--- _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 license: https://creativecommons.org/licenses/by/4.0/ 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' ...