--- _id: '13057' abstract: - lang: eng text: 'This dataset comprises all data shown in the figures of the submitted article "Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction". Additional raw data are available from the corresponding author on reasonable request.' article_processing_charge: No author: - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Grisha full_name: Szep, Grisha last_name: Szep - first_name: Andrea full_name: Trioni, Andrea id: 42F71B44-F248-11E8-B48F-1D18A9856A87 last_name: Trioni - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: 'Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. 2021. doi:10.5281/ZENODO.5592103' apa: 'Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M., & Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. Zenodo. https://doi.org/10.5281/ZENODO.5592103' chicago: 'Peruzzo, Matilda, Farid Hassani, Grisha Szep, Andrea Trioni, Elena Redchenko, Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5592103.' ieee: 'M. Peruzzo et al., “Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction.” Zenodo, 2021.' ista: 'Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM. 2021. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction, Zenodo, 10.5281/ZENODO.5592103.' mla: 'Peruzzo, Matilda, et al. Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction. Zenodo, 2021, doi:10.5281/ZENODO.5592103.' short: M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, (2021). date_created: 2023-05-23T13:42:27Z date_published: 2021-10-22T00:00:00Z date_updated: 2023-08-11T10:44:21Z day: '22' ddc: - '530' department: - _id: JoFi doi: 10.5281/ZENODO.5592103 license: https://creativecommons.org/licenses/by/4.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.5592104 month: '10' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '9928' relation: used_in_publication status: public status: public title: 'Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '9985' abstract: - lang: eng text: AMPA receptor (AMPAR) abundance and positioning at excitatory synapses regulates the strength of transmission. Changes in AMPAR localisation can enact synaptic plasticity, allowing long-term information storage, and is therefore tightly controlled. Multiple mechanisms regulating AMPAR synaptic anchoring have been described, but with limited coherence or comparison between reports, our understanding of this process is unclear. Here, combining synaptic recordings from mouse hippocampal slices and super-resolution imaging in dissociated cultures, we compare the contributions of three AMPAR interaction domains controlling transmission at hippocampal CA1 synapses. We show that the AMPAR C-termini play only a modulatory role, whereas the extracellular N-terminal domain (NTD) and PDZ interactions of the auxiliary subunit TARP γ8 are both crucial, and each is sufficient to maintain transmission. Our data support a model in which γ8 accumulates AMPARs at the postsynaptic density, where the NTD further tunes their positioning. This interplay between cytosolic (TARP γ8) and synaptic cleft (NTD) interactions provides versatility to regulate synaptic transmission and plasticity. acknowledgement: The authors are very grateful to Andrew Penn for advice and discussions on surface receptor labelling in slice tissue, dissociated culture transfection, and for providing tdTomato and BirAER expression plasmids. This work would not have been possible without support from the Biological Services teams at both the Laboratory of Molecular Biology and Ares facilities. We are also very grateful to Nick Barry and Jerome Boulanger of the LMB Light Microscopy facility for support with confocal and STORM imaging and analysis, Junichi Takagi for providing scFv-Clasp expression constructs, Veronica Chang for assistance with scFv-Clasp protein production, and Nejc Kejzar for assistance with cluster analysis. We would like to thank Teru Nakagawa and Ole Paulsen for critical reading of the manuscript and constructive feedback. This work was supported by grants from the Medical Research Council (MC_U105174197) and BBSRC (BB/N002113/1). article_number: '5083' article_processing_charge: Yes article_type: original author: - first_name: Jake full_name: Watson, Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Alexandra full_name: Pinggera, Alexandra last_name: Pinggera - first_name: Hinze full_name: Ho, Hinze last_name: Ho - first_name: Ingo H. full_name: Greger, Ingo H. last_name: Greger citation: ama: Watson J, Pinggera A, Ho H, Greger IH. AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-25281-4 apa: Watson, J., Pinggera, A., Ho, H., & Greger, I. H. (2021). AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-021-25281-4 chicago: Watson, Jake, Alexandra Pinggera, Hinze Ho, and Ingo H. Greger. “AMPA Receptor Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.” Nature Communications. Nature Publishing Group, 2021. https://doi.org/10.1038/s41467-021-25281-4. ieee: J. Watson, A. Pinggera, H. Ho, and I. H. Greger, “AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions,” Nature Communications, vol. 12, no. 1. Nature Publishing Group, 2021. ista: Watson J, Pinggera A, Ho H, Greger IH. 2021. AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications. 12(1), 5083. mla: Watson, Jake, et al. “AMPA Receptor Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.” Nature Communications, vol. 12, no. 1, 5083, Nature Publishing Group, 2021, doi:10.1038/s41467-021-25281-4. short: J. Watson, A. Pinggera, H. Ho, I.H. Greger, Nature Communications 12 (2021). date_created: 2021-09-05T22:01:23Z date_published: 2021-08-23T00:00:00Z date_updated: 2023-08-11T11:07:51Z day: '23' ddc: - '612' department: - _id: PeJo doi: 10.1038/s41467-021-25281-4 external_id: isi: - '000687672000006' pmid: - '34426577 ' file: - access_level: open_access checksum: 1bf4f6a561f96bc426d754de9cb57710 content_type: application/pdf creator: cchlebak date_created: 2021-09-08T12:57:06Z date_updated: 2021-09-08T12:57:06Z file_id: '9991' file_name: 2021_NatureCommunications_Watson.pdf file_size: 18310502 relation: main_file success: 1 file_date_updated: 2021-09-08T12:57:06Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Nature Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '9981' abstract: - lang: eng text: "The numerical simulation of dynamical phenomena in interacting quantum systems is a notoriously hard problem. Although a number of promising numerical methods exist, they often have limited applicability due to the growth of entanglement or the presence of the so-called sign problem. In this work, we develop an importance sampling scheme for the simulation of quantum spin dynamics, building on a recent approach mapping quantum spin systems to classical stochastic processes. The importance sampling scheme is based on identifying the classical trajectory that yields the largest contribution to a given quantum observable. An exact transformation is then carried out to preferentially sample trajectories that are close to the dominant one. We demonstrate that this approach is capable of reducing the temporal growth of fluctuations in the stochastic quantities, thus extending the range of accessible times and system sizes compared to direct sampling. We discuss advantages and limitations of the proposed approach, outlining directions\r\nfor further developments." article_number: '048' 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. Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. 2021;11(3). doi:10.21468/scipostphys.11.3.048 apa: De Nicola, S. (2021). Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. SciPost. https://doi.org/10.21468/scipostphys.11.3.048 chicago: De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation of Quantum Spin Dynamics.” SciPost Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.3.048. ieee: S. De Nicola, “Importance sampling scheme for the stochastic simulation of quantum spin dynamics,” SciPost Physics, vol. 11, no. 3. SciPost, 2021. ista: De Nicola S. 2021. Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. 11(3), 048. mla: De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation of Quantum Spin Dynamics.” SciPost Physics, vol. 11, no. 3, 048, SciPost, 2021, doi:10.21468/scipostphys.11.3.048. short: S. De Nicola, SciPost Physics 11 (2021). date_created: 2021-09-02T11:49:47Z date_published: 2021-09-02T00:00:00Z date_updated: 2023-08-11T10:59:29Z day: '02' ddc: - '519' department: - _id: MaSe doi: 10.21468/scipostphys.11.3.048 ec_funded: 1 external_id: arxiv: - '2103.16468' isi: - '000692534200001' file: - access_level: open_access checksum: e4ec69d893e31811efc6093cb6ea8eb7 content_type: application/pdf creator: cchlebak date_created: 2021-09-02T14:05:43Z date_updated: 2021-09-02T14:05:43Z file_id: '9984' file_name: 2021_SciPostPhys_DeNicola.pdf file_size: 373833 relation: main_file success: 1 file_date_updated: 2021-09-02T14:05:43Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '3' keyword: - General Physics and Astronomy language: - iso: eng month: '09' 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: eissn: - 2666-9366 issn: - 2542-4653 publication_status: published publisher: SciPost quality_controlled: '1' status: public title: Importance sampling scheme for the stochastic simulation of quantum spin dynamics tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2021' ... --- _id: '9951' abstract: - lang: eng text: "There has recently been a surge of interest in the computational and complexity properties of the population model, which assumes n anonymous, computationally-bounded nodes, interacting at random, with the goal of jointly computing global predicates. Significant work has gone towards investigating majority or consensus dynamics in this model: that is, assuming that every node is initially in one of two states X or Y, determine which state had higher initial count.\r\n\r\nIn this paper, we consider a natural generalization of majority/consensus, which we call comparison : in its simplest formulation, we are given two baseline states, X and Y, present in any initial configuration in fixed, but possibly small counts. One of these states has higher count than the other: we will assume |X_0| > C |Y_0| for some constant C > 1. The challenge is to design a protocol by which nodes can quickly and reliably decide on which of the baseline states X_0 and Y_0 has higher initial count. We begin by analyzing a simple and general dynamics solving the above comparison problem, which uses O( log n ) states per node, and converges in O(log n) (parallel) time, with high probability, to a state where the whole population votes on opinions X or Y at rates proportional to the initial concentrations of |X_0| vs. |Y_0|. We then describe how this procedure can be bootstrapped to solve comparison, i.e. have every node in the population reach the \"correct'' decision, with probability 1 - o(1), at the cost of O (log log n) additional states. Further, we prove that this dynamics is self-stabilizing, in the sense that it converges to the correct decision from arbitrary initial states, and leak-robust, in the sense that it can withstand spurious faulty reactions, which are known to occur in practical implementations of population protocols. Our analysis is based on a new martingale concentration result relating the discrete-time evolution of a population protocol to its expected (steady-state) analysis, which should be a useful tool when analyzing opinion dynamics and epidemic dissemination in the population model." acknowledgement: We would like to thank Rati Gelashvili for very useful discussions, and the PODC anonymous reviewers for their careful reading of our paper, and for their useful remarks. This work is partially supported by the Polish National Science Center (NCN) grant UMO2017/25/B/ST6/02010. article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Martin full_name: Töpfer, Martin id: 4B865388-F248-11E8-B48F-1D18A9856A87 last_name: Töpfer - first_name: Przemysław full_name: Uznański, Przemysław last_name: Uznański citation: ama: 'Alistarh D-A, Töpfer M, Uznański P. Comparison dynamics in population protocols. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:55-65. doi:10.1145/3465084.3467915' apa: 'Alistarh, D.-A., Töpfer, M., & Uznański, P. (2021). Comparison dynamics in population protocols. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 55–65). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467915' chicago: Alistarh, Dan-Adrian, Martin Töpfer, and Przemysław Uznański. “Comparison Dynamics in Population Protocols.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 55–65. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467915. ieee: D.-A. Alistarh, M. Töpfer, and P. Uznański, “Comparison dynamics in population protocols,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 55–65. ista: 'Alistarh D-A, Töpfer M, Uznański P. 2021. Comparison dynamics in population protocols. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 55–65.' mla: Alistarh, Dan-Adrian, et al. “Comparison Dynamics in Population Protocols.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 55–65, doi:10.1145/3465084.3467915. short: D.-A. Alistarh, M. Töpfer, P. Uznański, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 55–65. conference: end_date: 2021-07-30 location: Virtual, Italy name: 'PODC: Symposium on Principles of Distributed Computing' start_date: 2021-07-26 date_created: 2021-08-22T22:01:20Z date_published: 2021-07-21T00:00:00Z date_updated: 2023-08-11T10:56:04Z day: '21' department: - _id: DaAl doi: 10.1145/3465084.3467915 external_id: isi: - '000744439800005' isi: 1 language: - iso: eng month: '07' oa_version: None page: 55-65 publication: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing publication_identifier: isbn: - '9781450385480' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Comparison dynamics in population protocols type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9960' abstract: - lang: eng text: The control of many-body quantum dynamics in complex systems is a key challenge in the quest to reliably produce and manipulate large-scale quantum entangled states. Recently, quench experiments in Rydberg atom arrays [Bluvstein et al. Science 371, 1355 (2021)] demonstrated that coherent revivals associated with quantum many-body scars can be stabilized by periodic driving, generating stable subharmonic responses over a wide parameter regime. We analyze a simple, related model where these phenomena originate from spatiotemporal ordering in an effective Floquet unitary, corresponding to discrete time-crystalline behavior in a prethermal regime. Unlike conventional discrete time crystals, the subharmonic response exists only for Néel-like initial states, associated with quantum scars. We predict robustness to perturbations and identify emergent timescales that could be observed in future experiments. Our results suggest a route to controlling entanglement in interacting quantum systems by combining periodic driving with many-body scars. acknowledgement: We thank Dmitry Abanin, Ehud Altman, Iris Cong, Sepehr Ebadi, Alex Keesling, Harry Levine, Ahmed Omran, Hannes Pichler, Rhine Samajdar, Guilia Semeghini, Tout Wang, Norman Yao, and Harry Zhou or stimulating discussions. We acknowledge support from the Center for Ultracold Atoms, the National Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of Energy, the Army Research Office MURI, and the DARPA ONISQ program (M. L., N. M, W. W. H., D. B.); the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme Grant Agreement No. 850899 (A. M. and M. S.); the Department of Energy Computational Science Graduate Fellowship under Awards No. DESC0021110 (N. M.); the Moore Foundation EPiQS initiative Grant No. GBMF4306, the National University of Singapore (NUS) Development Grant AY2019/2020 and the Stanford Institute for Theoretical Physics (W. W. H.); the NSF Graduate Research Fellowship Program (Grant No. DGE1745303) and The Fannie and John Hertz Foundation (D. B.); the Miller Institute for Basic Research in Science (S. C.); DOE Quantum Systems Accelerator – Contract No. 7568717; and DOE Programmable Quantum Simulators for Lattice Gauge Theories and Gauge-Gravity Correspondence – Grant No. DE-SC0021013. article_number: '090602' article_processing_charge: No article_type: letter_note author: - first_name: N. full_name: Maskara, N. last_name: Maskara - first_name: Alexios full_name: Michailidis, Alexios id: 36EBAD38-F248-11E8-B48F-1D18A9856A87 last_name: Michailidis orcid: 0000-0002-8443-1064 - first_name: W. W. full_name: Ho, W. W. last_name: Ho - first_name: D. full_name: Bluvstein, D. last_name: Bluvstein - first_name: S. full_name: Choi, S. last_name: Choi - first_name: M. D. full_name: Lukin, M. D. last_name: Lukin - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: 'Maskara N, Michailidis A, Ho WW, et al. Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. Physical Review Letters. 2021;127(9). doi:10.1103/PhysRevLett.127.090602' apa: 'Maskara, N., Michailidis, A., Ho, W. W., Bluvstein, D., Choi, S., Lukin, M. D., & Serbyn, M. (2021). Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.127.090602' chicago: 'Maskara, N., Alexios Michailidis, W. W. Ho, D. Bluvstein, S. Choi, M. D. Lukin, and Maksym Serbyn. “Discrete Time-Crystalline Order Enabled by Quantum Many-Body Scars: Entanglement Steering via Periodic Driving.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.127.090602.' ieee: 'N. Maskara et al., “Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving,” Physical Review Letters, vol. 127, no. 9. American Physical Society, 2021.' ista: 'Maskara N, Michailidis A, Ho WW, Bluvstein D, Choi S, Lukin MD, Serbyn M. 2021. Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. Physical Review Letters. 127(9), 090602.' mla: 'Maskara, N., et al. “Discrete Time-Crystalline Order Enabled by Quantum Many-Body Scars: Entanglement Steering via Periodic Driving.” Physical Review Letters, vol. 127, no. 9, 090602, American Physical Society, 2021, doi:10.1103/PhysRevLett.127.090602.' short: N. Maskara, A. Michailidis, W.W. Ho, D. Bluvstein, S. Choi, M.D. Lukin, M. Serbyn, Physical Review Letters 127 (2021). date_created: 2021-08-28T08:08:58Z date_published: 2021-08-27T00:00:00Z date_updated: 2023-08-11T10:57:51Z day: '27' department: - _id: MaSe doi: 10.1103/PhysRevLett.127.090602 ec_funded: 1 external_id: arxiv: - '2102.13160' isi: - '000692200100002' intvolume: ' 127' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2102.13160 month: '08' oa: 1 oa_version: Submitted Version project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: 'Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 127 year: '2021' ... --- _id: '9961' abstract: - lang: eng text: The notion of Thouless energy plays a central role in the theory of Anderson localization. We investigate and compare the scaling of Thouless energy across the many-body localization (MBL) transition in a Floquet model. We use a combination of methods that are reliable on the ergodic side of the transition (e.g., spectral form factor) and methods that work on the MBL side (e.g., typical matrix elements of local operators) to obtain a complete picture of the Thouless energy behavior across the transition. On the ergodic side, Thouless energy decreases slowly with the system size, while at the transition it becomes comparable to the level spacing. Different probes yield consistent estimates of Thouless energy in their overlapping regime of applicability, giving the location of the transition point nearly free of finite-size drift. This work establishes a connection between different definitions of Thouless energy in a many-body setting and yields insights into the MBL transition in Floquet systems. acknowledgement: "We thank S. Garratt for useful comments on the manuscript. This work was supported by the Swiss National Science Foundation (M. Sonner and D.A.A.) and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (M. Serbyn, Grant Agreement No. 850899, and D.A.A., Grant Agreement No. 864597). Z.P. acknowledges support from EPSRC Grant No. EP/R020612/1 and from Leverhulme Trust Research Leadership Award No. RL-2019-015. The computations were performed on the Baobab cluster of the University\r\nof Geneva." article_number: L081112 article_processing_charge: No article_type: letter_note author: - first_name: Michael full_name: Sonner, Michael last_name: Sonner - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić - first_name: Dmitry A. full_name: Abanin, Dmitry A. last_name: Abanin citation: ama: Sonner M, Serbyn M, Papić Z, Abanin DA. Thouless energy across the many-body localization transition in Floquet systems. Physical Review B. 2021;104(8). doi:10.1103/PhysRevB.104.L081112 apa: Sonner, M., Serbyn, M., Papić, Z., & Abanin, D. A. (2021). Thouless energy across the many-body localization transition in Floquet systems. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.104.L081112 chicago: Sonner, Michael, Maksym Serbyn, Zlatko Papić, and Dmitry A. Abanin. “Thouless Energy across the Many-Body Localization Transition in Floquet Systems.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/PhysRevB.104.L081112. ieee: M. Sonner, M. Serbyn, Z. Papić, and D. A. Abanin, “Thouless energy across the many-body localization transition in Floquet systems,” Physical Review B, vol. 104, no. 8. American Physical Society, 2021. ista: Sonner M, Serbyn M, Papić Z, Abanin DA. 2021. Thouless energy across the many-body localization transition in Floquet systems. Physical Review B. 104(8), L081112. mla: Sonner, Michael, et al. “Thouless Energy across the Many-Body Localization Transition in Floquet Systems.” Physical Review B, vol. 104, no. 8, L081112, American Physical Society, 2021, doi:10.1103/PhysRevB.104.L081112. short: M. Sonner, M. Serbyn, Z. Papić, D.A. Abanin, Physical Review B 104 (2021). date_created: 2021-08-28T16:44:55Z date_published: 2021-08-15T00:00:00Z date_updated: 2023-08-11T10:57:09Z day: '15' department: - _id: MaSe doi: 10.1103/PhysRevB.104.L081112 ec_funded: 1 external_id: arxiv: - '2012.15676' isi: - '000689734500009' intvolume: ' 104' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2012.15676 month: '08' oa: 1 oa_version: Submitted Version project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Thouless energy across the many-body localization transition in Floquet systems type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 104 year: '2021' ... --- _id: '9957' abstract: - lang: eng text: The reflectance field of a face describes the reflectance properties responsible for complex lighting effects including diffuse, specular, inter-reflection and self shadowing. Most existing methods for estimating the face reflectance from a monocular image assume faces to be diffuse with very few approaches adding a specular component. This still leaves out important perceptual aspects of reflectance as higher-order global illumination effects and self-shadowing are not modeled. We present a new neural representation for face reflectance where we can estimate all components of the reflectance responsible for the final appearance from a single monocular image. Instead of modeling each component of the reflectance separately using parametric models, our neural representation allows us to generate a basis set of faces in a geometric deformation-invariant space, parameterized by the input light direction, viewpoint and face geometry. We learn to reconstruct this reflectance field of a face just from a monocular image, which can be used to render the face from any viewpoint in any light condition. Our method is trained on a light-stage training dataset, which captures 300 people illuminated with 150 light conditions from 8 viewpoints. We show that our method outperforms existing monocular reflectance reconstruction methods, in terms of photorealism due to better capturing of physical premitives, such as sub-surface scattering, specularities, self-shadows and other higher-order effects. acknowledgement: "We thank Tarun Yenamandra and Duarte David for helping us with the comparisons. This work was supported by the\r\nERC Consolidator Grant 4DReply (770784). We also acknowledge support from InterDigital." article_processing_charge: No author: - first_name: Mallikarjun full_name: B R, Mallikarjun last_name: B R - first_name: Ayush full_name: Tewari, Ayush last_name: Tewari - first_name: Tae-Hyun full_name: Oh, Tae-Hyun last_name: Oh - first_name: Tim full_name: Weyrich, Tim last_name: Weyrich - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Hans-Peter full_name: Seidel, Hans-Peter last_name: Seidel - first_name: Hanspeter full_name: Pfister, Hanspeter last_name: Pfister - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Mohamed full_name: Elgharib, Mohamed last_name: Elgharib - first_name: Christian full_name: Theobalt, Christian last_name: Theobalt citation: ama: 'B R M, Tewari A, Oh T-H, et al. Monocular reconstruction of neural face reflectance fields. In: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE; 2021:4791-4800. doi:10.1109/CVPR46437.2021.00476' apa: 'B R, M., Tewari, A., Oh, T.-H., Weyrich, T., Bickel, B., Seidel, H.-P., … Theobalt, C. (2021). Monocular reconstruction of neural face reflectance fields. In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (pp. 4791–4800). Nashville, TN, United States; Virtual: IEEE. https://doi.org/10.1109/CVPR46437.2021.00476' chicago: B R, Mallikarjun, Ayush Tewari, Tae-Hyun Oh, Tim Weyrich, Bernd Bickel, Hans-Peter Seidel, Hanspeter Pfister, Wojciech Matusik, Mohamed Elgharib, and Christian Theobalt. “Monocular Reconstruction of Neural Face Reflectance Fields.” In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 4791–4800. IEEE, 2021. https://doi.org/10.1109/CVPR46437.2021.00476. ieee: M. B R et al., “Monocular reconstruction of neural face reflectance fields,” in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Nashville, TN, United States; Virtual, 2021, pp. 4791–4800. ista: 'B R M, Tewari A, Oh T-H, Weyrich T, Bickel B, Seidel H-P, Pfister H, Matusik W, Elgharib M, Theobalt C. 2021. Monocular reconstruction of neural face reflectance fields. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 4791–4800.' mla: B R, Mallikarjun, et al. “Monocular Reconstruction of Neural Face Reflectance Fields.” Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2021, pp. 4791–800, doi:10.1109/CVPR46437.2021.00476. short: M. B R, A. Tewari, T.-H. Oh, T. Weyrich, B. Bickel, H.-P. Seidel, H. Pfister, W. Matusik, M. Elgharib, C. Theobalt, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2021, pp. 4791–4800. conference: end_date: 2021-06-25 location: Nashville, TN, United States; Virtual name: 'CVPR: Conference on Computer Vision and Pattern Recognition' start_date: 2021-06-20 date_created: 2021-08-24T06:03:00Z date_published: 2021-09-01T00:00:00Z date_updated: 2023-08-11T11:08:35Z day: '01' ddc: - '000' department: - _id: BeBi doi: 10.1109/CVPR46437.2021.00476 external_id: arxiv: - '2008.10247' isi: - '000739917304096' file: - access_level: open_access checksum: 961db0bde76dd87cf833930080bb9f38 content_type: application/pdf creator: bbickel date_created: 2021-08-24T06:02:15Z date_updated: 2021-08-24T06:02:15Z file_id: '9958' file_name: R_Monocular_Reconstruction_of_Neural_Face_Reflectance_Fields_CVPR_2021_paper[1].pdf file_size: 4746649 relation: main_file file_date_updated: 2021-08-24T06:02:15Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Preprint page: 4791-4800 publication: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition publication_identifier: isbn: - 978-166544509-2 issn: - 1063-6919 publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Monocular reconstruction of neural face reflectance fields type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9973' abstract: - lang: eng text: In this article we introduce a complete gradient estimate for symmetric quantum Markov semigroups on von Neumann algebras equipped with a normal faithful tracial state, which implies semi-convexity of the entropy with respect to the recently introduced noncommutative 2-Wasserstein distance. We show that this complete gradient estimate is stable under tensor products and free products and establish its validity for a number of examples. As an application we prove a complete modified logarithmic Sobolev inequality with optimal constant for Poisson-type semigroups on free group factors. acknowledgement: Both authors would like to thank Jan Maas for fruitful discussions and helpful comments. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Melchior full_name: Wirth, Melchior id: 88644358-0A0E-11EA-8FA5-49A33DDC885E last_name: Wirth orcid: 0000-0002-0519-4241 - first_name: Haonan full_name: Zhang, Haonan id: D8F41E38-9E66-11E9-A9E2-65C2E5697425 last_name: Zhang citation: ama: Wirth M, Zhang H. Complete gradient estimates of quantum Markov semigroups. Communications in Mathematical Physics. 2021;387:761–791. doi:10.1007/s00220-021-04199-4 apa: Wirth, M., & Zhang, H. (2021). Complete gradient estimates of quantum Markov semigroups. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-021-04199-4 chicago: Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum Markov Semigroups.” Communications in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s00220-021-04199-4. ieee: M. Wirth and H. Zhang, “Complete gradient estimates of quantum Markov semigroups,” Communications in Mathematical Physics, vol. 387. Springer Nature, pp. 761–791, 2021. ista: Wirth M, Zhang H. 2021. Complete gradient estimates of quantum Markov semigroups. Communications in Mathematical Physics. 387, 761–791. mla: Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum Markov Semigroups.” Communications in Mathematical Physics, vol. 387, Springer Nature, 2021, pp. 761–791, doi:10.1007/s00220-021-04199-4. short: M. Wirth, H. Zhang, Communications in Mathematical Physics 387 (2021) 761–791. date_created: 2021-08-30T10:07:44Z date_published: 2021-08-30T00:00:00Z date_updated: 2023-08-11T11:09:07Z day: '30' ddc: - '621' department: - _id: JaMa doi: 10.1007/s00220-021-04199-4 ec_funded: 1 external_id: arxiv: - '2007.13506' isi: - '000691214200001' file: - access_level: open_access checksum: 8a602f916b1c2b0dc1159708b7cb204b content_type: application/pdf creator: cchlebak date_created: 2021-09-08T07:34:24Z date_updated: 2021-09-08T09:46:34Z file_id: '9990' file_name: 2021_CommunMathPhys_Wirth.pdf file_size: 505971 relation: main_file file_date_updated: 2021-09-08T09:46:34Z has_accepted_license: '1' intvolume: ' 387' isi: 1 keyword: - Mathematical Physics - Statistical and Nonlinear Physics language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 761–791 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: Communications in Mathematical Physics publication_identifier: eissn: - 1432-0916 issn: - 0010-3616 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Complete gradient estimates of quantum Markov semigroups 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: 387 year: '2021' ... --- _id: '10000' abstract: - lang: eng text: Inhibition or targeted deletion of histone deacetylase 3 (HDAC3) is neuroprotective in a variety neurodegenerative conditions, including retinal ganglion cells (RGCs) after acute optic nerve damage. Consistent with this, induced HDAC3 expression in cultured cells shows selective toxicity to neurons. Despite an established role for HDAC3 in neuronal pathology, little is known regarding the mechanism of this pathology. acknowledgement: 'The authors thank Joel Dietz for maintaining the mice used in this study, Satoshi Kinoshita and the Translational Research Initiative in Pathology Laboratory at the University of Wisconsin-Madison for cutting retinal sections analyzed in this study, and Mark Banghart for statistical review of the data analysis. Supported by National Eye Institute Grants R01 EY012223 (RWN), R01 EY030123 (RWN), R01 EY029809 (LWG), R01 EY029809 (LWG) and a Vision Research CORE grant P30 EY016665, NRSA grant T32 GM081061, by an unrestricted research grant from Research to Prevent Blindness, Inc., and by a University of Wisconsin-Madison Vilas Life Cycle award and the Frederick A. Davis Research Chair (RWN). ' article_number: '14' article_processing_charge: Yes article_type: original author: - first_name: Heather M. full_name: Schmitt, Heather M. last_name: Schmitt - first_name: Rachel L. full_name: Fehrman, Rachel L. last_name: Fehrman - 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: Huan full_name: Yang, Huan last_name: Yang - first_name: Lian Wang full_name: Guo, Lian Wang last_name: Guo - first_name: Cassandra L. full_name: Schlamp, Cassandra L. last_name: Schlamp - first_name: Heather R. full_name: Pelzel, Heather R. last_name: Pelzel - first_name: Robert W. full_name: Nickells, Robert W. last_name: Nickells citation: ama: Schmitt HM, Fehrman RL, Maes ME, et al. Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology and Visual Science. 2021;62(10). doi:10.1167/IOVS.62.10.14 apa: Schmitt, H. M., Fehrman, R. L., Maes, M. E., Yang, H., Guo, L. W., Schlamp, C. L., … Nickells, R. W. (2021). Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology and Visual Science. Association for Research in Vision and Ophthalmology. https://doi.org/10.1167/IOVS.62.10.14 chicago: Schmitt, Heather M., Rachel L. Fehrman, Margaret E Maes, Huan Yang, Lian Wang Guo, Cassandra L. Schlamp, Heather R. Pelzel, and Robert W. Nickells. “Increased Susceptibility and Intrinsic Apoptotic Signaling in Neurons by Induced HDAC3 Expression.” Investigative Ophthalmology and Visual Science. Association for Research in Vision and Ophthalmology, 2021. https://doi.org/10.1167/IOVS.62.10.14. ieee: H. M. Schmitt et al., “Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression,” Investigative Ophthalmology and Visual Science, vol. 62, no. 10. Association for Research in Vision and Ophthalmology, 2021. ista: Schmitt HM, Fehrman RL, Maes ME, Yang H, Guo LW, Schlamp CL, Pelzel HR, Nickells RW. 2021. Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology and Visual Science. 62(10), 14. mla: Schmitt, Heather M., et al. “Increased Susceptibility and Intrinsic Apoptotic Signaling in Neurons by Induced HDAC3 Expression.” Investigative Ophthalmology and Visual Science, vol. 62, no. 10, 14, Association for Research in Vision and Ophthalmology, 2021, doi:10.1167/IOVS.62.10.14. short: H.M. Schmitt, R.L. Fehrman, M.E. Maes, H. Yang, L.W. Guo, C.L. Schlamp, H.R. Pelzel, R.W. Nickells, Investigative Ophthalmology and Visual Science 62 (2021). date_created: 2021-09-12T22:01:23Z date_published: 2021-08-16T00:00:00Z date_updated: 2023-08-14T06:35:17Z day: '16' ddc: - '570' department: - _id: SaSi doi: 10.1167/IOVS.62.10.14 external_id: isi: - '000695230000014' pmid: - '34398198' file: - access_level: open_access checksum: c430967746f653aa1ae84ee617f62b73 content_type: application/pdf creator: dernst date_created: 2022-05-13T07:40:15Z date_updated: 2022-05-13T07:40:15Z file_id: '11369' file_name: 2021_IOVS_Schmitt.pdf file_size: 19707796 relation: main_file success: 1 file_date_updated: 2022-05-13T07:40:15Z has_accepted_license: '1' intvolume: ' 62' isi: 1 issue: '10' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Investigative Ophthalmology and Visual Science publication_identifier: eissn: - 1552-5783 issn: - 0146-0404 publication_status: published publisher: Association for Research in Vision and Ophthalmology quality_controlled: '1' scopus_import: '1' status: public title: Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression 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: 62 year: '2021' ... --- _id: '9998' abstract: - lang: eng text: We define quantum equivariant K-theory of Nakajima quiver varieties. We discuss type A in detail as well as its connections with quantum XXZ spin chains and trigonometric Ruijsenaars-Schneider models. Finally we study a limit which produces a K-theoretic version of results of Givental and Kim, connecting quantum geometry of flag varieties and Toda lattice. acknowledgement: 'First of all we would like to thank Andrei Okounkov for invaluable discussions, advises and sharing with us his fantastic viewpoint on modern quantum geometry. We are also grateful to D. Korb and Z. Zhou for their interest and comments. The work of A. Smirnov was supported in part by RFBR Grants under Numbers 15-02-04175 and 15-01-04217 and in part by NSF Grant DMS–2054527. The work of P. Koroteev, A.M. Zeitlin and A. Smirnov is supported in part by AMS Simons travel Grant. A. M. Zeitlin is partially supported by Simons Collaboration Grant, Award ID: 578501. Open access funding provided by Institute of Science and Technology (IST Austria).' article_number: '87' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Peter full_name: Koroteev, Peter last_name: Koroteev - first_name: Petr full_name: Pushkar, Petr id: 151DCEB6-9EC3-11E9-8480-ABECE5697425 last_name: Pushkar - first_name: Andrey V. full_name: Smirnov, Andrey V. last_name: Smirnov - first_name: Anton M. full_name: Zeitlin, Anton M. last_name: Zeitlin citation: ama: Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. 2021;27(5). doi:10.1007/s00029-021-00698-3 apa: Koroteev, P., Pushkar, P., Smirnov, A. V., & Zeitlin, A. M. (2021). Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. Springer Nature. https://doi.org/10.1007/s00029-021-00698-3 chicago: Koroteev, Peter, Petr Pushkar, Andrey V. Smirnov, and Anton M. Zeitlin. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” Selecta Mathematica. Springer Nature, 2021. https://doi.org/10.1007/s00029-021-00698-3. ieee: P. Koroteev, P. Pushkar, A. V. Smirnov, and A. M. Zeitlin, “Quantum K-theory of quiver varieties and many-body systems,” Selecta Mathematica, vol. 27, no. 5. Springer Nature, 2021. ista: Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. 2021. Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. 27(5), 87. mla: Koroteev, Peter, et al. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” Selecta Mathematica, vol. 27, no. 5, 87, Springer Nature, 2021, doi:10.1007/s00029-021-00698-3. short: P. Koroteev, P. Pushkar, A.V. Smirnov, A.M. Zeitlin, Selecta Mathematica 27 (2021). date_created: 2021-09-12T22:01:22Z date_published: 2021-08-30T00:00:00Z date_updated: 2023-08-14T06:34:14Z day: '30' ddc: - '530' department: - _id: TaHa doi: 10.1007/s00029-021-00698-3 external_id: isi: - '000692795200001' file: - access_level: open_access checksum: beadc5a722ffb48190e1e63ee2dbfee5 content_type: application/pdf creator: cchlebak date_created: 2021-09-13T11:31:34Z date_updated: 2021-09-13T11:31:34Z file_id: '10010' file_name: 2021_SelectaMath_Koroteev.pdf file_size: 584648 relation: main_file success: 1 file_date_updated: 2021-09-13T11:31:34Z has_accepted_license: '1' intvolume: ' 27' isi: 1 issue: '5' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Selecta Mathematica publication_identifier: eissn: - 1420-9020 issn: - 1022-1824 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Quantum K-theory of quiver varieties and many-body systems tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 27 year: '2021' ... --- _id: '9999' abstract: - lang: eng text: 'The developmental strategies used by progenitor cells to endure a safe journey from their induction place towards the site of terminal differentiation are still poorly understood. Here we uncovered a progenitor cell allocation mechanism that stems from an incomplete process of epithelial delamination that allows progenitors to coordinate their movement with adjacent extra-embryonic tissues. Progenitors of the zebrafish laterality organ originate from the surface epithelial enveloping layer by an apical constriction process of cell delamination. During this process, progenitors retain long-term apical contacts that enable the epithelial layer to pull a subset of progenitors along their way towards the vegetal pole. The remaining delaminated progenitors follow apically-attached progenitors’ movement by a co-attraction mechanism, avoiding sequestration by the adjacent endoderm, ensuring their fate and collective allocation at the differentiation site. Thus, we reveal that incomplete delamination serves as a cellular platform for coordinated tissue movements during development. Impact Statement: Incomplete delamination serves as a cellular platform for coordinated tissue movements during development, guiding newly formed progenitor cell groups to the differentiation site.' article_number: e66483 article_processing_charge: Yes article_type: original author: - first_name: Eduardo full_name: Pulgar, Eduardo last_name: Pulgar - first_name: Cornelia full_name: Schwayer, Cornelia id: 3436488C-F248-11E8-B48F-1D18A9856A87 last_name: Schwayer orcid: 0000-0001-5130-2226 - first_name: Néstor full_name: Guerrero, Néstor last_name: Guerrero - first_name: Loreto full_name: López, Loreto last_name: López - first_name: Susana full_name: Márquez, Susana last_name: Márquez - first_name: Steffen full_name: Härtel, Steffen last_name: Härtel - first_name: Rodrigo full_name: Soto, Rodrigo last_name: Soto - first_name: Carl Philipp full_name: Heisenberg, Carl Philipp last_name: Heisenberg - first_name: Miguel L. full_name: Concha, Miguel L. last_name: Concha citation: ama: Pulgar E, Schwayer C, Guerrero N, et al. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. eLife. 2021;10. doi:10.7554/eLife.66483 apa: Pulgar, E., Schwayer, C., Guerrero, N., López, L., Márquez, S., Härtel, S., … Concha, M. L. (2021). Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.66483 chicago: Pulgar, Eduardo, Cornelia Schwayer, Néstor Guerrero, Loreto López, Susana Márquez, Steffen Härtel, Rodrigo Soto, Carl Philipp Heisenberg, and Miguel L. Concha. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.66483. ieee: E. Pulgar et al., “Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Pulgar E, Schwayer C, Guerrero N, López L, Márquez S, Härtel S, Soto R, Heisenberg CP, Concha ML. 2021. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. eLife. 10, e66483. mla: Pulgar, Eduardo, et al. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” ELife, vol. 10, e66483, eLife Sciences Publications, 2021, doi:10.7554/eLife.66483. short: E. Pulgar, C. Schwayer, N. Guerrero, L. López, S. Márquez, S. Härtel, R. Soto, C.P. Heisenberg, M.L. Concha, ELife 10 (2021). date_created: 2021-09-12T22:01:23Z date_published: 2021-08-27T00:00:00Z date_updated: 2023-08-14T06:53:33Z day: '27' ddc: - '570' department: - _id: CaHe doi: 10.7554/eLife.66483 ec_funded: 1 external_id: isi: - '000700428500001' pmid: - '34448451' file: - access_level: open_access checksum: a3f82b0499cc822ac1eab48a01f3f57e content_type: application/pdf creator: dernst date_created: 2022-05-13T08:03:37Z date_updated: 2022-05-13T08:03:37Z file_id: '11371' file_name: 2021_eLife_Pulgar.pdf file_size: 9010446 relation: main_file success: 1 file_date_updated: 2022-05-13T08:03:37Z has_accepted_license: '1' intvolume: ' 10' isi: 1 keyword: - cell delamination - apical constriction - dragging - mechanical forces - collective 18 locomotion - dorsal forerunner cells - zebrafish language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism 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: '10002' abstract: - lang: eng text: 'We present a faster symbolic algorithm for the following central problem in probabilistic verification: Compute the maximal end-component (MEC) decomposition of Markov decision processes (MDPs). This problem generalizes the SCC decomposition problem of graphs and closed recurrent sets of Markov chains. The model of symbolic algorithms is widely used in formal verification and model-checking, where access to the input model is restricted to only symbolic operations (e.g., basic set operations and computation of one-step neighborhood). For an input MDP with n vertices and m edges, the classical symbolic algorithm from the 1990s for the MEC decomposition requires O(n2) symbolic operations and O(1) symbolic space. The only other symbolic algorithm for the MEC decomposition requires O(nm−−√) symbolic operations and O(m−−√) symbolic space. A main open question is whether the worst-case O(n2) bound for symbolic operations can be beaten. We present a symbolic algorithm that requires O˜(n1.5) symbolic operations and O˜(n−−√) symbolic space. Moreover, the parametrization of our algorithm provides a trade-off between symbolic operations and symbolic space: for all 0<ϵ≤1/2 the symbolic algorithm requires O˜(n2−ϵ) symbolic operations and O˜(nϵ) symbolic space ( O˜ hides poly-logarithmic factors). Using our techniques we present faster algorithms for computing the almost-sure winning regions of ω -regular objectives for MDPs. We consider the canonical parity objectives for ω -regular objectives, and for parity objectives with d -priorities we present an algorithm that computes the almost-sure winning region with O˜(n2−ϵ) symbolic operations and O˜(nϵ) symbolic space, for all 0<ϵ≤1/2 .' acknowledgement: The authors are grateful to the anonymous referees for their valuable comments. A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15–003. K. C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and by the ERC CoG 863818 (ForM-SMArt). For M. H. the research leading to these results has received funding from the European Research Council under the European Unions Seventh Framework Programme (FP/2007–2013) / ERC Grant Agreement no. 340506. article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Wolfgang full_name: Dvorak, Wolfgang last_name: Dvorak - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Alexander full_name: Svozil, Alexander last_name: Svozil citation: ama: 'Chatterjee K, Dvorak W, Henzinger MH, Svozil A. Symbolic time and space tradeoffs for probabilistic verification. In: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers; 2021:1-13. doi:10.1109/LICS52264.2021.9470739' apa: 'Chatterjee, K., Dvorak, W., Henzinger, M. H., & Svozil, A. (2021). Symbolic time and space tradeoffs for probabilistic verification. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 1–13). Rome, Italy: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS52264.2021.9470739' chicago: Chatterjee, Krishnendu, Wolfgang Dvorak, Monika H Henzinger, and Alexander Svozil. “Symbolic Time and Space Tradeoffs for Probabilistic Verification.” In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, 1–13. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470739. ieee: K. Chatterjee, W. Dvorak, M. H. Henzinger, and A. Svozil, “Symbolic time and space tradeoffs for probabilistic verification,” in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Rome, Italy, 2021, pp. 1–13. ista: 'Chatterjee K, Dvorak W, Henzinger MH, Svozil A. 2021. Symbolic time and space tradeoffs for probabilistic verification. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 1–13.' mla: Chatterjee, Krishnendu, et al. “Symbolic Time and Space Tradeoffs for Probabilistic Verification.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13, doi:10.1109/LICS52264.2021.9470739. short: K. Chatterjee, W. Dvorak, M.H. Henzinger, A. Svozil, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13. conference: end_date: 2021-07-02 location: Rome, Italy name: 'LICS: Symposium on Logic in Computer Science' start_date: 2021-06-29 date_created: 2021-09-12T22:01:24Z date_published: 2021-07-07T00:00:00Z date_updated: 2023-08-14T06:51:33Z day: '07' department: - _id: KrCh doi: 10.1109/LICS52264.2021.9470739 ec_funded: 1 external_id: arxiv: - '2104.07466' isi: - '000947350400089' isi: 1 keyword: - Computer science - Computational modeling - Markov processes - Probabilistic logic - Formal verification - Game Theory language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2104.07466 month: '07' oa: 1 oa_version: Preprint page: 1-13 project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science publication_identifier: eisbn: - 978-1-6654-4895-6 isbn: - 978-1-6654-4896-3 issn: - 1043-6871 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Symbolic time and space tradeoffs for probabilistic verification type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '10024' abstract: - lang: eng text: In this paper, we introduce a random environment for the exclusion process in obtained by assigning a maximal occupancy to each site. This maximal occupancy is allowed to randomly vary among sites, and partial exclusion occurs. Under the assumption of ergodicity under translation and uniform ellipticity of the environment, we derive a quenched hydrodynamic limit in path space by strengthening the mild solution approach initiated in Nagy (2002) and Faggionato (2007). To this purpose, we prove, employing the technology developed for the random conductance model, a homogenization result in the form of an arbitrary starting point quenched invariance principle for a single particle in the same environment, which is a result of independent interest. The self-duality property of the partial exclusion process allows us to transfer this homogenization result to the particle system and, then, apply the tightness criterion in Redig et al. (2020). acknowledgement: The authors would like to thank Marek Biskup and Alberto Chiarini for useful suggestions and Cristian Giardina, Frank den Hollander and Shubhamoy Nandan for inspiring discussions. S.F. acknowledges Simona Villa for her help in creating the picture. Furthermore, the authors thank two anonymous referees for the careful reading of the manuscript. S.F. acknowledges financial support from NWO, The Netherlands via the grant TOP1.17.019. F.S. acknowledges financial support from NWO via the TOP1 grant 613.001.552 as well as 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 article_type: original author: - first_name: Simone full_name: Floreani, Simone last_name: Floreani - first_name: Frank full_name: Redig, Frank last_name: Redig - first_name: Federico full_name: Sau, Federico id: E1836206-9F16-11E9-8814-AEFDE5697425 last_name: Sau citation: ama: Floreani S, Redig F, Sau F. Hydrodynamics for the partial exclusion process in random environment. Stochastic Processes and their Applications. 