random number generation with flexible assumptions. Npj Quantum Information. Springer Nature. https://doi.org/10.1038/s41534-021-00387-1 chicago: Pivoluska, Matej, Martin Plesch, Máté Farkas, Natalia Ruzickova, Clara Flegel, Natalia Herrera Valencia, Will Mccutcheon, Mehul Malik, and Edgar A. Aguilar. “Semi-Device-Independent Random Number Generation with Flexible Assumptions.” Npj Quantum Information. Springer Nature, 2021. https://doi.org/10.1038/s41534-021-00387-1. ieee: M. Pivoluska et al., “Semi-device-independent random number generation with flexible assumptions,” npj Quantum Information, vol. 7. Springer Nature, 2021. ista: Pivoluska M, Plesch M, Farkas M, Ruzickova N, Flegel C, Valencia NH, Mccutcheon W, Malik M, Aguilar EA. 2021. Semi-device-independent random number generation with flexible assumptions. npj Quantum Information. 7, 50. mla: Pivoluska, Matej, et al. “Semi-Device-Independent Random Number Generation with Flexible Assumptions.” Npj Quantum Information, vol. 7, 50, Springer Nature, 2021, doi:10.1038/s41534-021-00387-1. short: M. Pivoluska, M. Plesch, M. Farkas, N. Ruzickova, C. Flegel, N.H. Valencia, W. Mccutcheon, M. Malik, E.A. Aguilar, Npj Quantum Information 7 (2021). date_created: 2021-03-21T23:01:19Z date_published: 2021-03-15T00:00:00Z date_updated: 2023-08-07T14:17:26Z day: '15' ddc: - '530' department: - _id: FyKo doi: 10.1038/s41534-021-00387-1 external_id: isi: - '000629173100001' file: - access_level: open_access checksum: 26d3f2a2c8c8fa8c1002028326b45f64 content_type: application/pdf creator: dernst date_created: 2021-03-22T11:09:34Z date_updated: 2021-03-22T11:09:34Z file_id: '9274' file_name: 2021_NPJQuantumInformation_Pivoluska.pdf file_size: 1360271 relation: main_file success: 1 file_date_updated: 2021-03-22T11:09:34Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: npj Quantum Information publication_identifier: eissn: - 2056-6387 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Semi-device-independent random number generation with flexible assumptions 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: 7 year: '2021' ... --- _id: '9260' abstract: - lang: eng text: We study the density of rational points on a higher-dimensional orbifold (Pn−1,Δ) when Δ is a Q-divisor involving hyperplanes. This allows us to address a question of Tanimoto about whether the set of rational points on such an orbifold constitutes a thin set. Our approach relies on the Hardy–Littlewood circle method to first study an asymptotic version of Waring’s problem for mixed powers. In doing so we make crucial use of the recent resolution of the main conjecture in Vinogradov’s mean value theorem, due to Bourgain–Demeter–Guth and Wooley. acknowledgement: While working on this paper the authors were both supported by EPSRC grant EP/P026710/1, and the second author received additional support from the NWO Veni Grant 016.Veni.192.047. Thanks are due to Marta Pieropan, Arne Smeets and Sho Tanimoto for useful conversations related to this topic, and to the anonymous referee for numerous helpful suggestions. article_processing_charge: No article_type: original author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Shuntaro full_name: Yamagishi, Shuntaro last_name: Yamagishi citation: ama: Browning TD, Yamagishi S. Arithmetic of higher-dimensional orbifolds and a mixed Waring problem. Mathematische Zeitschrift. 2021;299:1071–1101. doi:10.1007/s00209-021-02695-w apa: Browning, T. D., & Yamagishi, S. (2021). Arithmetic of higher-dimensional orbifolds and a mixed Waring problem. Mathematische Zeitschrift. Springer Nature. https://doi.org/10.1007/s00209-021-02695-w chicago: Browning, Timothy D, and Shuntaro Yamagishi. “Arithmetic of Higher-Dimensional Orbifolds and a Mixed Waring Problem.” Mathematische Zeitschrift. Springer Nature, 2021. https://doi.org/10.1007/s00209-021-02695-w. ieee: T. D. Browning and S. Yamagishi, “Arithmetic of higher-dimensional orbifolds and a mixed Waring problem,” Mathematische Zeitschrift, vol. 299. Springer Nature, pp. 1071–1101, 2021. ista: Browning TD, Yamagishi S. 2021. Arithmetic of higher-dimensional orbifolds and a mixed Waring problem. Mathematische Zeitschrift. 299, 1071–1101. mla: Browning, Timothy D., and Shuntaro Yamagishi. “Arithmetic of Higher-Dimensional Orbifolds and a Mixed Waring Problem.” Mathematische Zeitschrift, vol. 299, Springer Nature, 2021, pp. 1071–1101, doi:10.1007/s00209-021-02695-w. short: T.D. Browning, S. Yamagishi, Mathematische Zeitschrift 299 (2021) 1071–1101. date_created: 2021-03-21T23:01:21Z date_published: 2021-03-05T00:00:00Z date_updated: 2023-08-07T14:20:00Z day: '05' ddc: - '510' department: - _id: TiBr doi: 10.1007/s00209-021-02695-w external_id: isi: - '000625573800002' file: - access_level: open_access checksum: 8ed9f49568806894744096dbbca0ad7b content_type: application/pdf creator: dernst date_created: 2021-03-22T12:41:26Z date_updated: 2021-03-22T12:41:26Z file_id: '9279' file_name: 2021_MathZeitschrift_Browning.pdf file_size: 492685 relation: main_file success: 1 file_date_updated: 2021-03-22T12:41:26Z has_accepted_license: '1' intvolume: ' 299' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1071–1101 project: - _id: 26A8D266-B435-11E9-9278-68D0E5697425 grant_number: EP-P026710-2 name: Between rational and integral points publication: Mathematische Zeitschrift publication_identifier: eissn: - 1432-1823 issn: - 0025-5874 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Arithmetic of higher-dimensional orbifolds and a mixed Waring problem tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 299 year: '2021' ... --- _id: '9258' acknowledgement: 'We thank S. van der Walt and K. Marchuk for discussion during development. This project was funded by Packard Fellowship and Chan Zuckerberg Biohub Investigator Awards to L.W.; STROBE: A NSF Science and Technology Center; an NSF Graduate Research Fellowship awarded to H.P.; a Berkeley Institute for Data Science/UCSF Bakar Computational Health Sciences Institute Fellowship awarded to H.P. with support from the Koret Foundation, the Gordon and Betty Moore Foundation, and the Alfred P. Sloan Foundation to the University of California, Berkeley. K.W.E., B.L. and M.T. were funded by the Chan Zuckerberg Initiative and NIH grant P41GM135019.' article_processing_charge: No article_type: letter_note author: - first_name: Henry full_name: Pinkard, Henry last_name: Pinkard - first_name: Nico full_name: Stuurman, Nico last_name: Stuurman - first_name: Ivan E. full_name: Ivanov, Ivan E. last_name: Ivanov - first_name: Nicholas M. full_name: Anthony, Nicholas M. last_name: Anthony - first_name: Wei full_name: Ouyang, Wei last_name: Ouyang - first_name: Bin full_name: Li, Bin last_name: Li - first_name: Bin full_name: Yang, Bin last_name: Yang - first_name: Mark A. full_name: Tsuchida, Mark A. last_name: Tsuchida - first_name: Bryant full_name: Chhun, Bryant last_name: Chhun - first_name: Grace full_name: Zhang, Grace last_name: Zhang - first_name: Ryan full_name: Mei, Ryan last_name: Mei - first_name: Michael full_name: Anderson, Michael last_name: Anderson - first_name: Douglas P. full_name: Shepherd, Douglas P. last_name: Shepherd - first_name: Ian full_name: Hunt-Isaak, Ian last_name: Hunt-Isaak - first_name: Raymond L. full_name: Dunn, Raymond L. last_name: Dunn - first_name: Wiebke full_name: Jahr, Wiebke id: 425C1CE8-F248-11E8-B48F-1D18A9856A87 last_name: Jahr - first_name: Saul full_name: Kato, Saul last_name: Kato - first_name: Loïc A. full_name: Royer, Loïc A. last_name: Royer - first_name: Jay R. full_name: Thiagarajah, Jay R. last_name: Thiagarajah - first_name: Kevin W. full_name: Eliceiri, Kevin W. last_name: Eliceiri - first_name: Emma full_name: Lundberg, Emma last_name: Lundberg - first_name: Shalin B. full_name: Mehta, Shalin B. last_name: Mehta - first_name: Laura full_name: Waller, Laura last_name: Waller citation: ama: 'Pinkard H, Stuurman N, Ivanov IE, et al. Pycro-Manager: Open-source software for customized and reproducible microscope control. Nature Methods. 2021;18(3):226-228. doi:10.1038/s41592-021-01087-6' apa: 'Pinkard, H., Stuurman, N., Ivanov, I. E., Anthony, N. M., Ouyang, W., Li, B., … Waller, L. (2021). Pycro-Manager: Open-source software for customized and reproducible microscope control. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-021-01087-6' chicago: 'Pinkard, Henry, Nico Stuurman, Ivan E. Ivanov, Nicholas M. Anthony, Wei Ouyang, Bin Li, Bin Yang, et al. “Pycro-Manager: Open-Source Software for Customized and Reproducible Microscope Control.” Nature Methods. Springer Nature, 2021. https://doi.org/10.1038/s41592-021-01087-6.' ieee: 'H. Pinkard et al., “Pycro-Manager: Open-source software for customized and reproducible microscope control,” Nature Methods, vol. 18, no. 3. Springer Nature, pp. 226–228, 2021.' ista: 'Pinkard H, Stuurman N, Ivanov IE, Anthony NM, Ouyang W, Li B, Yang B, Tsuchida MA, Chhun B, Zhang G, Mei R, Anderson M, Shepherd DP, Hunt-Isaak I, Dunn RL, Jahr W, Kato S, Royer LA, Thiagarajah JR, Eliceiri KW, Lundberg E, Mehta SB, Waller L. 2021. Pycro-Manager: Open-source software for customized and reproducible microscope control. Nature Methods. 18(3), 226–228.' mla: 'Pinkard, Henry, et al. “Pycro-Manager: Open-Source Software for Customized and Reproducible Microscope Control.” Nature Methods, vol. 18, no. 3, Springer Nature, 2021, pp. 226–28, doi:10.1038/s41592-021-01087-6.' short: H. Pinkard, N. Stuurman, I.E. Ivanov, N.M. Anthony, W. Ouyang, B. Li, B. Yang, M.A. Tsuchida, B. Chhun, G. Zhang, R. Mei, M. Anderson, D.P. Shepherd, I. Hunt-Isaak, R.L. Dunn, W. Jahr, S. Kato, L.A. Royer, J.R. Thiagarajah, K.W. Eliceiri, E. Lundberg, S.B. Mehta, L. Waller, Nature Methods 18 (2021) 226–228. date_created: 2021-03-21T23:01:20Z date_published: 2021-03-01T00:00:00Z date_updated: 2023-08-07T14:19:08Z day: '01' department: - _id: JoDa doi: 10.1038/s41592-021-01087-6 external_id: isi: - '000625600600007' pmid: - '33674797' intvolume: ' 18' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41592-021-01087-6 month: '03' oa: 1 oa_version: Published Version page: 226-228 pmid: 1 publication: Nature Methods publication_identifier: eissn: - 1548-7105 issn: - 1548-7091 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Pycro-Manager: Open-source software for customized and reproducible microscope control' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 18 year: '2021' ... --- _id: '9306' abstract: - lang: eng text: Assemblies of actin and its regulators underlie the dynamic morphology of all eukaryotic cells. To understand how actin regulatory proteins work together to generate actin-rich structures such as filopodia, we analyzed the localization of diverse actin regulators within filopodia in Drosophila embryos and in a complementary in vitro system of filopodia-like structures (FLSs). We found that the composition of the regulatory protein complex where actin is incorporated (the filopodial tip complex) is remarkably heterogeneous both in vivo and in vitro. Our data reveal that different pairs of proteins correlate with each other and with actin bundle length, suggesting the presence of functional subcomplexes. This is consistent with a theoretical framework where three or more redundant subcomplexes join the tip complex stochastically, with any two being sufficient to drive filopodia formation. We provide an explanation for the observed heterogeneity and suggest that a mechanism based on multiple components allows stereotypical filopodial dynamics to arise from diverse upstream signaling pathways. acknowledgement: "This work was supported by European Research Council grant 281971, Wellcome Trust Research Career Development Fellowship WT095829AIA and Wellcome Trust Senior Research\r\nFellowship 219482/Z/19/Z to J.L. Gallop, a Wellcome Trust Senior Investigator Award 098357 to B.D. Simons, and an Austrian Science Fund grant (P31639) to E. Hannezo. We acknowledge\r\ncore funding by the Wellcome Trust (092096) and Cancer Research UK (C6946/A14492). U. Dobramysl was supported by a Wellcome Trust Junior Interdisciplinary Fellowship grant\r\n(105602/Z/14/Z) and a Herchel Smith Postdoctoral Fellowship. H. Shimo was supported by a Funai Foundation Overseas scholarship." article_number: e202003052 article_processing_charge: No article_type: original author: - first_name: Ulrich full_name: Dobramysl, Ulrich last_name: Dobramysl - first_name: Iris Katharina full_name: Jarsch, Iris Katharina last_name: Jarsch - first_name: Yoshiko full_name: Inoue, Yoshiko last_name: Inoue - first_name: Hanae full_name: Shimo, Hanae last_name: Shimo - first_name: Benjamin full_name: Richier, Benjamin last_name: Richier - first_name: Jonathan R. full_name: Gadsby, Jonathan R. last_name: Gadsby - first_name: Julia full_name: Mason, Julia last_name: Mason - first_name: Alicja full_name: Szałapak, Alicja last_name: Szałapak - first_name: Pantelis Savvas full_name: Ioannou, Pantelis Savvas last_name: Ioannou - first_name: Guilherme Pereira full_name: Correia, Guilherme Pereira last_name: Correia - first_name: Astrid full_name: Walrant, Astrid last_name: Walrant - first_name: Richard full_name: Butler, Richard last_name: Butler - 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: Benjamin D. full_name: Simons, Benjamin D. last_name: Simons - first_name: Jennifer L. full_name: Gallop, Jennifer L. last_name: Gallop citation: ama: Dobramysl U, Jarsch IK, Inoue Y, et al. Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. Journal of Cell Biology. 2021;220(4). doi:10.1083/jcb.202003052 apa: Dobramysl, U., Jarsch, I. K., Inoue, Y., Shimo, H., Richier, B., Gadsby, J. R., … Gallop, J. L. (2021). Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202003052 chicago: Dobramysl, Ulrich, Iris Katharina Jarsch, Yoshiko Inoue, Hanae Shimo, Benjamin Richier, Jonathan R. Gadsby, Julia Mason, et al. “Stochastic Combinations of Actin Regulatory Proteins Are Sufficient to Drive Filopodia Formation.” Journal of Cell Biology. Rockefeller University Press, 2021. https://doi.org/10.1083/jcb.202003052. ieee: U. Dobramysl et al., “Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation,” Journal of Cell Biology, vol. 220, no. 4. Rockefeller University Press, 2021. ista: Dobramysl U, Jarsch IK, Inoue Y, Shimo H, Richier B, Gadsby JR, Mason J, Szałapak A, Ioannou PS, Correia GP, Walrant A, Butler R, Hannezo EB, Simons BD, Gallop JL. 2021. Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. Journal of Cell Biology. 220(4), e202003052. mla: Dobramysl, Ulrich, et al. “Stochastic Combinations of Actin Regulatory Proteins Are Sufficient to Drive Filopodia Formation.” Journal of Cell Biology, vol. 220, no. 4, e202003052, Rockefeller University Press, 2021, doi:10.1083/jcb.202003052. short: U. Dobramysl, I.K. Jarsch, Y. Inoue, H. Shimo, B. Richier, J.R. Gadsby, J. Mason, A. Szałapak, P.S. Ioannou, G.P. Correia, A. Walrant, R. Butler, E.B. Hannezo, B.D. Simons, J.L. Gallop, Journal of Cell Biology 220 (2021). date_created: 2021-04-04T22:01:21Z date_published: 2021-03-19T00:00:00Z date_updated: 2023-08-07T14:32:28Z day: '19' ddc: - '576' department: - _id: EdHa doi: 10.1083/jcb.202003052 external_id: isi: - '000663160600002' pmid: - '33740033' file: - access_level: open_access checksum: 4739ffd90f2c7e05ac5b00f057c58aa2 content_type: application/pdf creator: dernst date_created: 2021-04-06T10:39:08Z date_updated: 2021-04-06T10:39:08Z file_id: '9310' file_name: 2021_JCB_Dobramysl.pdf file_size: 9019720 relation: main_file success: 1 file_date_updated: 2021-04-06T10:39:08Z has_accepted_license: '1' intvolume: ' 220' isi: 1 issue: '4' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 268294B6-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31639 name: Active mechano-chemical description of the cell cytoskeleton publication: Journal of Cell Biology publication_identifier: eissn: - '15408140' publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation 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: 220 year: '2021' ... --- _id: '9307' abstract: - lang: eng text: We establish finite time extinction with probability one for weak solutions of the Cauchy–Dirichlet problem for the 1D stochastic porous medium equation with Stratonovich transport noise and compactly supported smooth initial datum. Heuristically, this is expected to hold because Brownian motion has average spread rate O(t12) whereas the support of solutions to the deterministic PME grows only with rate O(t1m+1). The rigorous proof relies on a contraction principle up to time-dependent shift for Wong–Zakai type approximations, the transformation to a deterministic PME with two copies of a Brownian path as the lateral boundary, and techniques from the theory of viscosity solutions. acknowledgement: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 . I am very grateful to M. Gerencsér and J. Maas for proposing this problem as well as helpful discussions. Special thanks go to F. Cornalba for suggesting the additional κ-truncation in Proposition 5. I am also indebted to an anonymous referee for pointing out a gap in a previous version of the proof of Lemma 9 (concerning the treatment of the noise term). The issue is resolved in this version. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Sebastian full_name: Hensel, Sebastian id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87 last_name: Hensel orcid: 0000-0001-7252-8072 citation: ama: 'Hensel S. Finite time extinction for the 1D stochastic porous medium equation with transport noise. Stochastics and Partial Differential Equations: Analysis and Computations. 2021;9:892–939. doi:10.1007/s40072-021-00188-9' apa: 'Hensel, S. (2021). Finite time extinction for the 1D stochastic porous medium equation with transport noise. Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-021-00188-9' chicago: 'Hensel, Sebastian. “Finite Time Extinction for the 1D Stochastic Porous Medium Equation with Transport Noise.” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2021. https://doi.org/10.1007/s40072-021-00188-9.' ieee: 'S. Hensel, “Finite time extinction for the 1D stochastic porous medium equation with transport noise,” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 9. Springer Nature, pp. 892–939, 2021.' ista: 'Hensel S. 2021. Finite time extinction for the 1D stochastic porous medium equation with transport noise. Stochastics and Partial Differential Equations: Analysis and Computations. 9, 892–939.' mla: 'Hensel, Sebastian. “Finite Time Extinction for the 1D Stochastic Porous Medium Equation with Transport Noise.” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 9, Springer Nature, 2021, pp. 892–939, doi:10.1007/s40072-021-00188-9.' short: 'S. Hensel, Stochastics and Partial Differential Equations: Analysis and Computations 9 (2021) 892–939.' date_created: 2021-04-04T22:01:21Z date_published: 2021-03-21T00:00:00Z date_updated: 2023-08-07T14:31:59Z day: '21' ddc: - '510' department: - _id: JuFi doi: 10.1007/s40072-021-00188-9 ec_funded: 1 external_id: isi: - '000631001700001' file: - access_level: open_access checksum: 6529b609c9209861720ffa4685111bc6 content_type: application/pdf creator: dernst date_created: 2021-04-06T09:31:28Z date_updated: 2021-04-06T09:31:28Z file_id: '9309' file_name: 2021_StochPartDiffEquation_Hensel.pdf file_size: 727005 relation: main_file success: 1 file_date_updated: 2021-04-06T09:31:28Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 892–939 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: 'Stochastics and Partial Differential Equations: Analysis and Computations' publication_identifier: eissn: - 2194-041X issn: - 2194-0401 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Finite time extinction for the 1D stochastic porous medium equation with transport noise tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2021' ... --- _id: '9297' abstract: - lang: eng text: 'We report the results of an experimental investigation into the decay of turbulence in plane Couette–Poiseuille flow using ‘quench’ experiments where the flow laminarises after a sudden reduction in Reynolds number Re. Specifically, we study the velocity field in the streamwise–spanwise plane. We show that the spanwise velocity containing rolls decays faster than the streamwise velocity, which displays elongated regions of higher or lower velocity called streaks. At final Reynolds numbers above 425, the decay of streaks displays two stages: first a slow decay when rolls are present and secondly a more rapid decay of streaks alone. The difference in behaviour results from the regeneration of streaks by rolls, called the lift-up effect. We define the turbulent fraction as the portion of the flow containing turbulence and this is estimated by thresholding the spanwise velocity component. It decreases linearly with time in the whole range of final Re. The corresponding decay slope increases linearly with final Re. The extrapolated value at which this decay slope vanishes is Reaz≈656±10, close to Reg≈670 at which turbulence is self-sustained. The decay of the energy computed from the spanwise velocity component is found to be exponential. The corresponding decay rate increases linearly with Re, with an extrapolated vanishing value at ReAz≈688±10. This value is also close to the value at which the turbulence is self-sustained, showing that valuable information on the transition can be obtained over a wide range of Re.' acknowledgement: "We gratefully acknowledge Joran Rolland, Yohann Duguet, Romain Monchaux, S´ebastien Gom´e, Laurette Tuckerman, Dwight Barkley, Olivier Dauchot and Sabine Bottin for fruitful discussions. We thank Xavier Benoit-Gonin, Amaury Fourgeaud, Thierry Darnige, Olivier Brouard and Justine Laurent for technical help. This work has benefited from the ANR TransFlow, and by starting grants obtained by B.S. from CNRS (INSIS) and ESPCI. T.M. was\r\nsupported by a Joliot visiting professorship grant from ESPCI." article_number: A65 article_processing_charge: No article_type: original author: - first_name: T. full_name: Liu, T. last_name: Liu - first_name: B. full_name: Semin, B. last_name: Semin - first_name: Lukasz full_name: Klotz, Lukasz id: 2C9AF1C2-F248-11E8-B48F-1D18A9856A87 last_name: Klotz orcid: 0000-0003-1740-7635 - first_name: R. full_name: Godoy-Diana, R. last_name: Godoy-Diana - first_name: J. E. full_name: Wesfreid, J. E. last_name: Wesfreid - first_name: T. full_name: Mullin, T. last_name: Mullin citation: ama: Liu T, Semin B, Klotz L, Godoy-Diana R, Wesfreid JE, Mullin T. Decay of streaks and rolls in plane Couette-Poiseuille flow. Journal of Fluid Mechanics. 