2021;142:124-158. doi:10.1016/j.spa.2021.08.006 apa: Floreani, S., Redig, F., & Sau, F. (2021). Hydrodynamics for the partial exclusion process in random environment. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2021.08.006 chicago: Floreani, Simone, Frank Redig, and Federico Sau. “Hydrodynamics for the Partial Exclusion Process in Random Environment.” Stochastic Processes and Their Applications. Elsevier, 2021. https://doi.org/10.1016/j.spa.2021.08.006. ieee: S. Floreani, F. Redig, and F. Sau, “Hydrodynamics for the partial exclusion process in random environment,” Stochastic Processes and their Applications, vol. 142. Elsevier, pp. 124–158, 2021. ista: Floreani S, Redig F, Sau F. 2021. Hydrodynamics for the partial exclusion process in random environment. Stochastic Processes and their Applications. 142, 124–158. mla: Floreani, Simone, et al. “Hydrodynamics for the Partial Exclusion Process in Random Environment.” Stochastic Processes and Their Applications, vol. 142, Elsevier, 2021, pp. 124–58, doi:10.1016/j.spa.2021.08.006. short: S. Floreani, F. Redig, F. Sau, Stochastic Processes and Their Applications 142 (2021) 124–158. date_created: 2021-09-19T22:01:25Z date_published: 2021-08-27T00:00:00Z date_updated: 2023-08-14T06:52:43Z day: '27' ddc: - '519' department: - _id: JaMa doi: 10.1016/j.spa.2021.08.006 ec_funded: 1 external_id: arxiv: - '1911.12564' isi: - '000697748500005' file: - access_level: open_access checksum: 56768c553d7218ee5714902ffec90ec4 content_type: application/pdf creator: dernst date_created: 2022-05-13T07:55:50Z date_updated: 2022-05-13T07:55:50Z file_id: '11370' file_name: 2021_StochasticProcessesAppl_Floreani.pdf file_size: 2115791 relation: main_file success: 1 file_date_updated: 2022-05-13T07:55:50Z has_accepted_license: '1' intvolume: ' 142' isi: 1 keyword: - hydrodynamic limit - random environment - random conductance model - arbitrary starting point quenched invariance principle - duality - mild solution language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 124-158 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Stochastic Processes and their Applications publication_identifier: issn: - 0304-4149 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Hydrodynamics for the partial exclusion process in random environment 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: 142 year: '2021' ... --- _id: '10004' abstract: - lang: eng text: 'Markov chains are the de facto finite-state model for stochastic dynamical systems, and Markov decision processes (MDPs) extend Markov chains by incorporating non-deterministic behaviors. Given an MDP and rewards on states, a classical optimization criterion is the maximal expected total reward where the MDP stops after T steps, which can be computed by a simple dynamic programming algorithm. We consider a natural generalization of the problem where the stopping times can be chosen according to a probability distribution, such that the expected stopping time is T, to optimize the expected total reward. Quite surprisingly we establish inter-reducibility of the expected stopping-time problem for Markov chains with the Positivity problem (which is related to the well-known Skolem problem), for which establishing either decidability or undecidability would be a major breakthrough. Given the hardness of the exact problem, we consider the approximate version of the problem: we show that it can be solved in exponential time for Markov chains and in exponential space for MDPs.' acknowledgement: We are grateful to the anonymous reviewers of LICS 2021 and of a previous version of this paper for insightful comments that helped improving the presentation. This research was partially supported by the grant ERC CoG 863818 (ForM-SMArt). article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen citation: ama: 'Chatterjee K, Doyen L. Stochastic processes with expected stopping time. In: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers; 2021:1-13. doi:10.1109/LICS52264.2021.9470595' apa: 'Chatterjee, K., & Doyen, L. (2021). Stochastic processes with expected stopping time. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 1–13). Rome, Italy: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS52264.2021.9470595' chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected Stopping Time.” In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, 1–13. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470595. ieee: K. Chatterjee and L. Doyen, “Stochastic processes with expected stopping time,” in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Rome, Italy, 2021, pp. 1–13. ista: 'Chatterjee K, Doyen L. 2021. Stochastic processes with expected stopping time. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 1–13.' mla: Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected Stopping Time.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13, doi:10.1109/LICS52264.2021.9470595. short: K. Chatterjee, L. Doyen, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13. conference: end_date: 2021-07-02 location: Rome, Italy name: 'LICS: Symposium on Logic in Computer Science' start_date: 2021-06-29 date_created: 2021-09-12T22:01:25Z date_published: 2021-07-07T00:00:00Z date_updated: 2023-08-14T06:52:07Z day: '07' department: - _id: KrCh doi: 10.1109/LICS52264.2021.9470595 ec_funded: 1 external_id: arxiv: - '2104.07278' isi: - '000947350400036' isi: 1 keyword: - Computer science - Heuristic algorithms - Memory management - Automata - Markov processes - Probability distribution - Complexity theory language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2104.07278 month: '07' oa: 1 oa_version: Preprint page: 1-13 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science publication_identifier: eisbn: - 978-1-6654-4895-6 isbn: - 978-1-6654-4896-3 issn: - 1043-6871 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Stochastic processes with expected stopping time type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '10053' abstract: - lang: eng text: 'This paper characterizes the latency of the simplified successive-cancellation (SSC) decoding scheme for polar codes under hardware resource constraints. In particular, when the number of processing elements P that can perform SSC decoding operations in parallel is limited, as is the case in practice, the latency of SSC decoding is O(N1−1 μ+NPlog2log2NP), where N is the block length of the code and μ is the scaling exponent of polar codes for the channel. Three direct consequences of this bound are presented. First, in a fully-parallel implementation where P=N2 , the latency of SSC decoding is O(N1−1/μ) , which is sublinear in the block length. This recovers a result from an earlier work. Second, in a fully-serial implementation where P=1 , the latency of SSC decoding scales as O(Nlog2log2N) . The multiplicative constant is also calculated: we show that the latency of SSC decoding when P=1 is given by (2+o(1))Nlog2log2N . Third, in a semi-parallel implementation, the smallest P that gives the same latency as that of the fully-parallel implementation is P=N1/μ . The tightness of our bound on SSC decoding latency and the applicability of the foregoing results is validated through extensive simulations.' acknowledgement: "S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council\r\nof Canada (NSERC) and by Huawei. M. Mondelli is partially supported by the 2019 Lopez-Loreta Prize. A. Fazeli and A. Vardy were supported in part by the National Science Foundation under Grant CCF-1764104." article_processing_charge: No author: - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Arman full_name: Fazeli, Arman last_name: Fazeli - first_name: Alexander full_name: Vardy, Alexander last_name: Vardy - first_name: John full_name: Cioffi, John last_name: Cioffi - first_name: Andrea full_name: Goldsmith, Andrea last_name: Goldsmith citation: ama: 'Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. In: 2021 IEEE International Symposium on Information Theory. Institute of Electrical and Electronics Engineers; 2021:2369-2374. doi:10.1109/ISIT45174.2021.9518153' apa: 'Hashemi, S. A., Mondelli, M., Fazeli, A., Vardy, A., Cioffi, J., & Goldsmith, A. (2021). Parallelism versus latency in simplified successive-cancellation decoding of polar codes. In 2021 IEEE International Symposium on Information Theory (pp. 2369–2374). Melbourne, Australia: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/ISIT45174.2021.9518153' chicago: Hashemi, Seyyed Ali, Marco Mondelli, Arman Fazeli, Alexander Vardy, John Cioffi, and Andrea Goldsmith. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” In 2021 IEEE International Symposium on Information Theory, 2369–74. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/ISIT45174.2021.9518153. ieee: S. A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, and A. Goldsmith, “Parallelism versus latency in simplified successive-cancellation decoding of polar codes,” in 2021 IEEE International Symposium on Information Theory, Melbourne, Australia, 2021, pp. 2369–2374. ista: 'Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. 2021. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. 2021 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 2369–2374.' mla: Hashemi, Seyyed Ali, et al. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” 2021 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2021, pp. 2369–74, doi:10.1109/ISIT45174.2021.9518153. short: S.A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, A. Goldsmith, in:, 2021 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2021, pp. 2369–2374. conference: end_date: 2021-07-20 location: Melbourne, Australia name: 'ISIT: International Symposium on Information Theory' start_date: 2021-07-12 date_created: 2021-09-27T14:33:14Z date_published: 2021-09-01T00:00:00Z date_updated: 2023-08-14T06:55:58Z day: '01' department: - _id: MaMo doi: 10.1109/ISIT45174.2021.9518153 external_id: arxiv: - '2012.13378' isi: - '000701502202078' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2012.13378 month: '09' oa: 1 oa_version: Preprint page: 2369-2374 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: 2021 IEEE International Symposium on Information Theory publication_identifier: eisbn: - 978-1-5386-8209-8 isbn: - 978-1-5386-8210-4 issn: - 2157-8095 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' related_material: record: - id: '10364' relation: later_version status: public scopus_import: '1' status: public title: Parallelism versus latency in simplified successive-cancellation decoding of polar codes type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '10033' abstract: - lang: eng text: The ⊗*-monoidal structure on the category of sheaves on the Ran space is not pro-nilpotent in the sense of [3]. However, under some connectivity assumptions, we prove that Koszul duality induces an equivalence of categories and that this equivalence behaves nicely with respect to Verdier duality on the Ran space and integrating along the Ran space, i.e. taking factorization homology. Based on ideas sketched in [4], we show that these results also offer a simpler alternative to one of the two main steps in the proof of the Atiyah-Bott formula given in [7] and [5]. acknowledgement: 'The author would like to express his gratitude to D. Gaitsgory, without whose tireless guidance and encouragement in pursuing this problem, this work would not have been possible. The author is grateful to his advisor B.C. Ngô for many years of patient guidance and support. This paper is revised while the author is a postdoc in Hausel group at IST Austria. We thank him and the group for providing a wonderful research environment. The author also gratefully acknowledges the support of the Lise Meitner fellowship “Algebro-Geometric Applications of Factorization Homology,” Austrian Science Fund (FWF): M 2751.' article_number: '107992' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Quoc P full_name: Ho, Quoc P id: 3DD82E3C-F248-11E8-B48F-1D18A9856A87 last_name: Ho orcid: 0000-0001-6889-1418 citation: ama: Ho QP. The Atiyah-Bott formula and connectivity in chiral Koszul duality. Advances in Mathematics. 2021;392. doi:10.1016/j.aim.2021.107992 apa: Ho, Q. P. (2021). The Atiyah-Bott formula and connectivity in chiral Koszul duality. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2021.107992 chicago: Ho, Quoc P. “The Atiyah-Bott Formula and Connectivity in Chiral Koszul Duality.” Advances in Mathematics. Elsevier, 2021. https://doi.org/10.1016/j.aim.2021.107992. ieee: Q. P. Ho, “The Atiyah-Bott formula and connectivity in chiral Koszul duality,” Advances in Mathematics, vol. 392. Elsevier, 2021. ista: Ho QP. 2021. The Atiyah-Bott formula and connectivity in chiral Koszul duality. Advances in Mathematics. 392, 107992. mla: Ho, Quoc P. “The Atiyah-Bott Formula and Connectivity in Chiral Koszul Duality.” Advances in Mathematics, vol. 392, 107992, Elsevier, 2021, doi:10.1016/j.aim.2021.107992. short: Q.P. Ho, Advances in Mathematics 392 (2021). date_created: 2021-09-21T15:58:59Z date_published: 2021-09-21T00:00:00Z date_updated: 2023-08-14T06:54:35Z day: '21' ddc: - '514' department: - _id: TaHa doi: 10.1016/j.aim.2021.107992 external_id: arxiv: - '1610.00212' isi: - '000707040300031' file: - access_level: open_access checksum: f3c0086d41af11db31c00014efb38072 content_type: application/pdf creator: qho date_created: 2021-09-21T15:58:52Z date_updated: 2021-09-21T15:58:52Z file_id: '10034' file_name: 1-s2.0-S000187082100431X-main.pdf file_size: 840635 relation: main_file file_date_updated: 2021-09-21T15:58:52Z has_accepted_license: '1' intvolume: ' 392' isi: 1 keyword: - Chiral algebras - Chiral homology - Factorization algebras - Koszul duality - Ran space language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 26B96266-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02751 name: Algebro-Geometric Applications of Factorization Homology publication: Advances in Mathematics publication_identifier: eissn: - 1090-2082 issn: - 0001-8708 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: The Atiyah-Bott formula and connectivity in chiral Koszul duality 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: 392 year: '2021' ... --- _id: '10051' abstract: - lang: eng text: 'Rab-interacting molecule (RIM)-binding protein 2 (BP2) is a multidomain protein of the presynaptic active zone (AZ). By binding to RIM, bassoon (Bsn), and voltage-gated Ca2+ channels (CaV), it is considered to be a central organizer of the topography of CaV and release sites of synaptic vesicles (SVs) at the AZ. Here, we used RIM-BP2 knock-out (KO) mice and their wild-type (WT) littermates of either sex to investigate the role of RIM-BP2 at the endbulb of Held synapse of auditory nerve fibers (ANFs) with bushy cells (BCs) of the cochlear nucleus, a fast relay of the auditory pathway with high release probability. Disruption of RIM-BP2 lowered release probability altering short-term plasticity and reduced evoked EPSCs. Analysis of SV pool dynamics during high-frequency train stimulation indicated a reduction of SVs with high release probability but an overall normal size of the readily releasable SV pool (RRP). The Ca2+-dependent fast component of SV replenishment after RRP depletion was slowed. Ultrastructural analysis by superresolution light and electron microscopy revealed an impaired topography of presynaptic CaV and a reduction of docked and membrane-proximal SVs at the AZ. We conclude that RIM-BP2 organizes the topography of CaV, and promotes SV tethering and docking. This way RIM-BP2 is critical for establishing a high initial release probability as required to reliably signal sound onset information that we found to be degraded in BCs of RIM-BP2-deficient mice in vivo. SIGNIFICANCE STATEMENT: Rab-interacting molecule (RIM)-binding proteins (BPs) are key organizers of the active zone (AZ). Using a multidisciplinary approach to the calyceal endbulb of Held synapse that transmits auditory information at rates of up to hundreds of Hertz with submillisecond precision we demonstrate a requirement for RIM-BP2 for normal auditory signaling. Endbulb synapses lacking RIM-BP2 show a reduced release probability despite normal whole-terminal Ca2+ influx and abundance of the key priming protein Munc13-1, a reduced rate of SV replenishment, as well as an altered topography of voltage-gated (CaV)2.1 Ca2+ channels, and fewer docked and membrane proximal synaptic vesicles (SVs). This hampers transmission of sound onset information likely affecting downstream neural computations such as of sound localization.' acknowledgement: This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the Collaborative Sensory Research Center 1286 [to C.W. (A4) and T.M. (B5)] and under Germany’s Excellence Strategy Grant EXC 2067/1-390729940. We thank S. Gerke, A.J. Goldak, and C. Senger-Freitag for expert technical assistance; G. Hoch for developing image analysis routines; and S. Chepurwar and N. Strenzke for technical support and discussion regarding in vivo experiments. We also thank Dr. Christian Rosenmund, Dr. Katharina Grauel, and Dr. Stephan Sigrist for providing RIM-BP2 KO mice and Dr. Masahiko Watanabe for providing the anti-neurexin-antibody, and Dr. Toshihisa Ohtsuka for the anti-ELKS-antibody. J. Neef for help with the STED imaging and image analysis; E. Neher and S. Rizzoli for discussion and comments on the manuscript; K. Eguchi for help with the statistical analysis; and C. H. Huang and J. Neef for constant support and scientific discussion. article_processing_charge: No article_type: original author: - first_name: Tanvi full_name: Butola, Tanvi last_name: Butola - first_name: Theocharis full_name: Alvanos, Theocharis last_name: Alvanos - first_name: Anika full_name: Hintze, Anika last_name: Hintze - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: David full_name: Kleindienst, David id: 42E121A4-F248-11E8-B48F-1D18A9856A87 last_name: Kleindienst - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Carolin full_name: Wichmann, Carolin last_name: Wichmann - first_name: Tobias full_name: Moser, Tobias last_name: Moser citation: ama: Butola T, Alvanos T, Hintze A, et al. RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse. Journal of Neuroscience. 2021;41(37):7742-7767. doi:10.1523/JNEUROSCI.0586-21.2021 apa: Butola, T., Alvanos, T., Hintze, A., Koppensteiner, P., Kleindienst, D., Shigemoto, R., … Moser, T. (2021). RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0586-21.2021 chicago: Butola, Tanvi, Theocharis Alvanos, Anika Hintze, Peter Koppensteiner, David Kleindienst, Ryuichi Shigemoto, Carolin Wichmann, and Tobias Moser. “RIM-Binding Protein 2 Organizes Ca21 Channel Topography and Regulates Release Probability and Vesicle Replenishment at a Fast Central Synapse.” Journal of Neuroscience. Society for Neuroscience, 2021. https://doi.org/10.1523/JNEUROSCI.0586-21.2021. ieee: T. Butola et al., “RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse,” Journal of Neuroscience, vol. 41, no. 37. Society for Neuroscience, pp. 7742–7767, 2021. ista: Butola T, Alvanos T, Hintze A, Koppensteiner P, Kleindienst D, Shigemoto R, Wichmann C, Moser T. 2021. RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse. Journal of Neuroscience. 41(37), 7742–7767. mla: Butola, Tanvi, et al. “RIM-Binding Protein 2 Organizes Ca21 Channel Topography and Regulates Release Probability and Vesicle Replenishment at a Fast Central Synapse.” Journal of Neuroscience, vol. 41, no. 37, Society for Neuroscience, 2021, pp. 7742–67, doi:10.1523/JNEUROSCI.0586-21.2021. short: T. Butola, T. Alvanos, A. Hintze, P. Koppensteiner, D. Kleindienst, R. Shigemoto, C. Wichmann, T. Moser, Journal of Neuroscience 41 (2021) 7742–7767. date_created: 2021-09-27T14:33:13Z date_published: 2021-09-15T00:00:00Z date_updated: 2023-08-14T06:56:30Z day: '15' ddc: - '570' department: - _id: RySh doi: 10.1523/JNEUROSCI.0586-21.2021 external_id: isi: - '000752287700005' pmid: - '34353898' file: - access_level: open_access checksum: 769ab627c7355a50ccfd445e43a5f351 content_type: application/pdf creator: dernst date_created: 2022-05-31T09:10:15Z date_updated: 2022-05-31T09:10:15Z file_id: '11423' file_name: 2021_JourNeuroscience_Butola.pdf file_size: 11571961 relation: main_file success: 1 file_date_updated: 2022-05-31T09:10:15Z has_accepted_license: '1' intvolume: ' 41' isi: 1 issue: '37' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 7742-7767 pmid: 1 publication: Journal of Neuroscience publication_identifier: eissn: - 1529-2401 issn: - 0270-6474 publication_status: published publisher: Society for Neuroscience quality_controlled: '1' scopus_import: '1' status: public title: RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse 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: '10055' abstract: - lang: eng text: "Repeated idempotent elements are commonly used to characterise iterable behaviours in abstract models of computation. Therefore, given a monoid M, it is natural to ask how long a sequence of elements of M needs to be to ensure the presence of consecutive idempotent factors. This question is formalised through the notion of the Ramsey function R_M associated to M, obtained by mapping every k ∈ ℕ to the minimal integer R_M(k) such that every word u ∈ M^* of length R_M(k) contains k consecutive non-empty factors that correspond to the same idempotent element of M. In this work, we study the behaviour of the Ramsey function R_M by investigating the regular \U0001D49F-length of M, defined as the largest size L(M) of a submonoid of M isomorphic to the set of natural numbers {1,2, …, L(M)} equipped with the max operation. We show that the regular \U0001D49F-length of M determines the degree of R_M, by proving that k^L(M) ≤ R_M(k) ≤ (k|M|⁴)^L(M). To allow applications of this result, we provide the value of the regular \U0001D49F-length of diverse monoids. In particular, we prove that the full monoid of n × n Boolean matrices, which is used to express transition monoids of non-deterministic automata, has a regular \U0001D49F-length of (n²+n+2)/2." acknowledgement: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. I wish to thank Michaël Cadilhac, Emmanuel Filiot and Charles Paperman for their valuable insights concerning Green’s relations. alternative_title: - LIPIcs article_number: '44' article_processing_charge: No author: - first_name: Ismael R full_name: Jecker, Ismael R id: 85D7C63E-7D5D-11E9-9C0F-98C4E5697425 last_name: Jecker citation: ama: 'Jecker IR. A Ramsey theorem for finite monoids. In: 38th International Symposium on Theoretical Aspects of Computer Science. Vol 187. Schloss Dagstuhl - Leibniz Zentrum für Informatik; 2021. doi:10.4230/LIPIcs.STACS.2021.44' apa: 'Jecker, I. R. (2021). A Ramsey theorem for finite monoids. In 38th International Symposium on Theoretical Aspects of Computer Science (Vol. 187). Saarbrücken, Germany: Schloss Dagstuhl - Leibniz Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2021.44' chicago: Jecker, Ismael R. “A Ramsey Theorem for Finite Monoids.” In 38th International Symposium on Theoretical Aspects of Computer Science, Vol. 187. Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.STACS.2021.44. ieee: I. R. Jecker, “A Ramsey theorem for finite monoids,” in 38th International Symposium on Theoretical Aspects of Computer Science, Saarbrücken, Germany, 2021, vol. 187. ista: 'Jecker IR. 2021. A Ramsey theorem for finite monoids. 38th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 187, 44.' mla: Jecker, Ismael R. “A Ramsey Theorem for Finite Monoids.” 38th International Symposium on Theoretical Aspects of Computer Science, vol. 187, 44, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021, doi:10.4230/LIPIcs.STACS.2021.44. short: I.R. Jecker, in:, 38th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021. conference: end_date: 2021-03-19 location: Saarbrücken, Germany name: 'STACS: Symposium on Theoretical Aspects of Computer Science' start_date: 2021-03-16 date_created: 2021-09-27T14:33:15Z date_published: 2021-03-10T00:00:00Z date_updated: 2023-08-14T07:03:23Z day: '10' ddc: - '000' department: - _id: KrCh doi: 10.4230/LIPIcs.STACS.2021.44 ec_funded: 1 external_id: isi: - '000635691700044' file: - access_level: open_access checksum: 17432a05733f408de300e17e390a90e4 content_type: application/pdf creator: cchlebak date_created: 2021-10-01T09:55:00Z date_updated: 2021-10-01T09:55:00Z file_id: '10063' file_name: 2021_LIPIcs_Jecker.pdf file_size: 720250 relation: main_file success: 1 file_date_updated: 2021-10-01T09:55:00Z has_accepted_license: '1' intvolume: ' 187' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: 38th International Symposium on Theoretical Aspects of Computer Science publication_identifier: isbn: - 978-3-9597-7180-1 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: A Ramsey theorem for finite monoids 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 volume: 187 year: '2021' ... --- _id: '10069' abstract: - lang: eng text: 'The extent to which women differ in the course of blood cell counts throughout pregnancy, and the importance of these changes to pregnancy outcomes has not been well defined. Here, we develop a series of statistical analyses of repeated measures data to reveal the degree to which women differ in the course of pregnancy, predict the changes that occur, and determine the importance of these changes for post-partum hemorrhage (PPH) which is one of the leading causes of maternal mortality. We present a prospective cohort of 4082 births recorded at the University Hospital, Lausanne, Switzerland between 2009 and 2014 where full labour records could be obtained, along with complete blood count data taken at hospital admission. We find significant differences, at a [Formula: see text] level, among women in how blood count values change through pregnancy for mean corpuscular hemoglobin, mean corpuscular volume, mean platelet volume, platelet count and red cell distribution width. We find evidence that almost all complete blood count values show trimester-specific associations with PPH. For example, high platelet count (OR 1.20, 95% CI 1.01-1.53), high mean platelet volume (OR 1.58, 95% CI 1.04-2.08), and high erythrocyte levels (OR 1.36, 95% CI 1.01-1.57) in trimester 1 increased PPH, but high values in trimester 3 decreased PPH risk (OR 0.85, 0.79, 0.67 respectively). We show that differences among women in the course of blood cell counts throughout pregnancy have an important role in shaping pregnancy outcome and tracking blood count value changes through pregnancy improves identification of women at increased risk of postpartum hemorrhage. This study provides greater understanding of the complex changes in blood count values that occur through pregnancy and provides indicators to guide the stratification of patients into risk groups.' acknowledgement: This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria. We would like to thank the participants of the study and all the midwives and doctors for the computerized obstetrical data. article_number: '19238' article_processing_charge: Yes article_type: original author: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Marion full_name: Patxot, Marion last_name: Patxot - first_name: Miloš full_name: Stojanov, Miloš last_name: Stojanov - first_name: Sabine full_name: Blum, Sabine last_name: Blum - first_name: David full_name: Baud, David last_name: Baud citation: ama: Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. Scientific Reports. 2021;11. doi:10.1038/s41598-021-98411-z apa: Robinson, M. R., Patxot, M., Stojanov, M., Blum, S., & Baud, D. (2021). Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-98411-z chicago: Robinson, Matthew Richard, Marion Patxot, Miloš Stojanov, Sabine Blum, and David Baud. “Postpartum Hemorrhage Risk Is Driven by Changes in Blood Composition through Pregnancy.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-98411-z. ieee: M. R. Robinson, M. Patxot, M. Stojanov, S. Blum, and D. Baud, “Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy,” Scientific Reports, vol. 11. Springer Nature, 2021. ista: Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. 2021. Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. Scientific Reports. 11, 19238. mla: Robinson, Matthew Richard, et al. “Postpartum Hemorrhage Risk Is Driven by Changes in Blood Composition through Pregnancy.” Scientific Reports, vol. 11, 19238, Springer Nature, 2021, doi:10.1038/s41598-021-98411-z. short: M.R. Robinson, M. Patxot, M. Stojanov, S. Blum, D. Baud, Scientific Reports 11 (2021). date_created: 2021-10-03T22:01:21Z date_published: 2021-09-28T00:00:00Z date_updated: 2023-08-14T07:05:15Z day: '28' ddc: - '618' department: - _id: MaRo doi: 10.1038/s41598-021-98411-z external_id: isi: - '000701575500083' pmid: - '34584125' file: - access_level: open_access checksum: f002ec22f609f58e1263b79e7f79601e content_type: application/pdf creator: cchlebak date_created: 2021-10-05T14:56:48Z date_updated: 2021-10-05T14:56:48Z file_id: '10091' file_name: 2021_ScientificReports_Robinson.pdf file_size: 6970368 relation: main_file success: 1 file_date_updated: 2021-10-05T14:56:48Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Scientific Reports publication_identifier: eissn: - 2045-2322 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy 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: '10025' abstract: - lang: eng text: Ferromagnetism is most common in transition metal compounds but may also arise in low-density two-dimensional electron systems, with signatures observed in silicon, III-V semiconductor systems, and graphene moiré heterostructures. Here we show that gate-tuned van Hove singularities in rhombohedral trilayer graphene drive the spontaneous ferromagnetic polarization of the electron system into one or more spin- and valley flavors. Using capacitance measurements on graphite-gated van der Waals heterostructures, we find a cascade of density- and electronic displacement field tuned phase transitions marked by negative electronic compressibility. The transitions define the boundaries between phases where quantum oscillations have either four-fold, two-fold, or one-fold degeneracy, associated with a spin and valley degenerate normal metal, spin-polarized `half-metal', and spin and valley polarized `quarter metal', respectively. For electron doping, the salient features are well captured by a phenomenological Stoner model with a valley-anisotropic Hund's coupling, likely arising from interactions at the lattice scale. For hole filling, we observe a richer phase diagram featuring a delicate interplay of broken symmetries and transitions in the Fermi surface topology. Finally, by rotational alignment of a hexagonal boron nitride substrate to induce a moiré superlattice, we find that the superlattice perturbs the preexisting isospin order only weakly, leaving the basic phase diagram intact while catalyzing the formation of topologically nontrivial gapped states whenever itinerant half- or quarter metal states occur at half- or quarter superlattice band filling. Our results show that rhombohedral trilayer graphene is an ideal platform for well-controlled tests of many-body theory and reveal magnetism in moiré materials to be fundamentally itinerant in nature. acknowledgement: "The authors acknowledge discussions with A. Macdonald, L. Fu, F. Wang and M. Zaletel. AFY acknowledges support of the National Science Foundation under DMR1654186, and the Gordon and Betty Moore Foundation under award GBMF9471. The authors acknowledge the use of the research facilities within the California NanoSystems Institute, supported by the University of California, Santa Barbara and the University of California, Office of the President.\r\nK.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, Grant Number JPMXP0112101001 and JSPS KAKENHI, Grant Number JP20H00354. EB and TH were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799). A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement\r\nNo. 754411.\r\n" article_processing_charge: No article_type: original author: - first_name: Haoxin full_name: Zhou, Haoxin last_name: Zhou - first_name: Tian full_name: Xie, Tian last_name: Xie - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Tobias full_name: Holder, Tobias last_name: Holder - first_name: James R. full_name: Ehrets, James R. last_name: Ehrets - first_name: Eric M. full_name: Spanton, Eric M. last_name: Spanton - first_name: Takashi full_name: Taniguchi, Takashi last_name: Taniguchi - first_name: Kenji full_name: Watanabe, Kenji last_name: Watanabe - first_name: Erez full_name: Berg, Erez last_name: Berg - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Andrea F. full_name: Young, Andrea F. last_name: Young citation: ama: Zhou H, Xie T, Ghazaryan A, et al. Half and quarter metals in rhombohedral trilayer graphene. Nature. 2021. doi:10.1038/s41586-021-03938-w apa: Zhou, H., Xie, T., Ghazaryan, A., Holder, T., Ehrets, J. R., Spanton, E. M., … Young, A. F. (2021). Half and quarter metals in rhombohedral trilayer graphene. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03938-w chicago: Zhou, Haoxin, Tian Xie, Areg Ghazaryan, Tobias Holder, James R. Ehrets, Eric M. Spanton, Takashi Taniguchi, et al. “Half and Quarter Metals in Rhombohedral Trilayer Graphene.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03938-w. ieee: H. Zhou et al., “Half and quarter metals in rhombohedral trilayer graphene,” Nature. Springer Nature, 2021. ista: Zhou H, Xie T, Ghazaryan A, Holder T, Ehrets JR, Spanton EM, Taniguchi T, Watanabe K, Berg E, Serbyn M, Young AF. 2021. Half and quarter metals in rhombohedral trilayer graphene. Nature. mla: Zhou, Haoxin, et al. “Half and Quarter Metals in Rhombohedral Trilayer Graphene.” Nature, Springer Nature, 2021, doi:10.1038/s41586-021-03938-w. short: H. Zhou, T. Xie, A. Ghazaryan, T. Holder, J.R. Ehrets, E.M. Spanton, T. Taniguchi, K. Watanabe, E. Berg, M. Serbyn, A.F. Young, Nature (2021). date_created: 2021-09-19T22:01:25Z date_published: 2021-09-01T00:00:00Z date_updated: 2023-08-14T07:04:06Z day: '01' department: - _id: MaSe - _id: MiLe doi: 10.1038/s41586-021-03938-w ec_funded: 1 external_id: arxiv: - '2104.00653' isi: - '000706977400002' isi: 1 keyword: - condensed matter - mesoscale and nanoscale physics - condensed matter - strongly correlated electrons - multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2104.00653 month: '09' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41586-021-04181-z scopus_import: '1' status: public title: Half and quarter metals in rhombohedral trilayer graphene type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '10076' abstract: - lang: eng text: We present a novel approach for blockchain asset owners to reclaim their funds in case of accidental private-key loss or transfer to a mistyped address. Our solution can be deployed upon failure or absence of proactively implemented backup mechanisms, such as secret sharing and cold storage. The main advantages against previous proposals is it does not require any prior action from users and works with both single-key and multi-sig accounts. We achieve this by a 3-phase Commit()→Reveal()→Claim()−or−Challenge() smart contract that enables accessing funds of addresses for which the spending key is not available. We provide an analysis of the threat and incentive models and formalize the concept of reactive KEy-Loss Protection (KELP). acknowledgement: The authors would like to thank all anonymous reviewers of FC21 WTSC workshop for comments and suggestions that greatly improved the quality of this paper. alternative_title: - LNCS article_processing_charge: No author: - first_name: Sam full_name: Blackshear, Sam last_name: Blackshear - first_name: Konstantinos full_name: Chalkias, Konstantinos last_name: Chalkias - first_name: Panagiotis full_name: Chatzigiannis, Panagiotis last_name: Chatzigiannis - first_name: Riyaz full_name: Faizullabhoy, Riyaz last_name: Faizullabhoy - first_name: Irakliy full_name: Khaburzaniya, Irakliy last_name: Khaburzaniya - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Joshua full_name: Lind, Joshua last_name: Lind - first_name: David full_name: Wong, David last_name: Wong - first_name: Tim full_name: Zakian, Tim last_name: Zakian citation: ama: 'Blackshear S, Chalkias K, Chatzigiannis P, et al. Reactive key-loss protection in blockchains. In: FC 2021 Workshops. Vol 12676. Springer Nature; 2021:431-450. doi:10.1007/978-3-662-63958-0_34' apa: 'Blackshear, S., Chalkias, K., Chatzigiannis, P., Faizullabhoy, R., Khaburzaniya, I., Kokoris Kogias, E., … Zakian, T. (2021). Reactive key-loss protection in blockchains. In FC 2021 Workshops (Vol. 12676, pp. 431–450). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-63958-0_34' chicago: Blackshear, Sam, Konstantinos Chalkias, Panagiotis Chatzigiannis, Riyaz Faizullabhoy, Irakliy Khaburzaniya, Eleftherios Kokoris Kogias, Joshua Lind, David Wong, and Tim Zakian. “Reactive Key-Loss Protection in Blockchains.” In FC 2021 Workshops, 12676:431–50. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-63958-0_34. ieee: S. Blackshear et al., “Reactive key-loss protection in blockchains,” in FC 2021 Workshops, Virtual, 2021, vol. 12676, pp. 431–450. ista: 'Blackshear S, Chalkias K, Chatzigiannis P, Faizullabhoy R, Khaburzaniya I, Kokoris Kogias E, Lind J, Wong D, Zakian T. 2021. Reactive key-loss protection in blockchains. FC 2021 Workshops. FC: International Conference on Financial Cryptography and Data Security, LNCS, vol. 12676, 431–450.' mla: Blackshear, Sam, et al. “Reactive Key-Loss Protection in Blockchains.” FC 2021 Workshops, vol. 12676, Springer Nature, 2021, pp. 431–50, doi:10.1007/978-3-662-63958-0_34. short: S. Blackshear, K. Chalkias, P. Chatzigiannis, R. Faizullabhoy, I. Khaburzaniya, E. Kokoris Kogias, J. Lind, D. Wong, T. Zakian, in:, FC 2021 Workshops, Springer Nature, 2021, pp. 431–450. conference: end_date: 2021-03-05 location: Virtual name: 'FC: International Conference on Financial Cryptography and Data Security' start_date: 2021-03-01 date_created: 2021-10-03T22:01:24Z date_published: 2021-09-17T00:00:00Z date_updated: 2023-08-14T07:06:16Z day: '17' department: - _id: ElKo doi: 10.1007/978-3-662-63958-0_34 external_id: isi: - '000713005000034' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://research.fb.com/publications/reactive-key-loss-protection-in-blockchains/ month: '09' oa: 1 oa_version: Preprint page: 431-450 publication: FC 2021 Workshops publication_identifier: eisbn: - 978-3-662-63958-0 eissn: - 1611-3349 isbn: - 978-3-6626-3957-3 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Reactive key-loss protection in blockchains type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: '12676 ' year: '2021' ... --- _id: '10070' abstract: - lang: eng text: We extensively discuss the Rademacher and Sobolev-to-Lipschitz properties for generalized intrinsic distances on strongly local Dirichlet spaces possibly without square field operator. We present many non-smooth and infinite-dimensional examples. As an application, we prove the integral Varadhan short-time asymptotic with respect to a given distance function for a large class of strongly local Dirichlet forms. acknowledgement: 'The authors are grateful to Professor Kazuhiro Kuwae for kindly providing a copy of [49]. They are also grateful to Dr. Bang-Xian Han for helpful discussions on the Sobolev-to-Lipschitz property on metric measure spaces. They wish to express their deepest gratitude to an anonymous Reviewer, whose punctual remarks and comments greatly improved the accessibility and overall quality of the initial submission. This work was completed while L.D.S. was a member of the Institut für Angewandte Mathematik of the University of Bonn. He acknowledges funding of his position at that time by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the Sonderforschungsbereich (Sfb, Collaborative Research Center) 1060 - project number 211504053. He also acknowledges funding of his current position by the Austrian Science Fund (FWF) grant F65, and by the European Research Council (ERC, grant No. 716117, awarded to Prof. Dr. Jan Maas). K.S. gratefully acknowledges funding by: the JSPS Overseas Research Fellowships, Grant Nr. 290142; World Premier International Research Center Initiative (WPI), MEXT, Japan; and JSPS Grant-in-Aid for Scientific Research on Innovative Areas “Discrete Geometric Analysis for Materials Design”, Grant Number 17H06465.' article_number: '109234' article_processing_charge: No article_type: original author: - first_name: Lorenzo full_name: Dello Schiavo, Lorenzo id: ECEBF480-9E4F-11EA-B557-B0823DDC885E last_name: Dello Schiavo orcid: 0000-0002-9881-6870 - first_name: Kohei full_name: Suzuki, Kohei last_name: Suzuki citation: ama: Dello Schiavo L, Suzuki K. Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. 2021;281(11). doi:10.1016/j.jfa.2021.109234 apa: Dello Schiavo, L., & Suzuki, K. (2021). Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109234 chicago: Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” Journal of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109234. ieee: L. Dello Schiavo and K. Suzuki, “Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces,” Journal of Functional Analysis, vol. 281, no. 11. Elsevier, 2021. ista: Dello Schiavo L, Suzuki K. 2021. Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. 281(11), 109234. mla: Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” Journal of Functional Analysis, vol. 281, no. 11, 109234, Elsevier, 2021, doi:10.1016/j.jfa.2021.109234. short: L. Dello Schiavo, K. Suzuki, Journal of Functional Analysis 281 (2021). date_created: 2021-10-03T22:01:21Z date_published: 2021-09-15T00:00:00Z date_updated: 2023-08-14T07:05:44Z day: '15' department: - _id: JaMa doi: 10.1016/j.jfa.2021.109234 ec_funded: 1 external_id: arxiv: - '2008.01492' isi: - '000703896600005' intvolume: ' 281' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2008.01492 month: '09' oa: 1 oa_version: Preprint project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics publication: Journal of Functional Analysis publication_identifier: eissn: - 1096-0783 issn: - 0022-1236 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 281 year: '2021' ... --- _id: '10123' abstract: - lang: eng text: Solution synthesis of particles emerged as an alternative to prepare thermoelectric materials with less demanding processing conditions than conventional solid-state synthetic methods. However, solution synthesis generally involves the presence of additional molecules or ions belonging to the precursors or added to enable solubility and/or regulate nucleation and growth. These molecules or ions can end up in the particles as surface adsorbates and interfere in the material properties. This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically adsorbed in SnSe particles synthesized in water and play a crucial role not only in directing the material nano/microstructure but also in determining the transport properties of the consolidated material. In dense pellets prepared by sintering SnSe particles, Na remains within the crystal lattice as dopant, in dislocations, precipitates, and forming grain boundary complexions. These results highlight the importance of considering all the possible unintentional impurities to establish proper structure-property relationships and control material properties in solution-processed thermoelectric materials. acknowledged_ssus: - _id: EM-Fac - _id: NanoFab acknowledgement: 'Y.L. and M.C. contributed equally to this work. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union''s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. M.C. has received funding from the European Union''s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385. Y.Y. and O.C.-M. acknowledge the financial support from DFG within the project SFB 917: Nanoswitches. J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia program. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N.' article_number: '2106858' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Mariano full_name: Calcabrini, Mariano id: 45D7531A-F248-11E8-B48F-1D18A9856A87 last_name: Calcabrini orcid: 0000-0003-4566-5877 - first_name: Yuan full_name: Yu, Yuan last_name: Yu - first_name: Aziz full_name: Genç, Aziz last_name: Genç - first_name: Cheng full_name: Chang, Cheng id: 9E331C2E-9F27-11E9-AE48-5033E6697425 last_name: Chang orcid: 0000-0002-9515-4277 - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - 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: Jordi full_name: Llorca, Jordi last_name: Llorca - first_name: Oana full_name: Cojocaru‐Mirédin, Oana last_name: Cojocaru‐Mirédin - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 citation: ama: 'Liu Y, Calcabrini M, Yu Y, et al. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 2021;33(52). doi:10.1002/adma.202106858' apa: 'Liu, Y., Calcabrini, M., Yu, Y., Genç, A., Chang, C., Costanzo, T., … Ibáñez, M. (2021). The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202106858' chicago: 'Liu, Yu, Mariano Calcabrini, Yuan Yu, Aziz Genç, Cheng Chang, Tommaso Costanzo, Tobias Kleinhanns, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” Advanced Materials. Wiley, 2021. https://doi.org/10.1002/adma.202106858.' ieee: 'Y. Liu et al., “The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe,” Advanced Materials, vol. 33, no. 52. Wiley, 2021.' ista: 'Liu Y, Calcabrini M, Yu Y, Genç A, Chang C, Costanzo T, Kleinhanns T, Lee S, Llorca J, Cojocaru‐Mirédin O, Ibáñez M. 2021. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 33(52), 2106858.' mla: 'Liu, Yu, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” Advanced Materials, vol. 33, no. 52, 2106858, Wiley, 2021, doi:10.1002/adma.202106858.' short: Y. Liu, M. Calcabrini, Y. Yu, A. Genç, C. Chang, T. Costanzo, T. Kleinhanns, S. Lee, J. Llorca, O. Cojocaru‐Mirédin, M. Ibáñez, Advanced Materials 33 (2021). date_created: 2021-10-11T20:07:24Z date_published: 2021-12-29T00:00:00Z date_updated: 2023-08-14T07:25:27Z day: '29' ddc: - '620' department: - _id: EM-Fac - _id: MaIb doi: 10.1002/adma.202106858 ec_funded: 1 external_id: isi: - '000709899300001' pmid: - '34626034' file: - access_level: open_access checksum: 990bccc527c64d85cf1c97885110b5f4 content_type: application/pdf creator: cchlebak date_created: 2022-02-03T13:16:14Z date_updated: 2022-02-03T13:16:14Z file_id: '10720' file_name: 2021_AdvancedMaterials_Liu.pdf file_size: 5595666 relation: main_file success: 1 file_date_updated: 2022-02-03T13:16:14Z has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '52' keyword: - mechanical engineering - mechanics of materials - general materials science language: - iso: eng month: '12' 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 - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A grant_number: M02889 name: Bottom-up Engineering for Thermoelectric Applications - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' publication: Advanced Materials publication_identifier: eissn: - 1521-4095 issn: - 0935-9648 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '12885' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe' 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: 33 year: '2021' ... --- _id: '10117' abstract: - lang: eng text: Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism. acknowledgement: We thank de Bono lab members for helpful comments on the manuscript, IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions and comments for the optimization of mass spec analyses of worm samples. The biotin auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg). Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University of Vienna). article_number: '101094' article_processing_charge: Yes article_type: original author: - first_name: Murat full_name: Artan, Murat id: C407B586-6052-11E9-B3AE-7006E6697425 last_name: Artan orcid: 0000-0001-8945-6992 - first_name: Stephen full_name: Barratt, Stephen id: 57740d2b-2a88-11ec-97cf-d9e6d1b39677 last_name: Barratt - first_name: Sean M. full_name: Flynn, Sean M. last_name: Flynn - first_name: Farida full_name: Begum, Farida last_name: Begum - first_name: Mark full_name: Skehel, Mark last_name: Skehel - first_name: Armel full_name: Nicolas, Armel id: 2A103192-F248-11E8-B48F-1D18A9856A87 last_name: Nicolas - first_name: Mario full_name: De Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: De Bono orcid: 0000-0001-8347-0443 citation: ama: Artan M, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 2021;297(3). doi:10.1016/J.JBC.2021.101094 apa: Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., & de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. Elsevier. https://doi.org/10.1016/J.JBC.2021.101094 chicago: Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel, Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry. Elsevier, 2021. https://doi.org/10.1016/J.JBC.2021.101094. ieee: M. Artan et al., “Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling,” Journal of Biological Chemistry, vol. 297, no. 3. Elsevier, 2021. ista: Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 297(3), 101094. mla: Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry, vol. 297, no. 3, 101094, Elsevier, 2021, doi:10.1016/J.JBC.2021.101094. short: M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021). date_created: 2021-10-10T22:01:23Z date_published: 2021-09-01T00:00:00Z date_updated: 2023-08-14T07:24:09Z day: '01' ddc: - '612' department: - _id: MaDe - _id: LifeSc doi: 10.1016/J.JBC.2021.101094 ec_funded: 1 external_id: isi: - '000706409200006' file: - access_level: open_access checksum: 19e39d36c5b9387c6dc0e89c9ae856ab content_type: application/pdf creator: cchlebak date_created: 2021-10-11T12:20:58Z date_updated: 2021-10-11T12:20:58Z file_id: '10121' file_name: 2021_JBC_Artan.pdf file_size: 1680010 relation: main_file success: 1 file_date_updated: 2021-10-11T12:20:58Z has_accepted_license: '1' intvolume: ' 297' isi: 1 issue: '3' language: - iso: eng month: '09' 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 Biological Chemistry publication_identifier: eissn: - 1083-351X issn: - 0021-9258 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling 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: 297 year: '2021' ... --- _id: '10108' abstract: - lang: eng text: We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs. acknowledgement: The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Mae Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper. alternative_title: - LNCS article_processing_charge: No author: - first_name: Fabian full_name: Mühlböck, Fabian id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425 last_name: Mühlböck orcid: 0000-0003-1548-0177 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: 'Mühlböck F, Henzinger TA. Differential monitoring. In: International Conference on Runtime Verification. Vol 12974. Cham: Springer Nature; 2021:231-243. doi:10.1007/978-3-030-88494-9_12' apa: 'Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. In International Conference on Runtime Verification (Vol. 12974, pp. 231–243). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-88494-9_12' chicago: 'Mühlböck, Fabian, and Thomas A Henzinger. “Differential Monitoring.” In International Conference on Runtime Verification, 12974:231–43. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_12.' ieee: F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in International Conference on Runtime Verification, Virtual, 2021, vol. 12974, pp. 231–243. ista: 'Mühlböck F, Henzinger TA. 2021. Differential monitoring. International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 231–243.' mla: Mühlböck, Fabian, and Thomas A. Henzinger. “Differential Monitoring.” International Conference on Runtime Verification, vol. 12974, Springer Nature, 2021, pp. 231–43, doi:10.1007/978-3-030-88494-9_12. short: F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 231–243. conference: end_date: 2021-10-14 location: Virtual name: 'RV: Runtime Verification' start_date: 2021-10-11 date_created: 2021-10-07T23:30:10Z date_published: 2021-10-06T00:00:00Z date_updated: 2023-08-14T07:20:30Z day: '06' ddc: - '005' department: - _id: ToHe doi: 10.1007/978-3-030-88494-9_12 external_id: isi: - '000719383800012' file: - access_level: open_access checksum: 554c7fdb259eda703a8b6328a6dad55a content_type: application/pdf creator: fmuehlbo date_created: 2021-10-07T23:32:18Z date_updated: 2021-10-07T23:32:18Z file_id: '10109' file_name: differentialmonitoring-cameraready-openaccess.pdf file_size: 350632 relation: main_file success: 1 file_date_updated: 2021-10-07T23:32:18Z has_accepted_license: '1' intvolume: ' 12974' isi: 1 keyword: - run-time verification - software engineering - implicit specification language: - iso: eng month: '10' oa: 1 oa_version: Preprint page: 231-243 place: Cham project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: International Conference on Runtime Verification publication_identifier: eisbn: - 978-3-030-88494-9 eissn: - 1611-3349 isbn: - 978-3-030-88493-2 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '9946' relation: extended_version status: public scopus_import: '1' status: public title: Differential monitoring type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12974 year: '2021' ... --- _id: '10116' abstract: - lang: eng text: The ubiquitous Ca2+ sensor calmodulin (CaM) binds and regulates many proteins, including ion channels, CaM kinases, and calcineurin, according to Ca2+-CaM levels. What regulates neuronal CaM levels, is, however, unclear. CaM-binding transcription activators (CAMTAs) are ancient proteins expressed broadly in nervous systems and whose loss confers pleiotropic behavioral defects in flies, mice, and humans. Using Caenorhabditis elegans and Drosophila, we show that CAMTAs control neuronal CaM levels. The behavioral and neuronal Ca2+ signaling defects in mutants lacking camt-1, the sole C. elegans CAMTA, can be rescued by supplementing neuronal CaM. CAMT-1 binds multiple sites in the CaM promoter and deleting these sites phenocopies camt-1. Our data suggest CAMTAs mediate a conserved and general mechanism that controls neuronal CaM levels, thereby regulating Ca2+ signaling, physiology, and behavior. acknowledgement: The authors thank the MRC-LMB Flow Cytometry facility and Imaging Service for support, the Cancer Research UK Cambridge Institute Genomics Core for Next Generation Sequencing, Julie Ahringer and Alex Appert for advice and technical help for ChIP-seq experiments, Paula Freire-Pritchett, Tim Stevens, and Gurpreet Ghattaoraya for RNA-seq and ChIP-seq analyses, Nikos Chronis for the TN-XL plasmid, Hong-Sheng Li and Daisuke Yamamoto for generously sending the tes2 and cro mutants, Daria Siekhaus for hosting the fly work, Michaela Misova for technical assistance. The authors are very grateful to Salihah Ece Sönmez for teaching us how to dissect, mount and stain Drosophila retinae. This work was supported by an Advanced ERC grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB, and an IST Plus Fellowship to TV-B (Marie Sklodowska-Curie Agreement no 754411). article_number: e68238 article_processing_charge: No article_type: original author: - first_name: Thanh full_name: Vuong-Brender, Thanh id: D389312E-10C4-11EA-ABF4-A4B43DDC885E last_name: Vuong-Brender - first_name: Sean full_name: Flynn, Sean last_name: Flynn - first_name: Yvonne full_name: Vallis, Yvonne id: 05A2795C-31B5-11EA-83A7-7DA23DDC885E last_name: Vallis - first_name: Mario full_name: De Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: De Bono orcid: 0000-0001-8347-0443 citation: ama: Vuong-Brender T, Flynn S, Vallis Y, de Bono M. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife. 2021;10. doi:10.7554/eLife.68238 apa: Vuong-Brender, T., Flynn, S., Vallis, Y., & de Bono, M. (2021). Neuronal calmodulin levels are controlled by CAMTA transcription factors. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.68238 chicago: Vuong-Brender, Thanh, Sean Flynn, Yvonne Vallis, and Mario de Bono. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.68238. ieee: T. Vuong-Brender, S. Flynn, Y. Vallis, and M. de Bono, “Neuronal calmodulin levels are controlled by CAMTA transcription factors,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Vuong-Brender T, Flynn S, Vallis Y, de Bono M. 2021. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife. 10, e68238. mla: Vuong-Brender, Thanh, et al. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” ELife, vol. 10, e68238, eLife Sciences Publications, 2021, doi:10.7554/eLife.68238. short: T. Vuong-Brender, S. Flynn, Y. Vallis, M. de Bono, ELife 10 (2021). date_created: 2021-10-10T22:01:22Z date_published: 2021-09-17T00:00:00Z date_updated: 2023-08-14T07:23:39Z day: '17' ddc: - '610' department: - _id: MaDe doi: 10.7554/eLife.68238 ec_funded: 1 external_id: isi: - '000695716100001' pmid: - '34499028' file: - access_level: open_access checksum: b465e172d2b1f57aa26a2571a085d052 content_type: application/pdf creator: cchlebak date_created: 2021-10-11T14:15:07Z date_updated: 2021-10-11T14:15:07Z file_id: '10122' file_name: 2021_eLife_VuongBrender.pdf file_size: 1774624 relation: main_file success: 1 file_date_updated: 2021-10-11T14:15:07Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Neuronal calmodulin levels are controlled by CAMTA transcription factors 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: '10103' abstract: - lang: eng text: The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses. acknowledgement: We thank Volker M. Vogt for his critical comments in preparation of the review. article_number: '1853' article_processing_charge: Yes article_type: original author: - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr orcid: 0000-0003-1756-6564 - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Robert A. full_name: Dick, Robert A. last_name: Dick citation: ama: Obr M, Schur FK, Dick RA. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 2021;13(9). doi:10.3390/v13091853 apa: Obr, M., Schur, F. K., & Dick, R. A. (2021). A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. MDPI. https://doi.org/10.3390/v13091853 chicago: Obr, Martin, Florian KM Schur, and Robert A. Dick. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses. MDPI, 2021. https://doi.org/10.3390/v13091853. ieee: M. Obr, F. K. Schur, and R. A. Dick, “A structural perspective of the role of IP6 in immature and mature retroviral assembly,” Viruses, vol. 13, no. 9. MDPI, 2021. ista: Obr M, Schur FK, Dick RA. 2021. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 13(9), 1853. mla: Obr, Martin, et al. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses, vol. 13, no. 9, 1853, MDPI, 2021, doi:10.3390/v13091853. short: M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021). date_created: 2021-10-07T09:13:29Z date_published: 2021-09-17T00:00:00Z date_updated: 2023-08-14T07:21:51Z day: '17' ddc: - '616' department: - _id: FlSc doi: 10.3390/v13091853 external_id: isi: - '000699841100001' pmid: - '34578434' file: - access_level: open_access checksum: bcfd72a12977d48e22df3d0cc55aacf1 content_type: application/pdf creator: cchlebak date_created: 2021-10-08T10:38:15Z date_updated: 2021-10-08T10:38:15Z file_id: '10115' file_name: 2021_Viruses_Obr.pdf file_size: 4146796 relation: main_file success: 1 file_date_updated: 2021-10-08T10:38:15Z has_accepted_license: '1' intvolume: ' 13' isi: 1 issue: '9' keyword: - virology - infectious diseases language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid publication: Viruses publication_identifier: issn: - 1999-4915 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: A structural perspective of the role of IP6 in immature and mature retroviral assembly tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2021' ... --- _id: '10067' abstract: - lang: eng text: The search for novel entangled phases of matter has lead to the recent discovery of a new class of “entanglement transitions,” exemplified by random tensor networks and monitored quantum circuits. Most known examples can be understood as some classical ordering transitions in an underlying statistical mechanics model, where entanglement maps onto the free-energy cost of inserting a domain wall. In this paper we study the possibility of entanglement transitions driven by physics beyond such statistical mechanics mappings. Motivated by recent applications of neural-network-inspired variational Ansätze, we investigate under what conditions on the variational parameters these Ansätze can capture an entanglement transition. We study the entanglement scaling of short-range restricted Boltzmann machine (RBM) quantum states with random phases. For uncorrelated random phases, we analytically demonstrate the absence of an entanglement transition and reveal subtle finite-size effects in finite-size numerical simulations. Introducing phases with correlations decaying as 1/r^α in real space, we observe three regions with a different scaling of entanglement entropy depending on the exponent α. We study the nature of the transition between these regions, finding numerical evidence for critical behavior. Our work establishes the presence of long-range correlated phases in RBM-based wave functions as a required ingredient for entanglement transitions. acknowledgement: We would like to thank S. De Nicola, P. Brighi, and V. Karle for fruitful discussions and valuable feedback on the manuscript. R.M. and M.S. acknowledge support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.V. acknowledges support from the US Department of Energy, Office of Science, Basic Energy Sciences, under Early Career Award No. DE-SC0019168, and the Alfred P. Sloan Foundation through a Sloan Research Fellowship. article_number: '104205' article_processing_charge: No article_type: original author: - first_name: Raimel A full_name: Medina Ramos, Raimel A id: CE680B90-D85A-11E9-B684-C920E6697425 last_name: Medina Ramos orcid: 0000-0002-5383-2869 - first_name: Romain full_name: Vasseur, Romain last_name: Vasseur - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Medina Ramos RA, Vasseur R, Serbyn M. Entanglement transitions from restricted Boltzmann machines. Physical Review B. 2021;104(10). doi:10.1103/physrevb.104.104205 apa: Medina Ramos, R. A., Vasseur, R., & Serbyn, M. (2021). Entanglement transitions from restricted Boltzmann machines. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.104.104205 chicago: Medina Ramos, Raimel A, Romain Vasseur, and Maksym Serbyn. “Entanglement Transitions from Restricted Boltzmann Machines.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/physrevb.104.104205. ieee: R. A. Medina Ramos, R. Vasseur, and M. Serbyn, “Entanglement transitions from restricted Boltzmann machines,” Physical Review B, vol. 104, no. 10. American Physical Society, 2021. ista: Medina Ramos RA, Vasseur R, Serbyn M. 2021. Entanglement transitions from restricted Boltzmann machines. Physical Review B. 104(10), 104205. mla: Medina Ramos, Raimel A., et al. “Entanglement Transitions from Restricted Boltzmann Machines.” Physical Review B, vol. 104, no. 10, 104205, American Physical Society, 2021, doi:10.1103/physrevb.104.104205. short: R.A. Medina Ramos, R. Vasseur, M. Serbyn, Physical Review B 104 (2021). date_created: 2021-10-02T09:03:42Z date_published: 2021-09-30T00:00:00Z date_updated: 2023-08-14T07:24:47Z day: '30' department: - _id: MaSe doi: 10.1103/physrevb.104.104205 ec_funded: 1 external_id: arxiv: - '2107.05735' isi: - '000704414400002' intvolume: ' 104' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2107.05735 month: '09' oa: 1 oa_version: Preprint project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Entanglement transitions from restricted Boltzmann machines type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 104 year: '2021' ... --- _id: '9946' abstract: - lang: eng text: We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs. acknowledgement: The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Matthew Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper. alternative_title: - IST Austria Technical Report article_processing_charge: No author: - first_name: Fabian full_name: Mühlböck, Fabian id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425 last_name: Mühlböck orcid: 0000-0003-1548-0177 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: Mühlböck F, Henzinger TA. Differential Monitoring. IST Austria; 2021. doi:10.15479/AT:ISTA:9946 apa: Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. IST Austria. https://doi.org/10.15479/AT:ISTA:9946 chicago: Mühlböck, Fabian, and Thomas A Henzinger. Differential Monitoring. IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9946. ieee: F. Mühlböck and T. A. Henzinger, Differential monitoring. IST Austria, 2021. ista: Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p. mla: Mühlböck, Fabian, and Thomas A. Henzinger. Differential Monitoring. IST Austria, 2021, doi:10.15479/AT:ISTA:9946. short: F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021. date_created: 2021-08-20T20:00:37Z date_published: 2021-09-01T00:00:00Z date_updated: 2023-08-14T07:20:29Z day: '01' ddc: - '005' department: - _id: ToHe doi: 10.15479/AT:ISTA:9946 file: - access_level: open_access checksum: 0f9aafd59444cb6bdca6925d163ab946 content_type: application/pdf creator: fmuehlbo date_created: 2021-08-20T19:59:44Z date_updated: 2021-09-03T12:34:28Z file_id: '9948' file_name: differentialmonitoring-techreport.pdf file_size: '320453' relation: main_file file_date_updated: 2021-09-03T12:34:28Z has_accepted_license: '1' keyword: - run-time verification - software engineering - implicit specification language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '17' project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria related_material: record: - id: '9281' relation: other status: public - id: '10108' relation: shorter_version status: public status: public title: Differential monitoring type: technical_report user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2021' ... --- _id: '10073' abstract: - lang: eng text: Thermoelectric materials enable the direct conversion between heat and electricity. SnTe is a promising candidate due to its high charge transport performance. Here, we prepared SnTe nanocomposites by employing an aqueous method to synthetize SnTe nanoparticles (NP), followed by a unique surface treatment prior NP consolidation. This synthetic approach allowed optimizing the charge and phonon transport synergistically. The novelty of this strategy was the use of a soluble PbS molecular complex prepared using a thiol-amine solvent mixture that upon blending is adsorbed on the SnTe NP surface. Upon consolidation with spark plasma sintering, SnTe-PbS nanocomposite is formed. The presence of PbS complexes significantly compensates for the Sn vacancy and increases the average grain size of the nanocomposite, thus improving the carrier mobility. Moreover, lattice thermal conductivity is also reduced by the Pb and S-induced mass and strain fluctuation. As a result, an enhanced ZT of ca. 0.8 is reached at 873 K. Our finding provides a novel strategy to conduct rational surface treatment on NP-based thermoelectrics. acknowledged_ssus: - _id: EM-Fac acknowledgement: "The authors thank the EMF facility in IST Austria for providing SEM and EDX measurements.\r\n" article_number: '5416' article_processing_charge: Yes article_type: original author: - first_name: Cheng full_name: Chang, Cheng id: 9E331C2E-9F27-11E9-AE48-5033E6697425 last_name: Chang orcid: 0000-0002-9515-4277 - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 citation: ama: Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 2021;14(18). doi:10.3390/ma14185416 apa: Chang, C., & Ibáñez, M. (2021). Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. MDPI. https://doi.org/10.3390/ma14185416 chicago: Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” Materials. MDPI, 2021. https://doi.org/10.3390/ma14185416. ieee: C. Chang and M. Ibáñez, “Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites,” Materials, vol. 14, no. 18. MDPI, 2021. ista: Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 14(18), 5416. mla: Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” Materials, vol. 14, no. 18, 5416, MDPI, 2021, doi:10.3390/ma14185416. short: C. Chang, M. Ibáñez, Materials 14 (2021). date_created: 2021-10-03T22:01:23Z date_published: 2021-09-19T00:00:00Z date_updated: 2023-08-14T08:00:01Z day: '19' ddc: - '540' department: - _id: MaIb doi: 10.3390/ma14185416 external_id: isi: - '000700689400001' pmid: - '34576640' file: - access_level: open_access checksum: 4929dfc673a3ae77c010b6174279cc1d content_type: application/pdf creator: cchlebak date_created: 2021-10-14T11:56:39Z date_updated: 2021-10-14T11:56:39Z file_id: '10140' file_name: 2021_Materials_Chang.pdf file_size: 4404141 relation: main_file success: 1 file_date_updated: 2021-10-14T11:56:39Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '18' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A grant_number: M02889 name: Bottom-up Engineering for Thermoelectric Applications publication: Materials publication_identifier: eissn: - 1996-1944 publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Enhanced thermoelectric performance by surface engineering in SnTe-PbS 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: 14 year: '2021' ... --- _id: '10167' abstract: - lang: eng text: Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group. acknowledged_ssus: - _id: ScienComp acknowledgement: The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V. article_processing_charge: No article_type: original author: - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 - first_name: Mikhail A. full_name: Moldovan, Mikhail A. id: c8bb7f32-3315-11ec-b58b-e5950e6c14a0 last_name: Moldovan orcid: 0000-0002-8876-6494 - first_name: Marion A L full_name: Picard, Marion A L id: 2C921A7A-F248-11E8-B48F-1D18A9856A87 last_name: Picard orcid: 0000-0002-8101-2518 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 2021. doi:10.1093/molbev/msab178 apa: Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., & Vicoso, B. (2021). Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. Oxford University Press . https://doi.org/10.1093/molbev/msab178 chicago: Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” Molecular Biology and Evolution. Oxford University Press , 2021. https://doi.org/10.1093/molbev/msab178. ieee: M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” Molecular Biology and Evolution. Oxford University Press , 2021. ista: Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. mla: Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” Molecular Biology and Evolution, Oxford University Press , 2021, doi:10.1093/molbev/msab178. short: M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution (2021). date_created: 2021-10-21T07:49:12Z date_published: 2021-06-19T00:00:00Z date_updated: 2023-08-14T08:03:06Z day: '19' ddc: - '610' department: - _id: BeVi doi: 10.1093/molbev/msab178 external_id: isi: - '000741368600009' pmid: - '34146097' file: - access_level: open_access checksum: 1b096702fb356d9c0eb88e1b3fcff5f8 content_type: application/pdf creator: dernst date_created: 2022-05-06T09:47:18Z date_updated: 2022-05-06T09:47:18Z file_id: '11352' file_name: 2021_MolecularBiolEvolution_Elkrewi.pdf file_size: 1008594 relation: main_file success: 1 file_date_updated: 2022-05-06T09:47:18Z has_accepted_license: '1' isi: 1 keyword: - sex chromosomes - evolutionary strata - W-linked gene - sex determining gene - schistosome parasites language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 250ED89C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28842-B22 name: Sex chromosome evolution under male- and female- heterogamety publication: Molecular Biology and Evolution publication_identifier: eissn: - 1537-1719 issn: - 0737-4038 publication_status: published publisher: 'Oxford University Press ' quality_controlled: '1' scopus_import: '1' status: public title: Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination 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 year: '2021' ... --- _id: '10163' abstract: - lang: eng text: The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay. acknowledgement: 'D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase; Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for design of the arrest assay sequences; Petra van der Lelij for help with generating mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing; Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis; staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support; Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for critical comments on the manuscript; Life Science Editors for editing assistance. M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K. is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S. is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic (CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement no. 649030); this publication reflects only the author’s view and the Research Executive Agency is not responsible for any use that may be made of the information it contains. M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276, P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative ‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action BM1405 Non-globular proteins - from sequence to structure, function and application in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF LS17-008), and by the University of Vienna. This project was funded by the MFPL start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”) to D.S.' article_number: '6078' article_processing_charge: No article_type: original author: - first_name: Lisa-Marie full_name: Appel, Lisa-Marie last_name: Appel - first_name: Vedran full_name: Franke, Vedran last_name: Franke - first_name: Melania full_name: Bruno, Melania last_name: Bruno - first_name: Irina full_name: Grishkovskaya, Irina last_name: Grishkovskaya - first_name: Aiste full_name: Kasiliauskaite, Aiste last_name: Kasiliauskaite - first_name: Tanja full_name: Kaufmann, Tanja last_name: Kaufmann - first_name: Ursula E. full_name: Schoeberl, Ursula E. last_name: Schoeberl - first_name: Martin G. full_name: Puchinger, Martin G. last_name: Puchinger - first_name: Sebastian full_name: Kostrhon, Sebastian last_name: Kostrhon - first_name: Carmen full_name: Ebenwaldner, Carmen last_name: Ebenwaldner - first_name: Marek full_name: Sebesta, Marek last_name: Sebesta - first_name: Etienne full_name: Beltzung, Etienne last_name: Beltzung - first_name: Karl full_name: Mechtler, Karl last_name: Mechtler - first_name: Gen full_name: Lin, Gen last_name: Lin - first_name: Anna full_name: Vlasova, Anna last_name: Vlasova - first_name: Martin full_name: Leeb, Martin last_name: Leeb - first_name: Rushad full_name: Pavri, Rushad last_name: Pavri - first_name: Alexander full_name: Stark, Alexander last_name: Stark - first_name: Altuna full_name: Akalin, Altuna last_name: Akalin - first_name: Richard full_name: Stefl, Richard last_name: Stefl - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 - first_name: Kristina full_name: Djinovic-Carugo, Kristina last_name: Djinovic-Carugo - first_name: Dea full_name: Slade, Dea last_name: Slade citation: ama: Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26360-2 apa: Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26360-2 chicago: Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26360-2. ieee: L.-M. Appel et al., “PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021. ista: Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078. mla: Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications, vol. 12, no. 1, 6078, Springer Nature, 2021, doi:10.1038/s41467-021-26360-2. short: L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T. Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta, E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A. Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications 12 (2021). date_created: 2021-10-20T14:40:32Z date_published: 2021-10-19T00:00:00Z date_updated: 2023-08-14T08:02:31Z day: '19' ddc: - '610' department: - _id: CaBe doi: 10.1038/s41467-021-26360-2 external_id: isi: - '000709050300001' file: - access_level: open_access checksum: d99fcd51aebde19c21314e3de0148007 content_type: application/pdf creator: cchlebak date_created: 2021-10-21T13:51:49Z date_updated: 2021-10-21T13:51:49Z file_id: '10169' file_name: 2021_NatComm_Appel.pdf file_size: 5111706 relation: main_file success: 1 file_date_updated: 2021-10-21T13:51:49Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' keyword: - general physics and astronomy - general biochemistry - genetics and molecular biology - general chemistry language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: 'Preprint ' relation: earlier_version url: https://www.biorxiv.org/content/10.1101/2020.02.11.943159 status: public title: PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '9547' abstract: - lang: eng text: With the wider availability of full-color 3D printers, color-accurate 3D-print preparation has received increased attention. A key challenge lies in the inherent translucency of commonly used print materials that blurs out details of the color texture. Previous work tries to compensate for these scattering effects through strategic assignment of colored primary materials to printer voxels. To date, the highest-quality approach uses iterative optimization that relies on computationally expensive Monte Carlo light transport simulation to predict the surface appearance from subsurface scattering within a given print material distribution; that optimization, however, takes in the order of days on a single machine. In our work, we dramatically speed up the process by replacing the light transport simulation with a data-driven approach. Leveraging a deep neural network to predict the scattering within a highly heterogeneous medium, our method performs around two orders of magnitude faster than Monte Carlo rendering while yielding optimization results of similar quality level. The network is based on an established method from atmospheric cloud rendering, adapted to our domain and extended by a physically motivated weight sharing scheme that substantially reduces the network size. We analyze its performance in an end-to-end print preparation pipeline and compare quality and runtime to alternative approaches, and demonstrate its generalization to unseen geometry and material values. This for the first time enables full heterogenous material optimization for 3D-print preparation within time frames in the order of the actual printing time. acknowledgement: We thank Sebastian Cucerca for processing and capturing the phys-cal printouts. This work was supported by the Charles University grant SVV-260588 and Czech Science Foundation grant 19-07626S. This project has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska Curie grant agreements No 642841 (DISTRO) and No765911 (RealVision), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE). article_processing_charge: No article_type: original author: - first_name: Tobias full_name: Rittig, Tobias last_name: Rittig - first_name: Denis full_name: Sumin, Denis last_name: Sumin - first_name: Vahid full_name: Babaei, Vahid last_name: Babaei - first_name: Piotr full_name: Didyk, Piotr last_name: Didyk - first_name: Alexey full_name: Voloboy, Alexey last_name: Voloboy - first_name: Alexander full_name: Wilkie, Alexander last_name: Wilkie - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Karol full_name: Myszkowski, Karol last_name: Myszkowski - first_name: Tim full_name: Weyrich, Tim last_name: Weyrich - first_name: Jaroslav full_name: Křivánek, Jaroslav last_name: Křivánek citation: ama: Rittig T, Sumin D, Babaei V, et al. Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. 2021;40(2):205-219. doi:10.1111/cgf.142626 apa: Rittig, T., Sumin, D., Babaei, V., Didyk, P., Voloboy, A., Wilkie, A., … Křivánek, J. (2021). Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.142626 chicago: Rittig, Tobias, Denis Sumin, Vahid Babaei, Piotr Didyk, Alexey Voloboy, Alexander Wilkie, Bernd Bickel, Karol Myszkowski, Tim Weyrich, and Jaroslav Křivánek. “Neural Acceleration of Scattering-Aware Color 3D Printing.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.142626. ieee: T. Rittig et al., “Neural acceleration of scattering-aware color 3D printing,” Computer Graphics Forum, vol. 40, no. 2. Wiley, pp. 205–219, 2021. ista: Rittig T, Sumin D, Babaei V, Didyk P, Voloboy A, Wilkie A, Bickel B, Myszkowski K, Weyrich T, Křivánek J. 2021. Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. 40(2), 205–219. mla: Rittig, Tobias, et al. “Neural Acceleration of Scattering-Aware Color 3D Printing.” Computer Graphics Forum, vol. 40, no. 2, Wiley, 2021, pp. 205–19, doi:10.1111/cgf.142626. short: T. Rittig, D. Sumin, V. Babaei, P. Didyk, A. Voloboy, A. Wilkie, B. Bickel, K. Myszkowski, T. Weyrich, J. Křivánek, Computer Graphics Forum 40 (2021) 205–219. date_created: 2021-06-13T22:01:32Z date_published: 2021-05-01T00:00:00Z date_updated: 2023-08-14T08:01:50Z day: '01' ddc: - '004' department: - _id: BeBi doi: 10.1111/cgf.142626 ec_funded: 1 external_id: isi: - '000657959600017' file: - access_level: open_access checksum: 33271724215f54a75c39d2ed40f2c502 content_type: application/pdf creator: bbickel date_created: 2021-10-11T12:06:50Z date_updated: 2021-10-11T12:06:50Z file_id: '10120' file_name: ScatteringAwareColor3DPrinting_authorVersion.pdf file_size: 26026501 relation: main_file success: 1 file_date_updated: 2021-10-11T12:06:50Z has_accepted_license: '1' intvolume: ' 40' isi: 1 issue: '2' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 205-219 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: Computer Graphics Forum publication_identifier: eissn: - 1467-8659 issn: - 0167-7055 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Neural acceleration of scattering-aware color 3D printing type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ... --- _id: '10177' abstract: - lang: eng text: Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane hyperbolic dispersion exhibit ray-like propagation with large wave vectors and enhanced density of optical states along certain directions on a surface. As such, they have raised a surge of interest, promising unprecedented manipulation of infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end, we developed metallic nanoantennas of convex geometries for both efficient launching and focusing of the polaritons. The foci obtained exhibit enhanced near-field confinement and absorption compared to foci produced by in-plane isotropic PhPs. Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces a first and most basic building block developing planar polariton optics using in-plane anisotropic van der Waals materials. acknowledgement: J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain and FSE (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). J.T.-G. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-18-PF-BP17-126). G.A.-P. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-20-PF-BP19-053). K.V.V. and V.S.V. acknowledge the financial support from the Ministry of Science and Higher Education of the Russian Federation (agreement no. 075-15-2021-606). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation, and Universities (national projects MAT2017-88358-C3-3-R and PID2020-115221GB-C42) and the Basque Department of Education (PIBA-2020-1-0014). R.H. acknowledges financial support from the Spanish Ministry of Science, Innovation, and Universities (national project number RTI2018-094830-B-100 and project number MDM-2016-0618 of the Marie de Maeztu Units of Excellence Program) and the Basque Government (grant number IT1164-19). article_number: abj0127 article_processing_charge: Yes article_type: original author: - first_name: Javier full_name: Martín-Sánchez, Javier last_name: Martín-Sánchez - first_name: Jiahua full_name: Duan, Jiahua last_name: Duan - first_name: Javier full_name: Taboada-Gutiérrez, Javier last_name: Taboada-Gutiérrez - first_name: Gonzalo full_name: Álvarez-Pérez, Gonzalo last_name: Álvarez-Pérez - first_name: Kirill V. full_name: Voronin, Kirill V. last_name: Voronin - first_name: Ivan full_name: Prieto Gonzalez, Ivan id: 2A307FE2-F248-11E8-B48F-1D18A9856A87 last_name: Prieto Gonzalez orcid: 0000-0002-7370-5357 - first_name: Weiliang full_name: Ma, Weiliang last_name: Ma - first_name: Qiaoliang full_name: Bao, Qiaoliang last_name: Bao - first_name: Valentyn S. full_name: Volkov, Valentyn S. last_name: Volkov - first_name: Rainer full_name: Hillenbrand, Rainer last_name: Hillenbrand - first_name: Alexey Y. full_name: Nikitin, Alexey Y. last_name: Nikitin - first_name: Pablo full_name: Alonso-González, Pablo last_name: Alonso-González citation: ama: Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, et al. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 2021;7(41). doi:10.1126/sciadv.abj0127 apa: Martín-Sánchez, J., Duan, J., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., … Alonso-González, P. (2021). Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abj0127 chicago: Martín-Sánchez, Javier, Jiahua Duan, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Kirill V. Voronin, Ivan Prieto Gonzalez, Weiliang Ma, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/sciadv.abj0127. ieee: J. Martín-Sánchez et al., “Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas,” Science Advances, vol. 7, no. 41. American Association for the Advancement of Science, 2021. ista: Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Ma W, Bao Q, Volkov VS, Hillenbrand R, Nikitin AY, Alonso-González P. 2021. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 7(41), abj0127. mla: Martín-Sánchez, Javier, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances, vol. 7, no. 41, abj0127, American Association for the Advancement of Science, 2021, doi:10.1126/sciadv.abj0127. short: J. Martín-Sánchez, J. Duan, J. Taboada-Gutiérrez, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, W. Ma, Q. Bao, V.S. Volkov, R. Hillenbrand, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021). date_created: 2021-10-24T22:01:33Z date_published: 2021-10-08T00:00:00Z date_updated: 2023-08-14T08:04:42Z day: '08' ddc: - '530' department: - _id: NanoFab doi: 10.1126/sciadv.abj0127 external_id: arxiv: - '2103.10852' isi: - '000704912700024' file: - access_level: open_access checksum: 0a470ef6a47d2b8a96ede4c4d28cfacd content_type: application/pdf creator: cziletti date_created: 2021-10-27T14:16:06Z date_updated: 2021-10-27T14:16:06Z file_id: '10189' file_name: 2021_ScienceAdv_Martin-Sanchez.pdf file_size: 2441163 relation: main_file success: 1 file_date_updated: 2021-10-27T14:16:06Z has_accepted_license: '1' intvolume: ' 7' isi: 1 issue: '41' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '10' oa: 1 oa_version: Published Version publication: Science Advances publication_identifier: eissn: - '23752548' publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 7 year: '2021' ... --- _id: '10146' abstract: - lang: eng text: The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2 (refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in mammals, but in contrast to CICIII2 and the respirasome, to date the only known eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and plants13, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly intermediates, in different conformations. We describe the assembly of CIII2CIV from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while its C terminus is integrated into CIV. Our structures (which include CICIII2 and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2 is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII2, explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer in the electron transport chain. acknowledged_ssus: - _id: PreCl - _id: EM-Fac - _id: ScienComp acknowledgement: We thank the pre-clinical facility of the IST Austria and A. Venturino for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan Krios data collection, performed at the IST Austria. The data processing was performed at the IST high-performance computing cluster. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411. article_processing_charge: No article_type: original author: - first_name: Irene full_name: Vercellino, Irene id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87 last_name: Vercellino orcid: 0000-0001-5618-3449 - 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: Vercellino I, Sazanov LA. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 2021;598(7880):364-367. doi:10.1038/s41586-021-03927-z apa: Vercellino, I., & Sazanov, L. A. (2021). Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03927-z chicago: Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03927-z. ieee: I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV,” Nature, vol. 598, no. 7880. Springer Nature, pp. 364–367, 2021. ista: Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 598(7880), 364–367. mla: Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature, vol. 598, no. 7880, Springer Nature, 2021, pp. 364–67, doi:10.1038/s41586-021-03927-z. short: I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367. date_created: 2021-10-17T22:01:17Z date_published: 2021-10-14T00:00:00Z date_updated: 2023-08-14T08:01:21Z day: '14' department: - _id: LeSa doi: 10.1038/s41586-021-03927-z ec_funded: 1 external_id: isi: - '000704581600001' pmid: - '34616041' intvolume: ' 598' isi: 1 issue: '7880' language: - iso: eng month: '10' oa_version: None page: 364-367 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Webpage relation: press_release url: https://ist.ac.at/en/news/boosting-the-cells-power-house/ scopus_import: '1' status: public title: Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 598 year: '2021' ... --- _id: '10176' abstract: - lang: eng text: "We give a combinatorial model for r-spin surfaces with parameterized boundary based on Novak (“Lattice topological field theories in two dimensions,” Ph.D. thesis, Universität Hamburg, 2015). The r-spin structure is encoded in terms of ℤ\U0001D45F-valued indices assigned to the edges of a polygonal decomposition. This combinatorial model is designed for our state-sum construction of two-dimensional topological field theories on r-spin surfaces. We show that an example of such a topological field theory computes the Arf-invariant of an r-spin surface as introduced by Randal-Williams [J. Topol. 7, 155 (2014)] and Geiges et al. [Osaka J. Math. 49, 449 (2012)]. This implies, in particular, that the r-spin Arf-invariant is constant on orbits of the mapping class group, providing an alternative proof of that fact." acknowledgement: We would like to thank Nils Carqueville, Tobias Dyckerhoff, Jan Hesse, Ehud Meir, Sebastian Novak, Louis-Hadrien Robert, Nick Salter, Walker Stern, and Lukas Woike for helpful discussions and comments. L.S. was supported by the DFG Research Training Group 1670 “Mathematics Inspired by String Theory and Quantum Field Theory.” article_number: '102302' article_processing_charge: No 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. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 2021;62(10). doi:10.1063/5.0037826 apa: Runkel, I., & Szegedy, L. (2021). Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0037826 chicago: Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” Journal of Mathematical Physics. AIP Publishing, 2021. https://doi.org/10.1063/5.0037826. ieee: I. Runkel and L. Szegedy, “Topological field theory on r-spin surfaces and the Arf-invariant,” Journal of Mathematical Physics, vol. 62, no. 10. AIP Publishing, 2021. ista: Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302. mla: Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” Journal of Mathematical Physics, vol. 62, no. 10, 102302, AIP Publishing, 2021, doi:10.1063/5.0037826. short: I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021). date_created: 2021-10-24T22:01:32Z date_published: 2021-10-01T00:00:00Z date_updated: 2023-08-14T08:04:12Z day: '01' department: - _id: MiLe doi: 10.1063/5.0037826 external_id: arxiv: - '1802.09978' isi: - '000755638500010' intvolume: ' 62' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.09978 month: '10' oa: 1 oa_version: Preprint publication: Journal of Mathematical Physics publication_identifier: issn: - '00222488' publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Topological field theory on r-spin surfaces and the Arf-invariant type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 62 year: '2021' ... --- _id: '10179' abstract: - lang: eng text: Inhibitory GABAergic interneurons migrate over long distances from their extracortical origin into the developing cortex. In humans, this process is uniquely slow and prolonged, and it is unclear whether guidance cues unique to humans govern the various phases of this complex developmental process. Here, we use fused cerebral organoids to identify key roles of neurotransmitter signaling pathways in guiding the migratory behavior of human cortical interneurons. We use scRNAseq to reveal expression of GABA, glutamate, glycine, and serotonin receptors along distinct maturation trajectories across interneuron migration. We develop an image analysis software package, TrackPal, to simultaneously assess 48 parameters for entire migration tracks of individual cells. By chemical screening, we show that different modes of interneuron migration depend on distinct neurotransmitter signaling pathways, linking transcriptional maturation of interneurons with their migratory behavior. Altogether, our study provides a comprehensive quantitative analysis of human interneuron migration and its functional modulation by neurotransmitter signaling. acknowledgement: We thank all Knoblich laboratory members for continued support and discussions. We thank the IMP/IMBA BioOptics facility, particularly Pawel Pasierbek, Alberto Moreno Cencerrado and Gerald Schmauss, the IMP/IMBA Molecular Biology Service, in particular Robert Heinen, the IMP Bioinformatics facility, in particular Thomas Burkard, the Vienna Biocenter Core Facilities (VBCF) Histopathology facility, in particular Tamara Engelmaier, and the VBCF Next Generation Sequencing Facility, notably Volodymyr Shubchynskyy and Carmen Czepe. We would also like to thank Simon Haendeler for advice on statistical analyses, Jose Guzman for discussions and assistance with slice culture setups, Oliver L. Eichmueller for discussions and assistance with microscopy, and E.H. Gustafson, S. Wolfinger, and D. Reumann for technical assistance regarding generation of cerebral organoids. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie fellowship agreement Nr.707109 awarded to J.A.B. Work in J.A.K.'s laboratory is supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, the City of Vienna, a Research Program of the Austrian Science Fund FWF (SFBF78 Stem Cell, F 7803-B) and a European Research Council (ERC) Advanced Grant under the European 20 Union’s Horizon 2020 program (grant agreement no. 695642). article_number: e108714 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Sunanjay full_name: Bajaj, Sunanjay last_name: Bajaj - first_name: Joshua A. full_name: Bagley, Joshua A. last_name: Bagley - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Abel full_name: Vertesy, Abel last_name: Vertesy - first_name: Sakurako full_name: Nagumo Wong, Sakurako last_name: Nagumo Wong - first_name: Veronica full_name: Krenn, Veronica last_name: Krenn - first_name: Julie full_name: Lévi-Strauss, Julie last_name: Lévi-Strauss - first_name: Juergen A. full_name: Knoblich, Juergen A. last_name: Knoblich citation: ama: Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 2021;40(23). doi:10.15252/embj.2021108714 apa: Bajaj, S., Bagley, J. A., Sommer, C. M., Vertesy, A., Nagumo Wong, S., Krenn, V., … Knoblich, J. A. (2021). Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2021108714 chicago: Bajaj, Sunanjay, Joshua A. Bagley, Christoph M Sommer, Abel Vertesy, Sakurako Nagumo Wong, Veronica Krenn, Julie Lévi-Strauss, and Juergen A. Knoblich. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2021108714. ieee: S. Bajaj et al., “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” EMBO Journal, vol. 40, no. 23. Embo Press, 2021. ista: Bajaj S, Bagley JA, Sommer CM, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss J, Knoblich JA. 2021. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 40(23), e108714. mla: Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” EMBO Journal, vol. 40, no. 23, e108714, Embo Press, 2021, doi:10.15252/embj.2021108714. short: S. Bajaj, J.A. Bagley, C.M. Sommer, A. Vertesy, S. Nagumo Wong, V. Krenn, J. Lévi-Strauss, J.A. Knoblich, EMBO Journal 40 (2021). date_created: 2021-10-24T22:01:34Z date_published: 2021-10-18T00:00:00Z date_updated: 2023-08-14T08:05:23Z day: '18' ddc: - '610' department: - _id: Bio doi: 10.15252/embj.2021108714 external_id: isi: - '000708012800001' pmid: - '34661293' file: - access_level: open_access checksum: 78d2d02e775322297e774f72810a41a4 content_type: application/pdf creator: alisjak date_created: 2021-12-13T14:54:14Z date_updated: 2021-12-13T14:54:14Z file_id: '10541' file_name: 2021_EMBO_Bajaj.pdf file_size: 7819881 relation: main_file success: 1 file_date_updated: 2021-12-13T14:54:14Z has_accepted_license: '1' intvolume: ' 40' isi: 1 issue: '23' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: EMBO Journal publication_identifier: eissn: - 1460-2075 issn: - 0261-4189 publication_status: published publisher: Embo Press quality_controlled: '1' scopus_import: '1' status: public title: Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ... --- _id: '10203' abstract: - lang: eng text: Single photon emitters in atomically-thin semiconductors can be deterministically positioned using strain induced by underlying nano-structures. Here, we couple monolayer WSe2 to high-refractive-index gallium phosphide dielectric nano-antennas providing both optical enhancement and monolayer deformation. For single photon emitters formed on such nano-antennas, we find very low (femto-Joule) saturation pulse energies and up to 104 times brighter photoluminescence than in WSe2 placed on low-refractive-index SiO2 pillars. We show that the key to these observations is the increase on average by a factor of 5 of the quantum efficiency of the emitters coupled to the nano-antennas. This further allows us to gain new insights into their photoluminescence dynamics, revealing the roles of the dark exciton reservoir and Auger processes. We also find that the coherence time of such emitters is limited by intrinsic dephasing processes. Our work establishes dielectric nano-antennas as a platform for high-efficiency quantum light generation in monolayer semiconductors. acknowledgement: L.S., P.G.Z., and A.I.T. thank the financial support of the European Graphene Flagship Project under grant agreements 881603 and EPSRC grant EP/S030751/1. L.S. and A.I.T. thank the European Union’s Horizon 2020 research and innovation programme under ITN Spin-NANO Marie Sklodowska-Curie grant agreement no. 676108. P.G.Z. and A.I.T. thank the European Union’s Horizon 2020 research and innovation programme under ITN 4PHOTON Marie Sklodowska-Curie grant agreement no. 721394. J.C., S.A.M., and R.S. acknowledge funding by EPSRC (EP/P033369 and EP/M013812). C.L.P., A.J.B., A.I.T., and A.M.F. acknowledge funding by EPSRC Programme Grant EP/N031776/1. S.A.M. acknowledges the Lee-Lucas Chair in Physics, the Solar Energies go Hybrid (SolTech) programme, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2089/1 - 390776260. article_number: '6063' article_processing_charge: No article_type: original author: - first_name: Luca full_name: Sortino, Luca last_name: Sortino - first_name: Panaiot G. full_name: Zotev, Panaiot G. last_name: Zotev - first_name: Catherine L. full_name: Phillips, Catherine L. last_name: Phillips - first_name: Alistair J. full_name: Brash, Alistair J. last_name: Brash - first_name: Javier full_name: Cambiasso, Javier last_name: Cambiasso - first_name: Elena full_name: Marensi, Elena id: 0BE7553A-1004-11EA-B805-18983DDC885E last_name: Marensi orcid: 0000-0001-7173-4923 - first_name: A. Mark full_name: Fox, A. Mark last_name: Fox - first_name: Stefan A. full_name: Maier, Stefan A. last_name: Maier - first_name: Riccardo full_name: Sapienza, Riccardo last_name: Sapienza - first_name: Alexander I. full_name: Tartakovskii, Alexander I. last_name: Tartakovskii citation: ama: Sortino L, Zotev PG, Phillips CL, et al. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. 2021;12. doi:10.1038/s41467-021-26262-3 apa: Sortino, L., Zotev, P. G., Phillips, C. L., Brash, A. J., Cambiasso, J., Marensi, E., … Tartakovskii, A. I. (2021). Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26262-3 chicago: Sortino, Luca, Panaiot G. Zotev, Catherine L. Phillips, Alistair J. Brash, Javier Cambiasso, Elena Marensi, A. Mark Fox, Stefan A. Maier, Riccardo Sapienza, and Alexander I. Tartakovskii. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26262-3. ieee: L. Sortino et al., “Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas,” Nature Communications, vol. 12. Springer Nature, 2021. ista: Sortino L, Zotev PG, Phillips CL, Brash AJ, Cambiasso J, Marensi E, Fox AM, Maier SA, Sapienza R, Tartakovskii AI. 2021. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. 12, 6063. mla: Sortino, Luca, et al. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” Nature Communications, vol. 12, 6063, Springer Nature, 2021, doi:10.1038/s41467-021-26262-3. short: L. Sortino, P.G. Zotev, C.L. Phillips, A.J. Brash, J. Cambiasso, E. Marensi, A.M. Fox, S.A. Maier, R. Sapienza, A.I. Tartakovskii, Nature Communications 12 (2021). date_created: 2021-10-31T23:01:30Z date_published: 2021-10-18T00:00:00Z date_updated: 2023-08-14T08:12:12Z day: '18' ddc: - '530' department: - _id: BjHo doi: 10.1038/s41467-021-26262-3 external_id: arxiv: - '2103.16986' isi: - '000708601800015' file: - access_level: open_access checksum: 8580d128389860f732028c521cd5949e content_type: application/pdf creator: cchlebak date_created: 2021-11-03T11:31:24Z date_updated: 2021-11-03T11:31:24Z file_id: '10212' file_name: 2021_NatComm_Sortino.pdf file_size: 1434201 relation: main_file success: 1 file_date_updated: 2021-11-03T11:31:24Z has_accepted_license: '1' intvolume: ' 12' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '10178' abstract: - lang: eng text: In dense biological tissues, cell types performing different roles remain segregated by maintaining sharp interfaces. To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic tension at the interface between two distinct cell types in a fully 3D Voronoi model for confluent tissues. We find that cells rapidly sort and self-organize to generate a tissue-scale interface between cell types, and cells adjacent to this interface exhibit signature geometric features including nematic-like ordering, bimodal facet areas, and registration, or alignment, of cell centers on either side of the two-tissue interface. The magnitude of these features scales directly with the magnitude of the imposed tension, suggesting that biologists can estimate the magnitude of tissue surface tension between two tissue types simply by segmenting a 3D tissue. To uncover the underlying physical mechanisms driving these geometric features, we develop two minimal, ordered models using two different underlying lattices that identify an energetic competition between bulk cell shapes and tissue interface area. When the interface area dominates, changes to neighbor topology are costly and occur less frequently, which generates the observed geometric features. acknowledgement: "We thank Paula Sanematsu, Matthias Merkel, Daniel Sussman, Cristina Marchetti and Edouard Hannezo for helpful discussions, and M Merkel for developing and sharing the original version of the 3D Voronoi code. This work was primarily funded by NSF-PHY-1607416, NSF-PHY-2014192 , and are in the division of physics at the National Science Foundation. PS and MLM acknowledge additional support from Simons Grant No. 454947.\r\n" article_number: '093043' article_processing_charge: Yes article_type: original author: - first_name: Preeti full_name: Sahu, Preeti id: 55BA52EE-A185-11EA-88FD-18AD3DDC885E last_name: Sahu - first_name: J. M. full_name: Schwarz, J. M. last_name: Schwarz - first_name: M. Lisa full_name: Manning, M. Lisa last_name: Manning citation: ama: Sahu P, Schwarz JM, Manning ML. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 2021;23(9). doi:10.1088/1367-2630/ac23f1 apa: Sahu, P., Schwarz, J. M., & Manning, M. L. (2021). Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac23f1 chicago: Sahu, Preeti, J. M. Schwarz, and M. Lisa Manning. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac23f1. ieee: P. Sahu, J. M. Schwarz, and M. L. Manning, “Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue,” New Journal of Physics, vol. 23, no. 9. IOP Publishing, 2021. ista: Sahu P, Schwarz JM, Manning ML. 2021. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 23(9), 093043. mla: Sahu, Preeti, et al. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” New Journal of Physics, vol. 23, no. 9, 093043, IOP Publishing, 2021, doi:10.1088/1367-2630/ac23f1. short: P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021). date_created: 2021-10-24T22:01:34Z date_published: 2021-09-29T00:00:00Z date_updated: 2023-08-14T08:10:31Z day: '29' ddc: - '570' department: - _id: EdHa doi: 10.1088/1367-2630/ac23f1 external_id: arxiv: - '2102.05397' isi: - '000702042400001' file: - access_level: open_access checksum: ace603e8f0962b3ba55f23fa34f57764 content_type: application/pdf creator: cziletti date_created: 2021-10-28T12:06:01Z date_updated: 2021-10-28T12:06:01Z file_id: '10193' file_name: 2021_NewJPhys_Sahu.pdf file_size: 2215016 relation: main_file success: 1 file_date_updated: 2021-10-28T12:06:01Z has_accepted_license: '1' intvolume: ' 23' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: New Journal of Physics publication_identifier: eissn: - '13672630' publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue 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: '10181' abstract: - lang: eng text: In this article we study some geometric properties of proximally smooth sets. First, we introduce a modification of the metric projection and prove its existence. Then we provide an algorithm for constructing a rectifiable curve between two sufficiently close points of a proximally smooth set in a uniformly convex and uniformly smooth Banach space, with the moduli of smoothness and convexity of power type. Our algorithm returns a reasonably short curve between two sufficiently close points of a proximally smooth set, is iterative and uses our modification of the metric projection. We estimate the length of the constructed curve and its deviation from the segment with the same endpoints. These estimates coincide up to a constant factor with those for the geodesics in a proximally smooth set in a Hilbert space. acknowledgement: Theorem 2 was obtained at Steklov Mathematical Institute RAS and supported by Russian Science Foundation, grant N 19-11-00087. article_processing_charge: No article_type: original author: - first_name: Grigory full_name: Ivanov, Grigory id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E last_name: Ivanov - first_name: Mariana S. full_name: Lopushanski, Mariana S. last_name: Lopushanski citation: ama: Ivanov G, Lopushanski MS. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. 2021. doi:10.1007/s11228-021-00612-1 apa: Ivanov, G., & Lopushanski, M. S. (2021). Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. Springer Nature. https://doi.org/10.1007/s11228-021-00612-1 chicago: Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” Set-Valued and Variational Analysis. Springer Nature, 2021. https://doi.org/10.1007/s11228-021-00612-1. ieee: G. Ivanov and M. S. Lopushanski, “Rectifiable curves in proximally smooth sets,” Set-Valued and Variational Analysis. Springer Nature, 2021. ista: Ivanov G, Lopushanski MS. 2021. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. mla: Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” Set-Valued and Variational Analysis, Springer Nature, 2021, doi:10.1007/s11228-021-00612-1. short: G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis (2021). date_created: 2021-10-24T22:01:35Z date_published: 2021-10-09T00:00:00Z date_updated: 2023-08-14T08:11:38Z day: '09' department: - _id: UlWa doi: 10.1007/s11228-021-00612-1 external_id: arxiv: - '2012.10691' isi: - '000705774800001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2012.10691 month: '10' oa: 1 oa_version: Published Version publication: Set-Valued and Variational Analysis publication_identifier: eissn: - 1877-0541 issn: - 0927-6947 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Rectifiable curves in proximally smooth sets type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '10202' abstract: - lang: eng text: Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant. acknowledgement: 'We are grateful to the members of C.-P.H. and SG lab for discussions. Authors thank Shubha Tole for providing embryonic mouse tissues. Authors are grateful to Alessandro Mongera and Chetana Sachidanandan for generous help with Tg: Sox10: GFP line. Authors would like to thank Satyajeet Khare, Vanessa Barone, Jyothish S., Shalini Mishra, Yoshita Bhide, and Keshav Jha for assistance in experiments. We would also like to thank Chaitanya Dingare for valuable suggestions. We thank Diana Pinhiero and Alexandra Schauer for critical reading of early versions of the manuscript. This work was supported by the Centre of Excellence in Epigenetics program of the Department of Biotechnology, Government of India Phase I (BT/01/COE/09/07) to S.G. and R.K.M., and Phase II (BT/COE/34/SP17426/2016) to S.G. and JC Bose Fellowship (JCB/2019/000013) from Science and Engineering Research Board, Government of India to S.G., DST-BMWF Indo-Austrian bilateral program grant to S.G. and C.-P.H. The work using animal models was partly supported by the infrastructure support grants from the Department of Biotechnology (National Facility for Laboratory Model Organisms: BT/INF/22/SP17358/2016 and Establishment of a Pune Biotech Cluster, Model Organism to Human Disease: B-2 Whole Animal Imaging & Tissue Processing FacilityBT/Pune-Biocluster/01/2015). S.J.P. was supported by Fellowship from the Council of Scientific and Industrial Research, India and travel fellowship from the Company of Biologists, UK. P.C.R. was supported by the Early Career Fellowship of the Wellcome Trust-DBT India Alliance (IA/E/16/1/503057). A.S. was supported by UGC and R.S. was supported by CSIR India. M.S. was supported by core funding from the Tata Institute of Fundamental Research (TIFR 12P-121).' article_number: '6094' article_processing_charge: Yes article_type: original author: - first_name: Saurabh J. full_name: Pradhan, Saurabh J. last_name: Pradhan - first_name: Puli Chandramouli full_name: Reddy, Puli Chandramouli last_name: Reddy - first_name: Michael full_name: Smutny, Michael id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87 last_name: Smutny orcid: 0000-0002-5920-9090 - first_name: Ankita full_name: Sharma, Ankita last_name: Sharma - first_name: Keisuke full_name: Sako, Keisuke id: 3BED66BE-F248-11E8-B48F-1D18A9856A87 last_name: Sako orcid: 0000-0002-6453-8075 - first_name: Meghana S. full_name: Oak, Meghana S. last_name: Oak - first_name: Rini full_name: Shah, Rini last_name: Shah - first_name: Mrinmoy full_name: Pal, Mrinmoy last_name: Pal - first_name: Ojas full_name: Deshpande, Ojas last_name: Deshpande - first_name: Greg full_name: Dsilva, Greg last_name: Dsilva - first_name: Yin full_name: Tang, Yin last_name: Tang - first_name: Rakesh full_name: Mishra, Rakesh last_name: Mishra - first_name: Girish full_name: Deshpande, Girish last_name: Deshpande - first_name: Antonio J. full_name: Giraldez, Antonio J. last_name: Giraldez - first_name: Mahendra full_name: Sonawane, Mahendra last_name: Sonawane - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Sanjeev full_name: Galande, Sanjeev last_name: Galande citation: ama: Pradhan SJ, Reddy PC, Smutny M, et al. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26234-7 apa: Pradhan, S. J., Reddy, P. C., Smutny, M., Sharma, A., Sako, K., Oak, M. S., … Galande, S. (2021). Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26234-7 chicago: Pradhan, Saurabh J., Puli Chandramouli Reddy, Michael Smutny, Ankita Sharma, Keisuke Sako, Meghana S. Oak, Rini Shah, et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26234-7. ieee: S. J. Pradhan et al., “Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021. ista: Pradhan SJ, Reddy PC, Smutny M, Sharma A, Sako K, Oak MS, Shah R, Pal M, Deshpande O, Dsilva G, Tang Y, Mishra R, Deshpande G, Giraldez AJ, Sonawane M, Heisenberg C-PJ, Galande S. 2021. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 12(1), 6094. mla: Pradhan, Saurabh J., et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications, vol. 12, no. 1, 6094, Springer Nature, 2021, doi:10.1038/s41467-021-26234-7. short: S.J. Pradhan, P.C. Reddy, M. Smutny, A. Sharma, K. Sako, M.S. Oak, R. Shah, M. Pal, O. Deshpande, G. Dsilva, Y. Tang, R. Mishra, G. Deshpande, A.J. Giraldez, M. Sonawane, C.-P.J. Heisenberg, S. Galande, Nature Communications 12 (2021). date_created: 2021-10-31T23:01:29Z date_published: 2021-10-19T00:00:00Z date_updated: 2023-08-14T10:32:48Z day: '19' ddc: - '570' department: - _id: CaHe doi: 10.1038/s41467-021-26234-7 external_id: isi: - '000709050300016' pmid: - '34667153' file: - access_level: open_access checksum: c40a69ae94435ecd3a30c9874a11ef2b content_type: application/pdf creator: cziletti date_created: 2021-11-09T13:59:26Z date_updated: 2021-11-09T13:59:26Z file_id: '10262' file_name: 2021_NatureComm_Pradhan.pdf file_size: 7144437 relation: main_file success: 1 file_date_updated: 2021-11-09T13:59:26Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: Preprint relation: earlier_version url: 'https://doi.org/10.1101/2020.11.23.394171 ' scopus_import: '1' status: public title: Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '10271' abstract: - lang: eng text: Understanding interactions between antibiotics used in combination is an important theme in microbiology. Using the interactions between the antifolate drug trimethoprim and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model, we applied a transcriptomic approach for dissecting interactions between two antibiotics with different modes of action. When trimethoprim and erythromycin were combined, the transcriptional response of genes from the sulfate reduction pathway deviated from the dominant effect of trimethoprim on the transcriptome. We successfully altered the drug interaction from additivity to suppression by increasing the sulfate level in the growth environment and identified sulfate reduction as an important metabolic determinant that shapes the interaction between the two drugs. Our work highlights the potential of using prioritization of gene expression patterns as a tool for identifying key metabolic determinants that shape drug-drug interactions. We further demonstrated that the sigma factor-binding protein gene crl shapes the interactions between the two antibiotics, which provides a rare example of how naturally occurring variations between strains of the same bacterial species can sometimes generate very different drug interactions. acknowledgement: High-throughput sequencing data were generated by the Vienna BioCenter Core Facilities. The authors would like to thank Karin Mitosch, Bor Kavcic, and Nadine Kraupner for their constructive feedback. The authors would also like to thank Gertraud Stift, Julia Flor, Renate Srsek, Agnieszka Wiktor, and Booshini Fernando for technical support. article_number: '760017' article_processing_charge: No article_type: original author: - first_name: Qin full_name: Qi, Qin id: 3B22D412-F248-11E8-B48F-1D18A9856A87 last_name: Qi orcid: 0000-0002-6148-2416 - first_name: S. Andreas full_name: Angermayr, S. Andreas last_name: Angermayr - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Qi Q, Angermayr SA, Bollenbach MT. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. 2021;12. doi:10.3389/fmicb.2021.760017 apa: Qi, Q., Angermayr, S. A., & Bollenbach, M. T. (2021). Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2021.760017 chicago: Qi, Qin, S. Andreas Angermayr, and Mark Tobias Bollenbach. “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia Coli.” Frontiers in Microbiology. Frontiers, 2021. https://doi.org/10.3389/fmicb.2021.760017. ieee: Q. Qi, S. A. Angermayr, and M. T. Bollenbach, “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli,” Frontiers in Microbiology, vol. 12. Frontiers, 2021. ista: Qi Q, Angermayr SA, Bollenbach MT. 2021. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. 12, 760017. mla: Qi, Qin, et al. “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia Coli.” Frontiers in Microbiology, vol. 12, 760017, Frontiers, 2021, doi:10.3389/fmicb.2021.760017. short: Q. Qi, S.A. Angermayr, M.T. Bollenbach, Frontiers in Microbiology 12 (2021). date_created: 2021-11-11T10:39:37Z date_published: 2021-10-20T00:00:00Z date_updated: 2023-08-14T11:43:23Z day: '20' ddc: - '610' doi: 10.3389/fmicb.2021.760017 ec_funded: 1 external_id: isi: - '000715997300001' pmid: - '34745067' file: - access_level: open_access checksum: d41321748e9588dd3cf03e9a7222127f content_type: application/pdf creator: cchlebak date_created: 2021-11-11T10:54:40Z date_updated: 2021-11-11T10:54:40Z file_id: '10272' file_name: 2021_FrontiersMicrob_Qi.pdf file_size: 2397203 relation: main_file success: 1 file_date_updated: 2021-11-11T10:54:40Z has_accepted_license: '1' intvolume: ' 12' isi: 1 keyword: - microbiology language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 25E83C2C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303507' name: Optimality principles in responses to antibiotics publication: Frontiers in Microbiology publication_identifier: eissn: - 1664-302X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '10221' abstract: - lang: eng text: We prove that any deterministic matrix is approximately the identity in the eigenbasis of a large random Wigner matrix with very high probability and with an optimal error inversely proportional to the square root of the dimension. Our theorem thus rigorously verifies the Eigenstate Thermalisation Hypothesis by Deutsch (Phys Rev A 43:2046–2049, 1991) for the simplest chaotic quantum system, the Wigner ensemble. In mathematical terms, we prove the strong form of Quantum Unique Ergodicity (QUE) with an optimal convergence rate for all eigenvectors simultaneously, generalizing previous probabilistic QUE results in Bourgade and Yau (Commun Math Phys 350:231–278, 2017) and Bourgade et al. (Commun Pure Appl Math 73:1526–1596, 2020). acknowledgement: 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: Giorgio full_name: Cipolloni, Giorgio id: 42198EFA-F248-11E8-B48F-1D18A9856A87 last_name: Cipolloni orcid: 0000-0002-4901-7992 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 citation: ama: Cipolloni G, Erdös L, Schröder DJ. Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. 2021;388(2):1005–1048. doi:10.1007/s00220-021-04239-z apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-021-04239-z chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” Communications in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s00220-021-04239-z. ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Eigenstate thermalization hypothesis for Wigner matrices,” Communications in Mathematical Physics, vol. 388, no. 2. Springer Nature, pp. 1005–1048, 2021. ista: Cipolloni G, Erdös L, Schröder DJ. 2021. Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. 388(2), 1005–1048. mla: Cipolloni, Giorgio, et al. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” Communications in Mathematical Physics, vol. 388, no. 2, Springer Nature, 2021, pp. 1005–1048, doi:10.1007/s00220-021-04239-z. short: G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics 388 (2021) 1005–1048. date_created: 2021-11-07T23:01:25Z date_published: 2021-10-29T00:00:00Z date_updated: 2023-08-14T10:29:49Z day: '29' ddc: - '510' department: - _id: LaEr doi: 10.1007/s00220-021-04239-z external_id: arxiv: - '2012.13215' isi: - '000712232700001' file: - access_level: open_access checksum: a2c7b6f5d23b5453cd70d1261272283b content_type: application/pdf creator: cchlebak date_created: 2022-02-02T10:19:55Z date_updated: 2022-02-02T10:19:55Z file_id: '10715' file_name: 2021_CommunMathPhys_Cipolloni.pdf file_size: 841426 relation: main_file success: 1 file_date_updated: 2022-02-02T10:19:55Z has_accepted_license: '1' intvolume: ' 388' isi: 1 issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1005–1048 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Communications in Mathematical Physics publication_identifier: eissn: - 1432-0916 issn: - 0010-3616 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Eigenstate thermalization hypothesis for Wigner matrices 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: 388 year: '2021' ... --- _id: '10224' abstract: - lang: eng text: We investigate the Fröhlich polaron model on a three-dimensional torus, and give a proof of the second-order quantum corrections to its ground-state energy in the strong-coupling limit. Compared to previous work in the confined case, the translational symmetry (and its breaking in the Pekar approximation) makes the analysis substantially more challenging. acknowledgement: "Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged. We would also like to thank Rupert Frank for many helpful discussions, especially related to the Gross coordinate transformation defined in Def. 4.7.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria)." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Dario full_name: Feliciangeli, Dario id: 41A639AA-F248-11E8-B48F-1D18A9856A87 last_name: Feliciangeli orcid: 0000-0003-0754-8530 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. 2021;242(3):1835–1906. doi:10.1007/s00205-021-01715-7' apa: 'Feliciangeli, D., & Seiringer, R. (2021). The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01715-7' chicago: 'Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01715-7.' ieee: 'D. Feliciangeli and R. Seiringer, “The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics,” Archive for Rational Mechanics and Analysis, vol. 242, no. 3. Springer Nature, pp. 1835–1906, 2021.' ista: 'Feliciangeli D, Seiringer R. 2021. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. 242(3), 1835–1906.' mla: 'Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational Mechanics and Analysis, vol. 242, no. 3, Springer Nature, 2021, pp. 1835–1906, doi:10.1007/s00205-021-01715-7.' short: D. Feliciangeli, R. Seiringer, Archive for Rational Mechanics and Analysis 242 (2021) 1835–1906. date_created: 2021-11-07T23:01:26Z date_published: 2021-10-25T00:00:00Z date_updated: 2023-08-14T10:32:19Z day: '25' ddc: - '530' department: - _id: RoSe doi: 10.1007/s00205-021-01715-7 ec_funded: 1 external_id: arxiv: - '2101.12566' isi: - '000710850600001' file: - access_level: open_access checksum: 672e9c21b20f1a50854b7c821edbb92f content_type: application/pdf creator: alisjak date_created: 2021-12-14T08:35:42Z date_updated: 2021-12-14T08:35:42Z file_id: '10544' file_name: 2021_Springer_Feliciangeli.pdf file_size: 990529 relation: main_file success: 1 file_date_updated: 2021-12-14T08:35:42Z has_accepted_license: '1' intvolume: ' 242' isi: 1 issue: '3' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1835–1906 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: - 1432-0673 issn: - 0003-9527 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '9787' relation: earlier_version status: public scopus_import: '1' status: public title: 'The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics' 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: 242 year: '2021' ... --- _id: '10281' abstract: - lang: eng text: Mutations affecting mTOR or RAS signaling underlie defined syndromes (the so-called mTORopathies and RASopathies) with high risk for Autism Spectrum Disorder (ASD). These syndromes show a broad variety of somatic phenotypes including cancers, skin abnormalities, heart disease and facial dysmorphisms. Less well studied are the neuropsychiatric symptoms such as ASD. Here, we assess the relevance of these signalopathies in ASD reviewing genetic, human cell model, rodent studies and clinical trials. We conclude that signalopathies have an increased liability for ASD and that, in particular, ASD individuals with dysmorphic features and intellectual disability (ID) have a higher chance for disruptive mutations in RAS- and mTOR-related genes. Studies on rodent and human cell models confirm aberrant neuronal development as the underlying pathology. Human studies further suggest that multiple hits are necessary to induce the respective phenotypes. Recent clinical trials do only report improvements for comorbid conditions such as epilepsy or cancer but not for behavioral aspects. Animal models show that treatment during early development can rescue behavioral phenotypes. Taken together, we suggest investigating the differential roles of mTOR and RAS signaling in both human and rodent models, and to test drug treatment both during and after neuronal development in the available model systems acknowledgement: 'This review was funded by the IMI2 Initiative under the grant AIMS-2-TRIALS No 777394, by the Hessian Ministry for Science and Arts; State of Hesse Ministry for Science and Arts: LOEWE-Grant to the CePTER-Consortium (www.uni-frankfurt.de/67689811); Research (BMBF) under the grant RAISE-genic No 779282 all to AGC. This work was also supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM) and by the Austrian Science Fund (FWF) (DK W1232-B24) both to G.N. and both BMBF GeNeRARe 01GM1519A and CRC 1080, project B10, of the German Research Foundation (DFG) to M.J.S, respectively. We want to thank R. Waltes for her support in preparing this manuscript.' alternative_title: - Special Issue "From Genes to Therapy in Autism Spectrum Disorder" article_number: '1746' article_processing_charge: No article_type: original author: - first_name: Verica full_name: Vasic, Verica last_name: Vasic - first_name: Mattson S.O. full_name: Jones, Mattson S.O. last_name: Jones - first_name: Denise full_name: Haslinger, Denise id: 76922BDA-3D3B-11EA-90BD-A44F3DDC885E last_name: Haslinger - first_name: Lisa full_name: Knaus, Lisa id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87 last_name: Knaus - first_name: Michael J. full_name: Schmeisser, Michael J. last_name: Schmeisser - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Andreas G. full_name: Chiocchetti, Andreas G. last_name: Chiocchetti citation: ama: 'Vasic V, Jones MSO, Haslinger D, et al. Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. 2021;12(11). doi:10.3390/genes12111746' apa: 'Vasic, V., Jones, M. S. O., Haslinger, D., Knaus, L., Schmeisser, M. J., Novarino, G., & Chiocchetti, A. G. (2021). Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. MDPI. https://doi.org/10.3390/genes12111746' chicago: 'Vasic, Verica, Mattson S.O. Jones, Denise Haslinger, Lisa Knaus, Michael J. Schmeisser, Gaia Novarino, and Andreas G. Chiocchetti. “Translating the Role of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12111746.' ieee: 'V. Vasic et al., “Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment,” Genes, vol. 12, no. 11. MDPI, 2021.' ista: 'Vasic V, Jones MSO, Haslinger D, Knaus L, Schmeisser MJ, Novarino G, Chiocchetti AG. 2021. Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. 12(11), 1746.' mla: 'Vasic, Verica, et al. “Translating the Role of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” Genes, vol. 12, no. 11, 1746, MDPI, 2021, doi:10.3390/genes12111746.' short: V. Vasic, M.S.O. Jones, D. Haslinger, L. Knaus, M.J. Schmeisser, G. Novarino, A.G. Chiocchetti, Genes 12 (2021). date_created: 2021-11-14T23:01:24Z date_published: 2021-10-30T00:00:00Z date_updated: 2023-08-14T11:46:12Z day: '30' ddc: - '570' department: - _id: GaNo doi: 10.3390/genes12111746 ec_funded: 1 external_id: isi: - '000834044200002' file: - access_level: open_access checksum: 256cb832a9c3051c7dc741f6423b8cbd content_type: application/pdf creator: dernst date_created: 2022-05-16T07:02:27Z date_updated: 2022-05-16T07:02:27Z file_id: '11380' file_name: 2021_Genes_Vasic.pdf file_size: 1335308 relation: main_file success: 1 file_date_updated: 2022-05-16T07:02:27Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '11' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication: Genes publication_identifier: eissn: - 2073-4425 publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: 'Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '10282' abstract: - lang: eng text: Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development. acknowledgement: We thank Claus Schwechheimer for the pin34 and pin347 seeds, Yuliia Mironova for technical assistance, Ksenia Timofeyenko and Dmitry Konovalov for help with the evolutional analysis, Konstantin Kutashev and Siarhei Dabravolski for assistance with FRET-FLIM, Huibin Han for advice with hypocotyl imaging, Karel Müller for the initial qRT-PCR on the tobacco cell lines, Stano Pekár for suggestions regarding the statistical analysis of the morphodynamic measurements, and Jozef Mravec, Dolf Weijers and Lindy Abas for their comments on the manuscript. This work was supported by the Czech Science Foundation (projects 16-26428S and 19-23773S to IK, MH and KRůžička, 19-18917S to JHumpolíčková and 18-26981S to JF), and the Ministry of Education, Youth and Sports of the Czech Republic (MEYS, CZ.02.1.01/0.0/0.0/16_019/0000738) to KRůžička and JHejátko. The imaging facilities of the Institute of Experimental Botany and CEITEC are supported by MEYS (LM2018129 – Czech BioImaging and CZ.02.1.01/0.0/0.0/16_013/0001775). The authors declare no competing interests. article_processing_charge: No article_type: original author: - first_name: Ivan full_name: Kashkan, Ivan last_name: Kashkan - first_name: Mónika full_name: Hrtyan, Mónika id: 45A71A74-F248-11E8-B48F-1D18A9856A87 last_name: Hrtyan - first_name: Katarzyna full_name: Retzer, Katarzyna last_name: Retzer - first_name: Jana full_name: Humpolíčková, Jana last_name: Humpolíčková - first_name: Aswathy full_name: Jayasree, Aswathy last_name: Jayasree - first_name: Roberta full_name: Filepová, Roberta last_name: Filepová - first_name: Zuzana full_name: Vondráková, Zuzana last_name: Vondráková - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Debbie full_name: Rombaut, Debbie last_name: Rombaut - first_name: Thomas B. full_name: Jacobs, Thomas B. last_name: Jacobs - first_name: Mikko J. full_name: Frilander, Mikko J. last_name: Frilander - first_name: Jan full_name: Hejátko, Jan last_name: Hejátko - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Kamil full_name: Růžička, Kamil last_name: Růžička citation: ama: Kashkan I, Hrtyan M, Retzer K, et al. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 2021;233:329-343. doi:10.1111/nph.17792 apa: Kashkan, I., Hrtyan, M., Retzer, K., Humpolíčková, J., Jayasree, A., Filepová, R., … Růžička, K. (2021). Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. Wiley. https://doi.org/10.1111/nph.17792 chicago: Kashkan, Ivan, Mónika Hrtyan, Katarzyna Retzer, Jana Humpolíčková, Aswathy Jayasree, Roberta Filepová, Zuzana Vondráková, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17792. ieee: I. Kashkan et al., “Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana,” New Phytologist, vol. 233. Wiley, pp. 329–343, 2021. ista: Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J, Růžička K. 2021. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 233, 329–343. mla: Kashkan, Ivan, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist, vol. 233, Wiley, 2021, pp. 329–43, doi:10.1111/nph.17792. short: I. Kashkan, M. Hrtyan, K. Retzer, J. Humpolíčková, A. Jayasree, R. Filepová, Z. Vondráková, S. Simon, D. Rombaut, T.B. Jacobs, M.J. Frilander, J. Hejátko, J. Friml, J. Petrášek, K. Růžička, New Phytologist 233 (2021) 329–343. date_created: 2021-11-14T23:01:24Z date_published: 2021-11-05T00:00:00Z date_updated: 2023-08-14T11:46:43Z day: '05' department: - _id: JiFr doi: 10.1111/nph.17792 external_id: isi: - '000714678100001' pmid: - '34637542' intvolume: ' 233' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2 month: '11' oa: 1 oa_version: Preprint page: 329-343 pmid: 1 publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 233 year: '2021' ... --- _id: '10220' abstract: - lang: eng text: "We study conditions under which a finite simplicial complex K can be mapped to ℝd without higher-multiplicity intersections. An almost r-embedding is a map f: K → ℝd such that the images of any r pairwise disjoint simplices of K do not have a common point. We show that if r is not a prime power and d ≥ 2r + 1, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost r-embedding of the (d +1)(r − 1)-simplex in ℝd. This improves on previous constructions of counterexamples (for d ≥ 3r) based on a series of papers by M. Özaydin, M. Gromov, P. Blagojević, F. Frick, G. Ziegler, and the second and fourth present authors.\r\n\r\nThe counterexamples are obtained by proving the following algebraic criterion in codimension 2: If r ≥ 3 and if K is a finite 2(r − 1)-complex, then there exists an almost r-embedding K → ℝ2r if and only if there exists a general position PL map f: K → ℝ2r such that the algebraic intersection number of the f-images of any r pairwise disjoint simplices of K is zero. This result can be restated in terms of a cohomological obstruction and extends an analogous codimension 3 criterion by the second and fourth authors. As another application, we classify ornaments f: S3 ⊔ S3 ⊔ S3 → ℝ5 up to ornament concordance.\r\n\r\nIt follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for r = 2 is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample." acknowledgement: Research supported by the Swiss National Science Foundation (Project SNSF-PP00P2-138948), by the Austrian Science Fund (FWF Project P31312-N35), by the Russian Foundation for Basic Research (Grants No. 15-01-06302 and 19-01-00169), by a Simons-IUM Fellowship, and by the D. Zimin Dynasty Foundation Grant. We would like to thank E. Alkin, A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful comments and discussions. article_processing_charge: No article_type: original author: - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Isaac full_name: Mabillard, Isaac id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87 last_name: Mabillard - first_name: Arkadiy B. full_name: Skopenkov, Arkadiy B. last_name: Skopenkov - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 2021;245:501–534. doi:10.1007/s11856-021-2216-z apa: Avvakumov, S., Mabillard, I., Skopenkov, A. B., & Wagner, U. (2021). Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-021-2216-z chicago: Avvakumov, Sergey, Isaac Mabillard, Arkadiy B. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel Journal of Mathematics. Springer Nature, 2021. https://doi.org/10.1007/s11856-021-2216-z. ieee: S. Avvakumov, I. Mabillard, A. B. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections. III. Codimension 2,” Israel Journal of Mathematics, vol. 245. Springer Nature, pp. 501–534, 2021. ista: Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. 2021. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 245, 501–534. mla: Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel Journal of Mathematics, vol. 245, Springer Nature, 2021, pp. 501–534, doi:10.1007/s11856-021-2216-z. short: S. Avvakumov, I. Mabillard, A.B. Skopenkov, U. Wagner, Israel Journal of Mathematics 245 (2021) 501–534. date_created: 2021-11-07T23:01:24Z date_published: 2021-10-30T00:00:00Z date_updated: 2023-08-14T11:43:55Z day: '30' department: - _id: UlWa doi: 10.1007/s11856-021-2216-z external_id: arxiv: - '1511.03501' isi: - '000712942100013' intvolume: ' 245' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.03501 month: '10' oa: 1 oa_version: Preprint page: '501–534 ' project: - _id: 26611F5C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31312 name: Algorithms for Embeddings and Homotopy Theory publication: Israel Journal of Mathematics publication_identifier: eissn: - 1565-8511 issn: - 0021-2172 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8183' relation: earlier_version status: public - id: '9308' relation: earlier_version status: public scopus_import: '1' status: public title: Eliminating higher-multiplicity intersections. III. Codimension 2 type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 245 year: '2021' ... --- _id: '13061' abstract: - lang: eng text: Infections early in life can have enduring effects on an organism’s development and immunity. In this study, we show that this equally applies to developing “superorganisms” – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen’s immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen’s pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism. article_processing_charge: No author: - first_name: Barbara E full_name: Casillas Perez, Barbara E id: 351ED2AA-F248-11E8-B48F-1D18A9856A87 last_name: Casillas Perez - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: Filip full_name: Naiser, Filip last_name: Naiser - first_name: Elisabeth full_name: Naderlinger, Elisabeth last_name: Naderlinger - first_name: Jiri full_name: Matas, Jiri last_name: Matas - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. 2021. doi:10.5061/DRYAD.7PVMCVDTJ apa: Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., & Cremer, S. (2021). Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. Dryad. https://doi.org/10.5061/DRYAD.7PVMCVDTJ chicago: Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger, Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” Dryad, 2021. https://doi.org/10.5061/DRYAD.7PVMCVDTJ. ieee: B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S. Cremer, “Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies.” Dryad, 2021. ista: Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2021. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies, Dryad, 10.5061/DRYAD.7PVMCVDTJ. mla: Casillas Perez, Barbara E., et al. Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies. Dryad, 2021, doi:10.5061/DRYAD.7PVMCVDTJ. short: B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, (2021). date_created: 2023-05-23T16:14:35Z date_published: 2021-10-29T00:00:00Z date_updated: 2023-08-14T11:45:28Z day: '29' ddc: - '570' department: - _id: SyCr doi: 10.5061/DRYAD.7PVMCVDTJ ec_funded: 1 license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.7pvmcvdtj month: '10' oa: 1 oa_version: Published Version project: - _id: 2649B4DE-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771402' name: Epidemics in ant societies on a chip publisher: Dryad related_material: record: - id: '10284' relation: used_in_publication status: public status: public title: Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '10301' abstract: - lang: eng text: De novo protein synthesis is required for synapse modifications underlying stable memory encoding. Yet neurons are highly compartmentalized cells and how protein synthesis can be regulated at the synapse level is unknown. Here, we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR activation and restricts the mTOR-dependent translation of specific activity-regulated mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent protein synthesis, and facilitates the consolidation of associative and spatial memories in mice. The memory enhancement becomes evident with light or spaced training, can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood, and does not compromise other aspects of cognition such as memory flexibility or extinction. Our findings provide mechanistic insight into synaptic translational control and reveal a potentially selective target for cognitive enhancement. acknowledgement: We thank Stuart Lipton and Nobuki Nakanishi for providing the Grin3a knockout mice, Beverly Davidson for the AAV-caRheb, Jose Esteban for help with behavioral and biochemical experiments, and Noelia Campillo, Rebeca Martínez-Turrillas, and Ana Navarro for expert technical help. Work was funded by the UTE project CIMA; fellowships from the Fundación Tatiana Pérez de Guzmán el Bueno, FEBS, and IBRO (to M.J.C.D.), Generalitat Valenciana (to O.E.-Z.), Juan de la Cierva (to L.G.R.), FPI-MINECO (to E.R.V., to S.N.) and Intertalentum postdoctoral program (to V.B.); ANR (GluBrain3A) and ERC Advanced Grants (#693021) (to P.P.); Ramón y Cajal program RYC2014-15784, RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077 FEDER funds (to R.A.); RETOS-MINECO SAF2017-87928-R (to A.B.); an NIH grant (NS76637) and UTHSC College of Medicine funds (to S.J.T.); and NARSAD Independent Investigator Award and grants from the MINECO (CSD2008-00005, SAF2013-48983R, SAF2016-80895-R), Generalitat Valenciana (PROMETEO 2019/020)(to I.P.O.) and Severo-Ochoa Excellence Awards (SEV-2013-0317, SEV-2017-0723). article_number: e71575 article_processing_charge: No article_type: original author: - first_name: María J full_name: Conde-Dusman, María J last_name: Conde-Dusman - first_name: Partha N full_name: Dey, Partha N last_name: Dey - first_name: Óscar full_name: Elía-Zudaire, Óscar last_name: Elía-Zudaire - first_name: Luis E full_name: Garcia Rabaneda, Luis E id: 33D1B084-F248-11E8-B48F-1D18A9856A87 last_name: Garcia Rabaneda - first_name: Carmen full_name: García-Lira, Carmen last_name: García-Lira - first_name: Teddy full_name: Grand, Teddy last_name: Grand - first_name: Victor full_name: Briz, Victor last_name: Briz - first_name: Eric R full_name: Velasco, Eric R last_name: Velasco - first_name: Raül full_name: Andero Galí, Raül last_name: Andero Galí - first_name: Sergio full_name: Niñerola, Sergio last_name: Niñerola - first_name: Angel full_name: Barco, Angel last_name: Barco - first_name: Pierre full_name: Paoletti, Pierre last_name: Paoletti - first_name: John F full_name: Wesseling, John F last_name: Wesseling - first_name: Fabrizio full_name: Gardoni, Fabrizio last_name: Gardoni - first_name: Steven J full_name: Tavalin, Steven J last_name: Tavalin - first_name: Isabel full_name: Perez-Otaño, Isabel last_name: Perez-Otaño citation: ama: Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 2021;10. doi:10.7554/elife.71575 apa: Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E., García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.71575 chicago: Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.71575. ieee: M. J. Conde-Dusman et al., “Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Garcia Rabaneda LE, García-Lira C, Grand T, Briz V, Velasco ER, Andero Galí R, Niñerola S, Barco A, Paoletti P, Wesseling JF, Gardoni F, Tavalin SJ, Perez-Otaño I. 2021. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 10, e71575. mla: Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife, vol. 10, e71575, eLife Sciences Publications, 2021, doi:10.7554/elife.71575. short: M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira, T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti, J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021). date_created: 2021-11-18T06:59:45Z date_published: 2021-11-17T00:00:00Z date_updated: 2023-08-14T11:50:50Z day: '17' ddc: - '570' department: - _id: GaNo doi: 10.7554/elife.71575 external_id: isi: - '000720945900001' file: - access_level: open_access checksum: 59318e9e41507cec83c2f4070e6ad540 content_type: application/pdf creator: lgarciar date_created: 2021-11-18T07:02:02Z date_updated: 2021-11-18T07:02:02Z file_id: '10302' file_name: elife-71575-v1.pdf file_size: 2477302 relation: main_file success: 1 file_date_updated: 2021-11-18T07:02:02Z has_accepted_license: '1' intvolume: ' 10' isi: 1 keyword: - general immunology and microbiology - general biochemistry - genetics and molecular biology - general medicine - general neuroscience language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' status: public title: Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2021' ... --- _id: '10283' abstract: - lang: eng text: 'During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research.' acknowledgement: This EQIPD project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement no. 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and EFPIA. LR was supported by the Faculty of Biology and Medicine, University of Lausanne. VV was supported by Biocenter Finland and the Jane and Aatos Erkko Foundation. CP and IKB received funding from the Federal Ministry of Education and Research (BMBF, grant 01PW18001). SB from the Vienna BioCenter Core Facilities (VBCF) Preclinical Phenotyping Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna. MT is an incumbent of the Carolito Stiftung Research Fellow Chair in Neurodegenerative Diseases. We thank Dr. Katja Kivinen (Helsinki Institute of Life Science) for discussions and feedback. article_number: e53824 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Leonardo full_name: Restivo, Leonardo last_name: Restivo - first_name: Björn full_name: Gerlach, Björn last_name: Gerlach - first_name: Michael full_name: Tsoory, Michael last_name: Tsoory - first_name: Lior full_name: Bikovski, Lior last_name: Bikovski - first_name: Sylvia full_name: Badurek, Sylvia last_name: Badurek - first_name: Claudia full_name: Pitzer, Claudia last_name: Pitzer - first_name: Isabelle C. full_name: Kos-Braun, Isabelle C. last_name: Kos-Braun - first_name: Anne Laure Mj full_name: Mausset-Bonnefont, Anne Laure Mj last_name: Mausset-Bonnefont - first_name: Jonathan full_name: Ward, Jonathan last_name: Ward - first_name: Michael full_name: Schunn, Michael id: 4272DB4A-F248-11E8-B48F-1D18A9856A87 last_name: Schunn orcid: 0000-0003-4326-5300 - first_name: Lucas P.J.J. full_name: Noldus, Lucas P.J.J. last_name: Noldus - first_name: Anton full_name: Bespalov, Anton last_name: Bespalov - first_name: Vootele full_name: Voikar, Vootele last_name: Voikar citation: ama: 'Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research: Role of academic core facilities. EMBO Reports. 2021;22. doi:10.15252/embr.202153824' apa: 'Restivo, L., Gerlach, B., Tsoory, M., Bikovski, L., Badurek, S., Pitzer, C., … Voikar, V. (2021). Towards best practices in research: Role of academic core facilities. EMBO Reports. EMBO Press. https://doi.org/10.15252/embr.202153824' chicago: 'Restivo, Leonardo, Björn Gerlach, Michael Tsoory, Lior Bikovski, Sylvia Badurek, Claudia Pitzer, Isabelle C. Kos-Braun, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports. EMBO Press, 2021. https://doi.org/10.15252/embr.202153824.' ieee: 'L. Restivo et al., “Towards best practices in research: Role of academic core facilities,” EMBO Reports, vol. 22. EMBO Press, 2021.' ista: 'Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LPJJ, Bespalov A, Voikar V. 2021. Towards best practices in research: Role of academic core facilities. EMBO Reports. 22, e53824.' mla: 'Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports, vol. 22, e53824, EMBO Press, 2021, doi:10.15252/embr.202153824.' short: L. Restivo, B. Gerlach, M. Tsoory, L. Bikovski, S. Badurek, C. Pitzer, I.C. Kos-Braun, A.L.M. Mausset-Bonnefont, J. Ward, M. Schunn, L.P.J.J. Noldus, A. Bespalov, V. Voikar, EMBO Reports 22 (2021). date_created: 2021-11-14T23:01:24Z date_published: 2021-11-04T00:00:00Z date_updated: 2023-08-14T11:47:35Z day: '04' ddc: - '570' department: - _id: PreCl doi: 10.15252/embr.202153824 external_id: isi: - '000714350000001' file: - access_level: open_access checksum: 74743baa6ef431ef60c3de3bc4da045a content_type: application/pdf creator: dernst date_created: 2022-05-16T07:07:41Z date_updated: 2022-05-16T07:07:41Z file_id: '11381' file_name: 2021_EmboReports_Restivo.pdf file_size: 488583 relation: main_file success: 1 file_date_updated: 2022-05-16T07:07:41Z has_accepted_license: '1' intvolume: ' 22' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: EMBO Reports publication_identifier: eissn: - 1469-3178 issn: - 1469-221X publication_status: published publisher: EMBO Press quality_controlled: '1' scopus_import: '1' status: public title: 'Towards best practices in research: Role of academic core facilities' 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: 22 year: '2021' ... --- _id: '10310' abstract: - lang: eng text: A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700. acknowledgement: We are grateful for additional support and valuable scientific input for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata, Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias Rögner. Parts of this research were funded by the German Research Council (DFG) within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the Platform Project for Supporting Drug Discovery and Life Science Research [Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.), 17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED to K.N. and G.K. article_number: '304' article_processing_charge: No article_type: original author: - first_name: Mehmet Orkun full_name: Çoruh, Mehmet Orkun id: d25163e5-8d53-11eb-a251-e6dd8ea1b8ef last_name: Çoruh orcid: 0000-0002-3219-2022 - first_name: Anna full_name: Frank, Anna last_name: Frank - first_name: Hideaki full_name: Tanaka, Hideaki last_name: Tanaka - first_name: Akihiro full_name: Kawamoto, Akihiro last_name: Kawamoto - first_name: Eithar full_name: El-Mohsnawy, Eithar last_name: El-Mohsnawy - first_name: Takayuki full_name: Kato, Takayuki last_name: Kato - first_name: Keiichi full_name: Namba, Keiichi last_name: Namba - first_name: Christoph full_name: Gerle, Christoph last_name: Gerle - first_name: Marc M. full_name: Nowaczyk, Marc M. last_name: Nowaczyk - first_name: Genji full_name: Kurisu, Genji last_name: Kurisu citation: ama: Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 2021;4(1). doi:10.1038/s42003-021-01808-9 apa: Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T., … Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. Springer . https://doi.org/10.1038/s42003-021-01808-9 chicago: Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk, and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology. Springer , 2021. https://doi.org/10.1038/s42003-021-01808-9. ieee: M. O. Çoruh et al., “Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” Communications Biology, vol. 4, no. 1. Springer , 2021. ista: Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 4(1), 304. mla: Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology, vol. 4, no. 1, 304, Springer , 2021, doi:10.1038/s42003-021-01808-9. short: M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K. Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021). date_created: 2021-11-19T11:37:29Z date_published: 2021-03-08T00:00:00Z date_updated: 2023-08-14T11:51:19Z day: '08' ddc: - '570' department: - _id: LeSa doi: 10.1038/s42003-021-01808-9 external_id: isi: - '000627440700001' pmid: - '33686186' file: - access_level: open_access checksum: 8ffd39f2bba7152a2441802ff313bf0b content_type: application/pdf creator: cchlebak date_created: 2021-11-19T15:09:18Z date_updated: 2021-11-19T15:09:18Z file_id: '10318' file_name: 2021_CommBio_Çoruh.pdf file_size: 6030261 relation: main_file success: 1 file_date_updated: 2021-11-19T15:09:18Z has_accepted_license: '1' intvolume: ' 4' isi: 1 issue: '1' keyword: - general agricultural and biological Sciences - general biochemistry - genetics and molecular biology - medicine (miscellaneous) language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: Communications Biology publication_identifier: issn: - 2399-3642 publication_status: published publisher: 'Springer ' quality_controlled: '1' scopus_import: '1' status: public title: Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster 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: 4 year: '2021' ... --- _id: '10270' abstract: - lang: eng text: Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development. acknowledgement: 'e are grateful Richard Smith, Anne-Lise Routier, Crisanto Gutierrez and Juergen Kleine-Vehn for providing critical comments on the manuscript. Funding: This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016–0672 (2017–2021) to KW via the CBGP). In the frame of SEV-2016–0672 funding MM is supported with a postdoctoral contract. KW was supported by Programa Estatal de Generacion del Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I 2019 (PGC2018-093387-A-I00) from MICIU (to KW). MG is recipient of an IST Interdisciplinary Project (IC1022IPC03).' article_number: '72132' article_processing_charge: Yes article_type: original author: - first_name: Marco full_name: Marconi, Marco last_name: Marconi - first_name: Marçal full_name: Gallemi, Marçal id: 460C6802-F248-11E8-B48F-1D18A9856A87 last_name: Gallemi orcid: 0000-0003-4675-6893 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Krzysztof full_name: Wabnik, Krzysztof last_name: Wabnik citation: ama: Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 2021;10. doi:10.7554/elife.72132 apa: Marconi, M., Gallemi, M., Benková, E., & Wabnik, K. (2021). A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.72132 chicago: Marconi, Marco, Marçal Gallemi, Eva Benková, and Krzysztof Wabnik. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72132. ieee: M. Marconi, M. Gallemi, E. Benková, and K. Wabnik, “A coupled mechano-biochemical model for cell polarity guided anisotropic root growth,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Marconi M, Gallemi M, Benková E, Wabnik K. 2021. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 10, 72132. mla: Marconi, Marco, et al. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife, vol. 10, 72132, eLife Sciences Publications, 2021, doi:10.7554/elife.72132. short: M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021). date_created: 2021-11-11T10:05:18Z date_published: 2021-11-01T00:00:00Z date_updated: 2023-08-14T11:49:23Z day: '01' ddc: - '570' department: - _id: EvBe doi: 10.7554/elife.72132 external_id: isi: - '000734671200001' pmid: - '34723798' file: - access_level: open_access checksum: fad13c509b53bb7a2bef9c946a7ca60a content_type: application/pdf creator: dernst date_created: 2022-05-13T09:00:29Z date_updated: 2022-05-13T09:00:29Z file_id: '11372' file_name: 2021_eLife_Marconi.pdf file_size: 14137503 relation: main_file success: 1 file_date_updated: 2022-05-13T09:00:29Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: A coupled mechano-biochemical model for cell polarity guided anisotropic root growth 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: '10299' abstract: - lang: eng text: Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number. acknowledgement: We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg, and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft research unit FOR 2688. article_number: e2102350118 article_processing_charge: No article_type: original author: - first_name: George H full_name: Choueiri, George H id: 448BD5BC-F248-11E8-B48F-1D18A9856A87 last_name: Choueiri - first_name: Jose M full_name: Lopez Alonso, Jose M id: 40770848-F248-11E8-B48F-1D18A9856A87 last_name: Lopez Alonso orcid: 0000-0002-0384-2022 - first_name: Atul full_name: Varshney, Atul id: 2A2006B2-F248-11E8-B48F-1D18A9856A87 last_name: Varshney orcid: 0000-0002-3072-5999 - first_name: Sarath full_name: Sankar, Sarath last_name: Sankar - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 2021;118(45). doi:10.1073/pnas.2102350118 apa: Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., & Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2102350118 chicago: Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar, and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2102350118. ieee: G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental observation of the origin and structure of elastoinertial turbulence,” Proceedings of the National Academy of Sciences, vol. 118, no. 45. National Academy of Sciences, 2021. ista: Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 118(45), e2102350118. mla: Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:10.1073/pnas.2102350118. short: G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences 118 (2021). date_created: 2021-11-17T13:24:24Z date_published: 2021-11-03T00:00:00Z date_updated: 2023-08-14T11:50:10Z day: '03' department: - _id: BjHo doi: 10.1073/pnas.2102350118 external_id: arxiv: - '2103.00023' isi: - '000720926900019' pmid: - ' 34732570' intvolume: ' 118' isi: 1 issue: '45' keyword: - multidisciplinary - elastoinertial turbulence - viscoelastic flows - elastic instability - drag reduction language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2103.00023 month: '11' oa: 1 oa_version: Preprint pmid: 1 project: - _id: 238B8092-32DE-11EA-91FC-C7463DDC885E call_identifier: FWF grant_number: I04188 name: Instabilities in pulsating pipe flow of Newtonian and complex fluids publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Experimental observation of the origin and structure of elastoinertial turbulence type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 118 year: '2021' ... --- _id: '10280' abstract: - lang: eng text: 'Machines enabled the Industrial Revolution and are central to modern technological progress: A machine’s parts transmit forces, motion, and energy to one another in a predetermined manner. Today’s engineering frontier, building artificial micromachines that emulate the biological machinery of living organisms, requires faithful assembly and energy consumption at the microscale. Here, we demonstrate the programmable assembly of active particles into autonomous metamachines using optical templates. Metamachines, or machines made of machines, are stable, mobile and autonomous architectures, whose dynamics stems from the geometry. We use the interplay between anisotropic force generation of the active colloids with the control of their orientation by local geometry. This allows autonomous reprogramming of active particles of the metamachines to achieve multiple functions. It permits the modular assembly of metamachines by fusion, reconfiguration of metamachines and, we anticipate, a shift in focus of self-assembly towards active matter and reprogrammable materials.' acknowledgement: The authors thank R. Jazzar for useful advice regarding the synthesis of heterodimers. We thank S. Sacanna for critical reading. This material is based upon work supported by the National Science Foundation under Grant No. DMR-1554724 and Department of Army Research under grant W911NF-20-1-0112. article_number: '6398' article_processing_charge: Yes article_type: original author: - first_name: Antoine full_name: Aubret, Antoine last_name: Aubret - first_name: Quentin full_name: Martinet, Quentin id: b37485a8-d343-11eb-a0e9-df8c484ef8ab last_name: Martinet orcid: 0000-0002-2916-6632 - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 citation: ama: Aubret A, Martinet Q, Palacci JA. Metamachines of pluripotent colloids. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26699-6 apa: Aubret, A., Martinet, Q., & Palacci, J. A. (2021). Metamachines of pluripotent colloids. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26699-6 chicago: Aubret, Antoine, Quentin Martinet, and Jérémie A Palacci. “Metamachines of Pluripotent Colloids.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26699-6. ieee: A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021. ista: Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids. Nature Communications. 12(1), 6398. mla: Aubret, Antoine, et al. “Metamachines of Pluripotent Colloids.” Nature Communications, vol. 12, no. 1, 6398, Springer Nature, 2021, doi:10.1038/s41467-021-26699-6. short: A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021). date_created: 2021-11-14T23:01:23Z date_published: 2021-11-04T00:00:00Z date_updated: 2023-08-14T11:48:37Z day: '04' ddc: - '530' department: - _id: JePa doi: 10.1038/s41467-021-26699-6 external_id: isi: - '000714754400010' pmid: - '34737315' file: - access_level: open_access checksum: 1c392b12b9b7b615d422d9fabe19cdb9 content_type: application/pdf creator: cchlebak date_created: 2021-11-15T13:25:52Z date_updated: 2021-11-15T13:25:52Z file_id: '10292' file_name: 2021_NatComm_Aubret.pdf file_size: 6282703 relation: main_file success: 1 file_date_updated: 2021-11-15T13:25:52Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Metamachines of pluripotent colloids tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '10322' abstract: - lang: eng text: To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell autonomous. We have discovered that, in Caenorhabditis elegans, neuronal heat shock factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR), causes extensive fat remodeling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodeling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone morphogenetic protein (BMP) are required for signaling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodeling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell nonautonomously coordinate membrane saturation and composition across tissues in a multicellular animal. acknowledgement: We dedicate this work to the memory of Michael J.O. Wakelam. We would like to acknowledge Michael Fasseas (Invermis, Magnitude Biosciences) for plasmid injections and Sunny Biotech for transgenics; Catalina Vallejos and John Marioni for statistical advice at the beginning of the work; Simon Walker, Imaging, Bioinformatics and Lipidomics Facilities at Babraham Institute for technical support; and Cindy Voisine, Michael Witting, Jon Houseley, Len Stephens, Carmen Nussbaum Krammer, Rebeca Aldunate, Patricija van Oosten-Hawle, Jean-Louis Bessereau, and Jane Alfred for feedback on the manuscript. We thank Andy Dillin, Atsushi Kuhara, Amy Walker, Andrew Leifer, Yun Zhang, and Michalis Barkoulas for reagents and Julie Ahringer, Anne Ferguson-Smith, and Anne Corcoran for support and helpful discussions. We also acknowledge Babraham Institute Facilities. article_number: e3001431 article_processing_charge: No article_type: original author: - first_name: Laetitia full_name: Chauve, Laetitia last_name: Chauve - first_name: Francesca full_name: Hodge, Francesca last_name: Hodge - first_name: Sharlene full_name: Murdoch, Sharlene last_name: Murdoch - first_name: Fatemah full_name: Masoudzadeh, Fatemah last_name: Masoudzadeh - first_name: Harry Jack full_name: Mann, Harry Jack last_name: Mann - first_name: Andrea full_name: Lopez-Clavijo, Andrea last_name: Lopez-Clavijo - first_name: Hanneke full_name: Okkenhaug, Hanneke last_name: Okkenhaug - first_name: Greg full_name: West, Greg last_name: West - first_name: Bebiana C. full_name: Sousa, Bebiana C. last_name: Sousa - first_name: Anne full_name: Segonds-Pichon, Anne last_name: Segonds-Pichon - first_name: Cheryl full_name: Li, Cheryl last_name: Li - first_name: Steven full_name: Wingett, Steven last_name: Wingett - first_name: Hermine full_name: Kienberger, Hermine last_name: Kienberger - first_name: Karin full_name: Kleigrewe, Karin last_name: Kleigrewe - first_name: Mario full_name: De Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: De Bono orcid: 0000-0001-8347-0443 - first_name: Michael full_name: Wakelam, Michael last_name: Wakelam - first_name: Olivia full_name: Casanueva, Olivia last_name: Casanueva citation: ama: Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. 2021;19(11). doi:10.1371/journal.pbio.3001431 apa: Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H. J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3001431 chicago: Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” PLoS Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pbio.3001431. ieee: L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans,” PLoS Biology, vol. 19, no. 11. Public Library of Science, 2021. ista: Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann HJ, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. 19(11), e3001431. mla: Chauve, Laetitia, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” PLoS Biology, vol. 19, no. 11, e3001431, Public Library of Science, 2021, doi:10.1371/journal.pbio.3001431. short: L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, PLoS Biology 19 (2021). date_created: 2021-11-21T23:01:28Z date_published: 2021-11-01T00:00:00Z date_updated: 2023-08-14T11:53:27Z day: '01' ddc: - '570' department: - _id: MaDe doi: 10.1371/journal.pbio.3001431 external_id: isi: - '000715818400001' pmid: - '34723964' file: - access_level: open_access checksum: 0c61b667f814fd9435b3ac42036fc36d content_type: application/pdf creator: cchlebak date_created: 2021-11-22T09:34:03Z date_updated: 2021-11-22T09:34:03Z file_id: '10330' file_name: 2021_PLoSBio_Chauve.pdf file_size: 4069215 relation: main_file success: 1 file_date_updated: 2021-11-22T09:34:03Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Biology publication_identifier: eissn: - 1545-7885 issn: - 1544-9173 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '13069' relation: research_data status: public scopus_import: '1' status: public title: Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans 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: 19 year: '2021' ... --- _id: '10222' abstract: - lang: eng text: Consider a random set of points on the unit sphere in ℝd, which can be either uniformly sampled or a Poisson point process. Its convex hull is a random inscribed polytope, whose boundary approximates the sphere. We focus on the case d = 3, for which there are elementary proofs and fascinating formulas for metric properties. In particular, we study the fraction of acute facets, the expected intrinsic volumes, the total edge length, and the distance to a fixed point. Finally we generalize the results to the ellipsoid with homeoid density. acknowledgement: "This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.\r\nWe are grateful to Dmitry Zaporozhets and Christoph Thäle for valuable comments and for directing us to relevant references. We also thank to Anton Mellit for a useful discussion on Bessel functions." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Anton full_name: Nikitenko, Anton id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87 last_name: Nikitenko orcid: 0000-0002-0659-3201 citation: ama: Akopyan A, Edelsbrunner H, Nikitenko A. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics. 2021:1-15. doi:10.1080/10586458.2021.1980459 apa: Akopyan, A., Edelsbrunner, H., & Nikitenko, A. (2021). The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics. Taylor and Francis. https://doi.org/10.1080/10586458.2021.1980459 chicago: Akopyan, Arseniy, Herbert Edelsbrunner, and Anton Nikitenko. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics. Taylor and Francis, 2021. https://doi.org/10.1080/10586458.2021.1980459. ieee: A. Akopyan, H. Edelsbrunner, and A. Nikitenko, “The beauty of random polytopes inscribed in the 2-sphere,” Experimental Mathematics. Taylor and Francis, pp. 1–15, 2021. ista: Akopyan A, Edelsbrunner H, Nikitenko A. 2021. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics., 1–15. mla: Akopyan, Arseniy, et al. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics, Taylor and Francis, 2021, pp. 1–15, doi:10.1080/10586458.2021.1980459. short: A. Akopyan, H. Edelsbrunner, A. Nikitenko, Experimental Mathematics (2021) 1–15. date_created: 2021-11-07T23:01:25Z date_published: 2021-10-25T00:00:00Z date_updated: 2023-08-14T11:57:07Z day: '25' ddc: - '510' department: - _id: HeEd doi: 10.1080/10586458.2021.1980459 ec_funded: 1 external_id: arxiv: - '2007.07783' isi: - '000710893500001' file: - access_level: open_access checksum: 3514382e3a1eb87fa6c61ad622874415 content_type: application/pdf creator: dernst date_created: 2023-08-14T11:55:10Z date_updated: 2023-08-14T11:55:10Z file_id: '14053' file_name: 2023_ExperimentalMath_Akopyan.pdf file_size: 1966019 relation: main_file success: 1 file_date_updated: 2023-08-14T11:55:10Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1-15 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: The Wittgenstein Prize - _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316 grant_number: I4887 name: Discretization in Geometry and Dynamics - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: Experimental Mathematics publication_identifier: eissn: - 1944-950X issn: - 1058-6458 publication_status: published publisher: Taylor and Francis quality_controlled: '1' scopus_import: '1' status: public title: The beauty of random polytopes inscribed in the 2-sphere 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '10323' abstract: - lang: eng text: Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity. acknowledgement: We thank Juan C. Fontecilla-Camps for insightful discussions related to ATP-driven machineries, and Elif Karagöz for providing the structural model of the Hsp90-Tau complex. This study was supported by the European Research Council (StG-2012-311318-ProtDyn2Function) and the Agence Nationale de la Recherche (ANR-18-CE92-0032-MitoMemProtImp). article_number: '762005' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Iva full_name: Sučec, Iva last_name: Sučec - first_name: Beate full_name: Bersch, Beate last_name: Bersch - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Sučec I, Bersch B, Schanda P. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 2021;8. doi:10.3389/fmolb.2021.762005 apa: Sučec, I., Bersch, B., & Schanda, P. (2021). How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. Frontiers. https://doi.org/10.3389/fmolb.2021.762005 chicago: Sučec, Iva, Beate Bersch, and Paul Schanda. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences. Frontiers, 2021. https://doi.org/10.3389/fmolb.2021.762005. ieee: I. Sučec, B. Bersch, and P. Schanda, “How do chaperones bind (partly) unfolded client proteins?,” Frontiers in Molecular Biosciences, vol. 8. Frontiers, 2021. ista: Sučec I, Bersch B, Schanda P. 2021. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 8, 762005. mla: Sučec, Iva, et al. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences, vol. 8, 762005, Frontiers, 2021, doi:10.3389/fmolb.2021.762005. short: I. Sučec, B. Bersch, P. Schanda, Frontiers in Molecular Biosciences 8 (2021). date_created: 2021-11-21T23:01:29Z date_published: 2021-10-25T00:00:00Z date_updated: 2023-08-14T11:55:04Z day: '25' ddc: - '547' department: - _id: PaSc doi: 10.3389/fmolb.2021.762005 external_id: isi: - '000717241700001' pmid: - '34760928' file: - access_level: open_access checksum: a5c9dbf80dc2c5aaa737f456c941d964 content_type: application/pdf creator: cchlebak date_created: 2021-11-23T15:06:58Z date_updated: 2021-11-23T15:06:58Z file_id: '10333' file_name: 2021_FrontiersMolBioSc_Sučec.pdf file_size: 4700798 relation: main_file success: 1 file_date_updated: 2021-11-23T15:06:58Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Molecular Biosciences publication_identifier: eissn: - 2296-889X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: How do chaperones bind (partly) unfolded client 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: 8 year: '2021' ... --- _id: '10326' abstract: - lang: eng text: Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot branching and communications between host plants and symbiotic fungi or root parasitic plants. Extensive studies have identified the key components participating in SL biosynthesis and signalling, whereas the catabolism or deactivation of endogenous SLs in planta remains largely unknown. Here, we report that the Arabidopsis carboxylesterase 15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently hydrolyse SLs both in vitro and in planta. We also provide evidence that AtCXE15 is capable of catalysing hydrolysis of diverse SL analogues and that such CXE15-dependent catabolism of SLs is evolutionarily conserved in seed plants. These results disclose a catalytic mechanism underlying homoeostatic regulation of SLs in plants, which also provides a rational approach to spatial-temporally manipulate the endogenous SLs and thus architecture of crops and ornamental plants. acknowledgement: We thank J. Li (Institute of Genetics and Developmental Biology, China) for providing the at14-1, atmax2-1, atmax3-9, atmax4-1, atmax1-1, kai2-2 (Col-0 background) mutants and B. Xu for providing the complementary DNA of P. patens. We are grateful to L. Wang for assistance with MST, B. Han for assistance with UPLC–MS, J. Li for assistance with confocal microscopy and B. Mikael and J. Zhang for their comments on the manuscript. This work was supported by grants from Strategic Priority Research Program of Chinese Academy of Sciences (Y.H., XDB27030102) and the National Natural Science Foundation of China (E.X., 31700253; Y.H., 31830055). article_processing_charge: No article_type: original author: - first_name: Enjun full_name: Xu, Enjun last_name: Xu - first_name: Liang full_name: Chai, Liang last_name: Chai - first_name: Shiqi full_name: Zhang, Shiqi last_name: Zhang - first_name: Ruixue full_name: Yu, Ruixue last_name: Yu - first_name: Xixi full_name: Zhang, Xixi id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A last_name: Zhang orcid: 0000-0001-7048-4627 - first_name: Chongyi full_name: Xu, Chongyi last_name: Xu - first_name: Yuxin full_name: Hu, Yuxin last_name: Hu citation: ama: Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 2021;7:1495–1504. doi:10.1038/s41477-021-01011-y apa: Xu, E., Chai, L., Zhang, S., Yu, R., Zhang, X., Xu, C., & Hu, Y. (2021). Catabolism of strigolactones by a carboxylesterase. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-021-01011-y chicago: Xu, Enjun, Liang Chai, Shiqi Zhang, Ruixue Yu, Xixi Zhang, Chongyi Xu, and Yuxin Hu. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants. Springer Nature, 2021. https://doi.org/10.1038/s41477-021-01011-y. ieee: E. Xu et al., “Catabolism of strigolactones by a carboxylesterase,” Nature Plants, vol. 7. Springer Nature, pp. 1495–1504, 2021. ista: Xu E, Chai L, Zhang S, Yu R, Zhang X, Xu C, Hu Y. 2021. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 7, 1495–1504. mla: Xu, Enjun, et al. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants, vol. 7, Springer Nature, 2021, pp. 1495–1504, doi:10.1038/s41477-021-01011-y. short: E. Xu, L. Chai, S. Zhang, R. Yu, X. Zhang, C. Xu, Y. Hu, Nature Plants 7 (2021) 1495–1504. date_created: 2021-11-21T23:01:30Z date_published: 2021-11-11T00:00:00Z date_updated: 2023-08-14T11:54:02Z day: '11' department: - _id: JiFr doi: 10.1038/s41477-021-01011-y external_id: isi: - '000717408000002' pmid: - '34764442' intvolume: ' 7' isi: 1 language: - iso: eng month: '11' oa_version: None page: '1495–1504 ' pmid: 1 publication: Nature Plants publication_identifier: eissn: - 2055-0278 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Catabolism of strigolactones by a carboxylesterase type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 7 year: '2021' ... --- _id: '13069' abstract: - lang: eng text: To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal. article_processing_charge: No author: - first_name: Laetitia full_name: Chauve, Laetitia last_name: Chauve - first_name: Francesca full_name: Hodge, Francesca last_name: Hodge - first_name: Sharlene full_name: Murdoch, Sharlene last_name: Murdoch - first_name: Fatemah full_name: Masoudzadeh, Fatemah last_name: Masoudzadeh - first_name: Harry-Jack full_name: Mann, Harry-Jack last_name: Mann - first_name: Andrea full_name: Lopez-Clavijo, Andrea last_name: Lopez-Clavijo - first_name: Hanneke full_name: Okkenhaug, Hanneke last_name: Okkenhaug - first_name: Greg full_name: West, Greg last_name: West - first_name: Bebiana C. full_name: Sousa, Bebiana C. last_name: Sousa - first_name: Anne full_name: Segonds-Pichon, Anne last_name: Segonds-Pichon - first_name: Cheryl full_name: Li, Cheryl last_name: Li - first_name: Steven full_name: Wingett, Steven last_name: Wingett - first_name: Hermine full_name: Kienberger, Hermine last_name: Kienberger - first_name: Karin full_name: Kleigrewe, Karin last_name: Kleigrewe - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: Michael full_name: Wakelam, Michael last_name: Wakelam - first_name: Olivia full_name: Casanueva, Olivia last_name: Casanueva citation: ama: Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. 2021. doi:10.5281/ZENODO.5519410 apa: Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H.-J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. Zenodo. https://doi.org/10.5281/ZENODO.5519410 chicago: Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry-Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5519410. ieee: L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans.” Zenodo, 2021. ista: Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann H-J, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans, Zenodo, 10.5281/ZENODO.5519410. mla: Chauve, Laetitia, et al. Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans. Zenodo, 2021, doi:10.5281/ZENODO.5519410. short: L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.-J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, (2021). date_created: 2023-05-23T16:40:56Z date_published: 2021-12-25T00:00:00Z date_updated: 2023-08-14T11:53:26Z day: '25' ddc: - '570' department: - _id: MaDe doi: 10.5281/ZENODO.5519410 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.5547464 month: '12' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '10322' relation: used_in_publication status: public status: public title: Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '10325' abstract: - lang: eng text: Since the inception of Bitcoin, a plethora of distributed ledgers differing in design and purpose has been created. While by design, blockchains provide no means to securely communicate with external systems, numerous attempts towards trustless cross-chain communication have been proposed over the years. Today, cross-chain communication (CCC) plays a fundamental role in cryptocurrency exchanges, scalability efforts via sharding, extension of existing systems through sidechains, and bootstrapping of new blockchains. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence in their correctness and composability. We provide the first systematic exposition of cross-chain communication protocols. We formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. With this result in mind, we develop a framework to design new and evaluate existing CCC protocols, focusing on the inherent trust assumptions thereof, and derive a classification covering the field of cross-chain communication to date. We conclude by discussing open challenges for CCC research and the implications of interoperability on the security and privacy of blockchains. acknowledgement: 'We would like express our gratitude to Georgia Avarikioti, Daniel Perez and Dominik Harz for helpful comments and feedback on earlier versions of this manuscript. We also thank Nicholas Stifter, Aljosha Judmayer, Philipp Schindler, Edgar Weippl, and Alistair Stewart for insightful discussions during the early stages of this research. We also wish to thank the anonymous reviewers for their valuable comments that helped improve the presentation of our results. This research was funded by Bridge 1 858561 SESC; Bridge 1 864738 PR4DLT (all FFG); the Christian Doppler Laboratory for Security and Quality Improvement in the Production System Lifecycle (CDL-SQI); the competence center SBA-K1 funded by COMET; Chaincode Labs through the project SLN: Scalability for the Lightning Network; and by the Austrian Science Fund (FWF) through the Meitner program (project M-2608). Mustafa Al-Bassam is funded by a scholarship from the Alan Turing Institute. Alexei Zamyatin conducted the early stages of this work during his time at SBA Research, and was supported by a Binance Research Fellowship.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Alexei full_name: Zamyatin, Alexei last_name: Zamyatin - first_name: Mustafa full_name: Al-Bassam, Mustafa last_name: Al-Bassam - first_name: Dionysis full_name: Zindros, Dionysis last_name: Zindros - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Pedro full_name: Moreno-Sanchez, Pedro last_name: Moreno-Sanchez - first_name: Aggelos full_name: Kiayias, Aggelos last_name: Kiayias - first_name: William J. full_name: Knottenbelt, William J. last_name: Knottenbelt citation: ama: 'Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. In: 25th International Conference on Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:3-36. doi:10.1007/978-3-662-64331-0_1' apa: 'Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., & Knottenbelt, W. J. (2021). SoK: Communication across distributed ledgers. In 25th International Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 3–36). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_1' chicago: 'Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK: Communication across Distributed Ledgers.” In 25th International Conference on Financial Cryptography and Data Security, 12675:3–36. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_1.' ieee: 'A. Zamyatin et al., “SoK: Communication across distributed ledgers,” in 25th International Conference on Financial Cryptography and Data Security, Virtual, 2021, vol. 12675, pp. 3–36.' ista: 'Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias A, Knottenbelt WJ. 2021. SoK: Communication across distributed ledgers. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 3–36.' mla: 'Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” 25th International Conference on Financial Cryptography and Data Security, vol. 12675, Springer Nature, 2021, pp. 3–36, doi:10.1007/978-3-662-64331-0_1.' short: A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 3–36. conference: end_date: 2021-03-05 location: Virtual name: 'FC: Financial Cryptography' start_date: 2021-03-01 date_created: 2021-11-21T23:01:29Z date_published: 2021-10-23T00:00:00Z date_updated: 2023-08-14T12:59:26Z day: '23' department: - _id: ElKo doi: 10.1007/978-3-662-64331-0_1 external_id: isi: - '000712016200001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2019/1128 month: '10' oa: 1 oa_version: Preprint page: 3-36 publication: 25th International Conference on Financial Cryptography and Data Security publication_identifier: eisbn: - 978-3-662-64331-0 eissn: - 1611-3349 isbn: - 9-783-6626-4330-3 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'SoK: Communication across distributed ledgers' type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: '12675 ' year: '2021' ... --- _id: '10324' abstract: - lang: eng text: Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee’s approval for the last valid state. Additionally, Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead, Brick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. We formally define and prove for Brick the properties a payment channel construction should fulfill. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity. acknowledgement: We would like to thank Kaoutar Elkhiyaoui for her valuable feedback as well as Jakub Sliwinski for his impactful contribution to this work. alternative_title: - LNCS article_processing_charge: No author: - first_name: Zeta full_name: Avarikioti, Zeta last_name: Avarikioti - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Roger full_name: Wattenhofer, Roger last_name: Wattenhofer - first_name: Dionysis full_name: Zindros, Dionysis last_name: Zindros citation: ama: 'Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous incentive-compatible payment channels. In: 25th International Conference on Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:209-230. doi:10.1007/978-3-662-64331-0_11' apa: 'Avarikioti, Z., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (2021). Brick: Asynchronous incentive-compatible payment channels. In 25th International Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 209–230). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_11' chicago: 'Avarikioti, Zeta, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Incentive-Compatible Payment Channels.” In 25th International Conference on Financial Cryptography and Data Security, 12675:209–30. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_11.' ieee: 'Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous incentive-compatible payment channels,” in 25th International Conference on Financial Cryptography and Data Security, Virtual, 2021, vol. 12675, pp. 209–230.' ista: 'Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. 2021. Brick: Asynchronous incentive-compatible payment channels. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 209–230.' mla: 'Avarikioti, Zeta, et al. “Brick: Asynchronous Incentive-Compatible Payment Channels.” 25th International Conference on Financial Cryptography and Data Security, vol. 12675, Springer Nature, 2021, pp. 209–30, doi:10.1007/978-3-662-64331-0_11.' short: Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 209–230. conference: end_date: 2021-03-05 location: Virtual name: 'FC: Financial Cryptography' start_date: 2021-03-01 date_created: 2021-11-21T23:01:29Z date_published: 2021-10-23T00:00:00Z date_updated: 2023-08-14T12:59:58Z day: '23' department: - _id: ElKo doi: 10.1007/978-3-662-64331-0_11 external_id: arxiv: - '1905.11360' isi: - '000712016200011' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1905.11360 month: '10' oa: 1 oa_version: Preprint page: 209-230 publication: 25th International Conference on Financial Cryptography and Data Security publication_identifier: eisbn: - 978-3-662-64331-0 eissn: - 1611-3349 isbn: - 9-783-6626-4330-3 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Brick: Asynchronous incentive-compatible payment channels' type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: '12675 ' year: '2021' ... --- _id: '10363' abstract: - lang: eng text: Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death, but its pro-thrombotic activity is problematic for use of erythropoietin in treating hypoxia. We constructed a fusion protein that stimulates red blood cell production and neuroprotection without triggering platelet production, a marker for thrombosis. The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant (L108A). The mutation reduces activation of erythropoietin receptor homodimers that induce erythropoiesis and thrombosis, but maintains the tissue-protective signaling. The binding of the nanobody element to glycophorin A rescues homodimeric erythropoietin receptor activation on red blood cell precursors. In a cell proliferation assay, the fusion protein is active at 10−14 M, allowing an estimate of the number of receptor–ligand complexes needed for signaling. This fusion protein stimulates erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity in vitro. Our erythropoietin fusion protein presents a novel molecule for treating hypoxia. acknowledgement: This work was supported by funds from the Wyss Institute for Biologically Inspired Engineering and the Boston Biomedical Innovation Center (Pilot Award 112475; Drive Award U54HL119145). J.L., K.M.K., D.R.B., J.C.W. and P.A.S. were supported by the Harvard Medical School Department of Systems Biology. J.C.W. was further supported by the Harvard Medical School Laboratory of Systems Pharmacology. A.V., D.R.B. and P.A.S. were further supported by the Wyss Institute for Biologically Inspired Engineering. N.G.G. was sponsored by the Army Research Office under Grant Number W911NF-17-2-0092. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein. We sincerely thank Amanda Graveline and the Wyss Institute at Harvard for their scientific support. article_number: gzab025 article_processing_charge: No article_type: original author: - first_name: Jungmin full_name: Lee, Jungmin last_name: Lee - first_name: Andyna full_name: Vernet, Andyna last_name: Vernet - first_name: Nathalie full_name: Gruber, Nathalie id: 2C9C8316-AA17-11E9-B5C2-8BC2E5697425 last_name: Gruber - first_name: Kasia M. full_name: Kready, Kasia M. last_name: Kready - first_name: Devin R. full_name: Burrill, Devin R. last_name: Burrill - first_name: Jeffrey C. full_name: Way, Jeffrey C. last_name: Way - first_name: Pamela A. full_name: Silver, Pamela A. last_name: Silver citation: ama: Lee J, Vernet A, Gruber N, et al. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 2021;34. doi:10.1093/protein/gzab025 apa: Lee, J., Vernet, A., Gruber, N., Kready, K. M., Burrill, D. R., Way, J. C., & Silver, P. A. (2021). Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. Oxford University Press. https://doi.org/10.1093/protein/gzab025 chicago: Lee, Jungmin, Andyna Vernet, Nathalie Gruber, Kasia M. Kready, Devin R. Burrill, Jeffrey C. Way, and Pamela A. Silver. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection. Oxford University Press, 2021. https://doi.org/10.1093/protein/gzab025. ieee: J. Lee et al., “Rational engineering of an erythropoietin fusion protein to treat hypoxia,” Protein Engineering, Design and Selection, vol. 34. Oxford University Press, 2021. ista: Lee J, Vernet A, Gruber N, Kready KM, Burrill DR, Way JC, Silver PA. 2021. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 34, gzab025. mla: Lee, Jungmin, et al. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection, vol. 34, gzab025, Oxford University Press, 2021, doi:10.1093/protein/gzab025. short: J. Lee, A. Vernet, N. Gruber, K.M. Kready, D.R. Burrill, J.C. Way, P.A. Silver, Protein Engineering, Design and Selection 34 (2021). date_created: 2021-11-28T23:01:28Z date_published: 2021-11-01T00:00:00Z date_updated: 2023-08-14T13:01:38Z day: '01' department: - _id: CaGu doi: 10.1093/protein/gzab025 external_id: isi: - '000746596900001' pmid: - '34725710' intvolume: ' 34' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/protein/gzab025 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Protein Engineering, Design and Selection publication_identifier: eissn: - 1741-0134 issn: - 1741-0126 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Rational engineering of an erythropoietin fusion protein to treat hypoxia type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 34 year: '2021' ... --- _id: '10366' article_number: '203758' article_processing_charge: No article_type: letter_note author: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Ana Maria full_name: Lennon, Ana Maria last_name: Lennon - first_name: Roberto full_name: Mayor, Roberto last_name: Mayor - first_name: Guillaume full_name: Salbreux, Guillaume last_name: Salbreux citation: ama: 'Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. 2021;168(12). doi:10.1016/j.cdev.2021.203758' apa: 'Heisenberg, C.-P. J., Lennon, A. M., Mayor, R., & Salbreux, G. (2021). Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. Elsevier. https://doi.org/10.1016/j.cdev.2021.203758' chicago: 'Heisenberg, Carl-Philipp J, Ana Maria Lennon, Roberto Mayor, and Guillaume Salbreux. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development. Elsevier, 2021. https://doi.org/10.1016/j.cdev.2021.203758.' ieee: 'C.-P. J. Heisenberg, A. M. Lennon, R. Mayor, and G. Salbreux, “Special rebranding issue: ‘Quantitative cell and developmental biology,’” Cells and Development, vol. 168, no. 12. Elsevier, 2021.' ista: 'Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. 2021. Special rebranding issue: “Quantitative cell and developmental biology”. Cells and Development. 168(12), 203758.' mla: 'Heisenberg, Carl-Philipp J., et al. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development, vol. 168, no. 12, 203758, Elsevier, 2021, doi:10.1016/j.cdev.2021.203758.' short: C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development 168 (2021). date_created: 2021-11-28T23:01:30Z date_published: 2021-11-17T00:00:00Z date_updated: 2023-08-14T13:02:40Z day: '17' department: - _id: CaHe doi: 10.1016/j.cdev.2021.203758 external_id: isi: - '000974771600028' pmid: - '34800748' intvolume: ' 168' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cdev.2021.203758 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Cells and Development publication_identifier: issn: - 2667-2901 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Special rebranding issue: “Quantitative cell and developmental biology”' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 168 year: '2021' ... --- _id: '10402' abstract: - lang: eng text: Branching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales. acknowledgement: We thank all members of our respective groups for helpful discussion on the paper. The authors are also grateful to Prof. Abdel El. Manira for support and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core from the Karolinska Institutet for technical support. This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.); Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L. and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.); Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.). article_number: '6830' article_processing_charge: No article_type: original author: - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 - first_name: Dmitrii full_name: Kamenev, Dmitrii last_name: Kamenev - first_name: Kazunori full_name: Sunadome, Kazunori last_name: Sunadome - first_name: Dominik C full_name: Fachet, Dominik C id: 14FDD550-AA41-11E9-A0E5-1ACCE5697425 last_name: Fachet - first_name: Francois full_name: Lallemend, Francois last_name: Lallemend - first_name: Igor full_name: Adameyko, Igor last_name: Adameyko - first_name: Saida full_name: Hadjab, Saida last_name: Hadjab - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 2021;12. doi:10.1038/s41467-021-27135-5 apa: Ucar, M. C., Kamenev, D., Sunadome, K., Fachet, D. C., Lallemend, F., Adameyko, I., … Hannezo, E. B. (2021). Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-27135-5 chicago: Ucar, Mehmet C, Dmitrii Kamenev, Kazunori Sunadome, Dominik C Fachet, Francois Lallemend, Igor Adameyko, Saida Hadjab, and Edouard B Hannezo. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-27135-5. ieee: M. C. Ucar et al., “Theory of branching morphogenesis by local interactions and global guidance,” Nature Communications, vol. 12. Springer Nature, 2021. ista: Ucar MC, Kamenev D, Sunadome K, Fachet DC, Lallemend F, Adameyko I, Hadjab S, Hannezo EB. 2021. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 12, 6830. mla: Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications, vol. 12, 6830, Springer Nature, 2021, doi:10.1038/s41467-021-27135-5. short: M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021). date_created: 2021-12-05T23:01:40Z date_published: 2021-11-24T00:00:00Z date_updated: 2023-08-14T13:18:46Z day: '24' ddc: - '573' department: - _id: EdHa doi: 10.1038/s41467-021-27135-5 ec_funded: 1 external_id: isi: - '000722322900020' pmid: - '34819507' file: - access_level: open_access checksum: 63c56ec75314a71e63e7dd2920b3c5b5 content_type: application/pdf creator: cchlebak date_created: 2021-12-10T08:54:09Z date_updated: 2021-12-10T08:54:09Z file_id: '10529' file_name: 2021_NatComm_Ucar.pdf file_size: 2303405 relation: main_file success: 1 file_date_updated: 2021-12-10T08:54:09Z has_accepted_license: '1' intvolume: ' 12' isi: 1 language: - iso: eng month: '11' 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 - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '13058' relation: research_data status: public scopus_import: '1' status: public title: Theory of branching morphogenesis by local interactions and global guidance tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '10407' abstract: - lang: eng text: Digital hardware Trojans are integrated circuits whose implementation differ from the specification in an arbitrary and malicious way. For example, the circuit can differ from its specified input/output behavior after some fixed number of queries (known as “time bombs”) or on some particular input (known as “cheat codes”). To detect such Trojans, countermeasures using multiparty computation (MPC) or verifiable computation (VC) have been proposed. On a high level, to realize a circuit with specification F one has more sophisticated circuits F⋄ manufactured (where F⋄ specifies a MPC or VC of F ), and then embeds these F⋄ ’s into a master circuit which must be trusted but is relatively simple compared to F . Those solutions impose a significant overhead as F⋄ is much more complex than F , also the master circuits are not exactly trivial. In this work, we show that in restricted settings, where F has no evolving state and is queried on independent inputs, we can achieve a relaxed security notion using very simple constructions. In particular, we do not change the specification of the circuit at all (i.e., F=F⋄ ). Moreover the master circuit basically just queries a subset of its manufactured circuits and checks if they’re all the same. The security we achieve guarantees that, if the manufactured circuits are initially tested on up to T inputs, the master circuit will catch Trojans that try to deviate on significantly more than a 1/T fraction of the inputs. This bound is optimal for the type of construction considered, and we provably achieve it using a construction where 12 instantiations of F need to be embedded into the master. We also discuss an extremely simple construction with just 2 instantiations for which we conjecture that it already achieves the optimal bound. alternative_title: - LNCS article_processing_charge: No author: - first_name: Suvradip full_name: Chakraborty, Suvradip id: B9CD0494-D033-11E9-B219-A439E6697425 last_name: Chakraborty - first_name: Stefan full_name: Dziembowski, Stefan last_name: Dziembowski - first_name: Małgorzata full_name: Gałązka, Małgorzata last_name: Gałązka - first_name: Tomasz full_name: Lizurej, Tomasz last_name: Lizurej - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Michelle X full_name: Yeo, Michelle X id: 2D82B818-F248-11E8-B48F-1D18A9856A87 last_name: Yeo citation: ama: 'Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. Trojan-resilience without cryptography. In: Vol 13043. Springer Nature; 2021:397-428. doi:10.1007/978-3-030-90453-1_14' apa: 'Chakraborty, S., Dziembowski, S., Gałązka, M., Lizurej, T., Pietrzak, K. Z., & Yeo, M. X. (2021). Trojan-resilience without cryptography (Vol. 13043, pp. 397–428). Presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_14' chicago: Chakraborty, Suvradip, Stefan Dziembowski, Małgorzata Gałązka, Tomasz Lizurej, Krzysztof Z Pietrzak, and Michelle X Yeo. “Trojan-Resilience without Cryptography,” 13043:397–428. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_14. ieee: 'S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K. Z. Pietrzak, and M. X. Yeo, “Trojan-resilience without cryptography,” presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 397–428.' ista: 'Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. 2021. Trojan-resilience without cryptography. TCC: Theory of Cryptography Conference, LNCS, vol. 13043, 397–428.' mla: Chakraborty, Suvradip, et al. Trojan-Resilience without Cryptography. Vol. 13043, Springer Nature, 2021, pp. 397–428, doi:10.1007/978-3-030-90453-1_14. short: S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K.Z. Pietrzak, M.X. Yeo, in:, Springer Nature, 2021, pp. 397–428. conference: end_date: 2021-11-11 location: Raleigh, NC, United States name: 'TCC: Theory of Cryptography Conference' start_date: 2021-11-08 date_created: 2021-12-05T23:01:42Z date_published: 2021-11-04T00:00:00Z date_updated: 2023-08-14T13:07:46Z day: '04' department: - _id: KrPi doi: 10.1007/978-3-030-90453-1_14 ec_funded: 1 external_id: isi: - '000728364000014' intvolume: ' 13043' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2021/1224 month: '11' oa: 1 oa_version: Preprint page: 397-428 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: eissn: - 1611-3349 isbn: - 9-783-0309-0452-4 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Trojan-resilience without cryptography type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13043 year: '2021' ... --- _id: '10403' abstract: - lang: eng text: Synaptic transmission, connectivity, and dendritic morphology mature in parallel during brain development and are often disrupted in neurodevelopmental disorders. Yet how these changes influence the neuronal computations necessary for normal brain function are not well understood. To identify cellular mechanisms underlying the maturation of synaptic integration in interneurons, we combined patch-clamp recordings of excitatory inputs in mouse cerebellar stellate cells (SCs), three-dimensional reconstruction of SC morphology with excitatory synapse location, and biophysical modeling. We found that postnatal maturation of postsynaptic strength was homogeneously reduced along the somatodendritic axis, but dendritic integration was always sublinear. However, dendritic branching increased without changes in synapse density, leading to a substantial gain in distal inputs. Thus, changes in synapse distribution, rather than dendrite cable properties, are the dominant mechanism underlying the maturation of neuronal computation. These mechanisms favor the emergence of a spatially compartmentalized two-stage integration model promoting location-dependent integration within dendritic subunits. acknowledgement: This study was supported by the Centre National de la Recherche Scientifique and the Agence Nationale de la Recherche (ANR-13-BSV4-00166, to LC and DAD). TA was supported by fellowships from the Fondation pour la Recherche Medicale and the Swedish Research Council. We thank Dmitry Ershov from the Image Analysis Hub of the Institut Pasteur, Elodie Le Monnier, Elena Hollergschwandtner, Vanessa Zheden, and Corinne Nantet for technical support and Haining Zhong for providing the Venus-tagged PSD95 mouse line. We would like to thank Alberto Bacci, Ann Lohof, and Nelson Rebola for comments on the manuscript. article_number: e65954 article_processing_charge: No article_type: original author: - first_name: Celia full_name: Biane, Celia last_name: Biane - first_name: Florian full_name: Rückerl, Florian last_name: Rückerl - first_name: Therese full_name: Abrahamsson, Therese last_name: Abrahamsson - first_name: Cécile full_name: Saint-Cloment, Cécile last_name: Saint-Cloment - first_name: Jean full_name: Mariani, Jean last_name: Mariani - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: David A. full_name: Digregorio, David A. last_name: Digregorio - first_name: Rachel M. full_name: Sherrard, Rachel M. last_name: Sherrard - first_name: Laurence full_name: Cathala, Laurence last_name: Cathala citation: ama: Biane C, Rückerl F, Abrahamsson T, et al. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 2021;10. doi:10.7554/eLife.65954 apa: Biane, C., Rückerl, F., Abrahamsson, T., Saint-Cloment, C., Mariani, J., Shigemoto, R., … Cathala, L. (2021). Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.65954 chicago: Biane, Celia, Florian Rückerl, Therese Abrahamsson, Cécile Saint-Cloment, Jean Mariani, Ryuichi Shigemoto, David A. Digregorio, Rachel M. Sherrard, and Laurence Cathala. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.65954. ieee: C. Biane et al., “Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Biane C, Rückerl F, Abrahamsson T, Saint-Cloment C, Mariani J, Shigemoto R, Digregorio DA, Sherrard RM, Cathala L. 2021. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 10, e65954. mla: Biane, Celia, et al. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife, vol. 10, e65954, eLife Sciences Publications, 2021, doi:10.7554/eLife.65954. short: C. Biane, F. Rückerl, T. Abrahamsson, C. Saint-Cloment, J. Mariani, R. Shigemoto, D.A. Digregorio, R.M. Sherrard, L. Cathala, ELife 10 (2021). date_created: 2021-12-05T23:01:40Z date_published: 2021-11-03T00:00:00Z date_updated: 2023-08-14T13:12:07Z day: '03' ddc: - '570' department: - _id: RySh doi: 10.7554/eLife.65954 external_id: isi: - '000715789500001' file: - access_level: open_access checksum: c7c33c3319428d56e332e22349c50ed3 content_type: application/pdf creator: cchlebak date_created: 2021-12-10T08:31:41Z date_updated: 2021-12-10T08:31:41Z file_id: '10528' file_name: 2021_eLife_Biane.pdf file_size: 13131322 relation: main_file success: 1 file_date_updated: 2021-12-10T08:31:41Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons 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: '10401' abstract: - lang: eng text: Theoretical and experimental studies of the interaction between spins and temperature are vital for the development of spin caloritronics, as they dictate the design of future devices. In this work, we propose a two-terminal cold-atom simulator to study that interaction. The proposed quantum simulator consists of strongly interacting atoms that occupy two temperature reservoirs connected by a one-dimensional link. First, we argue that the dynamics in the link can be described using an inhomogeneous Heisenberg spin chain whose couplings are defined by the local temperature. Second, we show the existence of a spin current in a system with a temperature difference by studying the dynamics that follows the spin-flip of an atom in the link. A temperature gradient accelerates the impurity in one direction more than in the other, leading to an overall spin current similar to the spin Seebeck effect. acknowledgement: The authors acknowledge support from the European QuantERA ERA-NET Cofund in Quantum Technologies (Project QTFLAG Grant Agreement No. 731473) (R.E.B), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) Brazil (A.F.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V.), the Independent Research Fund Denmark, the Carlsberg Foundation, and Aarhus University Research Foundation under the Jens Christian Skou fellowship program (N.T.Z). article_number: '252' article_processing_charge: No article_type: original author: - first_name: Rafael E. full_name: Barfknecht, Rafael E. last_name: Barfknecht - first_name: Angela full_name: Foerster, Angela last_name: Foerster - first_name: Nikolaj T. full_name: Zinner, Nikolaj T. last_name: Zinner - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Barfknecht RE, Foerster A, Zinner NT, Volosniev A. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 2021;4(1). doi:10.1038/s42005-021-00753-7 apa: Barfknecht, R. E., Foerster, A., Zinner, N. T., & Volosniev, A. (2021). Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-021-00753-7 chicago: Barfknecht, Rafael E., Angela Foerster, Nikolaj T. Zinner, and Artem Volosniev. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics. Springer Nature, 2021. https://doi.org/10.1038/s42005-021-00753-7. ieee: R. E. Barfknecht, A. Foerster, N. T. Zinner, and A. Volosniev, “Generation of spin currents by a temperature gradient in a two-terminal device,” Communications Physics, vol. 4, no. 1. Springer Nature, 2021. ista: Barfknecht RE, Foerster A, Zinner NT, Volosniev A. 2021. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 4(1), 252. mla: Barfknecht, Rafael E., et al. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics, vol. 4, no. 1, 252, Springer Nature, 2021, doi:10.1038/s42005-021-00753-7. short: R.E. Barfknecht, A. Foerster, N.T. Zinner, A. Volosniev, Communications Physics 4 (2021). date_created: 2021-12-05T23:01:39Z date_published: 2021-11-26T00:00:00Z date_updated: 2023-08-14T13:04:34Z day: '26' ddc: - '530' department: - _id: MiLe doi: 10.1038/s42005-021-00753-7 ec_funded: 1 external_id: arxiv: - '2101.02020' isi: - 10.1038/s42005-021-00753-7 file: - access_level: open_access checksum: 9097319952cb9a3d96e7fd3aa9813a03 content_type: application/pdf creator: alisjak date_created: 2021-12-06T14:53:41Z date_updated: 2021-12-06T14:53:41Z file_id: '10420' file_name: 2021_NatComm_Barfknecht.pdf file_size: 1068984 relation: main_file success: 1 file_date_updated: 2021-12-06T14:53:41Z has_accepted_license: '1' intvolume: ' 4' issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Communications Physics publication_identifier: eissn: - '23993650' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Generation of spin currents by a temperature gradient in a two-terminal device 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: 4 year: '2021' ... --- _id: '10404' abstract: - lang: eng text: While convolutional neural networks (CNNs) have found wide adoption as state-of-the-art models for image-related tasks, their predictions are often highly sensitive to small input perturbations, which the human vision is robust against. This paper presents Perturber, a web-based application that allows users to instantaneously explore how CNN activations and predictions evolve when a 3D input scene is interactively perturbed. Perturber offers a large variety of scene modifications, such as camera controls, lighting and shading effects, background modifications, object morphing, as well as adversarial attacks, to facilitate the discovery of potential vulnerabilities. Fine-tuned model versions can be directly compared for qualitative evaluation of their robustness. Case studies with machine learning experts have shown that Perturber helps users to quickly generate hypotheses about model vulnerabilities and to qualitatively compare model behavior. Using quantitative analyses, we could replicate users’ insights with other CNN architectures and input images, yielding new insights about the vulnerability of adversarially trained models. acknowledgement: "We thank Robert Geirhos and Roland Zimmermann for their participation in the case study and valuable feedback, Chris Olah and Nick Cammarata for valuable discussions in the early phase of the project, as well as the Distill Slack workspace as a platform for discussions. M.L. is supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). J.B. is supported by the German Federal Ministry of Education and Research\r\n(BMBF) through the Competence Center for Machine Learning (TUE.AI, FKZ 01IS18039A) and the International Max Planck Research School for Intelligent Systems (IMPRS-IS). R.H. is partially supported by Boeing and Horizon-2020 ECSEL (grant 783163, iDev40).\r\n" article_processing_charge: No article_type: original author: - first_name: Stefan full_name: Sietzen, Stefan last_name: Sietzen - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Judy full_name: Borowski, Judy last_name: Borowski - first_name: Ramin full_name: Hasani, Ramin last_name: Hasani - first_name: Manuela full_name: Waldner, Manuela last_name: Waldner citation: ama: Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis of CNN robustness. Computer Graphics Forum. 2021;40(7):253-264. doi:10.1111/cgf.14418 apa: Sietzen, S., Lechner, M., Borowski, J., Hasani, R., & Waldner, M. (2021). Interactive analysis of CNN robustness. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.14418 chicago: Sietzen, Stefan, Mathias Lechner, Judy Borowski, Ramin Hasani, and Manuela Waldner. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.14418. ieee: S. Sietzen, M. Lechner, J. Borowski, R. Hasani, and M. Waldner, “Interactive analysis of CNN robustness,” Computer Graphics Forum, vol. 40, no. 7. Wiley, pp. 253–264, 2021. ista: Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis of CNN robustness. Computer Graphics Forum. 40(7), 253–264. mla: Sietzen, Stefan, et al. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum, vol. 40, no. 7, Wiley, 2021, pp. 253–64, doi:10.1111/cgf.14418. short: S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics Forum 40 (2021) 253–264. date_created: 2021-12-05T23:01:40Z date_published: 2021-11-27T00:00:00Z date_updated: 2023-08-14T13:11:42Z day: '27' department: - _id: ToHe doi: 10.1111/cgf.14418 external_id: arxiv: - '2110.07667' isi: - '000722952000024' intvolume: ' 40' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2110.07667 month: '11' oa: 1 oa_version: Preprint page: 253-264 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Computer Graphics Forum publication_identifier: eissn: - 1467-8659 issn: - 0167-7055 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Interactive analysis of CNN robustness type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ... --- _id: '10406' abstract: - lang: eng text: Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future. acknowledgement: The authors would like to thank Feyza Nur Arslan, Suyash Naik, Diana Pinheiro, Alexandra Schauer, and Shayan Shamipour for their comments on the draft. N.M. is supported by an ISTplus postdoctoral fellowship (H2020 Marie-Sklodowska-Curie COFUND Action). article_processing_charge: No article_type: original author: - first_name: Nikhil full_name: Mishra, Nikhil id: C4D70E82-1081-11EA-B3ED-9A4C3DDC885E last_name: Mishra orcid: 0000-0002-6425-5788 - 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: Mishra N, Heisenberg C-PJ. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 2021;55:209-233. doi:10.1146/annurev-genet-071819-103748 apa: Mishra, N., & Heisenberg, C.-P. J. (2021). Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genet-071819-103748 chicago: Mishra, Nikhil, and Carl-Philipp J Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics. Annual Reviews, 2021. https://doi.org/10.1146/annurev-genet-071819-103748. ieee: N. Mishra and C.-P. J. Heisenberg, “Dissecting organismal morphogenesis by bridging genetics and biophysics,” Annual Review of Genetics, vol. 55. Annual Reviews, pp. 209–233, 2021. ista: Mishra N, Heisenberg C-PJ. 2021. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 55, 209–233. mla: Mishra, Nikhil, and Carl-Philipp J. Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics, vol. 55, Annual Reviews, 2021, pp. 209–33, doi:10.1146/annurev-genet-071819-103748. short: N. Mishra, C.-P.J. Heisenberg, Annual Review of Genetics 55 (2021) 209–233. date_created: 2021-12-05T23:01:41Z date_published: 2021-08-30T00:00:00Z date_updated: 2023-08-14T13:05:13Z day: '30' department: - _id: CaHe doi: 10.1146/annurev-genet-071819-103748 ec_funded: 1 external_id: isi: - '000747220900010' pmid: - '34460295' intvolume: ' 55' isi: 1 keyword: - morphogenesis - forward genetics - high-resolution microscopy - biophysics - biochemistry - patterning language: - iso: eng month: '08' oa_version: None page: 209-233 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Annual Review of Genetics publication_identifier: eissn: - 1545-2948 issn: - 0066-4197 publication_status: published publisher: Annual Reviews quality_controlled: '1' scopus_import: '1' status: public title: Dissecting organismal morphogenesis by bridging genetics and biophysics type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 55 year: '2021' ... --- _id: '13058' abstract: - lang: eng text: The zip file includes source data used in the main text of the manuscript "Theory of branching morphogenesis by local interactions and global guidance", as well as a representative Jupyter notebook to reproduce the main figures. A sample script for the simulations of branching and annihilating random walks is also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary branched networks under external guidance. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt. article_processing_charge: No author: - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 citation: ama: Ucar MC. Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” 2021. doi:10.5281/ZENODO.5257160 apa: Ucar, M. C. (2021). Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” Zenodo. https://doi.org/10.5281/ZENODO.5257160 chicago: Ucar, Mehmet C. “Source Data for the Manuscript ‘Theory of Branching Morphogenesis by Local Interactions and Global Guidance.’” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5257160. ieee: M. C. Ucar, “Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance.’” Zenodo, 2021. ista: Ucar MC. 2021. Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance’, Zenodo, 10.5281/ZENODO.5257160. mla: Ucar, Mehmet C. Source Data for the Manuscript “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Zenodo, 2021, doi:10.5281/ZENODO.5257160. short: M.C. Ucar, (2021). date_created: 2023-05-23T13:46:34Z date_published: 2021-08-25T00:00:00Z date_updated: 2023-08-14T13:18:46Z day: '25' ddc: - '570' department: - _id: EdHa doi: 10.5281/ZENODO.5257160 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.5257161 month: '08' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '10402' relation: used_in_publication status: public status: public title: Source data for the manuscript "Theory of branching morphogenesis by local interactions and global guidance" tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '10408' abstract: - lang: eng text: 'Key trees are often the best solution in terms of transmission cost and storage requirements for managing keys in a setting where a group needs to share a secret key, while being able to efficiently rotate the key material of users (in order to recover from a potential compromise, or to add or remove users). Applications include multicast encryption protocols like LKH (Logical Key Hierarchies) or group messaging like the current IETF proposal TreeKEM. A key tree is a (typically balanced) binary tree, where each node is identified with a key: leaf nodes hold users’ secret keys while the root is the shared group key. For a group of size N, each user just holds log(N) keys (the keys on the path from its leaf to the root) and its entire key material can be rotated by broadcasting 2log(N) ciphertexts (encrypting each fresh key on the path under the keys of its parents). In this work we consider the natural setting where we have many groups with partially overlapping sets of users, and ask if we can find solutions where the cost of rotating a key is better than in the trivial one where we have a separate key tree for each group. We show that in an asymptotic setting (where the number m of groups is fixed while the number N of users grows) there exist more general key graphs whose cost converges to the cost of a single group, thus saving a factor linear in the number of groups over the trivial solution. As our asymptotic “solution” converges very slowly and performs poorly on concrete examples, we propose an algorithm that uses a natural heuristic to compute a key graph for any given group structure. Our algorithm combines two greedy algorithms, and is thus very efficient: it first converts the group structure into a “lattice graph”, which is then turned into a key graph by repeatedly applying the algorithm for constructing a Huffman code. To better understand how far our proposal is from an optimal solution, we prove lower bounds on the update cost of continuous group-key agreement and multicast encryption in a symbolic model admitting (asymmetric) encryption, pseudorandom generators, and secret sharing as building blocks.' acknowledgement: B. Auerbach, M.A. Baig and K. Pietrzak—received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Karen Klein was supported in part by ERC CoG grant 724307 and conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Guillermo Pascual-Perez was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385; Michael Walter conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT). alternative_title: - LNCS article_processing_charge: No author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Benedikt full_name: Auerbach, Benedikt id: D33D2B18-E445-11E9-ABB7-15F4E5697425 last_name: Auerbach orcid: 0000-0002-7553-6606 - first_name: Mirza Ahad full_name: Baig, Mirza Ahad id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425 last_name: Baig - first_name: Miguel full_name: Cueto Noval, Miguel id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc last_name: Cueto Noval - first_name: Karen full_name: Klein, Karen id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87 last_name: Klein - first_name: Guillermo full_name: Pascual Perez, Guillermo id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87 last_name: Pascual Perez orcid: 0000-0001-8630-415X - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Michael full_name: Walter, Michael id: 488F98B0-F248-11E8-B48F-1D18A9856A87 last_name: Walter orcid: 0000-0003-3186-2482 citation: ama: 'Alwen JF, Auerbach B, Baig MA, et al. Grafting key trees: Efficient key management for overlapping groups. In: 19th International Conference. Vol 13044. Springer Nature; 2021:222-253. doi:10.1007/978-3-030-90456-2_8' apa: 'Alwen, J. F., Auerbach, B., Baig, M. A., Cueto Noval, M., Klein, K., Pascual Perez, G., … Walter, M. (2021). Grafting key trees: Efficient key management for overlapping groups. In 19th International Conference (Vol. 13044, pp. 222–253). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90456-2_8' chicago: 'Alwen, Joel F, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” In 19th International Conference, 13044:222–53. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90456-2_8.' ieee: 'J. F. Alwen et al., “Grafting key trees: Efficient key management for overlapping groups,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13044, pp. 222–253.' ista: 'Alwen JF, Auerbach B, Baig MA, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ, Walter M. 2021. Grafting key trees: Efficient key management for overlapping groups. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13044, 222–253.' mla: 'Alwen, Joel F., et al. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” 19th International Conference, vol. 13044, Springer Nature, 2021, pp. 222–53, doi:10.1007/978-3-030-90456-2_8.' short: J.F. Alwen, B. Auerbach, M.A. Baig, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 222–253. conference: end_date: 2021-11-11 location: Raleigh, NC, United States name: 'TCC: Theory of Cryptography' start_date: 2021-11-08 date_created: 2021-12-05T23:01:42Z date_published: 2021-11-04T00:00:00Z date_updated: 2023-08-14T13:19:39Z day: '04' department: - _id: KrPi doi: 10.1007/978-3-030-90456-2_8 ec_funded: 1 external_id: isi: - '000728363700008' intvolume: ' 13044' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2021/1158 month: '11' oa: 1 oa_version: Preprint page: 222-253 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: 19th International Conference publication_identifier: eisbn: - 978-3-030-90456-2 eissn: - 1611-3349 isbn: - 9-783-0309-0455-5 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Grafting key trees: Efficient key management for overlapping groups' type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13044 year: '2021' ... --- _id: '10527' abstract: - lang: eng text: We show that in a two-dimensional electron gas with an annular Fermi surface, long-range Coulomb interactions can lead to unconventional superconductivity by the Kohn-Luttinger mechanism. Superconductivity is strongly enhanced when the inner and outer Fermi surfaces are close to each other. The most prevalent state has chiral p-wave symmetry, but d-wave and extended s-wave pairing are also possible. We discuss these results in the context of rhombohedral trilayer graphene, where superconductivity was recently discovered in regimes where the normal state has an annular Fermi surface. Using realistic parameters, our mechanism can account for the order of magnitude of Tc, as well as its trends as a function of electron density and perpendicular displacement field. Moreover, it naturally explains some of the outstanding puzzles in this material, that include the weak temperature dependence of the resistivity above Tc, and the proximity of spin singlet superconductivity to the ferromagnetic phase. acknowledgement: We thank Yang-Zhi Chou, Andrey Chubukov, Johannes Hofmann, Steve Kivelson, Sri Raghu, and Sankar das Sarma, Jay Sau, Fengcheng Wu, and Andrea Young for many stimulating discussions and for their comments on the manuscript. E.B. thanks S. Chatterjee, T. Wang, and M. Zaletel for a collaboration on a related topic. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz. article_number: '247001' article_processing_charge: No article_type: original author: - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Tobias full_name: Holder, Tobias last_name: Holder - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Erez full_name: Berg, Erez last_name: Berg citation: ama: 'Ghazaryan A, Holder T, Serbyn M, Berg E. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 2021;127(24). doi:10.1103/physrevlett.127.247001' apa: 'Ghazaryan, A., Holder, T., Serbyn, M., & Berg, E. (2021). Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.127.247001' chicago: 'Ghazaryan, Areg, Tobias Holder, Maksym Serbyn, and Erez Berg. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.247001.' ieee: 'A. Ghazaryan, T. Holder, M. Serbyn, and E. Berg, “Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene,” Physical Review Letters, vol. 127, no. 24. American Physical Society, 2021.' ista: 'Ghazaryan A, Holder T, Serbyn M, Berg E. 2021. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 127(24), 247001.' mla: 'Ghazaryan, Areg, et al. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical Review Letters, vol. 127, no. 24, 247001, American Physical Society, 2021, doi:10.1103/physrevlett.127.247001.' short: A. Ghazaryan, T. Holder, M. Serbyn, E. Berg, Physical Review Letters 127 (2021). date_created: 2021-12-10T07:51:33Z date_published: 2021-12-09T00:00:00Z date_updated: 2023-08-14T13:19:13Z day: '09' department: - _id: MaSe doi: 10.1103/physrevlett.127.247001 ec_funded: 1 external_id: arxiv: - '2109.00011' isi: - '000923819400004' intvolume: ' 127' isi: 1 issue: '24' keyword: - general physics and astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2109.00011 month: '12' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - description: News on IST Webpage relation: press_release url: https://ist.ac.at/en/news/resolving-the-puzzles-of-graphene-superconductivity/ scopus_import: '1' status: public title: 'Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 127 year: '2021' ... --- _id: '10534' abstract: - lang: eng text: For many years, fullerene derivatives have been the main n-type material of organic electronics and optoelectronics. Recently, fullerene derivatives functionalized with ethylene glycol (EG) side chains have been showing important properties such as enhanced dielectric constants, facile doping and enhanced self-assembly capabilities. Here, we have prepared field-effect transistors using a series of these fullerene derivatives equipped with EG side chains of different lengths. Transport data show the beneficial effect of increasing the EG side chain. In order to understand the material properties, full structural determination of these fullerene derivatives has been achieved by coupling the X-ray data with molecular dynamics (MD) simulations. The increase in transport properties is paired with the formation of extended layered structures, efficient molecular packing and an increase in the crystallite alignment. The layer-like structure is composed of conducting layers, containing of closely packed C60 balls approaching the inter-distance of 1 nm, that are separated by well-defined EG layers, where the EG chains are rather splayed with the chain direction almost perpendicular to the layer normal. Such a layered structure appears highly ordered and highly aligned with the C60 planes oriented parallel to the substrate in the thin film configuration. The order inside the thin film increases with the EG chain length, allowing the systems to achieve mobilities as high as 0.053 cm2 V−1 s−1. Our work elucidates the structure of these interesting semiconducting organic molecules and shows that the synergistic use of X-ray structural analysis and MD simulations is a powerful tool to identify the structure of thin organic films for optoelectronic applications. acknowledgement: J. D. gratefully acknowledges the China Scholarship Council (CSC No. 201606340158) for supporting his PhD studies. S. S. thanks J. Antoja-Lleonart for insightful discussions on simulating the X-ray diffraction patterns. Part of the work was sponsored by NWO Exact and Natural Sciences for the use of supercomputer facilities (Contract no. 17197 7095). Regarding S. S., R. A., R. W. A. H., J. C. H., and M. A. L., this is a publication by the FOM Focus Group “Next Generation Organic Photovoltaics”, participating in the Dutch Institute for Fundamental Energy Research (DIFFER). The ESRF is acknowledged for providing the beamtime. J. D. and G. P. are grateful to the BM26B staff for their great support during the beamtime. M. A. L., D. M. B. are grateful for the financial support of the European Research Council via a Starting Grant (HySPOD, No. 306983). article_processing_charge: No article_type: original author: - first_name: Jingjin full_name: Dong, Jingjin last_name: Dong - first_name: Selim full_name: Sami, Selim last_name: Sami - first_name: Daniel full_name: Balazs, Daniel id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E last_name: Balazs orcid: 0000-0001-7597-043X - first_name: Riccardo full_name: Alessandri, Riccardo last_name: Alessandri - first_name: Fatimeh full_name: Jahani, Fatimeh last_name: Jahani - first_name: Li full_name: Qiu, Li last_name: Qiu - first_name: Siewert J. full_name: Marrink, Siewert J. last_name: Marrink - first_name: Remco W.A. full_name: Havenith, Remco W.A. last_name: Havenith - first_name: Jan C. full_name: Hummelen, Jan C. last_name: Hummelen - first_name: Maria A. full_name: Loi, Maria A. last_name: Loi - first_name: Giuseppe full_name: Portale, Giuseppe last_name: Portale citation: ama: 'Dong J, Sami S, Balazs D, et al. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. 2021;9(45):16217-16225. doi:10.1039/d1tc02753k' apa: 'Dong, J., Sami, S., Balazs, D., Alessandri, R., Jahani, F., Qiu, L., … Portale, G. (2021). Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. Royal Society of Chemistry. https://doi.org/10.1039/d1tc02753k' chicago: 'Dong, Jingjin, Selim Sami, Daniel Balazs, Riccardo Alessandri, Fatimeh Jahani, Li Qiu, Siewert J. Marrink, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” Journal of Materials Chemistry C. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1tc02753k.' ieee: 'J. Dong et al., “Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties,” Journal of Materials Chemistry C, vol. 9, no. 45. Royal Society of Chemistry, pp. 16217–16225, 2021.' ista: 'Dong J, Sami S, Balazs D, Alessandri R, Jahani F, Qiu L, Marrink SJ, Havenith RWA, Hummelen JC, Loi MA, Portale G. 2021. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. 9(45), 16217–16225.' mla: 'Dong, Jingjin, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” Journal of Materials Chemistry C, vol. 9, no. 45, Royal Society of Chemistry, 2021, pp. 16217–25, doi:10.1039/d1tc02753k.' short: J. Dong, S. Sami, D. Balazs, R. Alessandri, F. Jahani, L. Qiu, S.J. Marrink, R.W.A. Havenith, J.C. Hummelen, M.A. Loi, G. Portale, Journal of Materials Chemistry C 9 (2021) 16217–16225. date_created: 2021-12-12T23:01:27Z date_published: 2021-12-07T00:00:00Z date_updated: 2023-08-17T06:18:44Z day: '07' ddc: - '540' department: - _id: MaIb doi: 10.1039/d1tc02753k external_id: isi: - '000688135700001' file: - access_level: open_access checksum: 6b73c214ce54a6894a5854b4364413d7 content_type: application/pdf creator: cchlebak date_created: 2021-12-13T09:24:42Z date_updated: 2021-12-13T09:24:42Z file_id: '10538' file_name: 2021_JMaterChemC_Dong.pdf file_size: 4979390 relation: main_file success: 1 file_date_updated: 2021-12-13T09:24:42Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '45' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 16217-16225 publication: Journal of Materials Chemistry C publication_identifier: eissn: - 2050-7526 issn: - 2050-7534 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: 'Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2021' ... --- _id: '10533' abstract: - lang: eng text: Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin. acknowledgement: We thank X Feng for helpful comments on the manuscript. This work was supported by a European Research Council grant MaintainMeth (725746) to DZ. article_number: e72676 article_processing_charge: No article_type: original author: - first_name: Jaemyung full_name: Choi, Jaemyung last_name: Choi - first_name: David B full_name: Lyons, David B last_name: Lyons - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 2021;10. doi:10.7554/elife.72676 apa: Choi, J., Lyons, D. B., & Zilberman, D. (2021). Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.72676 chicago: Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72676. ieee: J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676. mla: Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” ELife, vol. 10, e72676, eLife Sciences Publications, 2021, doi:10.7554/elife.72676. short: J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021). date_created: 2021-12-10T13:12:08Z date_published: 2021-12-01T00:00:00Z date_updated: 2023-08-17T06:21:08Z day: '01' ddc: - '570' department: - _id: DaZi doi: 10.7554/elife.72676 ec_funded: 1 external_id: isi: - '000754832000001' pmid: - '34850679' file: - access_level: open_access checksum: 22ed4c55fb550f6da02ae55c359be651 content_type: application/pdf creator: dernst date_created: 2022-05-16T10:42:22Z date_updated: 2022-05-16T10:42:22Z file_id: '11384' file_name: 2021_eLife_Choi.pdf file_size: 2715200 relation: main_file success: 1 file_date_updated: 2022-05-16T10:42:22Z has_accepted_license: '1' intvolume: ' 10' isi: 1 keyword: - genetics and molecular biology language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 62935a00-2b32-11ec-9570-eff30fa39068 call_identifier: H2020 grant_number: '725746' name: Quantitative analysis of DNA methylation maintenance with chromatin publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin 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: '10536' abstract: - lang: eng text: TGFβ overexpression is commonly detected in cancer patients and correlates with poor prognosis and metastasis. Cancer progression is often associated with an enhanced recruitment of myeloid-derived cells to the tumor microenvironment. Here we show that functional TGFβ-signaling in myeloid cells is required for metastasis to the lungs and the liver. Myeloid-specific deletion of Tgfbr2 resulted in reduced spontaneous lung metastasis, which was associated with a reduction of proinflammatory cytokines in the metastatic microenvironment. Notably, CD8+ T cell depletion in myeloid-specific Tgfbr2-deficient mice rescued lung metastasis. Myeloid-specific Tgfbr2-deficiency resulted in reduced liver metastasis with an almost complete absence of myeloid cells within metastatic foci. On contrary, an accumulation of Tgfβ-responsive myeloid cells was associated with an increased recruitment of monocytes and granulocytes and higher proinflammatory cytokine levels in control mice. Monocytic cells isolated from metastatic livers of Tgfbr2-deficient mice showed increased polarization towards the M1 phenotype, Tnfα and Il-1β expression, reduced levels of M2 markers and reduced production of chemokines responsible for myeloid-cell recruitment. No significant differences in Tgfβ levels were observed at metastatic sites of any model. These data demonstrate that Tgfβ signaling in monocytic myeloid cells suppresses CD8+ T cell activity during lung metastasis, while these cells actively contribute to tumor growth during liver metastasis. Thus, myeloid cells modulate metastasis through different mechanisms in a tissue-specific manner. acknowledgement: The authors acknowledge the assistance of the Laboratory Animal Services Center (LASC) – UZH, Center for Microscopy and Image Analysis, and the Flow Cytometry Center of the University of Zurich. article_number: '765151' article_processing_charge: No article_type: original author: - first_name: Cristina full_name: Stefanescu, Cristina last_name: Stefanescu - first_name: Merel full_name: Van Gogh, Merel last_name: Van Gogh - first_name: Marko full_name: Roblek, Marko id: 3047D808-F248-11E8-B48F-1D18A9856A87 last_name: Roblek orcid: 0000-0001-9588-1389 - first_name: Mathias full_name: Heikenwalder, Mathias last_name: Heikenwalder - first_name: Lubor full_name: Borsig, Lubor last_name: Borsig citation: ama: Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 2021;11. doi:10.3389/fonc.2021.765151 apa: Stefanescu, C., Van Gogh, M., Roblek, M., Heikenwalder, M., & Borsig, L. (2021). TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. Frontiers. https://doi.org/10.3389/fonc.2021.765151 chicago: Stefanescu, Cristina, Merel Van Gogh, Marko Roblek, Mathias Heikenwalder, and Lubor Borsig. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” Frontiers in Oncology. Frontiers, 2021. https://doi.org/10.3389/fonc.2021.765151. ieee: C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, and L. Borsig, “TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms,” Frontiers in Oncology, vol. 11. Frontiers, 2021. ista: Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. 2021. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 11, 765151. mla: Stefanescu, Cristina, et al. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” Frontiers in Oncology, vol. 11, 765151, Frontiers, 2021, doi:10.3389/fonc.2021.765151. short: C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, L. Borsig, Frontiers in Oncology 11 (2021). date_created: 2021-12-12T23:01:27Z date_published: 2021-11-18T00:00:00Z date_updated: 2023-08-17T06:20:32Z day: '18' ddc: - '610' department: - _id: DaSi doi: 10.3389/fonc.2021.765151 external_id: isi: - '000726603400001' pmid: - '34868988' file: - access_level: open_access checksum: 56cbac80e6891ce750511a30161b7792 content_type: application/pdf creator: alisjak date_created: 2021-12-13T13:32:37Z date_updated: 2021-12-13T13:32:37Z file_id: '10539' file_name: 2021_Frontiers_Stefanescu.pdf file_size: 9245199 relation: main_file success: 1 file_date_updated: 2021-12-13T13:32:37Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Oncology publication_identifier: eissn: - 2234-943X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2021' ... --- _id: '10537' abstract: - lang: eng text: We consider the quantum many-body evolution of a homogeneous Fermi gas in three dimensions in the coupled semiclassical and mean-field scaling regime. We study a class of initial data describing collective particle–hole pair excitations on the Fermi ball. Using a rigorous version of approximate bosonization, we prove that the many-body evolution can be approximated in Fock space norm by a quasi-free bosonic evolution of the collective particle–hole excitations. acknowledgement: NB was supported by Gruppo Nazionale per la Fisica Matematica (GNFM). RS was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 694227). PTN was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC-2111-390814868). MP was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC StG MaMBoQ, Grant Agreement No. 802901). BS was supported by the NCCR SwissMAP, the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates,” and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program through the ERC-AdG CLaQS (Grant Agreement No. 834782). article_processing_charge: No article_type: original author: - first_name: Niels P full_name: Benedikter, Niels P id: 3DE6C32A-F248-11E8-B48F-1D18A9856A87 last_name: Benedikter orcid: 0000-0002-1071-6091 - first_name: Phan Thành full_name: Nam, Phan Thành last_name: Nam - first_name: Marcello full_name: Porta, Marcello last_name: Porta - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. 2021. doi:10.1007/s00023-021-01136-y apa: Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., & Seiringer, R. (2021). Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. Springer Nature. https://doi.org/10.1007/s00023-021-01136-y chicago: Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Bosonization of Fermionic Many-Body Dynamics.” Annales Henri Poincaré. Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01136-y. ieee: N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Bosonization of fermionic many-body dynamics,” Annales Henri Poincaré. Springer Nature, 2021. ista: Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2021. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. mla: Benedikter, Niels P., et al. “Bosonization of Fermionic Many-Body Dynamics.” Annales Henri Poincaré, Springer Nature, 2021, doi:10.1007/s00023-021-01136-y. short: N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Annales Henri Poincaré (2021). date_created: 2021-12-12T23:01:28Z date_published: 2021-12-02T00:00:00Z date_updated: 2023-08-17T06:19:14Z day: '02' department: - _id: RoSe doi: 10.1007/s00023-021-01136-y ec_funded: 1 external_id: arxiv: - '2103.08224' isi: - '000725405700001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2103.08224 month: '12' oa: 1 oa_version: Preprint project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Annales Henri Poincaré publication_identifier: issn: - 1424-0637 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Bosonization of fermionic many-body dynamics type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '10549' abstract: - lang: eng text: We derive optimal-order homogenization rates for random nonlinear elliptic PDEs with monotone nonlinearity in the uniformly elliptic case. More precisely, for a random monotone operator on \mathbb {R}^d with stationary law (that is spatially homogeneous statistics) and fast decay of correlations on scales larger than the microscale \varepsilon >0, we establish homogenization error estimates of the order \varepsilon in case d\geqq 3, and of the order \varepsilon |\log \varepsilon |^{1/2} in case d=2. Previous results in nonlinear stochastic homogenization have been limited to a small algebraic rate of convergence \varepsilon ^\delta . We also establish error estimates for the approximation of the homogenized operator by the method of representative volumes of the order (L/\varepsilon )^{-d/2} for a representative volume of size L. Our results also hold in the case of systems for which a (small-scale) C^{1,\alpha } regularity theory is available. acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). SN acknowledges partial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project number 405009441. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Stefan full_name: Neukamm, Stefan last_name: Neukamm citation: ama: Fischer JL, Neukamm S. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. 2021;242(1):343-452. doi:10.1007/s00205-021-01686-9 apa: Fischer, J. L., & Neukamm, S. (2021). Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01686-9 chicago: Fischer, Julian L, and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01686-9. ieee: J. L. Fischer and S. Neukamm, “Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems,” Archive for Rational Mechanics and Analysis, vol. 242, no. 1. Springer Nature, pp. 343–452, 2021. ista: Fischer JL, Neukamm S. 2021. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. 