2021;915. doi:10.1017/jfm.2021.89 apa: Liu, T., Semin, B., Klotz, L., Godoy-Diana, R., Wesfreid, J. E., & Mullin, T. (2021). Decay of streaks and rolls in plane Couette-Poiseuille flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2021.89 chicago: Liu, T., B. Semin, Lukasz Klotz, R. Godoy-Diana, J. E. Wesfreid, and T. Mullin. “Decay of Streaks and Rolls in Plane Couette-Poiseuille Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2021.89. ieee: T. Liu, B. Semin, L. Klotz, R. Godoy-Diana, J. E. Wesfreid, and T. Mullin, “Decay of streaks and rolls in plane Couette-Poiseuille flow,” Journal of Fluid Mechanics, vol. 915. Cambridge University Press, 2021. ista: Liu T, Semin B, Klotz L, Godoy-Diana R, Wesfreid JE, Mullin T. 2021. Decay of streaks and rolls in plane Couette-Poiseuille flow. Journal of Fluid Mechanics. 915, A65. mla: Liu, T., et al. “Decay of Streaks and Rolls in Plane Couette-Poiseuille Flow.” Journal of Fluid Mechanics, vol. 915, A65, Cambridge University Press, 2021, doi:10.1017/jfm.2021.89. short: T. Liu, B. Semin, L. Klotz, R. Godoy-Diana, J.E. Wesfreid, T. Mullin, Journal of Fluid Mechanics 915 (2021). date_created: 2021-03-28T22:01:42Z date_published: 2021-03-17T00:00:00Z date_updated: 2023-08-07T14:30:11Z day: '17' department: - _id: BjHo doi: 10.1017/jfm.2021.89 external_id: arxiv: - '2008.08851' isi: - '000629677500001' intvolume: ' 915' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2008.08851 month: '03' oa: 1 oa_version: Preprint publication: Journal of Fluid Mechanics publication_identifier: eissn: - 1469-7645 issn: - 0022-1120 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Decay of streaks and rolls in plane Couette-Poiseuille flow type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 915 year: '2021' ... --- _id: '9295' abstract: - lang: eng text: "Hill's Conjecture states that the crossing number cr(\U0001D43E\U0001D45B) \ of the complete graph \U0001D43E\U0001D45B in the plane (equivalently, the sphere) is 14⌊\U0001D45B2⌋⌊\U0001D45B−12⌋⌊\U0001D45B−22⌋⌊\U0001D45B−32⌋=\U0001D45B4/64+\U0001D442(\U0001D45B3) . Moon proved that the expected number of crossings in a spherical drawing in which the points are randomly distributed and joined by geodesics is precisely \ \U0001D45B4/64+\U0001D442(\U0001D45B3) , thus matching asymptotically the conjectured value of cr(\U0001D43E\U0001D45B) . Let cr\U0001D443(\U0001D43A) denote the crossing number of a graph \U0001D43A in the projective plane. Recently, Elkies proved that the expected number of crossings in a naturally defined random projective plane drawing of \U0001D43E\U0001D45B is (\U0001D45B4/8\U0001D70B2)+\U0001D442(\U0001D45B3) . In analogy with the relation of Moon's result to Hill's conjecture, Elkies asked if lim\U0001D45B→∞ cr\U0001D443(\U0001D43E\U0001D45B)/\U0001D45B4=1/8\U0001D70B2 . We construct drawings of \U0001D43E\U0001D45B in the projective plane that disprove this." acknowledgement: "We thank two reviewers for their corrections and suggestions on the original version of this\r\npaper. This project has received funding from NSERC Grant 50503-10940-500 and from the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie grant agreement No 754411, IST, Klosterneuburg, Austria." article_processing_charge: No article_type: original author: - first_name: Alan M full_name: Arroyo Guevara, Alan M id: 3207FDC6-F248-11E8-B48F-1D18A9856A87 last_name: Arroyo Guevara orcid: 0000-0003-2401-8670 - first_name: Dan full_name: Mcquillan, Dan last_name: Mcquillan - first_name: R. Bruce full_name: Richter, R. Bruce last_name: Richter - first_name: Gelasio full_name: Salazar, Gelasio last_name: Salazar - first_name: Matthew full_name: Sullivan, Matthew last_name: Sullivan citation: ama: Arroyo Guevara AM, Mcquillan D, Richter RB, Salazar G, Sullivan M. Drawings of complete graphs in the projective plane. Journal of Graph Theory. 2021;97(3):426-440. doi:10.1002/jgt.22665 apa: Arroyo Guevara, A. M., Mcquillan, D., Richter, R. B., Salazar, G., & Sullivan, M. (2021). Drawings of complete graphs in the projective plane. Journal of Graph Theory. Wiley. https://doi.org/10.1002/jgt.22665 chicago: Arroyo Guevara, Alan M, Dan Mcquillan, R. Bruce Richter, Gelasio Salazar, and Matthew Sullivan. “Drawings of Complete Graphs in the Projective Plane.” Journal of Graph Theory. Wiley, 2021. https://doi.org/10.1002/jgt.22665. ieee: A. M. Arroyo Guevara, D. Mcquillan, R. B. Richter, G. Salazar, and M. Sullivan, “Drawings of complete graphs in the projective plane,” Journal of Graph Theory, vol. 97, no. 3. Wiley, pp. 426–440, 2021. ista: Arroyo Guevara AM, Mcquillan D, Richter RB, Salazar G, Sullivan M. 2021. Drawings of complete graphs in the projective plane. Journal of Graph Theory. 97(3), 426–440. mla: Arroyo Guevara, Alan M., et al. “Drawings of Complete Graphs in the Projective Plane.” Journal of Graph Theory, vol. 97, no. 3, Wiley, 2021, pp. 426–40, doi:10.1002/jgt.22665. short: A.M. Arroyo Guevara, D. Mcquillan, R.B. Richter, G. Salazar, M. Sullivan, Journal of Graph Theory 97 (2021) 426–440. date_created: 2021-03-28T22:01:41Z date_published: 2021-03-23T00:00:00Z date_updated: 2023-08-07T14:26:15Z day: '23' department: - _id: UlWa doi: 10.1002/jgt.22665 ec_funded: 1 external_id: arxiv: - '2002.02287' isi: - '000631693200001' intvolume: ' 97' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2002.02287 month: '03' oa: 1 oa_version: Preprint page: 426-440 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of Graph Theory publication_identifier: eissn: - 1097-0118 issn: - 0364-9024 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Drawings of complete graphs in the projective plane type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 97 year: '2021' ... --- _id: '9294' abstract: - lang: eng text: In this issue of Developmental Cell, Doyle and colleagues identify periodic anterior contraction as a characteristic feature of fibroblasts and mesenchymal cancer cells embedded in 3D collagen gels. This contractile mechanism generates a matrix prestrain required for crawling in fibrous 3D environments. article_processing_charge: No article_type: original author: - first_name: Florian R full_name: Gärtner, Florian R id: 397A88EE-F248-11E8-B48F-1D18A9856A87 last_name: Gärtner orcid: 0000-0001-6120-3723 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Gärtner FR, Sixt MK. Engaging the front wheels to drive through fibrous terrain. Developmental Cell. 2021;56(6):723-725. doi:10.1016/j.devcel.2021.03.002 apa: Gärtner, F. R., & Sixt, M. K. (2021). Engaging the front wheels to drive through fibrous terrain. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2021.03.002 chicago: Gärtner, Florian R, and Michael K Sixt. “Engaging the Front Wheels to Drive through Fibrous Terrain.” Developmental Cell. Elsevier, 2021. https://doi.org/10.1016/j.devcel.2021.03.002. ieee: F. R. Gärtner and M. K. Sixt, “Engaging the front wheels to drive through fibrous terrain,” Developmental Cell, vol. 56, no. 6. Elsevier, pp. 723–725, 2021. ista: Gärtner FR, Sixt MK. 2021. Engaging the front wheels to drive through fibrous terrain. Developmental Cell. 56(6), 723–725. mla: Gärtner, Florian R., and Michael K. Sixt. “Engaging the Front Wheels to Drive through Fibrous Terrain.” Developmental Cell, vol. 56, no. 6, Elsevier, 2021, pp. 723–25, doi:10.1016/j.devcel.2021.03.002. short: F.R. Gärtner, M.K. Sixt, Developmental Cell 56 (2021) 723–725. date_created: 2021-03-28T22:01:41Z date_published: 2021-03-22T00:00:00Z date_updated: 2023-08-07T14:26:47Z day: '22' department: - _id: MiSi doi: 10.1016/j.devcel.2021.03.002 external_id: isi: - '000631681200004' pmid: - '33756118' intvolume: ' 56' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.devcel.2021.03.002 month: '03' oa: 1 oa_version: Published Version page: 723-725 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: Engaging the front wheels to drive through fibrous terrain type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 56 year: '2021' ... --- _id: '9329' abstract: - lang: eng text: "Background: To understand information coding in single neurons, it is necessary to analyze subthreshold synaptic events, action potentials (APs), and their interrelation in different behavioral states. However, detecting excitatory postsynaptic potentials (EPSPs) or currents (EPSCs) in behaving animals remains challenging, because of unfavorable signal-to-noise ratio, high frequency, fluctuating amplitude, and variable time course of synaptic events.\r\nNew method: We developed a method for synaptic event detection, termed MOD (Machine-learning Optimal-filtering Detection-procedure), which combines concepts of supervised machine learning and optimal Wiener filtering. Experts were asked to manually score short epochs of data. The algorithm was trained to obtain the optimal filter coefficients of a Wiener filter and the optimal detection threshold. Scored and unscored data were then processed with the optimal filter, and events were detected as peaks above threshold.\r\nResults: We challenged MOD with EPSP traces in vivo in mice during spatial navigation and EPSC traces in vitro in slices under conditions of enhanced transmitter release. The area under the curve (AUC) of the receiver operating characteristics (ROC) curve was, on average, 0.894 for in vivo and 0.969 for in vitro data sets, indicating high detection accuracy and efficiency.\r\nComparison with existing methods: When benchmarked using a (1 − AUC)−1 metric, MOD outperformed previous methods (template-fit, deconvolution, and Bayesian methods) by an average factor of 3.13 for in vivo data sets, but showed comparable (template-fit, deconvolution) or higher (Bayesian) computational efficacy.\r\nConclusions: MOD may become an important new tool for large-scale, real-time analysis of synaptic activity." acknowledged_ssus: - _id: SSU acknowledgement: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J.). We thank Drs. Jozsef Csicsvari, Christoph Lampert, and Federico Stella for critically reading previous manuscript versions. We are also grateful to Drs. Josh Merel and Ben Shababo for their help with applying the Bayesian detection method to our data. We also thank Florian Marr for technical assistance, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support. article_number: '109125' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Xiaomin full_name: Zhang, Xiaomin id: 423EC9C2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: 'Zhang X, Schlögl A, Vandael DH, Jonas PM. MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. 2021;357(6). doi:10.1016/j.jneumeth.2021.109125' apa: 'Zhang, X., Schlögl, A., Vandael, D. H., & Jonas, P. M. (2021). MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. Elsevier. https://doi.org/10.1016/j.jneumeth.2021.109125' chicago: 'Zhang, Xiaomin, Alois Schlögl, David H Vandael, and Peter M Jonas. “MOD: A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.” Journal of Neuroscience Methods. Elsevier, 2021. https://doi.org/10.1016/j.jneumeth.2021.109125.' ieee: 'X. Zhang, A. Schlögl, D. H. Vandael, and P. M. Jonas, “MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo,” Journal of Neuroscience Methods, vol. 357, no. 6. Elsevier, 2021.' ista: 'Zhang X, Schlögl A, Vandael DH, Jonas PM. 2021. MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. 357(6), 109125.' mla: 'Zhang, Xiaomin, et al. “MOD: A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.” Journal of Neuroscience Methods, vol. 357, no. 6, 109125, Elsevier, 2021, doi:10.1016/j.jneumeth.2021.109125.' short: X. Zhang, A. Schlögl, D.H. Vandael, P.M. Jonas, Journal of Neuroscience Methods 357 (2021). date_created: 2021-04-18T22:01:39Z date_published: 2021-03-09T00:00:00Z date_updated: 2023-08-07T14:36:14Z day: '09' ddc: - '570' department: - _id: PeJo - _id: ScienComp doi: 10.1016/j.jneumeth.2021.109125 ec_funded: 1 external_id: isi: - '000661088500005' file: - access_level: open_access checksum: 2a5800d91b96d08b525e17319dcd5e44 content_type: application/pdf creator: dernst date_created: 2021-04-19T08:30:22Z date_updated: 2021-04-19T08:30:22Z file_id: '9339' file_name: 2021_JourNeuroscienceMeth_Zhang.pdf file_size: 6924738 relation: main_file success: 1 file_date_updated: 2021-04-19T08:30:22Z has_accepted_license: '1' intvolume: ' 357' isi: 1 issue: '6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize publication: Journal of Neuroscience Methods publication_identifier: eissn: - 1872-678X issn: - 0165-0270 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 357 year: '2021' ... --- _id: '9316' abstract: - lang: eng text: Embryo morphogenesis is impacted by dynamic changes in tissue material properties, which have been proposed to occur via processes akin to phase transitions (PTs). Here, we show that rigidity percolation provides a simple and robust theoretical framework to predict material/structural PTs of embryonic tissues from local cell connectivity. By using percolation theory, combined with directly monitoring dynamic changes in tissue rheology and cell contact mechanics, we demonstrate that the zebrafish blastoderm undergoes a genuine rigidity PT, brought about by a small reduction in adhesion-dependent cell connectivity below a critical value. We quantitatively predict and experimentally verify hallmarks of PTs, including power-law exponents and associated discontinuities of macroscopic observables. Finally, we show that this uniform PT depends on blastoderm cells undergoing meta-synchronous divisions causing random and, consequently, uniform changes in cell connectivity. Collectively, our theoretical and experimental findings reveal the structural basis of material PTs in an organismal context. acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: We thank Carl Goodrich and the members of the Heisenberg and Hannezo groups, in particular Reka Korei, for help, technical advice, and discussions; and the Bioimaging and zebrafish facilities of the IST Austria for continuous support. This work was supported by the Elise Richter Program of Austrian Science Fund (FWF) to N.I.P. ( V 736-B26 ) and the European Union (European Research Council Advanced Grant 742573 to C.-P.H. and European Research Council Starting Grant 851288 to E.H.). article_processing_charge: No article_type: original author: - first_name: Nicoletta full_name: Petridou, Nicoletta id: 2A003F6C-F248-11E8-B48F-1D18A9856A87 last_name: Petridou orcid: 0000-0002-8451-1195 - first_name: Bernat full_name: Corominas-Murtra, Bernat id: 43BE2298-F248-11E8-B48F-1D18A9856A87 last_name: Corominas-Murtra orcid: 0000-0001-9806-5643 - 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: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. 2021;184(7):1914-1928.e19. doi:10.1016/j.cell.2021.02.017 apa: Petridou, N., Corominas-Murtra, B., Heisenberg, C.-P. J., & Hannezo, E. B. (2021). Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. Elsevier. https://doi.org/10.1016/j.cell.2021.02.017 chicago: Petridou, Nicoletta, Bernat Corominas-Murtra, Carl-Philipp J Heisenberg, and Edouard B Hannezo. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” Cell. Elsevier, 2021. https://doi.org/10.1016/j.cell.2021.02.017. ieee: N. Petridou, B. Corominas-Murtra, C.-P. J. Heisenberg, and E. B. Hannezo, “Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions,” Cell, vol. 184, no. 7. Elsevier, p. 1914–1928.e19, 2021. ista: Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. 2021. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. 184(7), 1914–1928.e19. mla: Petridou, Nicoletta, et al. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” Cell, vol. 184, no. 7, Elsevier, 2021, p. 1914–1928.e19, doi:10.1016/j.cell.2021.02.017. short: N. Petridou, B. Corominas-Murtra, C.-P.J. Heisenberg, E.B. Hannezo, Cell 184 (2021) 1914–1928.e19. date_created: 2021-04-11T22:01:14Z date_published: 2021-04-01T00:00:00Z date_updated: 2023-08-07T14:33:59Z day: '01' ddc: - '570' department: - _id: CaHe - _id: EdHa doi: 10.1016/j.cell.2021.02.017 ec_funded: 1 external_id: isi: - '000636734000022' pmid: - '33730596' file: - access_level: open_access checksum: 1e5295fbd9c2a459173ec45a0e8a7c2e content_type: application/pdf creator: cziletti date_created: 2021-06-08T10:04:10Z date_updated: 2021-06-08T10:04:10Z file_id: '9534' file_name: 2021_Cell_Petridou.pdf file_size: 11405875 relation: main_file success: 1 file_date_updated: 2021-06-08T10:04:10Z has_accepted_license: '1' intvolume: ' 184' isi: 1 issue: '7' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1914-1928.e19 pmid: 1 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis - _id: 2693FD8C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: V00736 name: Tissue material properties in embryonic development publication: Cell publication_identifier: eissn: - '10974172' issn: - '00928674' publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/embryonic-tissue-undergoes-phase-transition/ scopus_import: '1' status: public title: Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions 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: 184 year: '2021' ... --- _id: '9317' abstract: - lang: eng text: Given a locally finite X⊆Rd and a radius r≥0, the k-fold cover of X and r consists of all points in Rd that have k or more points of X within distance r. We consider two filtrations—one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k—and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in Rd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module of Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. acknowledgement: "This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha), and by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through Grant No. I02979-N35 of the Austrian Science Fund (FWF)\r\nOpen Access funding provided by the Institute of Science and Technology (IST Austria)." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Georg F full_name: Osang, Georg F id: 464B40D6-F248-11E8-B48F-1D18A9856A87 last_name: Osang citation: ama: Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. Discrete and Computational Geometry. 2021;65:1296–1313. doi:10.1007/s00454-021-00281-9 apa: Edelsbrunner, H., & Osang, G. F. (2021). The multi-cover persistence of Euclidean balls. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-021-00281-9 chicago: Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-021-00281-9. ieee: H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” Discrete and Computational Geometry, vol. 65. Springer Nature, pp. 1296–1313, 2021. ista: Edelsbrunner H, Osang GF. 2021. The multi-cover persistence of Euclidean balls. Discrete and Computational Geometry. 65, 1296–1313. mla: Edelsbrunner, Herbert, and Georg F. Osang. “The Multi-Cover Persistence of Euclidean Balls.” Discrete and Computational Geometry, vol. 65, Springer Nature, 2021, pp. 1296–1313, doi:10.1007/s00454-021-00281-9. short: H. Edelsbrunner, G.F. Osang, Discrete and Computational Geometry 65 (2021) 1296–1313. date_created: 2021-04-11T22:01:15Z date_published: 2021-03-31T00:00:00Z date_updated: 2023-08-07T14:35:44Z day: '31' ddc: - '516' department: - _id: HeEd doi: 10.1007/s00454-021-00281-9 ec_funded: 1 external_id: isi: - '000635460400001' file: - access_level: open_access checksum: 59b4e1e827e494209bcb4aae22e1d347 content_type: application/pdf creator: cchlebak date_created: 2021-12-01T10:56:53Z date_updated: 2021-12-01T10:56:53Z file_id: '10394' file_name: 2021_DisCompGeo_Edelsbrunner_Osang.pdf file_size: 677704 relation: main_file success: 1 file_date_updated: 2021-12-01T10:56:53Z has_accepted_license: '1' intvolume: ' 65' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1296–1313 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: Discrete and Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '187' relation: earlier_version status: public scopus_import: '1' status: public title: The multi-cover persistence of Euclidean balls 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: 65 year: '2021' ... --- _id: '9318' abstract: - lang: eng text: We consider a system of N bosons in the mean-field scaling regime for a class of interactions including the repulsive Coulomb potential. We derive an asymptotic expansion of the low-energy eigenstates and the corresponding energies, which provides corrections to Bogoliubov theory to any order in 1/N. acknowledgement: The first author gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 754411. The third author was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227). article_number: e28 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lea full_name: Bossmann, Lea id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425 last_name: Bossmann orcid: 0000-0002-6854-1343 - first_name: Sören P full_name: Petrat, Sören P id: 40AC02DC-F248-11E8-B48F-1D18A9856A87 last_name: Petrat orcid: 0000-0002-9166-5889 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Bossmann L, Petrat SP, Seiringer R. Asymptotic expansion of low-energy excitations for weakly interacting bosons. Forum of Mathematics, Sigma. 