242(1), 343–452. mla: Fischer, Julian L., and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” Archive for Rational Mechanics and Analysis, vol. 242, no. 1, Springer Nature, 2021, pp. 343–452, doi:10.1007/s00205-021-01686-9. short: J.L. Fischer, S. Neukamm, Archive for Rational Mechanics and Analysis 242 (2021) 343–452. date_created: 2021-12-16T12:12:33Z date_published: 2021-06-30T00:00:00Z date_updated: 2023-08-17T06:23:21Z day: '30' ddc: - '530' department: - _id: JuFi doi: 10.1007/s00205-021-01686-9 external_id: arxiv: - '1908.02273' isi: - '000668431200001' file: - access_level: open_access checksum: cc830b739aed83ca2e32c4e0ce266a4c content_type: application/pdf creator: cchlebak date_created: 2021-12-16T14:58:08Z date_updated: 2021-12-16T14:58:08Z file_id: '10558' file_name: 2021_ArchRatMechAnalysis_Fischer.pdf file_size: 1640121 relation: main_file success: 1 file_date_updated: 2021-12-16T14:58:08Z has_accepted_license: '1' intvolume: ' 242' isi: 1 issue: '1' keyword: - Mechanical Engineering - Mathematics (miscellaneous) - Analysis language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 343-452 publication: Archive for Rational Mechanics and Analysis publication_identifier: eissn: - 1432-0673 issn: - 0003-9527 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems 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: 242 year: '2021' ... --- _id: '10409' abstract: - lang: eng text: We show that Yao’s garbling scheme is adaptively indistinguishable for the class of Boolean circuits of size S and treewidth w with only a SO(w) loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly O(δwlog(S)) , δ being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity. with only a SO(w) loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly O(δwlog(S)) , δ being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity. acknowledgement: We are grateful to Daniel Wichs for helpful discussions on the landscape of adaptive security of Yao’s garbling. We would also like to thank Crypto 2021 and TCC 2021 reviewers for their detailed review and suggestions, which helped improve presentation considerably. alternative_title: - LNCS article_processing_charge: No author: - first_name: Chethan full_name: Kamath Hosdurg, Chethan id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87 last_name: Kamath Hosdurg - first_name: Karen full_name: Klein, Karen id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87 last_name: Klein - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Kamath Hosdurg C, Klein K, Pietrzak KZ. On treewidth, separators and Yao’s garbling. In: 19th International Conference. Vol 13043. Springer Nature; 2021:486-517. doi:10.1007/978-3-030-90453-1_17' apa: 'Kamath Hosdurg, C., Klein, K., & Pietrzak, K. Z. (2021). On treewidth, separators and Yao’s garbling. In 19th International Conference (Vol. 13043, pp. 486–517). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_17' chicago: Kamath Hosdurg, Chethan, Karen Klein, and Krzysztof Z Pietrzak. “On Treewidth, Separators and Yao’s Garbling.” In 19th International Conference, 13043:486–517. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_17. ieee: C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “On treewidth, separators and Yao’s garbling,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 486–517. ista: 'Kamath Hosdurg C, Klein K, Pietrzak KZ. 2021. On treewidth, separators and Yao’s garbling. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13043, 486–517.' mla: Kamath Hosdurg, Chethan, et al. “On Treewidth, Separators and Yao’s Garbling.” 19th International Conference, vol. 13043, Springer Nature, 2021, pp. 486–517, doi:10.1007/978-3-030-90453-1_17. short: C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, 19th International Conference, Springer Nature, 2021, pp. 486–517. conference: end_date: 2021-11-11 location: Raleigh, NC, United States name: 'TCC: Theory of Cryptography' start_date: 2021-11-08 date_created: 2021-12-05T23:01:43Z date_published: 2021-11-04T00:00:00Z date_updated: 2023-08-17T06:21:38Z day: '04' department: - _id: KrPi doi: 10.1007/978-3-030-90453-1_17 ec_funded: 1 external_id: isi: - '000728364000017' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2021/926 month: '11' oa: 1 oa_version: Preprint page: 486-517 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: 19th International Conference publication_identifier: eissn: - 1611-3349 isbn: - 9-783-0309-0452-4 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '10044' relation: earlier_version status: public scopus_import: '1' status: public title: On treewidth, separators and Yao’s garbling type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: '13043 ' year: '2021' ... --- _id: '10545' abstract: - lang: eng text: Classical models with complex energy landscapes represent a perspective avenue for the near-term application of quantum simulators. Until now, many theoretical works studied the performance of quantum algorithms for models with a unique ground state. However, when the classical problem is in a so-called clustering phase, the ground state manifold is highly degenerate. As an example, we consider a 3-XORSAT model defined on simple hypergraphs. The degeneracy of classical ground state manifold translates into the emergence of an extensive number of Z2 symmetries, which remain intact even in the presence of a quantum transverse magnetic field. We establish a general duality approach that restricts the quantum problem to a given sector of conserved Z2 charges and use it to study how the outcome of the quantum adiabatic algorithm depends on the hypergraph geometry. We show that the tree hypergraph which corresponds to a classically solvable instance of the 3-XORSAT problem features a constant gap, whereas the closed hypergraph encounters a second-order phase transition with a gap vanishing as a power-law in the problem size. The duality developed in this work provides a practical tool for studies of quantum models with classically degenerate energy manifold and reveals potential connections between glasses and gauge theories. acknowledgement: We would like to thank S. De Nicola, A. Michaidilis, T. Gulden, Y. Nez-Fernndez, P. Brighi, and S. Sack for fruitful discussions and valuable feedback on the manuscript. M.S. acknowledges useful discussions with E. Altman, L. Cugliandolo, and C. Laumann. We acknowledge support from the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreement No. 850899. article_number: '062423' article_processing_charge: No article_type: original author: - first_name: Raimel A full_name: Medina Ramos, Raimel A id: CE680B90-D85A-11E9-B684-C920E6697425 last_name: Medina Ramos orcid: 0000-0002-5383-2869 - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Medina Ramos RA, Serbyn M. Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. 2021;104(6). doi:10.1103/physreva.104.062423 apa: Medina Ramos, R. A., & Serbyn, M. (2021). Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.104.062423 chicago: Medina Ramos, Raimel A, and Maksym Serbyn. “Duality Approach to Quantum Annealing of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/physreva.104.062423. ieee: R. A. Medina Ramos and M. Serbyn, “Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT),” Physical Review A, vol. 104, no. 6. American Physical Society, 2021. ista: Medina Ramos RA, Serbyn M. 2021. Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. 104(6), 062423. mla: Medina Ramos, Raimel A., and Maksym Serbyn. “Duality Approach to Quantum Annealing of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” Physical Review A, vol. 104, no. 6, 062423, American Physical Society, 2021, doi:10.1103/physreva.104.062423. short: R.A. Medina Ramos, M. Serbyn, Physical Review A 104 (2021). date_created: 2021-12-14T20:46:07Z date_published: 2021-12-14T00:00:00Z date_updated: 2023-08-17T06:22:49Z day: '14' department: - _id: MaSe doi: 10.1103/physreva.104.062423 ec_funded: 1 external_id: arxiv: - '2106.06344' isi: - '000753659200004' intvolume: ' 104' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2106.06344 month: '12' oa: 1 oa_version: Preprint project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: Physical Review A publication_identifier: eissn: - 2469-9934 issn: - 2469-9926 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 104 year: '2021' ... --- _id: '10554' abstract: - lang: eng text: 'We present DAG-Rider, the first asynchronous Byzantine Atomic Broadcast protocol that achieves optimal resilience, optimal amortized communication complexity, and optimal time complexity. DAG-Rider is post-quantum safe and ensures that all values proposed by correct processes eventually get delivered. We construct DAG-Rider in two layers: In the first layer, processes reliably broadcast their proposals and build a structured Directed Acyclic Graph (DAG) of the communication among them. In the second layer, processes locally observe their DAGs and totally order all proposals with no extra communication.' acknowledgement: "Oded Naor is grateful to the Technion Hiroshi Fujiwara Cyber-Security Research Center for providing a research grant. Part of Oded’s work was done while at Novi Research. This work was funded by the Novi team at Facebook. We also wish to thank the Novi Research team for valuable feedback, and in particular George Danezis, Alberto Sonnino, and Dahlia Malkhi.\r\n" article_processing_charge: No author: - first_name: Idit full_name: Keidar, Idit last_name: Keidar - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Oded full_name: Naor, Oded last_name: Naor - first_name: Alexander full_name: Spiegelman, Alexander last_name: Spiegelman citation: ama: 'Keidar I, Kokoris Kogias E, Naor O, Spiegelman A. All You Need is DAG. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:165-175. doi:10.1145/3465084.3467905' apa: 'Keidar, I., Kokoris Kogias, E., Naor, O., & Spiegelman, A. (2021). All You Need is DAG. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 165–175). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467905' chicago: Keidar, Idit, Eleftherios Kokoris Kogias, Oded Naor, and Alexander Spiegelman. “All You Need Is DAG.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 165–75. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467905. ieee: I. Keidar, E. Kokoris Kogias, O. Naor, and A. Spiegelman, “All You Need is DAG,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 165–175. ista: 'Keidar I, Kokoris Kogias E, Naor O, Spiegelman A. 2021. All You Need is DAG. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 165–175.' mla: Keidar, Idit, et al. “All You Need Is DAG.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 165–75, doi:10.1145/3465084.3467905. short: I. Keidar, E. Kokoris Kogias, O. Naor, A. Spiegelman, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 165–175. conference: end_date: 2021-07-30 location: Virtual, Italy name: 'PODC: Principles of Distributed Computing' start_date: 2021-07-26 date_created: 2021-12-16T13:21:13Z date_published: 2021-07-21T00:00:00Z date_updated: 2023-08-17T06:24:44Z day: '21' department: - _id: ElKo doi: 10.1145/3465084.3467905 external_id: arxiv: - '2102.08325' isi: - '000744439800016' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2102.08325 month: '07' oa: 1 oa_version: Preprint page: 165-175 publication: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing publication_identifier: isbn: - 978-1-4503-8548-0 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: All You Need is DAG type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '10568' abstract: - lang: eng text: Genetic adaptation and phenotypic plasticity facilitate the migration into new habitats and enable organisms to cope with a rapidly changing environment. In contrast to genetic adaptation that spans multiple generations as an evolutionary process, phenotypic plasticity allows acclimation within the life-time of an organism. Genetic adaptation and phenotypic plasticity are usually studied in isolation, however, only by including their interactive impact, we can understand acclimation and adaptation in nature. We aimed to explore the contribution of adaptation and plasticity in coping with an abiotic (salinity) and a biotic (Vibrio bacteria) stressor using six different populations of the broad-nosed pipefish Syngnathus typhle that originated from either high [14–17 Practical Salinity Unit (PSU)] or low (7–11 PSU) saline environments along the German coastline of the Baltic Sea. We exposed wild caught animals, to either high (15 PSU) or low (7 PSU) salinity, representing native and novel salinity conditions and allowed animals to mate. After male pregnancy, offspring was split and each half was exposed to one of the two salinities and infected with Vibrio alginolyticus bacteria that were evolved at either of the two salinities in a fully reciprocal design. We investigated life-history traits of fathers and expression of 47 target genes in mothers and offspring. Pregnant males originating from high salinity exposed to low salinity were highly susceptible to opportunistic fungi infections resulting in decreased offspring size and number. In contrast, no signs of fungal infection were identified in fathers originating from low saline conditions suggesting that genetic adaptation has the potential to overcome the challenges encountered at low salinity. Offspring from parents with low saline origin survived better at low salinity suggesting genetic adaptation to low salinity. In addition, gene expression analyses of juveniles indicated patterns of local adaptation, trans-generational plasticity and developmental plasticity. In conclusion, our study suggests that pipefish are locally adapted to the low salinity in their environment, however, they are retaining phenotypic plasticity, which allows them to also cope with ancestral salinity levels and prevailing pathogens. acknowledgement: We are grateful for the help of Kristina Dauven, Andreas Ebner, Janina Röckner, and Paulina Urban for fish collection in the field and fish maintenance. Furthermore, we thank Fabian Wendt for setting up the aquaria system and Tatjana Liese, Paulina Urban, Jakob Gismann, and Thorsten Reusch for support with DNA extraction and analysis of pipefish population structure. The authors acknowledge support of Isabel Tanger, Agnes Piecyk, Jonas Müller, Grace Walls, Sebastian Albrecht, Julia Böge, and Julia Stefanschitz for their support in preparing cDNA and running of Fluidigm chips. A special thank goes to Diana Gill for general lab support, ordering materials and just being the good spirit of our molecular lab, to Till Bayer for bioinformatics support and to Melanie Heckwolf for fruitful discussion and feedback on the manuscript. HG is very grateful for inspirational office space with ocean view provided by Lisa Hentschel and family. This manuscript has been released as a pre-print at BIORXIV. article_number: '626442' article_processing_charge: No article_type: original author: - first_name: Henry full_name: Goehlich, Henry last_name: Goehlich - first_name: Linda full_name: Sartoris, Linda id: 2B9284CA-F248-11E8-B48F-1D18A9856A87 last_name: Sartoris - first_name: Kim-Sara full_name: Wagner, Kim-Sara last_name: Wagner - first_name: Carolin C. full_name: Wendling, Carolin C. last_name: Wendling - first_name: Olivia full_name: Roth, Olivia last_name: Roth citation: ama: Goehlich H, Sartoris L, Wagner K-S, Wendling CC, Roth O. Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. Frontiers in Ecology and Evolution. 2021;9. doi:10.3389/fevo.2021.626442 apa: Goehlich, H., Sartoris, L., Wagner, K.-S., Wendling, C. C., & Roth, O. (2021). Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. Frontiers in Ecology and Evolution. Frontiers Media. https://doi.org/10.3389/fevo.2021.626442 chicago: Goehlich, Henry, Linda Sartoris, Kim-Sara Wagner, Carolin C. Wendling, and Olivia Roth. “Pipefish Locally Adapted to Low Salinity in the Baltic Sea Retain Phenotypic Plasticity to Cope with Ancestral Salinity Levels.” Frontiers in Ecology and Evolution. Frontiers Media, 2021. https://doi.org/10.3389/fevo.2021.626442. ieee: H. Goehlich, L. Sartoris, K.-S. Wagner, C. C. Wendling, and O. Roth, “Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels,” Frontiers in Ecology and Evolution, vol. 9. Frontiers Media, 2021. ista: Goehlich H, Sartoris L, Wagner K-S, Wendling CC, Roth O. 2021. Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. Frontiers in Ecology and Evolution. 9, 626442. mla: Goehlich, Henry, et al. “Pipefish Locally Adapted to Low Salinity in the Baltic Sea Retain Phenotypic Plasticity to Cope with Ancestral Salinity Levels.” Frontiers in Ecology and Evolution, vol. 9, 626442, Frontiers Media, 2021, doi:10.3389/fevo.2021.626442. short: H. Goehlich, L. Sartoris, K.-S. Wagner, C.C. Wendling, O. Roth, Frontiers in Ecology and Evolution 9 (2021). date_created: 2021-12-20T07:53:19Z date_published: 2021-03-25T00:00:00Z date_updated: 2023-08-17T06:27:22Z day: '25' ddc: - '597' department: - _id: SyCr doi: 10.3389/fevo.2021.626442 external_id: isi: - '000637736300001' file: - access_level: open_access checksum: 8d6e2b767bb0240a9b5a3a3555be51fd content_type: application/pdf creator: alisjak date_created: 2021-12-20T10:44:20Z date_updated: 2021-12-20T10:44:20Z file_id: '10572' file_name: 2021_Frontiers_Goehlich.pdf file_size: 3175085 relation: main_file success: 1 file_date_updated: 2021-12-20T10:44:20Z has_accepted_license: '1' intvolume: ' 9' isi: 1 keyword: - ecology - evolution - behavior and systematics - trans-generational plasticity - genetic adaptation - local adaptation - phenotypic plasticity - Baltic Sea - climate change - salinity - syngnathids language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Frontiers in Ecology and Evolution publication_identifier: issn: - 2296-701X publication_status: published publisher: Frontiers Media quality_controlled: '1' scopus_import: '1' status: public title: Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2021' ... --- _id: '10586' abstract: - lang: eng text: A facile approach for developing an interfacial solar evaporator by heat localization of solar-thermal energy conversion at water-air liquid composed by in-situ polymerization of Fe2O3 nanoparticles (Fe2O3@PPy) deposited over a facial sponge is proposed. The demonstrated system consists of a floating solar receiver having a vertically cross-linked microchannel for wicking up saline water. The in situ polymerized Fe2O3@PPy interfacial layer promotes diffuse reflection and its rough black surface allows Omni-directional solar absorption (94%) and facilitates efficient thermal localization at the water/air interface and offers a defect-rich surface to promote heat localization (41.9 °C) and excellent thermal management due to cellulosic content. The self-floating composite foam reveals continuous vapors generation at a rate of 1.52 kg m−2 h−1 under one 1 kW m−2 and profound evaporating efficiency (95%) without heat losses that dissipates in its surroundings. Indeed, long-term evaporation experiments reveal the negligible disparity in continuous evaporation rate (33.84 kg m−2/8.3 h) receiving two sun solar intensity, and ensures the stability of the device under intense seawater conditions synchronized with excellent salt rejection potential. More importantly, Raman spectroscopy investigation validates the orange dye rejection via Fe2O3@PPy solar evaporator. The combined advantages of high efficiency, self-floating capability, multimedia rejection, low cost, and this configuration are promising for producing large-scale solar steam generating systems appropriate for commercial clean water yield due to their scalable fabrication. acknowledgement: The authors extend their appreciation to King Saud University for funding this work through Researchers Supporting Project number (RSP-2021/387), King Saud University, Riyadh, Saudi Arabia. alternative_title: - Hybrid and Composite Crystalline Materials article_number: '1509' article_processing_charge: No article_type: original author: - first_name: Yuzheng full_name: Lu, Yuzheng last_name: Lu - first_name: Naila full_name: Arshad, Naila last_name: Arshad - first_name: Muhammad Sultan full_name: Irshad, Muhammad Sultan last_name: Irshad - first_name: Iftikhar full_name: Ahmed, Iftikhar last_name: Ahmed - first_name: Shafiq full_name: Ahmad, Shafiq last_name: Ahmad - first_name: Lina Abdullah full_name: Alshahrani, Lina Abdullah last_name: Alshahrani - first_name: Muhammad full_name: Yousaf, Muhammad last_name: Yousaf - first_name: Abdelaty Edrees full_name: Sayed, Abdelaty Edrees last_name: Sayed - first_name: Muhammad full_name: Nauman, Muhammad id: 32c21954-2022-11eb-9d5f-af9f93c24e71 last_name: Nauman orcid: 0000-0002-2111-4846 citation: ama: Lu Y, Arshad N, Irshad MS, et al. Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination. Crystals. 2021;11(12). doi:10.3390/cryst11121509 apa: Lu, Y., Arshad, N., Irshad, M. S., Ahmed, I., Ahmad, S., Alshahrani, L. A., … Nauman, M. (2021). Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination. Crystals. MDPI. https://doi.org/10.3390/cryst11121509 chicago: Lu, Yuzheng, Naila Arshad, Muhammad Sultan Irshad, Iftikhar Ahmed, Shafiq Ahmad, Lina Abdullah Alshahrani, Muhammad Yousaf, Abdelaty Edrees Sayed, and Muhammad Nauman. “Fe2O3 Nanoparticles Deposited over Self-Floating Facial Sponge for Facile Interfacial Seawater Solar Desalination.” Crystals. MDPI, 2021. https://doi.org/10.3390/cryst11121509. ieee: Y. Lu et al., “Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination,” Crystals, vol. 11, no. 12. MDPI, 2021. ista: Lu Y, Arshad N, Irshad MS, Ahmed I, Ahmad S, Alshahrani LA, Yousaf M, Sayed AE, Nauman M. 2021. Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination. Crystals. 11(12), 1509. mla: Lu, Yuzheng, et al. “Fe2O3 Nanoparticles Deposited over Self-Floating Facial Sponge for Facile Interfacial Seawater Solar Desalination.” Crystals, vol. 11, no. 12, 1509, MDPI, 2021, doi:10.3390/cryst11121509. short: Y. Lu, N. Arshad, M.S. Irshad, I. Ahmed, S. Ahmad, L.A. Alshahrani, M. Yousaf, A.E. Sayed, M. Nauman, Crystals 11 (2021). date_created: 2022-01-02T23:01:34Z date_published: 2021-12-03T00:00:00Z date_updated: 2023-08-17T06:31:20Z day: '03' ddc: - '620' department: - _id: KiMo doi: 10.3390/cryst11121509 external_id: isi: - '000736602200001' file: - access_level: open_access checksum: 668e9d777608ce0a3bc2e305133bd06b content_type: application/pdf creator: alisjak date_created: 2022-01-03T09:46:53Z date_updated: 2022-01-03T09:46:53Z file_id: '10591' file_name: 2021_Crystals_Yuzheng.pdf file_size: 4569639 relation: main_file success: 1 file_date_updated: 2022-01-03T09:46:53Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Crystals publication_identifier: eissn: - 2073-4352 publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination 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: '10569' abstract: - lang: eng text: 'For animals to survive until reproduction, it is crucial that juveniles successfully detect potential predators and respond with appropriate behavior. The recognition of cues originating from predators can be innate or learned. Cues of various modalities might be used alone or in multi-modal combinations to detect and distinguish predators but studies investigating multi-modal integration in predator avoidance are scarce. Here, we used wild, naive tadpoles of the Neotropical poison frog Allobates femoralis ( Boulenger, 1884) to test their reaction to cues with two modalities from two different sympatrically occurring potential predators: heterospecific predatory Dendrobates tinctorius tadpoles and dragonfly larvae. We presented A. femoralis tadpoles with olfactory or visual cues, or a combination of the two, and compared their reaction to a water control in a between-individual design. In our trials, A. femoralis tadpoles reacted to multi-modal stimuli (a combination of visual and chemical information) originating from dragonfly larvae with avoidance but showed no reaction to uni-modal cues or cues from heterospecific tadpoles. In addition, visual cues from conspecifics increased swimming activity while cues from predators had no effect on tadpole activity. Our results show that A. femoralis tadpoles can innately recognize some predators and probably need both visual and chemical information to effectively avoid them. This is the first study looking at anti-predator behavior in poison frog tadpoles. We discuss how parental care might influence the expression of predator avoidance responses in tadpoles.' acknowledgement: We are grateful to Véronique Helfer, Walter Hödl, Lisa Schretzmeyer and Julia Wotke, who assisted with fieldwork in French Guiana. This work was supported by the Austrian Science Fund (FWF) [P24788, T699 and P31518 to E.R.; P33728 to M.R.; J3827 to Thomas Bugnyar, Tecumseh Fitch and Ludwig Huber]; and by the Austrian Bundesministerium für Wissenschaft, Forschung und Wirtschaft [IS761001 to J.O. (Tecumseh Fitch, Thomas Bugnyar and Ludwig Huber)]. A.P. was supported by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 835530. S.A.R. was supported by the HT faculty, Lund University. We thank the CNRS Nouragues Ecological Research Station, which benefited from the ‘Investissement d'Avenir’ grants managed by the Agence Nationale de la Recherche (AnaEE France ANR-11-INBS-0001; Labex CEBA ANR-10-LABX-25-01). Open access funding provided by University of Vienna. Deposited in PMC for immediate release. article_number: jeb243647 article_processing_charge: No article_type: original author: - first_name: B full_name: Szabo, B last_name: Szabo - first_name: R full_name: Mangione, R last_name: Mangione - first_name: M full_name: Rath, M last_name: Rath - first_name: A full_name: Pašukonis, A last_name: Pašukonis - first_name: SA full_name: Reber, SA 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: M full_name: Ringler, M last_name: Ringler - first_name: E full_name: Ringler, E last_name: Ringler citation: ama: Szabo B, Mangione R, Rath M, et al. Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles. Journal of Experimental Biology. 2021;224(24). doi:10.1242/jeb.243647 apa: Szabo, B., Mangione, R., Rath, M., Pašukonis, A., Reber, S., Oh, J., … Ringler, E. (2021). Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles. Journal of Experimental Biology. The Company of Biologists. https://doi.org/10.1242/jeb.243647 chicago: Szabo, B, R Mangione, M Rath, A Pašukonis, SA Reber, Jinook Oh, M Ringler, and E Ringler. “Naïve Poison Frog Tadpoles Use Bi-Modal Cues to Avoid Insect Predators but Not Heterospecific Predatory Tadpoles.” Journal of Experimental Biology. The Company of Biologists, 2021. https://doi.org/10.1242/jeb.243647. ieee: B. Szabo et al., “Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles,” Journal of Experimental Biology, vol. 224, no. 24. The Company of Biologists, 2021. ista: Szabo B, Mangione R, Rath M, Pašukonis A, Reber S, Oh J, Ringler M, Ringler E. 2021. Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles. Journal of Experimental Biology. 224(24), jeb243647. mla: Szabo, B., et al. “Naïve Poison Frog Tadpoles Use Bi-Modal Cues to Avoid Insect Predators but Not Heterospecific Predatory Tadpoles.” Journal of Experimental Biology, vol. 224, no. 24, jeb243647, The Company of Biologists, 2021, doi:10.1242/jeb.243647. short: B. Szabo, R. Mangione, M. Rath, A. Pašukonis, S. Reber, J. Oh, M. Ringler, E. Ringler, Journal of Experimental Biology 224 (2021). date_created: 2021-12-20T07:54:22Z date_published: 2021-12-16T00:00:00Z date_updated: 2023-08-17T06:26:15Z day: '16' ddc: - '573' department: - _id: SyCr doi: 10.1242/jeb.243647 external_id: isi: - '000738259300013' pmid: - '34845497' file: - access_level: open_access checksum: 75d13a5ec8e3b90e3bc02bd8a9c17eef content_type: application/pdf creator: cchlebak date_created: 2021-12-20T10:14:14Z date_updated: 2021-12-20T10:14:14Z file_id: '10571' file_name: 2021_JExpBio_Szabo.pdf file_size: 607096 relation: main_file success: 1 file_date_updated: 2021-12-20T10:14:14Z has_accepted_license: '1' intvolume: ' 224' isi: 1 issue: '24' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: Journal of Experimental Biology publication_identifier: eissn: - 1477-9145 issn: - 0022-0949 publication_status: published publisher: The Company of Biologists quality_controlled: '1' status: public title: Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles 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: 224 year: '2021' ... --- _id: '10575' abstract: - lang: eng text: The choice of the boundary conditions in mechanical problems has to reflect the interaction of the considered material with the surface. Still the assumption of the no-slip condition is preferred in order to avoid boundary terms in the analysis and slipping effects are usually overlooked. Besides the “static slip models”, there are phenomena that are not accurately described by them, e.g. at the moment when the slip changes rapidly, the wall shear stress and the slip can exhibit a sudden overshoot and subsequent relaxation. When these effects become significant, the so-called dynamic slip phenomenon occurs. We develop a mathematical analysis of Navier–Stokes-like problems with a dynamic slip boundary condition, which requires a proper generalization of the Gelfand triplet and the corresponding function space setting. acknowledgement: The research of A. Abbatiello is supported by Einstein Foundation, Berlin. A. Abbatiello is also member of the Italian National Group for the Mathematical Physics (GNFM) of INdAM. M. Bulíček acknowledges the support of the project No. 20-11027X financed by Czech Science Foundation (GACR). M. Bulíček is member of the Jindřich Nečas Center for Mathematical Modelling. E. Maringová acknowledges support from Charles University Research program UNCE/SCI/023, the grant SVV-2020-260583 by the Ministry of Education, Youth and Sports, Czech Republic and from the Austrian Science Fund (FWF), grants P30000, W1245, and F65. article_processing_charge: No article_type: original author: - first_name: Anna full_name: Abbatiello, Anna last_name: Abbatiello - first_name: Miroslav full_name: Bulíček, Miroslav last_name: Bulíček - first_name: Erika full_name: Maringová, Erika id: dbabca31-66eb-11eb-963a-fb9c22c880b4 last_name: Maringová citation: ama: Abbatiello A, Bulíček M, Maringová E. On the dynamic slip boundary condition for Navier-Stokes-like problems. Mathematical Models and Methods in Applied Sciences. 2021;31(11):2165-2212. doi:10.1142/S0218202521500470 apa: Abbatiello, A., Bulíček, M., & Maringová, E. (2021). On the dynamic slip boundary condition for Navier-Stokes-like problems. Mathematical Models and Methods in Applied Sciences. World Scientific Publishing. https://doi.org/10.1142/S0218202521500470 chicago: Abbatiello, Anna, Miroslav Bulíček, and Erika Maringová. “On the Dynamic Slip Boundary Condition for Navier-Stokes-like Problems.” Mathematical Models and Methods in Applied Sciences. World Scientific Publishing, 2021. https://doi.org/10.1142/S0218202521500470. ieee: A. Abbatiello, M. Bulíček, and E. Maringová, “On the dynamic slip boundary condition for Navier-Stokes-like problems,” Mathematical Models and Methods in Applied Sciences, vol. 31, no. 11. World Scientific Publishing, pp. 2165–2212, 2021. ista: Abbatiello A, Bulíček M, Maringová E. 2021. On the dynamic slip boundary condition for Navier-Stokes-like problems. Mathematical Models and Methods in Applied Sciences. 31(11), 2165–2212. mla: Abbatiello, Anna, et al. “On the Dynamic Slip Boundary Condition for Navier-Stokes-like Problems.” Mathematical Models and Methods in Applied Sciences, vol. 31, no. 11, World Scientific Publishing, 2021, pp. 2165–212, doi:10.1142/S0218202521500470. short: A. Abbatiello, M. Bulíček, E. Maringová, Mathematical Models and Methods in Applied Sciences 31 (2021) 2165–2212. date_created: 2021-12-26T23:01:27Z date_published: 2021-10-13T00:00:00Z date_updated: 2023-08-17T06:29:01Z day: '13' ddc: - '510' department: - _id: JuFi doi: 10.1142/S0218202521500470 external_id: arxiv: - '2009.09057' isi: - '000722309400001' file: - access_level: open_access checksum: 8c0a9396335f0b70e1f5cbfe450a987a content_type: application/pdf creator: dernst date_created: 2022-05-16T10:55:45Z date_updated: 2022-05-16T10:55:45Z file_id: '11385' file_name: 2021_MathModelsMethods_Abbatiello.pdf file_size: 795483 relation: main_file success: 1 file_date_updated: 2022-05-16T10:55:45Z has_accepted_license: '1' intvolume: ' 31' isi: 1 issue: '11' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 2165-2212 project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems - _id: 260788DE-B435-11E9-9278-68D0E5697425 call_identifier: FWF name: Dissipation and Dispersion in Nonlinear Partial Differential Equations publication: Mathematical Models and Methods in Applied Sciences publication_identifier: eissn: - 1793-6314 issn: - 0218-2025 publication_status: published publisher: World Scientific Publishing quality_controlled: '1' scopus_import: '1' status: public title: On the dynamic slip boundary condition for Navier-Stokes-like problems tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 31 year: '2021' ... --- _id: '10574' abstract: - lang: eng text: 'The understanding of material appearance perception is a complex problem due to interactions between material reflectance, surface geometry, and illumination. Recently, Serrano et al. collected the largest dataset to date with subjective ratings of material appearance attributes, including glossiness, metallicness, sharpness and contrast of reflections. In this work, we make use of their dataset to investigate for the first time the impact of the interactions between illumination, geometry, and eight different material categories in perceived appearance attributes. After an initial analysis, we select for further analysis the four material categories that cover the largest range for all perceptual attributes: fabric, plastic, ceramic, and metal. Using a cumulative link mixed model (CLMM) for robust regression, we discover interactions between these material categories and four representative illuminations and object geometries. We believe that our findings contribute to expanding the knowledge on material appearance perception and can be useful for many applications, such as scene design, where any particular material in a given shape can be aligned with dominant classes of illumination, so that a desired strength of appearance attributes can be achieved.' acknowledgement: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie, grant agreement N∘ 765911 (RealVision) and from the European Research Council (ERC), grant agreement N∘ 804226 (PERDY). Open Access funding enabled and organized by Projekt DEAL. article_processing_charge: Yes article_type: original author: - first_name: Bin full_name: Chen, Bin last_name: Chen - first_name: Chao full_name: Wang, Chao last_name: Wang - first_name: Michael full_name: Piovarci, Michael id: 62E473F4-5C99-11EA-A40E-AF823DDC885E last_name: Piovarci orcid: 0000-0002-5062-4474 - first_name: Hans Peter full_name: Seidel, Hans Peter last_name: Seidel - first_name: Piotr full_name: Didyk, Piotr last_name: Didyk - first_name: Karol full_name: Myszkowski, Karol last_name: Myszkowski - first_name: Ana full_name: Serrano, Ana last_name: Serrano citation: ama: Chen B, Wang C, Piovarci M, et al. The effect of geometry and illumination on appearance perception of different material categories. Visual Computer. 2021;37(12):2975-2987. doi:10.1007/s00371-021-02227-x apa: Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., Myszkowski, K., & Serrano, A. (2021). The effect of geometry and illumination on appearance perception of different material categories. Visual Computer. Springer Nature. https://doi.org/10.1007/s00371-021-02227-x chicago: Chen, Bin, Chao Wang, Michael Piovarci, Hans Peter Seidel, Piotr Didyk, Karol Myszkowski, and Ana Serrano. “The Effect of Geometry and Illumination on Appearance Perception of Different Material Categories.” Visual Computer. Springer Nature, 2021. https://doi.org/10.1007/s00371-021-02227-x. ieee: B. Chen et al., “The effect of geometry and illumination on appearance perception of different material categories,” Visual Computer, vol. 37, no. 12. Springer Nature, pp. 2975–2987, 2021. ista: Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K, Serrano A. 2021. The effect of geometry and illumination on appearance perception of different material categories. Visual Computer. 37(12), 2975–2987. mla: Chen, Bin, et al. “The Effect of Geometry and Illumination on Appearance Perception of Different Material Categories.” Visual Computer, vol. 37, no. 12, Springer Nature, 2021, pp. 2975–87, doi:10.1007/s00371-021-02227-x. short: B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, A. Serrano, Visual Computer 37 (2021) 2975–2987. date_created: 2021-12-26T23:01:26Z date_published: 2021-12-01T00:00:00Z date_updated: 2023-08-17T06:29:34Z day: '01' ddc: - '000' department: - _id: BeBi doi: 10.1007/s00371-021-02227-x external_id: isi: - '000673536600003' file: - access_level: open_access checksum: 244cfcac0479ca6e3444c098ab2860a1 content_type: application/pdf creator: cchlebak date_created: 2021-12-27T13:51:08Z date_updated: 2021-12-27T13:51:08Z file_id: '10578' file_name: 2021_VisComput_Chen.pdf file_size: 5741094 relation: main_file success: 1 file_date_updated: 2021-12-27T13:51:08Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 2975-2987 publication: Visual Computer publication_identifier: eissn: - 1432-2315 issn: - 0178-2789 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The effect of geometry and illumination on appearance perception of different material categories 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: 37 year: '2021' ... --- _id: '10573' abstract: - lang: eng text: How tissues acquire complex shapes is a fundamental question in biology and regenerative medicine. Zebrafish semicircular canals form from invaginations in the otic epithelium (buds) that extend and fuse to form the hubs of each canal. We find that conventional actomyosin-driven behaviors are not required. Instead, local secretion of hyaluronan, made by the enzymes uridine 5′-diphosphate dehydrogenase (ugdh) and hyaluronan synthase 3 (has3), drives canal morphogenesis. Charged hyaluronate polymers osmotically swell with water and generate isotropic extracellular pressure to deform the overlying epithelium into buds. The mechanical anisotropy needed to shape buds into tubes is conferred by a polarized distribution of actomyosin and E-cadherin-rich membrane tethers, which we term cytocinches. Most work on tissue morphogenesis ascribes actomyosin contractility as the driving force, while the extracellular matrix shapes tissues through differential stiffness. Our work inverts this expectation. Hyaluronate pressure shaped by anisotropic tissue stiffness may be a widespread mechanism for powering morphological change in organogenesis and tissue engineering. acknowledgement: We thank Ian Swinburne, Sandy Nandagopal, and Toru Kawanishi for support, discussions, and reagents. We thank Vanessa Barone, Joseph Nasser, and members of the Megason lab for useful comments on the manuscript and general feedback. We are grateful to the Heisenberg and Knaut labs for transgenic fish. Diagrams on the right in the graphical abstract were created using BioRender. This work was supported by NIH R01DC015478 and NIH R01GM107733 to S.G.M. A.M. was supported by Human Frontiers Science Program LTF and NIH K99HD098918. article_processing_charge: No article_type: original author: - first_name: Akankshi full_name: Munjal, Akankshi last_name: Munjal - 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: Tony Y.C. full_name: Tsai, Tony Y.C. last_name: Tsai - first_name: Timothy J. full_name: Mitchison, Timothy J. last_name: Mitchison - first_name: Sean G. full_name: Megason, Sean G. last_name: Megason citation: ama: Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. 2021;184(26):6313-6325.e18. doi:10.1016/j.cell.2021.11.025 apa: Munjal, A., Hannezo, E. B., Tsai, T. Y. C., Mitchison, T. J., & Megason, S. G. (2021). Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. Elsevier ; Cell Press. https://doi.org/10.1016/j.cell.2021.11.025 chicago: Munjal, Akankshi, Edouard B Hannezo, Tony Y.C. Tsai, Timothy J. Mitchison, and Sean G. Megason. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” Cell. Elsevier ; Cell Press, 2021. https://doi.org/10.1016/j.cell.2021.11.025. ieee: A. Munjal, E. B. Hannezo, T. Y. C. Tsai, T. J. Mitchison, and S. G. Megason, “Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis,” Cell, vol. 184, no. 26. Elsevier ; Cell Press, p. 6313–6325.e18, 2021. ista: Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. 2021. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. 184(26), 6313–6325.e18. mla: Munjal, Akankshi, et al. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” Cell, vol. 184, no. 26, Elsevier ; Cell Press, 2021, p. 6313–6325.e18, doi:10.1016/j.cell.2021.11.025. short: A. Munjal, E.B. Hannezo, T.Y.C. Tsai, T.J. Mitchison, S.G. Megason, Cell 184 (2021) 6313–6325.e18. date_created: 2021-12-26T23:01:26Z date_published: 2021-12-22T00:00:00Z date_updated: 2023-08-17T06:28:25Z day: '22' department: - _id: EdHa doi: 10.1016/j.cell.2021.11.025 external_id: isi: - '000735387500002' intvolume: ' 184' isi: 1 issue: '26' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.09.28.316042 month: '12' oa: 1 oa_version: Preprint page: 6313-6325.e18 publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier ; Cell Press quality_controlled: '1' scopus_import: '1' status: public title: Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 184 year: '2021' ... --- _id: '10674' abstract: - lang: eng text: 'In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner of the game. Such games are central in formal methods since they model the interaction between a non-terminating system and its environment. In bidding games the players bid for the right to move the token: in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Bidding games are known to have a clean and elegant mathematical structure that relies on the ability of the players to submit arbitrarily small bids. Many applications, however, require a fixed granularity for the bids, which can represent, for example, the monetary value expressed in cents. We study, for the first time, the combination of discrete-bidding and infinite-duration games. Our most important result proves that these games form a large determined subclass of concurrent games, where determinacy is the strong property that there always exists exactly one player who can guarantee winning the game. In particular, we show that, in contrast to non-discrete bidding games, the mechanism with which tied bids are resolved plays an important role in discrete-bidding games. We study several natural tie-breaking mechanisms and show that, while some do not admit determinacy, most natural mechanisms imply determinacy for every pair of initial budgets.' acknowledgement: "This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE), Z211-N23 (Wittgenstein Award), and M 2369-N33 (Meitner fellowship).\r\n" article_processing_charge: No article_type: original author: - first_name: Milad full_name: Aghajohari, Milad last_name: Aghajohari - 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 citation: ama: Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. 2021;17(1):10:1-10:23. doi:10.23638/LMCS-17(1:10)2021 apa: Aghajohari, M., Avni, G., & Henzinger, T. A. (2021). Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. International Federation for Computational Logic. https://doi.org/10.23638/LMCS-17(1:10)2021 chicago: Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding Infinite-Duration Games.” Logical Methods in Computer Science. International Federation for Computational Logic, 2021. https://doi.org/10.23638/LMCS-17(1:10)2021. ieee: M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding infinite-duration games,” Logical Methods in Computer Science, vol. 17, no. 1. International Federation for Computational Logic, p. 10:1-10:23, 2021. ista: Aghajohari M, Avni G, Henzinger TA. 2021. Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. 17(1), 10:1-10:23. mla: Aghajohari, Milad, et al. “Determinacy in Discrete-Bidding Infinite-Duration Games.” Logical Methods in Computer Science, vol. 17, no. 1, International Federation for Computational Logic, 2021, p. 10:1-10:23, doi:10.23638/LMCS-17(1:10)2021. short: M. Aghajohari, G. Avni, T.A. Henzinger, Logical Methods in Computer Science 17 (2021) 10:1-10:23. date_created: 2022-01-25T16:32:13Z date_published: 2021-02-03T00:00:00Z date_updated: 2023-08-17T06:56:42Z day: '03' ddc: - '510' department: - _id: ToHe doi: 10.23638/LMCS-17(1:10)2021 external_id: arxiv: - '1905.03588' isi: - '000658724600010' file: - access_level: open_access checksum: b35586a50ed1ca8f44767de116d18d81 content_type: application/pdf creator: alisjak date_created: 2022-01-26T08:04:50Z date_updated: 2022-01-26T08:04:50Z file_id: '10690' file_name: 2021_LMCS_AGHAJOHAR.pdf file_size: 819878 relation: main_file success: 1 file_date_updated: 2022-01-26T08:04:50Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '1' keyword: - computer science - computer science and game theory - logic in computer science language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 10:1-10:23 project: - _id: 264B3912-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02369 name: Formal Methods meets Algorithmic Game Theory - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Logical Methods in Computer Science publication_identifier: eissn: - 1860-5974 publication_status: published publisher: International Federation for Computational Logic quality_controlled: '1' scopus_import: '1' status: public title: Determinacy in discrete-bidding infinite-duration games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2021' ... --- _id: '10609' abstract: - lang: eng text: "We study Multi-party computation (MPC) in the setting of subversion, where the adversary tampers with the machines of honest parties. Our goal is to construct actively secure MPC protocols where parties are corrupted adaptively by an adversary (as in the standard adaptive security setting), and in addition, honest parties’ machines are compromised.\r\nThe idea of reverse firewalls (RF) was introduced at EUROCRYPT’15 by Mironov and Stephens-Davidowitz as an approach to protecting protocols against corruption of honest parties’ devices. Intuitively, an RF for a party P is an external entity that sits between P and the outside world and whose scope is to sanitize P ’s incoming and outgoing messages in the face of subversion of their computer. Mironov and Stephens-Davidowitz constructed a protocol for passively-secure two-party computation. At CRYPTO’20, Chakraborty, Dziembowski and Nielsen constructed a protocol for secure computation with firewalls that improved on this result, both by extending it to multi-party computation protocol, and considering active security in the presence of static corruptions. In this paper, we initiate the study of RF for MPC in the adaptive setting. We put forward a definition for adaptively secure MPC in the reverse firewall setting, explore relationships among the security notions, and then construct reverse firewalls for MPC in this stronger setting of adaptive security. We also resolve the open question of Chakraborty, Dziembowski and Nielsen by removing the need for a trusted setup in constructing RF for MPC. Towards this end, we construct reverse firewalls for adaptively secure augmented coin tossing and adaptively secure zero-knowledge protocols and obtain a constant round adaptively secure MPC protocol in the reverse firewall setting without setup. Along the way, we propose a new multi-party adaptively secure coin tossing protocol in the plain model, that is of independent interest." alternative_title: - LNCS article_processing_charge: No author: - first_name: Suvradip full_name: Chakraborty, Suvradip id: B9CD0494-D033-11E9-B219-A439E6697425 last_name: Chakraborty - first_name: Chaya full_name: Ganesh, Chaya last_name: Ganesh - first_name: Mahak full_name: Pancholi, Mahak last_name: Pancholi - first_name: Pratik full_name: Sarkar, Pratik last_name: Sarkar citation: ama: 'Chakraborty S, Ganesh C, Pancholi M, Sarkar P. Reverse firewalls for adaptively secure MPC without setup. In: 27th International Conference on the Theory and Application of Cryptology and Information Security. Vol 13091. Springer Nature; 2021:335-364. doi:10.1007/978-3-030-92075-3_12' apa: 'Chakraborty, S., Ganesh, C., Pancholi, M., & Sarkar, P. (2021). Reverse firewalls for adaptively secure MPC without setup. In 27th International Conference on the Theory and Application of Cryptology and Information Security (Vol. 13091, pp. 335–364). Virtual, Singapore: Springer Nature. https://doi.org/10.1007/978-3-030-92075-3_12' chicago: Chakraborty, Suvradip, Chaya Ganesh, Mahak Pancholi, and Pratik Sarkar. “Reverse Firewalls for Adaptively Secure MPC without Setup.” In 27th International Conference on the Theory and Application of Cryptology and Information Security, 13091:335–64. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-92075-3_12. ieee: S. Chakraborty, C. Ganesh, M. Pancholi, and P. Sarkar, “Reverse firewalls for adaptively secure MPC without setup,” in 27th International Conference on the Theory and Application of Cryptology and Information Security, Virtual, Singapore, 2021, vol. 13091, pp. 335–364. ista: 'Chakraborty S, Ganesh C, Pancholi M, Sarkar P. 2021. Reverse firewalls for adaptively secure MPC without setup. 27th International Conference on the Theory and Application of Cryptology and Information Security. ASIACRYPT: International Conference on Cryptology in Asia, LNCS, vol. 13091, 335–364.' mla: Chakraborty, Suvradip, et al. “Reverse Firewalls for Adaptively Secure MPC without Setup.” 