2021;9. doi:10.1017/fms.2021.22 apa: Bossmann, L., Petrat, S. P., & Seiringer, R. (2021). Asymptotic expansion of low-energy excitations for weakly interacting bosons. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2021.22 chicago: Bossmann, Lea, Sören P Petrat, and Robert Seiringer. “Asymptotic Expansion of Low-Energy Excitations for Weakly Interacting Bosons.” Forum of Mathematics, Sigma. Cambridge University Press, 2021. https://doi.org/10.1017/fms.2021.22. ieee: L. Bossmann, S. P. Petrat, and R. Seiringer, “Asymptotic expansion of low-energy excitations for weakly interacting bosons,” Forum of Mathematics, Sigma, vol. 9. Cambridge University Press, 2021. ista: Bossmann L, Petrat SP, Seiringer R. 2021. Asymptotic expansion of low-energy excitations for weakly interacting bosons. Forum of Mathematics, Sigma. 9, e28. mla: Bossmann, Lea, et al. “Asymptotic Expansion of Low-Energy Excitations for Weakly Interacting Bosons.” Forum of Mathematics, Sigma, vol. 9, e28, Cambridge University Press, 2021, doi:10.1017/fms.2021.22. short: L. Bossmann, S.P. Petrat, R. Seiringer, Forum of Mathematics, Sigma 9 (2021). date_created: 2021-04-11T22:01:15Z date_published: 2021-03-26T00:00:00Z date_updated: 2023-08-07T14:35:06Z day: '26' ddc: - '510' department: - _id: RoSe doi: 10.1017/fms.2021.22 ec_funded: 1 external_id: isi: - '000634006900001' file: - access_level: open_access checksum: 17a3e6786d1e930cf0c14a880a6d7e92 content_type: application/pdf creator: dernst date_created: 2021-04-12T07:15:58Z date_updated: 2021-04-12T07:15:58Z file_id: '9319' file_name: 2021_ForumMath_Bossmann.pdf file_size: 883851 relation: main_file success: 1 file_date_updated: 2021-04-12T07:15:58Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Forum of Mathematics, Sigma publication_identifier: eissn: - '20505094' publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Asymptotic expansion of low-energy excitations for weakly interacting bosons tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2021' ... --- _id: '9331' abstract: - lang: eng text: 'Quantum entanglement has been generated and verified in cold-atom experiments and used to make atom-interferometric measurements below the shot-noise limit. However, current state-of-the-art cold-atom devices exploit separable (i.e., unentangled) atomic states. This perspective piece asks the question: can entanglement usefully improve cold-atom sensors, in the sense that it gives new sensing capabilities unachievable with current state-of-the-art devices? We briefly review the state-of-the-art in precision cold-atom sensing, focusing on clocks and inertial sensors, identifying the potential benefits entanglement could bring to these devices, and the challenges that need to be overcome to realize these benefits. We survey demonstrated methods of generating metrologically useful entanglement in cold-atom systems, note their relative strengths and weaknesses, and assess their prospects for near-to-medium term quantum-enhanced cold-atom sensing.' acknowledgement: We acknowledge fruitful discussions with John Close, Chris Freier, Kyle Hardman, Joseph Hope, and Paul Wigley, and insightful suggestions made by Franck Pereira dos Santos on behalf of the Atom Interferometry and Inertial Sensors team at SYRTE. S.S.S. was supported by an Australian Research Council Discovery Early Career Researcher Award (DECRA), Project No. DE200100495. O.H. was supported by IST Austria. article_number: '140501' article_processing_charge: No article_type: original author: - first_name: Stuart S. full_name: Szigeti, Stuart S. last_name: Szigeti - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Simon A. full_name: Haine, Simon A. last_name: Haine citation: ama: 'Szigeti SS, Hosten O, Haine SA. Improving cold-atom sensors with quantum entanglement: Prospects and challenges. Applied Physics Letters. 2021;118(14). doi:10.1063/5.0050235' apa: 'Szigeti, S. S., Hosten, O., & Haine, S. A. (2021). Improving cold-atom sensors with quantum entanglement: Prospects and challenges. Applied Physics Letters. AIP Publishing. https://doi.org/10.1063/5.0050235' chicago: 'Szigeti, Stuart S., Onur Hosten, and Simon A. Haine. “Improving Cold-Atom Sensors with Quantum Entanglement: Prospects and Challenges.” Applied Physics Letters. AIP Publishing, 2021. https://doi.org/10.1063/5.0050235.' ieee: 'S. S. Szigeti, O. Hosten, and S. A. Haine, “Improving cold-atom sensors with quantum entanglement: Prospects and challenges,” Applied Physics Letters, vol. 118, no. 14. AIP Publishing, 2021.' ista: 'Szigeti SS, Hosten O, Haine SA. 2021. Improving cold-atom sensors with quantum entanglement: Prospects and challenges. Applied Physics Letters. 118(14), 140501.' mla: 'Szigeti, Stuart S., et al. “Improving Cold-Atom Sensors with Quantum Entanglement: Prospects and Challenges.” Applied Physics Letters, vol. 118, no. 14, 140501, AIP Publishing, 2021, doi:10.1063/5.0050235.' short: S.S. Szigeti, O. Hosten, S.A. Haine, Applied Physics Letters 118 (2021). date_created: 2021-04-18T22:01:40Z date_published: 2021-04-07T00:00:00Z date_updated: 2023-08-07T14:36:42Z day: '07' department: - _id: OnHo doi: 10.1063/5.0050235 external_id: arxiv: - '2010.09168' isi: - '000637702100001' intvolume: ' 118' isi: 1 issue: '14' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2010.09168 month: '04' oa: 1 oa_version: Preprint publication: Applied Physics Letters publication_identifier: issn: - '00036951' publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'Improving cold-atom sensors with quantum entanglement: Prospects and challenges' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 118 year: '2021' ... --- _id: '9330' abstract: - lang: eng text: In nerve cells the genes encoding for α2δ subunits of voltage-gated calcium channels have been linked to synaptic functions and neurological disease. Here we show that α2δ subunits are essential for the formation and organization of glutamatergic synapses. Using a cellular α2δ subunit triple-knockout/knockdown model, we demonstrate a failure in presynaptic differentiation evidenced by defective presynaptic calcium channel clustering and calcium influx, smaller presynaptic active zones, and a strongly reduced accumulation of presynaptic vesicle-associated proteins (synapsin and vGLUT). The presynaptic defect is associated with the downscaling of postsynaptic AMPA receptors and the postsynaptic density. The role of α2δ isoforms as synaptic organizers is highly redundant, as each individual α2δ isoform can rescue presynaptic calcium channel trafficking and expression of synaptic proteins. Moreover, α2δ-2 and α2δ-3 with mutated metal ion-dependent adhesion sites can fully rescue presynaptic synapsin expression but only partially calcium channel trafficking, suggesting that the regulatory role of α2δ subunits is independent from its role as a calcium channel subunit. Our findings influence the current view on excitatory synapse formation. First, our study suggests that postsynaptic differentiation is secondary to presynaptic differentiation. Second, the dependence of presynaptic differentiation on α2δ implicates α2δ subunits as potential nucleation points for the organization of synapses. Finally, our results suggest that α2δ subunits act as transsynaptic organizers of glutamatergic synapses, thereby aligning the synaptic active zone with the postsynaptic density. acknowledged_ssus: - _id: EM-Fac acknowledgement: "We thank Arnold Schwartz for providing α2δ-1 knockout mice; Ariane Benedetti, Sabine Baumgartner, Sandra Demetz, and Irene Mahlknecht for technical support; Nadine Ortner and Andreas Lieb for electrophysiological experiments; the team of the Electron Microscopy Facility at the Institute of Science and Technology Austria for technical support related to ultrastructural analysis; Hermann Dietrich and Anja Beierfuß and her team for animal care; Jutta Engel and Jörg Striessnig for critical discussions; and Bruno Benedetti and Bernhard Flucher for critical discussions and reading the manuscript. This study was supported by Austrian Science Fund Grants P24079, F44060, F44150, and DOC30-B30 (to G.J.O.) and T855 (to M.C.), European Research Council Grant AdG 694539 (to R.S.), Deutsche Forschungsgemeinschaft\r\nGrant SFB1348-TP A03 (to M.M.), and Interdisziplinäre Zentrum für Klinische Forschung Münster Grant Mi3/004/19 (to M.M.). This work is part of the PhD theses of C.L.S., S.M.G., and C.A." article_processing_charge: No article_type: original author: - first_name: Clemens L. full_name: Schöpf, Clemens L. last_name: Schöpf - first_name: Cornelia full_name: Ablinger, Cornelia last_name: Ablinger - first_name: Stefanie M. full_name: Geisler, Stefanie M. last_name: Geisler - first_name: Ruslan I. full_name: Stanika, Ruslan I. last_name: Stanika - first_name: Marta full_name: Campiglio, Marta last_name: Campiglio - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Benedikt full_name: Nimmervoll, Benedikt last_name: Nimmervoll - first_name: Bettina full_name: Schlick, Bettina last_name: Schlick - first_name: Johannes full_name: Brockhaus, Johannes last_name: Brockhaus - first_name: Markus full_name: Missler, Markus last_name: Missler - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Gerald J. full_name: Obermair, Gerald J. last_name: Obermair citation: ama: Schöpf CL, Ablinger C, Geisler SM, et al. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. PNAS. 2021;118(14). doi:10.1073/pnas.1920827118 apa: Schöpf, C. L., Ablinger, C., Geisler, S. M., Stanika, R. I., Campiglio, M., Kaufmann, W., … Obermair, G. J. (2021). Presynaptic α2δ subunits are key organizers of glutamatergic synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1920827118 chicago: Schöpf, Clemens L., Cornelia Ablinger, Stefanie M. Geisler, Ruslan I. Stanika, Marta Campiglio, Walter Kaufmann, Benedikt Nimmervoll, et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” PNAS. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.1920827118. ieee: C. L. Schöpf et al., “Presynaptic α2δ subunits are key organizers of glutamatergic synapses,” PNAS, vol. 118, no. 14. National Academy of Sciences, 2021. ista: Schöpf CL, Ablinger C, Geisler SM, Stanika RI, Campiglio M, Kaufmann W, Nimmervoll B, Schlick B, Brockhaus J, Missler M, Shigemoto R, Obermair GJ. 2021. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. PNAS. 118(14). mla: Schöpf, Clemens L., et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” PNAS, vol. 118, no. 14, National Academy of Sciences, 2021, doi:10.1073/pnas.1920827118. short: C.L. Schöpf, C. Ablinger, S.M. Geisler, R.I. Stanika, M. Campiglio, W. Kaufmann, B. Nimmervoll, B. Schlick, J. Brockhaus, M. Missler, R. Shigemoto, G.J. Obermair, PNAS 118 (2021). date_created: 2021-04-18T22:01:40Z date_published: 2021-04-06T00:00:00Z date_updated: 2023-08-08T13:08:47Z day: '06' ddc: - '570' department: - _id: EM-Fac - _id: RySh doi: 10.1073/pnas.1920827118 ec_funded: 1 external_id: isi: - '000637398300002' file: - access_level: open_access checksum: dd014f68ae9d7d8d8fc4139a24e04506 content_type: application/pdf creator: dernst date_created: 2021-04-19T10:10:56Z date_updated: 2021-04-19T10:10:56Z file_id: '9340' file_name: 2021_PNAS_Schoepf.pdf file_size: 2603911 relation: main_file success: 1 file_date_updated: 2021-04-19T10:10:56Z has_accepted_license: '1' intvolume: ' 118' isi: 1 issue: '14' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 25CA28EA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694539' name: 'In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour' publication: PNAS publication_identifier: eissn: - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Presynaptic α2δ subunits are key organizers of glutamatergic synapses 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: 118 year: '2021' ... --- _id: '9332' abstract: - lang: eng text: Lateral root (LR) formation is an example of a plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE (PKL) negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Here we show that PKL interacts with RETINOBLASTOMA-RELATED 1 (RBR1) to repress the LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) promoter activity. Since LBD16 function is required for the formative division of LR founder cells, repression mediated by the PKL–RBR1 complex negatively regulates formative division and LR formation. Inhibition of LR formation by PKL–RBR1 is counteracted by auxin, indicating that, in addition to auxin-mediated transcriptional responses, the fine-tuned process of LR formation is also controlled at the chromatin level in an auxin-signaling dependent manner. acknowledgement: "This research was supported by a postdoctoral fellowship of the Carl Tryggers Foundation (to K.Ö.) and by grants from Vetenskapsrådet (Nr.: 621-2004-2921 to L.B.) and VINNOVA (to L.B. and S.R.).\r\nWe thank Frederic Berger, Hidehiro Fukaki, Malcolm Bennett, Claudia Köhler, Jiri Friml for providing pRBR1::RBR1-RFP, ssl2-1, slr-1, pPKL::PKL-GFP seeds and the DR5 expressing vector, respectively. Authors are grateful to Hayashi Kenichiro for providing the auxinol compound and to Rishi Bhalerao for stimulating discussions. The technical help of Adeline Rigal and Thomas Vain with the auxinol experiments is much appreciated." article_number: '3862' article_processing_charge: No article_type: original author: - first_name: Krisztina full_name: Ötvös, Krisztina id: 29B901B0-F248-11E8-B48F-1D18A9856A87 last_name: Ötvös orcid: 0000-0002-5503-4983 - first_name: Pál full_name: Miskolczi, Pál last_name: Miskolczi - first_name: Peter full_name: Marhavý, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavý orcid: 0000-0001-5227-5741 - first_name: Alfredo full_name: Cruz-Ramírez, Alfredo last_name: Cruz-Ramírez - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: László full_name: Bakó, László last_name: Bakó citation: ama: Ötvös K, Miskolczi P, Marhavý P, et al. Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. International Journal of Molecular Sciences. 2021;22(8). doi:10.3390/ijms22083862 apa: Ötvös, K., Miskolczi, P., Marhavý, P., Cruz-Ramírez, A., Benková, E., Robert, S., & Bakó, L. (2021). Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22083862 chicago: Ötvös, Krisztina, Pál Miskolczi, Peter Marhavý, Alfredo Cruz-Ramírez, Eva Benková, Stéphanie Robert, and László Bakó. “Pickle Recruits Retinoblastoma Related 1 to Control Lateral Root Formation in Arabidopsis.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22083862. ieee: K. Ötvös et al., “Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis,” International Journal of Molecular Sciences, vol. 22, no. 8. MDPI, 2021. ista: Ötvös K, Miskolczi P, Marhavý P, Cruz-Ramírez A, Benková E, Robert S, Bakó L. 2021. Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. International Journal of Molecular Sciences. 22(8), 3862. mla: Ötvös, Krisztina, et al. “Pickle Recruits Retinoblastoma Related 1 to Control Lateral Root Formation in Arabidopsis.” International Journal of Molecular Sciences, vol. 22, no. 8, 3862, MDPI, 2021, doi:10.3390/ijms22083862. short: K. Ötvös, P. Miskolczi, P. Marhavý, A. Cruz-Ramírez, E. Benková, S. Robert, L. Bakó, International Journal of Molecular Sciences 22 (2021). date_created: 2021-04-18T22:01:41Z date_published: 2021-04-08T00:00:00Z date_updated: 2023-08-08T13:09:58Z day: '08' ddc: - '570' department: - _id: EvBe doi: 10.3390/ijms22083862 external_id: isi: - '000644394800001' file: - access_level: open_access checksum: 26ada2531ad1f9c01a1664de0431f1fe content_type: application/pdf creator: dernst date_created: 2021-04-19T10:54:55Z date_updated: 2021-04-19T10:54:55Z file_id: '9342' file_name: 2021_JourMolecularScience_Oetvoes.pdf file_size: 2769717 relation: main_file success: 1 file_date_updated: 2021-04-19T10:54:55Z has_accepted_license: '1' intvolume: ' 22' isi: 1 issue: '8' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: International Journal of Molecular Sciences publication_identifier: eissn: - 1422-0067 issn: - 1661-6596 publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 22 year: '2021' ... --- _id: '9333' abstract: - lang: eng text: We revise a previous result about the Fröhlich dynamics in the strong coupling limit obtained in Griesemer (Rev Math Phys 29(10):1750030, 2017). In the latter it was shown that the Fröhlich time evolution applied to the initial state φ0⊗ξα, where φ0 is the electron ground state of the Pekar energy functional and ξα the associated coherent state of the phonons, can be approximated by a global phase for times small compared to α2. In the present note we prove that a similar approximation holds for t=O(α2) if one includes a nontrivial effective dynamics for the phonons that is generated by an operator proportional to α−2 and quadratic in creation and annihilation operators. Our result implies that the electron ground state remains close to its initial state for times of order α2, while the phonon fluctuations around the coherent state ξα can be described by a time-dependent Bogoliubov transformation. acknowledgement: 'I thank Marcel Griesemer for many interesting discussions about the Fröhlich polaron and also for valuable comments on this manuscript. Helpful discussions with Nikolai Leopold and Robert Seiringer are also gratefully acknowledged. This work was partially supported by the Deutsche Forschungsgemeinschaft (DFG) through the Research Training Group 1838: Spectral Theory and Dynamics of Quantum Systems. Open Access funding enabled and organized by Projekt DEAL.' article_number: '45' article_processing_charge: No article_type: original author: - first_name: David Johannes full_name: Mitrouskas, David Johannes id: cbddacee-2b11-11eb-a02e-a2e14d04e52d last_name: Mitrouskas citation: ama: Mitrouskas DJ. A note on the Fröhlich dynamics in the strong coupling limit. Letters in Mathematical Physics. 2021;111. doi:10.1007/s11005-021-01380-7 apa: Mitrouskas, D. J. (2021). A note on the Fröhlich dynamics in the strong coupling limit. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-021-01380-7 chicago: Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong Coupling Limit.” Letters in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s11005-021-01380-7. ieee: D. J. Mitrouskas, “A note on the Fröhlich dynamics in the strong coupling limit,” Letters in Mathematical Physics, vol. 111. Springer Nature, 2021. ista: Mitrouskas DJ. 2021. A note on the Fröhlich dynamics in the strong coupling limit. Letters in Mathematical Physics. 111, 45. mla: Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong Coupling Limit.” Letters in Mathematical Physics, vol. 111, 45, Springer Nature, 2021, doi:10.1007/s11005-021-01380-7. short: D.J. Mitrouskas, Letters in Mathematical Physics 111 (2021). date_created: 2021-04-18T22:01:41Z date_published: 2021-04-05T00:00:00Z date_updated: 2023-08-08T13:09:28Z day: '05' ddc: - '510' department: - _id: RoSe doi: 10.1007/s11005-021-01380-7 external_id: isi: - '000637359300002' file: - access_level: open_access checksum: be56c0845a43c0c5c772ee0b5053f7d7 content_type: application/pdf creator: dernst date_created: 2021-04-19T10:40:01Z date_updated: 2021-04-19T10:40:01Z file_id: '9341' file_name: 2021_LettersMathPhysics_Mitrouskas.pdf file_size: 438084 relation: main_file success: 1 file_date_updated: 2021-04-19T10:40:01Z has_accepted_license: '1' intvolume: ' 111' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Letters in Mathematical Physics publication_identifier: eissn: - '15730530' issn: - '03779017' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A note on the Fröhlich dynamics in the strong coupling limit 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: 111 year: '2021' ... --- _id: '9335' abstract: - lang: eng text: 'Various degenerate diffusion equations exhibit a waiting time phenomenon: depending on the “flatness” of the compactly supported initial datum at the boundary of the support, the support of the solution may not expand for a certain amount of time. We show that this phenomenon is captured by particular Lagrangian discretizations of the porous medium and the thin film equations, and we obtain sufficient criteria for the occurrence of waiting times that are consistent with the known ones for the original PDEs. For the spatially discrete solution, the waiting time phenomenon refers to a deviation of the edge of support from its original position by a quantity comparable to the mesh width, over a mesh-independent time interval. Our proof is based on estimates on the fluid velocity in Lagrangian coordinates. Combining weighted entropy estimates with an iteration technique à la Stampacchia leads to upper bounds on free boundary propagation. Numerical simulations show that the phenomenon is already clearly visible for relatively coarse discretizations.' acknowledgement: This research was supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics”. article_processing_charge: No 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: Daniel full_name: Matthes, Daniel last_name: Matthes citation: ama: Fischer JL, Matthes D. The waiting time phenomenon in spatially discretized porous medium and thin film equations. SIAM Journal on Numerical Analysis. 