27th International Conference on the Theory and Application of Cryptology and Information Security, vol. 13091, Springer Nature, 2021, pp. 335–64, doi:10.1007/978-3-030-92075-3_12. short: S. Chakraborty, C. Ganesh, M. Pancholi, P. Sarkar, in:, 27th International Conference on the Theory and Application of Cryptology and Information Security, Springer Nature, 2021, pp. 335–364. conference: end_date: 2021-12-10 location: Virtual, Singapore name: 'ASIACRYPT: International Conference on Cryptology in Asia' start_date: 2021-12-06 date_created: 2022-01-09T23:01:27Z date_published: 2021-12-01T00:00:00Z date_updated: 2023-08-17T06:34:41Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-030-92075-3_12 ec_funded: 1 external_id: isi: - '000927876200012' intvolume: ' 13091' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2021/1262 month: '12' oa: 1 oa_version: Preprint page: 335-364 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: 27th International Conference on the Theory and Application of Cryptology and Information Security publication_identifier: eisbn: - 978-3-030-92075-3 eissn: - 1611-3349 isbn: - 978-3-030-92074-6 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Reverse firewalls for adaptively secure MPC without setup type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13091 year: '2021' ... --- _id: '10606' abstract: - lang: eng text: Cell division orientation is thought to result from a competition between cell geometry and polarity domains controlling the position of the mitotic spindle during mitosis. Depending on the level of cell shape anisotropy or the strength of the polarity domain, one dominates the other and determines the orientation of the spindle. Whether and how such competition is also at work to determine unequal cell division (UCD), producing daughter cells of different size, remains unclear. Here, we show that cell geometry and polarity domains cooperate, rather than compete, in positioning the cleavage plane during UCDs in early ascidian embryos. We found that the UCDs and their orientation at the ascidian third cleavage rely on the spindle tilting in an anisotropic cell shape, and cortical polarity domains exerting different effects on spindle astral microtubules. By systematically varying mitotic cell shape, we could modulate the effect of attractive and repulsive polarity domains and consequently generate predicted daughter cell size asymmetries and position. We therefore propose that the spindle position during UCD is set by the combined activities of cell geometry and polarity domains, where cell geometry modulates the effect of cortical polarity domain(s). acknowledged_ssus: - _id: NanoFab - _id: Bio acknowledgement: 'We thank members of the Heisenberg and McDougall groups for technical advice and discussion. We are grateful to the Bioimaging and Nanofabrication facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB) of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-0, for continuous support. This work was supported by a collaborative grant from the French Government funding agency Agence National de la Recherche to McDougall (ANR ''MorCell'': ANR-17-CE 13-0028) and the Austrian Science Fund to Heisenberg (FWF: I 3601-B27).' article_number: e75639 article_processing_charge: No article_type: original author: - first_name: Benoit G full_name: Godard, Benoit G id: 33280250-F248-11E8-B48F-1D18A9856A87 last_name: Godard - first_name: Remi full_name: Dumollard, Remi last_name: Dumollard - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Alex full_name: Mcdougall, Alex last_name: Mcdougall citation: ama: Godard BG, Dumollard R, Heisenberg C-PJ, Mcdougall A. Combined effect of cell geometry and polarity domains determines the orientation of unequal division. eLife. 2021;10. doi:10.7554/eLife.75639 apa: Godard, B. G., Dumollard, R., Heisenberg, C.-P. J., & Mcdougall, A. (2021). Combined effect of cell geometry and polarity domains determines the orientation of unequal division. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.75639 chicago: Godard, Benoit G, Remi Dumollard, Carl-Philipp J Heisenberg, and Alex Mcdougall. “Combined Effect of Cell Geometry and Polarity Domains Determines the Orientation of Unequal Division.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.75639. ieee: B. G. Godard, R. Dumollard, C.-P. J. Heisenberg, and A. Mcdougall, “Combined effect of cell geometry and polarity domains determines the orientation of unequal division,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Godard BG, Dumollard R, Heisenberg C-PJ, Mcdougall A. 2021. Combined effect of cell geometry and polarity domains determines the orientation of unequal division. eLife. 10, e75639. mla: Godard, Benoit G., et al. “Combined Effect of Cell Geometry and Polarity Domains Determines the Orientation of Unequal Division.” ELife, vol. 10, e75639, eLife Sciences Publications, 2021, doi:10.7554/eLife.75639. short: B.G. Godard, R. Dumollard, C.-P.J. Heisenberg, A. Mcdougall, ELife 10 (2021). date_created: 2022-01-09T23:01:26Z date_published: 2021-12-21T00:00:00Z date_updated: 2023-08-17T06:32:44Z day: '21' ddc: - '570' department: - _id: CaHe doi: 10.7554/eLife.75639 external_id: isi: - '000733610100001' file: - access_level: open_access checksum: 759c7a873d554c48a6639e6350746ca6 content_type: application/pdf creator: alisjak date_created: 2022-01-10T09:40:37Z date_updated: 2022-01-10T09:40:37Z file_id: '10611' file_name: 2021_eLife_Godard.pdf file_size: 7769934 relation: main_file success: 1 file_date_updated: 2022-01-10T09:40:37Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 2646861A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03601 name: Control of embryonic cleavage pattern publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Combined effect of cell geometry and polarity domains determines the orientation of unequal division 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: '10607' abstract: - lang: eng text: The evidence linking innate immunity mechanisms and neurodegenerative diseases is growing, but the specific mechanisms are incompletely understood. Experimental data suggest that microglial TLR4 mediates the uptake and clearance of α-synuclein also termed synucleinophagy. The accumulation of misfolded α-synuclein throughout the brain is central to Parkinson's disease (PD). The distribution and progression of the pathology is often attributed to the propagation of α-synuclein. Here, we apply a classical α-synuclein propagation model of prodromal PD in wild type and TLR4 deficient mice to study the role of TLR4 in the progression of the disease. Our data suggest that TLR4 deficiency facilitates the α-synuclein seed spreading associated with reduced lysosomal activity of microglia. Three months after seed inoculation, more pronounced proteinase K-resistant α-synuclein inclusion pathology is observed in mice with TLR4 deficiency. The facilitated propagation of α-synuclein is associated with early loss of dopamine transporter (DAT) signal in the striatum and loss of dopaminergic neurons in substantia nigra pars compacta of TLR4 deficient mice. These new results support TLR4 signaling as a putative target for disease modification to slow the progression of PD and related disorders. acknowledgement: This study was supported by grants of the Austrian Science Fund (FWF) F4414 and W1206-08. Electron microscopy was performed at the Scientific Service Units (SSU) of IST-Austria through resources provided by the Electron Microscopy Facility. article_processing_charge: No article_type: original author: - first_name: Serena full_name: Venezia, Serena last_name: Venezia - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Gregor K. full_name: Wenning, Gregor K. last_name: Wenning - first_name: Nadia full_name: Stefanova, Nadia last_name: Stefanova citation: ama: Venezia S, Kaufmann W, Wenning GK, Stefanova N. Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism & Related Disorders. 2021;91:59-65. doi:10.1016/j.parkreldis.2021.09.007 apa: Venezia, S., Kaufmann, W., Wenning, G. K., & Stefanova, N. (2021). Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism & Related Disorders. Elsevier. https://doi.org/10.1016/j.parkreldis.2021.09.007 chicago: Venezia, Serena, Walter Kaufmann, Gregor K. Wenning, and Nadia Stefanova. “Toll-like Receptor 4 Deficiency Facilitates α-Synuclein Propagation and Neurodegeneration in a Mouse Model of Prodromal Parkinson’s Disease.” Parkinsonism & Related Disorders. Elsevier, 2021. https://doi.org/10.1016/j.parkreldis.2021.09.007. ieee: S. Venezia, W. Kaufmann, G. K. Wenning, and N. Stefanova, “Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease,” Parkinsonism & Related Disorders, vol. 91. Elsevier, pp. 59–65, 2021. ista: Venezia S, Kaufmann W, Wenning GK, Stefanova N. 2021. Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism & Related Disorders. 91, 59–65. mla: Venezia, Serena, et al. “Toll-like Receptor 4 Deficiency Facilitates α-Synuclein Propagation and Neurodegeneration in a Mouse Model of Prodromal Parkinson’s Disease.” Parkinsonism & Related Disorders, vol. 91, Elsevier, 2021, pp. 59–65, doi:10.1016/j.parkreldis.2021.09.007. short: S. Venezia, W. Kaufmann, G.K. Wenning, N. Stefanova, Parkinsonism & Related Disorders 91 (2021) 59–65. date_created: 2022-01-09T23:01:26Z date_published: 2021-10-01T00:00:00Z date_updated: 2023-08-17T06:36:01Z day: '01' ddc: - '610' department: - _id: EM-Fac doi: 10.1016/j.parkreldis.2021.09.007 external_id: isi: - '000701142900012' pmid: - '34530328' file: - access_level: open_access checksum: 360681585acb51e80d17c6b213c56b55 content_type: application/pdf creator: alisjak date_created: 2022-01-10T13:41:40Z date_updated: 2022-01-10T13:41:40Z file_id: '10612' file_name: 2021_Parkinsonism_Venezia.pdf file_size: 6848513 relation: main_file success: 1 file_date_updated: 2022-01-10T13:41:40Z has_accepted_license: '1' intvolume: ' 91' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 59-65 pmid: 1 publication: Parkinsonism & Related Disorders publication_identifier: eissn: - 1873-5126 issn: - 1353-8020 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson's disease tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 91 year: '2021' ... --- _id: '10628' abstract: - lang: eng text: The surface states of 3D topological insulators in general have negligible quantum oscillations (QOs) when the chemical potential is tuned to the Dirac points. In contrast, we find that topological Kondo insulators (TKIs) can support surface states with an arbitrarily large Fermi surface (FS) when the chemical potential is pinned to the Dirac point. We illustrate that these FSs give rise to finite-frequency QOs, which can become comparable to the extremal area of the unhybridized bulk bands. We show that this occurs when the crystal symmetry is lowered from cubic to tetragonal in a minimal two-orbital model. We label such surface modes as 'shadow surface states'. Moreover, we show that the sufficient next-nearest neighbor out-of-plane hybridization leading to shadow surface states can be self-consistently stabilized for tetragonal TKIs. Consequently, shadow surface states provide an important example of high-frequency QOs beyond the context of cubic TKIs. acknowledgement: PG acknowledges support from National Science Foundation Awards No. DMR-1824265 for this work. AG acknowledges support from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. EMN is supported by ASU startup grant. OE is in part supported by NSF-DMR-1904716. article_number: '123042' article_processing_charge: No article_type: original author: - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Emilian M. full_name: Nica, Emilian M. last_name: Nica - first_name: Onur full_name: Erten, Onur last_name: Erten - first_name: Pouyan full_name: Ghaemi, Pouyan last_name: Ghaemi citation: ama: Ghazaryan A, Nica EM, Erten O, Ghaemi P. Shadow surface states in topological Kondo insulators. New Journal of Physics. 2021;23(12). doi:10.1088/1367-2630/ac4124 apa: Ghazaryan, A., Nica, E. M., Erten, O., & Ghaemi, P. (2021). Shadow surface states in topological Kondo insulators. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac4124 chicago: Ghazaryan, Areg, Emilian M. Nica, Onur Erten, and Pouyan Ghaemi. “Shadow Surface States in Topological Kondo Insulators.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac4124. ieee: A. Ghazaryan, E. M. Nica, O. Erten, and P. Ghaemi, “Shadow surface states in topological Kondo insulators,” New Journal of Physics, vol. 23, no. 12. IOP Publishing, 2021. ista: Ghazaryan A, Nica EM, Erten O, Ghaemi P. 2021. Shadow surface states in topological Kondo insulators. New Journal of Physics. 23(12), 123042. mla: Ghazaryan, Areg, et al. “Shadow Surface States in Topological Kondo Insulators.” New Journal of Physics, vol. 23, no. 12, 123042, IOP Publishing, 2021, doi:10.1088/1367-2630/ac4124. short: A. Ghazaryan, E.M. Nica, O. Erten, P. Ghaemi, New Journal of Physics 23 (2021). date_created: 2022-01-16T23:01:28Z date_published: 2021-12-23T00:00:00Z date_updated: 2023-08-17T06:54:54Z day: '23' ddc: - '530' department: - _id: MiLe doi: 10.1088/1367-2630/ac4124 ec_funded: 1 external_id: arxiv: - '2012.11625' isi: - '000734063700001' file: - access_level: open_access checksum: 0c3cb6816242fa8afd1cc87a5fe77821 content_type: application/pdf creator: cchlebak date_created: 2022-01-17T10:01:58Z date_updated: 2022-01-17T10:01:58Z file_id: '10632' file_name: 2021_NewJourPhys_Ghazaryan.pdf file_size: 2533102 relation: main_file success: 1 file_date_updated: 2022-01-17T10:01:58Z has_accepted_license: '1' intvolume: ' 23' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: New Journal of Physics publication_identifier: issn: - 1367-2630 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Shadow surface states in topological Kondo insulators 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: '10631' abstract: - lang: eng text: We combine experimental and theoretical approaches to explore excited rotational states of molecules embedded in helium nanodroplets using CS2 and I2 as examples. Laser-induced nonadiabatic molecular alignment is employed to measure spectral lines for rotational states extending beyond those initially populated at the 0.37 K droplet temperature. We construct a simple quantum-mechanical model, based on a linear rotor coupled to a single-mode bosonic bath, to determine the rotational energy structure in its entirety. The calculated and measured spectral lines are in good agreement. We show that the effect of the surrounding superfluid on molecular rotation can be rationalized by a single quantity, the angular momentum, transferred from the molecule to the droplet. acknowledgement: I.C. acknowledges the support by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665385. G.B. acknowledges support from the Austrian Science Fund (FWF), under project No. M2461-N27. M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.S acknowledges support from the European Research Council-AdG (Project No. 320459, DropletControl) and from The Villum Foundation through a Villum Investigator grant no. 25886. article_number: L061303 article_processing_charge: No article_type: original author: - first_name: Igor full_name: Cherepanov, Igor id: 339C7E5A-F248-11E8-B48F-1D18A9856A87 last_name: Cherepanov - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Constant A. full_name: Schouder, Constant A. last_name: Schouder - first_name: Adam S. full_name: Chatterley, Adam S. last_name: Chatterley - first_name: Simon H. full_name: Albrechtsen, Simon H. last_name: Albrechtsen - first_name: Alberto Viñas full_name: Muñoz, Alberto Viñas last_name: Muñoz - first_name: Lars full_name: Christiansen, Lars last_name: Christiansen - first_name: Henrik full_name: Stapelfeldt, Henrik last_name: Stapelfeldt - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Cherepanov I, Bighin G, Schouder CA, et al. Excited rotational states of molecules in a superfluid. Physical Review A. 2021;104(6). doi:10.1103/PhysRevA.104.L061303 apa: Cherepanov, I., Bighin, G., Schouder, C. A., Chatterley, A. S., Albrechtsen, S. H., Muñoz, A. V., … Lemeshko, M. (2021). Excited rotational states of molecules in a superfluid. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.104.L061303 chicago: Cherepanov, Igor, Giacomo Bighin, Constant A. Schouder, Adam S. Chatterley, Simon H. Albrechtsen, Alberto Viñas Muñoz, Lars Christiansen, Henrik Stapelfeldt, and Mikhail Lemeshko. “Excited Rotational States of Molecules in a Superfluid.” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/PhysRevA.104.L061303. ieee: I. Cherepanov et al., “Excited rotational states of molecules in a superfluid,” Physical Review A, vol. 104, no. 6. American Physical Society, 2021. ista: Cherepanov I, Bighin G, Schouder CA, Chatterley AS, Albrechtsen SH, Muñoz AV, Christiansen L, Stapelfeldt H, Lemeshko M. 2021. Excited rotational states of molecules in a superfluid. Physical Review A. 104(6), L061303. mla: Cherepanov, Igor, et al. “Excited Rotational States of Molecules in a Superfluid.” Physical Review A, vol. 104, no. 6, L061303, American Physical Society, 2021, doi:10.1103/PhysRevA.104.L061303. short: I. Cherepanov, G. Bighin, C.A. Schouder, A.S. Chatterley, S.H. Albrechtsen, A.V. Muñoz, L. Christiansen, H. Stapelfeldt, M. Lemeshko, Physical Review A 104 (2021). date_created: 2022-01-16T23:01:29Z date_published: 2021-12-30T00:00:00Z date_updated: 2023-08-17T06:52:17Z day: '30' department: - _id: MiLe doi: 10.1103/PhysRevA.104.L061303 ec_funded: 1 external_id: arxiv: - '2107.00468' isi: - '000739618300001' intvolume: ' 104' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://128.84.4.18/abs/2107.00468 month: '12' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 26986C82-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02641 name: A path-integral approach to composite impurities publication: Physical Review A publication_identifier: eissn: - 2469-9934 issn: - 2469-9926 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Excited rotational states of molecules in a superfluid type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 104 year: '2021' ... --- _id: '10597' abstract: - lang: eng text: We thank Emmanuel Abbe and Min Ye for providing us the implementation of RPA decoding. D. Fathollahi and M. Mondelli are partially supported by the 2019 Lopez-Loreta Prize. N. Farsad is supported by Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (NSERC) and Canada Foundation for Innovation (CFI), John R. Evans Leader Fund. S. A. Hashemi is supported by a Postdoctoral Fellowship from NSERC. article_processing_charge: No author: - first_name: Dorsa full_name: Fathollahi, Dorsa last_name: Fathollahi - first_name: Nariman full_name: Farsad, Nariman last_name: Farsad - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: 'Fathollahi D, Farsad N, Hashemi SA, Mondelli M. Sparse multi-decoder recursive projection aggregation for Reed-Muller codes. In: 2021 IEEE International Symposium on Information Theory. Institute of Electrical and Electronics Engineers; 2021:1082-1087. doi:10.1109/isit45174.2021.9517887' apa: 'Fathollahi, D., Farsad, N., Hashemi, S. A., & Mondelli, M. (2021). Sparse multi-decoder recursive projection aggregation for Reed-Muller codes. In 2021 IEEE International Symposium on Information Theory (pp. 1082–1087). Virtual, Melbourne, Australia: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/isit45174.2021.9517887' chicago: Fathollahi, Dorsa, Nariman Farsad, Seyyed Ali Hashemi, and Marco Mondelli. “Sparse Multi-Decoder Recursive Projection Aggregation for Reed-Muller Codes.” In 2021 IEEE International Symposium on Information Theory, 1082–87. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/isit45174.2021.9517887. ieee: D. Fathollahi, N. Farsad, S. A. Hashemi, and M. Mondelli, “Sparse multi-decoder recursive projection aggregation for Reed-Muller codes,” in 2021 IEEE International Symposium on Information Theory, Virtual, Melbourne, Australia, 2021, pp. 1082–1087. ista: 'Fathollahi D, Farsad N, Hashemi SA, Mondelli M. 2021. Sparse multi-decoder recursive projection aggregation for Reed-Muller codes. 2021 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 1082–1087.' mla: Fathollahi, Dorsa, et al. “Sparse Multi-Decoder Recursive Projection Aggregation for Reed-Muller Codes.” 2021 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2021, pp. 1082–87, doi:10.1109/isit45174.2021.9517887. short: D. Fathollahi, N. Farsad, S.A. Hashemi, M. Mondelli, in:, 2021 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2021, pp. 1082–1087. conference: end_date: 2021-07-20 location: Virtual, Melbourne, Australia name: 'ISIT: International Symposium on Information Theory' start_date: 2021-07-12 date_created: 2022-01-03T11:31:26Z date_published: 2021-09-01T00:00:00Z date_updated: 2023-08-17T06:32:06Z day: '01' department: - _id: MaMo doi: 10.1109/isit45174.2021.9517887 external_id: arxiv: - '2011.12882' isi: - '000701502201029' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2011.12882 month: '09' oa: 1 oa_version: Preprint page: 1082-1087 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: 2021 IEEE International Symposium on Information Theory publication_identifier: eisbn: - 978-1-5386-8209-8 isbn: - 978-1-5386-8210-4 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Sparse multi-decoder recursive projection aggregation for Reed-Muller codes type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '10666' abstract: - lang: eng text: Adversarial training is an effective method to train deep learning models that are resilient to norm-bounded perturbations, with the cost of nominal performance drop. While adversarial training appears to enhance the robustness and safety of a deep model deployed in open-world decision-critical applications, counterintuitively, it induces undesired behaviors in robot learning settings. In this paper, we show theoretically and experimentally that neural controllers obtained via adversarial training are subjected to three types of defects, namely transient, systematic, and conditional errors. We first generalize adversarial training to a safety-domain optimization scheme allowing for more generic specifications. We then prove that such a learning process tends to cause certain error profiles. We support our theoretical results by a thorough experimental safety analysis in a robot-learning task. Our results suggest that adversarial training is not yet ready for robot learning. acknowledgement: M.L. and T.A.H. are supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). R.H. and D.R. are supported by Boeing and R.G. by Horizon-2020 ECSEL Project grant no. 783163 (iDev40). article_processing_charge: No author: - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Ramin full_name: Hasani, Ramin last_name: Hasani - first_name: Radu full_name: Grosu, Radu last_name: Grosu - first_name: Daniela full_name: Rus, Daniela last_name: Rus - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: 'Lechner M, Hasani R, Grosu R, Rus D, Henzinger TA. Adversarial training is not ready for robot learning. In: 2021 IEEE International Conference on Robotics and Automation. ICRA. ; 2021:4140-4147. doi:10.1109/ICRA48506.2021.9561036' apa: Lechner, M., Hasani, R., Grosu, R., Rus, D., & Henzinger, T. A. (2021). Adversarial training is not ready for robot learning. In 2021 IEEE International Conference on Robotics and Automation (pp. 4140–4147). Xi’an, China. https://doi.org/10.1109/ICRA48506.2021.9561036 chicago: Lechner, Mathias, Ramin Hasani, Radu Grosu, Daniela Rus, and Thomas A Henzinger. “Adversarial Training Is Not Ready for Robot Learning.” In 2021 IEEE International Conference on Robotics and Automation, 4140–47. ICRA, 2021. https://doi.org/10.1109/ICRA48506.2021.9561036. ieee: M. Lechner, R. Hasani, R. Grosu, D. Rus, and T. A. Henzinger, “Adversarial training is not ready for robot learning,” in 2021 IEEE International Conference on Robotics and Automation, Xi’an, China, 2021, pp. 4140–4147. ista: 'Lechner M, Hasani R, Grosu R, Rus D, Henzinger TA. 2021. Adversarial training is not ready for robot learning. 2021 IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and AutomationICRA, 4140–4147.' mla: Lechner, Mathias, et al. “Adversarial Training Is Not Ready for Robot Learning.” 2021 IEEE International Conference on Robotics and Automation, 2021, pp. 4140–47, doi:10.1109/ICRA48506.2021.9561036. short: M. Lechner, R. Hasani, R. Grosu, D. Rus, T.A. Henzinger, in:, 2021 IEEE International Conference on Robotics and Automation, 2021, pp. 4140–4147. conference: end_date: 2021-06-05 location: Xi'an, China name: 'ICRA: International Conference on Robotics and Automation' start_date: 2021-05-30 date_created: 2022-01-25T15:44:54Z date_published: 2021-01-01T00:00:00Z date_updated: 2023-08-17T06:58:38Z ddc: - '000' department: - _id: GradSch - _id: ToHe doi: 10.1109/ICRA48506.2021.9561036 external_id: arxiv: - '2103.08187' isi: - '000765738803040' has_accepted_license: '1' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/3.0/ main_file_link: - open_access: '1' url: https://arxiv.org/abs/2103.08187 oa: 1 oa_version: None page: 4140-4147 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: 2021 IEEE International Conference on Robotics and Automation publication_identifier: eisbn: - 978-1-7281-9077-8 eissn: - 2577-087X isbn: - 978-1-7281-9078-5 issn: - 1050-4729 publication_status: published quality_controlled: '1' related_material: record: - id: '11362' relation: dissertation_contains status: public series_title: ICRA status: public title: Adversarial training is not ready for robot learning tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) short: CC BY-NC-ND (3.0) type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '10711' abstract: - lang: eng text: In this paper, we investigate the distribution of the maximum of partial sums of families of m -periodic complex-valued functions satisfying certain conditions. We obtain precise uniform estimates for the distribution function of this maximum in a near-optimal range. Our results apply to partial sums of Kloosterman sums and other families of ℓ -adic trace functions, and are as strong as those obtained by Bober, Goldmakher, Granville and Koukoulopoulos for character sums. In particular, we improve on the recent work of the third author for Birch sums. However, unlike character sums, we are able to construct families of m -periodic complex-valued functions which satisfy our conditions, but for which the Pólya–Vinogradov inequality is sharp. acknowledgement: We would like to thank the anonymous referees for carefully reading the paper and for their remarks and suggestions. article_processing_charge: No article_type: original author: - first_name: Pascal full_name: Autissier, Pascal last_name: Autissier - first_name: Dante full_name: Bonolis, Dante id: 6A459894-5FDD-11E9-AF35-BB24E6697425 last_name: Bonolis - first_name: Youness full_name: Lamzouri, Youness last_name: Lamzouri citation: ama: Autissier P, Bonolis D, Lamzouri Y. The distribution of the maximum of partial sums of Kloosterman sums and other trace functions. Compositio Mathematica. 2021;157(7):1610-1651. doi:10.1112/s0010437x21007351 apa: Autissier, P., Bonolis, D., & Lamzouri, Y. (2021). The distribution of the maximum of partial sums of Kloosterman sums and other trace functions. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/s0010437x21007351 chicago: Autissier, Pascal, Dante Bonolis, and Youness Lamzouri. “The Distribution of the Maximum of Partial Sums of Kloosterman Sums and Other Trace Functions.” Compositio Mathematica. Cambridge University Press, 2021. https://doi.org/10.1112/s0010437x21007351. ieee: P. Autissier, D. Bonolis, and Y. Lamzouri, “The distribution of the maximum of partial sums of Kloosterman sums and other trace functions,” Compositio Mathematica, vol. 157, no. 7. Cambridge University Press, pp. 1610–1651, 2021. ista: Autissier P, Bonolis D, Lamzouri Y. 2021. The distribution of the maximum of partial sums of Kloosterman sums and other trace functions. Compositio Mathematica. 157(7), 1610–1651. mla: Autissier, Pascal, et al. “The Distribution of the Maximum of Partial Sums of Kloosterman Sums and Other Trace Functions.” Compositio Mathematica, vol. 157, no. 7, Cambridge University Press, 2021, pp. 1610–51, doi:10.1112/s0010437x21007351. short: P. Autissier, D. Bonolis, Y. Lamzouri, Compositio Mathematica 157 (2021) 1610–1651. date_created: 2022-02-01T08:10:43Z date_published: 2021-06-28T00:00:00Z date_updated: 2023-08-17T06:59:16Z day: '28' department: - _id: TiBr doi: 10.1112/s0010437x21007351 external_id: arxiv: - '1909.03266' isi: - '000667289300001' intvolume: ' 157' isi: 1 issue: '7' keyword: - Algebra and Number Theory language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1909.03266 month: '06' oa: 1 oa_version: Preprint page: 1610-1651 publication: Compositio Mathematica publication_identifier: eissn: - 1570-5846 issn: - 0010-437X publication_status: published publisher: Cambridge University Press quality_controlled: '1' status: public title: The distribution of the maximum of partial sums of Kloosterman sums and other trace functions type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 157 year: '2021' ... --- _id: '10809' abstract: - lang: eng text: Thermoelectric materials are engines that convert heat into an electrical current. Intuitively, the efficiency of this process depends on how many electrons (charge carriers) can move and how easily they do so, how much energy those moving electrons transport, and how easily the temperature gradient is maintained. In terms of material properties, an excellent thermoelectric material requires a high electrical conductivity σ, a high Seebeck coefficient S (a measure of the induced thermoelectric voltage as a function of temperature gradient), and a low thermal conductivity κ. The challenge is that these three properties are strongly interrelated in a conflicting manner (1). On page 722 of this issue, Roychowdhury et al. (2) have found a way to partially break these ties in silver antimony telluride (AgSbTe2) with the addition of cadmium (Cd) cations, which increase the ordering in this inherently disordered thermoelectric material. article_processing_charge: No article_type: letter_note author: - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 citation: ama: Liu Y, Ibáñez M. Tidying up the mess. Science. 2021;371(6530):678-679. doi:10.1126/science.abg0886 apa: Liu, Y., & Ibáñez, M. (2021). Tidying up the mess. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abg0886 chicago: Liu, Yu, and Maria Ibáñez. “Tidying up the Mess.” Science. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/science.abg0886. ieee: Y. Liu and M. Ibáñez, “Tidying up the mess,” Science, vol. 371, no. 6530. American Association for the Advancement of Science, pp. 678–679, 2021. ista: Liu Y, Ibáñez M. 2021. Tidying up the mess. Science. 371(6530), 678–679. mla: Liu, Yu, and Maria Ibáñez. “Tidying up the Mess.” Science, vol. 371, no. 6530, American Association for the Advancement of Science, 2021, pp. 678–79, doi:10.1126/science.abg0886. short: Y. Liu, M. Ibáñez, Science 371 (2021) 678–679. date_created: 2022-03-03T09:51:48Z date_published: 2021-02-12T00:00:00Z date_updated: 2023-08-17T07:00:35Z day: '12' department: - _id: MaIb doi: 10.1126/science.abg0886 external_id: isi: - '000617551600027' pmid: - '33574201' intvolume: ' 371' isi: 1 issue: '6530' keyword: - multidisciplinary language: - iso: eng month: '02' oa_version: None page: 678-679 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Tidying up the mess type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 371 year: '2021' ... --- _id: '10858' abstract: - lang: eng text: The cost-effective conversion of low-grade heat into electricity using thermoelectric devices requires developing alternative materials and material processing technologies able to reduce the currently high device manufacturing costs. In this direction, thermoelectric materials that do not rely on rare or toxic elements such as tellurium or lead need to be produced using high-throughput technologies not involving high temperatures and long processes. Bi2Se3 is an obvious possible Te-free alternative to Bi2Te3 for ambient temperature thermoelectric applications, but its performance is still low for practical applications, and additional efforts toward finding proper dopants are required. Here, we report a scalable method to produce Bi2Se3 nanosheets at low synthesis temperatures. We studied the influence of different dopants on the thermoelectric properties of this material. Among the elements tested, we demonstrated that Sn doping resulted in the best performance. Sn incorporation resulted in a significant improvement to the Bi2Se3 Seebeck coefficient and a reduction in the thermal conductivity in the direction of the hot-press axis, resulting in an overall 60% improvement in the thermoelectric figure of merit of Bi2Se3. acknowledgement: "M.L., Y.Z., T.Z. and K.X. thank the China Scholarship Council for their scholarship\r\nsupport. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and\r\ninnovation program under the Marie Sklodowska-Curie grant agreement No. 754411. J.L. thanks the ICREA Academia program and projects MICINN/FEDER RTI2018-093996-B-C31 and G.C. 2017 SGR 128. ICN2 acknowledges funding from the Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO ENE2017-85087-C3." article_number: '1827' article_processing_charge: No article_type: original author: - first_name: Mengyao full_name: Li, Mengyao last_name: Li - first_name: Yu full_name: Zhang, Yu last_name: Zhang - first_name: Ting full_name: Zhang, Ting last_name: Zhang - first_name: Yong full_name: Zuo, Yong last_name: Zuo - first_name: Ke full_name: Xiao, Ke last_name: Xiao - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Jordi full_name: Llorca, Jordi last_name: Llorca - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Li M, Zhang Y, Zhang T, et al. Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping. Nanomaterials. 2021;11(7). doi:10.3390/nano11071827 apa: Li, M., Zhang, Y., Zhang, T., Zuo, Y., Xiao, K., Arbiol, J., … Cabot, A. (2021). Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping. Nanomaterials. MDPI. https://doi.org/10.3390/nano11071827 chicago: Li, Mengyao, Yu Zhang, Ting Zhang, Yong Zuo, Ke Xiao, Jordi Arbiol, Jordi Llorca, Yu Liu, and Andreu Cabot. “Enhanced Thermoelectric Performance of N-Type Bi2Se3 Nanosheets through Sn Doping.” Nanomaterials. MDPI, 2021. https://doi.org/10.3390/nano11071827. ieee: M. Li et al., “Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping,” Nanomaterials, vol. 11, no. 7. MDPI, 2021. ista: Li M, Zhang Y, Zhang T, Zuo Y, Xiao K, Arbiol J, Llorca J, Liu Y, Cabot A. 2021. Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping. Nanomaterials. 11(7), 1827. mla: Li, Mengyao, et al. “Enhanced Thermoelectric Performance of N-Type Bi2Se3 Nanosheets through Sn Doping.” Nanomaterials, vol. 11, no. 7, 1827, MDPI, 2021, doi:10.3390/nano11071827. short: M. Li, Y. Zhang, T. Zhang, Y. Zuo, K. Xiao, J. Arbiol, J. Llorca, Y. Liu, A. Cabot, Nanomaterials 11 (2021). date_created: 2022-03-18T09:45:02Z date_published: 2021-07-14T00:00:00Z date_updated: 2023-08-17T07:08:30Z day: '14' ddc: - '540' department: - _id: MaIb doi: 10.3390/nano11071827 ec_funded: 1 external_id: isi: - '000676570000001' file: - access_level: open_access checksum: f28a8b5cf80f5605828359bb398463b0 content_type: application/pdf creator: dernst date_created: 2022-03-18T09:53:15Z date_updated: 2022-03-18T09:53:15Z file_id: '10859' file_name: 2021_Nanomaterials_Li.pdf file_size: 4867547 relation: main_file success: 1 file_date_updated: 2022-03-18T09:53:15Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '7' keyword: - General Materials Science - General Chemical Engineering language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nanomaterials publication_identifier: issn: - 2079-4991 publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping 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: '10834' abstract: - lang: eng text: Hematopoietic-specific protein 1 (Hem1) is an essential subunit of the WAVE regulatory complex (WRC) in immune cells. WRC is crucial for Arp2/3 complex activation and the protrusion of branched actin filament networks. Moreover, Hem1 loss of function in immune cells causes autoimmune diseases in humans. Here, we show that genetic removal of Hem1 in macrophages diminishes frequency and efficacy of phagocytosis as well as phagocytic cup formation in addition to defects in lamellipodial protrusion and migration. Moreover, Hem1-null macrophages displayed strong defects in cell adhesion despite unaltered podosome formation and concomitant extracellular matrix degradation. Specifically, dynamics of both adhesion and de-adhesion as well as concomitant phosphorylation of paxillin and focal adhesion kinase (FAK) were significantly compromised. Accordingly, disruption of WRC function in non-hematopoietic cells coincided with both defects in adhesion turnover and altered FAK and paxillin phosphorylation. Consistently, platelets exhibited reduced adhesion and diminished integrin αIIbβ3 activation upon WRC removal. Interestingly, adhesion phenotypes, but not lamellipodia formation, were partially rescued by small molecule activation of FAK. A full rescue of the phenotype, including lamellipodia formation, required not only the presence of WRCs but also their binding to and activation by Rac. Collectively, our results uncover that WRC impacts on integrin-dependent processes in a FAK-dependent manner, controlling formation and dismantling of adhesions, relevant for properly grabbing onto extracellular surfaces and particles during cell edge expansion, like in migration or phagocytosis. acknowledgement: We are grateful to Silvia Prettin, Ina Schleicher, and Petra Hagendorff for expert technical assistance; David Dettbarn for animal keeping and breeding; and Lothar Gröbe and Maria Höxter for cell sorting. We also thank Werner Tegge for peptides and Giorgio Scita for antibodies. This work was supported, in part, by the Deutsche Forschungsgemeinschaft (DFG), Priority Programm SPP1150 (to T.E.B.S., K.R., and M. Sixt), and by DFG grant GRK2223/1 (to K.R.). T.E.B.S. acknowledges support by the Helmholtz Society through HGF impulse fund W2/W3-066 and M. Schnoor by the Mexican Council for Science and Technology (CONACyT, 284292 ), Fund SEP-Cinvestav ( 108 ), and the Royal Society, UK (Newton Advanced Fellowship, NAF/R1/180017 ). article_processing_charge: No article_type: original author: - first_name: Stephanie full_name: Stahnke, Stephanie last_name: Stahnke - first_name: Hermann full_name: Döring, Hermann last_name: Döring - first_name: Charly full_name: Kusch, Charly last_name: Kusch - first_name: David J.J. full_name: de Gorter, David J.J. last_name: de Gorter - first_name: Sebastian full_name: Dütting, Sebastian last_name: Dütting - first_name: Aleks full_name: Guledani, Aleks last_name: Guledani - first_name: Irina full_name: Pleines, Irina last_name: Pleines - first_name: Michael full_name: Schnoor, Michael last_name: Schnoor - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Robert full_name: Geffers, Robert last_name: Geffers - first_name: Manfred full_name: Rohde, Manfred last_name: Rohde - first_name: Mathias full_name: Müsken, Mathias last_name: Müsken - first_name: Frieda full_name: Kage, Frieda last_name: Kage - first_name: Anika full_name: Steffen, Anika last_name: Steffen - first_name: Jan full_name: Faix, Jan last_name: Faix - first_name: Bernhard full_name: Nieswandt, Bernhard last_name: Nieswandt - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner - first_name: Theresia E.B. full_name: Stradal, Theresia E.B. last_name: Stradal citation: ama: Stahnke S, Döring H, Kusch C, et al. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. 2021;31(10):2051-2064.e8. doi:10.1016/j.cub.2021.02.043 apa: Stahnke, S., Döring, H., Kusch, C., de Gorter, D. J. J., Dütting, S., Guledani, A., … Stradal, T. E. B. (2021). Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2021.02.043 chicago: Stahnke, Stephanie, Hermann Döring, Charly Kusch, David J.J. de Gorter, Sebastian Dütting, Aleks Guledani, Irina Pleines, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” Current Biology. Elsevier, 2021. https://doi.org/10.1016/j.cub.2021.02.043. ieee: S. Stahnke et al., “Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion,” Current Biology, vol. 31, no. 10. Elsevier, p. 2051–2064.e8, 2021. ista: Stahnke S, Döring H, Kusch C, de Gorter DJJ, Dütting S, Guledani A, Pleines I, Schnoor M, Sixt MK, Geffers R, Rohde M, Müsken M, Kage F, Steffen A, Faix J, Nieswandt B, Rottner K, Stradal TEB. 2021. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. 31(10), 2051–2064.e8. mla: Stahnke, Stephanie, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” Current Biology, vol. 31, no. 10, Elsevier, 2021, p. 2051–2064.e8, doi:10.1016/j.cub.2021.02.043. short: S. Stahnke, H. Döring, C. Kusch, D.J.J. de Gorter, S. Dütting, A. Guledani, I. Pleines, M. Schnoor, M.K. Sixt, R. Geffers, M. Rohde, M. Müsken, F. Kage, A. Steffen, J. Faix, B. Nieswandt, K. Rottner, T.E.B. Stradal, Current Biology 31 (2021) 2051–2064.e8. date_created: 2022-03-08T07:51:04Z date_published: 2021-05-24T00:00:00Z date_updated: 2023-08-17T07:01:14Z day: '24' department: - _id: MiSi doi: 10.1016/j.cub.2021.02.043 external_id: isi: - '000654652200002' pmid: - '33711252' intvolume: ' 31' isi: 1 issue: '10' keyword: - General Agricultural and Biological Sciences - General Biochemistry - Genetics and Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2020.03.24.005835 month: '05' oa: 1 oa_version: Preprint page: 2051-2064.e8 pmid: 1 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 31 year: '2021' ... --- _id: '9935' abstract: - lang: eng text: "We present a deterministic O(log log log n)-round low-space Massively Parallel Computation (MPC) algorithm for the classical problem of (Δ+1)-coloring on n-vertex graphs. In this model, every machine has sublinear local space of size n^φ for any arbitrary constant φ \\in (0,1). Our algorithm works under the relaxed setting where each machine is allowed to perform exponential local computations, while respecting the n^φ space and bandwidth limitations.\r\n\r\nOur key technical contribution is a novel derandomization of the ingenious (Δ+1)-coloring local algorithm by Chang-Li-Pettie (STOC 2018, SIAM J. Comput. 2020). The Chang-Li-Pettie algorithm runs in T_local =poly(loglog n) rounds, which sets the state-of-the-art randomized round complexity for the problem in the local model. Our derandomization employs a combination of tools, notably pseudorandom generators (PRG) and bounded-independence hash functions.\r\n\r\nThe achieved round complexity of O(logloglog n) rounds matches the bound of log(T_local ), which currently serves an upper bound barrier for all known randomized algorithms for locally-checkable problems in this model. Furthermore, no deterministic sublogarithmic low-space MPC algorithms for the (Δ+1)-coloring problem have been known before." acknowledgement: This work is partially supported by a Weizmann-UK Making Connections Grant, the Centre for Discrete Mathematics and its Applications (DIMAP), IBM Faculty Award, EPSRC award EP/V01305X/1, European Research Council (ERC) Grant No. 949083, the Minerva foundation with funding from the Federal German Ministry for Education and Research No. 713238, and the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No 754411. article_processing_charge: No author: - first_name: Artur full_name: Czumaj, Artur last_name: Czumaj - first_name: Peter full_name: Davies, Peter id: 11396234-BB50-11E9-B24C-90FCE5697425 last_name: Davies orcid: 0000-0002-5646-9524 - first_name: Merav full_name: Parter, Merav last_name: Parter citation: ama: 'Czumaj A, Davies P, Parter M. Improved deterministic (Δ+1) coloring in low-space MPC. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:469–479. doi:10.1145/3465084.3467937' apa: 'Czumaj, A., Davies, P., & Parter, M. (2021). Improved deterministic (Δ+1) coloring in low-space MPC. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 469–479). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467937' chicago: Czumaj, Artur, Peter Davies, and Merav Parter. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 469–479. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467937. ieee: A. Czumaj, P. Davies, and M. Parter, “Improved deterministic (Δ+1) coloring in low-space MPC,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 469–479. ista: 'Czumaj A, Davies P, Parter M. 2021. Improved deterministic (Δ+1) coloring in low-space MPC. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 469–479.' mla: Czumaj, Artur, et al. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 469–479, doi:10.1145/3465084.3467937. short: A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 469–479. conference: end_date: 2021-07-30 location: Virtual, Italy name: 'PODC: Symposium on Principles of Distributed Computing' start_date: 2021-07-26 date_created: 2021-08-17T18:14:15Z date_published: 2021-07-21T00:00:00Z date_updated: 2023-08-17T07:11:03Z day: '21' department: - _id: DaAl doi: 10.1145/3465084.3467937 ec_funded: 1 external_id: isi: - '000744439800048' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://wrap.warwick.ac.uk/153753 month: '07' oa: 1 oa_version: Submitted Version page: 469–479 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing publication_identifier: isbn: - 978-1-4503-8548-0 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' status: public title: Improved deterministic (Δ+1) coloring in low-space MPC type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '10856' abstract: - lang: eng text: "We study the properties of the maximal volume k-dimensional sections of the n-dimensional cube [−1, 1]n. We obtain a first order necessary condition for a k-dimensional subspace to be a local maximizer of the volume of such sections, which we formulate in a geometric way. We estimate the length of the projection of a vector of the standard basis of Rn onto a k-dimensional subspace that maximizes the volume of the intersection. We \x1Cnd the optimal upper bound on the volume of a planar section of the cube [−1, 1]n , n ≥ 2." acknowledgement: "The authors acknowledge the support of the grant of the Russian Government N 075-15-\r\n2019-1926. G.I.was supported also by the SwissNational Science Foundation grant 200021-179133. The authors are very grateful to the anonymous reviewer for valuable remarks." article_processing_charge: No article_type: original author: - first_name: Grigory full_name: Ivanov, Grigory id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E last_name: Ivanov - first_name: Igor full_name: Tsiutsiurupa, Igor last_name: Tsiutsiurupa citation: ama: Ivanov G, Tsiutsiurupa I. On the volume of sections of the cube. Analysis and Geometry in Metric Spaces. 2021;9(1):1-18. doi:10.1515/agms-2020-0103 apa: Ivanov, G., & Tsiutsiurupa, I. (2021). On the volume of sections of the cube. Analysis and Geometry in Metric Spaces. De Gruyter. https://doi.org/10.1515/agms-2020-0103 chicago: Ivanov, Grigory, and Igor Tsiutsiurupa. “On the Volume of Sections of the Cube.” Analysis and Geometry in Metric Spaces. De Gruyter, 2021. https://doi.org/10.1515/agms-2020-0103. ieee: G. Ivanov and I. Tsiutsiurupa, “On the volume of sections of the cube,” Analysis and Geometry in Metric Spaces, vol. 9, no. 1. De Gruyter, pp. 1–18, 2021. ista: Ivanov G, Tsiutsiurupa I. 2021. On the volume of sections of the cube. Analysis and Geometry in Metric Spaces. 9(1), 1–18. mla: Ivanov, Grigory, and Igor Tsiutsiurupa. “On the Volume of Sections of the Cube.” Analysis and Geometry in Metric Spaces, vol. 9, no. 1, De Gruyter, 2021, pp. 1–18, doi:10.1515/agms-2020-0103. short: G. Ivanov, I. Tsiutsiurupa, Analysis and Geometry in Metric Spaces 9 (2021) 1–18. date_created: 2022-03-18T09:25:14Z date_published: 2021-01-29T00:00:00Z date_updated: 2023-08-17T07:07:58Z day: '29' ddc: - '510' department: - _id: UlWa doi: 10.1515/agms-2020-0103 external_id: arxiv: - '2004.02674' isi: - '000734286800001' file: - access_level: open_access checksum: 7e615ac8489f5eae580b6517debfdc53 content_type: application/pdf creator: dernst date_created: 2022-03-18T09:31:59Z date_updated: 2022-03-18T09:31:59Z file_id: '10857' file_name: 2021_AnalysisMetricSpaces_Ivanov.pdf file_size: 789801 relation: main_file success: 1 file_date_updated: 2022-03-18T09:31:59Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' keyword: - Applied Mathematics - Geometry and Topology - Analysis language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 1-18 publication: Analysis and Geometry in Metric Spaces publication_identifier: issn: - 2299-3274 publication_status: published publisher: De Gruyter quality_controlled: '1' scopus_import: '1' status: public title: On the volume of sections of the cube tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2021' ...