2021;59(1):60-87. doi:10.1137/19M1300017 apa: Fischer, J. L., & Matthes, D. (2021). The waiting time phenomenon in spatially discretized porous medium and thin film equations. SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1300017 chicago: Fischer, Julian L, and Daniel Matthes. “The Waiting Time Phenomenon in Spatially Discretized Porous Medium and Thin Film Equations.” SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics, 2021. https://doi.org/10.1137/19M1300017. ieee: J. L. Fischer and D. Matthes, “The waiting time phenomenon in spatially discretized porous medium and thin film equations,” SIAM Journal on Numerical Analysis, vol. 59, no. 1. Society for Industrial and Applied Mathematics, pp. 60–87, 2021. ista: Fischer JL, Matthes D. 2021. The waiting time phenomenon in spatially discretized porous medium and thin film equations. SIAM Journal on Numerical Analysis. 59(1), 60–87. mla: Fischer, Julian L., and Daniel Matthes. “The Waiting Time Phenomenon in Spatially Discretized Porous Medium and Thin Film Equations.” SIAM Journal on Numerical Analysis, vol. 59, no. 1, Society for Industrial and Applied Mathematics, 2021, pp. 60–87, doi:10.1137/19M1300017. short: J.L. Fischer, D. Matthes, SIAM Journal on Numerical Analysis 59 (2021) 60–87. date_created: 2021-04-18T22:01:42Z date_published: 2021-01-01T00:00:00Z date_updated: 2023-08-08T13:10:40Z day: '01' department: - _id: JuFi doi: 10.1137/19M1300017 external_id: arxiv: - '1911.04185' isi: - '000625044600003' intvolume: ' 59' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1911.04185 month: '01' oa: 1 oa_version: Preprint page: 60-87 publication: SIAM Journal on Numerical Analysis publication_identifier: issn: - 0036-1429 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: The waiting time phenomenon in spatially discretized porous medium and thin film equations type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 59 year: '2021' ... --- _id: '9349' abstract: - lang: eng text: 'The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly enhanced our ability to observe and quantify spatiotemporal patterns of signalling, force generation, deformation, and flow in living cells and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation are allowing us to perturb the underlying machinery that generates these patterns in increasingly sophisticated ways. Rapid advances in theory and computing have made it possible to construct predictive models that describe how cell and tissue organization and dynamics emerge from the local coupling of biochemistry and mechanics. Together, these advances have opened up a wealth of new opportunities to explore how mechanochemical patterning shapes organismal development. In this roadmap, we present a series of forward-looking case studies on mechanochemical patterning in development, written by scientists working at the interface between the physical and biological sciences, and covering a wide range of spatial and temporal scales, organisms, and modes of development. Together, these contributions highlight the many ways in which the dynamic coupling of mechanics and biochemistry shapes biological dynamics: from mechanoenzymes that sense force to tune their activity and motor output, to collectives of cells in tissues that flow and redistribute biochemical signals during development.' acknowledgement: The AK group is supported by IST Austria and by the ERC under European Union Horizon 2020 research and innovation programme Grant 680037. Apologies to those whose work could not be mentioned due to limited space. We thank all my lab members, both past and present, for stimulating discussion. This work was funded by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis Corson for continuous discussion and collaboration contributing to these views and for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665807. Research in JG's laboratory is funded by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi for help with figure 5. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for fruitful discussions on these topics—and apologize for not being able to cite many very relevant publications due to the strict 10-reference limit. EH acknowledges the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreements (851288). The authors acknowledge the inspiring scientists whose work could not be cited in this perspective due to space constraints; the members of the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation, the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health, and the Centre for Cellular Construction, an NSF Science and Technology Centre. The Minc laboratory is currently funded by the CNRS and the European Research Council (CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche via the Fondation pour la Recherche Médicale, the European Research Council Starting Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas (HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005) grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02). We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported by NIH-R01GM122936. The authors acknowledge the support by a grant from the European Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements d'Avenir' French Government programme managed by the French National Research Agency (ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX, and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022). article_number: '041501' article_processing_charge: No article_type: original author: - first_name: Pierre François full_name: Lenne, Pierre François last_name: Lenne - first_name: Edwin full_name: Munro, Edwin last_name: Munro - first_name: Idse full_name: Heemskerk, Idse last_name: Heemskerk - first_name: Aryeh full_name: Warmflash, Aryeh last_name: Warmflash - first_name: Laura full_name: Bocanegra, Laura id: 4896F754-F248-11E8-B48F-1D18A9856A87 last_name: Bocanegra - first_name: Kasumi full_name: Kishi, Kasumi id: 3065DFC4-F248-11E8-B48F-1D18A9856A87 last_name: Kishi - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Yuchen full_name: Long, Yuchen last_name: Long - first_name: Antoine full_name: Fruleux, Antoine last_name: Fruleux - first_name: Arezki full_name: Boudaoud, Arezki last_name: Boudaoud - first_name: Timothy E. full_name: Saunders, Timothy E. last_name: Saunders - first_name: Paolo full_name: Caldarelli, Paolo last_name: Caldarelli - first_name: Arthur full_name: Michaut, Arthur last_name: Michaut - first_name: Jerome full_name: Gros, Jerome last_name: Gros - first_name: Yonit full_name: Maroudas-Sacks, Yonit last_name: Maroudas-Sacks - first_name: Kinneret full_name: Keren, Kinneret last_name: Keren - 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: Zev J. full_name: Gartner, Zev J. last_name: Gartner - first_name: Benjamin full_name: Stormo, Benjamin last_name: Stormo - first_name: Amy full_name: Gladfelter, Amy last_name: Gladfelter - first_name: Alan full_name: Rodrigues, Alan last_name: Rodrigues - first_name: Amy full_name: Shyer, Amy last_name: Shyer - first_name: Nicolas full_name: Minc, Nicolas last_name: Minc - first_name: Jean Léon full_name: Maître, Jean Léon last_name: Maître - first_name: Stefano full_name: Di Talia, Stefano last_name: Di Talia - first_name: Bassma full_name: Khamaisi, Bassma last_name: Khamaisi - first_name: David full_name: Sprinzak, David last_name: Sprinzak - first_name: Sham full_name: Tlili, Sham last_name: Tlili citation: ama: Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 2021;18(4). doi:10.1088/1478-3975/abd0db apa: Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi, K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical Biology. IOP Publishing. https://doi.org/10.1088/1478-3975/abd0db chicago: Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” Physical Biology. IOP Publishing, 2021. https://doi.org/10.1088/1478-3975/abd0db. ieee: P. F. Lenne et al., “Roadmap for the multiscale coupling of biochemical and mechanical signals during development,” Physical biology, vol. 18, no. 4. IOP Publishing, 2021. ista: Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J, Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 18(4), 041501. mla: Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” Physical Biology, vol. 18, no. 4, 041501, IOP Publishing, 2021, doi:10.1088/1478-3975/abd0db. short: P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi, A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A. Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B. Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia, B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021). date_created: 2021-04-25T22:01:29Z date_published: 2021-04-14T00:00:00Z date_updated: 2023-08-08T13:15:46Z day: '14' ddc: - '570' department: - _id: AnKi - _id: EdHa doi: 10.1088/1478-3975/abd0db ec_funded: 1 external_id: isi: - '000640396400001' pmid: - '33276350' file: - access_level: open_access checksum: 4f52082549d3561c4c15d4d8d84ca5d8 content_type: application/pdf creator: cziletti date_created: 2021-04-27T08:38:35Z date_updated: 2021-04-27T08:38:35Z file_id: '9355' file_name: 2021_PhysBio_Lenne.pdf file_size: 6296324 relation: main_file success: 1 file_date_updated: 2021-04-27T08:38:35Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: B6FC0238-B512-11E9-945C-1524E6697425 call_identifier: H2020 grant_number: '680037' name: Coordination of Patterning And Growth In the Spinal Cord - _id: 268294B6-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31639 name: Active mechano-chemical description of the cell cytoskeleton - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis publication: Physical biology publication_identifier: eissn: - 1478-3975 publication_status: published publisher: IOP Publishing quality_controlled: '1' related_material: record: - id: '13081' relation: dissertation_contains status: public scopus_import: '1' status: public title: Roadmap for the multiscale coupling of biochemical and mechanical signals during development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 18 year: '2021' ... --- _id: '9334' abstract: - lang: eng text: 'Polaritons with directional in-plane propagation and ultralow losses in van der Waals (vdW) crystals promise unprecedented manipulation of light at the nanoscale. However, these polaritons present a crucial limitation: their directional propagation is intrinsically determined by the crystal structure of the host material, imposing forbidden directions of propagation. Here, we demonstrate that directional polaritons (in-plane hyperbolic phonon polaritons) in a vdW crystal (α-phase molybdenum trioxide) can be directed along forbidden directions by inducing an optical topological transition, which emerges when the slab is placed on a substrate with a given negative permittivity (4H–silicon carbide). By visualizing the transition in real space, we observe exotic polaritonic states between mutually orthogonal hyperbolic regimes, which unveil the topological origin of the transition: a gap opening in the dispersion. This work provides insights into optical topological transitions in vdW crystals, which introduce a route to direct light at the nanoscale.' acknowledgement: 'G.Á.-P. and J.T.-G. acknowledge support through the Severo Ochoa Program from the government of the Principality of Asturias (grant nos. PA20-PF-BP19-053 and PA-18-PF-BP17-126, respectively). K.V.V. and V.S.V. acknowledge the Ministry of Science and Higher Education of the Russian Federation (no. 0714-2020-0002). J. M.-S. acknowledges financial support through the Ramón y Cajal Program from the government of Spain and FSE (RYC2018-026196-I). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation and Universities (national project no. MAT201788358-C3-3-R), and the Basque Department of Education (PIBA-2020-1-0014). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA. ' article_number: eabf2690 article_processing_charge: No article_type: original author: - first_name: J. full_name: Duan, J. last_name: Duan - first_name: G. full_name: Álvarez-Pérez, G. last_name: Álvarez-Pérez - first_name: K. V. full_name: Voronin, K. V. last_name: Voronin - first_name: Ivan full_name: Prieto Gonzalez, Ivan id: 2A307FE2-F248-11E8-B48F-1D18A9856A87 last_name: Prieto Gonzalez orcid: 0000-0002-7370-5357 - first_name: J. full_name: Taboada-Gutiérrez, J. last_name: Taboada-Gutiérrez - first_name: V. S. full_name: Volkov, V. S. last_name: Volkov - first_name: J. full_name: Martín-Sánchez, J. last_name: Martín-Sánchez - first_name: A. Y. full_name: Nikitin, A. Y. last_name: Nikitin - first_name: P. full_name: Alonso-González, P. last_name: Alonso-González citation: ama: Duan J, Álvarez-Pérez G, Voronin KV, et al. Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. 2021;7(14). doi:10.1126/sciadv.abf2690 apa: Duan, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., Taboada-Gutiérrez, J., Volkov, V. S., … Alonso-González, P. (2021). Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. AAAS. https://doi.org/10.1126/sciadv.abf2690 chicago: Duan, J., G. Álvarez-Pérez, K. V. Voronin, Ivan Prieto Gonzalez, J. Taboada-Gutiérrez, V. S. Volkov, J. Martín-Sánchez, A. Y. Nikitin, and P. Alonso-González. “Enabling Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological Transition.” Science Advances. AAAS, 2021. https://doi.org/10.1126/sciadv.abf2690. ieee: J. Duan et al., “Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition,” Science Advances, vol. 7, no. 14. AAAS, 2021. ista: Duan J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Taboada-Gutiérrez J, Volkov VS, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2021. Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. 7(14), eabf2690. mla: Duan, J., et al. “Enabling Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological Transition.” Science Advances, vol. 7, no. 14, eabf2690, AAAS, 2021, doi:10.1126/sciadv.abf2690. short: J. Duan, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, J. Taboada-Gutiérrez, V.S. Volkov, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021). date_created: 2021-04-18T22:01:42Z date_published: 2021-04-02T00:00:00Z date_updated: 2023-08-08T13:11:31Z day: '02' ddc: - '530' department: - _id: NanoFab doi: 10.1126/sciadv.abf2690 external_id: isi: - '000636455600027' pmid: - '33811076' file: - access_level: open_access checksum: 4b383d4a1d484a71bbc64ecf401bbdbb content_type: application/pdf creator: dernst date_created: 2021-04-19T11:17:29Z date_updated: 2021-04-19T11:17:29Z file_id: '9343' file_name: 2021_ScienceAdv_Duan.pdf file_size: 717489 relation: main_file success: 1 file_date_updated: 2021-04-19T11:17:29Z has_accepted_license: '1' intvolume: ' 7' isi: 1 issue: '14' language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: Science Advances publication_identifier: eissn: - '23752548' publication_status: published publisher: AAAS quality_controlled: '1' scopus_import: '1' status: public title: Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 7 year: '2021' ... --- _id: '9351' abstract: - lang: eng text: 'We consider the many-body quantum evolution of a factorized initial data, in the mean-field regime. We show that fluctuations around the limiting Hartree dynamics satisfy large deviation estimates that are consistent with central limit theorems that have been established in the last years. ' acknowledgement: The authors gratefully acknowledge Gérard Ben Arous for suggesting this kind of result. K.L.K. was partially supported by NSF CAREER Award DMS-125479 and a Simons Sabbatical Fellowship. S.R. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. B. S. gratefully acknowledges partial support from the NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose–Einstein condensates” and from the European Research Council through the ERC-AdG CLaQS. Funding Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Kay full_name: Kirkpatrick, Kay last_name: Kirkpatrick - first_name: Simone Anna Elvira full_name: Rademacher, Simone Anna Elvira id: 856966FE-A408-11E9-977E-802DE6697425 last_name: Rademacher orcid: 0000-0001-5059-4466 - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein citation: ama: Kirkpatrick K, Rademacher SAE, Schlein B. A large deviation principle in many-body quantum dynamics. Annales Henri Poincare. 2021;22:2595-2618. doi:10.1007/s00023-021-01044-1 apa: Kirkpatrick, K., Rademacher, S. A. E., & Schlein, B. (2021). A large deviation principle in many-body quantum dynamics. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-021-01044-1 chicago: Kirkpatrick, Kay, Simone Anna Elvira Rademacher, and Benjamin Schlein. “A Large Deviation Principle in Many-Body Quantum Dynamics.” Annales Henri Poincare. Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01044-1. ieee: K. Kirkpatrick, S. A. E. Rademacher, and B. Schlein, “A large deviation principle in many-body quantum dynamics,” Annales Henri Poincare, vol. 22. Springer Nature, pp. 2595–2618, 2021. ista: Kirkpatrick K, Rademacher SAE, Schlein B. 2021. A large deviation principle in many-body quantum dynamics. Annales Henri Poincare. 22, 2595–2618. mla: Kirkpatrick, Kay, et al. “A Large Deviation Principle in Many-Body Quantum Dynamics.” Annales Henri Poincare, vol. 22, Springer Nature, 2021, pp. 2595–618, doi:10.1007/s00023-021-01044-1. short: K. Kirkpatrick, S.A.E. Rademacher, B. Schlein, Annales Henri Poincare 22 (2021) 2595–2618. date_created: 2021-04-25T22:01:30Z date_published: 2021-04-08T00:00:00Z date_updated: 2023-08-08T13:14:40Z day: '08' ddc: - '530' department: - _id: RoSe doi: 10.1007/s00023-021-01044-1 ec_funded: 1 external_id: arxiv: - '2010.13754' isi: - '000638022600001' file: - access_level: open_access checksum: 1a0fb963f2f415ba470881a794f20eb6 content_type: application/pdf creator: cchlebak date_created: 2021-10-15T11:15:40Z date_updated: 2021-10-15T11:15:40Z file_id: '10143' file_name: 2021_Annales_Kirkpatrick.pdf file_size: 522669 relation: main_file success: 1 file_date_updated: 2021-10-15T11:15:40Z has_accepted_license: '1' intvolume: ' 22' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 2595-2618 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Annales Henri Poincare publication_identifier: issn: - 1424-0637 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A large deviation principle in many-body quantum dynamics 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: 22 year: '2021' ... --- _id: '9336' abstract: - lang: eng text: Mentorship is experience and/or knowledge‐based guidance. Mentors support, sponsor and advocate for mentees. Having one or more mentors when you seek advice can significantly influence and improve your research endeavours, well‐being and career development. Positive mentee–mentor relationships are vital for maintaining work–life balance and success in careers. Early‐career researchers (ECRs), in particular, can benefit from mentorship to navigate challenges in academic and nonacademic life and careers. Yet, strategies for selecting mentors and maintaining interactions with them are often underdiscussed within research environments. In this Words of Advice, we provide recommendations for ECRs to seek and manage mentorship interactions. Our article draws from our experiences as ECRs and published work, to provide suggestions for mentees to proactively promote beneficial mentorship interactions. The recommended practices highlight the importance of identifying mentorship needs, planning and selecting multiple and diverse mentors, setting goals, and maintaining constructive, and mutually beneficial working relationships with mentors. acknowledgement: The authors thank Nicholas Asby of the University of Chicago for valuable comments on an earlier version of this work. A.P.S. was partially supported by the NARSAD Young Investigator Grant 27705. S.J.H was supported by the National Institutes of Health grant R35GM133732. alternative_title: - Words of Advice article_processing_charge: No article_type: original author: - first_name: Sarvenaz full_name: Sarabipour, Sarvenaz last_name: Sarabipour - first_name: Sarah J. full_name: Hainer, Sarah J. last_name: Hainer - first_name: Feyza N full_name: Arslan, Feyza N id: 49DA7910-F248-11E8-B48F-1D18A9856A87 last_name: Arslan orcid: 0000-0001-5809-9566 - first_name: Charlotte M. full_name: De Winde, Charlotte M. last_name: De Winde - first_name: Emily full_name: Furlong, Emily last_name: Furlong - first_name: Natalia full_name: Bielczyk, Natalia last_name: Bielczyk - first_name: Nafisa M. full_name: Jadavji, Nafisa M. last_name: Jadavji - first_name: Aparna P. full_name: Shah, Aparna P. last_name: Shah - first_name: Sejal full_name: Davla, Sejal last_name: Davla citation: ama: Sarabipour S, Hainer SJ, Arslan FN, et al. Building and sustaining mentor interactions as a mentee. FEBS Journal. 2021. doi:10.1111/febs.15823 apa: Sarabipour, S., Hainer, S. J., Arslan, F. N., De Winde, C. M., Furlong, E., Bielczyk, N., … Davla, S. (2021). Building and sustaining mentor interactions as a mentee. FEBS Journal. Wiley. https://doi.org/10.1111/febs.15823 chicago: Sarabipour, Sarvenaz, Sarah J. Hainer, Feyza N Arslan, Charlotte M. De Winde, Emily Furlong, Natalia Bielczyk, Nafisa M. Jadavji, Aparna P. Shah, and Sejal Davla. “Building and Sustaining Mentor Interactions as a Mentee.” FEBS Journal. Wiley, 2021. https://doi.org/10.1111/febs.15823. ieee: S. Sarabipour et al., “Building and sustaining mentor interactions as a mentee,” FEBS Journal. Wiley, 2021. ista: Sarabipour S, Hainer SJ, Arslan FN, De Winde CM, Furlong E, Bielczyk N, Jadavji NM, Shah AP, Davla S. 2021. Building and sustaining mentor interactions as a mentee. FEBS Journal. mla: Sarabipour, Sarvenaz, et al. “Building and Sustaining Mentor Interactions as a Mentee.” FEBS Journal, Wiley, 2021, doi:10.1111/febs.15823. short: S. Sarabipour, S.J. Hainer, F.N. Arslan, C.M. De Winde, E. Furlong, N. Bielczyk, N.M. Jadavji, A.P. Shah, S. Davla, FEBS Journal (2021). date_created: 2021-04-18T22:01:43Z date_published: 2021-04-05T00:00:00Z date_updated: 2023-08-08T13:12:55Z day: '05' department: - _id: CaHe doi: 10.1111/febs.15823 external_id: isi: - '000636678800001' pmid: - '33818917' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/febs.15823 month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: FEBS Journal publication_identifier: eissn: - 1742-4658 issn: - 1742-464X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Building and sustaining mentor interactions as a mentee type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9350' abstract: - lang: eng text: Intercellular adhesion is the key to multicellularity, and its malfunction plays an important role in various developmental and disease-related processes. Although it has been intensively studied by both biologists and physicists, a commonly accepted definition of cell-cell adhesion is still being debated. Cell-cell adhesion has been described at the molecular scale as a function of adhesion receptors controlling binding affinity, at the cellular scale as resistance to detachment forces or modulation of surface tension, and at the tissue scale as a regulator of cellular rearrangements and morphogenesis. In this review, we aim to summarize and discuss recent advances in the molecular, cellular, and theoretical description of cell-cell adhesion, ranging from biomimetic models to the complexity of cells and tissues in an organismal context. In particular, we will focus on cadherin-mediated cell-cell adhesion and the role of adhesion signaling and mechanosensation therein, two processes central for understanding the biological and physical basis of cell-cell adhesion. acknowledgement: T.S. acknowledges funding by the research program “The Active Matter Physics of Collective Metastasis,” which is financed by the Dutch Research Council (NWO). article_processing_charge: No article_type: original author: - first_name: Feyza N full_name: Arslan, Feyza N id: 49DA7910-F248-11E8-B48F-1D18A9856A87 last_name: Arslan orcid: 0000-0001-5809-9566 - first_name: Julia full_name: Eckert, Julia last_name: Eckert - first_name: Thomas full_name: Schmidt, Thomas last_name: Schmidt - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: 'Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. Holding it together: when cadherin meets cadherin. Biophysical Journal. 2021;120:4182-4192. doi:10.1016/j.bpj.2021.03.025' apa: 'Arslan, F. N., Eckert, J., Schmidt, T., & Heisenberg, C.-P. J. (2021). Holding it together: when cadherin meets cadherin. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2021.03.025' chicago: 'Arslan, Feyza N, Julia Eckert, Thomas Schmidt, and Carl-Philipp J Heisenberg. “Holding It Together: When Cadherin Meets Cadherin.” Biophysical Journal. Biophysical Society, 2021. https://doi.org/10.1016/j.bpj.2021.03.025.' ieee: 'F. N. Arslan, J. Eckert, T. Schmidt, and C.-P. J. Heisenberg, “Holding it together: when cadherin meets cadherin,” Biophysical Journal, vol. 120. Biophysical Society, pp. 4182–4192, 2021.' ista: 'Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. 2021. Holding it together: when cadherin meets cadherin. Biophysical Journal. 120, 4182–4192.' mla: 'Arslan, Feyza N., et al. “Holding It Together: When Cadherin Meets Cadherin.” Biophysical Journal, vol. 120, Biophysical Society, 2021, pp. 4182–92, doi:10.1016/j.bpj.2021.03.025.' short: F.N. Arslan, J. Eckert, T. Schmidt, C.-P.J. Heisenberg, Biophysical Journal 120 (2021) 4182–4192. date_created: 2021-04-25T22:01:30Z date_published: 2021-10-05T00:00:00Z date_updated: 2023-08-08T13:14:10Z day: '05' department: - _id: CaHe doi: 10.1016/j.bpj.2021.03.025 external_id: isi: - '000704646900006' pmid: - '33794149' intvolume: ' 120' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://scholarlypublications.universiteitleiden.nl/access/item%3A3251048/view month: '10' oa: 1 oa_version: Published Version page: 4182-4192 pmid: 1 publication: Biophysical Journal publication_identifier: eissn: - 1542-0086 issn: - 0006-3495 publication_status: published publisher: Biophysical Society quality_controlled: '1' related_material: record: - id: '12368' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Holding it together: when cadherin meets cadherin' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 120 year: '2021' ... --- _id: '9348' abstract: - lang: eng text: We consider the stochastic quantization of a quartic double-well energy functional in the semiclassical regime and derive optimal asymptotics for the exponentially small splitting of the ground state energy. Our result provides an infinite-dimensional version of some sharp tunneling estimates known in finite dimensions for semiclassical Witten Laplacians in degree zero. From a stochastic point of view it proves that the L2 spectral gap of the stochastic one-dimensional Allen-Cahn equation in finite volume satisfies a Kramers-type formula in the limit of vanishing noise. We work with finite-dimensional lattice approximations and establish semiclassical estimates which are uniform in the dimension. Our key estimate shows that the constant separating the two exponentially small eigenvalues from the rest of the spectrum can be taken independently of the dimension. acknowledgement: GDG gratefully acknowledges the financial support of HIM Bonn in the framework of the 2019 Junior Trimester Programs “Kinetic Theory” and “Randomness, PDEs and Nonlinear Fluctuations” and the hospitality at the University of Rome La Sapienza during his frequent visits. article_number: '109029' article_processing_charge: No article_type: original author: - first_name: Morris full_name: Brooks, Morris id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425 last_name: Brooks orcid: 0000-0002-6249-0928 - first_name: Giacomo full_name: Di Gesù, Giacomo last_name: Di Gesù citation: ama: Brooks M, Di Gesù G. Sharp tunneling estimates for a double-well model in infinite dimension. Journal of Functional Analysis. 2021;281(3). doi:10.1016/j.jfa.2021.109029 apa: Brooks, M., & Di Gesù, G. (2021). Sharp tunneling estimates for a double-well model in infinite dimension. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109029 chicago: Brooks, Morris, and Giacomo Di Gesù. “Sharp Tunneling Estimates for a Double-Well Model in Infinite Dimension.” Journal of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109029. ieee: M. Brooks and G. Di Gesù, “Sharp tunneling estimates for a double-well model in infinite dimension,” Journal of Functional Analysis, vol. 281, no. 3. Elsevier, 2021. ista: Brooks M, Di Gesù G. 2021. Sharp tunneling estimates for a double-well model in infinite dimension. Journal of Functional Analysis. 281(3), 109029. mla: Brooks, Morris, and Giacomo Di Gesù. “Sharp Tunneling Estimates for a Double-Well Model in Infinite Dimension.” Journal of Functional Analysis, vol. 281, no. 3, 109029, Elsevier, 2021, doi:10.1016/j.jfa.2021.109029. short: M. Brooks, G. Di Gesù, Journal of Functional Analysis 281 (2021). date_created: 2021-04-25T22:01:29Z date_published: 2021-04-07T00:00:00Z date_updated: 2023-08-08T13:15:11Z day: '07' department: - _id: RoSe doi: 10.1016/j.jfa.2021.109029 external_id: arxiv: - '1911.03187' isi: - '000644702800005' intvolume: ' 281' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1911.03187 month: '04' oa: 1 oa_version: Preprint publication: Journal of Functional Analysis publication_identifier: eissn: - 1096-0783 issn: - 0022-1236 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Sharp tunneling estimates for a double-well model in infinite dimension type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 281 year: '2021' ... --- _id: '9352' abstract: - lang: eng text: This paper provides an a priori error analysis of a localized orthogonal decomposition method for the numerical stochastic homogenization of a model random diffusion problem. If the uniformly elliptic and bounded random coefficient field of the model problem is stationary and satisfies a quantitative decorrelation assumption in the form of the spectral gap inequality, then the expected $L^2$ error of the method can be estimated, up to logarithmic factors, by $H+(\varepsilon/H)^{d/2}$, $\varepsilon$ being the small correlation length of the random coefficient and $H$ the width of the coarse finite element mesh that determines the spatial resolution. The proof bridges recent results of numerical homogenization and quantitative stochastic homogenization. acknowledgement: 'This work was initiated while the authors enjoyed the kind hospitality of the Hausdorff Institute for Mathematics in Bonn during the trimester program Multiscale Problems: Algorithms, Numerical Analysis, and Computation. D. Peterseim would like to acknowledge the kind hospitality of the Erwin Schrödinger International Institute for Mathematics and Physics (ESI), where parts of this research were developed under the frame of the thematic program Numerical Analysis of Complex PDE Models in the Sciences.' article_processing_charge: No 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: Dietmar full_name: Gallistl, Dietmar last_name: Gallistl - first_name: Dietmar full_name: Peterseim, Dietmar last_name: Peterseim citation: ama: Fischer JL, Gallistl D, Peterseim D. A priori error analysis of a numerical stochastic homogenization method. SIAM Journal on Numerical Analysis. 2021;59(2):660-674. doi:10.1137/19M1308992 apa: Fischer, J. L., Gallistl, D., & Peterseim, D. (2021). A priori error analysis of a numerical stochastic homogenization method. SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1308992 chicago: Fischer, Julian L, Dietmar Gallistl, and Dietmar Peterseim. “A Priori Error Analysis of a Numerical Stochastic Homogenization Method.” SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics, 2021. https://doi.org/10.1137/19M1308992. ieee: J. L. Fischer, D. Gallistl, and D. Peterseim, “A priori error analysis of a numerical stochastic homogenization method,” SIAM Journal on Numerical Analysis, vol. 59, no. 2. Society for Industrial and Applied Mathematics, pp. 660–674, 2021. ista: Fischer JL, Gallistl D, Peterseim D. 2021. A priori error analysis of a numerical stochastic homogenization method. SIAM Journal on Numerical Analysis. 59(2), 660–674. mla: Fischer, Julian L., et al. “A Priori Error Analysis of a Numerical Stochastic Homogenization Method.” SIAM Journal on Numerical Analysis, vol. 59, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 660–74, doi:10.1137/19M1308992. short: J.L. Fischer, D. Gallistl, D. Peterseim, SIAM Journal on Numerical Analysis 59 (2021) 660–674. date_created: 2021-04-25T22:01:31Z date_published: 2021-03-09T00:00:00Z date_updated: 2023-08-08T13:13:37Z day: '09' department: - _id: JuFi doi: 10.1137/19M1308992 external_id: arxiv: - '1912.11646' isi: - '000646030400003' intvolume: ' 59' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.11646 month: '03' oa: 1 oa_version: Preprint page: 660-674 publication: SIAM Journal on Numerical Analysis publication_identifier: issn: - 0036-1429 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: A priori error analysis of a numerical stochastic homogenization method type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 59 year: '2021' ... --- _id: '9363' abstract: - lang: eng text: Optogenetics has been harnessed to shed new mechanistic light on current and future therapeutic strategies. This has been to date achieved by the regulation of ion flow and electrical signals in neuronal cells and neural circuits that are known to be affected by disease. In contrast, the optogenetic delivery of trophic biochemical signals, which support cell survival and are implicated in degenerative disorders, has never been demonstrated in an animal model of disease. Here, we reengineered the human and Drosophila melanogaster REarranged during Transfection (hRET and dRET) receptors to be activated by light, creating one-component optogenetic tools termed Opto-hRET and Opto-dRET. Upon blue light stimulation, these receptors robustly induced the MAPK/ERK proliferative signaling pathway in cultured cells. In PINK1B9 flies that exhibit loss of PTEN-induced putative kinase 1 (PINK1), a kinase associated with familial Parkinson’s disease (PD), light activation of Opto-dRET suppressed mitochondrial defects, tissue degeneration and behavioral deficits. In human cells with PINK1 loss-of-function, mitochondrial fragmentation was rescued using Opto-dRET via the PI3K/NF-кB pathway. Our results demonstrate that a light-activated receptor can ameliorate disease hallmarks in a genetic model of PD. The optogenetic delivery of trophic signals is cell type-specific and reversible and thus has the potential to inspire novel strategies towards a spatio-temporal regulation of tissue repair. acknowledgement: We thank R. Cagan, A. Whitworth and J. Nagpal for fly lines and advice, S. Herlitze for provision of a tissue culture illuminator, and Verian Bader for help with statistical analysis. article_processing_charge: No author: - first_name: Álvaro full_name: Inglés Prieto, Álvaro id: 2A9DB292-F248-11E8-B48F-1D18A9856A87 last_name: Inglés Prieto orcid: 0000-0002-5409-8571 - first_name: Nikolas full_name: Furthmann, Nikolas last_name: Furthmann - first_name: Samuel H. full_name: Crossman, Samuel H. last_name: Crossman - first_name: Alexandra Madelaine full_name: Tichy, Alexandra Madelaine last_name: Tichy - first_name: Nina full_name: Hoyer, Nina last_name: Hoyer - first_name: Meike full_name: Petersen, Meike last_name: Petersen - first_name: Vanessa full_name: Zheden, Vanessa id: 39C5A68A-F248-11E8-B48F-1D18A9856A87 last_name: Zheden - first_name: Julia full_name: Bicher, Julia id: 3CCBB46E-F248-11E8-B48F-1D18A9856A87 last_name: Bicher - first_name: Eva full_name: Gschaider-Reichhart, Eva id: 3FEE232A-F248-11E8-B48F-1D18A9856A87 last_name: Gschaider-Reichhart orcid: 0000-0002-7218-7738 - first_name: Attila full_name: György, Attila id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87 last_name: György orcid: 0000-0002-1819-198X - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Peter full_name: Soba, Peter last_name: Soba - first_name: Konstanze F. full_name: Winklhofer, Konstanze F. last_name: Winklhofer - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 citation: ama: Inglés Prieto Á, Furthmann N, Crossman SH, et al. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS genetics. 2021;17(4):e1009479. doi:10.1371/journal.pgen.1009479 apa: Inglés Prieto, Á., Furthmann, N., Crossman, S. H., Tichy, A. M., Hoyer, N., Petersen, M., … Janovjak, H. L. (2021). Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1009479 chicago: Inglés Prieto, Álvaro, Nikolas Furthmann, Samuel H. Crossman, Alexandra Madelaine Tichy, Nina Hoyer, Meike Petersen, Vanessa Zheden, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” PLoS Genetics. Public Library of Science, 2021. https://doi.org/10.1371/journal.pgen.1009479. ieee: Á. Inglés Prieto et al., “Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease,” PLoS genetics, vol. 17, no. 4. Public Library of Science, p. e1009479, 2021. ista: Inglés Prieto Á, Furthmann N, Crossman SH, Tichy AM, Hoyer N, Petersen M, Zheden V, Bicher J, Gschaider-Reichhart E, György A, Siekhaus DE, Soba P, Winklhofer KF, Janovjak HL. 2021. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS genetics. 17(4), e1009479. mla: Inglés Prieto, Álvaro, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” PLoS Genetics, vol. 17, no. 4, Public Library of Science, 2021, p. e1009479, doi:10.1371/journal.pgen.1009479. short: Á. Inglés Prieto, N. Furthmann, S.H. Crossman, A.M. Tichy, N. Hoyer, M. Petersen, V. Zheden, J. Bicher, E. Gschaider-Reichhart, A. György, D.E. Siekhaus, P. Soba, K.F. Winklhofer, H.L. Janovjak, PLoS Genetics 17 (2021) e1009479. date_created: 2021-05-02T22:01:29Z date_published: 2021-04-01T00:00:00Z date_updated: 2023-08-08T13:17:47Z day: '01' ddc: - '570' department: - _id: EM-Fac - _id: LoSw - _id: DaSi doi: 10.1371/journal.pgen.1009479 external_id: isi: - '000640606700001' file: - access_level: open_access checksum: 82a74668f863e8dfb22fdd4f845c92ce content_type: application/pdf creator: kschuh date_created: 2021-05-04T09:05:27Z date_updated: 2021-05-04T09:05:27Z file_id: '9369' file_name: 2021_PLOS_Ingles-Prieto.pdf file_size: 3072764 relation: main_file success: 1 file_date_updated: 2021-05-04T09:05:27Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: e1009479 publication: PLoS genetics publication_identifier: eissn: - '15537404' publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2021' ... --- _id: '9380' abstract: - lang: eng text: Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands. acknowledgement: We thank Fyodor Kondrashov for valuable advice and manuscript proofreading. We also thank Alla Mikheenko for assistance with Circos. article_number: '628622' article_processing_charge: No article_type: original author: - first_name: Zaira full_name: Seferbekova, Zaira last_name: Seferbekova - first_name: Alexey full_name: Zabelkin, Alexey last_name: Zabelkin - first_name: Yulia full_name: Yakovleva, Yulia last_name: Yakovleva - first_name: Robert full_name: Afasizhev, Robert last_name: Afasizhev - first_name: Natalia O. full_name: Dranenko, Natalia O. last_name: Dranenko - first_name: Nikita full_name: Alexeev, Nikita last_name: Alexeev - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 citation: ama: Seferbekova Z, Zabelkin A, Yakovleva Y, et al. High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. 2021;12. doi:10.3389/fmicb.2021.628622 apa: Seferbekova, Z., Zabelkin, A., Yakovleva, Y., Afasizhev, R., Dranenko, N. O., Alexeev, N., … Bochkareva, O. (2021). High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2021.628622 chicago: Seferbekova, Zaira, Alexey Zabelkin, Yulia Yakovleva, Robert Afasizhev, Natalia O. Dranenko, Nikita Alexeev, Mikhail S. Gelfand, and Olga Bochkareva. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” Frontiers in Microbiology. Frontiers, 2021. https://doi.org/10.3389/fmicb.2021.628622. ieee: Z. Seferbekova et al., “High rates of genome rearrangements and pathogenicity of Shigella spp,” Frontiers in Microbiology, vol. 12. Frontiers, 2021. ista: Seferbekova Z, Zabelkin A, Yakovleva Y, Afasizhev R, Dranenko NO, Alexeev N, Gelfand MS, Bochkareva O. 2021. High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. 12, 628622. mla: Seferbekova, Zaira, et al. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” Frontiers in Microbiology, vol. 12, 628622, Frontiers, 2021, doi:10.3389/fmicb.2021.628622. short: Z. Seferbekova, A. Zabelkin, Y. Yakovleva, R. Afasizhev, N.O. Dranenko, N. Alexeev, M.S. Gelfand, O. Bochkareva, Frontiers in Microbiology 12 (2021). date_created: 2021-05-09T22:01:38Z date_published: 2021-04-12T00:00:00Z date_updated: 2023-08-08T13:30:39Z day: '12' ddc: - '570' department: - _id: FyKo doi: 10.3389/fmicb.2021.628622 ec_funded: 1 external_id: isi: - '000643713300001' file: - access_level: open_access checksum: 2f856543add59273a482a7f326fc0400 content_type: application/pdf creator: kschuh date_created: 2021-05-11T13:05:52Z date_updated: 2021-05-11T13:05:52Z file_id: '9384' file_name: 2021_Frontiers_Microbiology_Seferbekova.pdf file_size: 14362316 relation: main_file success: 1 file_date_updated: 2021-05-11T13:05:52Z has_accepted_license: '1' intvolume: ' 12' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Frontiers in Microbiology publication_identifier: eissn: - 1664-302X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: High rates of genome rearrangements and pathogenicity of Shigella spp 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: 12 year: '2021' ... --- _id: '9359' abstract: - lang: eng text: "We prove that the factorization homologies of a scheme with coefficients in truncated polynomial algebras compute the cohomologies of its generalized configuration spaces. Using Koszul duality between commutative algebras and Lie algebras, we obtain new expressions for the cohomologies of the latter. As a consequence, we obtain a uniform and conceptual approach for treating homological stability, homological densities, and arithmetic densities of generalized configuration spaces. Our results categorify, generalize, and in fact provide a conceptual understanding of the coincidences appearing in the work of Farb--Wolfson--Wood. Our computation of the stable homological densities also yields rational homotopy types, answering a question posed by Vakil--Wood. Our approach hinges on the study of homological stability of cohomological Chevalley complexes, which is of independent interest.\r\n" acknowledgement: "This paper owes an obvious intellectual debt to the illuminating treatments of factorization homology by J.\r\nFrancis, D. Gaitsgory, and J. Lurie in [GL,G1, FG]. The author would like to thank B. Farb and J. Wolfson for\r\nbringing the question of explaining coincidences in homological densities to his attention. Moreover, the author\r\nthanks J. Wolfson for many helpful conversations on the subject, O. Randal-Williams for many comments which\r\ngreatly help improve the exposition, and G. C. Drummond-Cole for many useful conversations on L∞-algebras.\r\nFinally, the author is grateful to the anonymous referee for carefully reading the manuscript and for providing\r\nnumerous comments which greatly helped improve the clarity and precision of the exposition.\r\nThis work is supported by the Advanced Grant “Arithmetic and Physics of Higgs moduli spaces” No. 320593 of\r\nthe European Research Council and the Lise Meitner fellowship “Algebro-Geometric Applications of Factorization\r\nHomology,” Austrian Science Fund (FWF): M 2751." article_processing_charge: No article_type: original author: - first_name: Quoc P full_name: Ho, Quoc P id: 3DD82E3C-F248-11E8-B48F-1D18A9856A87 last_name: Ho citation: ama: Ho QP. Homological stability and densities of generalized configuration spaces. Geometry & Topology. 2021;25(2):813-912. doi:10.2140/gt.2021.25.813 apa: Ho, Q. P. (2021). Homological stability and densities of generalized configuration spaces. Geometry & Topology. Mathematical Sciences Publishers. https://doi.org/10.2140/gt.2021.25.813 chicago: Ho, Quoc P. “Homological Stability and Densities of Generalized Configuration Spaces.” Geometry & Topology. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/gt.2021.25.813. ieee: Q. P. Ho, “Homological stability and densities of generalized configuration spaces,” Geometry & Topology, vol. 25, no. 2. Mathematical Sciences Publishers, pp. 813–912, 2021. ista: Ho QP. 2021. Homological stability and densities of generalized configuration spaces. Geometry & Topology. 25(2), 813–912. mla: Ho, Quoc P. “Homological Stability and Densities of Generalized Configuration Spaces.” Geometry & Topology, vol. 25, no. 2, Mathematical Sciences Publishers, 2021, pp. 813–912, doi:10.2140/gt.2021.25.813. short: Q.P. Ho, Geometry & Topology 25 (2021) 813–912. date_created: 2021-05-02T06:59:33Z date_published: 2021-04-27T00:00:00Z date_updated: 2023-08-08T13:28:59Z day: '27' ddc: - '514' - '516' - '512' department: - _id: TaHa doi: 10.2140/gt.2021.25.813 ec_funded: 1 external_id: arxiv: - '1802.07948' isi: - '000682738600005' file: - access_level: open_access checksum: 643a8d2d6f06f0888dcd7503f55d0920 content_type: application/pdf creator: qho date_created: 2021-05-03T06:54:06Z date_updated: 2021-05-03T06:54:06Z file_id: '9366' file_name: densities.pdf file_size: 479268 relation: main_file success: 1 file_date_updated: 2021-05-03T06:54:06Z has_accepted_license: '1' intvolume: ' 25' isi: 1 issue: '2' keyword: - Generalized configuration spaces - homological stability - homological densities - chiral algebras - chiral homology - factorization algebras - Koszul duality - Ran space language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 813-912 project: - _id: 25E549F4-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '320593' name: Arithmetic and physics of Higgs moduli spaces - _id: 26B96266-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02751 name: Algebro-Geometric Applications of Factorization Homology publication: Geometry & Topology publication_identifier: issn: - 1364-0380 publication_status: published publisher: Mathematical Sciences Publishers quality_controlled: '1' status: public title: Homological stability and densities of generalized configuration spaces type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 25 year: '2021' ... --- _id: '9361' abstract: - lang: eng text: The multimeric matrix (M) protein of clinically relevant paramyxoviruses orchestrates assembly and budding activity of viral particles at the plasma membrane (PM). We identified within the canine distemper virus (CDV) M protein two microdomains, potentially assuming α-helix structures, which are essential for membrane budding activity. Remarkably, while two rationally designed microdomain M mutants (E89R, microdomain 1 and L239D, microdomain 2) preserved proper folding, dimerization, interaction with the nucleocapsid protein, localization at and deformation of the PM, the virus-like particle formation, as well as production of infectious virions (as monitored using a membrane budding-complementation system), were, in sharp contrast, strongly impaired. Of major importance, raster image correlation spectroscopy (RICS) revealed that both microdomains contributed to finely tune M protein mobility specifically at the PM. Collectively, our data highlighted the cornerstone membrane budding-priming activity of two spatially discrete M microdomains, potentially by coordinating the assembly of productive higher oligomers at the PM. acknowledgement: This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.). article_number: e01024-20 article_processing_charge: No author: - first_name: Matthieu full_name: Gast, Matthieu last_name: Gast - first_name: Nicole P. full_name: Kadzioch, Nicole P. last_name: Kadzioch - first_name: Doreen full_name: Milius, Doreen id: 384050BC-F248-11E8-B48F-1D18A9856A87 last_name: Milius - first_name: Francesco full_name: Origgi, Francesco last_name: Origgi - first_name: Philippe full_name: Plattet, Philippe last_name: Plattet citation: ama: Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. mSphere. 2021;6(2). doi:10.1128/mSphere.01024-20 apa: Gast, M., Kadzioch, N. P., Milius, D., Origgi, F., & Plattet, P. (2021). Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. MSphere. American Society for Microbiology. https://doi.org/10.1128/mSphere.01024-20 chicago: Gast, Matthieu, Nicole P. Kadzioch, Doreen Milius, Francesco Origgi, and Philippe Plattet. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” MSphere. American Society for Microbiology, 2021. https://doi.org/10.1128/mSphere.01024-20. ieee: M. Gast, N. P. Kadzioch, D. Milius, F. Origgi, and P. Plattet, “Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein,” mSphere, vol. 6, no. 2. American Society for Microbiology, 2021. ista: Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. 2021. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. mSphere. 6(2), e01024-20. mla: Gast, Matthieu, et al. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” MSphere, vol. 6, no. 2, e01024-20, American Society for Microbiology, 2021, doi:10.1128/mSphere.01024-20. short: M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021). date_created: 2021-05-02T22:01:28Z date_published: 2021-04-14T00:00:00Z date_updated: 2023-08-08T13:26:12Z day: '14' ddc: - '570' department: - _id: Bio doi: 10.1128/mSphere.01024-20 external_id: isi: - '000663823400025' pmid: - '33853875' file: - access_level: open_access checksum: 310748d140c8838335c1314431095898 content_type: application/pdf creator: kschuh date_created: 2021-05-04T12:41:38Z date_updated: 2021-05-04T12:41:38Z file_id: '9370' file_name: 2021_mSphere_Gast.pdf file_size: 3379349 relation: main_file success: 1 file_date_updated: 2021-05-04T12:41:38Z has_accepted_license: '1' intvolume: ' 6' isi: 1 issue: '2' language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: mSphere publication_identifier: eissn: - '23795042' publication_status: published publisher: American Society for Microbiology quality_controlled: '1' scopus_import: '1' status: public title: Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein 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: 6 year: '2021' ... --- _id: '9376' abstract: - lang: eng text: This paper presents a method for designing planar multistable compliant structures. Given a sequence of desired stable states and the corresponding poses of the structure, we identify the topology and geometric realization of a mechanism—consisting of bars and joints—that is able to physically reproduce the desired multistable behavior. In order to solve this problem efficiently, we build on insights from minimally rigid graph theory to identify simple but effective topologies for the mechanism. We then optimize its geometric parameters, such as joint positions and bar lengths, to obtain correct transitions between the given poses. Simultaneously, we ensure adequate stability of each pose based on an effective approximate error metric related to the elastic energy Hessian of the bars in the mechanism. As demonstrated by our results, we obtain functional multistable mechanisms of manageable complexity that can be fabricated using 3D printing. Further, we evaluated the effectiveness of our method on a large number of examples in the simulation and fabricated several physical prototypes. acknowledged_ssus: - _id: M-Shop acknowledgement: 'We would like to thank everyone who contributed to this paper, the authors of artworks for all the examples, including @macrovec-tor_official and Wikimedia for the FLAG semaphore, and @pikisuper-star for the FIGURINE. The photos of iconic poses in the teaser were supplied by (from left to right): Mike Hewitt/Olympics Day 8 - Athletics/Gettty Images, Oneinchpunch/Basketball player training on acourt in New york city/Shutterstock, and Andrew Redington/TigerWoods/Getty Images. We also want to express our gratitude to Christian Hafner for insightful discussions, the IST Austria machine shop SSU, all proof-readers, and anonymous reviewers. This project has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE).' article_number: '186' article_processing_charge: No article_type: original author: - first_name: Ran full_name: Zhang, Ran id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0002-3808-281X - first_name: Thomas full_name: Auzinger, Thomas id: 4718F954-F248-11E8-B48F-1D18A9856A87 last_name: Auzinger orcid: 0000-0002-1546-3265 - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: Zhang R, Auzinger T, Bickel B. Computational design of planar multistable compliant structures. ACM Transactions on Graphics. 2021;40(5). doi:10.1145/3453477 apa: Zhang, R., Auzinger, T., & Bickel, B. (2021). Computational design of planar multistable compliant structures. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3453477 chicago: Zhang, Ran, Thomas Auzinger, and Bernd Bickel. “Computational Design of Planar Multistable Compliant Structures.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453477. ieee: R. Zhang, T. Auzinger, and B. Bickel, “Computational design of planar multistable compliant structures,” ACM Transactions on Graphics, vol. 40, no. 5. Association for Computing Machinery, 2021. ista: Zhang R, Auzinger T, Bickel B. 2021. Computational design of planar multistable compliant structures. ACM Transactions on Graphics. 40(5), 186. mla: Zhang, Ran, et al. “Computational Design of Planar Multistable Compliant Structures.” ACM Transactions on Graphics, vol. 40, no. 5, 186, Association for Computing Machinery, 2021, doi:10.1145/3453477. short: R. Zhang, T. Auzinger, B. Bickel, ACM Transactions on Graphics 40 (2021). date_created: 2021-05-08T17:37:08Z date_published: 2021-10-08T00:00:00Z date_updated: 2023-08-08T13:31:38Z day: '08' ddc: - '000' department: - _id: BeBi doi: 10.1145/3453477 ec_funded: 1 external_id: isi: - '000752079300003' file: - access_level: open_access checksum: 8564b3118457d4c8939a8ef2b1a2f16c content_type: application/pdf creator: bbickel date_created: 2021-05-08T17:36:59Z date_updated: 2021-05-08T17:36:59Z file_id: '9377' file_name: Multistable-authorversion.pdf file_size: 18926557 relation: main_file - access_level: open_access checksum: 3b6e874e30bfa1bfc3ad3498710145a1 content_type: video/mp4 creator: bbickel date_created: 2021-05-08T17:38:22Z date_updated: 2021-05-08T17:38:22Z file_id: '9378' file_name: multistable-video.mp4 file_size: 76542901 relation: main_file success: 1 - access_level: open_access checksum: 20dc3bc42e1a912a5b0247c116772098 content_type: application/pdf creator: bbickel date_created: 2021-12-17T08:13:51Z date_updated: 2021-12-17T08:13:51Z description: This document provides additional results and analyzes the robustness and limitations of our approach. file_id: '10562' file_name: multistable-supplementary material.pdf file_size: 3367072 relation: supplementary_material title: Supplementary Material for “Computational Design of Planar Multistable Compliant Structures” file_date_updated: 2021-12-17T08:13:51Z has_accepted_license: '1' intvolume: ' 40' isi: 1 issue: '5' keyword: - multistability - mechanism - computational design - rigidity language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: ACM Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' status: public title: Computational design of planar multistable compliant structures tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ... --- _id: '9375' abstract: - lang: eng text: Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations. acknowledgement: 'We thank Felicity Jones for input into experimental design, helpful discussion and improving the manuscript. We thank the Rolian, Jiggins, Chan and Jones Labs members for support, insightful scientific discussion and improving the manuscript. We thank the Rolian lab members, the Animal Resource Centre staff at the University of Calgary, and Caroline Schmid and Ann-Katrin Geysel at the Friedrich Miescher Laboratory for animal husbandry. We thank Christa Lanz, Rebecca Schwab and Ilja Bezrukov for assistance with high-throughput sequencing and associated data processing; Andre Noll and the MPI Tübingen IT team for computational support. We thank Ben Haller and Richard Durbin for helpful discussions. We thank David M. Kingsley for thoughtful input that has greatly improved our manuscript. J.I.M. is supported by a Research Fellowship from St. John’s College, Cambridge. A.D. was supported by a European Research Council Consolidator Grant (No. 617279 “EvolRecombAdapt”, P/I Felicity Jones). C.R. is supported by Discovery Grant #4181932 from the Natural Sciences and Engineering Research Council of Canada and by the Faculty of Veterinary Medicine at the University of Calgary. C.D.J. is supported by a BBSRC grant BB/R007500 and a European Research Council Advanced Grant (No. 339873 “SpeciationGenetics”). M.K. and Y.F.C. are supported by the Max Planck Society and a European Research Council Starting Grant (No. 639096 “HybridMiX”).' article_number: e2015005118 article_processing_charge: No article_type: original author: - first_name: Joana I. full_name: Meier, Joana I. last_name: Meier - first_name: Patricio A. full_name: Salazar, Patricio A. last_name: Salazar - first_name: Marek full_name: Kučka, Marek last_name: Kučka - first_name: Robert William full_name: Davies, Robert William last_name: Davies - first_name: Andreea full_name: Dréau, Andreea last_name: Dréau - first_name: Ismael full_name: Aldás, Ismael last_name: Aldás - first_name: Olivia Box full_name: Power, Olivia Box last_name: Power - first_name: Nicola J. full_name: Nadeau, Nicola J. last_name: Nadeau - first_name: Jon R. full_name: Bridle, Jon R. last_name: Bridle - first_name: Campbell full_name: Rolian, Campbell last_name: Rolian - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: W. Owen full_name: McMillan, W. Owen last_name: McMillan - first_name: Chris D. full_name: Jiggins, Chris D. last_name: Jiggins - first_name: Yingguang Frank full_name: Chan, Yingguang Frank last_name: Chan citation: ama: Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 2021;118(25). doi:10.1073/pnas.2015005118 apa: Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I., … Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2015005118 chicago: Meier, Joana I., Patricio A. Salazar, Marek Kučka, Robert William Davies, Andreea Dréau, Ismael Aldás, Olivia Box Power, et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS. Proceedings of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2015005118. ieee: J. I. Meier et al., “Haplotype tagging reveals parallel formation of hybrid races in two butterfly species,” PNAS, vol. 118, no. 25. Proceedings of the National Academy of Sciences, 2021. ista: Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Power OB, Nadeau NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. 2021. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 118(25), e2015005118. mla: Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS, vol. 118, no. 25, e2015005118, Proceedings of the National Academy of Sciences, 2021, doi:10.1073/pnas.2015005118. short: J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B. Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins, Y.F. Chan, PNAS 118 (2021). date_created: 2021-05-07T17:10:21Z date_published: 2021-06-21T00:00:00Z date_updated: 2023-08-08T13:33:09Z day: '21' ddc: - '570' department: - _id: NiBa doi: 10.1073/pnas.2015005118 external_id: isi: - '000671755600001' pmid: - '34155138' file: - access_level: open_access checksum: cb30c6166b2132ee60d616b31a1a7c29 content_type: application/pdf creator: dernst date_created: 2022-03-08T08:18:16Z date_updated: 2022-03-08T08:18:16Z file_id: '10835' file_name: 2021_PNAS_Meier.pdf file_size: 20592929 relation: main_file success: 1 file_date_updated: 2022-03-08T08:18:16Z has_accepted_license: '1' intvolume: ' 118' isi: 1 issue: '25' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: PNAS publication_identifier: eissn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species 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: 118 year: '2021' ... --- _id: '9394' abstract: - lang: eng text: 'Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.' acknowledgement: 'We are very grateful to Irena Senčić for technical assistance and to Michelle Kortyna and Sean Holland at the Center for Anchored Phylogenomics for assistance with data collection. RKB was funded by the Natural Environment Research Council and by the European Research Council. KJ was funded by the Swedish Research Councils VR and Formas (Linnaeus Grant: 217‐2008‐1719). JL was funded by a studentship from the Leverhulme Centre for Advanced Biological Modelling. AMW was funded by the European Union''s Horizon 2020 research and innovation program under Marie Skłodowska‐Curie Grant agreement no. 797747. RF was funded by the European Union''s Horizon 2020 research and innovation programme under the Marie Sklodowska‐Curie Grant agreement No. 706376 and by FEDER Funds through the Operational Competitiveness Factors Program—COMPETE and by National Funds through FCT—Foundation for Science and Technology within the scope of the project “Hybrabbid” (PTDC/BIA‐EVL/30628/2017‐ POCI‐01‐0145‐FEDER‐030628). We are grateful to other members of the Littorina research group for helpful discussions. We thank Claire Mérot and an anonymous referee for insightful comments on an earlier version. ' article_processing_charge: No article_type: original author: - first_name: Eva L. full_name: Koch, Eva L. last_name: Koch - first_name: Hernán E. full_name: Morales, Hernán E. last_name: Morales - first_name: Jenny full_name: Larsson, Jenny last_name: Larsson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Alan R. full_name: Lemmon, Alan R. last_name: Lemmon - first_name: E. Moriarty full_name: Lemmon, E. Moriarty last_name: Lemmon - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 2021;5(3):196-213. doi:10.1002/evl3.227 apa: Koch, E. L., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.227 chicago: Koch, Eva L., Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters. Wiley, 2021. https://doi.org/10.1002/evl3.227. ieee: E. L. Koch et al., “Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis,” Evolution Letters, vol. 5, no. 3. Wiley, pp. 196–213, 2021. ista: Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 5(3), 196–213. mla: Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters, vol. 5, no. 3, Wiley, 2021, pp. 196–213, doi:10.1002/evl3.227. short: E.L. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, Evolution Letters 5 (2021) 196–213. date_created: 2021-05-16T22:01:47Z date_published: 2021-05-07T00:00:00Z date_updated: 2023-08-08T13:34:08Z day: '07' ddc: - '570' department: - _id: NiBa doi: 10.1002/evl3.227 ec_funded: 1 external_id: isi: - '000647846200001' file: - access_level: open_access checksum: 023b1608e311f0fda30593ba3d0a4e0b content_type: application/pdf creator: cchlebak date_created: 2021-10-15T08:26:02Z date_updated: 2021-10-15T08:26:02Z file_id: '10142' file_name: 2021_EvolutionLetters_Koch.pdf file_size: 3021108 relation: main_file success: 1 file_date_updated: 2021-10-15T08:26:02Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '3' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 196-213 project: - _id: 265B41B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '797747' name: Theoretical and empirical approaches to understanding Parallel Adaptation publication: Evolution Letters publication_identifier: eissn: - 2056-3744 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '12987' relation: research_data status: public scopus_import: '1' status: public title: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 5 year: '2021' ... --- _id: '9381' abstract: - lang: eng text: 'A game of rock-paper-scissors is an interesting example of an interaction where none of the pure strategies strictly dominates all others, leading to a cyclic pattern. In this work, we consider an unstable version of rock-paper-scissors dynamics and allow individuals to make behavioural mistakes during the strategy execution. We show that such an assumption can break a cyclic relationship leading to a stable equilibrium emerging with only one strategy surviving. We consider two cases: completely random mistakes when individuals have no bias towards any strategy and a general form of mistakes. Then, we determine conditions for a strategy to dominate all other strategies. However, given that individuals who adopt a dominating strategy are still prone to behavioural mistakes in the observed behaviour, we may still observe extinct strategies. That is, behavioural mistakes in strategy execution stabilise evolutionary dynamics leading to an evolutionary stable and, potentially, mixed co-existence equilibrium.' acknowledgement: Authors would like to thank Christian Hilbe and Martin Nowak for their inspiring and very helpful feedback on the manuscript. article_number: e1008523 article_processing_charge: No article_type: original author: - first_name: Maria full_name: Kleshnina, Maria id: 4E21749C-F248-11E8-B48F-1D18A9856A87 last_name: Kleshnina - first_name: Sabrina S. full_name: Streipert, Sabrina S. last_name: Streipert - first_name: Jerzy A. full_name: Filar, Jerzy A. last_name: Filar - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: Kleshnina M, Streipert SS, Filar JA, Chatterjee K. Mistakes can stabilise the dynamics of rock-paper-scissors games. PLoS Computational Biology. 2021;17(4). doi:10.1371/journal.pcbi.1008523 apa: Kleshnina, M., Streipert, S. S., Filar, J. A., & Chatterjee, K. (2021). Mistakes can stabilise the dynamics of rock-paper-scissors games. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008523 chicago: Kleshnina, Maria, Sabrina S. Streipert, Jerzy A. Filar, and Krishnendu Chatterjee. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008523. ieee: M. Kleshnina, S. S. Streipert, J. A. Filar, and K. Chatterjee, “Mistakes can stabilise the dynamics of rock-paper-scissors games,” PLoS Computational Biology, vol. 17, no. 4. Public Library of Science, 2021. ista: Kleshnina M, Streipert SS, Filar JA, Chatterjee K. 2021. Mistakes can stabilise the dynamics of rock-paper-scissors games. PLoS Computational Biology. 17(4), e1008523. mla: Kleshnina, Maria, et al. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.” PLoS Computational Biology, vol. 17, no. 4, e1008523, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1008523. short: M. Kleshnina, S.S. Streipert, J.A. Filar, K. Chatterjee, PLoS Computational Biology 17 (2021). date_created: 2021-05-09T22:01:38Z date_published: 2021-04-01T00:00:00Z date_updated: 2023-08-08T13:31:08Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.1371/journal.pcbi.1008523 ec_funded: 1 external_id: isi: - '000639711200001' file: - access_level: open_access checksum: a94ebe0c4116f5047eaa6029e54d2dac content_type: application/pdf creator: kschuh date_created: 2021-05-11T13:50:06Z date_updated: 2021-05-11T13:50:06Z file_id: '9385' file_name: 2021_pcbi_Kleshnina.pdf file_size: 1323820 relation: main_file success: 1 file_date_updated: 2021-05-11T13:50:06Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: PLoS Computational Biology publication_identifier: eissn: - '15537358' issn: - 1553734X publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Mistakes can stabilise the dynamics of rock-paper-scissors games 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: 17 year: '2021' ... --- _id: '9392' abstract: - lang: eng text: 'Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not.' acknowledgement: We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger K. Butlin and members of the University of Sheffield Speciation Journal Club for feedback on draft survey questions and/or comments on a draft manuscript. Three anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to everyone who took part in the survey. Ethical approval for the survey was obtained through the University of Sheffield Ethics Review Procedure (Application 029768). S.S. was supported by a NERC grant awarded to Roger K. Butlin. article_processing_charge: No article_type: original author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Mark full_name: Ravinet, Mark last_name: Ravinet citation: ama: Stankowski S, Ravinet M. Quantifying the use of species concepts. Current Biology. 2021;31(9):R428-R429. doi:10.1016/j.cub.2021.03.060 apa: Stankowski, S., & Ravinet, M. (2021). Quantifying the use of species concepts. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2021.03.060 chicago: Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology. Cell Press, 2021. https://doi.org/10.1016/j.cub.2021.03.060. ieee: S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” Current Biology, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021. ista: Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429. mla: Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:10.1016/j.cub.2021.03.060. short: S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429. date_created: 2021-05-16T22:01:46Z date_published: 2021-05-10T00:00:00Z date_updated: 2023-08-08T13:34:38Z day: '10' department: - _id: NiBa doi: 10.1016/j.cub.2021.03.060 external_id: isi: - '000654741200004' pmid: - '33974865' intvolume: ' 31' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2021.03.060 month: '05' oa: 1 oa_version: Published Version page: R428-R429 pmid: 1 publication: Current Biology publication_identifier: eissn: - '18790445' issn: - '09609822' publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: Quantifying the use of species concepts type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 31 year: '2021' ... --- _id: '9387' abstract: - lang: eng text: We report the complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This result suggests that fixation of a deleterious allele that follows a click of the Muller’s ratchet is governed by natural selection, instead of random drift. acknowledgement: This work was supported by the Russian Science Foundation grant N 16-14-10173. article_number: '110729' article_processing_charge: No article_type: original author: - first_name: Kseniia full_name: Khudiakova, Kseniia id: 4E6DC800-AE37-11E9-AC72-31CAE5697425 last_name: Khudiakova orcid: 0000-0002-6246-1465 - first_name: Tatiana Yu. full_name: Neretina, Tatiana Yu. last_name: Neretina - first_name: Alexey S. full_name: Kondrashov, Alexey S. last_name: Kondrashov citation: ama: Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 2021;524. doi:10.1016/j.jtbi.2021.110729 apa: Khudiakova, K., Neretina, T. Y., & Kondrashov, A. S. (2021). Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. Elsevier . https://doi.org/10.1016/j.jtbi.2021.110729 chicago: Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal of Theoretical Biology. Elsevier , 2021. https://doi.org/10.1016/j.jtbi.2021.110729. ieee: K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under mutation-selection balance and Muller’s ratchet,” Journal of Theoretical Biology, vol. 524. Elsevier , 2021. ista: Khudiakova K, Neretina TY, Kondrashov AS. 2021. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 524, 110729. mla: Khudiakova, Kseniia, et al. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal of Theoretical Biology, vol. 524, 110729, Elsevier , 2021, doi:10.1016/j.jtbi.2021.110729. short: K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology 524 (2021). date_created: 2021-05-12T05:58:42Z date_published: 2021-04-24T00:00:00Z date_updated: 2023-08-08T13:32:40Z day: '24' department: - _id: GradSch doi: 10.1016/j.jtbi.2021.110729 external_id: isi: - '000659161500002' intvolume: ' 524' isi: 1 keyword: - General Biochemistry - Genetics and Molecular Biology - Modelling and Simulation - Statistics and Probability - General Immunology and Microbiology - Applied Mathematics - General Agricultural and Biological Sciences - General Medicine language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/477489v1 month: '04' oa: 1 oa_version: Preprint publication: Journal of Theoretical Biology publication_identifier: issn: - 0022-5193 publication_status: published publisher: 'Elsevier ' quality_controlled: '1' status: public title: Two linked loci under mutation-selection balance and Muller’s ratchet type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 524 year: '2021' ... --- _id: '12987' abstract: - lang: eng text: Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome. article_processing_charge: No author: - first_name: Eva full_name: Koch, Eva last_name: Koch - first_name: Hernán E. full_name: Morales, Hernán E. last_name: Morales - first_name: Jenny full_name: Larsson, Jenny last_name: Larsson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Alan R. full_name: Lemmon, Alan R. last_name: Lemmon - first_name: E. Moriarty full_name: Lemmon, E. Moriarty last_name: Lemmon - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: 'Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:10.5061/DRYAD.ZGMSBCCB4' apa: 'Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4' chicago: 'Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.' ieee: 'E. Koch et al., “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.' ista: 'Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.' mla: 'Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.' short: E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021). date_created: 2023-05-16T12:34:09Z date_published: 2021-04-10T00:00:00Z date_updated: 2023-08-08T13:34:07Z day: '10' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.ZGMSBCCB4 has_accepted_license: '1' license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.zgmsbccb4 month: '04' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '9394' relation: used_in_publication status: public status: public title: 'Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '9408' abstract: - lang: eng text: We present a computational design system that assists users to model, optimize, and fabricate quad-robots with soft skins. Our system addresses the challenging task of predicting their physical behavior by fully integrating the multibody dynamics of the mechanical skeleton and the elastic behavior of the soft skin. The developed motion control strategy uses an alternating optimization scheme to avoid expensive full space time-optimization, interleaving space-time optimization for the skeleton, and frame-by-frame optimization for the full dynamics. The output are motor torques to drive the robot to achieve a user prescribed motion trajectory. We also provide a collection of convenient engineering tools and empirical manufacturing guidance to support the fabrication of the designed quad-robot. We validate the feasibility of designs generated with our system through physics simulations and with a physically-fabricated prototype. acknowledgement: The authors would like to thank anonymous reviewers for their constructive comments. Weiwei Xu is partially supported by Zhejiang Lab. Yin Yang is partially spported by NSF under Grant Nos. CHS 1845024 and 1717972. Weiwei Xu and Hujun Bao are supported by Fundamental Research Funds for the Central Universities. This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (Grant agreement No 715767). article_number: 2881-2895 article_processing_charge: No author: - first_name: Xudong full_name: Feng, Xudong last_name: Feng - first_name: Jiafeng full_name: Liu, Jiafeng last_name: Liu - first_name: Huamin full_name: Wang, Huamin last_name: Wang - first_name: Yin full_name: Yang, Yin last_name: Yang - first_name: Hujun full_name: Bao, Hujun last_name: Bao - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Weiwei full_name: Xu, Weiwei last_name: Xu citation: ama: Feng X, Liu J, Wang H, et al. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 2021;27(6). doi:10.1109/TVCG.2019.2957218 apa: Feng, X., Liu, J., Wang, H., Yang, Y., Bao, H., Bickel, B., & Xu, W. (2021). Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2019.2957218 chicago: Feng, Xudong, Jiafeng Liu, Huamin Wang, Yin Yang, Hujun Bao, Bernd Bickel, and Weiwei Xu. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2021. https://doi.org/10.1109/TVCG.2019.2957218. ieee: X. Feng et al., “Computational design of skinned Quad-Robots,” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6. IEEE, 2021. ista: Feng X, Liu J, Wang H, Yang Y, Bao H, Bickel B, Xu W. 2021. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 27(6), 2881–2895. mla: Feng, Xudong, et al. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6, 2881–2895, IEEE, 2021, doi:10.1109/TVCG.2019.2957218. short: X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions on Visualization and Computer Graphics 27 (2021). date_created: 2021-05-23T22:01:42Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-08-08T13:45:46Z day: '01' ddc: - '000' department: - _id: BeBi doi: 10.1109/TVCG.2019.2957218 ec_funded: 1 external_id: isi: - '000649620700009' pmid: - '31804937' file: - access_level: open_access checksum: a78e6ac94e33ade4ffaea66943d5f7dc content_type: application/pdf creator: kschuh date_created: 2021-05-25T15:08:49Z date_updated: 2021-05-25T15:08:49Z file_id: '9427' file_name: 2021_TVCG_Feng.pdf file_size: 6183002 relation: main_file success: 1 file_date_updated: 2021-05-25T15:08:49Z has_accepted_license: '1' intvolume: ' 27' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: IEEE Transactions on Visualization and Computer Graphics publication_identifier: eissn: - '10772626' issn: - '19410506' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Computational design of skinned Quad-Robots 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: 27 year: '2021' ... --- _id: '9410' abstract: - lang: eng text: Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains. acknowledgement: We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton, Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall, Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and Michael Whitlock for insightful support. article_number: '20200913' article_processing_charge: No author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Hildegard full_name: Uecker, Hildegard id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87 last_name: Uecker orcid: 0000-0001-9435-2813 - first_name: Paul full_name: Neve, Paul last_name: Neve citation: ama: Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913 apa: Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2020.0913 chicago: Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters. Royal Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913. ieee: M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal Society of London, 2021. ista: Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913. mla: Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:10.1098/rsbl.2020.0913. short: M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021). date_created: 2021-05-23T22:01:43Z date_published: 2021-05-12T00:00:00Z date_updated: 2023-08-08T13:44:35Z day: '12' ddc: - '570' department: - _id: NiBa doi: 10.1098/rsbl.2020.0913 ec_funded: 1 external_id: isi: - '000651501400001' pmid: - ' 33975485' file: - access_level: open_access checksum: 9c13c1f5af7609c97c741f11d293188a content_type: application/pdf creator: kschuh date_created: 2021-05-25T14:09:03Z date_updated: 2021-05-25T14:09:03Z file_id: '9425' file_name: 2021_BiologyLetters_Lagator.pdf file_size: 726759 relation: main_file success: 1 file_date_updated: 2021-05-25T14:09:03Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Biology letters publication_identifier: eissn: - 1744957X publication_status: published publisher: Royal Society of London quality_controlled: '1' scopus_import: '1' status: public title: Adaptation at different points along antibiotic concentration gradients 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: 17 year: '2021' ... --- _id: '9412' abstract: - lang: eng text: We extend our recent result [22] on the central limit theorem for the linear eigenvalue statistics of non-Hermitian matrices X with independent, identically distributed complex entries to the real symmetry class. We find that the expectation and variance substantially differ from their complex counterparts, reflecting (i) the special spectral symmetry of real matrices onto the real axis; and (ii) the fact that real i.i.d. matrices have many real eigenvalues. Our result generalizes the previously known special cases where either the test function is analytic [49] or the first four moments of the matrix elements match the real Gaussian [59, 44]. The key element of the proof is the analysis of several weakly dependent Dyson Brownian motions (DBMs). The conceptual novelty of the real case compared with [22] is that the correlation structure of the stochastic differentials in each individual DBM is non-trivial, potentially even jeopardising its well-posedness. article_number: '24' article_processing_charge: No author: - first_name: Giorgio full_name: Cipolloni, Giorgio id: 42198EFA-F248-11E8-B48F-1D18A9856A87 last_name: Cipolloni orcid: 0000-0002-4901-7992 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 citation: ama: Cipolloni G, Erdös L, Schröder DJ. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 2021;26. doi:10.1214/21-EJP591 apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/21-EJP591 chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2021. https://doi.org/10.1214/21-EJP591. ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular law for random matrices with real entries,” Electronic Journal of Probability, vol. 26. Institute of Mathematical Statistics, 2021. ista: Cipolloni G, Erdös L, Schröder DJ. 2021. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 26, 24. mla: Cipolloni, Giorgio, et al. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” Electronic Journal of Probability, vol. 26, 24, Institute of Mathematical Statistics, 2021, doi:10.1214/21-EJP591. short: G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 26 (2021). date_created: 2021-05-23T22:01:44Z date_published: 2021-03-23T00:00:00Z date_updated: 2023-08-08T13:39:19Z day: '23' ddc: - '510' department: - _id: LaEr doi: 10.1214/21-EJP591 ec_funded: 1 external_id: arxiv: - '2002.02438' isi: - '000641855600001' file: - access_level: open_access checksum: 864ab003ad4cffea783f65aa8c2ba69f content_type: application/pdf creator: kschuh date_created: 2021-05-25T13:24:19Z date_updated: 2021-05-25T13:24:19Z file_id: '9423' file_name: 2021_EJP_Cipolloni.pdf file_size: 865148 relation: main_file success: 1 file_date_updated: 2021-05-25T13:24:19Z has_accepted_license: '1' intvolume: ' 26' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Electronic Journal of Probability publication_identifier: eissn: - '10836489' publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' scopus_import: '1' status: public title: Fluctuation around the circular law for random matrices with real entries tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 26 year: '2021' ... --- _id: '9407' abstract: - lang: eng text: 'High impact epidemics constitute one of the largest threats humanity is facing in the 21st century. In the absence of pharmaceutical interventions, physical distancing together with testing, contact tracing and quarantining are crucial in slowing down epidemic dynamics. Yet, here we show that if testing capacities are limited, containment may fail dramatically because such combined countermeasures drastically change the rules of the epidemic transition: Instead of continuous, the response to countermeasures becomes discontinuous. Rather than following the conventional exponential growth, the outbreak that is initially strongly suppressed eventually accelerates and scales faster than exponential during an explosive growth period. As a consequence, containment measures either suffice to stop the outbreak at low total case numbers or fail catastrophically if marginally too weak, thus implying large uncertainties in reliably estimating overall epidemic dynamics, both during initial phases and during second wave scenarios.' acknowledgement: The authors thank Malte Schröder for valuable discussions and creating the scale-free network topologies. B.H. thanks Mukund Vasudevan for helpful discussion. The research by M.T. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany´s Excellence Strategy–EXC-2068–390729961–Cluster of Excellence Physics of Life of TU Dresden. article_number: '2586' article_processing_charge: No article_type: original author: - first_name: Davide full_name: Scarselli, Davide id: 40315C30-F248-11E8-B48F-1D18A9856A87 last_name: Scarselli orcid: 0000-0001-5227-4271 - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Marc full_name: Timme, Marc last_name: Timme - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Scarselli D, Budanur NB, Timme M, Hof B. Discontinuous epidemic transition due to limited testing. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-22725-9 apa: Scarselli, D., Budanur, N. B., Timme, M., & Hof, B. (2021). Discontinuous epidemic transition due to limited testing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-22725-9 chicago: Scarselli, Davide, Nazmi B Budanur, Marc Timme, and Björn Hof. “Discontinuous Epidemic Transition Due to Limited Testing.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-22725-9. ieee: D. Scarselli, N. B. Budanur, M. Timme, and B. Hof, “Discontinuous epidemic transition due to limited testing,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021. ista: Scarselli D, Budanur NB, Timme M, Hof B. 2021. Discontinuous epidemic transition due to limited testing. Nature Communications. 12(1), 2586. mla: Scarselli, Davide, et al. “Discontinuous Epidemic Transition Due to Limited Testing.” Nature Communications, vol. 12, no. 1, 2586, Springer Nature, 2021, doi:10.1038/s41467-021-22725-9. short: D. Scarselli, N.B. Budanur, M. Timme, B. Hof, Nature Communications 12 (2021). date_created: 2021-05-23T22:01:42Z date_published: 2021-05-10T00:00:00Z date_updated: 2023-08-08T13:45:13Z day: '10' ddc: - '570' department: - _id: BjHo doi: 10.1038/s41467-021-22725-9 external_id: isi: - '000687305500044' file: - access_level: open_access checksum: fe26c1b8a7da1ae07a6c03f80ff06ea1 content_type: application/pdf creator: kschuh date_created: 2021-05-25T14:18:40Z date_updated: 2021-05-25T14:18:40Z file_id: '9426' file_name: 2021_NatureCommunications_Scarselli.pdf file_size: 1176573 relation: main_file success: 1 file_date_updated: 2021-05-25T14:18:40Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - '20411723' 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/smashing-the-covid-curve/ scopus_import: '1' status: public title: Discontinuous epidemic transition due to limited testing 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: 12 year: '2021' ... --- _id: '9411' abstract: - lang: eng text: The dynamics of a triangular magnetocapillary swimmer is studied using the lattice Boltzmann method. We extend on our previous work, which deals with the self-assembly and a specific type of the swimmer motion characterized by the swimmer’s maximum velocity centred around the particle’s inverse viscous time. Here, we identify additional regimes of motion. First, modifying the ratio of surface tension and magnetic forces allows to study the swimmer propagation in the regime of significantly lower frequencies mainly defined by the strength of the magnetocapillary potential. Second, introducing a constant magnetic contribution in each of the particles in addition to their magnetic moment induced by external fields leads to another regime characterized by strong in-plane swimmer reorientations that resemble experimental observations. acknowledgement: This work was financially supported by the DFG Priority Programme SPP 1726 “Microswimmers–From Single Particle Motion to Collective Behaviour” (HA 4382/5-1). We further acknowledge the Jülich Supercomputing Centre (JSC) and the High Performance Computing Centre Stuttgart (HLRS) for the allocation of computing time. article_number: '59' article_processing_charge: No author: - first_name: Alexander full_name: Sukhov, Alexander last_name: Sukhov - first_name: Maxime full_name: Hubert, Maxime last_name: Hubert - first_name: Galien M full_name: Grosjean, Galien M id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425 last_name: Grosjean orcid: 0000-0001-5154-417X - first_name: Oleg full_name: Trosman, Oleg last_name: Trosman - first_name: Sebastian full_name: Ziegler, Sebastian last_name: Ziegler - first_name: Ylona full_name: Collard, Ylona last_name: Collard - first_name: Nicolas full_name: Vandewalle, Nicolas last_name: Vandewalle - first_name: Ana Sunčana full_name: Smith, Ana Sunčana last_name: Smith - first_name: Jens full_name: Harting, Jens last_name: Harting citation: ama: Sukhov A, Hubert M, Grosjean GM, et al. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 2021;44(4). doi:10.1140/epje/s10189-021-00065-2 apa: Sukhov, A., Hubert, M., Grosjean, G. M., Trosman, O., Ziegler, S., Collard, Y., … Harting, J. (2021). Regimes of motion of magnetocapillary swimmers. European Physical Journal E. Springer. https://doi.org/10.1140/epje/s10189-021-00065-2 chicago: Sukhov, Alexander, Maxime Hubert, Galien M Grosjean, Oleg Trosman, Sebastian Ziegler, Ylona Collard, Nicolas Vandewalle, Ana Sunčana Smith, and Jens Harting. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E. Springer, 2021. https://doi.org/10.1140/epje/s10189-021-00065-2. ieee: A. Sukhov et al., “Regimes of motion of magnetocapillary swimmers,” European Physical Journal E, vol. 44, no. 4. Springer, 2021. ista: Sukhov A, Hubert M, Grosjean GM, Trosman O, Ziegler S, Collard Y, Vandewalle N, Smith AS, Harting J. 2021. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 44(4), 59. mla: Sukhov, Alexander, et al. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E, vol. 44, no. 4, 59, Springer, 2021, doi:10.1140/epje/s10189-021-00065-2. short: A. Sukhov, M. Hubert, G.M. Grosjean, O. Trosman, S. Ziegler, Y. Collard, N. Vandewalle, A.S. Smith, J. Harting, European Physical Journal E 44 (2021). date_created: 2021-05-23T22:01:44Z date_published: 2021-04-24T00:00:00Z date_updated: 2023-08-08T13:36:28Z day: '24' ddc: - '530' department: - _id: ScWa doi: 10.1140/epje/s10189-021-00065-2 external_id: isi: - '000643251300001' file: - access_level: open_access checksum: 0ef342d011afbe3c5cb058fda9a3f395 content_type: application/pdf creator: kschuh date_created: 2021-05-25T11:32:14Z date_updated: 2021-05-25T11:32:14Z file_id: '9422' file_name: 2021_EPJE_Sukhov.pdf file_size: 2507870 relation: main_file success: 1 file_date_updated: 2021-05-25T11:32:14Z has_accepted_license: '1' intvolume: ' 44' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: European Physical Journal E publication_identifier: eissn: - 1292895X issn: - '12928941' publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Regimes of motion of magnetocapillary swimmers 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: 44 year: '2021' ... --- _id: '9414' abstract: - lang: eng text: Microtubule plus-end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing in Xenopus egg extract. We observed strong spatial regulation of depolymerization rates, which were higher in the aster interior compared with the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and microtubule-associated proteins (MAPs) in the interior cytosol compared with that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density. acknowledgement: The authors thank the members of Mitchison, Brugués, and Jay Gatlin groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG) for frog maintenance. We thank Nikon for microscopy support at Marine Biological Laboratory (MBL). K.I. was supported by fellowships from the Honjo International Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C. is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research is supported by National Institutes of Health Grant no. R35GM131753. article_processing_charge: No article_type: original author: - first_name: Keisuke full_name: Ishihara, Keisuke last_name: Ishihara - first_name: Franziska full_name: Decker, Franziska last_name: Decker - first_name: Paulo R full_name: Dos Santos Caldas, Paulo R id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87 last_name: Dos Santos Caldas orcid: 0000-0001-6730-4461 - first_name: James F. full_name: Pelletier, James F. last_name: Pelletier - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Jan full_name: Brugués, Jan last_name: Brugués - first_name: Timothy J. full_name: Mitchison, Timothy J. last_name: Mitchison citation: ama: Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 2021;32(9):869-879. doi:10.1091/MBC.E20-11-0723 apa: Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose, M., Brugués, J., & Mitchison, T. J. (2021). Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/MBC.E20-11-0723 chicago: Ishihara, Keisuke, Franziska Decker, Paulo R Dos Santos Caldas, James F. Pelletier, Martin Loose, Jan Brugués, and Timothy J. Mitchison. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell. American Society for Cell Biology, 2021. https://doi.org/10.1091/MBC.E20-11-0723. ieee: K. Ishihara et al., “Spatial variation of microtubule depolymerization in large asters,” Molecular Biology of the Cell, vol. 32, no. 9. American Society for Cell Biology, pp. 869–879, 2021. ista: Ishihara K, Decker F, Dos Santos Caldas PR, Pelletier JF, Loose M, Brugués J, Mitchison TJ. 2021. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 32(9), 869–879. mla: Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell, vol. 32, no. 9, American Society for Cell Biology, 2021, pp. 869–79, doi:10.1091/MBC.E20-11-0723. short: K. Ishihara, F. Decker, P.R. Dos Santos Caldas, J.F. Pelletier, M. Loose, J. Brugués, T.J. Mitchison, Molecular Biology of the Cell 32 (2021) 869–879. date_created: 2021-05-23T22:01:45Z date_published: 2021-04-19T00:00:00Z date_updated: 2023-08-08T13:36:02Z day: '19' department: - _id: MaLo doi: 10.1091/MBC.E20-11-0723 ec_funded: 1 external_id: isi: - '000641574700005' intvolume: ' 32' isi: 1 issue: '9' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/3.0/ main_file_link: - open_access: '1' url: https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723 month: '04' oa: 1 oa_version: Published Version page: 869-879 project: - _id: 2595697A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '679239' name: Self-Organization of the Bacterial Cell - _id: 260D98C8-B435-11E9-9278-68D0E5697425 name: Reconstitution of Bacterial Cell Division Using Purified Components publication: Molecular Biology of the Cell publication_identifier: eissn: - 1939-4586 issn: - 1059-1524 publication_status: published publisher: American Society for Cell Biology quality_controlled: '1' scopus_import: '1' status: public title: Spatial variation of microtubule depolymerization in large asters tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0) short: CC BY-NC-SA (3.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 32 year: '2021' ... --- _id: '9356' abstract: - lang: eng text: 'In runtime verification, a monitor watches a trace of a system and, if possible, decides after observing each finite prefix whether or not the unknown infinite trace satisfies a given specification. We generalize the theory of runtime verification to monitors that attempt to estimate numerical values of quantitative trace properties (instead of attempting to conclude boolean values of trace specifications), such as maximal or average response time along a trace. Quantitative monitors are approximate: with every finite prefix, they can improve their estimate of the infinite trace''s unknown property value. Consequently, quantitative monitors can be compared with regard to a precision-cost trade-off: better approximations of the property value require more monitor resources, such as states (in the case of finite-state monitors) or registers, and additional resources yield better approximations. We introduce a formal framework for quantitative and approximate monitoring, show how it conservatively generalizes the classical boolean setting for monitoring, and give several precision-cost trade-offs for monitors. For example, we prove that there are quantitative properties for which every additional register improves monitoring precision.' acknowledgement: We thank the anonymous reviewers for their helpful comments. This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). article_number: '9470547' article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Naci E full_name: Sarac, Naci E id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425 last_name: Sarac citation: ama: 'Henzinger TA, Sarac NE. Quantitative and approximate monitoring. In: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers; 2021. doi:10.1109/LICS52264.2021.9470547' apa: 'Henzinger, T. A., & Sarac, N. E. (2021). Quantitative and approximate monitoring. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Online: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS52264.2021.9470547' chicago: Henzinger, Thomas A, and Naci E Sarac. “Quantitative and Approximate Monitoring.” In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470547. ieee: T. A. Henzinger and N. E. Sarac, “Quantitative and approximate monitoring,” in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Online, 2021. ista: 'Henzinger TA, Sarac NE. 2021. Quantitative and approximate monitoring. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 9470547.' mla: Henzinger, Thomas A., and Naci E. Sarac. “Quantitative and Approximate Monitoring.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, 9470547, Institute of Electrical and Electronics Engineers, 2021, doi:10.1109/LICS52264.2021.9470547. short: T.A. Henzinger, N.E. Sarac, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021. conference: end_date: 2021-07-02 location: Online name: 'LICS: Symposium on Logic in Computer Science' start_date: 2021-06-29 date_created: 2021-04-30T17:30:47Z date_published: 2021-06-29T00:00:00Z date_updated: 2023-08-08T13:52:56Z day: '29' ddc: - '000' department: - _id: GradSch - _id: ToHe doi: 10.1109/LICS52264.2021.9470547 external_id: arxiv: - '2105.08353' isi: - '000947350400021' file: - access_level: open_access checksum: 6e4cba3f72775f479c5b1b75d1a4a0c4 content_type: application/pdf creator: esarac date_created: 2021-06-16T08:23:54Z date_updated: 2021-06-16T08:23:54Z file_id: '9557' file_name: qam.pdf file_size: 641990 relation: main_file success: 1 file_date_updated: 2021-06-16T08:23:54Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Quantitative and approximate monitoring type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9439' abstract: - lang: eng text: The ability to adapt to changes in stimulus statistics is a hallmark of sensory systems. Here, we developed a theoretical framework that can account for the dynamics of adaptation from an information processing perspective. We use this framework to optimize and analyze adaptive sensory codes, and we show that codes optimized for stationary environments can suffer from prolonged periods of poor performance when the environment changes. To mitigate the adversarial effects of these environmental changes, sensory systems must navigate tradeoffs between the ability to accurately encode incoming stimuli and the ability to rapidly detect and adapt to changes in the distribution of these stimuli. We derive families of codes that balance these objectives, and we demonstrate their close match to experimentally observed neural dynamics during mean and variance adaptation. Our results provide a unifying perspective on adaptation across a range of sensory systems, environments, and sensory tasks. acknowledgement: We thank D. Kastner and T. Münch for generously providing figures from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy for useful discussions and feedback on the manuscript. W.F.M. was funded by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute. article_processing_charge: No article_type: original author: - first_name: Wiktor F full_name: Mlynarski, Wiktor F id: 358A453A-F248-11E8-B48F-1D18A9856A87 last_name: Mlynarski - first_name: Ann M. full_name: Hermundstad, Ann M. last_name: Hermundstad citation: ama: Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0 apa: Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0 chicago: Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0. ieee: W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,” Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021. ista: Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes. Nature Neuroscience. 24, 998–1009. mla: Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009, doi:10.1038/s41593-021-00846-0. short: W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009. date_created: 2021-05-30T22:01:24Z date_published: 2021-05-20T00:00:00Z date_updated: 2023-08-08T13:51:14Z day: '20' department: - _id: GaTk doi: 10.1038/s41593-021-00846-0 ec_funded: 1 external_id: isi: - '000652577300003' intvolume: ' 24' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/669200 ' month: '05' oa: 1 oa_version: Preprint page: 998-1009 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature Neuroscience publication_identifier: eissn: - 1546-1726 issn: - 1097-6256 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Efficient and adaptive sensory codes type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 24 year: '2021' ... --- _id: '9443' abstract: - lang: eng text: Endoplasmic reticulum–plasma membrane contact sites (ER–PM CS) play fundamental roles in all eukaryotic cells. Arabidopsis thaliana mutants lacking the ER–PM protein tether synaptotagmin1 (SYT1) exhibit decreased PM integrity under multiple abiotic stresses, such as freezing, high salt, osmotic stress, and mechanical damage. Here, we show that, together with SYT1, the stress-induced SYT3 is an ER–PM tether that also functions in maintaining PM integrity. The ER–PM CS localization of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated by abiotic stress. Lipidomic analysis revealed that cold stress increased the accumulation of diacylglycerol at the PM in a syt1/3 double mutant relative to wild-type while the levels of most glycerolipid species remain unchanged. In addition, the SYT1-green fluorescent protein fusion preferentially binds diacylglycerol in vivo with little affinity for polar glycerolipids. Our work uncovers a SYT-dependent mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol at the PM produced during episodes of abiotic stress. acknowledgement: "We would also like to thank Lothar Willmitzer for the lipidomic analysis at the Max Planck Institute of Molecular Plant Physiology (Potsdam, Germany). We thank Manuela Vega from SCI for her technical assistance in image analysis. We thank John R. Pearson and the Bionand Nanoimaging Unit, F. David Navas Fernández and the SCAI Imaging Facility and The Plant Cell Biology facility at the Shanghai Center for Plant Stress Biology for assistance with confocal microscopy. The FaFAH1 clone was a gift from Iraida Amaya Saavedra (IFAPA-Centro de Churriana, Málaga, Spain). The AHA3 antibody against the H+-ATPase was a gift from Ramón Serrano Salom (Instituto de Biología Molecular y Celular de Plantas, Valencia, Spain). The MAP-mTU2-SAC1 construct was provided by Yvon Jaillais (Laboratoire Reproduction et Développement des Plantes, Univ Lyon, France). The pGWB5 from the pGWB vector series, was provided by Tsuyoshi Nakagawa (Department of Molecular and Functional Genomics, Shimane University). We thank Plan Propio from the University of Málaga for financial support.\r\nFunding" article_processing_charge: No article_type: original author: - first_name: N full_name: Ruiz-Lopez, N last_name: Ruiz-Lopez - first_name: J full_name: Pérez-Sancho, J last_name: Pérez-Sancho - first_name: A full_name: Esteban Del Valle, A last_name: Esteban Del Valle - first_name: RP full_name: Haslam, RP last_name: Haslam - first_name: S full_name: Vanneste, S last_name: Vanneste - first_name: R full_name: Catalá, R last_name: Catalá - first_name: C full_name: Perea-Resa, C last_name: Perea-Resa - first_name: D full_name: Van Damme, D last_name: Van Damme - first_name: S full_name: García-Hernández, S last_name: García-Hernández - first_name: A full_name: Albert, A last_name: Albert - first_name: J full_name: Vallarino, J last_name: Vallarino - first_name: J full_name: Lin, J last_name: Lin - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: AP full_name: Macho, AP last_name: Macho - first_name: J full_name: Salinas, J last_name: Salinas - first_name: A full_name: Rosado, A last_name: Rosado - first_name: JA full_name: Napier, JA last_name: Napier - first_name: V full_name: Amorim-Silva, V last_name: Amorim-Silva - first_name: MA full_name: Botella, MA last_name: Botella citation: ama: Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, et al. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 2021;33(7):2431-2453. doi:10.1093/plcell/koab122 apa: Ruiz-Lopez, N., Pérez-Sancho, J., Esteban Del Valle, A., Haslam, R., Vanneste, S., Catalá, R., … Botella, M. (2021). Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab122 chicago: Ruiz-Lopez, N, J Pérez-Sancho, A Esteban Del Valle, RP Haslam, S Vanneste, R Catalá, C Perea-Resa, et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab122. ieee: N. Ruiz-Lopez et al., “Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress,” Plant Cell, vol. 33, no. 7. American Society of Plant Biologists, pp. 2431–2453, 2021. ista: Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, Haslam R, Vanneste S, Catalá R, Perea-Resa C, Van Damme D, García-Hernández S, Albert A, Vallarino J, Lin J, Friml J, Macho A, Salinas J, Rosado A, Napier J, Amorim-Silva V, Botella M. 2021. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 33(7), 2431–2453. mla: Ruiz-Lopez, N., et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell, vol. 33, no. 7, American Society of Plant Biologists, 2021, pp. 2431–53, doi:10.1093/plcell/koab122. short: N. Ruiz-Lopez, J. Pérez-Sancho, A. Esteban Del Valle, R. Haslam, S. Vanneste, R. Catalá, C. Perea-Resa, D. Van Damme, S. García-Hernández, A. Albert, J. Vallarino, J. Lin, J. Friml, A. Macho, J. Salinas, A. Rosado, J. Napier, V. Amorim-Silva, M. Botella, Plant Cell 33 (2021) 2431–2453. date_created: 2021-06-02T13:13:58Z date_published: 2021-07-01T00:00:00Z date_updated: 2023-08-08T13:54:32Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1093/plcell/koab122 ec_funded: 1 external_id: isi: - '000703938100026' pmid: - '33944955' file: - access_level: open_access checksum: 22d596678d00310d793611864a6d0fcd content_type: application/pdf creator: cchlebak date_created: 2021-10-14T13:36:38Z date_updated: 2021-10-14T13:36:38Z file_id: '10141' file_name: 2021_PlantCell_RuizLopez.pdf file_size: 2952028 relation: main_file success: 1 file_date_updated: 2021-10-14T13:36:38Z has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 2431-2453 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Plant Cell publication_identifier: eissn: - 1532-298x issn: - 1040-4651 publication_status: published publisher: American Society of Plant Biologists quality_controlled: '1' scopus_import: '1' status: public title: Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress 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: 33 year: '2021' ...